Life with 6000 Genes

The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.

[1]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

[2]  B. Tye,et al.  Autonomously replicating sequences in Saccharomyces cerevisiae. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[3]  J. Broach,et al.  The Molecular biology of the yeast Saccharomyces : metabolism and gene expression , 1982 .

[4]  H. Feldmann,et al.  Ty1 and delta elements occur adjacent to several tRNA genes in yeast. , 1982, The EMBO journal.

[5]  R. Rothstein.  One-step gene disruption in yeast. , 1983, Methods in enzymology.

[6]  J. Yates,et al.  A vector that replicates as a plasmid and can be efficiently selected in B-lymphoblasts transformed by Epstein-Barr virus , 1985, Molecular and cellular biology.

[7]  Ronald W. Davis,et al.  Mitotic stability of yeast chromosomes: A colony color assay that measures nondisjunction and chromosome loss , 1985, Cell.

[8]  Paul Russell,et al.  Schizosaccharomyces pombe and saccharomyces cerevisiae: A look at yeasts divided , 1986, Cell.

[9]  R. Anwar,et al.  A 'hot-spot' for Ty transposition on the left arm of yeast chromosome III. , 1986, Nucleic acids research.

[10]  J R Johnston,et al.  Genealogy of principal strains of the yeast genetic stock center. , 1986, Genetics.

[11]  G. Fink,et al.  Pseudogenes in yeast? , 1987, Cell.

[12]  M. J. Charron,et al.  Molecular evolution of the telomere-associated MAL loci of Saccharomyces. , 1989, Genetics.

[13]  H. Y. Steensma,et al.  Enhanced meiotic recombination on the smallest chromosome of Saccharomyces cerevisiae. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[14]  M V Olson,et al.  Physical map of the Saccharomyces cerevisiae genome at 110-kilobase resolution. , 1991, Genetics.

[15]  J. Broach,et al.  Genome dynamics, protein synthesis, and energetics , 1991 .

[16]  Daniel F. Voytas,et al.  Yeast retrotransposon revealed , 1992, Nature.

[17]  B. Dujon,et al.  The complete DNA sequence of yeast chromosome III , 1992, Nature.

[18]  E J Louis,et al.  The structure and evolution of subtelomeric Y' repeats in Saccharomyces cerevisiae. , 1992, Genetics.

[19]  A. Sherman,et al.  Multiple sites for double‐strand breaks in whole meiotic chromosomes of Saccharomyces cerevisiae. , 1992, The EMBO journal.

[20]  AC Tose.  Cell , 1993, Cell.

[21]  P. Sharp,et al.  Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure. , 1993, Nucleic acids research.

[22]  G. Natsoulis,et al.  Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences , 1993, Cell.

[23]  F. Sherman,et al.  The gene clusters ARC and COR on chromosomes 5 and 10, respectively, of Saccharomyces cerevisiae share a common ancestry. , 1993, Journal of molecular biology.

[24]  M. Olson,et al.  Physical maps of the six smallest chromosomes of Saccharomyces cerevisiae at a resolution of 2.6 kilobase pairs. , 1993, Genetics.

[25]  O. Ozier-Kalogeropoulos,et al.  A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. , 1993, Nucleic acids research.

[26]  Hans Lehrach,et al.  High resolution cosmid and P1 maps spanning the 14 Mb genome of the fission yeast S. pombe , 1993, Cell.

[27]  S. Oliver,et al.  The eukaryotic genome: organisation and regulation. , 1993 .

[28]  P. T. Magee,et al.  Construction of an SfiI macrorestriction map of the Candida albicans genome , 1993, Journal of bacteriology.

[29]  G Muthukumar,et al.  Seripauperins of Saccharomyces cerevisiae: a new multigene family encoding serine-poor relatives of serine-rich proteins. , 1994, Gene.

[30]  M. Aigle,et al.  Complete DNA sequence of yeast chromosome II. , 1994, The EMBO journal.

[31]  C. Newlon,et al.  A physical comparison of chromosome III in six strains of Saccharomyces cerevisiae , 1994, Yeast.

[32]  Jonathan A. Cooper,et al.  Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII. , 1994, Science.

[33]  P. Philippsen,et al.  New heterologous modules for classical or PCR‐based gene disruptions in Saccharomyces cerevisiae , 1994, Yeast.

[34]  W. H. Mager,et al.  Global regulators of ribosome biosynthesis in yeast. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[35]  Terrance G. Cooper,et al.  Complilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae , 1995 .

[36]  R. Waterston,et al.  The Nematode Caenorhabditis elegans and Its Genome , 1995, Science.

[37]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[38]  E. Naumova,et al.  Genetic mapping of the α‐galactosidase MEL gene family on right and left telomeres of Saccharomyces cerevisiae , 1995, Yeast.

[39]  B. Dujon,et al.  Construction of a complete genomic library of Saccharomyces cerevisiae and physical mapping of chromosome XI at 3·7 kb resolution , 1995, Yeast.

[40]  E. Louis,et al.  The chromosome ends of Saccharomyces cerevisiae , 1995, Yeast.

[41]  H. Bussey,et al.  The nucleotide sequence of chromosome I from Saccharomyces cerevisiae. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[42]  E. Jacobs,et al.  A method for performing precise alterations in the yeast genome using a recycable selectable marker. , 1995, Nucleic acids research.

[43]  M. Yamazaki,et al.  Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae , 1995, Nature Genetics.

[44]  B. Barrell,et al.  The Saccharomyces cerevisiae genome on the World Wide Web. , 1996, Trends in genetics : TIG.

[45]  B. Dujon.  The yeast genome project: what did we learn? , 1996, Trends in genetics : TIG.

[46]  K. Heumann,et al.  Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X. , 1996, The EMBO journal.

[47]  S. Oliver.  A network approach to the systematic analysis of yeast gene function. , 1996, Trends in genetics : TIG.

[48]  A. Podtelejnikov,et al.  Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[49]  S. Oliver.  From DNA sequence to biological function , 1996, Nature.

[50]  Douglas E. Bassett,et al.  Yeast genes and human disease , 1996, Nature.

[51]  D. Hochstrasser,et al.  From Proteins to Proteomes: Large Scale Protein Identification by Two-Dimensional Electrophoresis and Arnino Acid Analysis , 1996, Bio/Technology.

[52]  R. Wilson,et al.  High throughput fingerprint analysis of large-insert clones. , 1997, Genome research.

[53]  S. Schreiber,et al.  A yeast genetic system for selecting small molecule inhibitors of protein-protein interactions in nanodroplets. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[54]  M. Boguski,et al.  Functional genomics: it's all how you read it. , 1997, Science.

[55]  S. Jackson,et al.  Identification of Saccharomyces cerevisiae DNA ligase IV: involvement in DNA double‐strand break repair , 1997, The EMBO journal.

[56]  J M Cherry,et al.  Molecular linguistics: extracting information from gene and protein sequences. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[57]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[58]  M. Olson,et al.  Multiple-complete-digest restriction fragment mapping: generating sequence-ready maps for large-scale DNA sequencing. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[59]  R. Weinberg,et al.  The catalytic subunit of yeast telomerase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[60]  J. Boeke,et al.  Small open reading frames: beautiful needles in the haystack. , 1997, Genome research.

[61]  R. Lester,et al.  Synthesis of Mannose-(inositol-P)2-ceramide, the Major Sphingolipid in Saccharomyces cerevisiae, Requires the IPT1 (YDR072c) Gene* , 1997, The Journal of Biological Chemistry.

[62]  S Povey,et al.  Dynamic molecular combing: stretching the whole human genome for high-resolution studies. , 1997, Science.

[63]  A. Nicolas,et al.  Clustering of meiotic double-strand breaks on yeast chromosome III. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[64]  D. Inzé,et al.  Efficient gene tagging in Arabidopsis thaliana using a gene trap approach. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[65]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[66]  G. Mahairas,et al.  Sequencing the human genome. , 1997, Science.

[67]  D. Glerum,et al.  COX15 Codes for a Mitochondrial Protein Essential for the Assembly of Yeast Cytochrome Oxidase* , 1997, The Journal of Biological Chemistry.

[68]  M. Roth,et al.  Transcription units as RNA processing units. , 1997, Genes & development.

[69]  J. McCarthy,et al.  Posttranscriptional Control of Gene Expression in Yeast , 1998, Microbiology and Molecular Biology Reviews.

[70]  J. Berg.  Genome sequence of the nematode C. elegans: a platform for investigating biology. , 1998, Science.

[71]  S. Jackson,et al.  Components of the Ku‐dependent non‐homologous end‐joining pathway are involved in telomeric length maintenance and telomeric silencing , 1998, The EMBO journal.

[72]  P. Agre,et al.  Aquaporins in Saccharomyces GENETIC AND FUNCTIONAL , 1998 .

[73]  Michael Y. Galperin,et al.  Analogous enzymes: independent inventions in enzyme evolution. , 1998, Genome research.

[74]  S Audic,et al.  Self-identification of protein-coding regions in microbial genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[75]  I. Jonassen,et al.  Predicting gene regulatory elements in silico on a genomic scale. , 1998, Genome research.

[76]  K. Kang,et al.  Deoxyhypusine Synthase Activity Is Essential for Cell Viability in the Yeast Saccharomyces cerevisiae * , 1998, The Journal of Biological Chemistry.

[77]  R. G. Kulka,et al.  Degradation signals for ubiquitin system proteolysis in Saccharomyces cerevisiae , 1998, The EMBO journal.

[78]  H. Bussey,et al.  The Candida albicans KRE9 gene is required for cell wall beta-1, 6-glucan synthesis and is essential for growth on glucose. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[79]  W. Tanner,et al.  New Potential Cell Wall Glucanases ofSaccharomyces cerevisiae and Their Involvement in Mating , 1998, Journal of bacteriology.

[80]  M W Simmen,et al.  Gene number in an invertebrate chordate, Ciona intestinalis. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[81]  P. Manivasakam,et al.  Nonhomologous End Joining during Restriction Enzyme-Mediated DNA Integration in Saccharomyces cerevisiae , 1998, Molecular and Cellular Biology.

[82]  Radhey S. Gupta.  Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes , 1998, Microbiology and Molecular Biology Reviews.

[83]  T. Bennett,et al.  The Saccharomyces cerevisiae RAD9Checkpoint Reduces the DNA Damage-Associated Stimulation of Directed Translocations , 1998, Molecular and Cellular Biology.

[84]  P. T. Magee,et al.  A physical map of chromosome 7 of Candida albicans. , 1998, Genetics.

[85]  R. Camerini-Otero,et al.  Sequence-specific ligation of DNA using RecA protein. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[86]  T. Kobayashi,et al.  Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I. , 1998, Genes & development.

[87]  Alex van Belkum,et al.  Short-Sequence DNA Repeats in Prokaryotic Genomes , 1998, Microbiology and Molecular Biology Reviews.

[88]  M. Mann,et al.  Analysis of the Saccharomyces Spindle Pole by Matrix-assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry , 1998, The Journal of cell biology.

[89]  J. Drake,et al.  Rates of spontaneous mutation. , 1998, Genetics.

[90]  Mario J. Borgnia,et al.  The Aquaporins, Blueprints for Cellular Plumbing Systems* , 1998, The Journal of Biological Chemistry.

[91]  M. Werner-Washburne,et al.  The Highly Conserved, Coregulated SNOand SNZ Gene Families in Saccharomyces cerevisiaeRespond to Nutrient Limitation , 1998, Journal of bacteriology.

[92]  J. Pronk,et al.  The Saccharomyces cerevisiae NDE1 andNDE2 Genes Encode Separate Mitochondrial NADH Dehydrogenases Catalyzing the Oxidation of Cytosolic NADH* , 1998, The Journal of Biological Chemistry.