Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae

OMICS A Journal of Integrative Biology

Volumn 7, Issue 2, 2003, Pages 193-202

  Förster, Jochen ^a   Famili, Iman ^b   Palsson, Bernhard Ø ^b   Nielsen, Jens ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGY; COMPARATIVE STUDY; COMPUTER PROGRAM; FUNGUS GROWTH; FUNGUS MUTANT; GENE CONTROL; GENE DELETION; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; GENOME; GENOME ANALYSIS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; METHODOLOGY; NONHUMAN; OPEN READING FRAME; PHENOTYPE; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; STANDARD; STOICHIOMETRY; STRUCTURAL GENE;

FUNGI; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0042816453     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/153623103322246584     Document Type: Article

References (48)

1. BARD, M., WOODS, R.A., BARTON, D.H., et al. (1977). Sterol mutants of Saccharomyces cerevisiae: chromatographic analyses. Lipids 12, 645-654.
2. BASSINGTHWAIGHTE, J.B. (2000). Strategies for the physiome project. Ann Biomed Eng 28, 1043-1058.
3. BAXEVANIS, A.D. (2002). The molecular biology database collection: 2002 update. Nucleic Acids Res 30, 1-12.
4. BELL, W., SUN, W., HOHMANN, S., et al. (1998). Composition and functional analysis of the Saccharomyces cerevisiae trehalose synthase complex. J Biol Chem 273, 33311-33319.
5. BIRNER, R., BURGERMEISTER, M., SCHNEITER, R., et al. (2001). Roles of phosphatidylethanolamine and of its several biosynthetic pathways in Saccharomyces cerevisiae. Mol Biol Cell 12, 997-1007.
6. BOLES, E., SCHULTE, F., MIOSGA, T., et al. (1997). Characterization of a glucose-repressed pyruvate kinase (Pyk2p) in Saccharomyces cerevisiae that is catalytically insensitive to fructose-1,6-bisphosphate. J Bacteriol 179, 2987-2993.
7. BOUROT, S., and KARST, F. (1995). Isolation and characterization of the Saccharomyces cerevisiae SUT gene involved in sterol uptake. Gene 165, 97-102.
8. BRENT, R. (2000). Genomic biology. Cell 100, 169-183.
9. CHERRY, J.M., ADLER, C., BALL, C., et al. (1998). SGD: Saccharomyces genome database. Nucleic Acids Res 26, 73-79.
10. CIRIACY, M., and BREITENBACH, I. (1979). Physiological effects of seven different blocks in glycolysis in Saccharomyces cerevisiae. J Bacteriol 139, 152-160.
11. COVERT, M.W., and PALSSON, B.Ø. (2002). Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 277, 28058-28064.
12. COVERT, M.W., SCHILLING, C.H., FAMILI, I., et al. (2001). Metabolic modeling of microbial strains in silico. Trends Biochem Sci 26, 179-186.
13. DAUM, G., LEES, N.D., BARD, M., et al. (1998). Biochemistry, cell biology and molecular biology of lipids of Saccharomyces cerevisiae. Yeast 14, 1471-1510.
14. DAUM, G., TULLER, G., NEMEC, T., et al. (1999). Systematic analysis of yeast strains with possible defects in lipid metabolism. Yeast 15, 601-614.
15. DICKINSON, J.R. (1998). Nitrogen metabolism. In The Metabolism and Molecular Physiology of Saccharomyces cerevisiae. J.R. Dickinson and M. Schweizer, eds. (Taylor & Francis, London), pp. 57-77.
16. EDWARDS, J.S., and PALSSON, B.Ø. (2000). The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97, 5528-5533.
17. EDWARDS, J.S., RAMAKRISHNA, R., SCHILLING, C.H., et al. (1999). Metabolic flux balance analysis. In Metabolic Engineering, S.Y. Lee and E.T. Papoutsakis, eds. (Marcel Dekker, New York), pp. 13-57.
18. FAMILI, I., FÖRSTER, J., FU, P., et al. (2003). Computing phenotypes from a reconstructed genome-scale metabolic network for Saccharomyces cerevisiae (submitted).
19. FÖRSTER, J., FAMILI, I., FU, P., et al. (2003). Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13, 244-253.
20. FUKUCHI, T., NIKAWA, J., KIMURA, N., et al. (1993). Isolation, overexpression and disruption of a Saccharomyces cerevisiae YNK gene encoding nucleoside diphosphate kinase. Gene 129, 141-146.
21. GUETSOVA, M.L., LECOQ, K., and DAIGNAN-FORNIER, B. (1997). The isolation and characterization of Saccharomyces cerevisiae mutants that constitutively express purine biosynthetic genes. Genetics 147, 383-397.
22. 28-14C]ergosta-5,7-dien-3 beta-o with the mutant. J Biochem (Tokyo) 94, 501-510.
23. IDEKER, T., GALITSKI, T., and HOOD, L. (2001). A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2, 343-372.
24. JOSHI, A., and PALSSON, B.Ø. (1989). Metabolic dynamics in the human red cell. Part I - A comprehensive kinetic model. J Theor Biol 141, 515-528.
25. KITANO, H. (2000). Perspectives on systems biology. New Generation Comput 18, 199-216.
26. LACROUTE, F. (1968). Regulation of pyrimidine biosynthesis in Saccharomyces cerevisiae. J Bacteriol 95, 824-832.
27. LOPEZ, F., LEUBE, M., GIL-MASCARELL, R., et al. (1999). The yeast inositol monophosphatase is a lithium- and sodium-sensitive enzyme encoded by a non-essential gene pair. Mol Microbiol 31, 1255-1264.
28. MEWES, H.W., ALBERMANN, K., HEUMANN, K., et al. (1997). MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Res 25, 28-30.
29. MITCHELL, A.P. (1985). The GLN1 locus of Saccharomyces cerevisiae encodes glutamine synthetase. Genetics 111, 243-258.
30. MURRAY, M., and GREENBERG, M.L. (2000). Expression of yeast INM1 encoding inositol monophosphatase is regulated by inositol, carbon source and growth stage and is decreased by lithium and valproate. Mol Microbiol 36, 651-661.
31. MÜLLER, S., and ENTIAN, K.-D. (1997). Enolase. In Yeast Sugar Metabolism. F.K. Zimmerman and K.-D. Entian, eds. (Technomic Publishing, Lancaster, U.K.), pp. 157-170.
32. NIELSEN, J. (1998). Metabolic engineering: techniques for analysis of targets for genetic manipulations. Biotechnol Bioeng 58, 125-132.
33. NIELSEN, J., and OLSSON, L. (2002). An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology. FEMS Yeast Res 2, 175-181.
34. PALSSON, B.Ø. (2000). The challenges of in silico biology. Nat Biotechnol 18, 1147-1150.
35. PARKS, L.W., CROWLEY, J.H., LEAK, F.W., et al. (1999). Use of sterol mutants as probes for sterol functions in the yeast, Saccharomyces cerevisiae. Crit Rev Biochem Mol Biol 34, 399-404.
36. PERSSON, B.L., PETERSSON, J., FRISTEDT, U., et al. (1999). Phosphate permeases of Saccharomyces cerevisiae: structure, function and regulation. Biochim Biophys Acta 1422, 255-272.
37. SCHILLING, C.H., COVERT, M.W., FAMILI, I., et al. (2002). Genome-scale metabolic models of less-characterized organisms - a case study for Helicobacter pylori. J Bacteriol 184, 4582-4593.
38. SCHWEIZER, M. (1998). Lipids and membranes. In The Metabolism and Molecular Physiology of Saccharomyces cerevisiae. J.R. Dickinson and M. Schweizer, eds. (Taylor & Francis, London), pp. 79-155.
39. SILVE, S., LEPLATOIS, P., JOSSE, A., et al. (1996). The immunosuppressant SR 31747 blocks cell proliferation by inhibiting a steroid isomerase in Saccharomyces cerevisiae. Mol Cellular Biol 16, 2719-2727.
40. STÜCKRATH, I., LANGE, H.C., KOTTER, P., et al. (2002). Characterization of null mutants of the glyoxylate cycle and gluconeogenic enzymes in S. cerevisiae through metabolic network modeling verified by chemostat cultivation. Biotechnol Bioeng 77, 61-72.
41. SUMMERS, E.F., LETTS, V.A., MCGRAW, P., et al. (1988). Saccharomyces cerevisiae cho2 mutants are deficient in phospholipid methylation and cross-pathway regulation of inositol synthesis. Genetics 120, 909-922.
42. THOMAS, D., and SURDIN-KERJAN, Y. (1997). Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 61, 503-532.
43. TOMITA, M., HASHIMOTO, K., TAKAHASHI, K., et al. (1999). E-CELL: software environment for whole-cell simulation. Bioinformatics 15, 72-84.
44. TROTTER, P.J., WU, W.I., PEDRETTI, J., et al. (1998). A genetic screen for aminophospholipid transport mutants identifies the phosphatidylinositol 4-kinase, STT4p, as an essential component in phosphatidylserine metabolism. J Biol Chem 273, 13189-13196.
45. VAN DEN BERG, M.A., and STEENSMA, H.Y. (1995). ACS2, a Saccharomyces cerevisiae gene encoding acetyl-coenzyme A synthetase, essential for growth on glucose. Eur J Biochem 231, 704-713.
46. WHITE, W.H., GUNYUZLU, P.L., and TOYN, J.H. (2001). Saccharomyces cerevisiae is capable of de novo pantothenic acid biosynthesis involving a novel pathway of beta-alanine production from spermine. J Biol Chem 276, 10794-10800.
47. WINZELER, E.A., SHOEMAKER, D.D., ASTROMOFF, A., et al. (1999). Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906.
48. ZWEYTICK, D., HRASTNIK, C., KOHLWEIN, S.D., et al. (2000). Biochemical characterization and subcellular localization of the sterol C-24(28) reductase, erg4p, from the yeast Saccharomyces cerevisiae. FEBS Lett 470, 83-87.