S S Single letter code for serine. S1 (1) A soluble fragment (102 kDa) of heavy meromyosin produced by papain cleavage: it retains the ATPase and actin-binding activity and motor function, and can be used to decorate actin filaments for identification by electron microscopy. (2) Ribosomal protein S1 plays a critical role in translation initiation and elongation in E. coli and is believed to stabilize mRNA on the ribosome. (3) See S1 nuclease.
S1 mapping See Berk-Sharp technique and S1 nuclease.
S1 nuclease (1) A single-strand specific nuclease (EC 3.1.30.1, 287aa), usually isolated from certain Neurospora and Aspergillus species, that degrades single-stranded nucleic acids and is more active against DNA than RNA. Used in the Berk-Sharp technique (S1 nuclease mapping) and to remove single-stranded extensions from DNA to produce blunt ends. (2) Ribonuclease S-1 (EC 3.1.27.1, 228aa) from Pyrus pyrifolia (Japanese pear) is an endonuclease and is involved in self-incompatibility. (3) See pyocin-S1.
S2 Fibrous fragment of heavy meromyosin (HMM). Links the S1 head to the light meromyosin (LMM) region that lies in the body of the thick filament and acts as a flexible hinge.
S6 kinase A family of serine/threonine kinases, activated by MAP kinase, that phosphorylate ribosomal protein S6 to elevate protein production in cells stimulated by a mitogen. One example is S6 kinase alpha-1 (EC 2.7.11.1, MAP kinase-activated protein kinase 1a, 735aa) which may be involved in activating CREB.
S9 (1) Post-mitochondrial supernatant fraction of liver hom*ogenate rich in drug-metabolising enzymes (cytochrome P450s), sometimes used in the Ames test. (2) A ribosomal protein found ubiquitously in the small subunit of ribosomes of prokaryotes and eukaryotes. (3) See dermaseptins.
S100 A large family of calcium-binding proteins containing an EF-hand. They also bind zinc at a different site and with higher affinity. S100A1 (94aa) is found particularly in heart but also other tissues. S100A4 (placental calcium-binding protein, Mts1, metastasin, p9Ka, pEL98, CAPL, calvasculin, Fsp-1, 101aa) is ubiquitously expressed and upregulated in various pathological conditions. S100A6 is calcyclin. S100A7 (101aa) is highly upregulated in psoriatic skin. S100A8 (calgranulin A) and S100A9
(calgranulin B) form heterodimeric calprotectin. S100A10 (97aa) is the light chain of calpactin, S100A12 (92aa) is calgranulin C. S100B (92aa) is involved with the regulation of protein phosphorylation in brain and has neurotrophic and mitogenic activity. Other members of the family include calmodulin and troponin.
S180 sarcoma 180 Highly malignant mouse sarcoma cells, often passaged in ascites form. Used in some of the classical studies on contact inhibition of locomotion.
Sab Protein (SH3BP5, 455aa) that binds selectively to SH3 domain of btk and binds to and serves as a substrate for JNK.
Sabouraud’s
dextrose broth A culture medium used for moulds, yeasts and pathogenic fungi, particularly those associated with skin infections. It is acidic (pH 5.6) and selective for fungi. Informative supplier website: http://www.condalab. com/pdf/1205.pdf
SAC complex A multiprotein complex composed of crumbs, patj and sdt involved in determining polarity of epithelial cells.
saccade An eye movement in which the eyes jump from one point to another; the images are integrated centrally to give the impression that the whole field of view is being seen.
saccharomicins Saccharomicins A and B are heptadecaglycoside antibiotics isolated from the fermentation broth of the rare actinomycete Saccharothrix espanaensis. They are active both in vitro and in vivo against bacteria and yeast by disrupting membranes. http://www.ncbi.nlm.nih.gov/ pmc/articles/PMC90028/
Saccharomyces Genus of Ascomycetes; yeasts. Normally haploid unicellular fungi that reproduce asexually by budding but have a sexual cycle in which cells of different mating types fuse to form a diploid zygote. Economically important in brewing and baking, and are also suitable eukaryotic cells for the processes of genetic engineering, and for the analysis of, for example, cell division cycle control by selecting for mutants (see cdc genes). S. cerevisiae is baker’s yeast; S. carlsbergensis is now the major brewer’s yeast. See also Schizosaccharomyces pombe.
Saccharomyces Genome Database A scientific database of the molecular biology and genetics of baker’s yeast, Saccharomyces cerevisiae. Link to database: http://www.yeastgenome.org/
The Dictionary of Cell and Molecular Biology. DOI: http://dx.doi.org/10.1016/B978-0-12-384931-1.00019-2 r 2013 Elsevier Ltd. All rights reserved.
saccharopine
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sallimus
saccharopine An intermediate in the aminoadipic
SAGA complex A multisubunit histone acetyl-
pathway for the synthesis or degradation of lysine, synthesized from lysine and α-oxoglutarate in mammalian liver.
transferase complex (Spt-Ada-Gcn5-acetyltransferase) originally described as being involved in transcriptional regulation in S. cerevisiae, required for RNA polymerase II-dependent transcription of several genes and that facilitates the binding of TATA-binding protein (TBP) during transcriptional activation. Components include ataxin-7, ataxin-7-like protein 3, enhancer of yellow 2 transcription factor hom*ologue (ENY2), histone acetyltransferase GCN5L2, transcription initiation protein SPT3 hom*ologue (SUPT3H), transcription factor II (TFIID) subunit TAF10, transformation/transcription domain-associated protein (TRRAP) and ubiquitin carboxyl-terminal hydrolase 22 (USP22).
saccharopine
dehydrogenase Cytoplasmic enzyme (EC 1.5.1.9, 429aa) that catalyzes the NAD1dependent cleavage of saccharopine to L-lysine and 2-oxoglutarate. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase, the first two linked enzymes of lysine catabolism. One of the AlaDH/PNT (alanine dehydrogenase/pyridine nucleotide transhydrogenase) family of enzymes.
sacsin A protein (4579aa) that is highly expressed in the central nervous system where it may act as a chaperone in protein folding. Mutations in the gene cause autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), an early onset neurodegenerative disease.
sad1 (1) Constitutive membrane-bound component (514aa) of the yeast spindle pole body (SPB) that interact with Kms1. See sun proteins. (2) PremRNA-splicing factor (snRNP assembly-defective protein 1, 448aa) required for splicing of pre-mRNA in S. cerevisiae. (3) A serine/threonine kinase (BR serine/threonine-protein kinase 1, EC 2.7.11.1, 794aa) required for the differentiation of forebrain neurons. (4) SUN domain-containing protein 1 (812aa), a component of SUN-protein-containing complexes (LINC complexes) which link the nucleoskeleton and cytoskeleton. (5) Arabidopsis SAD1 (supersensitive to ABA and drought) mutation increases plant sensitivity to drought stress and abscissic acid in seed germination. (6) Mycobacterial semialdehyde dehydrogenases, Sad1 and Sad2.
S-adenosyl methionine An activated derivative of methionine (S-(50 -deoxyadenosine-50 )-methionine), produced by methionine adenosyltransferase, that functions as a methyl group donor, in (for example) phospholipid methylation and bacterial chemotaxis.
Saethre-Chotzen
syndrome An
autosomal dominant syndrome in which there is fusion of bones (craniosynostosis) in the skull that are normally separate, caused by loss-of-function mutation in twist-1.
safranin A histological stain (safranin O, basic red 2), a mixture of dimethyl and trimethyl safranin, used as a counterstain. It stains nuclei red and metachromatically stains cartilage yellow.
SAGE Serial Analysis of Gene Expression A method for analysing overall gene expression patterns by generating short sequence tags (10214 bp), each uniquely identifying a transcript, linking these together to produce a long serial molecule that can be cloned and sequenced and then quantifying the number of times a particular tag is observed, this being a measure of the expression level of the corresponding transcript. The necessary software is freely available. Link to Sagenet homepage: http://www. sagenet.org/
sagittal section Section through the median vertical longitudinal plane of an animal.
salicylic acid A naturally occuring antiseptic and anti-inflammatory compound (2-hydroxybenzoic acid) found especially in the bark of willow (Salix); the acetylated form is aspirin (acetylsalicylic acid). The ester, ethyl salicylate, is oil of wintergreen. In plants can act as a hormone and is a second messenger of oxidative stress signalling. It is involved in plant defence responses, senescence and regulation of flowering time.
salinosporamide A A potent proteasome inhibitor from the marine bacterium, Salinispora tropica. Currently in clinical trials for the treatment of multiple myeloma.
SALL proteins A family of zinc-finger transcription factors (SALL1, sal-like 1, 1324aa) involved in organogenesis. SALL1 defects cause Townes-Brock syndrome. It is the human hom*ologue of the homeotic gene spalt (sal) of Drosophila required for the specification of posterior head and anterior tail regions in development. Other related proteins are known (SALL2, 1007; SALL3, 1300). SALL4 (1054aa) defects are associated with upper limb abnormalities.
Salla disease See sialin.
SAGA (1) See SAGA complex. (2) In Aspergillus
sallimus One of two proteins in insects (projectin
fumigatus a component of the actin cytoskeletonregulatory complex (sagA, endocytosis protein 3, end3, 404aa) required for the internalization of endosomes.
and sallimus) that are functional hom*ologues of vertebrate titin. The Drosophila gene sallimus (sls) encodes a protein of 2 MDa. The 50 half of sls codes for zormin and kettin; both proteins contain Ig
Salmonella
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domains and can be expressed as separate isoforms. Abstract of article: http://www.ncbi.nlm.nih.gov/ pubmed/17316686
Salmonella Genus of Enterobacteriaceae; motile, Gram-negative bacteria that, if invasive, cause enteric fevers (e.g. typhoid, caused by S. typhi), food-poisoning (usually S. typhimurium or S. enteridis, the latter notorious for contamination of poultry), and occasionally septicaemia in non-intestinal tissues.
SALT See skin associated lymphoid tissue. saltatory Describing a pattern of movement in which there are distinct jumps (kangaroos move in a saltatory fashion). Intracellular particles can exhibit saltatory movements although the mechanism is unclear. Saltatory conduction is the rapid method by which nerve impulses move down a myelinated axon with excitation occurring only at nodes of Ranvier. This reduces the capacitance of the neuron, allowing much faster transmission. See myelin, Schwann cells. Saltatory replication is the sudden amplification (in generational terms) of a DNA sequence to generate many tandem copies, possibly the way in which satellite DNA arose.
salusins Bioactive peptides (salusin-alpha, 28aa; salusin-beta, 20aa) derived from torsin 2A. Salusinalpha has mild hypotensive effects; salusin-beta stimulates arginine-vasopressin release from rat pituitary and causes rapid and profound hypotension and bradycardia. Informative supplier webpage: http:// www.phoenixbiotech.net/Catalog%20Files/Salusin/ Salusin.htm
salvador See Salvador-Warts-Hippo pathway. Salvador-Warts-Hippo pathway A tumoursuppressor signalling pathway involved in tissue growth control and axis specification in Drosophila. The pathway is a ser/thr kinase cascade in which hippo (STE20-like kinase MST, 669aa), in complex with its regulatory scaffold protein salvador (608aa), phosphorylates and activates the ser/thr kinase warts (1105aa) that is complexed with its regulatory protein Mats (Mps one binder kinase activator-like 1, 219aa), which in turn phosphorylates and inactivates the yorkie oncoprotein. It also seems to be important in mammalian tumours by limiting activity of the yorkie oncoprotein; hom*ologues of all the Drosophila components are found in humans. Research article: http://www.sciencedirect.com/ science/article/pii/S0960982207020751
salvage pathways Metabolic pathways that allow synthesis of important intermediates from materials that would otherwise be waste products. An experimentally important pathway is that from hypoxanthine to nucleotides. See HGPRT.
SAP
SAM domain A protein interaction module (sterile
alpha motif domain, B70aa) found in diverse signaltransducing proteins including EPH-related receptor tyrosine kinases, serine/threonine protein kinases, cytoplasmic scaffolding and adaptor proteins, regulators of lipid metabolism, GTPases and transcription factors. SAM domains are known to form hom*oand hetero-oligomers. Structural information: http:// 130.15.90.72/sam_domain.htm
sam68 Protein (src-associated in mitosis, 68 kDa, 443aa) that associates with and is tyrosine phosphorylated by src in a mitosis-specific manner. Has KH-type RNA-binding, SH2 and SH3 domains. Interacts with RNA, src-family kinases, grb2 and PLCγ. Inhibition of phosphorylation of sam68 by radicicol will block exit from mitosis.
Sandhoff’s disease A lysosomal disease (storage disease) caused by mutation in the gene encoding the beta subunit of hexosaminidase (EC 3.2.1.52). GM2 gangliosides accumulate, particularly in neurons, leading to progressive neurodegeneration. Clinically indistinguishable from Tay-Sachs disease.
SANDO See sensory ataxic neuropathy. Sanfilippo
syndrome A lysosomal disease (mucopolysaccharidosis type III) characterized by severe central nervous system degeneration. There are four sub-types in which different enzymes are affected (heparan N-sulfatase in type A; alpha-N-acetylglucosaminidase in type B; acetyl CoA:alpha-glucosaminide acetyltransferase in type C; N-acetylglucosamine 6-sulphatase I in type D). Cross correction (complementation) of co-cultured fibroblasts from apparently clinically-identical patients can occur if a different enzyme is missing.
Sanger-Coulson method See dideoxy sequencing. Sanjad-Sakati syndrome See hypoparathyroidism.
SANS Scaffold protein containing ankyrin repeats and SAM domain. A scaffold protein (461aa) found in the apical region of cochlear and vestibular hair cells but not in stereocilia. It interacts with harmonin and myosin 7A. Mutations cause a form of deafness (Usher Syndrome 1G).
S-antigen (1) An abundant protein (S-arrestin, 409aa) of the retina and pineal gland that elicits experimental autoimmune uveitis. See arrestins. (2) Soluble heat-stable antigens (2502650aa, very variable between isolates) from the surface of Plasmodium falciparum that are responsible for antigenic heterogeneity and are found in sera of some infected individuals.
SAP (1) See serum amyloid P-component. (2) SLAM-associated protein. (3) See saposin. (4)
sapecin
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Spliceosome-associated proteins of various sizes (e.g. SAP145, pre-mRNA-splicing factor SF3b 145 kDa subunit, 895aa). (5) SIT4-associating protein SAP155 in S. cerevisiae, a positive regulator of protein phosphatase SIT4. (6) Histone deacetylase complex subunit SAP30 (sin3-associated polypeptide p30, 220aa). (7) Receptor-type tyrosine-protein phosphatase H (EC 3.1.3.48, stomach cancer-associated protein tyrosine phosphatase 1, SAP-1, 1115aa). (8) See sapintoxin D (SAPD).
sapecin A defensin produced by the flesh fly, Sarcophaga peregrina.
sapintoxin D Fluorescent, highly potent phorbol ester (12-N-methylanthraniloylphorbol 13-acetate; SAPD) that is a selective activator of protein kinase C (PKC)-alpha.
SAPK4 (1) Stress-activated protein kinase 4, one of the MAP kinase family (EC 2.7.11.24, MAPK13, 365aa), closely related to p38 MAP kinase (MAPK11, SAPK2, 364aa), both of which can be activated by proinflammatory cytokines and cellular stress. Transcription factor ATF2, and stathmin are substrates of SAPK4. (2) SNF1-type serine-threonine protein kinase (SAPK4, EC 2.7.11.1, osmotic stress/ abscisic acid-activated protein kinase, 4360aa) regulates stress-responsive gene expression in rice. There are many similar stress-responsive kinases in rice (SAPK1- SAPK10).
saponins Glycosidic surfactants produced by plant cells. Used to permeabilise membranes (being less harsh than, for example, Triton X-100) and as foaming agents in some beverages.
saporin A ribosome-inactivating protein (253aa), from seeds of the plant Saponaria officinalis (soapwort). Acts as an RNA-N-glycosidase, specifically depurinising the 28S RNA of ribosomes.
saposins Small (B80aa), heat-stable glycoprotein activators of lysosomal glycosphingolipid hydrolases (saposins A, B, C and D) derived by proteolysis from a single precursor, prosaposin. Lysosomal degradation of several sphingolipids requires the presence of saposins and they are important for exchange of lipids from CD1 molecules to lysosomal antigens. Other functions include neuritogenic/neuroprotection effects and induction of membrane fusion. Saposins B, C, and D share common structural features including a lack of tryptophan, a single glycosylation sequence, the presence of three conserved disulphide bonds, and a common helical bundle motif. Saposin A contains an additional glycosylation site and a single tryptophan. Saposin-like proteins (SAPLIPs) have the same motif and similar location of six cysteines; they include surfactant protein B (SP-B), Entamoeba histolytica pore-forming peptide, granulysin, NK-lysin, acid sphingomyelinase and acyloxyacyl hydrolase. Deficiency of saposin A causes atypical Krabbe’s disease, deficiency of
sarcolemma saposin B causes metachromatic leukodystrophy, deficiency of saposin C causes an atypical form of Gaucher’s disease.
sapoviruses A genus of the Calicivirus family responsible for mild gastroenteritis in infants.
saprophyte Organism that feeds on complex organic materials, often the dead and decaying bodies of other organisms. Many fungi are saprophytic
SAR (1) See structure-activity relationship and systemic acquired resistance. (2) Secretion-associated and ras-related protein (sar1p). In yeast, a small GTPase (190aa) that controls the assembly of the coat protein complex II (COPII) that surrounds vesicles that are involved in export from the ER. The Sar1p-GTP complex initiates membrane curvature during vesicle biogenesis. The human hom*ologue is SAR1 (SAR1A and SAR1B, both 198aa); mutations in SAR1B are associated with Anderson disease and chylomicron retention disease.
sarafotoxins Group of cardiotoxic venoms (SRTX, 21aa) from Atractaspis engaddensis (burrowing asp), structurally related to the endothelins.
sarcin/ricin loop A highly conserved sequence found in the RNA of all large ribosomal subunits. Alpha-sarcin and ricin both inactivate ribosomes by cleaving a single bond in the loop. This prevents the interaction with elongation factors and stops translation.
sarcodictyins Tricyclic compounds isolated from the Japanese soft coral Bellonella albiflora, that stabilize microtubule bundles.
Sarcodina A large phylum of aquatic protozoa that includes Amoebae, Foraminifera and Radiolaria.
sarcoglycans Transmembrane proteins that associate with dystroglycan in the sarcolemma and together with dystrophin and syntrophins link the contractile machinery to the extracellular matrix. The sarcoglycans are subdivided into the sarcoglycan alpha/epsilon and sarcoglycan beta/delta/gamma/ zeta families. Alpha-sarcoglycan (50DAG, A2, adhalin, 387aa), β-sarcoglycan (43DAG, A3b, 318aa), γ-sarcoglycan (35DAG, A4, 294aa), δ-sarcoglycan (289aa), ε-sarcoglycan (437aa) and ζ-sarcoglycan (299aa). Defects in sarcoglycans have been shown to be associated with autosomally inherited muscular dystrophy.
sarcoidosis Disease (Besnier-Boeck disease) of unknown aetiology in which there are chronic inflammatory granulomatous lesions in lymph nodes and other organs with an accumulation of CD41 T-cells and a Th1 immune response.
sarcolemma Plasma membrane of a striated muscle fibre.
sarcolipin
585
saturation
sarcolipin A proteolipid (31aa) that inhibits the car-
SARPs Streptomyces Antibiotic Regulatory Proteins.
sarcoma A malignant tumour derived from connec-
Pathway-specific regulatory proteins encoded within antibiotic biosynthetic-gene clusters in several antibiotic pathways in Streptomyces. They activate transcription by binding to a tandemly arrayed set of heptameric, direct repeats located around the -35 region of their cognate promoters. There are also pleiotropic regulatory genes. Review: http:// mic.sgmjournals.org/cgi/reprint/142/6/1335?view5 long&pmid58704973
diac sarcoplasmic reticulum Ca21 ATPase (SERCA2a) by direct binding and is superinhibitory if it binds as a binary complex with phospholamban (PLN). tive tissue cells, e.g. osteosarcoma (from bone). Some sarcomas are of viral origin: see Rous sarcoma virus, and src gene. Less common than carcinomas but tend to have an earlier onset and a worse prognosis.
sarcoma virus Virus that causes tumours that
SARS Severe Acute Respiratory Syndrome. A highly
originate from cells of connective tissue such as fibroblasts. See Rous sarcoma virus and src gene.
infectious respiratory disease caused by a coronavirus, first recognised in the Far East in 2003 where it caused a major epidemic with a fatality rate of 11%.
Sarcomastigophora Phylum of unicellular pro-
satellite cell (1) Sparse population of mononucle-
tozoa with pseudopodia or flagella or both.
sarcomere Repeating subunit from which the myofibrils of striated muscle are built. Has A- and I-bands, the I-band being subdivided by the Z-disc, and the A-band being split by the M-line and the H-zone.
sarcoplasm Cytoplasm of striated muscle fibre. sarcoplasmic reticulum Endoplasmic reticulum of striated muscle, specialized for the sequestration of calcium ions that are released upon receipt of a signal relayed by the T tubules from the neuromuscular junction.
sarcoplasmic-endoplasmic reticulum Ca21ATPase SERCA The calcium-ATPase pump (EC 3.6.3.8, 1043aa) of the sarcoplasmic reticulum (SR) that moves calcium ions from the sarcoplasm into the SR, reducing the calcium concentration around the myofibrils and allowing the muscle to relax. A different ATPase, the plasma-membrane Ca21 ATPase (PMCA, EC 3.6.3.8, 1258aa), pumps calcium to the extracellular space. There are muscle type-specific and non-muscle isoforms.
sarcosine A natural amino acid (N-methyl glycine) found in muscle and other tissues; has a sweet taste and is used in toothpaste. Reported to be an endogenous antagonist of glycine transporter-1 and have some beneficial effects in treating schizophrenia.
ate cells found in close contact with muscle fibres in vertebrate skeletal muscle. Seem normally to be inactive, but may be important in regeneration after damage. May be considered a quiescent stem cell. (2) An alternative name for glial cell.
satellite chromosome A small segment of a chromosome that is connected, usually to the short arm of an acrocentric chromosome, by a narrow neck (satellite stalk) which appears as an unstained gap in chromosome preparations. In humans chromosomes 13215 and 21222 have satellites. Cf. satellite DNA.
satellite DNA DNA containing highly repetitive sequences, that has a base composition (and thus density in ultracentrifugation) significantly different from normal DNA. Typically 10% of mammalian, and 50% of insect genomes are composed of satellites. As satellites are dispersed widely in the genome, are easily detectable (with a highly repetitive probe) and are frequently polymorphic in length, they are ideal markers for linkage studies of disease or inheritance, and for genomics. Minisatellites (variable number of tandem repeats, VNTRs) have core repeats of 9280 bp, microsatellites (short tandem repeats, STRs, simple sequence repeats, SSRs) have repeats of only 226 bp. See also Fragile X, Huntington’s chorea.
satellite virus A term used in plant virology for a
sarcosyl sarkosyl A mild, biodegradable anionic
virus associated functionally, at least for the purpose of its own replication, with another virus.
surfactant (N-lauroyl-sarcosine) derived from fatty acids and sarcosine, used in preparing solubilised fractions of biological materials.
saturated fatty acids Fatty acids without double
sarcotoxins Potent bactericidal proteins produced by insects in response to injury. They are cytotoxic to Gram-positive and Gram-negative bacteria. Sarcotoxin-1A (63aa) from Sarcophaga peregrina (Flesh fly) is a cecropin, as are the other sarcotoxin-1 variants: sarcotoxin-2 forms (e.g. sarcotoxin-2A, 294aa) are related to attacins.
sarin Nerve gas; inhibitor of acetylcholine esterase.
bonds. In eukaryotic membranes mostly stearic, palmitic and myristic acids, linear aliphatic chains with no double bonds. Prokaryotes have numerous branched-chain saturated fatty acids.
saturation The state in which all receptors or binding sites are effectively occupied all the time, can be said to occur in a simple binding equilibrium when the concentration of ligand is more than five times the Kd value, although strictly it will only be true at infinite ligand concentration.
saturation density
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scanning transmission electron
saturation density The maximal population den-
scaffolding proteins In general, proteins that
sity achieved by a cell type grown under particular in vitro culture conditions. Although transformed cells generally grow to a higher saturation density than normal cells this is not necessarily the case. Many factors affect the final density achieved by a cell population; the critical factor may be availability of surface upon which to spread or the serum concentration in the medium. Population densities in culture never approach those found in whole organisms.
assist in the formation of large multi-molecular complexes. The term is applied, for example, to proteins that maintain the clustering of particular receptors at synapses (see, inter alia, caveolins, flotillins), to proteins involved in assembling the viral capsid, and to proteins involved in eukaryotic chromosome structure. See also AKAP79, involucrin, titin.
sauvagine Peptide (40aa) originally isolated from the skin of the frog, Phyllomedusa sauvagei, closely related to corticotrophin releasing factor and to urotensin I.
sax saxophone The receptor in Drosophila for gbb, the ortholog of the human Activin Receptor-Like Kinase-1 and -2. A serine/threonine protein kinase (570aa). Research article: http://www.genetics.org/ content/183/2/563.long
saxitoxin STX Neurotoxin produced by the ‘red tide’ dinoflagellates, particularly Alexandrium (formerly Gonyaulax) catenella. It accumulates in shellfish and when ingested binds to the sodium channel, blocking the passage of action potentials. Its action closely resembles that of tetrodotoxin. The toxin was originally isolated from the clam, Saxidomus giganteus and is responsible for paralytic shellfish poisoning.
sbcc protein In E. coli, a nuclease (1048aa) that cleaves DNA hairpin structures. Forms a heterodimer with sbcD.
scaffoldins A family of proteins (CipA, cipB etc.,
B2000aa) of the bacterial cellulosome that organize and position other protein subunits into the complex. The scaffoldins (scaA (cipBc), scaB, scaC, and scaD) can also serve as an attachment device for fastening the cellulosome to the cell surface and/or for its targeting to cellulose substrate.
SCAMPs See secretory carrier-associated membrane proteins.
scanning
electron microscopy SEM Technique of electron microscopy in which the specimen is coated with heavy metal, and then scanned by an electron beam. The image is built up on a monitor screen, in the same way as the raster builds an image on a cathode ray tube. The resolution is not so great as with transmission electron microscopy, but preparation is easier (often by fixation followed by critical point drying), the depth of focus is relatively enormous, the surface of a specimen can be seen (though not the interior unless the specimen is cracked open), and the image is aesthetically pleasing.
scanning ion conductance microscopy A
mite Sarcoptes scabiei which burrows in the horny layer of the skin and causes an inflammatory reaction.
contact-free scanning technique which uses electrical resistance changes to detect the distance between the scanning tip, a glass microelectrode, and an insulator, which can be the surface of a live cell. Variants of the technique involve using current pulses to avoid electrode drift and other interference. Article: http://www.formatex.org/microscopy3/pdf/pp968975.pdf
scaffold-attachment regions Specific DNA
scanning probe microscopy SPM Methods
sequences involved in interactions with the protein nuclear scaffold. Scaffold attached regions (SARs) are thought to be the bases of DNA loops and are sections of genome of variable length.
for visualizing surfaces at microscopic scale that rely on moving a tiny probe over a surface (usually in an x-y scan), and recording some property of interest (current, force) at each coordinate. These techniques have the ability to resolve detail down to single atoms. See also scanning tunnelling microscopy, scanning ion conductance microscopy and atomic force microscopy.
SBDS See Shwachman-Diamond syndrome. SC-35 See ASF/SF-2. scabies A contagious skin disease caused by the
scaffold/radial loop model Model for chromatin organization in eukaryotic metaphase chromosomes. Involves a non-histone protein core that is coiled and to which the linear DNA molecule has an ordered series of attachment points every 30290 kbp, with intervening DNA forming a loop that is supercoiled or folded. The 1502200 nmdiameter central core contains structural maintenance of chromosomes 2 (SMC2) protein and topoisomerase II.
scanning transmission electron microscopy STEM Method of electron microscopy in which image formation depends upon analysis of the pattern of energies of electrons that pass through the specimen. Has comparable resolving power to conventional transmission EM.
scanning tunnelling microscopy
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SCG10 gene
scanning tunnelling microscopy STM A form
Scatchard plot A method for analysing data for
of ultra-high resolution microscopy of a surface in which a very small current is passed through a surface and is detected by a microprobe of atomic dimensions at its tip that scans the surface by use of a piezodrive. In the simplest form the current transferred to the probe is recorded as an indication of the contours of molecules on the surface above the local plane. In more complex forms feedback is used to hold the probe at a constant difference and the signal in the feedback loop indicates the contours of the molecule. Capable of resolving single atoms and known to work for non-conducting molecules as well as conducting ones.
freely reversible ligand/receptor binding interactions. The graphical plot is: (Bound ligand/Free ligand) against (Bound ligand); the slope gives the negative reciprocal of the binding affinity, the intercept on the x-axis the number of receptors (Bound/Free becomes zero at infinite ligand concentration). The Scatchard plot is preferable to the Eadie-Hoffstee plot for binding data because it is more dependent upon the values at high ligand concentration, the most reliable values. A non-linear Scatchard plot is often taken to indicate heterogeneity of receptors, although this is not the only explanation possible.
scatter factor A motility factor (motogen) isolated
a protein involved in feedback inhibition of the sterol regulatory element-binding protein (SREBP) pathway. Sterols prevent movement of the SCAP/ SREBP complex from the endoplasmic reticulum to the Golgi, where proteolytic cleavage of SREBPs would release the transcription factor domain and activate genes for lipid biosynthesis.
from conditioned medium in which human fibroblasts have been grown. It causes colonies of epithelial and endothelial cells, in culture, to separate into single cells that move apart i.e. they scatter. It has been shown to be identical to human hepatocyte growth factor (728aa), but it is not mitogenic for all cell types. Defects are responsible for a form of autosomal recessive deafness.
SCAPER S phase cyclin A-associated protein in the
scavenger receptors Structurally diverse family
SCAP SREBP cleavage-activating protein (1279aa),
endoplasmic reticulum. A zinc-finger regulatory protein (1399aa) that transiently maintains the cyclinA2CDK2 complex in the cytoplasm. Does not interact with cyclinA2 uncomplexed with CDK2, nor with other cyclin-CDC complexes.
scar A WASP-related protein, binds the p21 subunit of the Arp 2/3 complex and is an endogenous activator of actin polymerization. See WAVEs.
scarb Gene family that encodes scavenger receptors of class B. These receptors bind ligands such as phospholipids, cholesterol ester, lipoproteins, phosphatidylserine and apoptotic cells and are located in caveolae. They facilitate the flux of free and esterified cholesterol between the cell surface and extracellular donors and acceptors. Scarb1 (CD36-like 1, 552aa), scarb2 (CD36L-2, 478aa).
SCARECROW Transcription factor (GRAS-family protein 20, 653aa) required for quiescent centre specification and maintenance of surrounding stem cells, and for the asymmetric cell division involved in radial pattern formation in roots. Also required for normal shoot gravitropism. There is a family of Scarecrow-like (SCL) putative transcription factors. See GRAS family.
SCARF Endothelial cell scavenger receptors. SCARF1 (scavenger receptor class F, member 1, acetyl LDL receptor, 830aa) is involved in the binding and degradation of acetylated low density lipoprotein but also in heterophilic adhesion. SCARF2 (scavenger receptor expressed by endothelial cells 2, 866aa) is probably an adhesion protein mediating hom*ophilic and heterophilic interactions. Mutations in SCARF2 are associated with Van Den Ende-Gupta syndrome.
of receptors on macrophages that are involved in the uptake of modified LDL and have been implicated in development of atherosclerotic lesions. Six classes are recognized with different binding preferences. Macrophage scavenger receptors Class A bind a wide range of ligands, including bacteria and scavenger receptors may be important in recognizing apoptotic cells. See collectins and scarb.
Scenedesmus A non-motile colonial alga, of the Order Chlorococcales, consisting of 2, 4 or 8 elongated cells, often with long spines on the terminal cells. Common in ponds and as planktonic forms in rivers and lakes.
S cells See secretin. SCF (1) See stem cell factor. (2) SCF complexes are a class of E3 ubiquitin protein ligases (a multiprotein aggregate of Skp1p-cdc53p-F-box protein) that play a role in regulation of cell division. The F-box component of the complex gives substrate specificity for ubiquitinylation. See skp and cullin.
scFv Single-chain variable fragment. A fusion of the variable regions of the immunoglobulin heavy and light chains linked together with a short peptide linker and produced by recombinant methods in bacteria. Can be selected to be specific for antigens of choice by various selection methods.
SCG10 gene A neural-specific gene (superior cervical ganglion-10) that encodes a growth-associated protein (179aa) expressed early in the development of neuronal derivatives of the neural crest and that is associated with the membranous organelles that accumulate in growth cones. SCG10-like protein (SCLIP, stathmin-like 3, 180aa) forms a complex
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(2 tubulins: 1 stathmin-like protein) thereby affecting microtubule dynamics. See stathmin.
Scheie syndrome Mucopolysaccharidosis (lysosomal disease) in which there is a defect in α-L-iduronidase. Fibroblasts from Scheie syndrome patients do not cross-correct fibroblasts from Hurler’s disease; Hurler and Scheie syndromes represent phenotypes at the severe and mild ends of the clinical spectrum.
Schick test A test, introduced by Schick in 1913, to assess the degree of susceptibility or immunity of individuals to diphtheria by challenging with a small amount of diphtheria toxin injected intracutaneously into one forearm.
scintillation proximity assay
schizogony The division of cells, especially of protozoans, in non-sexual stages of the life history of the organism.
Schizosaccharomyces pombe Species of fission yeast commonly used for studies on cell cycle control because there is a distinct G2 phase to the cycle. Only distantly related to the budding yeast Saccharomyces cerevisiae. A further advantage for experimental studies is that some mammalian introns are processed correctly.
Schmidt’s syndrome See autoimmune polyendocrinopathy syndrome.
Schulman-Upshaw syndrome See thrombotic thrombocytopenic purpura.
Schiff base The product of the reaction of a pri-
Schultz-Charlton test Old test for scarlet fever
mary amine with an aldehyde or ketone, an imine. When an arylamine is used the Schiff base may form an intermediate in a staining reaction, e.g. for polysaccharides.
in which antibody to erythrogenic toxin of Streptococcus pyogenes is injected subcutaneously.
Schiff’s reagent See periodic acid-Schiff reaction. Schilder’s disease A rare progressive demyelinating disorder (myelinoclastic diffuse sclerosis, diffuse sclerosis, encephalitis periaxialis) which usually begins in childhood, a variant of multiple sclerosis.
schistocytes Fragments of red blood cells found in the circulation.
schistosomiasis bilharzia Disease caused by trematode worms (flukes). Three main species, Schistosoma haematobium, S. japonicum, and S. mansoni, cause disease in man. Larval forms of the parasite live in freshwater snails; cercariae liberated from the snail burrow into skin, transform to the schistosomulum stage, and migrate to the urinary tract (S. haematobium), liver or intestine (S. japonicum, S.mansoni) where the adult worms develop. Eggs are shed into the urinary tract or the intestine and hatch to form miracidia which then infect snails, completing the life cycle. Adult worms cause substantial damage to tissue and seem to resist immune damage by mechanisms that are not fully understood.
schistosomulum Pl. schistosomula. See schistosomiasis.
schizocoel Coelom that is developed within the mass of mesoderm by splitting or cleavage. Cf. enterocoel.
schizogeny A mechanism of aerenchyma formation in plants in which development results in the cell separation. Schizogenous aerenchyma is common in wetland species like Rumex (dock) and is formed by cell separation, without the cells dying. See lysigeny.
Schwann cell A specialized glial cell that wraps around vertebrate axons providing extremely good electrical insulation. Separated by nodes of Ranvier about once every millimetre, at which the axon surface is exposed to the environment. See saltatory conduction, myelin.
Schwannoma-derived growth factor SDGF See amphiregulin.
Schwartz-Jampel syndrome A progressive growth disorder. Type 1 (SJS1) is caused by mutation in the gene encoding perlecan. The SilvermanHandmaker type of dyssegmental dysplasia is caused by a different mutation in the same gene and has a more severe phenotype. Neonatal Schwartz-Jampel syndrome type 2 (Stuve-Wiedemann syndrome) has a more severe phenotype caused by mutation in the leukaemia inhibitory factor receptor (LIFR} gene.
Schwartzmann
reaction Mis-spelling
of
Shwartzman reaction.
SCID See severe combined immunodeficiency disease.
scinderin See adseverin. scintillation counting Technique for measuring quantity of a radioactive isotope present in a sample. In biology, liquid scintillation counting is mainly used for β emitters such as 14C, 35S and 32P and particularly for the low energy β emission of 3H. Gamma emissions are often measured by counting the scintillations that they cause in a crystal. Autoradiographic images can be enhanced by using a screen of scintillant behind the film.
scintillation proximity assay Assay system in which antibody or receptor molecule is bound to a bead that will emit light when β emission from an isotope occurs in close proximity, i.e. from a
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radioactively-labelled ligand. Avoids the need for scintillant in order to measure the amount of bound isotope and thus the amount of antigen or ligand present.
scintillons Cytoplasmic bodies (ca. 0.5 μm in diameter) found in the cortical region of dinoflagellates as an outpocket of the main cell vacuole. They contain luciferase and luciferin and are responsible for the production of luminescence, a brief (0.1 sec) blue flash (max 476 nm) when stimulated, usually by mechanical disturbance. Dinoflagellates produce most of the bioluminescence in the oceans.
SCIP POU-domain transcription factor (Oct-6, Tst-1, 451aa) expressed by promyelinating Schwann cells (where it represses expression of the myelin structural genes) and, in tissue culture, by oligodendrocyte progenitors.
scirrhous carcinoma Carcinoma having a hard structure because of excessive production of dense connective tissue.
sclereid Type of sclerenchyma cell that differs from the fibre cell by not being greatly elongated. Often occurs singly (an idioblast) or in small groups, giving rise to a gritty texture in, for instance, the pear fruit, where it is known as a ‘stone cell’. May also occur in layers, e.g. in hard seed coats.
sclerenchyma Plant cell type with thick lignified walls, normally dead at maturity and specialized for structural strength. Includes fibre cells, that are greatly elongated, and sclereids, that are more isodiametric. Intermediate types exist.
scleritis An inflammatory disease that affects the conjunctiva, sclera, and episclera (the connective tissue between the conjunctiva and sclera). It is associated with underlying systemic diseases such as Wegener’s granulomatosis or rheumatoid arthritis in about half of the cases.
scleroderma A chronic autoimmune connective tissue disorder (systematic sclerosis) in which there is immune activation, vascular damage, and fibrosis of the skin and major internal organs. There are some genetic predisposing factors and antibodies to fibrillarin are found in some cases. See CREST syndrome, RNaseP.
sclerosis Pathological hardening of tissue. But see amyotrophic lateral sclerosis, Balo’s concentric sclerosis, multiple sclerosis, Schilder’s disease, scleroderma, tuberous sclerosis.
sclerosteosis A rare autosomal recessive bone dysplasia affecting mainly the skull and mandible and leading to facial paralysis and hearing loss. Caused by mutation in the coding region of the gene for sclerostin. In van Buchem’s disease there is down-regulation of sclerostin production.
scorpion toxins
sclerostin An antagonist (213aa) for bone morphogenic protein (BMP) that represses osteoblast differentiation and function but in turn is inactivated by noggin. Sclerostin has a cystine knot motif (residues 802167) similar to that in the cer/dan family. The gene is mutated in sclerosteosis and downregulated in van Buchem’s disease. Sclerostin-domain containing protein-1 (ectodin, 206aa) inhibits BMP2, BMP4, BMP6, and BMP7.
sclerotia Quiescent, multicellular aggregates of vegetative hyphae (several mm to several cm in size) which allow species of the fungus Sclerotinia to survive for long periods of time under adverse conditions. They have a black, melanized rind which is resistant to microbial invasion and physical insult. Sclerotia can undergo myceliogenic or carpogenic germination to produce infective hyphae or apothecia.
sclerotin Hard, dark-coloured cross-linked (tanned) protein found in the cuticle of insects and some other arthropods.
Sclerotinia sclerotiorum A nonspecific, ascomycete pathogen of plants. The fungus infects 64 families of plants, many of economic importance. About 90% of the life cycle of Sclerotinia species is spent in soil as sclerotia, which germinate under the right conditions to form a mycelium which can infect a host, or an apothecium. Resource page: http://www.sclerotia.org/
SCN (1) The suprachiasmatic nucleus of the hypothalamus. (2) The thiocyanate anion (SCN2). (3) See voltage-gated sodium channels.
SCO-spondin See spondins. scoliosis An abnormal lateral curvature of the spine which may be idiopathic or a secondary feature of disorders including Marfan’s syndrome, dysautonomia, neurofibromatosis, Friedreich’s ataxia and muscular dystrophies.
scombrotoxin Causative agent of scombroid poisoning (histamine poisoning), caused by eating foods (spoiled fish, some cheeses) with high levels of histamine and possibly other vasoactive amines and compounds produced by bacteria.
scopolamine hyoscine An alkaloid found in thorn apple (Datura stramonium). Related to atropine both in effects and structure and acts as a muscarinic acetylcholine receptor antagonist.
scopoletin A naturally occurring fluorescent component (7-hydroxy-6-methoxycoumarin) of some plants that acts as a plant growth inhibitor. Said to lower blood pressure in hypertension and raise it in hypotension; also to be bacteriostatic and antiinflammatory. An acetylcholine esterase inhibitor.
scorpion toxins Polypeptide toxins (B7 kDa) with four disulphide bridges. The α-toxins are found in
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venom of Old World scorpions, β-toxins in those of the New World. Bind with high affinity to the voltage-sensitive sodium channel of nerve and muscle (α and β toxins bind to different sites).
scotophobin Peptide (15aa) isolated from brains of rats trained to avoid the dark that will transfer this aversion to naive animals. The original claim was treated with considerable scepticism and the topic remains contentious.
scramblases A family of cytoplasmic membraneassociated proteins (phospholipid scramblase-1, PLSCR1, 318aa; PLSCR2, 224aa; PLSCR3, 295aa; PLSCR4, 329aa) that mediate an ATP-independent Ca21-dependent transbilayer flip/flop of membrane lipids, causing the loss of the normal phospholipid asymmetry of the plasma membrane. They have some similarities with tubby. May have a role in initiating fibrin clot formation, activating mast cells, the recognition of apoptotic and injured cells and amplifying the interferon response. Research article: http://bioinformatics.oxfordjournals.org/content/25/2/ 159.long
scrapie A chronic neurological disease of sheep and goats, similar to other spongiform encephalopathies and much used as a model for studying the diseases. Controversy still surrounds the nature of the transmissible agent, although the idea of slow viruses has been overtaken by Prusiner’s prion hypothesis, which is now fairly generally accepted. Atypical forms of the disease seem to be emerging in sheep of the genotypes that are resistant to the classical form.
screw A protein (400aa) in Drosophila that acts together with decapentaplegic in specifying dorsal cell fates in the embryo.
scRNP Small cytoplasmic ribonucleoprotein. See small interfering RNA.
scrub typhus See shimamushi fever. scruin Actin-binding protein (alpha, 918aa; beta,
SDH
scurvy Disease caused by vitamin C deficiency. The effects are due to a failure of the hydroxylation of proline residues in collagen synthesis, and the consequent failure of fibroblasts to produce mature collagen. See hydroxyproline.
scutellum Part of the embryo in seeds of the Poaceae (grasses). Can be considered equivalent to the cotyledon of other monocotyledenous seeds. During germination, absorbs degraded storage material from the endosperm and transfers it to the growing axis.
SCY cytokine superfamily A superfamily of small cytokines with chemokine activity. The SCYA family are CC-chemokines (CCL12CCL28), the SCYB family are CXC chemokines (CXCL12 CXCL16), the SCYC family are the C-chemokines (XCL1 and XCL2). SCYD1 is fractalkine (neurotactin, CX3CL1); SCYE1 is the gene for EMAP-II. See Table C3.
scyllatoxin Toxin (31aa) from the scorpion Leiurus quinquestriatus hebraeus that specifically blocks low conductance calcium-dependent potassium channels (SK channels) that are also a target for apamin.
scyphozoa Jellyfish. A class within the phylum Cnidaria in which the polyp stage is inconspicuous or completely absent. Fuller description: http:// www.mbl.edu/BiologicalBulletin/KEYS/INVERTS/3/ Dscyphozoakeys.htm
scytalidopepsins Pepstatin-insensitive acid endopeptidases from the fungus Scytalidium lignicolum. Scytalidopepsin A (EC 3.4.23.31) is one of the sedolisin family of serine-carboxyl peptidases. Scytalidopepsin B (EC 3.4.23.32, scytalidoglutamic peptidase, 260aa) is the type peptidase of the glutamic (G1) peptidase family (See MEROPS).
SD sequence See Shine-Dalgarno region. SDAM An autosomal dominant form of caudal dysgenesis (sacral defect with anterior meningocele) caused by mutations in the VANGL1 gene that encodes vang-like protein 1.
916aa) found associated with the acrosomal process of Limulus polyphemus sperm. Scruin holds the microfilaments of the core process in a strained configuration so that the process is coiled. The myosin binding sites on the microfilaments are blocked so HMM decoration is impossible, indicating that there is an unusual packing conformation; when the scruin-actin binding is released the process straightens, the conformation of the actin changes and myosin binding is possible.
SDF-1 A chemokine (stromal cell derived factor-1,
scurfy A murine X-linked lymphoproliferative dis-
nase. The SDHA, SDHB, SDHC and SDHD genes encode the subunits of succinate dehydrogenase (succinate: ubiquinone oxidoreductase), a component of both the Krebs cycle and the mitochondrial respiratory chain. Less often: (2) Sorbitol dehydrogenase.
ease, similar to the Wiskott-Aldrich syndrome in humans, caused by mutation of the foxp3 gene which affects the development and maintenance of CD41 regulatory T-cells.
CXCL12, 93aa) that controls many aspects of stem cell function, including trafficking and proliferation. The receptor is CXCR4. Originally known as pre-B cell growth-stimulating factor and identical to human intercrine reduced in hepatomas (hIRH).
SDGF Schwannoma-derived growth factor. See amphiregulin.
SDH Most commonly, (1) Succinate dehydroge-
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(3) Saccharopine dehydrogenase. (4) Serine dehydratase. (5) Shikimate 5-dehydrogenase.
SDS Sodium dodecyl sulphate (sodium lauryl sulphate). Anionic detergent that at millimolar concentrations will bind to and denature proteins, forming an SDS-protein complex. The amount of SDS bound is proportional to the molecular weight of the protein, and each SDS molecule, bound by its hydrophobic domain, contributes one negative charge to the protein thus swamping its intrinsic charge. This property is exploited in the separation of proteins by SDS-PAGE.
SDS-PAGE Polyacrylamide gel electrophoresis (PAGE) in which the charge on the proteins results from their binding of SDS. Since the charge is proportional to the surface area of the protein, and the resistance to movement proportional to diameter, small proteins migrate further.
sdt In Drosophila a protein (stardust, EC 2.7.4.8) with guanylate kinase activity that is a component of the SAC complex that determines epithelial polarity. There are multiple isoforms rannging from 731aa to 2020aa.
sea An oncogene (S13 avian erythroblastosis oncogene hom*ologue) that encodes a member of the Met/ hepatocyte growth factor/scatter factor family of receptor tyrosine kinases.
SEA0400 Potent and selective inhibitor of the Na1/
Ca21 exchanger. Research article: http://www.ncbi. nlm.nih.gov/pmc/articles/PMC1575948/?tool 5 pubmed
sea-blue histiocyte disease A disorder caused by a defect in apolipoprotein E. There is splenomegaly, mild thrombocytopenia and many histiocytes in the bone marrow with cytoplasmic granules that stain bright blue (hence the name).
sea hare See Aplysia. seam cells Specialised epithelial cells in C. elegans that lie along the apical midline of the hypodermis, at the extreme left and right sides between nose and tail. During postembryonic development, they can act as stem cells to produce neurons and are responsible for production of the cuticular alae in L1 stage, dauer larvae, and adults. See let-7. Description: http://www. wormatlas.org/handbook/anatomyintro/anatomyintro.htm
sebacic acid A naturally occurring dicarboxylic acid commercially produced from castor oil and used in production of various plastics. As a copolymer with glycerol (poly(glycerol sebacate)) has promising properties for tissue engineering. Website of commercial supplier: http://www.sebacicacid.com/
Sebastian syndrome See May-Hegglin anomaly.
second messenger
SEC (1) Serpin-enzyme complex, see serpins. (2) Selenocysteine (Sec). (3) Size-exclusion chromatography (SEC). (4) The general secretory (sec) pathway in bacteria (see sec-dependent transport). (5) See sec proteins.
SecA A bacterial protein (901aa in E. coli) that couples ATP hydrolysis to the transfer of proteins into and across the cell membrane. Acts as a receptor for the preprotein-secB complex and as an ATPdriven molecular motor. Interacts with the secYEG preprotein conducting channel. See sec-dependent transport.
sec-dependent
transport Pathway for the secretion of proteins across the inner membrane into the periplasm of Gram-negative bacteria using the general translocase SecYEG. The SecA protein recognises the signal sequence of proteins destined for export. Also used for the insertion of inner membrane proteins, in some cases in association with YidC. Other translocation mechanisms involve the Tat system and YidC. SecYEG is a trimeric complex where Y and E are related to sec61α and γ subunits (see secA).
sec proteins Proteins involved in sec-dependent transport. In S. cerevisiae Sec 1 (724aa) is involved in the final stage of protein secretion. Sec7 has a domain of around 200aa that is found in several GEFs for ADP ribosylation factors (ARFs); mutations lead to accumulation of Golgi cisternae and loss of secretory granules. Various other Sec proteins (Sec13, Sec16, Sec23, Sec24, Sec31) are components of the COPII coat protein complex. Sec61 is a conserved heterotrimeric protein-conducting channel (translocon) in eukaryotes (hom*ologous to the SecY channel in eubacteria and archaea) that associates with the sub-complex Sec62/Sec63 and translocates proteins across cellular membranes and integrates proteins containing hydrophobic transmembrane segments into lipid bilayers. Sec61a (Ssh1, 476aa) is a multispanning membrane protein, Sec61b (SEB2, 88aa) kinetically facilitates cotranslational translocation and interacts with the 25-kD subunit of the signal peptidase complex (SPC25), Sec61γ (SSS1, 80aa) is the third component. Sec65 in S. cerevisiae is a subunit of the signal recognition particle similar to mammalian SRP19. See also exocyst complex.
secernins A subfamily of the peptidase C69 family. Secernin-1 (p50, 414aa) was originally isolated from bovine brain cytosol and shown to regulate exocytosis in mast cells. Secernin-2 (425aa) and secernin-3 (424aa) are known. Research article: http://www. molbiolcell.org/cgi/content/full/13/9/3344
second messenger The intracellular mediator of responses to signalling substances such as peptide hormones that do not cross the plasma membrane but bind to receptors on the cell surface. The second
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messenger may be the same for several different intercellular signalling molecules and may therefore integrate signals. Examples include cyclic AMP, cyclic GMP, IP3 and diacylglycerol.
secondary granules See specific granules. secondary immune response The response of the immune system to the second or subsequent occasion on which it encounters a specific antigen.
secondary lymphoid tissue See lymphoid tissue.
secretion systems peptidase that generates the N-terminus of the beta-amyloid protein from APP; further cleavage is then carried out by gamma-secretase. It is an integral membrane protein. Beta-secretase-2 (EC 3.4.23.45, theta-secretase, memapsin-1, 518aa) has similar activity. Gamma-secretase is a multi-protein complex that will cleave amyloid precursor protein (APP) and other type I transmembrane proteins such as notch and E-cadherin. There are four components, presenilin, nicastrin, APH-1 and PEN-2, all required for proteolytic activity, and a fifth component, CD147, with a regulatory role.
secondary lysosome Term used to describe
secretin Peptide hormone (27aa derived from a
intracellular vacuoles formed by the fusion of lysosomes with organelles (autosomes) or with primary phagosomes. Residual bodies are the remnants of secondary lysosomes containing indigestible material.
121aa precursor peptide) secreted by S cells in the duodenal mucosa. Stimulates secretion of pepsin by the pancreas and bile, but inhibits secretion of gastric acid. One of the secretin family of hormones that also includes gastric inhibitory peptide, glucagon, glucagon like peptide-1, growth hormone releasing hormone, helodermin, peptide histidine methionine, pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal peptide. The receptor (440aa) is G-protein coupled.
secondary metabolite A product excreted by a microorganism as it enters stationary phase.
secondary phloem Phloem formed during secondary growth by the activity of a vascular cambium as opposed to primary phloem that is derived from procambium.
secondary product An end-product of plant cell metabolism, which accumulates in, or is secreted from, the cell. Includes anthocyanins, alkaloids, amongst others. Some are of major economic importance, e.g. as drugs. In contrast to a primary product that is involved in the vital metabolism of the plant.
secondary structure See primary structure. secondary wall That part of the plant cell wall which is laid down on top of the primary cell wall after the wall has ceased to increase in surface area. Only occurs in certain cell types, e.g. tracheids, vessel elements and sclerenchyma. Differs from the primary wall both in composition and structure, and is often diagnostic for a particular cell type.
secondary xylem Xylem formed by the activity of a vascular cambium as a plant grows. Wood is composed largely of secondary xylem.
secretagogue Substance that induces secretion from cells; originally applied to peptides inducing gastric and pancreatic secretion.
secretases A family of peptidases involved in processing of membrane-bound precursor molecules. Alpha-secretase (ADAM10, EC 3.4.24.81, CD156c, 748aa) has broad proteolytic activity and cleaves amyloid precursor protein (APP) to the soluble non-amyloidogenic product sAPP alpha. It also processes heparin-binding epidermal growth-like factor, ephrin-A2 and TNF. Beta-secretase-1 (BACE-1, Beta-site APP cleaving enzyme 1, EC 3.4.23.46, 501aa) is the major beta-secretase in vivo, an aspartic
secretion Release of synthesized product from cells. Release may be of membrane-bounded vesicles (merocrine secretion) or of vesicle content following fusion of the vesicle with the plasma membrane (apocrine secretion). In holocrine secretion whole cells are released.
secretion systems There are various different bacterial secretory systems. In the Type I secretion system (T1SS, TOSS) there is a contiguous channel that traverses the inner and outer membranes of Gram-negative bacteria. There are only three protein subunits: the ABC protein, membrane fusion protein (MFP), and outer membrane protein (OMP). The Type I secretion system transports various molecules including ions, drugs and proteins of various sizes (202900 kDa). The Type II system (T2SS) in Gramnegative bacteria depends upon the Sec or Tat system for initial transport of proteins into the periplasm from where they pass through the outer membrane via a multimeric (12214 subunits) complex of pore forming secretin proteins. In addition to the secretin proteins, 10215 other inner and outer membrane proteins compose the full secretion apparatus, many with as yet unknown function. In some bacteria, certain proteins are shared between the pilus complex and the type II system. The Type III system (TTSS, T3SS) is essential for pathogenicity of many Gram-negative bacteria, and allows them to translocate proteins into eukaryotic host cells. The type III secretion apparatus (T3SA) is a multisubunit membrane-spanning macromolecular assembly comprising more than 20 different protein, some of which have sequence hom*ology with flagellar proteins. The TTSS encoded in Salmonella Pathogenicity Island 2 (SPI2) is critical for adaptation to the intracellular environment within both
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phagocytic and epithelial cell types. The Type IV secretion system (T4SS, TFSS) is hom*ologous to the conjugation machinery of bacteria and to archaeal flagella. It is capable of transporting both DNA and proteins. Discovered in Agrobacterium tumefaciens which uses this system to introduce the T-DNA portion of the Ti plasmid into the plant host, which in turn causes the development of a crown gall.
secretogranins See granins. secretoneurin A polypeptide (33aa) derived by proteolytic cleavage from secretogranin II (617aa; see granins) that stimulates dopamine release from striatal neurons, and gonadotropin II secretion from the pituitary; inhibits serotonin and melatonin release from pinealocytes. Activates monocyte migration, and probably has a role in neurogenic inflammation. The receptor is G-protein coupled.
secretor A person who secretes ABO blood group substances into mucous secretions, e.g. saliva; at least 80% of humans are secretors.
secretory carrier-associated membrane proteins A family of integral membrane proteins (SCAMPs, tetraspan vesicle membrane proteins) of post-Golgi membranes that function as recycling carriers to the cell surface. At least five members of the family have been identified ( SCAMP1, 338aa; SCAMP2, 329aa; SCAMP3, 347aa, SCAMP4, 229aa; SCAMP5, 235aa) with different tissue distributions and transport activities. In Arabidopsis similar proteins (e.g. SCAMP1, 282aa) are probably involved in membrane trafficking.
secretory cells Cells specialized for secretion, usually epithelial. Those that secrete proteins characteristically have well developed rough endoplasmic reticulum, whereas conspicuous smooth endoplasmic reticulum is typical of cells that secrete lipid or lipid-derived products (e.g. steroids). In plants secretory cells release substances such as mucins and latex.
secretory component secretory piece A secreted polypeptide chain (585aa) cleaved from the polyimmunoglobulin receptor (764aa). This receptor binds polymeric IgA and IgM at the basolateral surface of epithelial cells, the complex is then transported across the cell and is secreted at the apical surface. During the secretory process the secretory component is cleaved from the transmembrane segment of the receptor.
secretory proteins In eukaryotes, proteins synthesized on rough endoplasmic reticulum and destined for export. Nearly all proteins secreted from cells are glycosylated in the Golgi apparatus, although there are exceptions (e.g. albumin). In prokaryotes, secreted proteins may be synthesized on
Segawa syndrome ribosomes associated with the plasma membrane or exported post-translation.
secretory vesicle Membrane-bounded vesicle derived from the Golgi apparatus and containing material that is to be released from the cell. The contents may be densely packed, often in an inactive precursor form (zymogen).
securin An inhibitor (pituitary tumour-transforming gene 1 protein, 202aa) of the anaphase activator separin (separase/Esp1p). It is ubiquitinated by activated anaphase-promoting complex; loss of securin leads to proteolytic cleavage of cohesin. Defects in securin may contribute to chromosomal instability.
sedimentation Settling of a component of a mixture under the influence of gravity or centrifugation so that the mixture separates into two or more phases or zones.
sedimentation coefficient The ratio of the velocity of sedimentation of a molecule to the centrifugal force required to produce this sedimentation. It is a constant for a particular species of molecule, and the value is given in Svedberg units (S) that are non-additive.
sedimentation test A standard blood test that involves measuring the rate of settling of erythrocytes in anti-coagulant treated blood. Erythrocyte sedimentation rates (ESR) are increased in inflammation.
sedlin An evolutionarily conserved protein (140 aa), a subunit of the Transport Protein Particle (TRAPP) complex, involved in targeting and fusion of endoplasmic reticulum (ER)-derived transport vesicles to the Golgi acceptor compartment. Encoded by the causative gene SEDL for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder. The intracellular chloride channel protein CLIC1 has been shown to associate with sedlin by yeast two-hybrid screening. Research article: http://www.ncbi.nlm.nih. gov/pmc/articles/PMC2871040/?tool 5 pubmed
sedoheptulose Seven-carbon sugar, whose phosphate derivatives are involved in the pentose phosphate pathway and the Calvin-Benson cycle.
seed fern Pteridospermae A group of extinct ferns that flourished in the Devonian period.
Segawa syndrome A childhood disorder (infantile Parkinsonism) in which there is severe motor retardation. The autosomal recessive form is caused by mutation in the tyrosine hydroxylase gene and an autosomal dominant form by mutation in the gene that encodes GTP cyclohydrolase I (EC 3.5.4.16), the rate-limiting enzyme in synthesis of tetrahydrobiopterin, an essential cofactor for phenylalanine, tyrosine, and tryptophan hydroxylases. Infantile parkinsonism-dystonia syndrome is caused
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by mutation in the SLC6A3 gene that encodes a dopamine transporter.
segment long-spacing collagen See SLS collagen.
segmentation Organization of the body into repeating units called segments, a common feature of several phyla, e.g. arthropods and annelids, although the segments arise by very different mechanisms. Segmentation also occurs during embryonic development in vertebrates, e.g. partition of the mesoderm into somites, and is a feature of early CNS development. See rhombomeres, neuromeres.
segmentation gene Genes required for the establishment of segmentation in the embryo. In Drosophila about 20 such genes are required, for example gooseberry.
Seip syndrome A rare autosomal recessive disease (Berardinelli-Seip congenital lipodystrophy type 2) characterised by an almost complete absence of adipose tissue and severe insulin resistance. It is caused by mutation in the gene encoding seipin. See lipodystrophy.
seipin A single-pass membrane protein (398aa) of the endoplasmic reticulum, highly expressed in the brain and testis. Seipin mutations are involved in various disorders including congenital lipodystrophy type 2, Silver syndrome and distal hereditary motor neuropathy type V.
seismonasty The movement of a plant part in response to vibration (a special case of the response to touch, the thigmonastic response). The folding of the leaflets of Mimosa is the classic example. Informative webpages: http://www.biologie.unihamburg.de/b-online/e32/32d.htm
selectins addressins A family of cell adhesion molecules that have selective carbohydrate-binding capacity (selective lectins, hence the name). They are integral membrane glycoproteins with an N-terminal, C-type lectin domain, followed by an EGF-like domain, a variable number of repeats of the short consensus sequence of complement regulatory proteins and a single transmembrane domain. The prefix letter is based on the site of their original identification, although they are not restricted to these locations. E-selectin (endothelial selectin, CD62E, endothelial leukocyte adhesion molecule-1, ELAM-1, 610aa) is upregulated on endothelial cells of postcapillary venules where it is important for neutrophil margination during acute inflammation; it binds sialylated Lewis X and a particular glycoform of ESL-1 that is present on myeloid cells. L-selectin (leucocyteendothelial cell adhesion molecule, LECAM, CD62L, LAM-1, MEL-14 antigen, leu-8, 372aa) is also involved in leucocyte-endothelial adhesion, for lymphocyte homing to high endothelial venules and for implantation of the embryo to the uterine wall.
selenoprotein It binds to carbohydrates on CD34, CD162, GlyCam and MAdCAM. Once the leucocytes have migrated into tissue (diapedesis) the L-selectin is enzymatically removed by a membrane-associated metallopeptidase, a sheddase. P-selectin (platelet selectin CD62P, PADGEM, GMP-140, LECAM-3, 830aa) is rapidly upregulated in platelets and endothelial cells when activated, but only transiently expressed. It mediates rolling of neutrophils, platelets and some T-cell subsets to the endothelial lining of blood vessels. Although knock-out animals show defective cellular infiltration into inflammatory sites it is necessary to inhibit both P-selectin and E-selectin to see total blockade.
selective serotonin re-uptake inhibitors SSRIs A class of drugs that inhibit the uptake of serotonin into presynaptic cells. This increases the duration of the signal and also reduces serotonin production through a feedback mechanism. They are extensively prescribed for depression, anxiety disorders, and some personality disorders. An example is Prozac.
selector genes A group of genes that determines which part of a developmental pattern cells will be allocated within a developmental segment. Antennapedia is an example and the neural selector gene cut, that encodes a homeobox transcription factor, is required for the specification of the correct identity of external (bristle-type) sensory organs in Drosophila.
selenium Se An essential trace element that must be added as a supplement in serum-free culture media for most animal cells. Some plant species are Se tolerant and will accumulate very high concentrations of Se (accumulators), but most plants are Se non-accumulators and are Se-sensitive. See selenocysteine and selenoprotein. Review: http:// arjournals.annualreviews.org/doi/abs/10.1146/annurev. arplant.51.1.401
selenocysteine Sec An unusual amino acid of proteins, the selenium analogue of cysteine, the selenium atom replacing sulphur. Involved in the catalytic mechanism of seleno-enzymes such as formate dehydrogenase of E. coli, and mammalian glutathione peroxidase. A special opal suppressor tRNA that recognizes certain UGA nonsense codons allow it to be genomically encoded.
selenoprotein A protein that contains selenocysteine. Selenoprotein N (590aa) contains a single selenocysteine residue and is a glycoprotein localized within the endoplasmic reticulum and found in brain, muscle, lung and placenta. Mutations in the gene lead to rigid-spine muscular dystrophy. Selenoprotein P (381aa) has multiple selenocysteine residues and may be involved in antioxidant activity and possibly in selenium transport. Mitochondrial capsule selenoprotein (116aa) is important for the maintenance and stabilization of the crescent
self-antigens
595
structure of the sperm mitochondria. Selenoprotein W (87aa) may be involved in redox-related processes and may have a role in the myopathies of selenium deficiency. Selenoprotein Z (524aa) is thioredoxin reductase 2 (EC 1.6.4.5). Various other selenoproteins are known and many are involved in redox reactions.
self-antigens autoantigens Normal components of the body that can be antigens in an autoimmune response.
senataxin plexins; see also collapsin response-mediator proteins. See Table S1.
semelparity The production of offspring only once in the lifetime of the organism. Adj. semelparous.
semiautonomous Describing systems or processes that are not wholly independent of other systems or processes.
semiconservative replication The system of
structures from subunits (protomers) without any external source of information (priming structures or templates).
replication of DNA found in all cells in which each daughter cell receives one old strand of DNA and one strand newly synthesized at the preceding S phase. The existence of semiconservative replication was demonstrated by the Meselson-Stahl experiment and implied the two- or multi-strandedness of DNA.
self-cloning Any system in which inappropriate
semigamy A rare type of facultative apomixis in
cell types or organisms are eliminated because they possess some character that allows them to die or to remove themselves from the system. Thus a transfected cell with genetic material including a drug resistance marker will be self-cloning in the presence of the drug and non-transfected cells will die.
plants controlled by an incompletely dominant autosomal gene. During semigamy, the sperm and egg cells undergo cellular fusion, but the sperm and egg nucleus fail to fuse in the embryo sac, giving rise to diploid, haploid, or chimeric embryos composed of sectors of paternal and maternal origin. Early report: http:// jhered.oxfordjournals.org/content/71/2/117.extract
self-incompatibility The inability of pollen grains
semipermeable membrane A membrane that
to fertilize flowers of the same plant or its close relatives. It is a mechanism to ensure out-breeding within some plant species, e.g. in the case of the S gene complex in Brassicas where the genes encoding for SI specificity in pistil (SRK) and pollen (SCR) are thought to be preserved because there is rarely or never any recombination.
is selectively permeable to only one (or a few) solutes. The potential developed across a membrane permeable to only one ionic species is given by the Nernst equation for the species: this is the basis for the operation of ion-selective electrodes.
self-assembly The formation of higher-order
self-replicating Literally, replication of a system by itself without outside intervention. In practice often taken to refer to systems that replicate without the contribution of any information from outside the system.
self-splicing Self-catalysed removal of group 5 introns from mRNA, mediated by six paired conserved regions.
sem-5 A cell-signalling gene of C. elegans that encodes a protein (228aa) with SH2 and SH3 domains; acts in vulval development and sex myoblast migration.
semaphorins Family of proteins that mediate neuronal guidance by inhibiting nerve growth cone movement. Both transmembrane and secreted proteins are included and many domains of the proteins are highly conserved between invertebrates and vertebrates. Most are around 750aa with a conserved ‘sema’ domain of up to 500aa extracellularly with a single immunoglobulin C2-type domain C-terminally to this. Collapsin, responsible for the collapse of nerve growth cones of chick sensory neurites in culture following contact with retinal axons was one of the first semaphorins described. Receptors are
Semliki forest virus Enveloped virus of the alphavirus group of Togaviridae. First isolated from mosquitoes in the Semliki Forest in Uganda; not known to cause any human illness although it causes a lethal encephalitis in rodents. The synthesis and export of its three spike glycoproteins, via the endoplasmic reticulum and Golgi complex, have been used as a model for the synthesis and export of plasma membrane proteins.
SEN1 See senataxin. Senarmont
compensation In interference microscopy, compensation for the phase difference introduced by the object, measured by introducing a quarter-wavelength plate and rotating the analyser: the angle of rotation is proportional to the optical path difference.
senataxin A protein (2,677aa), probably a helicase (EC 3.6.1.-), which may be involved in RNA maturation. Involved in DNA double-strand break response generated by oxidative stress. The gene is mutated in spinocerebellar ataxia autosomal recessive Type 1 and in a rare autosomal dominant form of juvenile amyotrophic lateral sclerosis. Has hom*ology to SEN1 of S. cerevisiae, a helicase required for endonucleolytic cleavage of introns from all families of precursor tRNAs. It is essential for vegetative growth of the yeast.
Table S1
596
Table S1
TABLE S1. Semaphorins Class
New Name
Old name
Features of Class
Sema-1a
G-Sema I, D-Sema I, T-sema I, Ce-Sema I
TM domain and short cytoplasmic tail
Sema-1b
Sema 1b
Sema 2a
D-Sema II, Ce-Sema II, gSemaII
Secreted and have Ig domain
Sema3A
C-Collapsin-1 (Coll-1), H-Sema III, M-SemD, R-Sema III, Sema-Z1a
Ig domain, short basic domain, secreted
Sema3B
M-SemaA, H-SemaA, H-Sema V
Sema3C
M-SemE, C-Coll-3, H-Sema E
Sema3D
C-Coll-2, Sema-Z2
Sema3E
C-Coll-5, M-Sema H
Sema3F
H-Sema IV, M-Sema IV, H-Sema-3F
Sema4A
M-SemB
Sema4B Sema4C
M-SemC M-sema F
Sema4D
CD100. M-Sema G, C-Coll-4 Sema-Z7
Invertebrate Class 1
Class 2 Vertebrate Class 3
Class 4
Sema4E Sema4F
Ig domain, TM domain, short cytoplasmic domain
M-Sema W, R-Sema W, H-Sema W
Sema4G Class 5
Class 6
Class 7
Sema5A
M-SemF
Sema5B
M-SemG
7 thrombospondin repeats, TM and short cytoplasmic domain
Sema6A
M-Sema Via
Sema6B
M-SemaVIb, R-Sema Z
TM and cytoplasmic domain
Sema6C
M-Sema Y, R-Sema Y
Sema7A
H-Sema K1, H-Sema L, M-Sema L, M-Sema K1
Ig domain and GPI anchor
SEMAVA
Vaccinia sema, Variola sema
Truncated sema domain
SEMAVB
AHV sema
Sema domain 1 Ig domain
Viral Class V
Based upon Recommendation of Semaphorin Nomenclature Committee. (1999) Cell 97: 551552. All have Sema domain which is also found in some functionally unrelated proteins.
Sendai virus
597
Sendai virus Haemagglutinating virus of Japan (HVJ) Parainfluenza virus type 1 (Paramyxoviridae). Can cause fatal pneumonia in mice, and may cause respiratory disease in humans. The ability of ultraviolet-inactivated virus to fuse mammalian cells has been extensively used in the study of heterokaryons and hybrid cell lines.
senescent cell antigen An antigen (62 kDa) that appears on the surface of senescent erythrocytes and is immunologically cross-reactive with isolated band III. Seems to be recognized by an autoantibody, and the immunoglobulin-coated erythrocyte is then removed from circulation by cells such as Kuppfer cells of the liver that have Fc receptors. Intracellular cleavage of intact band III by a calcium-activated peptidase, calpain, may reveal the antigen in situ. See LIM kinases.
senile plaque Characteristic feature of the brains of Alzheimer’s disease patients and aged monkeys, consisting of a core of amyloid fibrils surrounded by dystrophic neurites. The principal component of amyloid fibrils in senile plaques is B/A4, a peptide of about 4 kDa that is derived from the larger amyloid precursor protein (APP). The B/A4 sequence is located near the C-terminus of APP.
Senior-Loken syndrome An autosomal recessive disease characterised by nephronophthisis and Leber congenital amaurosis. Various forms of the disorder are caused by mutations in genes encoding nephrocystins.
sensitization A state of increased responsiveness, usually referring to the state of an animal after primary challenge with an antigen. The term is frequently used in the context of hypersensitivity.
sensory ataxic neuropathy A clinically heterogeneous systemic disorder with variable features resulting from mitochondrial dysfunction. Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis (SANDO) is caused by mutation in the nuclear gene that encodes DNA polymerase-gamma or by mutation in the gene for twinkle. Spinocerebellar ataxia with epilepsy (SCAE) is similar.
sensory neuron (1) A neuron that receives input from sensory cells. (2) Sensory cells such as cutaneous mechanoreceptors and muscle receptors.
SEPALLATA A MADS-box subfamily of transcription factors that interact with ABCD floral homeotic genes in specifying different floral whorls. SEPALLATA1 (SEP1, agamous-like MADS-box protein AGL2, 215aa) forms a heterodimer with AGAMOUS and interacts with other members of the family.
separin A caspase-like cysteine endopeptidase (separase, EC 3.4.22.49, 2120aa), involved in cleaving the cohesin complex that links sister chromatids
septins until the metaphase to anaphase transition. Separin activity is inhibited until securin is ubiquitinated by the anaphase-promoting complex and proteolytically degraded. Cyclin-dependent kinase-1 (CDK1) phosphorylates securin and blocks ubiquitination by the APC. In S. cerevisiae separin is Esp1.
Sephacryl Trade-name for a covalently crosslinked allyl dextrose gel formed into beads. Used in gel filtration columns for separating molecules in the size range 5 kDa to 1.5 million Da.
Sephadex Trade-name for a cross-linked dextran gel in bead form used for gel filtration columns: by varying the degree of cross-linking the effective fractionation range of the gel can be altered.
Sepharose Trade-name for a gel of agarose in bead form from which charged polysaccharides have been removed. Used in gel filtration columns.
septate junction An intercellular junction found in invertebrate epithelia that is characterized by a ladder-like appearance in electron micrographs. Thought to provide structural strength and to provide a barrier to diffusion of solutes through the intercellular space. Occurs widely in transporting epithelia, and is (perhaps controversially) considered analogous to tight junctions (zonula occludens).
septic shock Condition of clinical shock caused by endotoxin in the blood. A serious complication of severe burns and abdominal wounds, frequently fatal. Part of the problem seems to be due to increased leucocyte adhesiveness, which leads to massive sequestration of neutrophils in the lung, increased vascular permeability, and acute (adult) respiratory distress syndrome.
septicaemia A potentially life-threatening infection in which many bacteria are present in the blood. Commonly referred to as blood poisoning. See bacteraemia.
septins Family of evolutionary conserved proteins (cytoskeletal GTPases, peanut-like proteins, cell division control-related proteins, B350aa) that polymerize into hetero-oligomeric complexes that form filaments, and associate with cellular membranes, actin filaments and microtubules. GTPase activity is required for filament formation. They were first identified in S. cerevisiae where they are associated with cytokinesis and septum formation and form a ring of 10 nm filaments underlying the plasma membrane in the mother-bud neck. hom*ologous proteins, associated with cleavage furrows, are reported from Drosophila, amphibians and mammals but not from protozoa or plants, and they are also involved in membrane dynamics, vesicle trafficking, apoptosis, and cytoskeletal remodelling. There are at least 14 human septins with tissue-specific isoforms in many cases. A deficiency in septin-5 degradation may contribute to the development of early onset Parkinson’s
septum
598
disease 2, septin-7 interacts with CENP-E at the kinetochore. Mutations in septin-9 are associated with hereditary neuralgic amyotrophy. Review: http://genomebiology.com/2003/4/11/236
septum Literally a separating wall. Mainly applied to the structure composed of plasmalemmae and cell wall material formed in cell division in prokaryotes and fungi. Also applied to the sealing layers in various packages of sterile fluids, or barriers through which injections, needles etc., may be passed.
Seqboot A data-analysis package that allows
SERK genes concentrate positively charged proteases, histamine and other molecules within the storage granules.
sericin A serine-rich protein (1186aa in Bombyx mori) found in silk. It forms a sticky coat on the fibroin threads and cements them together. It is finding a range of uses in biotechnological applications.
serinc Class of carrier proteins (serine incorporators, e.g,, serinc-1, 453aa; serinc-2, 456aa) that facilitate the synthesis of serine-derived lipids, phosphatidylserine and sphingolipids. Serinc is a unique protein family that shows no amino acid hom*ology to other proteins but is highly conserved among eukaryotes. The members contain 11 transmembrane domains. Research article: http://www.jbc.org/content/280/42/ 35776.long
bootstrap, jackknife, or permutation resampling of molecular sequence, restriction site, gene frequency or character data. It can be used to generate multiple data sets that are resampled versions of the input data set. Link to webpage: http://cmgm.stanford.edu/ phylip/seqboot.html
serine One of the amino acids (Ser, S, 105 Da)
Sequenase™ Proprietary name for a genetically
found in proteins and that can be phosphorylated. See Table A1.
engineered form of T7 DNA polymerase (EC. 2.7.7.7) used in DNA sequencing. Affymetrix homepage: http://www.affymetrix.com/estore/index.jsp
sequence hom*ology Strictly, refers to the situation where nucleic acid or protein sequences are similar because they have a common evolutionary origin. Often used loosely to indicate that sequences are very similar. Sequence similarity is observable; hom*ology is an hypothesis based on observation.
sequestosome aggresome Protein aggregates (perinuclear inclusion bodies) composed of ubiquitin-linked proteins destined for degradation. Sequestosome-1 (ubiquitin-binding protein p62, 440aa) is an adapter protein which binds ubiquitin and may regulate the activation of NFκB1 by TNFα, nerve growth factor (NGF) and interleukin-1 and may regulate various signalling cascades. One form of Paget’s disease of bone is caused by mutation in the gene. Overexpression of parkin or disruption of microtubules apparently blocks the formation of aggresomes.
sequon A consensus sequence of amino acids, as for example the tripeptide motif Asn-Xaa-Ser/Thr that is the site for N-linked glycosylation.
SER See smooth endoplasmic reticulum. SERCA See sarcoplasmic-endoplasmic reticulum Ca21-ATPase.
serglycin proteoglycan 1 An intracellular proteoglycan, found particularly in the storage granules of connective tissue mast cells. The core protein consists of 153aa with 24 serine-glycine repeats between amino acids 89 and 137, hence the name. The serine-glycine repeats are the linkage sites for around 15 glycosaminoglycan chains that are either heparin or highly sulphated chondroitin sulphate. These negatively charged chains are thought to
serine dehydratase A gluconeogenic enzyme (EC 4.2.1.13, SDH, 328aa), one of the beta-family of pyridoxal phosphate-dependent (PLP) enzymes, catalyzes the deamination of L-serine and L-threonine to yield pyruvate or 2-oxobutyrate.
serine hydroxymethyltransferase One of the alpha- class of pyridoxal phosphate enzymes (EC 2.1.2.1, SHMT1, 444 and 483aa isoforms; SHMT2, 494aa is mitochondrial), a catabolic enzyme involved in converting serine to glycine and a key enzyme in the formation and regulation of the folate one-carbon pool. E. coli SHMT (417aa) has little sequence similarity to the enzyme family. See mimosine.
serine peptidases Peptidases (serine proteases) that share a common reaction mechanism based on formation of an acyl-enzyme intermediate on a specific active serine residue. Most are inhibited by generic serine peptidase inhibitors (serpins) and irreversibly inactivated by a series of organophosphorus esters, such as di-isopropylfluorophosphate (DFP). They are, however, diverse in molecular structure and catalytic mechanisms and are not hom*ologues of each other. Examples are trypsin, chymotrypsin and the bacterial enzyme subtilisin.
SERK genes Plant genes that encode somatic embryogenesis receptor-like kinases. SERK1 (EC 2.7.10.1, 625aa) is a dual specificity kinase that will phosphorylate serine/threonine- and tyrosinecontaining substrates. It is involved in the brassinolide signalling pathway. SERK1 and SERK2 act redundantly and double mutants of SERK1 and SERK2 are completely male sterile. SERK3 (BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1, 615aa) forms a heterodimer with BRI1 which it can phosphorylate; this may changie the equilibrium between plasma membrane-located BRI1 hom*odimers and endocytosed BRI1-BAK1
serogroup
599
heterodimers. SERK4 and SERK5 are also known but their function is unclear.
serogroup A group of bacteria or other microorganisms that have a certain antigen in common.
serosa (1) A serous epithelium, having serous glands or cells, as opposed to a mucous membrane. (2) Thin infolding of the lining of the peritoneal cavity that forms the omentum.
serotonin A
neurotransmitter and hormone (5-hydroxytryptamine, 5-HT, 176 Da), found in vertebrates, invertebrates and plants. It is important in the mammalian CNS and various psychoactive drugs (such as selective serotinin-reuptake inhibitors) are extensively used to treat depression. Serotonin is produced by enterochromaffin cells in the gut and is stored in platelets. Most receptors are G-protein coupled except for the 5-HT3 receptor which is a ligand gated ion channel permeable to sodium, potassium, and calcium ions. In plants serotonin may be present at high levels in fruits.
serum requirement and activation. ShlA not only forms pores in erythrocytes but also in fibroblasts and epithelial cells. Haemolysin: http://iai.asm.org/cgi/reprint/72/ 1/611.pdf
Sertoli cell Tall columnar cells found in the mammalian testis closely associated with developing spermatocytes and spermatids. Probably provide appropriate microenvironment for sperm differentiation and phagocytose degenerate sperm.
serum Fluid that is left when blood clots; the cells are enmeshed in fibrin and the clot retracts because of the contraction of platelets. It differs from plasma in having lost various proteins involved in clot formation (fibrinogen, prothrombin, various bloodclotting factors such as Hagemann factor, Factor VIII etc.) and in containing various platelet-released factors, notably platelet-derived growth factor. For this reason serum is a better supplement for cell culture medium than defibrinated plasma (plasmaderived serum).
serotype The genotype of a unicellular organism as
serum amyloid The fibrils deposited in tissues in
defined by antisera directed against antigenic determinants expressed on the surface.
secondary amyloidosis which are unrelated to immunoglobulin light chains (in contrast to the situation in primary amyloidosis) and are made of amyloid A protein (AA protein). This is derived from serum amyloid A (SAA) that is the apolipoprotein of a high-density lipoprotein and an acute phase protein. Partial proteolysis converts SAA into the beta pleated sheet configuration of the amyloid fibrils. Amyloid P protein is also found as a minor component of the fibrils (in both primary and secondary amyloidosis) and is derived from serum amyloid P a pentraxin with similarity to C-reactive protein. The physiological role remains obscure.
serous gland An exocrine gland that produces a watery, protein-rich secretion, as opposed to a carbohydrate-rich mucous secretion.
serpentine receptors See G-protein-coupled receptors.
serpins Superfamily of proteins, mostly serine peptidase inhibitors, that includes alpha 1-antitrypsin, complement C1 inhibitor, plasminogen activator inhibitor 1, maspin, PEDF, protease nexin-1 and vaspin. The serpin-enzyme complex (SEC) formed from a serpin and a serine peptidase binds to a hepatocyte receptor (SEC receptor) that mediates catabolism of α-1-antitrypsin/elastase complexes and elevates α-1-antitrypsin synthesis.
serrate (1) The transmembrane ligand (1404aa) for Notch, contains 14 repeats of the EGF-like domain, expressed on dorsal cells of Drosophila wing, activates Notch on ventral cells and induces the expression of delta protein. Serrate protein expression is reciprocally induced by delta and modulated by fringe. (2) In plants, a zinc finger protein, (SERRATE, 720aa) that is required for proper processing of primary miRNAs to miRNAs, for pre-mRNA splicing and for the accumulation of the trans-acting small interfering RNA (ta-siRNA).
Serratia marcescens A Gram-negative bacterium that is very common in soil and water; most strains produce a characteristic pigment, prodigiosin. Opportunistic human pathogen, infecting mainly hospital patients. Serratia marcescens haemolysin (ShlA, 1608aa) is an unusual pore-forming toxin, that requires ShlB (557aa) for its secretion
serumand glucocorticoid-inducible kinases Serine/threonine protein kinases (SGKs, of which several isoforms have been identified) that are transcriptionally regulated by corticoids, serum, and cell volume. SGK1 (EC 2.7.11.1, 431aa) activates certain potassium, sodium, and chloride channels and plays an important role in the regulation of epithelial ion transport by inactivating (by phosphorylation) Nedd4-2, an E3 ubiquitin-protein ligase that targets the epithelial Na1 channel (ENaC) and the excitatory amino acid transporter (EAAT-2) for degradation. SGK2 (427aa) is involved in the activation of potassium channels. SGK3 (496aa) also activates potassium channels and mediates IL-3-dependent survival signals. SGKs belong to the AGC Ser/Thr protein kinase family that includes Akt.
serum hepatitis See hepatitis B. serum requirement The amount of serum that must be added to culture medium to permit growth of an animal cell in culture. Transformed cells frequently have less stringent serum requirements than their normal counterparts.
serum response element
600
serum response element SRE DNA motif (20 bp) found (for example) in the c-fos promoter, which is bound by the serum response factor.
serum response factor Transcription factor (SRF, p67SRF) which interacts with Elk-1 (p62TCF) to bind the serum response element promoter motif found in many growth-related genes.
serum sickness A hypersensitivity response (Type III) to the injection of large amounts of antigen, as might happen when large amounts of antiserum are given in a passive immunization. The effects are caused by the presence of soluble immune complexes in the tissues.
sestrins A family of conserved proteins that accumulate in cells exposed to stress and whose expression is modulated by p53. They are involved in reducing peroxiredoxins which have been overoxidised by hydrogen peroxide, thereby regenerating their protective anti-oxidant function. Sestrins contain a predicted redox-active domain hom*ologous to bacterial AhpD. May also be regulators of cellular growth. In humans sestrin-2 (480aa) and sestrin-3 (492aa) are also known. Defects in sestrin-1 (SESN1, p53-regulated protein PA26, 492aa) may be involved in heterotaxia. In Drosophila, dSesn (sestrin hom*ologue, 497aa) appears to be a negative feedback regulator of TOR. Weblog: http://antiagingfirewalls.com/2010/03/07/sestrins-longevity-andcancers/
SET complex An endoplasmic reticulum-associated complex, originally discovered as a granzyme A (GzmA) target in cells undergoing caspase-independent T cell-mediated death, that contains 3 DNases (the base excision repair endonuclease APE1, 50230 exonuclease TREX1, and endonuclease NM23-H1). NM23-H1 and TREX1 are activated by GzmA cleavage of the inhibitor SET protein to cause single-stranded DNA damage Other components include a DNA binding protein (HMGB2) that preferentially binds to distorted or damaged DNA, and the PP2A inhibitor pp32/PHAP-I. The SET complex plays an important role in the early phase of the HIV-1 lifecycle by inhibiting autointegration.
SET protein A protein (suppressor of variegation, enhancer of zeste, and trithorax, 290aa) involved in apoptosis, transcription, nucleosome assembly and histone binding. It is a specific inhibitor of protein phosphatase 2A and modifies phosphorylation of histone H4 with effects on nucleosome structure. The SET domain is found in a number of proteins involved in embryonic development in plants and animals. For example, SETD8 (SET domain-containing protein 8, histone-lysine N-methyltransferase SETD8, EC 2.1.1.43, 393aa) specifically monomethylates Lys20 of histone H4, probably contributing to the maintenance of proper higher order structure of DNA during mitosis. See SET complex.
sex-duction
seven-membrane spanning receptors See G-protein-coupled receptors.
sevenless A Drosophila gene (sev) that is required for development of the R7 cell in each ommatidium in the eye. Gene product is a receptor tyrosine kinase (EC 2.7.10.1, 2554aa), related to the insulin receptor, for which the ligand is the product of the bride of sevenless gene. In the downstream signalling cascade son-of-sevenless plays an important part.
severe combined immunodeficiency disease A range of serious disorders of the immune system (severe congenital immunodeficiency disease, SCID). In all forms there is deficiency in T cell-mediated immune responses (T2) but B-cells and NK cells may or may not be affected. The commonest form is caused by mutation in the interleukin 2-receptor (IL2RG) gene (X-linked SCID; T2, B1, NK2). Autosomal recessive SCID (T2, B1, NK2 SCID) is caused by mutation in the JAK3 gene; T2, B1, NK1 SCID is caused by mutation in the IL7R gene, the CD45 gene, or the CD3D gene; T2, B2, NK2 SCID is caused by mutation in the ADA (adenosine deaminase ) gene; T2, B2, NK1 SCID is caused by mutation in the RAG1 and 2 genes; T2, B2, NK1 SCID combined with sensitivity to ionizing radiation is caused by mutation in the artemis gene. Gene therapy has been used to treat some patients with ADA deficiency.
severin A protein (362aa) of the villin/gelsolin family from Dictyostelium that binds to the barbed ends of F-actin microfilaments in a Ca21-dependent manner, blocking further assembly. Not, apparently, essential for movement.
sex chromatin Condensed chromatin of the inactivated X chromosome in female mammals (Barr body).
sex chromosome The chromosome that determines the sex of an animal. In humans the two sex chromosomes (X and Y) are dissimilar, the female has two X chromosomes (XX), and the male is heterogametic (XY); sperm are either X or Y. A portion of the X and Y chromosomes is similar and is known as the pseudoautosomal region. In many organisms, there is only one sex chromosome, and one sex is XX, the other X0. A different system operates in birds, some fish and crustaceans, and some insects; the the ovum determines the sex, the male being hom*ogametic (ZZ) and the female ZW. There is apparently no hom*ology between the XY and ZW systems.
sex-duction The transfer of genes from one bacterium to another by the process of conjugation. May involve one bacterium with an F0 -plasmid, in which case the process is called F-duction.
sex hormone
601
shadoo
sex hormone Hormone that is secreted by gonads,
SGS3 (1) In Arabidopsis, a protein (SUPPRESSOR
or that influences gonadal development. Examples are estrogen, testosterone, gonadotrophins.
OF GENE SILENCING 3, 626aa) required for posttranscriptional gene silencing and natural virus resistance. May bind nucleic acids and is essential for the biogenesis of trans-acting siRNAs. (2) In Drosophila, a protein (salivary glue protein, Sgs-3, 307aa) expressed in the salivary glands of mid- to late-instar larvae.
sex-linked disorder A genetic defect most commonly seen in heterogametic individuals (males in mammals), the consequence of a mutation in a gene on the unpaired portion of the X chromosome so that there is only one copy of the allele. Only hom*ozygous females will show the defect.
sex pili Fine filamentous projections (pili) on the surface of a bacterium that are important in conjugation. Often seem to be coded for by plasmids that confer conjugative potential on the host; in the case of the F-plasmid, the F-pili are 829 nm diameter and several microns long, composed of pilin. Whether the pili merely serve to establish and maintain adhesive contact between the partners in conjugation, or whether DNA is actually transferred through the central core of the pilus is still unresolved, although a simple adhesion role is more generally accepted.
Sezary cells See Sezary syndrome. Sezary syndrome A cutaneous T-cell lymphoma,
affecting CD41 cells, an advanced form of mycosis fungoides, in which skin all over the body is reddened, itchy, peeling, and painful. There may also be patches, plaques, or tumours on the skin. Cancerous T-cells (Sezary cells) are found in the blood and infiltrating the skin.
Sf9 cells Insect cell line derived from Spodoptera frugiperda much used for production of recombinant protein. The gene to be expressed is incorporated into a baculovirus vector which is used to infect the cells.
S gene complex Genes coding for molecular components of the pollen-stigma recognition system in the cabbage genus (Brassica). The gene products govern the self-incompatibility response and include a glycoprotein found on the stigma surface and a lectin on the pollen grain surface that binds to the stigma glycoprotein.
SGK See serum- and glucocorticoid-inducible kinases.
SGOT Enzyme (serum glutamic-oxaloacetic transaminase, aspartate transaminase-1, EC 2.6.1.1, 413aa) that reversibly catalyses the transfer of an amine group from glutamic acid to oxaloacetic acid, forming alpha-ketoglutaric acid and aspartic acid. High levels in serum are an indication of liver or heart damage. There are cytoplasmic, mitochondrial and chloroplastic isozymes.
SGPT Old name for serum glutamic-pyruvic transaminase (alanine aminotransferase-2, EC 2.6.1.2, 523aa).
sgRNA See subgenomic RNA.
SGT-1 In S. cerevisiae a protein (SGT1, 395aa) involved in ubiquitination by associating with the SCF (Skp1p/Cdc53p/F box protein) ubiquitin ligase complex. (See skp). Required for both entry into S phase and kinetochore function. Also involved in the cyclic AMP (cAMP) pathway, possibly involved in the assembly or the conformational activation of specific multiprotein complexes. The human Sgt1 (suppressor of G2 allele of SKP1 hom*ologue, 365aa, product of the SUGT1 gene ) will work in yeast and is also thought to be involved in ubiquitinylation, whereas SGT1 (ecdysoneless hom*ologue, 644aa) is a regulator of p53 stability and function. The Drosophila hom*ologue (ecdysoneless, 684aa) is required for oocyte development. Plant hom*ologues (643aa in Arabidopsis) are required for disease resistance mediated by nucleotide-binding site/leucinerich repeat (NBS-LRR) proteins.
SGTx1 A peptide toxin (34aa) from the venom of the tarantula, Scodra griseipes. Inhibits Kv2.1 potassium channels in rat cerebellar granule neurons and is a gating-modifier. hom*ologous to hanatoxin.
SH domains Domains (Src hom*ology domains) within proteins that, from their hom*ology with src, are involved in the interaction with phosphorylated tyrosine residues on other proteins (SH2 domains) or with proline-rich sections of other proteins (SH3 domains). The SH1 domain has tyrosine kinase activity, the SH4 domain has myristoylation and membrane-localisation sites.
SH1, SH2, etc. See SH domains. SH3BP4 A protein (SH3-domain binding protein 4, TTP, 963aa) involved in cargo-specific control of clathrin-mediated endocytosis, specifically controlling the internalization of the transferrin receptor (TfR). It interacts with endocytic proteins, including clathrin, dynamin, and the TfR, and localizes selectively to TfR-containing coated-pits and -vesicles. There are 3 Asn-Pro-Phe (NPF) motifs, an SH3 domain, a PXXP motif, a bipartite nuclear targeting signal, and a tyrosine phosphorylation site. See TTP which has alternative meanings.
shadoo A GPI-linked protein (151aa) expressed in the brain. The gene (SPRN, ‘shadow of prion protein’) is a paralog of PRNP that encodes the prion proteins (PrP) and is highly conserved from fish to mammals. Evolution of Vertebrate Genes Related to Prion and Shadoo Proteins Clues from
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Comparative Genomic Analysis; http://mbe.oxfordjournals.org/cgi/content/full/21/12/2210
shadowing Procedure used in electron microscopy, in which a thin layer of material, usually heavy metal or carbon, is deposited onto a surface from one side, in such a way as to cast ‘shadows’. Deposition is usually done by vaporizing the metal on an electrode under vacuum.
shaker Drosophila gene encoding a subunit of the Kv1.1 voltage-gated potassium channel (a heterotetramer that includes shaker, 655aa) involved in regulation of sleep; the legs of mutant flies shake when they are anaesthetised. Related genes, shab, shal and shaw are known in flies and humans. Mutations in the human gene can cause episodic ataxia Type 1. In Arabidopsis the hom*ologue (potassium channel AKT6, 888aa) is a selective inward-rectifying potassium channel that plays an important role in pollen tube development.
SHANKs A family of adapter proteins (SH3 and multiple ankyrin repeat domains proteins), SHANK1 (somatostatin receptor-interacting protein, 2161aa), SHANK2 (cortactin-binding protein 1, 1253aa) and SHANK3 (proline-rich synapse-associated protein 2, 1741aa). They are important for the formation of postsynaptic densities in excitatory synapses and control dendritic spine morphology. Shank-interacting protein-like 1 (sharpin, SHANK-associated RH domain-interacting protein, 387aa) may be involved in development of the immune system and controlling inflammation; it is commonly up-regulated in multiple human cancer types
sharpin See SHANKs. shc A family of proteins (SHC-transforming proteins, SH2 domain-containing-transforming proteins C, Shc1, 583aa; Shc2, 582aa; Shc3, 594aa; Shc4, 630aa) that couple activated growth factor receptors to signalling pathways in various tissues. Isoforms p46Shc and p52Shc of Shc1, once phosphorylated, couple activated receptor tyrosine kinases to ras via the recruitment of the GRB-2/sos complex. p66Shc is involved in signal transduction pathways that regulate the response to oxidative stress and life span. Overexpression of shc will transform fibroblasts. Shc SH2 domain-binding protein 1 (SHCBP1, 672aa) interacts with p52shc and may be part of a different downstream signalling pathway.
shear stress response element SSRE A response element proposed to activate gene expression in response to fluid shear stress. In the human PDGFA promoter there is a GC-rich region near the TATA box that is required for shear-inducible reporter gene expression. There have been suggestions, however, that the signalling is through the ras pathway.
Sheldon-Hall syndrome See arthrogryposis.
Shine-Dalgarno region
shelterin A protein complex that protects chromosome ends from all aspects of the DNA damage response and regulates telomere maintenance. Components include telomeric repeat binding factors (TRF1 and TRF2), TRF1-interacting factors 1 and 2 (TIN2 and PINX1), TRF2-interacting protein, protection of telomeres 1 (POT1), TIN2-interacting protein and accessory proteins such as apollo. There are other non-shelterin proteins at chromosome ends. Research article: http://genesdev. cshlp.org/content/19/18/2100.full
shibire Drosophila gene that encodes dynamin (EC 3.6.5.5, 877aa). Shibire is temperature sensitive and in affected flies synaptic vesicles are depleted at high temperatures but are restored in nerve terminals when endocytosis resumes at lower temperatures.
shiga toxin Bacterial AB toxin from Shigella dysenteriae. The B (binding) subunit (89aa) interacts with globotriaosylceramide in human intestinal microvilli. The A subunit (EC 3.2.2.22, 315aa) inactivates 60S ribosomal subunits thereby blocking eukaryotic protein synthesis. Shiga-like toxins (e.g. SLT-1 and SLT-2, verotoxin, of E. coli) are structurally-related toxins that cleave a single residue from the 28S rRNA subunit of ribosomes thus blocking interaction with elongation factors eEF-1 and eEF-2.
Shigella Genus of non-motile Gram-negative enterobacteria (Escherichiae group): cause dysentery. See shiga toxin.
shikimate 5-dehydrogenase A key enzyme (SDH, SKDH, EC 1.1.1.25, 272aa in E. coli) in the aromatic amino acid biosynthesis pathway (shikimic acid pathway), catalyzes the reversible reduction of 3-dehydroshikimate to shikimate.
shikimic acid pathway Metabolic pathway in plants and microorganisms, by which the aromatic amino acids (phenylalanine, tyrosine and tryptophan) are formed from phosphoenolpyruvate and erythrose-4-phosphate via shikimic acid. The aromatic amino acids in turn serve as precursors for the formation of lignin and other phenolic compounds in plants. Inhibitors of this pathway are used as herbicides. Diagram: http://4e.plantphys. net/article.php?ch 5 t&id 5 23
shimamushi fever An acute fever (scrub typhus, flood fever, Japanese river fever, tsutsugamushi fever) caused by Rickettsia tsutsugamushi, transmitted by the bite of a larval mite (chigger), Leptotrombidium akamushi.
Shine-Dalgarno region A poly-purine sequence found in bacterial mRNA about 7 nucleotides in front of the initiation codon, AUG. The complete sequence is 50 -AGGAGG-30 and almost all messengers contain at least half of this sequence. It is complementary to a highly-conserved sequence at the 30 end of 16S ribosomal RNA, 30 -UCCUCC-50 , and it
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is thought to be involved in the binding of the mRNA to the ribosome.
shingles Disease in adults caused by Varicella zoster virus (Herpetoviridae), that in children causes chicken pox. Disease arises by reactivation (usually associated with a decline in cell-mediated immunity) of latent virus that persists in spinal or cranial sensory nerve ganglia.
SHIP Lipid phosphatase (SH2-containing inositol phosphatase, 1188aa) containing an SH2 domain; dephosphorylates 50 -inositol phosphate and thus modulates PI3-kinase signalling downstream of growth factor and insulin receptors. Important in regulation of mast cell degranulation and cytokine signal transduction in lymphoid and myeloid cells. Negative signalling through SHIP appears to inhibit the ras pathway by competition with GRB-2 and shc for SH2 domain binding.
ShK toxin A toxin (35aa) from the sea anemone Stichodactyla helianthus that blocks the voltagegated potassium channel Kv1.3 in T-cells.
shmoo Polarized morphological form of the yeast S. cerevisiae that has been exposed to mating pheromone. (either alpha factor or a-factor). The cytoskeleton and proteins involved in mating are localized to a cell-surface projection; the tips of the projections from the two cells eventually fuse.
shoot apical meristem The small number of cytoplasmically dense cells at the shoot tip, comprising the apical dome. Division of these cells generates other aerial primordia and all subapical tissue.
shootin A protein (631aa) involved in the generation of internal asymmetric signals required for neuronal polarization. Acts upstream of PI3K (phosphoinositide 3-kinase), being required for spatially localized PI3K activity.
SHOOTMERISTEMLESS A KNOX1 homeobox gene involved in maintaining the undifferentiated state of the shoot apical meristem.
Shope fibroma virus Poxvirus associated with the production of benign skin tumours in cottontail (but not domestic) rabbits.
Shope papilloma virus A member of the Papillomaviridae that produces papillomas (warts) in cottontail rabbits.
short hairpin RNA See shRNA. short interfering RNA See small interfering RNA.
short interspersed nuclear elements SINEs Retrotransposons (short interspersed nucleotide elements) around 300 bp found in most animal genomes in very large numbers. They lack long terminal repeats and are nonautonomous, relying on the reverse
Shp transcriptase of the long interspersed nucleotide element LINE1 to replicate. The best known is the human Alu repeat but most others are derived from tRNAs. See mammalian-wide interspersed repeats (MIRs).
short QT syndrome A disorder in which the QT interval in the cardiac cycle is short and there can be paroxysmal atrial fibrillation and sudden cardiac failure. There are various forms, all caused by mutations in potassium channels: in short QT syndrome-1 (SQT1) the KCNH2 gene product hERG, in SQT2 the KCNQ1 gene for the shakerrelated subfamily of potassium channels, and in SQT3 the KCNJ2 gene product (Kir2.1). See long QT syndrome.
SHORT ROOT A transcription factor (531aa) of the GRAS family, required for specification of the quiescent centre and maintenance of surrounding stem cells, and for the asymmetric cell divisions involved in radial pattern formation in shoots and roots. Required for normal shoot gravitropism. Controls the transcription of SCARECROW.
short stop In Drosophila a spectraplakin hom*ologue with many (.12) isoforms, including the short stop/Kakapo long isoform (5201aa) encoded by the gene shot. Shot isoforms are similar to spectrin and dystrophin, with an actin-binding domain followed by spectrin repeats. In short stop plakin repeats are inserted between the actin-binding domain and spectrin repeats of shot. Localized to adherens junctions of embryonic and follicular epithelia.
short tandem repeat See satellite DNA. shot (1) A Drosophila plakin family member with actin binding and microtubule binding domains. In Drosophila, it is required for a wide range of processes, including axon extension, dendrite formation, axonal terminal arborization at the neuromuscular junction, tendon cell development, and adhesion of wing epithelium. See short stop. (2) Short stature homeobox protein 2 (Paired-related homeobox protein SHOT, 331aa) expressed during cranofacial development as well as in heart.
shotgun approach Casual term for any approach that analyses a large number of small samples rather than a single large one: a shotgun fires many small pellets over a wider area whereas a rifle fires a single large bullet. Generally used in the context of sequence analysis (shotgun sequencing) carried out by chopping DNA (or even the whole genome) into many small sections of random length, sequencing them all, some many times, and pasting them together using computer methods that recognise overlap, as opposed to working systematically from one end.
Shp (1) Protein tyrosine phosphatases with SH2 domains that are recruited to the ITIM motif of receptor tyrosine kinases and play an important role
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in the control of cytokine signalling. Shp-1 (haematopoietic cell phosphatase, PTP1C, PTPN6, 595aa) is important in regulating antigen responses in T-cells. See motheaten. Shp-2 (Syp, PTP2C, PTPN11, 593aa) functions downstream of several growth factor receptors and has a role in cell spreading and migration; the hom*ozygous mutation in mice is lethal. Mutations can lead to Noonan’s syndrome or LEOPARD syndrome. Shp-substrate 1 (signal regulatory protein alpha-1, SIRP-alpha-1, 503aa) is an Ig-like cell surface receptor for CD47 that may play a role in synaptogenesis. and is involved in the negative regulation of receptor tyrosine kinase-coupled cellular responses induced by cell adhesion, growth factors or insulin. CD47 binding prevents maturation of immature dendritic cells and inhibits cytokine production by mature dendritic cells. (2) Small heterodimer partner (shp, 257aa) an orphan nuclear receptor belonging to the nuclear receptor superfamily of transcription factors. May be a negative regulator of signalling pathways.
SIC1 various other abnormalities, caused by mutations in the SBDS gene. Heterozygous mutations in the SBDS gene have been associated with predisposition to aplastic anaemia. The gene product (250aa) may be involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes.
Shwartzman reaction Reaction that occurs when two injections of endotoxin are given to the same animal, particularly rabbits, 24 hours apart. In the local Shwartzman reaction the first injection is given intradermally, the second intravenously, and a haemorrhagic reaction develops at the dermal site. If both injections are intravenous the result is a generalized Shwartzman reaction, often accompanied by disseminated intravascular coagulation. The reaction depends upon the response of platelets and neutrophils to endotoxin.
sialic acid See neuraminic acid.
shRNA short hairpin RNA Small RNA molecules
sialidase See neuraminidase.
(502100 bases) generated from plasmids that are processed by the cellular machinery to produce small interfering RNA (siRNA) and thus suppress the targeted gene. Research article: http://www.ncbi.nlm. nih.gov/pmc/articles/PMC1343552/?tool 5 pmcentrez
sialidosis See mucolipidosis.
shrooms A family of actin-binding proteins with PDZ domains and the Apx/Shrm domain 2 (ASD2), involved in regulating cell shape during morphogenesis. Originally identified as being important in neural tube development in mice; mutations lead to the ‘mushrooming’ outward of the neural folds. Shroom 1 (852aa) may be involved in the assembly of microtubule arrays during cell elongation, Shroom 2 (1616aa) is involved in morphological changes in endothelial cells during spreading and may interact with gamma-tubulin. Shroom 3 (1986aa) interacts with microfilament bundles and also gamma-tubulin. Shroom 4 (1498aa) may regulate the spatial distribution of myosin II. A Drosophila hom*ologue (1576aa) is involved in cell elongation by regulating the formation of microtubule arrays.
SH-SY5Y cells A dopaminergic neuroblastoma cell line, derived by multiple subcloning of SK-N-SH cells, from a four year-old girl.
shuttle flow See cytoplasmic streaming. shuttle vector A cloning vector that will replicate in cells of more than one organism, e.g. E. coli and yeast. This combination allows DNA from yeast to be grown in E. coli and tested directly for complementation in yeast. Shuttle vectors are constructed so that they have the origins of replication of the various hosts.
sialin A tetraspanin lysosomal protein (solute carrier family 17 member 5, 495aa) responsible for export of anionic substances, particularly sialic acid. Defects lead to Salla disease or infantile free sialic acid storage disease, both neurodegenerative conditions.
sialoglycoprotein Glycoprotein in which the N- or O-glycan chains include residues of neuraminic acid.
sialophorin See leukosialin. sialyl Lewis x Sialylated form of CD15 (sLex, CD15s), the ligand for E-, P- and L-selectins and an important blood group antigen. Expressed on neutrophils, basophils and monocytes and only some lymphocytes. Also present on some HEV. Deficiency in sialyl Lewis-X will cause leucocyte adhesion deficiency Type II.
sialylate To add sialic acid to a glycoprotein or glycolipid, usually in a terminal position.
sialyltransferase A family of enzymes (EC 2.4.99.-, CMP-N-acetylneuraminate:acceptor N-acetylneuraminyl transferases) involved in the transfer of sialic acid (N-acetyl neuraminic acid) to oligosaccharide chains on glycoproteins or glycolipids. They are substratespecific.
siamois A
homeobox transcriptional activator (246aa) mediator of the dorsal Wnt signalling pathway, necessary for formation of the Spemann organizer and dorsoanterior development in Xenopus.
Shwachman-Diamond syndrome A disorder
SIC1 Substrate and inhibitor of the cyclin-dependent
(Shwachman-Bodian-Diamond syndrome) characterized by exocrine pancreatic insufficiency and
protein kinase CDC28 (284aa) from S. cerevisiae. Interacts with the MAP kinase HOG1. See Skp.
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sickle cell anaemia Disease common in ethnic groups originally from areas in which malaria is endemic. The cause is a point mutation in haemoglobin (valine instead of glutamic acid at position 6), and the altered haemoglobin (HbS) crystallizes readily at low oxygen tension. In consequence, erythrocytes from hom*ozygotes change from the normal discoid shape to a sickled shape when the oxygen tension is low, and these sickled cells become trapped in capillaries or damaged in transit, leading to severe anaemia. In heterozygotes, the disadvantages of the abnormal haemoglobin are apparently outweighed by increased resistance to Plasmodium falciparum malaria, probably because parasitized cells tend to sickle and are then removed from circulation.
sideramines See sideromycins. sideroblastic anaemia X-linked sideroblastic anaemia (XLSA) is caused by mutation in the gene encoding delta-aminolevulinate synthase-2 (ALA synthase), the enzyme that catalyzes the first committed step of haem biosynthesis. Sideroblastic anemia with spinocerebellar ataxia (ASAT) is an X-linked mitochondrial disease caused by mutation in ATP-binding cassette (ABC) transporter ABC7 (752aa) that is involved in iron homeostasis.
sideroblasts Nucleated red blood cells containing Pappenheimer bodies: small, deeply basophilic granules that contain ferric iron.
siderochromes See ferrichromes. sideromycins formerly
sideramines or siderochromes. Antibiotics covalently linked to siderophores that are actively transported into Gram-positive and Gram-negative bacteria. Examples include albomycin, a derivative of ferrichrome with a bound thioribosylpyrimidine moiety that inhibits seryl-t-RNA synthetase and salmycin, a ferrioxamine derivative with a bound aminodisaccharide, that is thought to inhibit protein synthesis. Research article: http://www.ncbi.nlm.nih. gov/pmc/articles/PMC2757582/?tool 5 pubmed
siderophilin See transferrin. siderophilins Family of non-haem iron chelating proteins (about 80 kDa) found in vertebrates. Examples are lactoferrin and transferrin.
siderophores Natural
iron-binding compounds that chelate ferric ions (which otherwise form insoluble colloidal hydroxides at neutral pH and are then inaccessible) and are then taken up together with the metal ion.
siderosis (1) A lung disease (a type of pneumonoconiosis) caused by the inhalation of metallic particles. (2) Excessive deposition of iron in tissues.
sieve plate The perforated end walls separating the component cells (sieve elements) that make up the
signal peptide peptidase phloem sieve tubes in angiosperms. The perforations permit the flow of water and dissolved organic solutes along the tube, and are lined with callose. The plates are readily blocked by further deposition of callose when the sieve tube is stressed or damaged.
sieve tube The structure within the phloem of higher plants that is responsible for transporting organic material (sucrose, raffinose, amino acids, etc.) from the photosynthetic tissues (e.g. leaves) to other parts of the plant. Made up of a column of cells (sieve elements) connected by sieve plates. In gymnosperms the sieve cells retain their nuclei and the conducting connections have less obvious pores than sieve plates.
sigma factors Prokaryotic initiation factors (σ factors) that promote attachment of DNA-dependent RNA polymerase to specific initiation sites. Every molecule of RNA polymerase has one sigma factor subunit which is released following attachment and different sigma factors are involved under different environmental conditions. For example, in E. coli, σ70 (RpoD, 613aa) is the primary sigma factor for housekeeping proteins, σ54 (RpoN, 477aa) is involved under conditions of nitrogen limitation, σ38 (RpoS, 111aa) under starvation conditions, amongst others.
sigma receptors Receptors originally identified by their ability to bind various psychoactive drugs but then shown to be non-opioid receptors. Sigma receptor 1 (sigma non-opioid intracellular receptor 1, 223aa) is widely expressed and involved in lipid transport from the ER, regulates various other receptors and potassium channels and has a role in calcium signalling. Considered to be involved in learning, memory and mood alteration. Sigma 2 receptors, unlike sigma-1 are not coupled to Gi/o proteins and sigma-2 receptor specific ligands induce apoptosis in a dose-dependent fashion.
signal peptidase complex SPC A multi subunit serine peptidase (protease) complex located in the ER membrane that cleaves the signal sequence from proteins that are destined for export. Cleavage occurs as soon as the cleavage site of the translocating polypeptide is exposed in the lumen of the ER. Mammalian signal peptidase is a complex of five different polypeptide chains; SPC12 and SPC25 have substantial cytoplasmic domains and span the membrane twice, SPC18, SPC21, SPC22/23 are single-spanning membrane proteins mostly exposed to the lumen of the endoplasmic reticulum. See also sec61.
signal peptide See signal sequence. signal peptide peptidase SPP Like gammasecretase, an unusual aspartyl peptidase (presenilinlike protein 3, EC 3.4.23.-, 377aa) that catalyzes the intramembrane proteolysis of some signal peptides
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after they have been cleaved from a preprotein. A family of SPP-like proteins (SPPLs) of unknown function has been identified.
signal recognition particle SRP A complex between a 7S RNA and six proteins. The SRP binds to the nascent polypeptide chain of eukaryotic proteins with a signal sequence and halts further translation until the ribosome becomes associated with the rough endoplasmic reticulum. One of the SRP proteins (srp54) binds GTP and in association with 7S RNA and srp19 has GTPase activity.
signal recognition particle-receptor Receptor for the signal recognition particle (SRP) found in the membrane of the endoplasmic reticulum. Also known as docking protein. Heterodimeric, both protomers (α, 638aa; β, 271aa) having GTP-binding capacity, though dissimilar binding sites. Not until the complex of SRP, ribosome, message, and nascent polypeptide chain binds to the SRP-receptor is the block to further chain elongation released and concurrently the SRP is released, leaving the ribosome attached to the ER membrane. Co-translational transport of the polypeptide delivers it into the lumen of the ER.
signal sequence (1) An N-terminal sequence
(B20aa, usually hydrophobic but with some positive residues) that interacts with signal recognition particle and is present on proteins that are destined either to be secreted or to be membrane components. It is normally absent from the mature protein, having been removed from the growing peptide chain by the signal peptidase complex located on the cisternal face of the endoplasmic reticulum. (2) Any sequence that determines the organelle for which the protein is destined.
signal transduction Signal-response coupling The cascade of processes by which an extracellular signal (typically a hormone or neurotransmitter) interacts with a receptor at the cell surface, causing a change in the level of a second messenger (for example calcium or cyclic AMP) and ultimately effects a change in the cell’s functioning (for example, triggering glucose uptake, or initiating cell division). Can also be applied to sensory signal transduction, e.g. of light at photoreceptors.
simocyclinone D8
signet-ring cell An adipocyte with a large central fat-filled vacuole or an epithelial cell with a mucinfilled vesicle in which the nucleus is displaced to one side to give an appearance reminiscent of a signet ring.
silanization Modification (silanisation, silanizing) of hydroxyl groups on silica or glass surfaces with silane coupling agents e.g. (3-mercaptopropyl)-trimethoxysilane) to give the inactive -O-SiR3 grouping. Silanization can neutralize surface charges, thus eliminating non-specific binding. Often used to prepare surfaces for the binding of DNA fragments in microarrays.
silent gene A gene that is not phenotypically expressed. This can arise because of mutation of the gene itself (e.g. a nonsense codon causing premature termination of translation), a defect in some upstream control, or a mutation that renders the product inactive in some way.
silent mutation Mutations that have no effect on phenotype because they do not affect the activity of the product of the gene, usually because of codon ambiguity.
siliconization Non-covalent coating of surface with a layer of silicone oil making it less adhesive or reactive. See silanizing.
silicosis Inflammation of the lung caused by foreign bodies (inhaled particles of silica): leads to fibrosis but unlike asbestosis does not predispose to neoplasia.
siliqua A long dry dehiscent fruit of cruciferous plants, for example oilseed rape, divided into two compartments by a central septum to which the seeds are attached.
Silver-Russell syndrome See H19 gene. Silverman-Handmaker type dyssegmental dysplasia See Schwartz-Jampel syndrome. Simian Virus 40 See SV40. Simmonds’ disease hypopituitarism The failure
signal
of the anterior lobe of the pituitary to produce any one or more of its six hormones (ACTH, TSH, FSH, LH, GH, and prolactin).
signal-transducing adaptor proteins Adaptor
simocyclinone D8 A potent DNA gyrase inhibi-
molecules (signal-transducing adaptor molecule 1, STAM1, 540aa; STAM2, 525aa) that link cytokine and growth factor receptors and STATs. STAMbinding protein (EC 3.1.2.15, 424aa) is a zinc metallopeptidase that specifically cleaves ‘Lys-63’-linked polyubiquitin chains. It interacts with the SH3 domain of STAM1 and potentiates various signalling pathways.
tor, an aminocoumarin antibiotic produced by Streptomyces antibioticus Tu¨ 6040. The mode of action is atypical: it binds to the GyrA subunit of the enzyme and prevents binding to DNA. The producing organism is protected by the production of a specific efflux pump which prevents build-up of the metabolite. Research article: http://www.jic.ac.uk/STAFF/ mark-buttner/pdfs/SimR_MolMicro_2009.pdf
signal-response
coupling See
transduction.
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simple epithelium An epithelial layer composed
sirtuins experimentally by rapidly cooling heat-denatured DNA to prevent renaturation.
of a single layer of cells all of which are in contact with the basal lamina (see basem*nt membrane). May be cuboidal, columnar, squamous or pseudostratified. Images http://www.mhhe.com/biosci/ap/ histology_mh/simpleep.html
single-channel recording Variant of patch
simple sequence length polymorphism SSLP
single-stranded conformational polymorphism, SSCP Technique for detecting point muta-
Tandem repeat sequences that are of variable length in different individuals, i.e. exhibit polymorphism. Since the flanking sequences are the same in all individuals it is relatively easy to choose primers that will selectively amplify such repeat sequences and the length variation (diffence in repeat number) can be detected easily on the basis of the product size.
simple sequence repeats SSRs See satellite DNA.
Simpson-Golabi-Behmel
syndrome SGBS An X-linked disorder characterized by excessive growth, similar to Beckwith-Wiedemann syndrome. Type 1 is caused by mutation in the glycipan-3 gene which reduces the binding of insulin-like growth factor-2 which normally limits its availability. Type 2 has been associated with a mutation in the CXORF5 gene.
Sin3 Component of the multiprotein complex involved in repression of transcription. Sin3 is a corepressor (Sin3A, 1219aa; Sin3B, 1130aa) and forms a complex with Rpd3 histone deacetylase; the complex then interacts with DNA-binding proteins. Yeast SIN3 (1536aa) is involved in the repression of a diverse range of genes. Sin3 does not itself bind to DNA.
Sindbis virus Enveloped virus of the alphavirus group of Togaviridae. It is thought to be an infection of birds spread by fleas, and there is little evidence that it causes any serious infection in humans. The synthesis and export of the spike proteins, via the endoplasmic reticulum and Golgi complex, have been used as a model for the synthesis and export of plasma membrane proteins.
SINEs See short interspersed nuclear elements. single cell protein Protein(s) produced by single cells of pure or mixed cultures of algae, yeasts, fungi or bacteria. Of possible commercial importance in providing food sources from biotechnological processes.
single nucleotide polymorphism See SNP. single stranded DNA ssDNA DNA that consists of only one chain of nucleotides rather than the two base-pairing strands found in DNA in the doublehelix form. Parvoviridae have a single-stranded DNA genome. Single-stranded DNA can be produced
clamp technique in which the flow of ions through a single channel is recorded.
tions in genes by amplifying a region of genomic DNA (using asymmetric PCR) and running the resulting product on a high quality gel. Single base substitutions can alter the secondary structure of the fragment in the gel, producing a visible shift in its mobility. (1) O2 An energised but uncharged form of oxygen (the diamagnetic form of molecular oxygen) that is produced in the metabolic burst of leucocytes and that can be toxic to cells. One of the so-called ‘reactive oxygen species (ROS)’.
singlet oxygen
SipA An actin-binding protein from Salmonella enterica, (Salmonella invasion protein A, 685aa) that apparently stabilizes F-actin bundles by increasing polymerization and decreasing depolymerization. Salmonella force their way into nonphagocytic host intestinal cells to initiate infection. Uptake is triggered by delivery into the target cell of over thirty specialised effector proteins via two distinct type III secretion systems. SipA is one of the effectors of the Salmonella pathogenicity island-1 (SPI-1) type 3 secretion system. SipC is also involved in the process. Salmonella pathogenesis: http://www.ncbi.nlm. nih.gov/pubmed/19157959
sir2 Protein (silent information regulator-2 protein, 562aa) from Saccharomyces cerevisiae, original member of the sirtuin family to be identified. A NAD1-dependent protein histone deacetylase.
sirenin Sexual pheromone, a bicyclic sesquiterpenediol, produced by female gametes of the water moulds, Allomyces macrogynus,and A. arbuscula. Male gametes respond chemotactically.
siRNA See small interfering RNA. sirtuins Family of NAD-dependent protein histone deacetylases (HDACs, silent information regulator 2 (Sir2) enzymes) that includes Sir2 and its mammalian orthologues: play an important role in epigenetic gene silencing, DNA recombination, cellular differentiation and metabolism, and the regulation of aging. Human sirtuin 1 (SIRT1, 747aa) and sirtuin-2 (389aa) have greatest hom*ology with S. cerevisiae Sir2 protein; SIRT3 (399aa), SIRT4 (314aa) and SIRT5 (310aa) are mitochondrial and more closely resemble prokaryotic sirtuin sequences. SIRTs 1-5 are widely expressed in fetal and adult tissues. The class IV sirtuins include SIRT6 (355aa) which is chromatin-associated and involved in DNA repair,
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skin associated lymphoid tissue
SIRT7 (400aa) which is associated with active rRNA genes (rDNA) and histones.
syndrome) because ciliary function during development is necessary for the normal asymmetry.
sis (1) An oncogene, sis, originally identified in
SIV Simian immunodeficiency virus. Very similar to
monkey sarcoma, encoding a B-chain of PDGF. Human c-sis/PDGF-B proto-oncogene has been shown to be overexpressed in a large percentage of human tumour cells. (2) See macrophage inflammatory protein 1 α and β. (SIS). (3) Small intestinal submucosa: porcine SIS has been used as a cellfree, biocompatible biomaterial for surgical repair purposes.
sister chromatid One of the two chromatids making up a bivalent. Both are semi-conservative copies of the original chromatid.
SIT Transmembrane adaptor protein (TRAP), a disulphide-linked hom*odimer (SHP2-interacting transmembrane adapter protein, 196aa), that is expressed in lymphocytes. Interacts with the SH2-containing protein tyrosine phosphatase 2 (SHP2) via an immunoreceptor tyrosine-based inhibition motif (ITIM). Also interacts with grb2.
Site-1 protease S1P See ski. site-directed mutagenesis See site-specific mutagenesis.
site-specific mutagenesis An in vitro tech-
HIV and used extensively as an animal model.
Sixth disease A benign disease (roseola) of children under two years old caused by human herpes virus-6 and -7 (Roseolovirus). There is a transient rash following a brief fever.
Sjogren’s syndrome One of the so-called connective tissue diseases that also include rheumatoid arthritis, systemic lupus erythematosus and rheumatic fever. Characterized by inflammation of conjunctiva and cornea. It is an autoimmune disease associated with HLA alleles DRB1*03 and DQB1*02. See La protein.
SK channels A subfamily of voltage-independent
Ca21-activated potassium channels (small conductance calcium-activated potassium channels) with four members (SK1 (KCa2.1), 543aa; SK2 (KCa2.2), 579aa; SK3 (Kca2.3), 736aa; SK4 (KCa3.1), 427aa). The channel complex is composed of 4 subunits each of which binds to a calmodulin subunit giving the calcium sensitivity. They are thought to regulate neuronal excitability by contributing to slow afterhyperpolarization. Some are selectively inhibited by apamin and scyllatoxin, others by charybdotoxin.
nique (site-directed mutagenesis) in which an alteration is made at a specific site in a DNA molecule, which is then reintroduced into a cell. Various techniques are used; for the cell biologist, a very powerful approach to determining which parts of a protein or nucleotide sequence are critical to function. For proteins it is common to systematically substitute alanine for various residues (an alanine scan).
skelemin The murine hom*ologue of myomesin 1
site-specific recombination A type of recom-
skeletrophin A RING finger-dependent ubiquitin
bination that occurs between two specific short DNA sequences present in the same or in different molecules that are recognised by site-specific recombinases which bind, cleave, excise, exchange and rejoin the strands. Examples include the lox-Cre system, resolvases, Flp-Frt recombination, lambda integrase.
ligase (mindbomb hom*olog 2, MIB2, 1013aa), which mediates ubiquitination of delta receptors, that are ligands of Notch proteins. It is down-regulated in many melanomas.
sitosterolemia A disorder caused by a defect in ABC transporters (ABCG8 or ABCG5) that normally cooperate to limit absorption of sterols in the intestine and promote sterol secretion in bile. Affected individuals have very high levels of the plant sterol, sitosterol, in the plasma which can cause xanthomas and increases the risk of coronary artery disease.
situs inversus Condition in which the normal asymmetry of the body (in respect of the circulatory system and intestinal coiling) is reversed to produce a mirror image of the normal situation. It occurs in approximately 50% of patients with primary ciliary dyskinesia (immotile cilia syndrome, Kartagener’s
(1667aa).
skeletal muscle A rather nonspecific term usually applied to the striated muscle of vertebrates that is under voluntary control. The muscle fibres are syncytial and contain myofibrils, tandem arrays of sarcomeres.
ski (1) An oncogene, ski (Sloan-Kettering Institute proto-oncogene), identified in avian carcinoma, encoding a nuclear protein. C-ski is a regulating factor for fibroblast proliferation and an important co-repressor of Smad3. (2) Subtilisin/kexin isozyme-1 (SKI-1), otherwise known as Site-1 protease (S1P), a Golgi proteinase involved in activation of sterolregulated element-binding proteins (SREBPs). (3) The hom*ologue of Drosophila skinny hedgehog (SKI1, hedgehog acyltransferase, HHAT, EC 2.3.1.-, 493aa) that catalyses N-terminal palmitoylation of sonic hedgehog.
skin associated lymphoid tissue SALT The cells of the immune system associated with the dermis and epidermis. Includes Langerhans cells and resident phagocytes although some authors would include cutaneous nerve termini containing
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calcitonin gene-related peptide (CGRP): release of the peptide will stimulate mast cells to release cytokines such as IL-10 and TNFα. More of a concept than a morphological entity: cf. gut-, bronchus-, and mucosal-associated lymphoid tissue.
SKIP (1) Ski-interacting protein (nuclear receptor coactivator NCoA-62, SNW domain-containing protein 1, 536aa) involved in vitamin D-mediated transcription. See ski. (2) In Arabidopsis, a large family of F-box proteins (SKP1-interacting partners) that are components of SCF E3 ubiquitin ligase complexes. (3) The protein (SKIP, SifA and kinesin interacting protein, PH domain-containing family M member 2, 1019aa) that regulates kinesin, has a role in Golgi morphology and is necessary for Salmonella infectivity. The close proximity of the SCV (Salmonella containing vacuole) to the Golgi may facilitate interception of endocytic and exocytic transport vesicles to obtain nutrients. SifA binds SKIP and appears to be important for promoting bacterial replication. Efficient localisation of SifA to the SCV is mediated by the SPI-1 effector SipA. Research article: http://www.ncbi.nlm.nih.gov/pmc/ articles/PMC2647982/
SKL Carboxyl-terminal amino acid sequence (serinelysine-leucine, SKL), the consensus peroxisomal targeting sequence 1 (PTS1) that directs a polypeptide to peroxisomes in plants, animals, and yeasts.
Skn-1 (1) In C. elegans a maternally and zygotically expressed transcription factor (skinhead-1, 623aa) that specifies the fate of certain blastomeres during early development. Binds DNA with high affinity as a monomer even though it has a basic region similar to basic-leucine zipper (bZIP) proteins that only bind as dimers. (2) In S. cerevisiae, beta-glucan synthesis-associated protein (SKN1, 771aa) required for synthesis of the major beta-glucans of the yeast cell wall.
skotomorphogenesis etiolation
Development, growth and differentiation of a plant under conditions of darkness.
skp Components of the SCF complex, (S-phase kinase-associated proteins; p19, Skp1, 163aa; p45, Skp2, 424aa). The SCF (Skp1-cullin-F-box complex) ubiquitin protein ligase of S. cerevisiae triggers DNA replication by catalysing ubiquitinylation of the S phase cyclin-dependent kinase inhibitor, SIC1. The complex also regulates the function of NFκB. See Sgt1.
skyllocytosis Phagocytic process in Allogromia
sliding filament model including TATA-binding protein TBP. (2) Stemloop structure 1 (SL1), a characteristic feature of some viral RNAs.
Sla1p In yeast, an actin regulatory protein (1244aa) that, together with End3p and Sla2p is important in maintaining a rapid turnover of F-actin in cortical patches. Binds both to activators of actin dynamics (Las17p and Pan1p) and to cargo proteins, such as the pheromone receptor Ste2p.
SLAMs Signalling lymphocyte-activation molecules. A family of Ig superfamily receptors on T- and B-cells (SLAM1 is CD150, 335aa). They recruit various cytoplasmic signalling molecules and co-activate immune responses. SLAM-associated proteins (SAPs) are adaptors with SH2 domains. SAP (128aa) is T-cellspecific and blocks recruitment of Shp2, it is mutated in X-linked lymphoproliferative disease (XLP).
SLAP (1) Src-like adapter proteins (SLA1, 281aa; SLA2, 261aa), that have SH2 and SH3 domains and interact with zap-70, Syk, LAT, and T-cell receptor (TCR)-zeta chain as negative regulators of immune responses. (2) Sarcolemmal-associated protein (sarcolemmal membrane-associated protein, 828aa) that forms a hom*odimer which interacts with myosin and is found in transverse tubules, near the junctional sarcoplasmic reticulum and along the Z- and M-lines in cardiomyocytes. May play a role during myoblast fusion.
S layer A paracrystalline array which completely covers the surfaces of many pathogenic bacteria (Archaea and Bacteria). Usually consist of a single (glyco-) protein species with molecular masses ranging from about 40 to 200 kDa that form lattices of oblique, tetragonal, or hexagonal architecture, and probably represent the earliest cell wall structures. About 10 nm thick.
SLC (1) Secondary lymphoid-tissue chemokine (CCL21, 134aa) that is selectively chemotactic in vitro for thymocytes and activated T-cells, and may mediate homing of lymphocytes to secondary lymphoid organs. (2) Sodium-lithium countertransport. (3) A G-protein coupled receptor, somatostatin-like receptor 1 (SLC-1), for which the ligand is melanin-concentrating hormone (MCH).
sleeping sickness See Trypanosoma. SLEEPY In Arabidopsis an F-box protein (SLEEPY1, SLY1, 151aa) a subunit of a SCF E3 ubiquitin ligase complex that positively regulates gibberellic acid signalling. See also SNEEZY.
‘A marine rhizopod with which the general zoologist is usually acquainted’.
slicer activity The cleavage of target RNA by
SL1 (1) Transcription factor SL1/TIF-IB complex,
sliding filament model Generally accepted model
which is involved in the assembly of the preinitiation complex during RNA polymerase I-dependent transcription. The complex is composed of four proteins
for the way in which contraction occurs in the sarcomere of striated muscle, by the sliding of the thick filaments relative to the thin filaments.
enzymes such as argonaute in RNA interference.
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slime moulds Two distinct groups of organisms, the cellular slime moulds Acrasidae that include Dictyostelium, and the acellular slime moulds or Myxomycetes that include Physarum.
slingshot A family of protein tyrosine phosphatases that are involved in control of actin dynamics (human slingshot hom*ologue-1, SSH1, EC 3.1.3.48, EC 3.1.3.16, 1049aa). Cofilin is activated by dephosphorylation by slingshot (SSH) family phosphatases. SSH activity is strongly increased by binding to filamentous actin but is inhibited when phosphorylated itself. Calcineurin will dephosphorylate and activate slingshot; interaction with 14-3-3 proteins inhibits phosphatase activity and also blocks recruitment to lamellipodia and slingshot stimulation by actin.
SLIP1 (1) A protein (SLBP (stem loop binding
SLS collagen site selection. They may function as adapters for Src kinases during mitosis. Expression of SLM2 is reported to be upregulated in patients with various kidney diseases. (2) In S. cerevisiae, phosphatidylinositol 4,5-bisphosphate-binding proteins (SLM1, TORC2 effector protein, 686aa; SLM2, 656aa); the heterodimer of SLM1-SLM2 is the effector of the TORC2- and calcineurin-signaling pathways. (3) In S. cerevisiae SLM3 is mitochondrial tRNA-specific 2-thiouridylase 1 (EC 2.8.1.-, 417aa), SLM4 (162aa) is a component of the GSE and EGO complexes. SLM5 is the gene for mitochondrial asparaginyltRNA synthetase (EC 6.1.1.22, 492aa) and SLM6 that for methyl methanesulphonate-sensitivity protein 1 (1407aa), involved in protection against replicationdependent DNA damage. (4) In Silene latifolia (white campion) SLM proteins are transcription factors. (e.g. SLM1, 248aa, SLM5, 257aa).
protein)-interacting protein 1, 222aa) involved in replication-dependent translation of histone mRNAs that end with a stem-loop rather than a poly-A tail. (2) In Drosophila, Slo-interacting protein 1 (767aa) that may selectively reduce calcium-activated potassium channel (Slo) currents (see BK channels).
slot blot A dot blot in which samples are placed
slipped strand mispairing Mispairing of the
of the presynaptic membrane that follows an action potential. It is generated by the activation of smallconductance calcium-activated potassium channels (SK channels). The hyperpolarization limits the firing frequency of repetitive action potentials (spike-frequency adaption) and is essential for normal neurotransmission.
complementary DNA strands of a single DNA double helix during replication. Slippage can be either forward (causing deletion) or backward (causing insertion). Short tandem repeats are thought to be particularly prone to slipped strand mispairing
slit Family of proteins first identified in Drosophila and subsequently in many vertebrates. Secreted diffusible proteins (Slit1,1534aa; Slit2, 1529aa) that act as chemorepellants for migrating neurons during development. Slit genes are expressed in the ventral midline of the neural tube and the effect of the repulsion is to force neurons to move in the rostral migratory stream and prevents axons from crossing between hemispheres. Slit3 (1532aa) is expressed more strongly in peripheral tissues. Receptor is robo (roundabout). See slit and NTRK proteins.
SLIT and NTRK-like proteins A family of proteins that affect neuronal migration by stimulating or inhibiting neuronal outgrowth. SLIT and NTRK-like protein-1 (SLIK1, 696aa) enhances neuronal dendrite outgrowth; defects may be a cause of Gilles de la Tourette syndrome. SLIK2 (845aa), SLIK3 (977aa), SLIK4 (837aa), SLIK5 (958aa) and SLIK6 (841aa) suppress neurite outgrowth. NTRK1 is the high-affinity nerve growth factor receptor.
SLK A microtubule-associated kinase (Ste20-like kinase, 1235aa), one of the germinal centre sub-family of STE20-like kinases, involved in turnover of focal adhesions.
SLM (1) RNA-binding proteins, (STAR proteins) (Sam68-like mammalian proteins, SLM1, 346aa; SLM2, 349aa) related to SAM68, that regulate splice
on a membrane through a series of rectangular slots in a template. This has some advantages because hybridization artefacts are usually circular.
slow after hyperpolarization Hyperpolarization
slow muscle Striated muscle used for long-term activity (e.g. postural support). Depends on oxidative metabolism and has many mitochondria and abundant myoglobin.
slow reacting substance of anaphylaxis SRS-A Potent bronchoconstrictor and inflammatory agent released by mast cells; an important mediator of allergic bronchial asthma. A mixture of three leukotrienes (LTC4 mainly, LTD4 and LTE4).
slow virus (1) Specifically one of the Lentivirinae. (2) Any virus causing a disease that has a very slow onset. Diseases such as sub-acute spongiform encephalopathy, Aleutian disease of mink, scrapie, kuru, and Creutzfeldt-Jacob disease may be caused by slow viruses although this hypothesis has fallen out of favour. See also prion.
SLP-76 An adapter protein required for T-cell receptor (TCR) signalling. See TRAPS. Interacts with IL-2-inducible T-cell kinase.
SLRPs See small leucine-rich repeat proteoglycans. SLS collagen Segment long spacing collagen. Abnormal packing pattern of collagen molecules formed if ATP is added to acidic collagen solutions, in which lateral aggregates of molecules are produced. Each aggregate is 300 nm long, and the
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molecules are all in register. If SLS-aggregates are overlapped with a quarter-stagger, the 67 nm banding pattern of normal fibrils is reconstituted.
slug Snail-related zinc-finger transcription factor, slug (SNAI2, 268aa), is critical for the normal development of neural crest-derived cells and loss-offunction Slug mutations have been proven to cause piebaldism and Waardenburg’s syndrome type 2.
slurps Secreted
Ly6/PLAUR domain-containing proteins. Proteins with anti-tumour activity. Slurp 1 (103aa) is involved in maintaining the physiological and structural integrity of the keratinocyte layers of the skin, and defects are a cause of Meleda disease. Slurp 2 (97aa) is expressed in a wider range of tissues. Research article: http://www.ncbi.nlm.nih.gov/ pmc/articles/PMC2144295/pdf/10211827.pdf
Sly’s syndrome An autosomal recessive lysosomal storage disease (mucopolysaccharidosis type VII) caused by mutation in the gene encoding betaglucuronidase.
Sm proteins (1) Sm proteins were originally isolated as the antigens targeted by anti-Sm antibodies in a patient (Stephanie Smith) with systemic lupus erythematosus. They are RNA-binding proteins associated with a set of uridine-rich small nuclear RNA (snRNA) molecules U1, U2, U4 and U5. The Sm core proteins (SmB, SmB’, SmN, SmD1, SmD2, SmD3, SmE, SmF and SmG) combine with other proteins and snRNAs to form small nuclear ribonucleoproteins (snRNPs) which are components of the spliceosome. A related snRNA, U6, binds to a complex of seven Like Sm proteins. The seven Sm and eight LSm proteins are conserved in eukaryotes; related proteins are found in Archaea (Sm1 and Sm2) and in Bacteria (Hfq and YlxS hom*ologues). (2) Sec1/Munc18-like proteins (SM proteins, syntaxin-binding proteins) that bind to the SNARE complexes formed between SNARE molecules on the surfaces of vesicles and on their target membranes and regulate the process of membrane fusion. See Sec proteins. http://www.sciencemag.org/content/ 323/5913/474.short. (3) See SMN complex.
smac In humans, the hom*ologue of diablo (second mitochondria-derived activator of caspases, direct IAP binding protein with low isoelectric point; often smac/diablo, 239aa) promotes apoptosis by activating caspases in the cytochrome c/Apaf-1/caspase-9 pathway and opposes the effects of inhibitor of apoptosis proteins (IAPs). It is the mammalian functional hom*ologue of Drosophila Reaper, Grim and Hid. Smac export from mitochondria into the cytosol is provoked by cytotoxic drugs and DNA damage but release can be reduced if Bcl-2 is overexpressed.
Smad proteins Intracellular proteins (hom*ologues of Drosophila mothers against decapentaplegic, MAD-related proteins and C. elegans dwarfin/sma
smallpox proteins) that mediate signalling from receptors for extracellular TGFβ-related factors. At least eight are identified. Smad2 (467aa) is essential for embryonic mesoderm formation and establishment of anteriorposterior patterning. Smad4 (552aa) is important in gastrulation. Smads1 (465aa) and 5 (465aa) are activated (serine/threonine phosphorylated) by BMP receptors, Smad2 and 3 (425aa) by activin and TGFβ receptors. Smads activated by occupied receptors form complexes with Smad4/DPC4 and move into the nucleus where they regulate gene expression. Interact with forkhead activin signal transducer. See juvenile polyposis.
small acid-soluble spore proteins SASPs DNA-binding proteins in the spores of some bacteria, thought to stabilize the DNA in the A-DNA configuration, so protecting it from cleavage by enzymes or UV light.
small basic intrinsic proteins SIPs A subset of the aquaporins. SIP1 (small basic intrinsic protein 1-1, 240aa) is found in the endoplasmic reticulum of Arabidopsis.
small cell carcinoma Common malignant neoplasm of bronchus. Cells of the tumour have endocrine-like characteristics and may secrete one or more of a wide range of hormones, especially regulatory peptides like bombesin.
small interfering RNA siRNA Small doublestranded RNA molecules (20225 bp) that interfere with the expression of specific mRNAs (RNA interference). They are a powerful experimental method for investigating the function of particular genes and are being developed as potential therapeutic agents. Some will activate gene expression (small activating RNAs, saRNAs) and others will activate innate antiviral systems (see RIG1). Cf. microRNAs. See transacting siRNAs.
small leucine-rich repeat proteoglycans SLRPs A family of proteoglycans characterised by leucine-rich repeats. Includes asporin, decorin, biglycan, osteomodulin, fibromodulin, and osteoglycin (mimecan).
small nuclear RNA snRNA Abundant class of RNA found in the nucleus of eukaryotes, usually including those RNAs with sedimentation coefficients of 7S or less. They are about 1002300 nucleotides long. Although 5S rRNA and tRNA are of a similar size, they are not normally regarded as snRNAs. Most are found in complexes with proteins (see ribonucleoprotein particles, snRNPs) and at least some have a role in processing hnRNA.
small temporal RNAs stRNAs Early name for microRNAs.
smallpox See variola virus.
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smooth microsome
SMARC The SWI/SNF complex-related, matrix-
Smith-Magenis syndrome A set of complex
associated, actin-dependent regulators of chromatin (SMARC), also called BRG1-associated factors (BAFs), are components of human SWI/SNF-like chromatin-remodelling protein complexes. The SMARCA4 gene encodes the transcription activator BRG1 (EC 3.6.1.-, BRG1-associated factor 190A, 1647aa) an ATP-dependent helicase that interacts with nuclear hormone receptors to potentiate transcriptional activation.
developmental abnormalities generally caused by a 3.7-Mb interstitial deletion in chromosome 17p11.2, but occasionally by mutations in the RAI1 gene (retinoic acid inducible-1) which is located in this region. A milder phenotype is associated with duplication of the same chromosomal region.
SMART A free web-based resource, a ‘Simple Modular Architecture Research Tool’, that allows the identification and annotation of protein domains. SMART-7 (2012) has models for 1009 protein domains from more than 2 million proteins in 1133 species. Link to web-pages: http://smart.embl-heidelberg.de/
SMC proteins A family of proteins (structural maintenance of chromosomes proteins) involved in chromosome cohesion during the cell cycle and in DNA repair. They are the central components of the cohesin complex which forms a large ring structure that traps sister chromatids until the complex is degraded at anaphase; the complex may also play a role in spindle pole assembly during mitosis. Cohesin complexes are composed of SMC1 (1233aa)/SMC3 (1217aa) heterodimers attached via their hinge domain, RAD21 which links them and one STAG protein (STAG1, STAG2 or STAG3), which interacts with RAD21. Defects in SMCs are the cause of Cornelia de Lange syndrome. The SMC5 (1101aa)/SMC6 (1091aa) complex (in association with non-structural maintenance of chromosomes element 2 hom*ologue, NSMCE2) is involved in maintaining the integrity of DNA at double-strand breaks and promoting repair by hom*ologous recombination. Research article: http://www.nature.com/ emboj/journal/v25/n14/full/7601218a.html
SMCT A Na1-coupled transporter (sodium-coupled monocarboxylate transporter, SLC5A8, 610aa) for lactate, pyruvate and short-chain fatty acids. Resorbs lactate in the kidney and maintains blood lactate homeostasis.
SMG1C complex A mRNA surveillance complex that recognizes and degrades mRNAs containing premature translation termination codons. Components include a serine/threoinine kinase (SMG1, 3657aa), SMG8 (991aa) and SMG9 (512aa). The complex forms part of the larger SURF complex. Other SMG proteins are involved in different mRNA surveillance systems (nonsense-mediated mRNA decay) and in the telomerase complex.
Smith-Lemli-Opitz syndrome An autosomal recessive disorder in which there are multiple congenital malformations and mental retardation. Caused by mutations in the gene encoding sterol delta-7reductase (DHCR7).
Smith-McCort dysplasia A rare autosomal recessive osteochondrodysplasia caused by defects in dymeclin. Has features in common with DyggveMelchior-Clausen syndrome which is caused by mutation in the same gene.
Smith-Watermann alignment Algorithm for detecting sequence similarities when searching a genomic database.
SMMCI A disorder in which there is a solitary median maxillary central incisor (SMMCI) in both the deciduous and permanent dentition. Caused by a mutation in the sonic hedgehog gene.
SMN complex A large macromolecular complex (survival of motor neurons complex) found in all metazoan cells and involved in the production of spliceosomal small nuclear ribonucleoproteins (snRNPs). The complex is found in the cytoplasm and in the nucleus in Gems (gemini of the coiled bodies). The constituent proteins include SMN, Gemin2, Gemin3 (a DEAD-box RNA helicase), Gemin4, Gemin5 (a WD-repeat protein), Gemin6 and Gemin7. SMN protein (294aa) is the product of the survival of motor neurons (SMN) gene which is defective in spinal muscular atrophy. The complex binds to specific sequences in the snRNAs. SMN complex substrates include Sm proteins, like Sm proteins, RNA helicase A, fibrillarin and GAR1, the RNP proteins hnRNP U, Q and R, as well as p80coilin. Research article: http://hmg.oxfordjournals. org/cgi/content/full/14/12/1605
SMO (1) See smoothened. (2) Spermine oxidase. (3) The SMO genetic locus in strains of the fungus Magnaporthe grisea directs the formation of correct cell shapes in asexual spores, infection structures and asci.
smooth endoplasmic reticulum SER An internal membrane structure of the eukaryotic cell, similar to the rough endoplasmic reticulum (RER) but without the ribosome-binding function. Tends to be tubular rather than sheet-like, may be separate from the RER or may be an extension of it. Abundant in cells concerned with lipid metabolism and proliferates in hepatocytes when animals are challenged with lipophilic drugs.
smooth microsome Fraction produced by ultracentrifugation of a cellular hom*ogenate. It consists of membrane vesicles derived largely from the smooth endoplasmic reticulum.
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SNIP
smooth muscle Muscle tissue in vertebrates
snake A Drosophila serine peptidase (EC 3.4.21.-,
made up from long tapering cells that may be anything from 202500μm long. Smooth muscle is generally involuntary, and differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres, and the ability to contract to a much smaller fraction of its resting length. Smooth muscle cells are found particularly in blood vessel walls, surrounding the intestine (particularly the gizzard in birds), and in the uterus. The contractile system and its control resemble those of motile tissue cells (e.g. fibroblasts, leucocytes), and antibodies against smooth muscle myosin will cross-react with myosin from tissue cells, whereas antibodies against skeletal muscle myosin will not. See also dense bodies.
435aa) involved in activating easter, a key component of the dorso-ventral patterning pathway in development.
smooth strain See rough strain. smoothelin Actin-binding protein (917aa with multiple isoforms) expressed abundantly in visceral (smoothelin-A) and vascular (smoothelin-B) smooth muscle and often used as a marker protein for contractile smooth muscle cells. Co-localizes with alpha-smooth muscle actin in stress fibres, posesses a calponin hom*ology domain and is thought to have a role in the contractile process. Various smoothelinlike proteins are also known (e.g. smoothelin-like 1, CHASM, calponin hom*ology-associated smooth muscle, 457aa) although they do not bind to F-actin in vitro.
smoothened In Drosophila a G-protein coupled receptor (smo, 1036aa) that associates with patched protein that has bound sonic hedgehog and transmits its activation signal to a microtubule-associated hedgehog signalling complex. It is thought to convert the Gli family of transcription factors from transcriptional repressors to transcriptional activators. Protein kinase A (PKA) and casein kinase I (CKI) regulate Smo cell-surface accumulation and activity. In the absence of hedgehog patched represses the constitutive signalling activity of smo through fused. The mammalian smoothened hom*ologue (in humans, 787aa) is expressed on the primary cilium. See cyclopamine.
SMRT Nuclear
receptor co-repressor (silencing mediator of retinoic acid and thyroid hormone receptors, 2525aa) that mediates the transcriptional repression activity of some nuclear receptors by promoting chromatin condensation, thus preventing access of the basal transcription. Distinct from N-CoR.
snail A zinc-finger transcription factor (264aa) involved in epithelial-mesenchymal transition; binds conserved E-box elements in the prostaglandin dehydrogenase (PGDH) promoter to repress transcription and downregulates E-cadherin. The snail family includes slug which suppresses several epithelial markers and adhesion molecules.
SNAP (1) Originally, soluble NSF attachment (accessory) protein (SNAP), involved in the control of vesicle transport by binding together with NSF, to SNAREs. The name has morphed to become ‘synaptosomal-associated proteins’ with the size (kDa) as the suffix. SNAP23 (23 kDa, 211aa) is part of the high affinity receptor for the general membrane fusion machinery and an important regulator of transport vesicle docking and fusion. Binds snapin, multiple syntaxins and synaptobrevins/ VAMPs. SNAP25 (206aa) is a t-SNARE involved in regulating neurotransmitter release. SNAP29 (258aa) and SNAP47 (464aa) are involved in various membrane trafficking activities. In Arabidopsis SNAP33 (SNAP25 hom*ologous protein, 300aa) is ubiquitous and acts as a t-SNARE. (2) S-nitrosoN-acetyl penicillamine.
snapin A SNARE-associated protein (SNAP25binding protein, 136aa) involved in synaptic vesicle docking and fusion and also a component of the BLOC1 complex.
SNAREs Receptors for SNAPs. The neuronal receptor for vesicle-SNAPs, v-SNARE, is synaptobrevin, also known as VAMP-2. The target (t-SNARE) associated with the plasma membrane of the axonal terminal is syntaxin. The SNAP-SNARE complex is apparently responsible for regulating vesicle targeting: neurotoxins such as tetanus toxin and botulinum toxin selectively cleave SNAREs or SNAPs. See also cellubrevin.
SNEEZY SNE A plant F-box protein (SLEEPY (SLY1) hom*ologue, 157aa) a component of a SCFtype E3 ligase complex that positively regulates the gibberellin signalling pathway. SNEEZY can replace SLY1 in the gibberellic acid-induced proteolysis of RGA, one of the DELLA proteins.
Snf1 kinase In Saccharomyces a multimeric complex required for transcriptional, metabolic, and developmental adaptations in response to glucose limitation. The complex is heterotrimeric with a catalytic alpha subunit SNF1 (carbon catabolitederepressing protein kinase, EC 2.7.11.1, 633aa), one of the three related beta subunits SIP1, SIP2 or GAL83, and the regulatory gamma subunit SNF4. hom*ologous systems are found in plants (KIN10/11) and animals (SNF1-related kinase, SNRK).
SNIP (1) Smad nuclear-interacting protein 1 (396aa) that down-regulates NFκB signalling. (2) An enzyme (snRNA incomplete 30 processing) involved in processing snRNA in Trypanosoma brucei. The central 158aa domain of SNIP is related to the exonuclease III (ExoIII) domain of the 30 -50 proofreading
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epsilon subunit of E. coli DNA polymerase III. (3) SNAP-25-interacting protein (src kinase signalling inhibitor 1, 1055aa) is co-distributed with SNAP-25 in brain where it regulates dendritic spine morphology and is involved in calcium-dependent exocytosis.
snoRNA Small nucleolar ribonucleic acid; guide chemical modifications of ribosomal and transfer RNAs and other small nuclear RNAs (snRNAs). See fibrillarin.
sodium lithium countertransport substrate recognition component of an ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins and seems to recognize JAK2. Other SOCs family members are induced by different cytokines and have slightly different targets (e.g. SOCS2, 198aa, is a negative regulator in the growth hormone/IGF1 signalling pathway).
sodium channel (1) Voltage-gated sodium chan-
domain protein PRO40. Said to contribute to the sealing efficiency of pores plugged by Woronin bodies after hyphal injury.
nels (NaV1.1, etc.) are responsible for electrical excitability of neurons. They are multi-subunit transmembrane channels with an aqueous pore around 0.4 nm diameter, with a negatively charged region internally (the ‘selectivity filter’) that blocks the passage of anions. The alpha subunits form the pore itself, the beta subunits vary between tissues and regulate the sensitivity. The channel opens in response to a small depolarization of the cell (usually caused by an approaching action potential), by a multistep process. Around 1000 sodium ions pass in the next millisecond, before the channel spontaneously closes (an event with single-step kinetics). The channel is then refractory to further depolarizations until returned to near the resting potential. There are around 100 channels per mm2 in unmyelinated axons; in myelinated axons, they are concentrated at the nodes of Ranvier. Mutations are associated with various forms of epilepsy, muscular disorders (periodic paralysis, myotonia), long QT syndrome, Brugada’s syndrome-1, erythromelalgia, congenital insensitivity to pain and paroxysmal extreme pain disorder. Many toxins (e.g. tetrodotoxin) affect the channel. (2) Amiloride-sensitive sodium channels are a family of nonvoltage-gated sodiumpermeable ion channels inhibited by the diuretic drug, amiloride. They are well characterized in epithelia where they constitute the rate-limiting step for sodium ion reabsorption. They are heterotrimers of highly hom*ologous alpha, beta and gamma subunits which also have hom*ology with degenerins from C. elegans. Gain of function mutations in the beta or gamma subunits is the cause of Liddle’s disease. A delta subunit that will assemble with the beta and gamma subunits to form a functional channel is also known. See Apx/Shrm domains.
SOC media A cell growth medium used to ensure
sodium cromoglicate A drug (formerly sodium
SNP Single nucleotide polymorphism. Any of the variations in single nucleotides in a DNA sequence that contribute to human individuality; at least 10 million are known. Arbitrarily, SNPs are defined as variations that occur in 1% or more of the population. SNP-mapping is increasingly used in searching for genetic associations of disease and the International HapMap Project makes the data publicly available.
SnRKs SNF-related serine/threonine kinases (EC 2.7.11.1, 765aa). In Arabidopsis a superfamily of kinases (CDPK-SnRK superfamily) with at least 34 members from seven subclasses involved in a range of signalling activities. See Snf1 kinase. Research paper: http://www.plantphysiol.org/content/132/2/666.full
snRNA See small nuclear RNA. snRNP Small nuclear ribonucleoprotein. See small nuclear RNA.
SNRPN One of the Sm proteins (small nuclear ribonucleoprotein polypeptide N, 240aa) an important trans-acting factors in constitutive pre-mRNA splicing, found predominantly in central neurons. The gene encoding the peptide is bicistronic and encodes 2 polypeptides, the SmN splicing factor and the SNRPN upstream reading frame (SNURF) polypeptide. Deletion of the paternal copy leads to Prader-Willi syndrome, that of the maternal copy to Angelman syndrome.
SO In Neurospora crassa the hom*ologue of the WW
maximum transformation efficiency, it is ‘Super Optimal Broth’ with the ‘B’ in SOB changed to ‘C’, for catabolite repression, reflective of the added glucose. Details: http://openwetware.org/wiki/SOB
SOCS Family of proteins suppressor of cytokine signalling, SOCS 1-7 and CIS (cytokine-inducible SH2-containing protein, 258aa) with SH2 domains that are induced in response to cytokines and act as negative feedback regulator of JAKs in the intracellular signalling pathway. SOCS1 (JAK-binding protein, JAB, STAT-induced STAT inhibitor-1, SSI-1, 211aa) is induced by IL6 and is probably the
cromoglycate) used prophylactically for allergic asthma. It acts on mast cells to inhibit release of bronchoconstrictors by indirectly blocking calcium ion influx.
sodium cromoglycate See sodium cromoglicate. sodium dodecyl sulphate See SDS. sodium lithium countertransport Erythrocyte sodium/lithium countertransport (SLC, Na/LiCT), sodium-stimulated lithium efflux from lithium-loaded erythrocytes, has been observed to be abnormal in
sodium pump
615
several hypertension-related diseases and is increased in patients with diabetes mellitus. But see solute carrier family proteins.
sodium pump See sodium-potassium ATPase. sodium-potassium ATPase A major transport protein, not a sodium channel, the sodium pump of the plasma membrane. A multi-subunit enzyme (EC 3.6.1.3), having a catalytic alpha subunit with multiple isoforms and a smaller beta subunit. The pump moves 3 sodium ions out of the cell, and 2 potassium ions in, for each ATP hydrolyzed. The sodium gradient established is used for several purposes (see facilitated diffusion, action potential), while the potassium gradient is dissipated through the potassium leak channel.
sodoku Rat-bite fever, an infection by Streptobacillus moniliformis or Spirillum minus, following the bite of a rat or contact with rat saliva.
soft agar Semi-solid agar used to gelate medium for culture of animal cells. Placed in such a medium, over a denser agar layer, the cells are denied access to a solid substratum on which to spread, so that only cells that do not show anchorage-dependence (usually transformed cells) are able to grow.
SOK1 (1) A Ste20 protein kinase (Sterile 20/oxidant stress-response kinase 1, EC 2.7.11.1, 426aa) of the germinal centre kinase (GCK) family, that is activated by oxidant stress and chemical anoxia. It localizes to Golgi apparatus where it appears to regulate protein transport events, cell adhesion, and cell polarization for locomotion. (2) In S. cerevisiae a suppressor (901aa) of a cyclic AMP-dependent protein kinase mutant.
sol-gel transformation Transition between more
somatic mesoderm
Solanum tuberosum The potato. SolEST A database that integrates different EST datasets from both cultivated and wild Solanaceae species and from two species of the genus Coffea. Link to database: http://biosrv.cab.unina.it/solestdb
soluble tyrosine kinases An obsolete term for tyrosine kinases that are not membrane associated.
solurshin See PITX genes. solute carrier family proteins SLCs Superfamily of proteins involved in the transport of molecules across membranes. 46 sub-classes are recognised, each with several members. For example, solute carrier family 1 (SLC1) comprises neuronal/epithelial high affinity glutamate/ neutral amino acid transporters, SLC2 family is of facilitated glucose transporters (GLUT proteins) and has 14 members. The superfamily does not include ATP Binding Cassette (ABC) transporters, ion channels or aquaporins.
somaclone Plants derived from somatic cells that have been grown in culture. Somaclonal variation is variation seen after repeated subculture.
somatic cell Usually any cell of a multicellular organism that will not contribute to the production of gametes, i.e. most cells of which an organism is made: not a germ cell. Notice, however, the alternative use in somatic mesoderm.
somatic cell genetics Method for identifying the chromosomal location of a particular gene without sexual crossing. Unstable heterokaryons are made between the cell of interest and another cell with identifiably different characteristics (or without the gene in question), and a series of clones isolated. By correlating retention of gene expression with the remaining chromosomes, it is possible to deduce which chromosome must carry the gene. Humanmouse heterokaryons have been extensively used in this sort of work.
fluid cytoplasm (endoplasm) and stiffer gel-like ectoplasm proposed as a mechanism for amoeboid locomotion: since the endoplasm cannot really be considered a simple fluid and has viscoelastic properties like a gel, the term is misleading and the mechanism is not generally accepted.
somatic cell nuclear transfer Transfer of the
solanidine The aglycone of solanine and chaco-
nucleus of a somatic cell into an enucleated egg as a means of cloning.
nine that is produced by the action of solanidine UDP-glycosyltransferases. Solanine has a branched trisaccharide galactose-(glucose)- rhamnose moiety, chaconine a glucose-(rhamnose)-rhamnose moiety.
solanine A glycoalkaloid toxin found in species of the nightshade family (Solanaceae) that includes potatoes. It can occur naturally in the any part of the plant, including the leaves, fruit, and tubers. It is very toxic even in small quantities. Solanine has both fungicidal and pesticidal properties, and it is one of the plant’s natural defenses. Has sedative and anticonvulsant properties, and has been used as a treatment for bronchial asthma. See solanidine, chaconine.
somatic embryogenesis The process in plants (asexual embryogenesis) in which somatic cells differentiate into embryos and ultimately into plants via a series of characteristic morphological stages. Somatic cells in plants retain totipotency.
somatic hybrid Heterokaryon formed between two somatic cells, usually from different species. See somatic cell genetics.
somatic mesoderm That portion of the embryonic mesoderm that is associated with the body wall, and is divided from the splanchnic (visceral) mesoderm by the coelomic cavity.
somatic mutation
616
somatic mutation Mutation that occurs in the somatic tissues of an organism, and that will not, therefore, be heritable, since it is not present in the germ cells. Some neoplasia is due to somatic mutation; a more conspicuous example is the reversion of some branches of variegated shrubs to the wild-type (completely green) phenotype. Somatic mutation is probably also important in generating diversity in V-gene regions of immunoglobulins.
somatic recombination One of the mechanisms
sorocarp tube during development of the vertebrate embryo. Somites are formed sequentially, starting at the head. Each somite will give rise to muscle (from the myotome region), spinal column (from the sclerotome), and dermis (from dermatome).
son-of-sevenless Drosophila
ras-GRF (GDF releasing factor, 1956aa), mammalian hom*ologues of which play an important part in intracellular signalling. See sos.
used to generate diversity in antibody production is to rearrange the DNA in B-cells during their differentiation, a process that involves cutting and splicing the immunoglobulin genes. Somatic recombination via hom*ologous crossing-over occurs at a low frequency in Aspergillus, Drosophila and Saccharomyces and in mammalian cells in culture. It may be detected through the production of hom*ozygous patches or sectors after mitosis of cells heterozygous for suitable marker genes.
sonic hedgehog Secreted protein (Shh, 465aa)
somatocrinin Growth hormone-releasing factor.
sorbitol glucitol The polyol (polyhydric alcohol)
See growth hormone-releasing hormone.
somatoliberin Growth hormone-releasing factor, somatotropin-releasing factor. See growth-hormone releasing hormone.
processed in the same way as other members of the hedgehog family, involved in organization and patterning of several vertebrate tissues during development. The zone of polarizing activity (ZPA) that determines anterior-posterior patterning of the limb expresses sonic hedgehog. Defects in Shh or the downstream signalling pathway are a cause of holoprosencephaly 3, VACTERL syndrome and SMMCI. corresponding to glucose. Occurs naturally in some plants, is used as a growth substrate in some tests for bacteria, and is sometimes used to maintain the tonicity of low ionic strength media.
sorbitol dehydrogenase A member of the somatomedin Generic term for insulin-like growth factors (IGFs) produced in the liver and released in response to somatotropin. Somatomedins stimulate the growth of bone and muscle, and also influence calcium, phosphate, carbohydrate and lipid metabolism. Somatomedin A (180aa) is IGF-II, somatomedin C (153aa) is IGF-I. Somatomedin B is a serum factor of uncertain function derived by proteolytic cleavage from vitronectin. See somatostatin.
somatostatin Gastrointestinal and hypothalamic peptide hormone (two forms: 14 and 28aa); found in gastric mucosa, pancreatic islets, nerves of the gastrointestinal tract, in posterior pituitary and in the central nervous system. Inhibits gastric secretion and motility: in hypothalamus/pituitary inhibits somatotropin release. Somatostatin acts through five G protein-coupled receptor subtypes (SSTR1-5), displaying a tissue specific distribution with multiple subtypes present on many cells. A neuropeptide, cortistatin, strongly resembles somatostatin. See also Table H2.
somatotrope Cell in the anterior pituitary which secretes growth hormone.
somatotrophin US. somatropin. Hormone (human
superfamily of medium chain dehydrogenases/reductases, (EC 1.1.1.14, SORD, 357aa), the second enzyme in the polyol pathway; oxidizes sorbitol to fructose in the presence of NAD1.
sorbose A monosaccharide hexose: L-sorbose is an intermediate in the commercial synthesis of ascorbic acid.
soredium Pl. soredia. Specialised asexual reproductive products of lichens consisting of algal cells surrounded by fungal hypae; emerge from soralia on the lichen suface and are wind-dispersed.
Soret band A very strong absorption band in the blue region (414 nm) of the optical absorption spectrum of a haem protein.
Soret effect The mass diffusion of chemical species due to an imposed thermal gradient. A temperature gradient across a fluid or gaseous mixture generally leads to a net mass flux and the build-up of a concentration gradient. This effect is known as thermal diffusion or Ludwig-Soret-effect. The amplitude of the concentration gradient is determined by the Soret coefficient, ST.
growth hormone, hGH, 191aa) released by anterior pituitary that stimulates release of somatomedin, thereby causing growth. See also Table H2.
Sorghum bicolor An important cereal crop for
somites Segmentally arranged blocks of mesoderm
sorocarp Fruiting body formed by some cellular
lying on either side of the notochord and neural
food, fuel, and biofeedstock. Unlike rice it is a C4 plant. slime moulds; has both stalk and spore-mass.
sortilin
617
sortilin A sorting receptor (neurotensin receptor 3, 831aa) in the Golgi compartment and a clearance receptor on the cell surface. Required for protein transport from the Golgi to lysosomes and important for the sorting and trafficking of sphingolipid activator proteins (saposins).
sorting nexins A large family of proteins that characteristically have a phox-hom*ology (PX) domain and are required for the endocytosis and sorting of transmembrane proteins. Sorting nexin-1 (SNX1, 522aa) is a component of the mammalian retromer complex. Human SNX1, -2, and -4 have been proposed to play a role in receptor trafficking and have been shown to bind to several receptor tyrosine kinases. SNX-6 (406aa) interacts with members of the TGFβ family of receptor serine-threonine kinases. Yeast Vps5p is the orthologue of mammalian sorting nexin-1.
sorting out Phenomenon observed to occur when mixed aggregates of dissimilar embryonic cell types are formed in vitro. The original aggregate sorts out so that similar cells come together into hom*otypic domains, usually with one cell type sorting out to form a central mass that is surrounded by the other cell type. Much controversy has arisen over the years as to the underlying mechanism, whether there is specificity in the adhesive interactions (which would imply tissue-specific receptor-ligand interactions), or whether it is sufficient to suppose that there are quantitative differences in hom*o- and hetero-typic adhesion (the differential adhesion hypothesis). With the exception perhaps of the main protagonists, most cell biologists consider that there are probably elements both of tissue specificity (CAMs) and of quantitative adhesive differences involved.
sorus A group of sporangia or spore cases, e.g. on the underside of fern leaves.
sos (1) Guanine-nucleotide releasing factors (sos1, 1333aa; sos2, 1332aa), the mammalian hom*ologues of son-of-sevenless. The proline-rich region of sos binds to the SH3 domain of GRB2. Has hom*ology with CDC-25, the yeast GTP-releasing factor for ras. A family of related proteins are now known and include vav, C3G, Ost, NET1, Ect2, RCC1, tiam, RalGDS, and Dbl. (2) See SOS system.
SOS system The DNA repair system also known as error-prone repair in which apurinic DNA molecules are repaired by incorporation of a base that may be the wrong base but that permits replication. RecA protein is required for this type of repair. SOS genes function in control of the cell cycle in prokaryotes and eukaryotes. See lexA.
Sotos' syndrome A disorder of growth (cerebral gigantism) caused by mutation in the NSD1 gene (nuclear receptor-binding suppressor of variation,
spacer DNA enhancer of zeste, trithorax domain protein 1) that encodes a co-regulator of the androgen receptor (histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific, EC 2.1.1.43, 2696aa). See SET protein, SET complex.
source-sink relationship In plants, the balance between source tissues that produce sugars and amino acids by photosynthesis and the sink tissues that import these products.
Southern blots See blotting. Originally developed by Dr Ed Southern, hence the name.
sox (1) SoxR: Redox sensory protein in E. coli. (2) SOX syndrome: Sialadenitis, osteoarthritis and xerostomia syndrome. (3) Sox genes (Sry-related HMG-box genes) are a family of genes involved in many developmental processes. Sox-2 regulates transcription of FGF-4 gene, sox-3 is involved in neural tube closure and lens specification, sox-9 is related to sry and found in mouse testis, sox-10 is important in neural crest development.
soybean trypsin inhibitor SBTI A Kunitz-type trypsin inhibitor (181aa) that forms a stable, stoichiometric, enzymically-inactive complex with trypsin, chymotypsin, plasmin and related peptidases.
SP proteins (1) A family of Cys2His2 zinc finger transcription factors that bind with high affinity to GC-rich motifs and regulate the expression of a large number of genes involved in a variety of processes such as cell growth, apoptosis, differentiation and immune responses. Specificity protein 1 (Sp1, 785aa) has been linked to vascular endothelial growth factor (VEGF) expression in pancreatic cancer cells. Research article: http://cancerres.aacrjournals. org/content/64/18/6740.full.pdf 1 html (2) In Bombyx mori, a methionine-rich larval storage protein (747aa). (3) In Macrozoarces americanus (Ocean pout) an antifreeze protein (ice-structuring protein SP1, 63aa). (4) Tunichrome Sp-1 is a modified pentapeptide from the haemocytes of the ascidian Styela plicata. (5) In Crotalus adamanteus (Eastern diamondback rattlesnake) a venom serine peptidase (EC 3.4.21.-, 259aa).
Sp value The specificity score or profile determined, e.g. for PDZ domains. The score ranges from zero (least specific) at a given ligand position to one (most specific). It allows classification of the domains into specificity classes with preferences for particular ligands. Research article: http://www.plosbiology.org/ article/info:doi/10.1371/journal.pbio.0060239
SPA, SPD See surfactant proteins A and D. spacer DNA The DNA sequence between genes. In bacteria, only a few nucleotides long. In eukaryotes, can be extensive and include repetitive DNA, comprising the majority of the DNA of the genome. The term is used particularly for the spacer DNA
SPAK
618
between the many tandemly-repeated copies of the ribosomal RNA genes (see intergenic spacer and internal transcribed spacers).
SPAK A serine/threonine kinase (Ste20/SPS-1-related proline-, alanine-rich kinase, 547aa) that phosphorylates NKCC1 (Na1-K1-2Cl2 co-transporter-1), leading to its activation. SPAK and OSR1 (oxidative stressresponsive kinase-1) are phosphorylated and activated by WNKs (with no K (lysine) protein kinase-1).
SPARC A secreted protein, acidic and rich in cysteine (SPARC, 303aa) overexpressed in the fibroblasts of skin biopsy specimens obtained from patients with systemic sclerosis. See osteonectin.
sparsomycin An antibiotic from Streptomyces sparsogenes, that inhibits peptidyl transferase in both prokaryotes and eukaryotes by blocking the peptidyl transfer step on the 50S/60S ribosomal subunit. More detail: http://www.microbiologyprocedure. com/bacterial-cheomotherapy/sparsomycin.htm
species are responsible for most cases of autosomal dominant spastic paraplegia.
spastizin Zinc finger FYVE domain-containing protein (ZFYVE26, 2539aa) found in a wide range of tissues. Mutations in the encoding gene cause a form of autosomal recessive spastic paraplegia (Kjellin’s syndrome).
spatacsin A multi-pass membrane protein (spasticity with thin or atrophied corpus callosum syndrome protein, 2443 aa) expressed throughout the brain, and highly expressed in the cerebellum. The encoding gene is defective in autosomal recessive spastic paraplegia Type 11.
spatial sensing Mechanism of sensing a gradient in which the signal is compared at different points on the cell surface and cell movement directed accordingly. Translocation of all or part of the cell is not required. See temporal and pseudospatial gradient sensing.
spartin A cytosolic and membrane-associated protein (666aa) that may be implicated in endosomal trafficking. A frameshift mutation in the spartin gene is the cause of Troyer syndrome (a form of spastic paraplegia).
spasmin Protein (180aa in Vorticella) that forms the spasmoneme. Thought to change its shape when the calcium ion concentration rises, and to revert when the calcium concentration falls: the reversible shape change is used as a motor mechanism. Contraction does not require ATP, relaxation does, probably to pump calcium ions back into the smooth endoplasmic reticulum.
spasmoneme Contractile
organelle found in Vorticella and related ciliate protozoans. Capable of shortening faster than any actin-myosin system, and of expanding actively. See spasmin.
spastic paraplegias A set of neurodegenerative disorders in which there is lower-limb spasticity (increased muscle tone with involuntary spasms or sustained contractions) and muscle weakness with a variety of different causes. Various subtypes are caused by defects in atlastin, kinesin-5A, maspardin, myelin proteolipid protein, NIPA1, paraplegin, PNPLA6, protrudin, receptor expression-enhancing protein-1, spartin, spastin, spatacsin and strumpellin; in other forms the defect is mapped but the defective protein as yet unidentified. Inheritance is most commonly autosomal dominant, but X-linked and autosomal recessive forms also occur.
spastin An ATPase (EC 3.6.4.3, 616aa) of the AAA family, related to the microtubule-severing protein katanin. It is involved in membrane traffic from the endoplasmic reticulum to the Golgi and may have a role in axon growth and the formation of axonal branches. Mutations in the encoding gene (SPG4)
spätzle spaetzle The protein (326aa) that is proteolytically processed (see easter) to produce the ligand (spa¨tzle C-106) for toll in dorso-ventral polarity signalling in Drosophila development. In the adult it is involved in antifungal defense.
SPAZ domain A domain (serine- and proline-rich AZU-1 domain, 83aa) found in TACC2 (AZU-1), TACC1, TACC3 and the S. cerevisiae gene product BCK1, a member of the MAPK kinase kinase family of serine/threonine kinases. It is thought that the domain may be a member of the Ig superfamily and as such may function as a protein-binding interface.
speciation Formation of new biological species. Usually considered to require isolation of a subpopulation of the ancestral species either geographically (classically seen with remote islands), by occupying a different niche (adaptive radiation), through acquisition of behavioural changes that restrict mating, so that distinct genetic variations accumulate and prevent further interbreeding, or by polyploidy that makes interbreeding with the original species impossible. See sympatric speciation.
species A group of individuals that are capable of interbreeding with each other but not with members of other groups. Usually a result of some form of isolation; in the early stages speciation can be reversed if reproductive isolation is lost or the niches change and overlap. Species are grouped into genera and divided into subspecies and varieties or cultivars. The name of the genus should be capitalised and the species name should not thus hom*o sapiens, genus hom*o, species sapiens and both should be italicised. This nicety is increasingly neglected.
specific activity
619
specific activity The number of activity units (whatever is appropriate) per unit of mass, volume or molarity. Perhaps most often encountered in the context of radiochemicals, the number of microcuries per micromole.
specific granules One of the two main classes of granules (secondary granules) found in neutrophil leucocytes: contain lactoferrin, lysozyme, Vitamin B12 binding protein and elastase. Are released more readily than the azurophil (primary) granules which have typical lysosmal contents.
spectinomycin A bacteriostatic aminocycl*tol antibiotic produced by the soil bacterium, Streptomyces spectabilis; binds to the 30S subunit of the bacterial ribosome, thus inhibiting protein synthesis.
spectral karyotyping A technique that allows scientists to visualize all of the human chromosomes at one time by ‘painting’ each pair of chromosomes in a different fluorescent color; translocations show up very conspicuously because the affected chromosome is multi-coloured.
spectraplakins Large cytoskeletal linker proteins that bind cytoplasmic filaments (microfilaments, microtubules and intermediate filaments). They often have two calponin hom*ology domains, a plakin domain, a series of plectin repeats, numerous spectrin repeats and a GAS2 domain: multiple isoforms are produced from each gene. The human spectraplakin (macrophin 1, trabeculin-alpha, actin crosslinking factor 7, 5373aa) is ubiquitously expressed. See desmoplakin, envoplakin, epiplakin, kazrin, periplakin, plectin. In Drosophila short-stop is a spectraplakin hom*ologue.
spectrin Membrane-associated
dimeric protein (alpha, 2419aa; beta, 2137aa) of erythrocytes. Forms a complex with ankyrin, actin, and probably other components of the ‘membrane cytoskeleton’, a meshwork of proteins underlying the plasma membrane, potentially restricting the lateral mobility of integral proteins and providing mechanical stability. Isoforms have been described from other tissues (fodrin, TW-240/260 kDa protein), where they are assumed to play a similar role. Contains the EF-hand motif.
spectrophotometry Quantitative measurement of the absorption of visible, ultraviolet or infrared light to determine the concentrations of substances in the sample.
Spemann’s organizer Signalling region located on the dorsal lip of the blastopore in the early embryo, essential for defining the main body axis.
speract A peptide hormone, produced by proteolysis of sperm-activating peptide (296aa) in the the jelly coat of the eggs of the sea-urchins Strongylocentrotus purpuratus and Hemicentrotus pulcherrinus. Cleavage
spherical aberration produces speract and speract-like decapeptides that stimulate sperm respiration and motility. Receptors are a plasma-membrane guanylate cyclase (EC 4.6.1.2, 1125aa) and a scavenger receptor (532aa).
speriolin Spermatogenesis and centriole-associated protein 1 (591aa) that interacts with CDC20 (fizzy) and forms a complex with CDC20, CDC27 and gamma tubulin.
spermatids The haploid products of the second meiotic division in spermatogenesis. Differentiate into mature spermatozoa.
spermatocytes Cells of the male reproductive system that undergo two meiotic divisions to give haploid spermatids.
spermatogenesis The process whereby primordial germ cells form mature spermatozoa.
spermatogonium Plant gonad cell that undergoes repeated mitoses, leading to the production of spermatocytes.
Spermatophyte Division of the plant kingdom, consisting of plants (phanerogams) that reproduce by means of seeds. The existent groups are cycads, Ginkgo (the sole member of the group), conifers, gnetophytes and angiosperms; others are known from the fossil record (e.g. seed ferns).
spermatozoon Mature sperm cell (male gamete). spermidine A polybasic amine (polyamine), N-(3aminopropyl)-1,4-butanediamine; see spermine.
spermine Polybasic amine (polyamine), N, N0 bis (3-aminopropyl)-1,4-butanediamine. Found in human sperm, in ribosomes and in some viruses. Involved in nucleic acid packaging. Synthesis is regulated by ornithine decarboxylase which plays a key role in control of DNA replication.
spermine oxidase An inducible enzyme (SMO, EC 1.5.3.-, 555aa) that may play a direct role in the cellular response to the antitumour polyamine analogues. Oxidises both spermine and N(1)-acetylspermine, but not spermidine.
SPF Describing animals (specific pathogen free) that have been raised in carefully controlled conditions so that they are not infected with any known pathogens. Usually delivered by Caesarean section and raised in strict quarantine.
S phase The synthesis (S) phase of the cell cycle during which DNA replication occurs.
spherical aberration Deficiency in simple lenses in which the image is sharp in the centre but outof-focus at the periphery of the field, more a problem when taking photographs than when observing directly. Lenses compensated for this defect are referred to as plan- lenses (e.g. planapochromat).
spheroblast
620
spinal muscular atrophy
spheroblast spheroplast Bacterium or yeast that
sphingosine-1-phosphate A signalling mole-
has been treated in such a way as to have lost the outer cell wall. This makes the cell osmotically fragile but makes it easier to get large molecules across the plasma membrane in e.g. transfection.
cule released from activated platelets and by a number of other cell types in response to growth factors and cytokines. It acts extracellularly through G-protein coupled receptors (see EDGs) and intracellularly as a second messenger, reportedly inhibiting histone deacetylases (HDACs). The cellular effects include growth related effects, such as proliferation, differentiation, cell survival and apoptosis, and cytoskeletal effects, such as chemotaxis, aggregation, adhesion, morphological change and secretion.
spherocytosis A condition in which erythrocytes lose their biconcave shape and become spherical. It occurs as cells age, and is also found in individuals with abnormal cytoskeletal proteins such as spectrin. Hereditary spherocytosis can cause haemolytic anaemia.
spheroplast See spheroblast.
SPHK See sphingosine kinase.
spherosome Lysosome-like lipid body (oleosome)
Spi-1 (1) Proto-oncogene encoding a transcription
in plants that probably derives from the endoplasmic reticulum and is a site for lipid storage, particularly in oil-rich seeds.
sphingolipid Structural lipid of which the parent structure is sphingosine rather Synthesized in the Golgi complex.
than
glycerol.
sphingomyelin A sphingolipid in which the head group is phosphoryl choline. A close analogue of phosphatidyl choline. In many cells the concentration of sphingomyelin and phosphatidyl choline in the plasma membrane seems to bear a reciprocal relationship. See lipidoses.
factor (PU1) that binds to purine-rich sequences (PU boxes) expressed in haematopoietic cells. (2) Salmonella typhimurium pathogenicity island 1 (SPI-1), a region that carries genes mediating invasion into intestinal epithelial cells and that induce cell death in murine macrophages. (3) Vaccinia virus host range/antiapoptosis genes, SPI-1 and SPI-2. (4) In S. cerevisiae, a cell wall protein (stationary phase-induced protein 1, 148aa) with a role in adaptation and resistance to cell wall stress. (5) In S. pombe a GTP-binding protein (216aa) involved in nucleocytoplasmic transport.
spichthyin See NIPA1. spin labelling The technique of introducing a
sphingomyelinase A stress-activated enzyme (sphingomyelin phosphodiesterase-1, acid sphingomyelinase, EC 3.1.4.12, 629aa) that generates ceramide from sphingomyelin, which serves as a second messenger in initiating apoptotosis. Deficiency in the enzyme leads to Niemann-Pick disease. Neutral sphingomyelinases (sphingomyelinase 2, 3 and 4; 423aa, 655aa and 827aa respectively) are found in various tissues and have similar capabilities. Sphingomyelinases are components of some spider venoms.
sphingosine A long-chain amino alcohol that bears an approximate similarity to glycerol with a hydrophobic chain attached to the 3-carbon. Forms the class of sphingolipids when it carries an acyl group joined by an amide link to the nitrogen. Forms sphingomyelin when phosphoryl choline is attached to the 1-hydroxyl group. Gives rise to the cerebroside and ganglioside classes of glycolipids when oligosaccharides are attached to the 1-hydroxyl group. Not found in the free form. See sphingosine1-phosphate, sphingosine kinase.
sphingosine kinase The enzyme (sphinganine kinase, EC 2.7.1.91, SHPK1, 384aa) that catalyses the formation of the signalling molecule sphingosine-1-phosphate. Sphingosine kinase 2 (SHPK2, 654aa) is present in the nucleus in complexes with the histone deacetylases HDAC1 and HDAC2.
grouping with an unpaired electron to act as an electron spin resonance (ESR) reporter species. This is almost invariably a nitroxide compound (-N-O) in which the nitrogen forms part of a sterically hindered ring. See electron paramagnetic resonance.
spina bifida A neural tube defect in which the bones of the spinal canal fail to meet and fuse during development. Varies in severity depending upon the extent of the failure: mild forms (spina bifida occulta), where only the most posterior vertebrae are affected, may be almost asymptomatic. In more serious forms (myelomeningocele and meningocele) there can be severe disability. The addition of folic acid to the diet of women of child-bearing age significantly reduces the incidence of neural tube defects.
spinal cord Elongated, approximately cylindrical part of the central nervous system of vertebrates that lies in the vertebral canal, and from which the spinal nerves emerge.
spinal ganglion, dorsal root ganglion Enlargement of the dorsal root of the spinal cord containing cell bodies of afferent spinal neurons. Neural outgrowth from dorsal root ganglia has been studied extensively in vitro.
spinal muscular atrophy A group of autosomal recessive disorders with symmetrical muscle weakness and atrophy caused by degeneration of the
spindle
621
anterior horn cells of the spinal cord. They are all a result of mutation in the telomeric copy of the survival of motor neuron gene (SMN1; see SMN complex). The severity and age of onset are affected by variable expression of the centromeric SMN2 gene.
spindle See mitotic spindle, muscle spindle.
spokein examples are the spirochaetes Vibrio cholerae and Treponema pallidum, the causative agents of cholera and syphilis respectively.
Spirochaetes A phylum of Gram-negative bacteria, which have long, helically coiled cells. The phylum includes Treponema pallidum, the causative agent of syphilis, Leptospira, and Borrelia burgdorferi.
spindle fibres Microtubules of the spindle that
Spirogyra Genus of green filamentous algae found
interdigitate at the equatorial plane with microtubules of the opposite polarity derived from the opposite pole microtubule organizing centre. Usually distinguished from kinetochore fibres that are microtubules that link the poles with the kinetochore, although these could be included in a broader use of the term.
in freshwater ponds. Contain helically disposed ribbon-like chloroplasts.
spindle pole body In S. cerevisiae, the functional equivalent of the centrosome that organizes both the spindle and cytoplasmic microtubules throughout the cell cycle. It is anchored to the nuclear envelope. See sad1.
spinner culture Method for growing large numbers of cells in suspension by continuously rotating the culture vessel.
spinocerebellar ataxia A group of genetic disorders in which gait becomes uncoordinated, and there is slow and progressive loss of control of hands, speech, and eye movements. Identified defects are in genes for beta-III spectrin, FGF14, inositol 1,4,5-trisphosphate receptor, nesprin 1, PKC, puratrophin-1, senataxin, twinkle, twinky and the CABC1 gene that encodes a chaperonelike protein. Some forms are caused by expanded (CAG)n trinucleotide repeat in the ataxin or TATA box-binding protein genes, others by defects in voltage-dependent calcium or potassium channels or in the gene for the brain-specific regulatory subunit of protein phosphatase PP2A. Many other forms have yet to be linked to specific molecular defects.
spinophilin See neurabin. spiral cleavage Pattern of early cleavage found in molluscs and annelids (both mosaic eggs). The animal pole blastomeres are rotated with respect to those of the vegetal pole. The handedness of the spiral twist shows maternal inheritance.
spire Drosophila protein (1020aa) of the Spir family (interacts with cappuchino). Spir proteins nucleate actin polymerization by binding four actin monomers to a cluster of four WASP-hom*ology domain 2 (WH-2 domains) in the central region of the proteins. This mechanism is distinct from actin nucleation by the Arp2/3 complex or by formins. There are two human spire hom*ologues (756aa and 714aa).
spirillum Pl. spirilla. A fairly rigid helically twisted (corkscrew-shaped) bacterial cell often, but not necessarily, a member of the genus Spirillum. Common
Spiroplasma citri A plant-pathogenic mollicute phylogenetically related to Gram-positive bacteria. Spiroplasma cells are restricted to the phloem sieve tubes and are transmitted from plant to plant by the leafhopper vector Circulifer haematoceps.
Spirostomum Genus of large free-living ciliate protozoans with an elongated body.
splanchnic Relating to the viscera. See also splanchnic mesoderm.
splanchnic mesoderm That portion of the embryonic mesoderm that is associated with the inner (endodermal) part of the body in contrast to somatic mesoderm which is associated with the body wall. The two mesodermal regions are separated by the coelom.
splenocytes Vague term usually referring to lymphoid cells or mononuclear phagocytes of the spleen.
splice variants Proteins that are related but differ in their sequence as a result of alternative splicing. Alternative Splicing Database Project: http://www. ebi.ac.uk/asd/
spliceosomes The macromolecular RNA-protein complexes involved in intron removal and exon ligation as mRNA is processed. Components include U2, U5, and U6 snRNAs and Prp8 (see Prp proteins). Different sub-classes of spliceosome process particular classes of introns and the minor spliceosome, which contains U5, U11, U12, U4atac, and U6atac is involved in processing U12-dependent introns.
splicing See alternative splicing and spliceosome. split gene See introns. split ratio The fraction of the cells in a fully grown culture of cells that should be used to start a subsequent culture. Minimum may be dictated by inadequacies of the medium that result in poor growth of some cells at high dilution.
spokein Term formerly used for the constituent protein of the radial spokes of the ciliary axoneme. Since a number of complementary spoke mutants are known to occur in Chlamydomonas, and one mutant
spondins
622
sporophyte
lacks 17 proteins, it seems likely that spokein is a complex mixture. The radial spokes are regularly repeating axonemal structures composed of at least 23 proteins and are required for normal axonemal motility. See radial spoke proteins.
but without any nucleic acid present) is necessary. Controversy still surrounds the causative agent although general opinion now favours Prusiner’s prion hypothesis. See also fatal familial insomnia, Gerstmann-Straussler-Scheinker syndrome.
spondins A sub-family of thrombospondin type I
spongin Collagenous protein (with hom*ology to
proteins involved in axonal growth and guidance by affecting adhesion. Spondin 1 (F-spondin, vascular smooth muscle cell growth-promoting factor (VSGP), 624aa) is a secreted extracellular matrix protein that interacts with a central sequence of amyloid precursor protein (APP) and prevents proteolytic processing by beta-secretase. Spondin 2 (M-spondin, mindin, 331aa) is a ligand for neutrophil and macrophage integrins and binding via mindin regulates the expression of Rho GTPases in dendritic cells. Mindin-deficient mice exhibit defective inflammatory and immune responses. The R-spondins regulate beta-catenin signalling. R-spondin 1 (RSPO1, 263aa) is expressed in enteroendocrine cells as well as in epithelial cells from various tissues. Mutations are associated with palmoplantar hyperkeratosis with squamous cell carcinoma of skin and sex reversal. R-spondin 2 (cristin 2, 243aa) apparently functions in a positive feedback loop to stimulate the WNT/betacatenin cascade. RSPO3 (273aa) regulates kidney cell proliferation. RSPO4 and a RSPO4 splice variant induce epithelial proliferation in the gastrointestinal tract; mutations are associated with anonychia congenita. SCO-spondin (5147aa) is secreted by the subcommissural organ and is a constituent of Reissner’s fibres.
collagen IV) that forms the extracellular matrix of silicaceous sponges, a meshwork that links the silica-rich spicules. Research paper: http://mbe. oxfordjournals.org/cgi/content/full/23/12/2288?view5 long&pmid516945979
spondyloepiphyseal dysplasia A subclass of chondrodysplasia in which cartilage is defective either because of mutation in genes encoding collagen IIA1 or II or those for other extracellular matrix components such as the chondroitin 6-sulphotransferase 3 gene or the genes encoding aggrecan or sedlin. The consequence is short stature and spinal abnormalities. See pseudoachondroplasia.
spondylometaphyseal dysplasia A type of bone dysplasia affecting the spine and metaphyses of bones leading to extreme dwarfism and usually a range of other problems. In some cases (Strudwick type) a result of mutation in the collagen COL2A1 gene, in other cases (Kozlowski type) by mutation in a vanilloid receptor. Other types are known but the molecular defect uncharacterised as yet.
spongiform encephalopathies A group of unusual diseases with very long incubation periods and a fatal progressive course in which there is a characteristic spongiform degeneration of brain cortex. The two main human diseases are kuru and Creutzfeldt-Jakob disease, other forms are scrapie in sheep and goats, bovine spongiform encephalopathy (BSE) and mink encephalopathy. Experimentally can be studied in mice although intracortical transfer of infective material (usually affected brain tissue
spongioblast Cell found in developing nervous system: gives rise to astrocytes and oligodendrocytes.
spongioblastoma Rare tumours of childhood and adolescence, a glioma in which cells resemble embryonic spongioblasts. Although sometimes described as a class of neuroepithelial tumours, are probably not a distinct entity but could be considered either ependymomas or neuroblastomas.
spongiocytes Lipid droplet-rich cells from the middle region of the cortex of the adrenal gland.
spongy parenchyma Tissue usually found in the lower part of the leaf mesophyll. Consists of irregularly-shaped, photosynthetic parenchyma cells, separated by large air spaces.
spontaneous transformation Transformation of a cultured cell that occurs without the deliberate addition of a transforming agent. Cells from some species, especially rodents, are particularly prone to such spontaneous transformation.
sporadic Of a tumour or genetic disease, a novel occurrence without any previous family history of the disease (cf. inherited). Examples of diseases with both sporadic and inherited forms are retinoblastoma and Wilms’ tumour.
sporangium Spore case, within which asexual spores are produced. Cf. conidium.
spore Highly resistant dehydrated form of reproductive cell produced under conditions of environmental stress. Usually have very resistant cell walls (integument) and low metabolic rate until activated. Bacterial spores may survive quite extraordinary extremes of temperature, dehydration or chemical insult. Gives rise to a new individual without fusion with another cell.
sporocarp Multicellular structure in fungi, lichens, ferns or other plants, the site of spore formation.
sporophyte The spore-producing plant generation. The dominant generation in pteridophytes and higher plants, and alternates with the gametophyte generation.
sporopollenin
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SRE
sporopollenin Polymer of carotenoids, found in
squamous epithelium An epithelium in which
the exine of the pollen wall. Extremely resistant to chemical or enzymic degradation.
the cells are flattened. May be a simple epithelium (e.g. endothelium) or a stratified epithelium (e.g. epidermis).
sporotrichosis A fungal infection, usually of the skin, caused by Sporothrix schenckii. Mainly an occupational disease of farmers, gardeners, and horticulturists.
Sporozoa Class of spore-forming parasitic protozoa without cilia, flagella or pseudopodia. See Apicomplexa.
sporozoite Infective stage of the life cycle of Apicomplexa such as Plasmodium and Cryptosporidia.
spot
desmosome Macula
adherens:
see
desmosome.
SPRED A family of membrane-associated proteins (sprouty-related EVH1 domain-containg proteins, SPRED1, 444aa; SPRED2, 418aa; SPRED3, 410aa) that inhibit growth factor mediated activation of MAP kinase, possibly in collaboration with caveolin. Mutations in SPRED1 cause neurofibromatosis 1-like syndrome. See sprouty. Structure: http://www. thesgc.org/structures?terms 5 SPRED
sprouting (1) Production of new processes (outgrowths) by nerve cells: e.g. by embryonic neurons undergoing primary differentiation; by adult neurons in response to nervous system damage; or by dissociated neurons redifferentiating in culture. (2) Casual term for the germination of a seed.
sprout In Drosophila a protein (SPRY, 589aa) that inhibits tracheal branching by antagonizing the BNL-FGF pathway. Mammalian hom*ologues negatively regulate fibroblast growth factor signalling in a variety of systems. SPRY1 (sprouty hom*ologue 1, 319aa) is downregulated in approximately 40% of prostate cancers. SPRY2 (315aa) and SPRY3 (288aa) also inhibit FGF signalling; SPRY4, 299aa) suppresses the insulin receptor and EGFR-transduced MAPK signalling pathway. See SPRED.
Spumavirinae Formerly a subfamily of the Retroviridae, now considered a single genus (Spumavirus) of the subfamily Spumaretrovirinae. Single-stranded enveloped RNA viruses that will induce the formation of syncytia in susceptible cell cultures; the polykaryons then undergo a characteristic foamy degeneration.
squalene A 30-carbon isoprenoid lipid found in large quantities in shark liver oil and in smaller amounts in olive oil, wheat germ oil, rice bran oil and yeast. A key intermediate in the biosynthesis of cholesterol.
squames Flat, keratinised, dead cells shed from the outermost layer of a squamous stratified epithelium.
squamous-cell
carcinoma Carcinoma that develops from the squamous layer of the epithelium. Slow growing but more likely to be metastatic than basal cell carcinomas.
squid giant axon Large axons, up to 1 mm in diameter, that innervate the mantle of the squid. Because of their large size, many of the pioneering investigations of the mechanisms underlying resting and action potentials in excitable cells were done on these fibres.
squidulin Squid calcium-binding protein (SCaBP, 149aa) with four EF-hand motifs from the optic lobe of squid (Loligo pealeii),
S region (1) The non-MHC gene in the midst of the murine H-2 major histocompatibility complex that codes for complement component C4. Sometimes confusingly known as the gene for the type III MHC product in mice. (2) The switch region, a region 50 to each immunoglobulin heavy chain constant region, that is important in isotype switching. Research article: http://www.jbc.org/content/263/15/7397.full.pdf
SR proteins A family of highly conserved nuclear phosphoproteins required for constitutive pre-mRNA splicing and also influence alternative splicing. They are characterized by one or two N-terminal RNA-binding domains and a C-terminal SR domain enriched in serine-arginine dipeptides (RS domain). SR proteins influence splice site selection and are required at an early step in spliceosome assembly.
SRBC Sheep red blood cells, often used in immunological assays.
src family Family of protein tyrosine kinases of which src (p60-src, EC 2.7.10.2, 536aa) was the first example (see src gene). Includes fyn, yes, fgr, lyn, hck, lck, blk and yrk. All cells studied so far have at least one of these kinases which act in cellular control. Family members all have characteristic srchom*ology (SH domain) structure, a kinase domain (SH1), SH2 and SH3 domains, and a domain (SH4) which has myristoylation and membrane-localisation sites. Inter-domain interactions, themselves regulated by phosphorylation (see csk), regulate the activity of the kinase.
src gene The gene in Rous sarcoma virus that encodes an unregulated cytoplasmic tyrosine kinase (pp60-vsrc) and is responsible for the transforming activity. The normal c-src kinase is regulated and does not induce uncontrolled cell proliferation.
SRE (1) Serum response element. (2) Sterol regulatory element, see SREBP.
SREBP
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stacking gel
SREBP Family of transcription factors (sterol regu-
SSH (1) See suppression subtractive hybridization.
latory element-binding proteins, SREBP1, 1147aa; SREBP2, 1141aa) that bind to steroid response elements in the promoter regions of genes involved in the metabolism of cholesterol and fatty acids.
(2) Slingshot hom*ologue. (3) Sec sixty-one protein hom*olog, one component (Ssh1, 490aa) of the sec61 translocon complex in Saccharomyces.
SRF See serum response factor.
SSLP See simple sequence length polymorphism.
S-ring The M and S rings of the bacterial flagellar motor are actually a single, double-flanged ring made from subunits of just one protein (FliF, 552aa) and do not, contrary to earlier ideas, contribute to the generation of torque. See bacterial flagella.
SRK A putative serine/threonine-protein kinase receptor (S-receptor kinase, EC 2.7.11.1, 849aa in Brassica oleracea) found mainly in the pistil and anther and involved in the self-incompatibility system, probably acting in combination with S-locus-specific glycoproteins that are kinase-activating ligands.
SRP See signal recognition particle. SRS-A See slow reacting substance of anaphylaxis. SRTX See sarafotoxin. sry proteins Family of high-mobility group (HMG) proteins that bind to a subset of sequences recognized by C/EBP family of DNA-binding proteins. Sry (sex-related gene on Y) itself is the primary testis-determining gene on the Y chromosome. The protein product, Sry (testis determining factor, 204aa), binds to DNA and causes it to bend sharply thereby affecting the expression of other genes on the Y chromosome. Sox-10 is related to Sry.
SSB (1) Single-stranded DNA binding (SSB) protein (helix-destabilizing protein, 178aa in E. coli) that binds selectively to single-stranded DNA intermediates during DNA replication, recombination and repair. (2) Single-strand breaks (SSB) in DNA. (3) Gene encoding Lupus La protein, (Sjogren syndrome type B antigen, 408aa) the target antigen of autoantibodies in sera of patients with Sjogren’s syndrome and systemic lupus erythematosus (SLE).
SSCP See
single-stranded polymorphism.
SSI-1 See SOCS.
conformational
ssDNA phage Single-strand DNA phages such as MS2, FX174, as opposed to double-stranded DNA phages or RNA phages.
SSEA (1) Stage-specific embryonic antigen. (2) SseA is a key Salmonella virulence determinant, a small (secretion system effector A, 104aa), basic pI protein that serves as a type III secretion system chaperone for SseB and SseD. (3) SseA, the translation product of the E. coli sseA gene, is a protein (rhodanese-like protein, EC 2.8.1.2, 281aa) with 3-mercaptopyruvate: cyanide sulphurtransferase activity in vitro.
ssrA A bacterial gene that encodes a stable RNA (transfer-messenger RNA, tmRNA) for a peptide tag which is cotranslationally added to truncated polypeptides, targeting them for rapid proteolysis. This constitutes a general mechanism in bacteria to rescue stalled ribosomes, for example those that arrive at the end of an mRNA without a stop codon. Research article: www.ncbi.nlm.nih.gov/pmc/articles/ PMC95270/
SSRE See shear stress response element. SSRIs Antidepressant drugs (selective serotonin reuptake inhibitors) that inhibit reuptake of serotonin released in the brain, thereby prolonging its action as a neurotransmitter.
SSU rDNA Small subunit ribosomal DNA. The sequence of SSU rDNA has been extensively used in molecular taxonomy. The SSU rDNA (18S rDNA, 17S rDNA, 16S-like rDNA) sequences from ascomycetes are listed on Myconet. Myconet: http://fieldmuseum.org/explore/myconet
SSX proteins Products of the SSX gene family that has at least five functional and highly hom*ologous members, SSX1 to SSX5. They are localized in the nucleus, are diffusely distributed and may act as transcriptional repressors. SSX2 (synovial sarcoma, X breakpoint 2, 188aa) interacts with rabin. Abstract: http://www.ncbi.nlm.nih.gov/pubmed/12007189
stable nuclear transformation A hereditable change in a cell experimentally induced by introduction of a new gene which becomes integrated into the host DNA.
stable transfection When transfecting animal cells, a clone of cells in which the transgene has been physically incorporated into the genome. It thus provides stable, long-term expression although is more difficult to produce.
stachyose Digalactosyl-sucrose,
a compound involved in carbohydrate transport in the phloem of many plants, and also in carbohydrate storage in some seeds.
stacking gel An upper layer of weak gel at the top of a gel in which an electrophoretic separation is to be run. Because the upper stacking gel is weak all the large molecules move through it rapidly, accumulate at the very top of the separating gel and thus all start from the same level.
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STAG proteins Components of the cohesin complex that interact directly with RAD21. STAG1 (stromal antigen-1, 1258aa), STAG2 (1231aa) and STAG3 (1225aa).
STAGA complex A human chromatin-acetylating transcription coactivator that interacts with premRNA splicing and DNA damage-binding factors in vivo. Contains hom*ologues of most yeast SAGA complex components. See ataxin 7. Article: http:// www.ncbi.nlm.nih.gov/pubmed/11564863
stage-specific embryonic antigen A marker (SSEA1) for murine pluripotent stem cells that plays an important role in adhesion and migration of the cells in the preimplantation embryo. In humans it is the LewisX antigen (CD15, 3-fucosyl-N-acetyllactosamine) that can be used to define immature retinal progenitor cells (see sialyl Lewis X). Other SSEAa are cell surface antigens; SSEA-3 is the murine glycolipid GB5.
staggered cut Situation when the two strands of a DNA molecule are cut in different places, slightly offset so that the two halves have ‘sticky ends’, a short segment of single-stranded DNA overhanging the duplex.
stalked bacteria Bacteria (prosthecate bacteria) that have appendages that allow them to attach to surfaces in aquatic environments.
staminode A rudimentary, sterile or abortive stamen.
stanniocalcin Glycoprotein hormone (STC-1, 179aa in Oncorhynchus keta, Chum salmon), secreted by the corpuscle of Stannius, an endocrine gland in teleosts. Prevents hypercalcaemia and inhibits calcium uptake through gills. Mammalian hom*ologues (STC1, 247aa; STC2, 302aa) have been identified and are involved in various physiological processes, such as calcium and phosphate homeostasis.
stanol Plant-derived sterol (24-alpha-ethylcholestanol), similar to cholesterol but poorly absorbed from the intestine. Thought to compete with cholesterol for binding sites and by decreasing dietary intake of cholesterol helps lower blood levels.
Staphylococcal cassette chromosome elements Genomic islands ubiquitously disseminated among staphylococci, that capture foreign DNA segments The staphylococcal cassette chromosome mec elements (SCCmec) carry meticillinresistance. The SSCs have cassette chromosome recombinase genes (ccrA and ccrB) that encode polypeptides with partial hom*ology to recombinases of the invertase/resolvase family that catalyze precise excision of the SCC and other genes carried within the element.
STAR proteins
Staphylococcal scalded-skin syndrome See exfoliatin.
Staphylococcal toxins Staphylococcus aureus produces several membranolytic toxins, alpha-, beta-, gamma-, and delta-haemolysins and leucocidin. Alpha-toxin (319aa) is secreted as monomers which then associate to form heptameric oligomer with a pore of 1 nm: it preferentially attacks platelets and cultured monocytes. Beta-toxin is a Mg21dependent sphingomyelinase C. The gamma-toxin locus expresses three proteins, two class S components (HlgA and HlgC) and one class F component (HlgB) which form S/F heterodimers, have potent proinflammatory effects and may be important in pathogenesis of toxic shock syndrome. Delta toxin is a small peptide (26aa) that is very amphipathic and surface active and has properties similar to melittin. Staphylococcal virulence regulator protein A (Multidrug export protein mepA, 451aa) is involved in the export of the toxins from the cell.
staphylococcins Bacteriocins
produced
by
staphylococci.
Staphylococcus Genus of non-motile Grampositive bacteria that are found in clusters, and that produce important exotoxins (see Table E2). Staphylococcus aureus (S. pyogenes) is pyogenic, an opportunistic pathogen, and responsible for a range of infections. It has protein A on the surface of the cell wall. Coagulase production correlates with virulence: hyaluronidase, lipase, and staphylokinase are released in addition to the toxins.
staphylokinase Enzyme (streptokinase, EC 3.4.99.22, 163aa) released by Staphylococcus aureus that acts as a plasminogen activator.
STAR proteins (1) A family of of RNA-binding proteins (signal transduction and activation of RNA); evolutionarily conserved from yeast to humans and important for a number of developmental decisions. Contain a conserved KH domain as well as two conserved domains called QUA1 and QUA2. Examples include mouse quaking, C. elegans germline defective-1 (GLD-1) and human RNA-binding protein T-Star (Sam68-like mammalian protein 2, 346aa). (2) An intestine-specific membrane-bound guanylate cyclase that binds guanylin and is the receptor for bacterial heat-stable enterotoxins such as the E. coli ST toxin, STa. (3) In Drosophila, a protein (star, 597aa) involved in EGF receptor signalling and photoreceptor development. Interacts with the EGF receptor torpedo in the eye. (4) StAR-related lipid transfer proteins contain a START domain and are involved in lipid transport. Steroidogenic acute regulatory protein is STAR1. For example, StAR-related lipid transfer proteins 3, 4 and 5 (STARD3, 445aa; STARD4, 205aa; STARD5, 213aa) are involved in intracellular lipid and sterol transport, STARD8 (1023aa) accelerates GTPase activity of rhoA and
STAR syndrome
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STATs
cdc42, but not rac1. StARD9 (4614aa) is found in the CNS, muscle and a few other tissues. Several others are known.
interaction with the cytoskeleton during neurite outgrowth. Stathmin-3 (180aa) is also neuronspecific.
STAR syndrome A developmental disorder (syn-
statins Lipid-lowering drugs that inhibit HMG Co-A
dactyly, telecanthus, anogenital and renal malformations) caused by mutation in the FAM58A gene that encodes cyclin M.
starch Storage carbohydrate of plants made from branched and unbranched polymers of glucose. It is made in choroplasts by photosynthesis and is stored in the form of starch grains. Starch grains occur in storage organelles termed amyloplasts, ready for use. The potato tuber is a rich source of stored starch. In cells of the root cap, starch grains form statoliths, involved in the perception of gravity.
Stargardt’s disease A childhood disorder in which there is retinal degeneration in the central (macular) region, Various genetic defects can cause the disease including mutation in genes encoding the retina-specific ABC transporter-A4 or the cyclicnucleotide gated ion channel beta-4. Another form is caused by mutation in the ELOVL4 gene encoding elongation of very long-chain fatty acids-like 4 (314aa) a photoreceptor-specific component of the fatty acid elongation system. Mutation in peripherin are also implicated in some forms.
reductase, a key enzyme in cholesterol biosynthesis.
stationary night blindness A retinal disorder in which there are reduced numbers of retinal rods, the photoreceptors used for low-light vision. X-linked forms can be caused by mutation in nyctalopin or the retina-specific calcium channel alpha1-subunit. Autosomal forms can be caused by mutation in the metabotropic glutamate receptor-6, calcium-binding protein-4, rhodopsin, cyclic nucleotide phosphodiesterase-6B or in rod-specific transducin. The Oguchi-type in which dark adaptation is abnormally slow, is caused by mutation in arrestin or in rhodopsin kinase.
stationary phase The stage of a cell culture at which cell proliferation ceases, because of nutrient depletion, and before senescence and cell death begins to reduce numbers of live cells.
statocyst A sense organ used to perceive gravity and thus body orientation. It has a cavity enclosing a statolith that is lined with sensory cells.
stargazin A brain-specific murine protein (323aa),
statocyte A root-tip cell containing one or more
the gamma-2 subunit of a voltage-dependent calcium channel, structurally similar to clarins, mutated in the mouse mutant stargazin which has seizures characteristic of absence epilepsy. A related molecule (stargazin-like protein, 447aa) is found in Drosophila.
statolith (1) A type of amyloplast found in root-tip
start codon See initiation codon. start site Imprecise term for either a transcriptional or a translational start site.
startle disease stiff man syndrome A genetically heterogeneous disorder with neurologically-induced muscular rigidity and an exaggerated startle response (hyperexplexia). Can be caused by mutations in genes encoding the alpha-1 or beta subunits of the glycine receptor, the presynaptic glycine transporter2 (SLC6A5), gephyrin, and collybistin.
statherin An acidic tyrosine-rich phosphoprotein (62aa) secreted mainly by salivary glands. Binds fimbrillin.
stathmin A coiled-coil cytosolic phosphoprotein (oncoprotein 18, stathmin-1, 149aa) that binds to two tubulin heterodimers and increases the rate of rapid ‘catastrophic’ disassembly of microtubules. Overexpressed in some tumours and probably regulated by phosphorylation, possibly by SAPK4. Stathmin-2 (superior cervical ganglion-10 protein, 179aa) is neuron-specific and may be important in neuronal differentiation, and in modulating membrane
statoliths, involved in the detection of gravity in geotropism. cells of higher plants. It can sediment within the cell under the influence of gravity, and is thought to be involved in the detection of gravity in geotropism. (2) A solid particle found in the cavity of a statocyst. It stimulates sensory cells lining the cavity with which it comes in contact under the influence of gravity.
STATs A family of proteins (signal transducers and activators of transcription) that have SH2 domains which bind phosphotyrosine residues in receptors, particularly cytokine-type receptors; they are then phosphorylated by JAKs, dimerize and translocate to the nucleus and act as transcription factors. Many STATs are known; some are relatively receptorspecific, others more promiscuous, so that a wide range of responses is possible with some STATs being activated by several different receptors, sometimes acting synergistically with other STATs. STAT1 (750aa) mediates signalling by interferons alpha and gamma whereas STAT2 (851aa) is only activated by Type 1 interferons. STAT3 (770aa) binds to the interleukin-6 (IL-6)-responsive elements identified in the promoters of various acute-phase protein genes, STAT4 (748aa) is involved in IL12 signalling. Several others are known in humans and in a range of other metazoa. Mutations in STAT1 affect innate immunity, mutations in STAT3 are associated with
staufen
627
hyper-IgE syndrome (Job’s syndrome). See signaltransducing adaptor proteins.
staufen In Drosophila a RNA binding protein (1026aa) a maternal effect protein that binds to the 30 UTR of specific mRNAs and acts in their localization, particularly maintaining cellular asymmetry in the oocyte through interaction with microtubules. Mammalian hom*ologues staufen 1 (577aa) and staufen 2 (570aa) are also involved in the localization of mRNA. Staufen2, a brain-specific isoform has been shown to shuttle between nucleus and cytoplasm and can enter the nucleolus.
staurosporine Inhibitor of PKC-like protein kinases, originally derived from Streptomyces staurosporeus. Has a rather broad inhibitory spectrum.
STE20 Evolutionarily conserved serine/threonine kinases (EC 2.7.11.1), subdivided into the p21-activated kinase (PAK) and germinal centre kinase (GCK) families, that regulate fundamental cellular processes including the cell cycle, apoptosis, and stress responses. In S. cerevisiae Ste20p (sterile 20 protein, 939aa) is a mitogen-activated protein kinase kinase kinase kinase (MAP4K) involved in the mating pathway. Human hom*ologues (at least 28) have the kinase domain but linked to other domains that confer specificity.
stealth proteins A protein family that is conserved from bacteria to higher eukaryotes. In bacteria they help pathogens to avoid the host innate immune system and are involved in the biosynthesis of exopolysaccharides such as capsular polysaccharides of pathogenic streptocoocci. Stealth protein GNPTAB is involved in adding mannose residues to enzymes destined for lysosomes and is defective in human I-cell disease.
STEAP One of a small family of cell-surface antigens that are expressed in prostate cancer and are potential targets for antibody-mediated therapy and diagnosis. STEAP1 (six-transmembrane epithelial antigen of the prostate, EC 1.16.1.-, 339aa) is expressed at the cell-cell junctions of the secretory epithelium of prostate and strongly expressed in prostate cancer cells. It is a metalloreductase that can reduce Fe31 to Fe21 and Cu21 to Cu1 using NAD1 as an acceptor. STEAP2 (490aa), STEAP3 (488aa) and STEAP4 (459aa) have similar properties but some are more ubiquitously expressed. See papin, PSM, PTCA-1, PSCA.
stearic acid N-octadecanoic acid. See fatty acids. steatoblasts Cells that give rise to fat cells (adipocytes).
steel factor Murine equivalent of stem cell factor, the ligand (273aa) for kit.
stenohaline that can be caused by defects in tau protein although the more typical forms are linked to other loci. There are some features resembling Parkinson’s disease.
stefins Family of cysteine peptidase inhibitors. Stefin A (cystatin A, keratolinin, 98aa) inhibits cathepsins D, B, H and L. Stefin B (cystatin B, 98aa) has anti-peptidase activity against cathepsins L, H and B. Mutations in stefin B are associated with myoclonic epilepsy of Unverricht and Lundborg.
stele vascular cylinder The vascular tissue (xylem and phloem) inside the cortex of roots and stems of vascular plants.
stem cell (1) Cell that gives rise to a lineage of cells (progenitor cell). (2) More commonly used of a cell that, upon division, produces dissimilar daughters, one replacing the original stem cell, the other differentiating further (e.g. stem cells in basal layers of skin, in haematopoietic tissue, and in meristems). Embryonic stem cells (ES cells) are totipotent, able to produce any cell type; following modification in vitro they can be used to produce chimeric embryos and thus transgenic animals. Pluripotent stem cells are more limited and can produce only some differentiated cells. Quiescent stem cells may have a repair function and for example, the satellite cells in the skeletal muscles of mammals are quiescent myoblasts that will proliferate after wounding and give rise to more muscle cells by fusion. Induced pluripotent stem cells (iPSCs) are differentiated cells that have been experimentally induced to revert to a pluripotent state. Originally this required transfection of genes with the risk that the iPSCs were potentially neoplastic; the hope is that eventually it will be possible to take cells from a patient, revert them to pluripotency and use them therapeutically.
stem cell factor A growth factor (mast cell growth factor, 273aa, 245aa when processed), the ligand for kit. Stimulates proliferation of myeloid and lymphoid series. See steel factor.
stem
cell-derived tyrosine kinase The murine hom*ologue of the human ron receptor tyrosine kinase (STK, macrophage-stimulating protein receptor, EC 2.7.10.1, CD136, 1378aa). The precursor is cleaved into alpha (281aa) and beta (1068aa) chains which form a disulphide-linked heterodimer. Expressed on macrophages. Ligand is macrophagestimulating protein (MSP), a serum protein activated by the coagulation cascade.
stem-and-loop structure Term for the structure of tRNAs which has four base-paired ‘stems’ and three ‘loops’ (not base-paired), one of which contains the anticodon.
Steele-Richardson-Olszewski syndrome A
stenohaline Descriptive of an organism that is
neurological disorder (progressive supranuclear palsy)
unable to tolerate a range of salinities Cf euryhaline.
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STIM proteins
stenospermocarpy One cause of seedlessness
steroid response element DNA sequence in
in, for example, grapes. Pollination and fertilization occur as normal, but the embryo and/or endosperm abort two to four weeks after fertilization; seed development ceases but the ovary wall pericarp continues to grow and forms berries. See parthenocarpy.
the promoter region of a gene that is recognized and bound by a steroid receptor. Informative web-pages: http://www.ultranet.com/Bjkimball/BiologyPages/S/ SteroidREs.html
stent A device inserted into a blood vessel to keep it open, usually a small metal coil or mesh tube. Similar devices are used in the GI tract and ureter.
Stentor Genus of large multinucleate protozoa (up to 2 mm long) with a ring of apical cilia used in feeding on bacteria. Spirotrich ciliates. Usually attached to a surface in freshwater ponds etc. but can relocate. Sometimes called the ‘trumpet animalcule’ because of its shape.
stereocilium See stereovillus. stereotaxis A system by which the precise 3-D coordinates of a target site are identified, allowing focussed delivery of radiation or precise insertion of a microelectrode.
stereovillus Microfilament bundle-supported projection, several microns long, from the apical surface of sensory epithelial cells (hair cells) in inner ear: like a microvillus, but larger. It is stiff and may act as a transducer directly, or merely restrict the movement of the single sensory cilium (which does have an axoneme). Also described on cells of pseudostratified epithelium of the epididymal duct. Sometimes called stereocilia but they do not have axonemes so this is potentially confusing.
sterigmatocystin An intermediate in the biosynthetic pathway that generates aflatoxins.
Sternberg-Reed cells See Hodgkin’s disease. steroid finger motif See steroid receptor. steroid hormones A group of structurally related hormones, based on cholesterol from which they are synthesized. They control sex and growth characteristics, are highly lipophilic, so can readily cross the plasma membrane, and are unique in that their receptors are in the nucleus, rather than on the plasma membrane. The five major subgroups are glucocorticoids, mineralocorticoids, androgens, estrogens, and progestagens.
steroid receptors Receptors for steroid hormones that have a conserved domain (the ‘steroid finger’ motif) containing two C4-type zinc fingers. Type I are cytoplasmic until they bind a hormone and release a chaperone, then they move to the nucleus and act as transcription factors. Type II are nuclear transcription factors and other members of this type bind non-steroid ligands (thyroid hormone, vitamin A).
steroidogenic acute regulatory protein A mitochondrial protein (START domain-containing protein 1, StAR1, 285aa) that mediates cholesterol transfer and promotes steroid hormone production in the ovary, testis and adrenal gland. Defective in congenital lipoid adrenal hyperplasia (lipoid CAH).
sterol regulatory element SRE See sterol regulatory element-binding proteins, steroid response element.
sterol regulatory element binding proteins SREBPs A family of membrane-bound transcription factors important in both cholesterol and fatty acid metabolism. SREBPs (SREBP1, 1147aa; SREBP2, 1142aa) regulate the expression of over 30 genes. SREBPs are regulated by proteolytic cleavage (see insig-1, SCAP), rapid degradation by the ubiquitinproteasome pathway, and sumoylation.
sterols Molecules that have a 17-carbon steroid structure, but with additional alcohol groups and side chains. Commonest example is cholesterol.
Stickler’s syndrome An autosomal dominant connective tissue disorder in which there are ocular, orofacial, auditory, and skeletal anomalies. Type 1 is caused by mutation in the collagen 2A1 gene and is morphologically similar to Wagner’s syndrome, Type 2 is a result of mutation in collagen 11A1 and Type 3 by mutation in collagen 11A2. An autosomal recessive form can be caused by mutation in the COL9A1 gene.
sticky ends The short stretches of single-stranded DNA produced by cutting DNA with restriction endonucleases whose site of cleavage is not at the axis of symmetry. The cut generates two complementary sequences that will hybridize (stick) to one another or to the sequences on other DNA fragments produced by the same restriction endonuclease.
stilbene synthase Important enzymes (stilbene synthase 1, EC 2.3.1.95, 392aa in grape, Vitis vinifera; many others are known) in the stilbene pathway. The levels of stilbenes increases in grapevine in response to biotic and abiotic stress, but also during berry ripening. Resveratrol is a stilbene.
Still’s disease A systemic inflammatory disorder (systemic-onset juvenile rheumatoid arthritis). Adultonset Still’s disease is probably just the adult version of the same disorder.
STIM proteins Single-pass transmembrane proteins localized predominantly in the membrane of the
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endoplasmic reticulum that appear to function as sensors of ER Ca21 levels and redistribute into a punctate pattern when calcium levels are low. STIM1 (stromal interaction molecule 1, 685aa) communicates with and opens CRAC channels located in the plasma membrane by interacting with Orai1. STIM2 (746aa) can form heterodimers with STIM1 and may inhibit STIM1-mediated Ca21 influx.
stimulated emission depletion microscopy A method of obtaining greater resolution in optical microscopy than is possible with standard confocal techniques. A small region of the specimen is illuminated with a very brief flash of light that stimulates fluorescence but is followed by illumination with a ‘ring’ of light at a wavelenth that depletes the capacity to fluoresce. The net effect is to restict the stimulation of fluorescence to an extremely small spot, smaller than that set by the point source of a confocal microscope and improving the resolution by an order of magnitude.
stimulus-secretion coupling A term used to describe the events that link receipt of a stimulus with the release of materials from membrane-bounded vesicles (the analogy is with excitation-contraction coupling in the control of muscle contraction). A classical example is the link between membrane depolarization at the presynaptic terminal and the release of neurotransmitter into the synaptic cleft.
sting cells Nematocysts of coelenterates. stipe A stalk, especially of fungal fruiting bodies or of large brown algae.
stipule A small appendages at the base of a leafstalk in certain plants; usually paired.
STK (1) Stem cell-derived tyrosine kinase. (2) Serine/threonine protein kinase e.g. LKB1, p61. (3) An ambiguous abbreviation that can refer to flt3, Aurora kinase B, mitogen-activated protein kinase HOG1 in Setosphaeria turcica (Northern corn leaf blight disease fungus) and various serine/threonine kinases. (4) Streptokinase.
stochastic Random or probabilistic. stoichiometry Ratio of the participating molecules
in a reaction in the case of an enzyme-substrate or receptor-ligand interaction should be a small integer.
Stoke’s radius Stoke’s law of viscosity defines the frictional coefficient for a particle moving through a fluid, a coefficient that depends upon the viscosity of the fluid and the radius of the particle. The apparent radius of a molecule sedimenting under centrifugal force calculated from this law (the Stoke’s radius) is a feature of the tertiary structure and thus informative about the molecule in question.
STOP
stolon A creeping horizontal stem that forms roots. A characteristic method of spreading in plants such as the strawberry.
stoma Pl. stomata. Pore in the epidermis of leaves and some stems, which permits gas exchange through the epidermis. Can be open or closed, depending upon the physiological state of the plant. Flanked by stomatal guard cells.
STOMAGEN A mesophyll-derived factor (45aa) that promotes epidermal stomatal development in Arabidopsis, generated from a 102aa precursor. If overexpressed or externally applied it increases stomatal density. It may compete with EPIDERMAL PATTERNING FACTORs for binding to the receptor TOO MANY MOUTHS.
stomatin An erythrocyte integral membrane protein (Band 7.2b, 288aa), defective in overhydrated hereditary stomatocytosis. Stomatin is found in most tissues and extensively throughout the animal kingdom, although its function is unclear. Stomatinlike 1 (STOML1, SLP1, 394aa), STOML2 (356aa) and STOML3 (287aa) are known in humans; STOML2 is overexpressed in a range of epithelial tumours. Similar genes (mec-2, unc-24, unc-1) are found in C. elegans and mutations in all of these affect the nervous system.
stomatocytosis A condition in which erythrocytes adopt an abnormal shape because of ion leakage across the plasma membrane. In one form (hereditary stomatocytosis-I, overhydrated stomatocytosis) there appears to be a defect in stomatin. A second form, stomatocytosis-II, in which there is no increase in fragility, has been reported. A different disorder, dehydrated hereditary stomatocytosis (xerocytosis; desiccytosis), is caused by excessive leakage of potassium from the erythrocytes which lose water and become more fragile.
stone cell See sclereid. stonin A family of adapter proteins (stonin-1, stoned B-like factor, 735aa; stonin-2, stoned B, 905aa) that are involved in the endocytic machinery and may facilitate clathrin-coated vesicle uncoating. In Drosophila stoned B (1262aa) may mediate the retrieval of synaptotagmin from the plasma membrane.
STOP (1) A calmodulin-binding microtubule-stabilizing protein (stable tubulin-only protein, microtubule-associated protein 6, 813aa) that inhibits cold temperature-induced disassembly, particularly in neurites. A similar protein, MAP6 domain-containing protein 1 (199aa) probably has similar properties. (2) In Arabidopsis a protein, SENSITIVE TO PROTON RHIZOTOXICITY 1 (STOP1, 499aa) a zinc-finger transcription factor that is important in responding to major stress factors in acid soils such aluminum (Al31). (3) See short stop (shot).
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stop codon See termination codons. stop transfer sequence Amino acid sequence (membrane anchor sequence) that causes cessation of the co-translational transfer of a protein across a membrane and leaves the protein embedded in the membrane. Generally consists of long sequences of hydrophobic residues.
storage diseases See lysosomal diseases. storage granules (1) Membrane-bounded vesicles containing condensed secretory materials (often in an inactive, zymogen, form). Otherwise known as zymogen granules or condensing vacuoles. (2) Granules found in plastids, or in cytoplasm; assumed to be ‘food reserves’, often of glycogen or other carbohydrate polymer.
storage pool disease SPD Platelet defects in which the numbers and contents of granules are affected. In alpha-SPD (gray platelet syndrome) there are severe reductions in the alpha-granules and their contents, in delta-SPD the defect is only in the dense granules (delta-granules) and in a third form (alpha/delta-SPD) both types of granule are affected.
storage vacuole In plants, vacuoles used to sequester products used for defence, or toxins that would harm the plant, or materials for later use. Contrast with lytic vacuoles.
STR See satellite DNA strain birefringence See birefringence. Strasburger cell A nucleated cell in phloem tissue of gymnosperms, closely associated with a sieve cell.
stratified epithelium An epithelium composed of multiple layers of cells, only the basal layer being in contact with the basal lamina (see basem*nt membrane). The basal layer is of stem cells that divide to produce the cells of the upper layers; in skin, these become heavily keratinised before dying and being shed as squames. Stratified epithelia usually have a mechanical/protective role.
stratifin An adapter molecule (14-3-3-sigma, epithelial cell marker protein 1, 248aa) found mainly in tissues enriched in stratified squamous keratinizing epithelium. Has a modulatory role in a range of signalling pathways.
stratum corneum Outermost layer of skin, composed of clear, dead, scale-like cells with little remaining except keratin.
stratum granulosum Layer of granular cells underlying the stratum corneum in the skin of vertebrates. The cells accumulate keratin and gradually become compressed to form the cornified cells of the outermost layer.
Streptococcus
stratum lucidum A thin, clear layer of dead cells in vertebrate skin, lying between the stratum corneum and stratum granulosum of thick skin, as on palms of the hands and the soles of the feet.
stratum Malpighii One of the layers of the skin in vertebrates, lying between the proliferating cells of the basal layer (stratum germinatum) and the stratum granulosum where keratin deposition occurs. Also known as the prickle cell layer. Location of many of the disorders of the skin.
streptavidin A protein (183aa) from Streptomycetes avidinii that has an avidin domain and binds biotin with high affinity. Forms a hom*otetramer that binds four biotin molecules. A useful experimental tool although its biological function is unclear.
Streptobacillus A
Gram-negative bacterium (Streptobacillus moniliformis) infective agent of ratbite fever (sodoku).
streptococcal M-protein Cell wall protein of streptococci used as a taxonomic marker for different strains of Group A streptococci (more than 100 serotypes are known). The M-protein confers anti-phagocytic properties on the cell and is present as hair-like fimbriae on the surface. M-protein is an important virulence factor, and antibodies directed against M-protein are essential for phagocytic killing of the bacteria.
streptococcal toxins Group of haemolytic exo-
toxins released by Streptococcus spp. α-haemolysin: 26239 kDa (four types), forms ring-like structures in membranes (see streptolysin O). Lipid target unclear; β-haemolysin: a hot-cold haemolysin with sphingomyelinase C activity; γ-haemolysin: complex of two proteins (29 and 26 kDa) that act synergistically, rabbit erythrocytes particularly sensitive; δ-toxin: heat-stable peptide (5 kDa) with high proportion of hydrophobic amino acids. Seems to act in a detergent-like manner (cf. subtilysin), but may form hydrophilic transmembrane pores by cooperative interaction with other δ-toxin molecules; leucocidin (Panton-Valentine leucocidin): two components F (fast migration on CM-cellulose column: 32 kDa), and S (slow: 38 kDa). Mode of action contentious. See also Streptococcus, streptolysins O and S, erythrogenic toxin. Streptococcus pyogenes releases a range of pyogenic (fever-inducing) exotoxins, several of which are superantigens with sequence hom*ology to staphylococcal toxins (SPEA, erythrogenic toxin, 251aa; SPEC, 235aa). SPEB is a cysteine peptidase (streptopain, EC 3.4.22.10, 398aa).
streptococcins Bacteriocins
released
by
streptococci.
Streptococcus Genus of Gram-positive cocci that grow in chains. Some species (Strep. pyogenes in particular) are responsible for important diseases in humans (pharyngitis, scarlet fever, rheumatic
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fever): Strep. pneumoniae (Pneumococcus pneumoniae; Diplococcus pneumoniae; Fraenkel’s bacillus) is the main culprit in lobar- and broncho-pneumonia. Streptococci have anti-phagocytic components (hyaluronic acid-rich capsule and M-protein), and release various toxins (streptolysins O and S, erythrogenic toxin) and enzymes (streptokinase, streptodornase, hyaluronidase, and proteinase). The α-haemolytic streptococci (viridans streptococci) produce limited haemolysis on blood agar; include S. mutans, S. salivarius, S. pneumoniae. The β-haemolytic streptococci, of which S. pyogenes is the only species, though there are many serotypes, produce a broad zone of almost complete haemolysis on blood agar as a result of streptolysin O and S release. The γ-streptococci are nonhaemolytic (e.g. S. faecalis).
streptodornase Mixture of four DNAases (EC 3.1.21.1) released by streptococci. By digesting DNA released from dead cells the enzyme reduces the viscosity of pus and allows the organism greater motility.
stress-induced proteins candidate genes for chemical modification of the bacteriocin propeptide and self protection, an ABC transporter for export and maturation proteolysis of the leader peptide, and an internal terminator motif for differential transcription of structural gene and accessory gene mRNAs. Cf. streptolysin O. Article: http://www.ncbi.nlm.nih.gov/pmc/articles/ PMC143243/?tool 5 pmcentrez
Streptomyces Genus of Gram-positive sporeforming bacteria that grow slowly in soil or water as a branching filamentous mycelium similar to that of fungi. Important as the source of many antibiotics, e.g. streptomycin, tetracycline, chloramphenicol, macrolides.
streptomycin A water-soluble
aminoglycoside antibiotic from the bacterium Streptomyces griseus. Commonly used antibiotic in cell culture media: acts only on prokaryotes, and blocks transition from initiation complex to chain-elongating ribosome.
streptopain See streptococcal exotoxins.
streptogramins Group of antibiotics that consist
streptovaricins Antibiotics of the ansamycin
of mixtures of two structurally distinct compounds, type A and type B, which are separately bacteriostatic, but bactericidal in appropriate ratios. They act at the level of inhibition of translation through binding to the bacterial ribosome. An example is quinupristin.
class, produced by various Actinomycetes, that block initiation of transcription in prokaryotes. (Cf. rifamycins and rifampicin).
streptokinase A non-enzymic plasminogen activator (440aa) released by Streptococcus pyogenes. Activates plasminogen by forming a complex. There are various forms (streptokinases A, C, G).
streptolydigin Antibiotic produced by Streptomyces lydicus that blocks peptide chain elongation by binding to bacterial RNA polymerase. Research paper: http://www.jbc.org/content/270/41/23930.long
streptolysin
O Oxygen-labile
thiol-activated haemolysin (571aa). Haemolysis is inhibited by cholesterol, and only cells with cholesterol in their membranes are susceptible. Toxin aggregates are linked to cholesterol to form a channel 30 nm diameter in the membrane, and non-osmotic lysis follows. Markedly inhibits neutrophil movement and stimulates secretion, but has little effect on monocytes. Cf. streptolysin S.
streptolysin
S Oxygen-stable haemolysin of Streptococcus pyogenes. Thought to be a peptide of ca 28aa: causes zone of β-haemolysis around streptococcal colonies on blood agar. Like complement-mediated haemolysis it appears to act in a onehit mechanism. Toxic to leucocytes, platelets, and several cell lines. Has sequence hom*ologies to the bacteriocin class of antimicrobial peptides. A ninegene operon is required for SLS production: this includes a candidate gene for a bacteriocin prepropeptide, SagA, the likely SLS precursor and
streptozotocin Methyl
nitroso-urea with a 2-substituted glucose, used as an antibiotic (effective against growing Gram-positive and Gram-negative organisms), and also to induce a form of diabetes in experimental animals (rapidly induces pancreatic B cell necrosis if given in high dose). By using multiple low doses in a particular strain of mice, it is possible to produce insulitis followed later by diabetes, a model for Type 1 (juvenile-onset) diabetes in humans.
stress related genes The strongly regulated biotic stress related genes in plants include several PR-proteins (endochitinase (TC60929), chitinase (Q7XB39), osmotin-like proteins (P93621), thaumatin (Q7XAU7), disease response protein (Q45W75), tumour related proteins (P93378)), three 1,3β-glucanases and several proteinase inhibitors. Early induction of genes encoding chitinases and 1,3-β-glucanases is a typical response of plants towards fungal pathogens.
stress-fibres Bundle of microfilaments and other proteins found in fibroblasts, particularly slowmoving fibroblasts cultured on rigid substrata. Shown to be contractile; have a periodicity reminiscent of the sarcomere. Anchored at one end to a focal adhesion, although sometimes seem to stretch between two focal adhesions.
stress-induced proteins Alternative and preferable name for heat-shock proteins of eukaryotic cells, which emphasises that the same small group of
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proteins is stimulated both by heat and various other stresses.
stresscopin See urocortin III.
strongyloidiasis
strobilus Pl. strobili. (1) The cone-like reproductive structures of most gymnosperms and some pteridophytes. (2) An angiosperm inflorescence of cone-like appearance. Cf. strobila.
striated muscle Muscle in which the repeating
stroma (1) The soluble, aqueous phase within the
units (sarcomeres) of the contractile myofibrils are arranged in register throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope, e.g. the voluntary (skeletal) and cardiac muscle of vertebrates.
chloroplast, containing water-soluble enzymes such as those of the Calvin-Benson cycle. The site of the dark reaction of photosynthesis. (2) Loose connective tissue with few cells.
strigolactones Carotenoid-derived plant hormones (sesquiterpenes) implicated in inhibition of shoot branching. Strigolactones act as a host-recognition signal for arbuscular mycorrhizal fungi, are released by the host plant and stimulate hyphal branching ‘branching factors’. They are also seed germination stimulants for the parasitic weeds Striga and Orobanche.
string A Drosophila protein of the Cdc25 family (M-phase inducer phosphatase, EC 3.1.3.48, 479aa) that activates mitosis by hydrolyzing phosphotyrosine 15 of the cyclin dependent kinase Cdc2. String is activated by tribbles and is transcribed in a spatial pattern controlled by the anterior-posterior and dorsoventral patterning systems. Cf. cysteine string protein.
stringency In nucleic acid hybridization, the labelled probe is used to label matching sequences by base-pairing. Unbound probe is removed though a series of stringency washes. Low stringency washing (low temperature, high ionic strength), allows some mismatching of probe and target, and thus allows the detection of similar sequences at some cost in specificity. By contrast, high stringency conditions allow only closely matching sequence to remain base-paired.
stringent control One of the two regulatory mechanisms used by E. coli to adjust rRNA output to amino acid availability (cf. growth-rate dependent control). Stringent control is mediated by alarmone ppGpp.
striosome One of the components of the striatum region of the basal ganglia in the brain. The striatum is made of two parts, the matriosome and the striosome. Both receive input from the cortex (mostly frontal) and from dopaminergic (DA) neurons, but the striosome projects principally to DA neurons in the ventral tegmental area (VTA) and the substantia nigra (SN), the matriosome projects back to the frontal lobe.
strobila Pl. strobilae. A part or structure that buds to form a series of segments. In Scyphozoa, the sessile larval stage that produces medusoids by transverse fission. In Cestoda, the segmented body consisting of proglottides. Cf. strobilus.
stromal cell A non-committal name for a resident cell of loose fibrous connective tissue.
stromatolites Large rounded, multilayered fossils found in rocks dating from the Early Archaean (3.5mya), possibly before ‘modern’ cyanobacteria evolved. The layers are produced as a result of photosynthetic activity of bacterial colonies causing the precipitation of calcium carbonate that is combined with other sedimentary material trapped within the mucilage surrounding the colony. New layers of bacteria then develop on the outer surface. Modern equivalents are produced by cyanobacteria under certain circ*mstances e.g. on the beaches at Shark Bay in W. Australia.
stromelysins Matrix metallopeptidases (stromelysin-1, EC 3.4.24.17, MMP-3, 477aa; stromelysin-2, EC 3.4.24.22, MMP-10, 476aa; stromelysin-3, EC 3.4.24.-, MMP-11, 488aa) involved in breaking down the extracellular matrix.
stromovascular cells The non-adipocyte cells of adipose tissue, presumed to be mostly pre-adipocytes. Research article: http://jas.fass.org/content/82/2/429. full.pdf 1 html
stromule Dynamic tubular structures emerging from the surface of plastids. Their function is unclear but by increasing the plastid/cytoplasm contact area they may facilitate the exchange of metabolites or signals. Recent paper: http://www.biomedcentral.com/14712229/11/115/abstract
strong promoter Promoter that, when bound by a transcription factor, strongly activates expression of the associated gene. The term is widely used, but lacks precision.
Strongylocentrotus purpuratus Common sea urchin. Echinoderms are popular tools for developmental biology because the early embryo is transparent and cell movements can easily be observed. Sea urchin eggs are available in large numbers and were a convenient material for early biochemical studies on histones and mRNA. Because they are relatively large they have also been convenient for various electrophysiological studies.
strongyloidiasis Intestinal infestation (strongyloidosis) of man with the nematode worm, Strongyloides stercoralis.
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strophanthin Mixture
substance P
of glycosides from Strophanthus kombe (a tropical liana) with properties similar to those of digoxin and ouabain (strophanthin G). See digitalis.
Stylonychia mytilus Large ciliate protozoan of
STRP Short tandem repeat polymorphism. See sat-
tin produced by animal cells, the other being the Ctype lectins. The carbohydrate binding activity of the S-type lectins requires their cysteines to have free thiols and, unlike the C-type lectins, does not need divalent cations. They mostly have molecular masses in the range 14216 kDa and often form dimers and higher oligomers. The carbohydrate recognition domain contains a number of critically conserved amino acids and largely binds to β-galactosides. S-type lectins occur as cytoplasmic proteins and lack a signal sequence for secretion, yet do exist extracellularly.
ellite DNA.
structural bioinformatics The branch of bioinformatics associated with prediction of the secondary structure of proteins and nucleic acids. Much software has been developed to do this and there are a number of free packages available. The capabilities of such programs and the availability of software changes rapidly. See PyMol. RNA secondary structure: http://openwetware.org/wiki/Wikiomics: RNA_secondary_structure_prediction
structural gene A gene that codes for a product (e.g. an enzyme, structural protein, tRNA), as opposed to a gene that serves a regulatory role.
structure-activity relationship SAR The relationship between the strucure of a compound and its activity, usually done by systematically varying the structure and analysing binding or inhibitory activity. A more sophisticated analysis using complex computational methods to derive appropriate parameters of shape and electronic distribution produces a quantitative structure-activity relationship (QSAR). The hope is that eventually it will be possible to design better inhibitors (drugs) by this means, but rational design is not yet straightforward.
Strumpell’s
disease A spastic caused by a defect in strumpellin.
paraplegia
strumpellin A component (1159aa) of the WASH complex, ubiquitously expressed and defective in some forms of spastic paraplegia (Strumpell’s disease).
struvite A mineral composed of orthorhombic crystals of magnesium ammonium phosphate. Struvite stones in the kidney are composed of a struvite-carbonate-apatite matrix and are associated with urinary infections, particularly with urease-producing bacteria, including Ureaplasma urealyticum and Proteus.
strychnine Alkaloid obtained from the Indian tree Strychnos nux-vomica; specific blocking agent for the action of the amino acid transmitter glycine. Convulsive effects of strychnine are probably due to its blockage of inhibitory synapses onto spinal cord motoneurons.
Stuve-Wiedemann syndrome See SchwartzJampel syndrome.
the Order Hypotrichida, that has compound cilia (cirri) that can be used for walking or swimming.
S-type lectins galectins One of two classes of lec-
subacute Description of a disease that progresses more rapidly than a chronic disease and more slowly than an acute one.
subacute sclerosing panencephalitis SSPE Chronic progressive illness seen in children a few years after measles infection, and involving demyelination of the cerebral cortex. Virus apparently persists in brain cells: usually considered a slow virus disease.
subcommissural organ A brain gland (SCO) present in all vertebrate phyla. It secretes glycoproteins into the cerebrospinal fluid, where some aggregate to form Reissner’s fibres and others remain soluble. Among the secreted proteins is SCO-spondin which is probably involved in axonal growth and/or guidance. Research article: http://www.cerebrospinalfluidresearch.com/content/5/1/3
suberin Fatty substance, containing long-chain fatty acids and fatty esters, found in the cell walls of cork cells (phellem) in higher plants. Also found in the Casparian band. Renders the cell wall impervious to water.
subgenomic RNA sgRNA Copies of viral RNA from positive-strand RNA viruses that are truncated at the 50 ends, but have the same 30 ends. The viral genome has multiple open reading frames with only a single 30 end: the subgenomic RNA is a transcript of a downstream ORF which would not normally be expressed because the stop-site at the end of the upstream ORF terminates transcription. A special subgenomic promoter (RNA-promoter) between the ORFs permits this to happen. Helpful website: http:// www.dias.kvl.dk/Plantvirology/evirusgenes/evirsubgenomic.html
substance K Neurokinin A (neuromedin L). See tachykinins.
substance P A vasoactive intestinal peptide STX (1) See saxitoxin. (2) Shiga toxin. See shigalike toxin. (3) See sialyltransferase.
(11aa) derived from protachykinin-1 found in the brain, spinal ganglia and intestine of vertebrates.
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Induces vasodilation, salivation and increased capillary permeability. The receptor is G-protein coupled (neurokinin 1 receptor, 407aa).
substantia nigra Area of darkly pigmented dopaminergic neurons in the ventral midbrain thought to control movement and damaged in Parkinsonism.
substrate (1) A substance that is acted upon by an enzyme. (2) A culture medium containing suitable compounds to permit growth of a species of bacterium. (3) A surface. See substratum.
sulphatase-modifying factor 1 from succinate, to reduce ubiquinone to ubiquinol. (2) An enzyme (EC 1.3.99.1, fumarate reductase, fumarate dehydrogenase) that oxidises succinate to fumarate with the involvement of an acceptor. A bacterial enzyme or degraded form of mitochondrial SDH.
succinyl CoA An intermediate product in the tricarboxylic acid cycle, a combination of succinic acid and coenzyme A.
succinylcholine Cholinergic
moves, or upon which a cell grows: should be used in this sense in preference to substrate, to avoid confusion.
antagonist (suxamethonium chloride), two acetylcholine molecules linked by their acetyl groups. Binds to the acetylcholine receptor but unlike acetylcholine persists for long enough to cause the loss of electrical excitability and acts as a skeletal muscle relaxant.
subtilin Cationic pore-forming lantibiotic (56aa)
succulents Plants adapted to dry conditions.
substratum The solid surface over which a cell
produced by Bacillus subtilis. Acts preferentially on Gram-positive microorganisms but the producer cells have immunity mediated by the four genes spaIFEG. SpaFEG is an ABC transporter-2 subfamily member, a multidrug resistance protein. SpaI is a membrane-localised lipoprotein that may be a subtilin-intercepting protein. Mechanism of target recognition: http://aac.asm.org/content/52/2/612.full
subtilisin Extracellular serine endopeptidase (EC 3.4.21.62, B380aa) produced by Bacillus spp.
subtilysin Haemolytic
surfactant produced by Bacillus subtilis, a hexapeptide linked to a longchain fatty acid.
subtractive hybridization subtraction cloning Technique used to identify genes expressed differentially between two tissue samples. A large excess of mRNA from one sample is hybridized to cDNA from the other, and the double stranded hybrids removed by physical means. Remaining cDNAs are those not represented as RNA in the first sample, and thus presumably expressed uniquely in the second. To improve specificity, the process is often repeated several times. See also differential screening.
subunits Components from which a structure is built; thus myosin has six subunits, microtubules are built of tubulin subunits. In some cases it may be more informative to speak of protomers.
succinate Intermediate of the tricarboxylic acid cycle and glyoxylate cycle.
succinate dehydrogenase (1) SDH (EC 1.3.5.1, succinate-coenzyme Q reductase, complex II in electron transport, succinate-ubiquinone oxidoreductase). An enzyme complex of 4 subunits located in the inner mitochondrial membrane. It has two main activities, as part of the citric acid cycle, oxidizing succinate into fumarate while passing electrons on to FAD and as complex II of the electron transport chain, which uses electrons freed
Storage of water in leaves and other organs gives them their succulent or swollen appearance.
sucrase See invertase. sucrose Table sugar, a non-reducing disaccharide, α-D-glucopyranosyl-β-D-fructofuranose.
Sudan stains Histochemical stains used for lipids. sudden oak death A disease of oak trees caused by the fungus Phytophthora ramorum.
SUFU A negative regulator of the sonic hedgehog/ patched and beta-catenin signalling pathways in vertebrates (suppressor of fused, 484aa), part of a corepressor complex that downregulates GLI-1 (glioma-associated oncogene-1) transactivation and in the cytoplasm sequesters GLI1, GLI2 and GLI3, probably targeting them for proteosomal degradation. Defects in SUFU are a cause of medulloblastoma.
sugars See separate entries, and Table S2. sulcus Pl. sulci. A groove or furrow e.g. on the surface of the cerebrum in mammals.
sulfonamides Synthetic bacteriostatic antibiotics derived from sulphanilamide (a red dye) with a wide spectrum of activity against most Gram-positive and many Gram-negative organisms. Sulfonamides inhibit multiplication of bacteria by acting as competitive inhibitors of p-aminobenzoic acid in the folic acid metabolism cycle. In UK formerly sulphonamides but sulfonamide is the BAN.
sulfur, sulfo- The British spelling, sulphur, sulphois used throughout except where the British Approved Name (BAN) for drugs is the ‘sulf-’ spelling.
sulphatase-modifying factor 1 The enzyme in the endoplasmic reticulum (SUMF1, EC 1.8.99.-, 374aa) that catalyses the post-translational formation of C-alpha-formylglycine (FGly) from cysteine at the active site of sulphatases. Mutations lead to multiple sulphatase deficiency.
Table S2
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Table S2
TABLE S2. Sugars Monosaccharides PENTOSES L-arabinose
D-ribose
H
HOH2C
HO H
H OH H
D-xylose
O
H OH
H
H
H
H
H
OH
2-deoxy-D-ribose MW 134 1
H O HO
OH
O H OH H H
O
HOH2C H H
H
H H
OH
OH
OH
HEXOSES D-fructose
D-galactose
O
HOH2C H
H
CH2OH
H HO
HO
D-glucose
CH2OH H
H
CH2OH
O H
H
O
HO
H OH H
D-mannose
OH
CH2OH
O H
H OH H H
O H H OH HO O HO H
O
OH
H
H
Free amino-sugars are not found in structural oligosaccharides but N-acetyl aminohexoses are widely distributed. Most common are: N-acetylgalactosamine
N-acetylglucosamine
CH2OH
CH2OH
O H
HO H
H OH H H
O H H OH H O HO H
O
NH
H
NH
C O
C O
Other common components of structural oligosaccharides are: fucose
sialic acids (N-acetyl-neuraminic acid)
CH2OI
CH3 HO H
O H
H OH H H
O
OH
HO–C–H HOOC HO–C–H HO H
O OH OH H H
H
NHCOCH
Table S2
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Sun proteins
Hexose derivatives found in proteoglycans also include: D-glucuronic acid
muramic acid
COOH H HO
CH2OH
O O
H OH H H
O O H OH H H HO H
H
OH
H
NH
The list includes only the most common compounds found in metabolic pathways and in structural molecules. The structures are presented as Haworth models and it should be noted the configuration at the carbon which carries the carbonyl oxygen is not determined unless the hydroxyl-group takes part in a glycosidic linkage, which it always does in higher oligomers. The convention for depicting glycosidic linkages is: glycosyl carbon - acceptor hydroxyl. Configuration not defined in free molecule. Shaded regions have configurations that are not defined in free molecules. Sulphated derivatives of N-acetyl aminohexoses are also widespread and include the 4- and 6- sulphate esters of N-acetyl glucosamine and N-acetyl galactosamine.
Disaccharides and Polysaccharides These are fully specified by the residue names, sequence, bond-direction, and the position numbers of the carbon atoms giving rise to the linkage. The configuration around the glycosidic carbon is also specified as alpha or beta.
sulphatases Esterases (EC 3.1.6.-) that degrade sulphate esters such as heparan sulphate and dermatan sulphate. See, for example, aryl sulphatase also multiple sulphatase deficiency.
sulpholipids Any lipid containing sulphur although usually restricted to mean those in which the polar head group contains sulphate species. Sulpholipid-1 (SL-1) is an abundant sulphated glycolipid and potential virulence factor found in Mycobacterium tuberculosis. In plants they are important intermediates in the sulphur cycle.
sulphonylurea
receptor The sulphonylurea receptor-1 (ABCC8, SUR-1, 1581aa) is an ABC transporter that regulates glucose-induced insulin secretion by controlling K1-ATP channel activity of the pancreatic beta-cell membrane. They form a stoichiometric complex with 4 pore-forming inwardly-rectifying Kir6.2 molecules to produce the ATP-sensitive potassium (KATP) channels in neurons and neuroendocrine cells. SURs have two nucleotide-binding folds that sense changes in the metabolic status (ATP/ADP ratio) of the cell. Glibenclamide, a sulphonyl urea drug, binds to SUR and labelled forms of the drug can be used to show the distribution of the receptors.
sulphonylureas Group of drugs which act by augmenting insulin secretion. Used in the treatment of Type II diabetes. Examples include glibenclamide which is the sulphonylurea most commonly used in experimental studies. See sulphonylurea receptor.
sulphur-oxidising bacteria Aerobic chemolithotrophic bacteria that use sulphur or H2S as an
electron donor for oxygen to produce sulphate with release of energy.
sulphur-reducing bacteria Anaerobic bacteria (sulphate-reducing bacteria) that respire with sulphate or sulphur acting as electron acceptor instead of oxygen to produce H2S.
sulphydryl reagents Compounds that bind to SH groups. Include p-chlormercuribenzoate, N-ethyl maleimide, iodoacetamide. Very important in studies of protein structure because they affect disuphide bonding.
SUMO Small ubiquitin-related modifier proteins See sumoylation.
sumoylation Post-transcriptional modification of a protein by the conjugation of SUMO (small ubiquitinrelated modifier) proteins: stabilizes some proteins and may alter subcellular localization. Three different SUMO proteins are conjugated to proteins, SUMO-1, SUMO-2 and SUMO-3. The SUMO-2 and SUMO-3 genes are closely related, with 86% sequence identity while SUMO-1 is less closely related with about 50% sequence identity with SUMO-2 and SUMO-3. SUMO-1 (101aa) conjugates as a monomer, while SUMO-2 (95aa) and SUMO-3 (103aa) are conjugated to proteins as higher molecular weight polymers. Targets include p53, ran-Gap and various transcription factors, including C/EBP proteins and c-Myb.
Sun proteins A conserved family of proteins that have a Sun domain (Sad1/UNC-84 hom*ology domain). They are important components of various complexes involved in chromosomal movement, positioning
superantigen
637 suppression subtractive hybridization
of nuclear pore complexes and linkage of the nucleoskeleton with the cytoskeleton (the LINC complex). Interact with lamins and with nesprins. They were originally cloned by hom*ology with C. elegans protein UNC-84 that is involved in nuclear migration/positioning. In S. cerevisiae Sun 4 (septation protein SUN4, 420aa) is involved in the process of septum formation. The NSUN family (NOL1/NOP2/Sun domain family) are S-adenosylL-methionine-dependent methyltransferases, for example, Nsun2 (tRNA (cytosine-5-)-methyltransferase NSUN2, EC 2.1.1.29, 767aa).
superantigen Antigens, mostly of microbial origin, that activate all those T-lymphocytes that have a T-cell receptor with a particular Vβ sequence; as a consequence superantigens activate large numbers of T-cells and elicit an inappropriately strong immune response. Superantigens are presented on MHC Class II, but are not processed, and bind with high affinity but not in the normal peptide-binding groove of the MHC molecule. Presentation is not MHCrestricted. Staphylococcal enterotoxins are the best known superantigens and are pyrogenic, increase host susceptibility to endotoxic shock, suppress immunoglobulin production and stimulate CD41 T-cells. Superantigen diseases include Staphylococcus aureus food poisoning, toxic shock syndrome, and scarlet fever (produced by erythrogenic toxin of Streptococcus pyogenes). The Mls gene product in mice can act as a self-superantigen.
supercoiling In circular DNA or closed loops of DNA, twisting of the DNA about its own axis changes the number of turns of the double helix. If twisting is in the opposite direction to the turns of the double helix, i.e. anticlockwise, the DNA strands will either have to unwind or the whole structure will twist or supercoil - termed negative supercoiling. If twisting is in the same direction as the helix, clockwise, which winds the DNA up more tightly, positive supercoiling is generated. DNA that shows no supercoiling is said to be relaxed. Supercoiling in circular DNA can be detected by electrophoresis because supercoiled DNA migrates faster than relaxed DNA. Circular DNA is commonly negatively supercoiled and the DNA of eukaryotes largely exists as supercoils associated with protein in the nucleosome. The degree of supercoiling can be altered by topoisomerases.
superhelix A supercoil of a molecule, like DNA, that is already coiled.
SUPERMAN A transcriptional regulator (204aa) in Arabidopsis that acts indirectly to prevent the B class homeotic proteins APETALA3 and PISTILLATA from acting during flower development.
superoxide Term used interchangeably for the superoxide anion (.)O22, or the weak acid HO2(.). Superoxide is generated both by prokaryotes and
eukaryotes, and is an important product of the metabolic burst of neutrophil leucocytes. A very active oxygen species, it can cause substantial damage, and may be responsible for the inactivation of plasma antiproteases that contributes to the pathogenesis of emphysema.
superoxide dismutase Any of a range of metalloenzymes (EC 1.15.1.1) that catalyse the breakdown of superoxide to produce hydrogen peroxide and oxygen. The eukaryotic form (SOD1) is a copper-zinc enzyme (154aa) and the prokaryotic (SodA, 206aa in E. coli) and mitochondrial (SOD2, 222aa in humans) form has manganese as a cation. Other metal ions (iron, nickel) are found in some prokaryotes. They play an important role in protecting tissues from superoxide-induced damage. Superoxide dismutase copper chaperone (274aa) delivers copper and zinc to SOD1. See amyotrophic lateral sclerosis 1.
supershift Phenomenon in band-shift assays where the reduction in mobility on a gel induced by a binding interaction with a protein is enhanced by the addition of an antibody to the protein (or another interacting protein). Net result is that the mobility of the band of interest is further decreased (shifted).
supervillin An actin binding protein (2214aa) of the gelsolin/villin family, that forms a high-affinity link between the actin cytoskeleton and the membrane. Isoform 1 (archvillin) is muscle-specific and is important in myogenesis and the assembly of myosin II. Isoform 2 (supervillin) is more ubiquitously expressed, somewhat smaller (1788aa), and may down-regulate focal adhesions by binding to thyroid receptor-interacting protein 6 (TRIP6).
suppression PCR A modification of PCR, competition (or suppression) hybridization in which there is selective suppression of the amplification of one or more closely related sequences, useful when the target is present as a rare sequence in a large excess of a closely related sequence. A 50 extension is included in one (or both) primer(s) that will form a hairpin loop with internal sequence of the amplicon and is then refractory to further amplification. Sequences containing a perfect match to the 50 extension are not amplified (are suppressed) and only sequences containing mismatches or lacking the sequence is unaffected. Descriptive article: http:// www.ncbi.nlm.nih.gov/pmc/articles/PMC1184225/
suppression subtractive hybridization SSH A method developed for cDNA comparisons, based on PCR suppression by inverted terminal repeats (PS-effect). In complex mixtures, the PS-effect allows precise amplification only of molecules that are flanked by different adapters at opposing termini (asymmetrically flanked molecules). This principle is used in Suppression Subtractive Hybridization (SSH), where the molecules of interest, those unique to the
suppressor factor
638
test sample, are driven to the asymmetrically flanked state and selectively amplified.
suppressor factor (1) Factors released by T-suppressor cells (T-regulatory cells). (2) See suppressor mutation and termination codons.
suppressor mutation Mutation that alleviates the effect of a primary mutation at a different locus. May be through almost any mechanism that can give a primary mutation, but perhaps the most interesting class are the opal, amber and ochre suppressors, where the anticodon of the tRNA is altered so that it misreads the termination codon and inserts an amino acid, preventing premature termination of the peptide chain.
suppressor T-cells See T-regulatory cells. suprachiasmatic nucleus SCN A region in the hypothalamus, immediately above the optic chiasm. The SCN generates a circadian rhythm of neuronal activity, which regulates many different body functions. Melanopsin-containing ganglion cells in the retina have a direct connection to the SCN.
SUR See sulphonylurea receptor. suramin A
polysulphonated naphthylurea that uncouples G-proteins from receptors, inhibits phospholipase D and inhibits binding of EGF, PDGF to cell surface receptors. An antagonist of P2x and P2y purinergic receptors. Has been used in treatment of trypanosomiasis.
SURF complex A mRNA surveillance complex, composed of eukaryotic release factors 1 and 3 (ERF1, ERF3A or 3B), elongation factor (EEF2), regulator of nonsense transcripts 1 (UPF1/RENT1) and the SMG1C complex that includes the serine/ threonine-protein kinase SMG1.
surface plasmon resonance Alteration in light reflectance as a result of binding of molecules to a surface from which total internal reflection is occurring. Used in the Biacore (Pharmacia Trademark) machine that detects the binding of ligand to surfaceimmobilised receptor or antibody.
surface potential The electrostatic potential due to surface charged groups and adsorbed ions at a surface. It is usually measured as the zeta potential at the Helmholtz slipping plane outside the surface.
surface-active compound Usually, in biological systems, a detergent-like molecule that is amphipathic and that will bind to the plasma membrane, or to a surface with which cells come in contact, altering its properties from hydrophobic to hydrophilic, or vice versa.
surfactant A surface-active compound; the best known example of which is the lung surfactant (see surfactant proteins).
sustentacular
surfactant proteins Pulmonary surfactant is mainly (90%) lipid associated with four surfactant-associated proteins: 2 collagenous, carbohydrate-binding glycoproteins (SP-A and SP-D of the collectin family) and 2 small hydrophobic proteins (SP-B and SP-C). Production of surfactants at parturition allows the lungs to fill with air because the alveolar surface becomes hydrophobic. SP-A is oligomeric, consisting of 18 protomers (248aa) with lectin-like domains that recognize glycoconjugates, lipids and protein determinants on both host cells and invading microorganisms. SP-B (381aa) is a disulphide-linked hom*odimer. SP-C (197aa) is defective in a form of pulmonary surfactant metabolism dysfunction and variations are associated with respiratory distress syndrome in premature infants. SP-D (375aa), an oligomeric complex of 4 hom*otrimers, contributes to the lung’s defense against inhaled microorganisms. Binds maltose residues and other alpha-glucosyl moieties. It also occurs at the luminal surface of the gastric mucosa.
surfactin A lipopeptide biosurfactant (a cyclic heptapeptide coupled to an C132C15 acyl residue) produced by surfactin synthase (a heterotrimeric enzyme, 3587aa, 3583aa and 1275aa) in Bacillus subtilis. Because it can be produced from cheap feedstock by biofermentation it is being investigated for use in bioremediation. It has antibiotic properties. Swarming motility protein swrC (1052aa) confers self-resistance to surfactant on B. subtilis.
surrogate marker A readily measured parameter that is associated with a disease state and that can be monitored as a substitute for more complex clinical signs that may be less easy to quantify.
survivin See BIRCs. Sus scrofa Domestic pig. sushi domains Domains (complement control protein (CCP) modules, short consensus repeats (SCR), B60aa) identified in a wide variety of complement and adhesion proteins; involved in proteinprotein and protein-ligand interactions. Contain four cysteines forming two disulphide bonds in a 123 and 224 pattern. See sushi peptides.
sushi peptides Peptides derived from the lipopolysaccharide (LPS)-binding domains of an LPS-sensitive serine peptidase, Factor C, from the horseshoe crab (Carcinoscorpius rotundicauda); have potent antibacterial properties. See sushi domains.
suspensor cell Plant cell linking the growing embryo to the wall of the embryo sac in developing seeds.
sustentacular Something that supports or maintains. Sustentacular cells (Sertoli cells) of the testis are involved in support and possibly nutrition of developing sperm.
suxamethonium
639
suxamethonium See succinylcholine. SUZ12 A polycomb group protein (suppressor of zeste 12 protein hom*ologue, 739aa) that is a component of PRC2/EED-EZH complexes which methylate histone H3. See zeste, EZH.
SV2 (1) An integral membrane glycoprotein of synaptic vesicles, SV2 has several isoforms (A, 742aa; B and C) and is found in vertebrate neuronal and endocrine tissues, where it positively regulates vesicle fusion by maintaining the readily releasable pool of secretory vesicles. Interacts with synaptotagmin-1 in a calcium-dependent manner and binds adapter protein AP-2. Similar proteins have been found in invertebrates. Botulinum neurotoxin A binds to SV2 and is internalised. SV2 related protein (SVOP, 548aa) is probably an anion transporter (SLC22 family). (2) A line of immortal nontumorigenic human lung fibroblasts, MRC-5 SV2 cells.
SV3T3 Swiss 3T3 cells transformed with SV40. SV40 Simian virus 40. A small DNA tumour virus,
symbiosis of the Smith-Waterman or Needleman-Wunsch algorithms. Link to website: http://www.phrap.org/phredphrapconsed.html
SWI/SNF complex The SWI/SNF (Switch/Sucrose non-fermentable) complex remodels nucleosome structure in an ATP-dependent manner. In yeast the SWI/SNF chromatin remodelling complex has 11 tightly associated polypeptides (SWI1, SWI2, SWI3, SNF5, SNF6, SNF11, SWP82, SWP73, SWP59, SWP61, and SWP29). SWP59 and SWP61, encoded by the ARP9 and ARP7 genes respectively, are members of the actin-related protein (ARP) family. The similarity of ARP7 and ARP9 proteins to the heatshock protein and HSC family of ATPases suggests that chromatin remodelling may involve chaperonelike activities. See BAF complex, RSC complex.
Swiss 3T3 cells An immortal line of fibroblastlike cells established from whole trypsinised embryos of Swiss mice (not an inbred stock) under conditions that favour establishment of cells with low saturation density in culture.
member of the Papovaviridae. Isolated from monkey cells, which were being used for the preparation of poliovirus vaccine, and originally named ‘vacuolating agent’ owing to a cytopathic effect observed in infected cells. Found to induce tumours in newborn hamsters. In culture, transforms the cells of many non- and semi-permissive species, including mouse and human. See also T-antigen.
switch regions The nucleotide sequences in heavy
S value See Svedberg unit and sedimentation
forming a complex that absorbs at 488 nm and emits green light (λmax 522 nm). A much safer dye that has replaced ethidium bromide. Extensively used in quantitative PCR and in general gel staining.
coefficient.
Svedberg unit The unit named after a pioneer of the ultracentrifuge that is applied to the sedimentation coefficient of a particle in a high-speed or ultracentrifuge. The unit S is calculated as follows, S 5 rate of sedimentation 3 1/ρ2r, where ρ is the speed of rotation in radians per second and r is the radius to a chosen point in the centrifuge tube. 1 Svedberg unit is defined as the time taken to travel unit distance for a particle under the influence of unit centrifugal acceleration, 10213 seconds. The units are non-additive: a particle formed from two 5S particles will not have a sedimentation coefficient of 10S.
swainsonine Fungal indolizidine alkaloid that is a reversible inhibitor of lysosomal alpha-mannosidase and of the Golgi complex alpha-mannosidase II that is involved in processing the oligosaccharide chains of glycoproteins.
chain immunoglobulin genes located in the introns at the 50 end of each CH locus concerned with DNA recombination events that lead to changes in the type of heavy chain produced by a B-cell, e.g. IgM to IgG switching. These regions are highly conserved. See isotype switching.
Sybr green A cyanine dye that binds to DNA
Sydenham’s chorea A condition, ‘Saint Vitus’ Dance’ characterized by rapid, uncoordinated jerking movements (chorea). Caused by childhood infection with Group A beta-haemolytic streptococci (which also cause rheumatic fever) that leads to an autoimmune response that destroys cells in the basal ganglia.
SYFPEITHI A database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. Link to database: http://www.syfpeithi.de/
syk A non-receptor tyrosine kinase (spleen tyrosine
SWAM In mouse an antibacterial protein (SWAM1,
kinase, 630aa), an effector of the B-cell receptor signalling pathway. Contains two tandem SH2 domains through which it interacts with the ITAM motif. More widely distributed than zap70 and important in signalling in both myeloid and lymphoid cells.
single WAP motif protein 1, elafin-like protein 1, 80aa; SWAM2, 85aa).
symbiont One of the partners in a symbiotic
swat A program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation
relationship.
symbiosis Living together for mutual benefit. See symbiont, symbiotic algae.
symbiotic algae
640
synaptic transmission
symbiotic algae Algae (often Chlorella spp.) that
synapse A connection between excitable cells, by
live intracellularly in animal cells (e.g. endoderm of Hydra viridis). The relationship is complex, because lysosomes do not fuse with the vacuoles containing the algae, and the growth rates of both cells are regulated to maintain the symbiosis. There is considerable strain-specificity. The term is imprecise, since there are many other symbiotic algae (as in lichens) where the relationship is different.
which an excitation is conveyed from one to the other. (1) Chemical synapse: one in which an action potential causes the exocytosis of neurotransmitter from the presynaptic cell, which diffuses across the synaptic cleft and binds to ligand-gated ion channels on the postsynaptic cell. These ion channels then affect the resting potential of the postsynaptic cell. (2) Electrical synapse: one in which electrical connection is made directly through the cytoplasm, via gap junctions. (3) Rectifying synapse: one in which action potentials can only pass across the synapse in one direction (all chemical and some electrical synapses). (4) Excitatory synapse: one in which the firing of the presynaptic cell increases the probability of firing of the postsynaptic cell. (5) Inhibitory synapse: one in which the firing of the presynaptic cell reduces the probability of firing of the postsynaptic cell. (6) See immunological synapse.
sympathetic nervous system One of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord, and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera, and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter.
sympathetic
ophthalmia An autoimmune response in which there is inflammatory disease in the undamaged eye following perforating injury to the other eye.
synapsins Family of phosphoproteins that coat
sympatric speciation Development of a new spe-
synaptic vesicles and bind to the cytoskeleton. Synapsin Ia and Ib (Brain protein 4.1, 705aa) are alternatively spliced variants as are synapsins IIa and IIb (582aa). Synapsin III (580aa) has a more restricted distribution. The synapsins are implicated in neurotransmitter release, axonogenesis and synaptogenesis. Can be phosphorylated by several protein kinases and interact with small G proteins such as rab. Synapsin 1 forms a ternary complex with nitric oxide synthase and CAPON. Mutations in synapsin 1 are associated with a form of X-linked epilepsy.
cies without (geographical) isolation. Controversial. See speciation.
synapsis (1) The specific pairing of the chromatids
sympathomimetic Mimicking the sympathetic nervous system. Sympathomimetic drugs mimic the stimulation of the sympathetic nervous system to produce, for example, tachycardia and increased output from the heart or bronchodilatation and vasodilatation.
Symphyta Symphyta (sawflies) are a sub-order of the Hymenoptera. Website: http://www.earthlife.net/ insects/symphyta.html
symplast The intracellular compartment of plants, consisting of the cytosol of a large number of cells connected by plasmodesmata. See apoplast.
symplectic metachronism See metachronism. symplesiomorphic See apomorphic. symport A mechanism of transport across a membrane in which two different molecules move in the same direction. Often, one molecule can move up an electrochemical gradient because the movement of the other molecule is more favourable (see facilitated diffusion). Example: the sodium/glucose cotransport. See antiport, uniport.
synaphin See complexin. synapomorph Apomorphic features possessed by two or more taxa in common. Phylogenic trees are based upon identifying groups united by synapomorphies.
of hom*ologous chromosomes during prophase I of meiosis. It allows crossing-over to take place. (2) Process that brings the ends of double-strand breaks in DNA together, prior to end joining in NHEJ. Synapsis results in the autophosphorylation of DNA-PKcs, which is required to make the DNA ends available for ligation.
synaptic cleft The narrow space between the presynaptic cell and the postsynaptic cell in a chemical synapse, across which the neurotransmitter diffuses.
synaptic facilitation See facilitation. synaptic plasticity Change in the properties of a synapse, usually in the context of learning and memory. Very few synapses provide simple 1:1 transfer of action potentials, and very small changes in the efficiency of a synapse (usually mediated by changes in either the pre- or postsynaptic membrane) can have profound influences on the electrical properties of a neuronal circuit. See also neuronal plasticity.
synaptic transmission The process of propagating a signal from one cell to another via a synapse.
synaptic vesicle
641
synaptic vesicle Intracellular vesicles containing neurotransmitter found in the presynaptic terminals of chemical synapses.
synaptobrevins Small integral membrane proteins of synaptic vesicles that have v-SNARE coiled-coil hom*ology domains and interact with target-SNARES. Two neuronal isoforms, VAMP1 (118aa) and VAMP2 (116aa) are known that bind SNAPs and syntaxin. Clostridial toxins encoding zinc endopeptidases, such as tetanus toxin and botulinum toxin, block synaptic release by degrading synaptobrevins. Other related proteins occur in other tissues serving a similar role in vesicle targeting through interactions with SNAREs. VAMP3 (100aa) is cellubrevin and involved in protein recycling. VAMP4 (141) is involved in removing an inhibitor (probably synaptotagmin-4) of calcium-triggered exocytosis during the maturation of secretory granules. VAMP5 (myobrevin, 102aa) is found in muscle. VAMP7 (synaptobrevinlike protein 1, 220aa) is ubiquitous and involved in endosome-lysosome transport. VAMP8 (endobrevin, 100aa) is associated with dense-granule secretion in platelets. VAMP-like proteins are found in a wide range of organisms, including protozoa, yeasts and Arabidopsis.
synaptogenesis Formation of a synapse. synaptogyrin A family of proteins involved in synaptic plasticity (synaptogyrin 1, SYNGR1, 233aa; SYNGR2, (cellugyrin), 224aa, SYNGR3, 229aa; SYNGR4 234aa). Synaptogyrin-3 is involved in the positive regulation of dopamine transporter activity.
synaptojanins Inositol 5-phosphatases involved in vesicle recycling; the amino-terminal region has hom*ology with yeast Sac1 (involved in phospholipid metabolism) and the C-terminal region has prolinerich sequences that probably interact with SH3 domains of amphiphysin and grb-2. Synaptojanin-1 (EC 3.1.3.36, 1573aa) is involved in clathrin-mediated endocytosis in presynaptic terminals through an interaction with dynamin, Eps15 and amphiphysin. Synaptojanin-2 (1496) has a much wider tissue distribution but a similar role in vesicle recycling. Synaptojanin-2-binding protein (145aa) is a mitochondrial outer-membrane protein.
synaptomorphic See apomorphic. synaptonemal complex Structure, identified by electron microscopy, lying between chromosomes during synapsis; consists of two lateral plates closely apposed to the chromosomes and connected to a central plate by filaments. It appears to act as a scaffold, but is not apparently essential for crossing-over. In S. cerevisiae, a mutation eliminating the synaptonemal complex protein, Zip1 (875aa), increases the meiosis I nondisjunction rate of nonexchange chromosomes, suggesting it is a backup system for those chromosome where recombination has not occurred. Various
SynCAMs synaptonemal proteins have been identified (SYCP1, 976aa; SYCP2, 1,530aa; SYCP3, 236aa and synaptosomal central element proteins, Syce 1, 329aa and Syce2, 171aa). Research article: http://www.pnas.org/ content/107/2/781.full.pdf 1 html
synaptophysin Abundant glycoprotein component (major synaptic vesicle protein p38, 313aa) of small synaptic vesicle with four transmembrane domains; both N- and C-termini are located cytoplasmically. The transmembrane organization and putative quaternary structure resemble that of connexins. Synaptophysin-like protein 2 (mitsugumin-29, 264aa) is involved in communication between the T-tubular and junctional sarcoplasmic reticulum (SR) membranes. See synaptoporin.
synaptopodin An
actin-associated proline-rich protein (929aa) found in kidney podocytes and a subset of mature telencephalic dendritic spines of neurons; a regulator of rhoA signalling and cell migration. Blocks Smurf1-mediated ubiquitination of rhoA, thereby preventing the targeting of rhoA for proteasomal degradation. May be involved in synaptic plasticity in telencephalic neurons. Synaptopodin2 (myopodin, 1093aa) is skeletal muscle-specific and localized to the Z-disc in mature muscle. Shuttles between the nucleus and the cytoplasm in a differentiation-dependent and stress-induced fashion.
synaptoporin SPO
Putative channel protein (265aa) of synaptic vesicles, and a member of the synaptophysin/connexin superfamily. It has 58% amino acid identity to synaptophysin, with highly conserved transmembrane segments but a divergent cytoplasmic tail.
synaptosome A subcellular fraction prepared from tissues rich in chemical synapses, used in biochemical studies. Consists mainly of vesicles from presynaptic terminals.
synaptotagmins Calcium-binding synaptic vesicle proteins that bind acidic phospholipids and recognize the cytoplasmic domain of the neurexins. Function as Ca21 sensors that facilitate SNAREmediated membrane fusion. Synaptotagmin-1 (SYT1, p65, 422aa) is only one of a large family (at least 15 members) that probably differ subtly in their binding partners. SYT1 forms a complex with SV2B (synaptic vesicle glycoprotein 2B), syntaxin 1 and SNAP25; SYT2 (419aa) interacts with stonin-2 and SCAMP5 (secretory carrier-associated membrane protein-5). Similar proteins are found in many metazoa.
SynCAMs Synaptic
cell adhesion molecules. Immunoglobulin superfamily adhesion molecules of the nectin subfamily (for example, syncam-1, cell adhesion molecule 1, nectin-like protein 2, 442aa) involved in calcium-independent hom*o- and heterotypic cell adhesion, not restricted to neuronal cells. Syncam 1 is implicated in presynaptic
synchronous cell population
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differentiation along with β-neurexin/neuroligin. It also interacts with poliovirus receptor-related protein 3 (nectin-3) and is involved in a wide range of other activities, acting as a tumour suppressor, promoting natural killer cell cytotoxicity amongst other things.
synchronous cell population A culture of cells that all divide in synchrony. Particularly useful for certain studies of the cell cycle, cells can be made synchronous by depriving them of essential molecules, which are then restored. Synchronization breaks down after a few cycles, however, as individual cells have unique division rates.
syncoilin An intermediate filament-type III protein (482aa) found in striated and cardiac muscle where it binds to desmin and to α-dystrobrevin and thereby to the dystrophin-associated protein complex.
syncollin Protein (134aa) found within zymogen granules that is required for efficient regulated exocytosis. Normally exists as a doughnut-shaped hom*o-oligomer (possibly a hexamer) in close association with the luminal surface of the zymogen granule membrane.
syncytin Membrane proteins encoded by human endogenous retroviruses genes that have retained their original fusogenic properties and participate in trophoblast fusion (formation of the syncytiotrophoblast) during placental morphogenesis. Syncytin 1 (538aa), the product of a HERV-W gene, is cleaved into a surface protein (SU, gp50, 297aa) that mediates recognition of the type D mammalian retrovirus receptors SLC1A4 and SLC1A5, and a transmembrane protein (TM, gp24, 221aa) that acts a class I viral fusion protein. SU and TM form a heterodimer. Syncytin 2 (product of a HERV-FRD gene, 538aa) is similar.
synergy
syndecans Integral membrane proteoglycans associated largely with epithelial cells. The core protein has an extracellular domain that is modified by addition of multiple heparan sulphate, chondroitin or dermatan sulphate chains and N-linked oligosaccharide. The heparan sulphate chains bind to proteins of the extracellular matrix, including collagens, fibronectin and tenascin. The cytoplasmic domain is thought to interact with actin filaments thus linking the cytoskeleton with fibrous elements of the extracellular matrix. Members of the family include syndecan-1 (CD138, 310aa), syndecan-2 (fibroglycan, heparan sulphate proteoglycan core protein, 201aa). Syndecan-3 (442aa) may have a role in signalling and binding of heparin-binding growthassociated molecule increases phosphorylation of c-src and cortactin. Syndecan-4 (amphiglycan, ryudocan core protein, 198aa) interacts with CUB domaincontaining protein 1, the adaptor proteins syntenin-1 and -2 (syndecan binding protein, SDBP1, melanoma differentiation-associated protein 9, scaffold protein Pbp1, 298aa; SDBP2, 292aa) and various other proteins. Syndecans bind gp120 of HIV and mediate viral entry to the host cell. The Drosophila protein (399aa) is required for axonal and myotube guidance and is a necessary component in slit/robo signalling.
syne proteins See nesprins. Synechocystis A
freshwater cyanobacterium capable of both phototrophic growth in sunlight and heterotrophic growth in darkness. Synechocystis sp. PCC6803 is well studied and exhibits circadian rhythms.
Synedra A genus of freshwater diatoms. Details: http://craticula.ncl.ac.uk/EADiatomKey/html/Synedra. html
synemin A typeVI intermediate filament isolated
the outermost fetal layer in the placenta and is thus the interface with maternal tissue. Has invasive capacity though in a regulated manner. See syncytin.
from avian smooth muscle (1604aa in Gallus gallus), but a hom*ologue (synemin, desmuslin, 1565aa) is also found in mammalian muscle. Forms heteropolymeric IFs with desmin and/or vimentin that link to adherens-type junctions. Three synemin isoforms, (339aa, 1251aa and 1563aa) are produced by alternative splicing and have different tissue distributions.
syncytium An epithelium or tissue in which there
synergids Cells of the egg apparatus in plants; two
syncytiotrophoblast Syncytial layer that forms
is cytoplasmic continuity between the constituent cells. Striated muscle is the classic example.
cells at the apex of the embryo sac closely associated with the egg cell and directly involved with the process of fertilisation.
syndactyly A relatively common congenital abnor-
Synergistetes A phylum of bacteria; Gram-negative,
mality in which the webbing between finger or toes persists because of a failure in the normal developmental programmed death of inter-digital tissue. Can be caused by mutation variously in genes encoding connexin-43, homeobox HOXD13, fibulin-1, low density lipoprotein receptor-related protein 4 or regulatory elements of the sonic hedgehog system. Syndactyly is associated with several other disorders although the mutations responsible are unclear.
rod-shaped obligate anaerobes. Some species have been implicated in periodontal disease, gastrointestinal infections and soft tissue infections.
synergy An interaction that produces a more-thanadditive effect. Demonstrating a synergistic effect requires that the second compound produces an additional effect in the presence of a maximally-effective level of the other. This criterion is not always met.
synexin
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synexin Annexin 8. See Table A2. syngamy Fusion of two haploid gametic nuclei to form the diploid nucleus of the zygote.
syngeneic Organisms that are antigenically identical monozygotic twins or highly inbred strains of animals. Cells or tissues introduced into a syngeneic host will not be rejected because they are histocompatible (do not differ in histocompatibility antigens).
synkaryon A somatic hybrid cell in which chromosomes from two different parental cells are enveloped in a single nucleus.
synoecious Describing the condition in which there are both male and female flowers in a single composite inflorescence or, in the case of bryophytes, having male and female organs together on a branch.
synomone See allomone. synoviocytes Fibroblastic cells of the synovial membrane (lining) that produce synovial fluid and the extracellular matrix of the bearing surface of the joint.
synovium Connective tissue that forms the bearing surface of the joint and that is eroded in arthritis.
synphilin A neural protein (alpha-synuclein-interacting protein, synphilin-1, 919aa with alternatively spliced isoforms). Isoforms 1 and 2 form a heterodimer: isoform 2 inhibits E3 ubiquitin-protein ligase (SIAH1) and inhibits proteasomal degradation of target proteins. Can be ubiquitinylated by parkin to produce cytoplasmic inclusions resembling Lewy bodies. Defects may cause Parkinson’s disease. See synuclein.
synpolydactyly See syndactyly. syntaxins A large family of receptors (t-SNAREs)
systemic acquired resistance
synthetase Enzymes of Class 6 in the E classification; catalyse synthesis of molecules, their activity being coupled to the breakdown of a nucleotide triphosphate.
syntrophins A family of adapter proteins that interact with dystrophin, dystrobrevin and diacylglycerol kinase (DGK)-zeta at the plasma membrane of muscle and nerve and may link receptors to the actin cytoskeleton. Alpha-1-syntrophin-alpha (syntrophin-1, Pro-TGFα cytoplasmic domaininteracting protein 1, TACIP1, 505aa) is mainly expressed in skeletal muscle and heart, and is important in synapse formation. Beta-1-syntrophin (syntrophin-2, 538aa) and beta-2-syntrophin (syntrophin-3, 540aa) are ubiquitous and interact with the other members of the syntrophin family. Gamma1-syntrophin (syntrophin-4, 517aa) is brain-specific but gamma-2-syntrophin (syntrophin-5, 539aa) is widely expressed. See dystrophin-associated protein complex.
synuclein Family of proteins (α-synuclein, 140aa;
β-, 134aa; γ-, 127aa) with structural resemblance to apolipoproteins, abundant in neuronal cytosol and particularly in presynaptic terminals where they may be involved in the regulation of dopamine release. In Alzheimer’s disease α-synuclein is a component of plaque amyloid; mutations in the α-synuclein gene are the cause of various forms of Parkinson’s disease (types 1 and 4) and the protein accumulates in Lewy bodies. Interacts with synphilin.
syphilis A contagious sexually-transmitted disease caused by infection with the spirochaete Treponema pallidum. Can also be vertically transmitted from mother to fetus.
syringomycin A phytotoxic lipopeptide produced by Pseudomonas syringae that form pores in plasma membranes and is also a powerful surfactant. Syringopeptin has similar effects.
for intracellular transport vesicles that bind synaptotagmin and taxilins in a calcium-dependent fashion and interact with voltage dependent calcium and potassium channels. Syntaxins have a hydrophobic C-terminal region that anchors the protein on the cytoplasmic surface of cellular membranes, a central conserved region and a variable N-terminal cytoplasmic domain. Syntaxin 1 (288aa) is mainly expressed in brain tissue and is thought to function specifically in neurotransmitter release, whereas syntaxin 2, 3, and 4 are involved in more general vesicle trafficking. In Arabidopsis, syntaxin 121 (syntaxin-related protein At-Syr1, 346aa) functions in the secretory pathway and binds to SNAP33.
syringopeptin A phytotoxic cyclic lipodepsipep-
syntenic Describing genes that lie on the same
systemic acquired resistance SAR In plants,
chromosome. Some loci are syntenic in both human and mouse, others are not.
syntenin See syndecans.
tide produced by Pseudomonas syringae that oligomerizes to form pores in cell membranes.
syringyl alcohol A phenylpropanoid alcohol (sinapyl alcohol), one of the three precursors of lignin.
systematic sclerosis See scleroderma, fibrillarin. systemic Describing something with global rather than local effects: systemic insecticides, for example, become distributed throughout a plant, systemic diseases affect the whole body. long-term resistance to pathogen attack, triggered by elicitors released by the pathogen (e.g. bacteria). In contrast to the hypersensitive response, which is a localized response involving cell death at the site of
systemic carnitine deficiency
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infection, SAR is displayed by the whole plant. SAR is associated with the expression and activity of a set of SAR genes which include the pathogenesisrelated (PR) genes.
systemic carnitine deficiency A condition in which carnitine levels are low in non-muscle tissue. Mutations in the SLC22A5 gene, which encodes the sodium ion-dependent carnitine transporter (OctN2), cause a failure of reabsorption of carnitine in the kidney. Myopathic carnitine deficiency is caused by a different mutation and is restricted to skeletal muscle.
systemic lupus erythematosus SLE An autoimmune disease with antinuclear and other antibodies (often anti-RNA) in plasma. Immune complex deposition in the glomerular capillaries is a particular problem. Multiple genes affect susceptibility, mostly genes that regulate the immune suystem although resistance is associated with a polymorphism in the Toll-like receptor-5 gene. See lupus erythematosus.
systemin An 18aa wound hormone released from sites on tomato leaves damaged mechanically or by insects. Through the systemin receptor regulates more than 20 defensive genes. Produced, by proteolytic cleavage, from prosystemin (200aa).
systemin receptor A leucine-rich repeat (LRR) receptor with serine/threonine-protein kinase activity
syzygy in Solanum peruvianum (Peruvian tomato) (EC 2.7.11.1, brassinosteroid LRR receptor kinase, 1207aa). Almost identical to the brassinosteroid receptor in Solanum lycopersicum (tomato) although brassinosteroid and systemin bind to different sites. The receptor regulates an intracellular cascade including, depolarization of the plasma membrane, the opening of ion channels, an increase in intracellular Ca21, activation of a MAP kinase activity and a phospholipase A2 activity. As a consequence linolenic acid, is released from plant membranes and converted to jasmonic acid.
systems biology Fashionable term for an integrated approach to biology in which effects on the whole organism are studied as opposed to the reductionist approaches of modern molecular bioscience. This Dictionary deliberately contains definitions that span a wide range of biological sub-specialities since molecular cell biologists are generally well aware of the importance of putting their work into context, but may need a glossary for some of the more arcane terminologies.
syzygy (1) In some parasitic protozoa the pairing of gamonts prior to sexual fusion. (2) In gregarines the end-to-end attachment of the sporonts. (3) In some crinoids the fusion of organs or skeletal elements.
