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EMBO J. 1994 Feb 1; 13(3): 493–503.
PMCID: PMC394838

Yeast chromosome III: new gene functions.


One year after the release of the sequence of yeast chromosome III, we have re-examined its open reading frames (ORFs) by computer methods. More than 61% of the 171 probable gene products have significant sequence similarities in the current databases; as many as 54% have already known functions or are related to functionally characterized proteins, allowing partial prediction of protein function, 11 percentage points more than reported a year ago; 19% are similar to proteins of known three-dimensional structure, allowing model building by homology. The most interesting new identifications include a sugar kinase distantly related to ribokinases, a phosphatidyl serine synthetase, a putative transcription regulator, a flavodoxin-like protein, and a zinc finger protein belonging to a distinct subfamily. Several ORFs have similarities to uncharacterized proteins, resulting in new families in search of a function'. About 54% of ORFs match sequences from other phyla, including numerous fragments in the database of expressed sequence tags (ESTs). Most significant similarities to ESTs are with proteins in conserved families widely represented in the databases. About 30% of ORFs contain one or more predicted transmembrane segments. The increase in the power of functional and structural prediction comes from improvements in sequence analysis and from richer databases and is expected to facilitate substantially the experimental effort in characterizing the function of new gene products.

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  • Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet. 1993 Mar;3(3):266–272. [PubMed]
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed]
  • Amakasu H, Suzuki Y, Nishizawa M, Fukasawa T. Isolation and characterization of SGE1: a yeast gene that partially suppresses the gal11 mutation in multiple copies. Genetics. 1993 Jul;134(3):675–683. [PMC free article] [PubMed]
  • Bairoch A. The PROSITE dictionary of sites and patterns in proteins, its current status. Nucleic Acids Res. 1993 Jul 1;21(13):3097–3103. [PMC free article] [PubMed]
  • Bairoch A, Boeckmann B. The SWISS-PROT protein sequence data bank, recent developments. Nucleic Acids Res. 1993 Jul 1;21(13):3093–3096. [PMC free article] [PubMed]
  • Barker WC, George DG, Mewes HW, Pfeiffer F, Tsugita A. The PIR-International databases. Nucleic Acids Res. 1993 Jul 1;21(13):3089–3092. [PMC free article] [PubMed]
  • Benson D, Lipman DJ, Ostell J. GenBank. Nucleic Acids Res. 1993 Jul 1;21(13):2963–2965. [PMC free article] [PubMed]
  • Boguski MS, Lowe TM, Tolstoshev CM. dbEST--database for "expressed sequence tags". Nat Genet. 1993 Aug;4(4):332–333. [PubMed]
  • Bork P. Hundreds of ankyrin-like repeats in functionally diverse proteins: mobile modules that cross phyla horizontally? Proteins. 1993 Dec;17(4):363–374. [PubMed]
  • Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Sci. 1992 Dec;1(12):1677–1690. [PMC free article] [PubMed]
  • Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. What's in a genome? Nature. 1992 Jul 23;358(6384):287–287. [PubMed]
  • Bork P, Sander C, Valencia A. Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases. Protein Sci. 1993 Jan;2(1):31–40. [PMC free article] [PubMed]
  • Claverie JM. Database of ancient sequences. Nature. 1993 Jul 1;364(6432):19–20. [PubMed]
  • Collart MA, Struhl K. CDC39, an essential nuclear protein that negatively regulates transcription and differentially affects the constitutive and inducible HIS3 promoters. EMBO J. 1993 Jan;12(1):177–186. [PMC free article] [PubMed]
  • Edman JC, Goldstein AL, Erbe JG. Para-aminobenzoate synthase gene of Saccharomyces cerevisiae encodes a bifunctional enzyme. Yeast. 1993 Jun;9(6):669–675. [PubMed]
  • Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol. 1984 Oct 15;179(1):125–142. [PubMed]
  • Franco L, Jiménez A, Demolder J, Molemans F, Fiers W, Contreras R. The nucleotide sequence of a third cyclophilin-homologous gene from Saccharomyces cerevisiae. Yeast. 1991 Dec;7(9):971–979. [PubMed]
  • Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet. 1993 Mar;3(3):266–272. [PubMed]
  • Goffeau A, Nakai K, Slonimski P, Risler JL, Slominski P [corrected to Slonimski P] The membrane proteins encoded by yeast chromosome III genes. FEBS Lett. 1993 Jun 28;325(1-2):112–117. [PubMed]
  • Goffeau A, Slonimski P, Nakai K, Risler JL. How many yeast genes code for membrane-spanning proteins? Yeast. 1993 Jul;9(7):691–702. [PubMed]
  • Gorbalenya AE, Blinov VM, Donchenko AP, Koonin EV. An NTP-binding motif is the most conserved sequence in a highly diverged monophyletic group of proteins involved in positive strand RNA viral replication. J Mol Evol. 1989 Mar;28(3):256–268. [PubMed]
  • Green P, Lipman D, Hillier L, Waterston R, States D, Claverie JM. Ancient conserved regions in new gene sequences and the protein databases. Science. 1993 Mar 19;259(5102):1711–1716. [PubMed]
  • Gribskov M, McLachlan AD, Eisenberg D. Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355–4358. [PMC free article] [PubMed]
  • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915–10919. [PMC free article] [PubMed]
  • Higgins DG, Bleasby AJ, Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189–191. [PubMed]
  • Hjelmstad RH, Bell RM. sn-1,2-diacylglycerol choline- and ethanolaminephosphotransferases in Saccharomyces cerevisiae. Nucleotide sequence of the EPT1 gene and comparison of the CPT1 and EPT1 gene products. J Biol Chem. 1991 Mar 15;266(8):5094–5103. [PubMed]
  • Janitor M, Subík J. Molecular cloning of the PEL1 gene of Saccharomyces cerevisiae that is essential for the viability of petite mutants. Curr Genet. 1993 Oct;24(4):307–312. [PubMed]
  • Karlin S, Altschul SF. Applications and statistics for multiple high-scoring segments in molecular sequences. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5873–5877. [PMC free article] [PubMed]
  • Kern L. The URK1 gene of Saccharomyces cerevisiae encoding uridine kinase. Nucleic Acids Res. 1990 Sep 11;18(17):5279–5279. [PMC free article] [PubMed]
  • Koonin EV. Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and lambda 2 protein of reovirus. J Gen Virol. 1993 Apr;74(Pt 4):733–740. [PubMed]
  • Lalo D, Stettler S, Mariotte S, Slonimski PP, Thuriaux P. Two yeast chromosomes are related by a fossil duplication of their centromeric regions. C R Acad Sci III. 1993;316(4):367–373. [PubMed]
  • Mehta PK, Christen P. Homology of pyridoxal-5'-phosphate-dependent aminotransferases with the cobC (cobalamin synthesis), nifS (nitrogen fixation), pabC (p-aminobenzoate synthesis) and malY (abolishing endogenous induction of the maltose system) gene products. Eur J Biochem. 1993 Jan 15;211(1-2):373–376. [PubMed]
  • Moore J, Engelberg A, Bairoch A. Using PC/GENE for protein and nucleic acid analysis. Biotechniques. 1988 Jun;6(6):566–572. [PubMed]
  • Navarre C, Ghislain M, Leterme S, Ferroud C, Dufour JP, Goffeau A. Purification and complete sequence of a small proteolipid associated with the plasma membrane H(+)-ATPase of Saccharomyces cerevisiae. J Biol Chem. 1992 Mar 25;267(9):6425–6428. [PubMed]
  • Nikawa J, Kodaki T, Yamashita S. Primary structure and disruption of the phosphatidylinositol synthase gene of Saccharomyces cerevisiae. J Biol Chem. 1987 Apr 5;262(10):4876–4881. [PubMed]
  • Oliver SG, van der Aart QJ, Agostoni-Carbone ML, Aigle M, Alberghina L, Alexandraki D, Antoine G, Anwar R, Ballesta JP, Benit P, et al. The complete DNA sequence of yeast chromosome III. Nature. 1992 May 7;357(6373):38–46. [PubMed]
  • Ouzounis C, Sander C. Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes. FEBS Lett. 1993 May 10;322(2):159–164. [PubMed]
  • Pang AS, Nathoo S, Wong SL. Cloning and characterization of a pair of novel genes that regulate production of extracellular enzymes in Bacillus subtilis. J Bacteriol. 1991 Jan;173(1):46–54. [PMC free article] [PubMed]
  • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. [PMC free article] [PubMed]
  • Mohana Rao JK, Argos P. A conformational preference parameter to predict helices in integral membrane proteins. Biochim Biophys Acta. 1986 Jan 30;869(2):197–214. [PubMed]
  • Rice CM, Fuchs R, Higgins DG, Stoehr PJ, Cameron GN. The EMBL data library. Nucleic Acids Res. 1993 Jul 1;21(13):2967–2971. [PMC free article] [PubMed]
  • Rohde K, Bork P. A fast, sensitive pattern-matching approach for protein sequences. Comput Appl Biosci. 1993 Apr;9(2):183–189. [PubMed]
  • Rothe B, Rothe B, Roggentin P, Schauer R. The sialidase gene from Clostridium septicum: cloning, sequencing, expression in Escherichia coli and identification of conserved sequences in sialidases and other proteins. Mol Gen Genet. 1991 Apr;226(1-2):190–197. [PubMed]
  • Sander C, Schneider R. The HSSP data base of protein structure-sequence alignments. Nucleic Acids Res. 1993 Jul 1;21(13):3105–3109. [PMC free article] [PubMed]
  • Savakis C, Doelz R. Contamination of cDNA sequences in databases. Science. 1993 Mar 19;259(5102):1677–1678. [PubMed]
  • Schuler GD, Altschul SF, Lipman DJ. A workbench for multiple alignment construction and analysis. Proteins. 1991;9(3):180–190. [PubMed]
  • Sor F, Chéret G, Fabre F, Faye G, Fukuhara H. Sequence of the HMR region on chromosome III of Saccharomyces cerevisiae. Yeast. 1992 Mar;8(3):215–222. [PubMed]
  • Tanaka S, Isono K. Correlation between observed transcripts and sequenced ORFs of chromosome III of Saccharomyces cerevisiae. Nucleic Acids Res. 1993 Mar 11;21(5):1149–1153. [PMC free article] [PubMed]
  • Tomoyasu T, Yuki T, Morimura S, Mori H, Yamanaka K, Niki H, Hiraga S, Ogura T. The Escherichia coli FtsH protein is a prokaryotic member of a protein family of putative ATPases involved in membrane functions, cell cycle control, and gene expression. J Bacteriol. 1993 Mar;175(5):1344–1351. [PMC free article] [PubMed]
  • Van Dyck E, Foury F, Stillman B, Brill SJ. A single-stranded DNA binding protein required for mitochondrial DNA replication in S. cerevisiae is homologous to E. coli SSB. EMBO J. 1992 Sep;11(9):3421–3430. [PMC free article] [PubMed]
  • Van Dyck L, Purnelle B, Skala J, Goffeau A. An 11.4 kb DNA segment on the left arm of yeast chromosome II carries the carboxypeptidase Y sorting gene PEP1, as well as ACH1, FUS3 and a putative ARS. Yeast. 1992 Sep;8(9):769–776. [PubMed]
  • Voytas DF, Boeke JD. Yeast retrotransposon revealed. Nature. 1992 Aug 27;358(6389):717–717. [PubMed]
  • Wickner RB, Fujimura T, Esteban R. Overview of double-stranded RNA replication in Saccharomyces cerevisiae. Basic Life Sci. 1986;40:149–163. [PubMed]
  • Yang W, Ni L, Somerville RL. A stationary-phase protein of Escherichia coli that affects the mode of association between the trp repressor protein and operator-bearing DNA. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5796–5800. [PMC free article] [PubMed]
  • Zhu G, Muller EG, Amacher SL, Northrop JL, Davis TN. A dosage-dependent suppressor of a temperature-sensitive calmodulin mutant encodes a protein related to the fork head family of DNA-binding proteins. Mol Cell Biol. 1993 Mar;13(3):1779–1787. [PMC free article] [PubMed]

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