THE YEAST GENOME: SYSTEMATIC ANALYSIS OF DNA SEQUENCE AND BIOLOGICAL FUNCTION

Genomics: Commercial Opportunities from a Scientific Revolution

Volumn , Issue , 2023, Pages 37-51

  Oliver, Stephen G ^a   Baganz, Frank ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

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EID: 0006617064     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781003423782-5     Document Type: Chapter

References (81)

1. Amberg, D. C., Botstein, D. and Beasley, E. M. (1995) Precise gene disruption in Saccharomyces cerevisiae by double fusion polymerase chain reaction. Yeast 11, 1275-1280.
2. Bartel, P. L., Roecklein, J. A., SenGupta, D. and Fields, S. (1996) A protein linkage map of Escherichia coli bacteriophage T7. Nature Genetics 12, 72-77.
3. Baganz, F., Hayes, A., Marren, D., Gardner, D. C. J. and Oliver, S.G. (1997a) Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae. Yeast 13, 1563-1573.
4. Baganz, F., Hayes, A., Farquhar, R., Gardner, D. C. J. and Oliver, S.G. (1997b) Quantitative analysis of yeast gene function using competition experiments in continuous culture. (In preparation.)
5. Baudin, A., Ozier-Kalogeropoulos, O., Denouel, A., Lacroute, F. and Cullin, C. (1993) A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Research 21, 3329-3330.
6. Baudin-Baillieu, A., Guillemet, E., Cullin, C. and Lacroute, F. (1997) Construction of a yeast strain deleted for the TRP1 promoter and coding region that enhances the efficiency of the polymerase chain reaction-disruption method. Yeast 13, 353-356.
7. Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F. et al. (1997) The complete genome sequence of Escherichia coli K-12 Science 277, 1453-1462.
8. Bork, P., Ouzounis, C. and Sander, C. (1994) From genome sequences to protein function. Current Opinion in Structural Biology 4, 393-403.
9. Brand, M. D. (1996) Top-down metabolic control analysis. Journal of Theoretical Biology 182, 351-360.
10. Burns, N., Grimwade, B., Ross-Macdonald, P. B., Choi, E. Y., Finberg, K., Roeder, G. S. and Snyder, M. (1994) Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes & Development 8, 1087-1105.
11. Cornish-Bowden, A. (1995) Metabolic control analysis in theory and practice. Advances in Molecular & Cellular Biology 11, 21-64.
12. Cubbitt, A. B., Heim, R., Adams, S. R., Boyd, A. E., Gross, L. A. and Tsien, R. Y. (1995) Understanding, improving and using green fluorescent proteins. Trends in Biochemical Sciences 20, 448-455.
13. Danhash, N., Gardner, D. C. J. and Oliver, S. G. (1991) Heritable damage to yeast caused by transformation. Bio/Technology 9, 179-182.
14. Dang, V. D., Valens, M., Bolotin-Fukuhara, M. and Daignan-Fornier, B. (1994) A genetic screen to isolate genes regulated by the yeast CCAAT-box binding protein Hap2p. Yeast 10, 1273-1283.
15. Delseny, M., Cooke, R., Comella, P., Wu, H.J., Raynal, M., and Grellet, F. (1997) The Arabidopsis thaliana genome project. Comptes Rendus Hebdomadaires des Seances, Academie des Sciences, Paris (III) 320, 589-599.
16. DeRisi, J. L., Vishwanath, R. I. and Brown, P. 0. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
17. Dujon, B. (1996) The yeast genome project: What did we learn? Trends in Genetics 12, 263-270.
18. Fell, D. A. (1992) Metabolic control analysis: a survey of its theoretical and experimental development. Biochemical Journal 286, 313-330.
19. Fey, S. J., Nawrocki, A., Larsen, M. R., Gorg, A., Roepstorff, P., Skews, G.N.,Williams, R. and Larsen, P. M. (1997) Proteome analysis of Saccharomyces cerevisiae: A methodological outline. Electrophoresis 18, 1361-1372.
20. Foury, F. (1997) Human genetic diseases: A cross-talk between man and yeast Gene 195, 1-10.
21. Fromont-Racine, M., Rain, J.C. and Legrain, P. (1997) Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nat. Genet. 16, 277-282.
22. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M. et al. (1996) Life with 6000 genes. Science 274, 546-567.
23. Goffeau A., Aert, R., Agostine-Carbone, A., Ahmed, A., Aigle, M., Alberghina, L., Albermann, K., Albers, M., Aldea, M., Alexandraki, D. et al. (1997) The yeast genome directory. Nature 387, 5-105.
24. Goodacre, R., Timmins, E. M., Rooney, P. J., Rowland, J. J. and Kell, D. B. (1996) Rapid identification of streptococcus and enterococcus species using diffuse reflectance-absorbency Fourier-transform Infrared-spectroscopy and artificial neural networks. FEMS Microbiology Letters 140, 233-239.
25. Güildener, U., Heck, S., Fiedler, T., Beinhauer, J. and Hegemann, J. H. (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Research 24, 2519-2524.
26. Haber, J.E. (1992) Mating-type gene switching in Saccharomyces cerevisiae. Trends in Genetics 8, 446-452.
27. Hammond, J. R. M., Lancashire, W. D., Meaden, P. G., Oliver, S. G. and Smith, N. A. (1994) Stability of genetically modified yeasts in relation to beer of good and consistent quality. MAFF (Ministry of Agriculture, Fisheries and Food; UK) Report 07/63M.
28. Heinrich, R. and Rapoport, T. (1974) A linear steady-state treatment of enzymatic chains. European Journal of Biochemistry 42, 89-95.
29. Hieter, P. and Boguski, M. (1997) Functional genomics: It's all how you read it. Science 278, 601-602.
30. Jia, Y. K., Becam, A. M. and Herbert, C. J. (1997) The CIT3 gene of Saccharomyces cerevisiae encodes a second mitochondrial isoform of citrate synthase. Molecular Microbiology 24, 53-59.
31. Jiminez, A. and Davis, J. (1980) Expression of transposable antibiotic resistance elements in Saccharomyces cerevisiae. Nature 287, 869-871.
32. Kaeser, H. and Bums, J. A. (1973) The control of flux. Symposia of the Society of Experimental Biology 27, 65-104.
33. Kai, A. J. (1997) Transcriptional regulation of genes encoding peroxisomal proteins in Saccharomyces cerevisiae. Ph.D. Thesis, University of Amsterdam.
34. Keogh, R. S., Seoghe, C. and Wolfe, K. H. (1997) Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces, and related fungi. Yeast (In press.)
35. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessieres, P., Bolotin, A., Borchert, S. et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390, 249-256.
36. Lalo, D., Stettler, S., Mariotte, S., Slonimski, P. P. and Thuriaux, P. (1993) 2 yeast chromosomes are related by a fossil duplication of their centromeric regions. Comptes Rendus Hebdomadaires des Seances, Academie des Sciences, Paris (III) 316, 367-373.
37. Langle-Rouault, F. and Jacobs, E. (1995) A method for performing precise alterations in the yeast genome using a recyclable selectable marker. Nucleic Acids Research. 23, 3079-308 I.
38. Leong-Morgenthaler, P., Oliver, S. G., Hottinger, H. and Soll, D. (1994) A Lactobacillus nifS-like gene suppresses an Escherichia coli transaminase B mutation. Biochimie 76, 45-49.
39. Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H. and Brown E. L. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14, 1675-1680.
40. Metha, P. and Christen, P (1993) Homology of pyridoxal-5' -phosphate-dependent aminotransferases with the cobC (cobalamin synthesis), nijS (nitrogen fixation), pabC (p-amino benzoate synthesis) and malY (abolishing endogenous induction of the maltose system) gene products. European Journal of Biochemistry 211, 373-376.
41. Mewes, H.W., Albermann, K., Bahr, M., Frishman, D., Gleissner, A., Hani, I. Heumann, K., Kleine, K., Maierl, A., Oliver, S.G., Pfeiffer F., and Zollner, A. (1997) Overview of the yeast genome. Nature 387 (Supp.), 7-65.
42. Mortimer, R. K. and Johnston, J. R. (1986) Genealogy of principal strains of the yeast genetic stock center. Genetics 113, 35-43.
43. Mortimer, R. K., Contopoulou, C. R. and King, J. S. (1992) Genetic and physical maps of Saccharomyces cerevisiae. Edition 11. Yeast 8, 817-902.
44. Naumann, D., Schultz, C. and Helm, D. (1996) What can infrared spectroscopy tell us about the structure and composition of intact bacterial cells? In Mantsch, H. H. and Chapmann, D. (Eds) Infrared spectroscopy of biomolecules. Wiley-Liss, New York, 279-310.
45. Niederberger, P., Prasad, R., Miozzari, G. and Kaeser, H. (1992) A strategy for increasing an in vivo flux by genetic manipulations - the tryptophan system of yeast. Biochemical Journal 287, 473-479.
46. Newlon, C. S. (1988) Yeast chromosome replication and segregation. Microbiolical Reviews 52, 568-601.
47. Oka, A., Sugisaki, H. and Takanami, M. (1981) Nucleotide sequence of the kanamycin resistance transposon Tn903. Journal of Molecular Biology 147, 217-226.
48. Olesen, J., Hahn, S. and Guarente, L. (1987) Yeast HAP2 and HAP3 activators bind to the CYCl activation site, UAS2, in an independent manner. Cell 51, 953-961.
49. Oliver, S.G., van der Aart, Q. J. M., Agostoni-Carbone, M. L., Aigle, M., Alberghina, L., Alexandraki, D., Antoine, G., Anwar, R., Ballesta, J.P. G., Benit, P. (1992) The complete DNA sequence of yeast chromosome III. Nature 357, 38-46.
50. Oliver, S.G., James, C. M., Gent M. E., and Indge, K. J. (1993) The great wall: sequencing the yeast genome. In Heslop-Harrison, J. S. and Flavell, R. B. (Eds), The Chromosome. J3ios Science Publishers, Oxford, 233-245.
51. Oliver, S. G. (1996a) From DNA sequence to biological function. Nature 379, 597-600.
52. Oliver, S. G. (1996b) A network approach to the systematic analysis of yeast gene function. Trends in Genetics 12, 241-242.
53. Oliver, S. G. (1997a) From gene to screen with yeast. Current Opinion in Genetics & Development 7, 405-409.
54. Oliver, S. G. (1997b) Yeast as a navigational aid in genome analysis. Microbiology- 143, 1483-1487
55. Olson, M.V. (1991) Genome structure and organization in Saccharomyces cerevisiae. In: The molecular and cellular biology of the yeast Saccharomyces cerevisiae, J. Broach, J. R., Pringle, and E.W. Jones (Eds), New York: Cold Spring Harbor Lab. Press, pp. 1-39.
56. Ouzounis, C. and Sander, C. (1993) Homology of the NifS family of proteins to a new class of pyridoxal phosphate-dependent enzymes. FEES Letters 322, 159-164.
57. Rashed, M. S., Oznand, P. T., Bucknall, M. P. and Little, D. (1995) Diagnosis of inborn errors of metabolism from bloodspots by acylcamitines and amino acids profiling using automated tandem mass spectrometry. Pediatric Research 38, 324-331.
58. Rieger, K.-J., Kaniak, A., Coppee, J.-Y., Aljinovic, G., Baudin-Baillieu, A., Orlowska, G., Gromadka, R., Groudinsky, o., di Rago, J.-P. and Slonimski, P.P.Large-scale phenotypic analysis - the pilot project on yeast chromosome III. Yeast (In Press).
59. Rohwer, J. M., Schuster, S. and Westerhoff, H. V. (1996) How to recognize monofunctional units in a metabolic system. Journal of Theoretical Biology 179, 213-228.
60. Ross-Macdonald, P., Erdman, S., Agarwal, S., Bums, N., Sheehan, A., Malczynski, M., Roeder, G. S. and Snyder, M. (1997) Large scale functional analysis of the Saccharomyces cerevisisae genome. Yeast 13, SlO.
61. Rothstein, R. J. (1983) One-step gene disruption in yeast. Methods in Enzymology 101, 3694-3698.
62. Sagliocco, F., Guillemot, J., Monribot, C., Capdevielle M., Perrot, M., Ferran, E., Ferrara, P. and Boucherie, H. (1996) Identification of proteins of the yeast protein map using genetically manipulated strains and peptide-mass fingerprinting. Yeast 12, 1519-1534.
63. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. O. and Davis, R. W. (1996) Parallel human genome analysis-microarray-based expression monitoring of 1000 genes. Proceedings of the National Academy of Science, USA 93, 10614-10619.
64. Shevchenko, A., Jense genome and proteome by mass spectrometry - large-scale identification of yeast proteins from 2-dimensional gels. Proceedings of the National Academy of Science, USA 93, 14440-14445.
65. Shoemaker, D. D., Lashkari, D. A., Morris, D., Mittmann, M. and Davis, R. W. (1996) Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nature Genetics 14, 450-456.
66. Smith, V., Botstein, D. and Brown, P. O. (1995) Genetic footprinting - a genomic strategy for determining a gene's function given its sequence. Proceedings of the National Academy of Science, USA 92, 6479-6483.
67. Smith, V., Chou, K. N., Lashkari, D., Botstein, D. and Brown, P. 0. (1996) Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science 274, 2069-2074.
68. Steiner, S. and Philippsen, P. (1994) Sequence and promoter analysis of the highly expressed TEF gene of the filamentous fungus Ashbya gossypii. Genetics 119, 249-260.
69. Sun, D. and Setlow, P. J. (1993) Cloning and nucleotide sequence of the Bacillus subtilis nadB gene and a nifS-like gene both of which are essential for NAD biosynthesis. Journal of Bacteriology 175, 1423-1432.
70. Teusink, B., Baganz, F., Westerhoff, H. V. and Oliver, S. G. (1998) Metabolic control analysis as a tool in the elucidation of the function of novel genes. In: Methods in Microbiology 26, 297-336.
71. Velculescu, V. E., Zhang, L., Vogelstein, B. and Kinzler, K. W. (1995) Serial analysis of gene expression. Science 38, 484-487.
72. Velculescu, V. E., Zhang, L., Vogelstein, J., Basrai, M. A., Bassett D. E. Jr, Hieter, P., Vogelstein, B. and Kinzler, K. W. (1996) Characterization of the yeast transcriptome. Cell 88, 243-251.
73. Wach, A., Brachat, A., Pohlmann, R. and Philippsen, P. (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10, 1793-1808.
74. Wach, A. (1996) PCR-synthesis of marker cassettes with long flanking homology regions for gene disruptions in S. cerevisiae. Yeast 12, 259-265.
75. Wach, A., Brachat, A., Alberti-Segui, C., Rebischung, C. and Philippsen, P. (1997) Heterologous HIS3 marker and GFP reporter modules for PCR-targeting in Saccharomyces cerevisiae. Yeast 13, 1065-1075.
76. Walmsley, R. M., Billinton, N. and Heyer, W.-D. (1997) Green fluorescent protein as a reporter for the DNA damage-induced gene RAD54 in Saccharomyces cerevisiae. Yeast (In press.)
77. Waterson, R. and Sulston, J. (1995) The genome of Caenorhabditis elegans. Proc. Nat. Acad. Sci. USA 92, 10836-10840.
78. Wilkins, M. R., Pasquali, C., Appel, R. D., Ou, K., Golaz, O., Sanchez, J.C., Yan, J. X., Gooley, A. A., Hughes, G., Humphrey-Smith, I. et al. (1996) From proteins to proteomes - large-scale protein identification by 2-dimensional electrophoreses and amino-acid-analysis. Bio/Technology 14, 61-65.
79. Wolfe, K. H. and Shields, D. C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713.
80. Yocum, R. (l 986) Genetic engineering of industrial yeasts. Proceedings Bio Expo 86, 17.
81. Zheng, L., White, R.H., Cash, V. L., Jack, R. F., and Dean, D.R. (1993) Cysteine desulfurase activity indicates a role for NifS I metallocluster biosynthesis. Proceedings of the National Academy of Science, USA 90, 2754-2758.