Sequencing and functional analysis of the yeast genome

Acta Biochimica Polonica

Volumn 45, Issue 3, 1998, Pages 627-643

  Zagulski, Marek ^a   Herbert, Christopher J ^b   Rytka, Joanna ^a  

^a INSTITUTE OF BIOCHEMISTRY AND BIOPHYSICS   (Poland)

^b CENTRE DE GÉNÉTIQUE MOLÉCULAIRE   (France)

Author keywords

Gene function; Genome sequence; Genomics; Saccharomyces cerevisiae; Yeast

Indexed keywords

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

GENETICS; GENOME; REVIEW; SACCHAROMYCES CEREVISIAE; SUPPRESSOR GENE;

GENES, SUPPRESSOR; GENOME, FUNGAL; SACCHAROMYCES CEREVISIAE;

EID: 0032238937     PISSN: 0001527X     EISSN: None     Source Type: Journal    
DOI: 10.18388/abp.1998_4201     Document Type: Review

References (52)

1. Barton, A.B. & Kaback, D.B. (1994) Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: Analysis of the genes in the FUN38-MAK16-SPO7 region. J. Bacteriol. 176, 1872-1880.
2. Becam, A.-M., Cullin, C., Grzybowska, E., Lacroute, F., Nasr, F., Ozier-Kalogeropoulos, O., Pałucha, A., Słonimski, P.P., Zagulski, M. & Herbert, C.J. (1994) The sequence of 29.7 kb from right arm of chromosome II reveals 13 complete open reading frames, of which ten correspond to new genes. Yeast 10, S1-S11.
3. Bennetzen, J.L. & Hall, B.D. (1982) Codon selection in yeast. J. Biol. Chem. 257, 3026-3031.
4. Boeke, J.D., LaCroute, F. & Fink, G.R. (1984) A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-Fluoro-orotic acid resistance. Mol. Gen. Genet. 197, 345-346.
5. Botstein, D. & Cherry, J.M. (1997) Molecular linguistics: Extracting information from gene and protein sequences. Proc. Natl. Acad. Sci. U.S.A. 94, 5506-5507.
6. Boucherie, H., Dujardin, G., Kermorgant, M., Monribot, C., Slonimski, P. & Perrot, M. (1995) Two-dimensional protein map of Saccharomyces cerevisiae: Construction of a gene- protein index. Yeast 11, 601-613.
7. Burns, N., Grimwade, B., Ross-Macdonald, P.B., Choi, E.Y., Finberg, K., Roeder, G.S. & Snyder, M. (1994) Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8, 1087-1105.
8. DeRisi, J.L., Iyer, V.R. & Brown, P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
9. Feng, D.F. & Doolittle, R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351-360.
10. Fields, S. & Song, O-k. (1989) A novel genetic system to detect protein-protein interactions. Nature 340, 245-246.
11. Fields, S. & Sternglanz, R. (1994) The two-hybrid system: An assay for protein-protein interactions. Trends Genet. 10, 286-292.
12. Greener, A., Callahan, M. & Jerpseth, B.A. (1997) An efficient random mutagenesis technique using an E. coli mutator strain. Mol. Biotechnol. 7, 189-195.
13. Gromadka, R., Góra, M., Zielenkiewicz, U., Słonimski, P.P. & Rytka, J. (1996a) Subtelomeric duplications in Saccharomyces cerevisiae chromosomes III and XI: Topology, arrangements, correction of sequence and strain- specific polymorphism. Yeast 12, 583-591.
14. Gromadka, R., Kaniak, A., Słonimski, P.P. & Rytka, J. (1996b) A novel cross phylum of proteins comprises a KRR1 (YCL 059c) gene which is essential for viability of Saccharomyces cerevisiae. Gene 171, 27-32.
15. Guarente, L. & Ptashne, M. (1981) Fusion of Escherichia coli lacZ to the cytochrome c gene of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 78, 2199-2203.
16. Guarente, L. (1983) Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. Methods Enzymol. 101, 181-191.
17. Hinnebusch, A.G. & Fink, G.R. (1983) Positive regulation in the general amino acid control of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 80, 5374-5378.
18. Huffaker, T.C., Hoyt, M.A. & Botstein, D. (1987) Genetic analysis of the yeast cytoskeleton. Annu. Rev. Genet. 21, 259-284.
19. Jimenez, A. & Davies, J. (1980) Expression of a transposable antibiotic resistance element in Saccharomyces. Nature 287, 869-871.
20. Kaback, D.B., Angerer, L.M. & Davidson, N. (1979) Improved methods for the formation and stabilization of R-loops. Nucleic Acids Res. 6, 2499-2317.
21. Kahn, P. (1995) From genome to proteome: Looking at a cell's proteins. Science 270, 369-370.
22. Karlin, S. & Altschul, S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. U.S.A. 87, 2264-2268.
23. Kucharczyk, R., Zagulski, M., Rytka, J. & Herbert, C.J. (1998) The yeast gene YJR025c encodes a 3-hydroxyanthranilic acid dioxygenase and is involved in nicotinic acid biosynthesis. FEBS Lett. 424, 127-130.
24. Mewes, H.W., Albermann, K., Bahr, M., Frishman, D. et al. (1997) Overview of the yeast genome. Nature (Suppl.) 387, 7-65.
25. Oka, A., Sugisaki, H. & Takanami, M. (1981) Nucleotide sequence of the kanamycin resistance transposon Tn903. J. Mol. Biol. 147, 217-226.
26. Park, E.C., Finley, D. & Szostak, J.W. (1992) A strategy for the generation of conditional mutations by protein destabilization. Proc. Natl. Acad. Sci. U.S.A. 89, 1249-1252.
27. Pearson, W.R. & Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 85, 2444-2448.
28. Reisdorf, P., Maarse, A.C. & Daignan-Fornier, B. (1993) Epitope-tagging vectors designed for yeast. Curr. Genet. 23, 181-183.
29. Richard, G.F., Fairhead, C. & Dujon, B. (1997) Complete transcriptional map of yeast chromosome XI in different life conditions. J. Mol. Biol. 268, 303-321.
30. Rieger, K.-J., Kaniak, A., Coppee, J.-Y., Aljinovic, G., Baudin-Baillieu, A., Orłowska, G., Gromadka, R., Groudinsky, O., Di Rago, J.-P. & Słonimski, P.P. (1997) Large scale phenotypic analysis. The pilot project on yeast chromosome III. Yeast 13, 1547-1562.
31. Rine, J. (1991) Gene overexpression in studies of Saccharomyces cerevisiae. Methods Enzymol. 194, 239-251.
32. Rose, M.D., Casadaban, M.J. & Botstein, D. (1981) Yeast genes fused to beta-galactosidase in Escherichia coli can be expressed normally in yeast. Proc. Natl. Acad. Sci. U.S.A. 78, 2460-2464.
33. Rose, M.D. & Fink, G.R. (1987) KAR 1, a gene required for function of both intracellular and extracellular microtubules in yeast. Cell 48, 1047-1060.
34. Schena, M., Picard, D. & Yamamoto, K.R. (1991) Vectors for constitutive and inducible gene expression in yeast. Methods Enzymol. 194, 389-398.
35. Shevchenko, A., Jensen, O.N., Podtelejnikov, A.V., Sagliocco, F., Wilm, M., Vorm, O., Mortensen, P., Shevchenko, A., Boucherie, H. & Mann, M. (1996) Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. U.S.A. 93, 14440-14445.
36. Shoemaker, D.D., Lashkari, D.A., Morris, D., Mittmann, M. & Davis, R.W. (1996) Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy Nature Genet. 14, 450-456.
37. Slonimski, P.P. & Brouillet, S. (1993) A data-base of chromosome III of Saccharomyces cerevisiae. Yeast 9, 941-1029.
38. Smith, R.C. & Waterman, M.S. (1981) Comparison of bio-sequences. Adv. Appl. Math. 2, 482-489.
39. Smith, V., Chou, K.N., Lashkari, D., Botstein, D. & Brown, P.O. (1996) Functional analysis of the genes of yeast chromosome V by genetic foot- printing. Science 274, 2069-2074.
40. Spee, J.H., de Vos, W.M. & Kuipers, O.P. (1993) Efficient random mutagenesis method with adjustable mutation frequency by use of PCR and dITP. Nucleic Acids Res. 21, 777-778.
41. Steiner, S. & Philippsen, P. (1994) Sequence and promoter analysis of the highly expressed TEF gene of the filamentous fungus Ashbya gossypii. Mol. Gen. Genet. 242, 263-271.
42. Struhl, K. (1986) Constitutive and inducible Saccharomyces cerevisiae promoters: Evidence for two distinct molecular mechanisms. Mol. Cell Biol. 6, 3847-3853.
43. Wach, A. (1996) PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12, 259-265.
44. Wach, A., Brachat, A., Pohlmann, R. & Philippsen, P. (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10, 1793-1808.
45. Wach, A., Brachat, A., Alberti-Segui, C., Rebischung, C. & Philippsen, P. (1997) Heterologous HIS3 marker and GFP reporter modules for PCR-targeting in Saccharomyces cerevisiae. Yeast 13, 1065-1075.
46. Wilkins, M.R., Sanchez, J.C., Gooley, A.A., Appel, R.D., Humphery-Smith, I., Hochstrasser, D.F. & Williams, K.L. (1996) Progress with proteome projects: Why all proteins expressed by a genome should be identified and how to do it Biotechnol. Genet. Eng. Rev. 13, 19-50.
47. Vallen, E.A., Ho, W., Winey, M. & Rose, M.-D. (1994) Genetic interactions between CDC31 and KAR1, two genes required for duplication of the microtubule organizing center in Saccharomyces cerevisiae. Genetics 137, 407-422.
48. Velculescu, V.E., Zhang, L., Vogelstein, B. & Kanzler, K.W. (1995) Serial analysis of gene expression. Science 270, 484-487.
49. Velculescu, V.E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M.A., Bassett, D.E., Jr., Hieter, P., Vogelstein, B. & Kinzler, K.W. (1997) Characterization of the yeast transcriptome. Cell 88, 243-251.
50. Yoshikawa, A. & Isono, K. (1990) Chromosome III of Saccharomyces cerevisiae: An ordered clone bank, a detailed restriction map and analysis of transcripts suggest the presence of 160 genes. Yeast 6, 383-401.
51. Yoshikawa, A. & Isono, K. (1991) Construction of an ordered clone bank and systematic analysis of the whole transcripts of chromosome VI of Saccharomyces cerevisiae. Nucleic Acids Res. 19, 1189-1195.
52. Zagulski, M., Babinska, B., Gromadka, R., Migdalski, A., Rytka, J., Sulicka, J. & Herbert, C.J. (1995) The sequence of 24.3 kb from chromosome X reveals 5 complete open reading frames all of which correspond to new genes, and a tandem insertion of a Ty1 transposon. Yeast 11, 1179-1186.