Global expression profiling of yeast treated with an inhibitor of amino acid biosynthesis, sulfometuron methyl

Physiological Genomics

Volumn 2000, Issue 3, 2000, Pages 83-92

  Jia, Melissa H ^a   Larossa, Robert A ^a   Lee, Jian Ming ^a,b   Rafalski, Antoni ^a   Derose, Ellen ^a   Gonye, Greg ^a   Xue, Zhixiong ^a  

^a DUPONT COMPANY   (United States)

^b HOFFMANN LA ROCHE INC   (United States)

Author keywords

DNA microarray; Metabolic regulation; Sulfometuron methyl

Indexed keywords

ACETOLACTATE SYNTHASE; AMINO ACID; DNA BINDING PROTEIN; ERGOSTEROL; FUNGAL PROTEIN; FUNGAL RNA; HERBICIDE; MESSENGER RNA; PROTEIN KINASE; SACCHAROMYCES CEREVISIAE PROTEIN; SULFOMETURON METHYL; SULFONYLUREA DERIVATIVE;

ARTICLE; BIOSYNTHESIS; DNA MICROARRAY; DOWN REGULATION; DRUG ANTAGONISM; DRUG EFFECT; FUNGAL GENE; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MICROBIOLOGICAL EXAMINATION; OPEN READING FRAME; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; UPREGULATION;

ACETOLACTATE SYNTHASE; AMINO ACIDS; DNA-BINDING PROTEINS; DOWN-REGULATION; ERGOSTEROL; FUNGAL PROTEINS; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; HERBICIDES; MICROBIAL SENSITIVITY TESTS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; PROTEIN KINASES; RNA, FUNGAL; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SULFONYLUREA COMPOUNDS; UP-REGULATION;

EID: 0034625801     PISSN: 15312267     EISSN: None     Source Type: Journal    
DOI: 10.1152/physiolgenomics.2000.3.2.83     Document Type: Article

References (59)

1. Alwine JC, Kemp DJ, Parker BA, and Stark GR. Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci USA 74: 5350-5354, 1977.
2. Benson PF and Fensom AH. Genetic Biochemical Disorders. New York: Oxford University Press, 1984, p. 274-305.
3. Bitter GA and Egan KM. Expression of heterologous genes in Saccharomyces cerevisiae from vectors utilizing the glyceraldehyde-3-phosphate dehydrogenase gene promoter. Gene 32: 263-274, 1984.
4. Bogosian G, Violand BN, Dorward-King EJ, Workman WE, Jung PE, and Kane JF. Biosynthesis and incorporation into protein of norleucine by Escherichia coli. J Biol Chem 264: 531-539, 1989.
5. Botstein D, Chervitz SA, and Cherry JM. Yeast as a model organism. Science 277: 1259-1260, 1997.
6. Boucherie H, Sagliocco F, Joubert R, Maillet I, Labarre J, and Perrot M. Two-dimensional gel protein database of Saccharomyces cerevisiae. Electrophoresis 17: 1683-1699, 1996.
7. Chervitz SA, Aravind L, Sherlock G, Ball CA, Koonin EV, Dwight SS, Harris MA, Dolinski K, Mohr S, Smith T, Weng S, Cherry JM, and Botstein D. Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science 282: 2022-2028, 1998.
8. Daignan-Fornier B and Fink GR. Coregulation of purine and histidine biosynthesis by the transcriptional activators BAS1 and BAS2. Proc Natl Acad Sci USA 89: 6746-6750, 1992.
9. Denis V, Boucherie H, Monribot C, and Daignan-Fornier B. Role of the myb-like protein bas1p in Saccharomyces cerevisiae: a proteome analysis. Mol Microbiol 30: 557-566, 1998.
10. DeRisi JL, Iye VR, and Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686, 1997.
11. Ehrenshaft M, Bilski P, Li MY, Chignell CF, and Daub ME. A highly conserved sequence is a novel gene involved in de novo vitamin B6 biosynthesis. Proc Natl Acad Sci USA 96: 9374-9378, 1999.
12. Engelberg D, Klein C, Martinetto H, Struhl K, and Karin M. The UV response involving the Ras signaling pathway and AP-1 transcription factors is conserved between yeast and mammals. Cell 77: 381-390, 1994.
13. Epelbaum S, LaRossa RA, Van Dyk T, Elkayam T, Chipman DM, and Barak Z. Branched-chain amino acid biosynthesis in Salmonella typhimurium: a quantitative analysis. J Bacterial 180: 4056-4067, 1998.
14. Falco SC and Dumas KS. Genetic analysis of mutants of Saccharomyces cerevisiae resistant to the herbicide sulfometuron methyl. Genetics 109: 21-35, 1985.
15. s is positively regulated by ppGpp. J Bacteriol 175: 7982-7989, 1993.
16. Goffeau A, Barrel BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, and Oliver SG. Life with 6000 genes. Science 25: 546, 563-567, 1996.
17. Guarente L. Messenger RNA transcription and its control in Saccharomyces cerevisiae. In: The Molecular and Cellular Biology of the Yeast Saccharomyces, edited by Jones EW, Pringle JR, and Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1992, p. 49-98.
18. Guetsova ML, Lecoq K, and Daignan-Fornier B. The isolation and characterization of Saccharomyces cerevisiae mutants that constitutively express purine biosynthetic genes. Genetics 147: 383-397, 1997.
19. Hardwick JS, Kuruvilla FG, Tong JK, Shamji AF, and Schreiber SL. Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. Proc Natl Acad Sci USA 96: 14866-14870, 1999.
20. Hereford LM and Rosbash M. Number and distribution of polyadenylated RNA sequences in yeast. Cell 10: 453-462, 1977.
21. Hinnebusch AG and Fink GR. Positive regulation in the general amino acid control of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 80: 5374-5378, 1983.
22. Hinnebusch AG. General and pathway-specific regulatory mechanisms controlling the synthesis of amino acid biosynthetic enzymes in Saccharomyces cerevisiae. In: The Molecular and Cellular Biology of the Yeast Saccharomyces, edited by Jones EW, Pringle JR, and Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1992, p. 319-414.
23. Hodges PE, McKee AHZ, Davis BP, Payne WE, and Garrels JL. Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data. Nucleic Acids Res 27: 69-73, 1999.
24. Iraqui I, Vissers S, Bernard F, de Craene JO, Boles E, Urrestarazu A, and Andre B. Amino acid signaling in Saccharomyces cerevisiae: a permease-like sensor of external amino acids and F-Box protein grr1p are required for transcriptional induction of the AGP1 gene, which encodes a broad-specificity amino acid permease. Mol Cell Biol 19: 989-1001, 1999.
25. Ito H, Jukuda Y, Murata K, and Kimura A. Transformation of intact yeast cells treated with alkaline cations. J Bacteriol 153: 163-168, 1983.
26. Jelinsky SA, and Samson LD. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc Natl Acad Sci USA 96: 1486-1491, 1999.
27. Jones EW and Fink GR. Regulation of amino acid and nucleotide biosynthesis in yeast. In: The Molecular Biology of the Yeast Saccharomyces, edited by Strathern JN, Jones EW, and Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1982, p. 181-299.
28. Keaveney M and Struhl K. Activator-mediated recruitment of the RNA polymerase II machinery is the predominant mechanism for transcriptional activation in yeast. Mol Cell 1: 917-924, 1998.
29. s subunit of RNA polymerase in Escherichia coli. J Bacteriol 177: 4676-4680, 1995.
30. LaRossa RA and Falco SC. Amino acid biosynthetic enzymes as targets of herbicides. Trends Biotech 2: 158-161, 1984.
31. LaRossa RA and Scholss JV. The sulfonylurea herbicide sulfometuron methyl is an extremely potent and selective inhibitor of acetolactate synthase in Salmonella typhimurium. J Biol Chem 259: 8753-8757, 1984.
32. LaRossa RA and Van Dyk TK. Utilization of sulfometuron methyl, an acetolactate synthase inhibitor, in molecular biological and metabolic studies of plants and microbes. Methods Enzymol 166: 97-107, 1988.
33. LaRossa RA and Van Dyk TK. Metabolic mayhem caused by 2-ketoacid imbalance. Bioessays 7: 125-130, 1989.
34. LaRossa RA, Van Dyk T, and Smulski DR. Toxic accumulation of a-ketobutyrate caused by inhibition of the branched-chain amino acid biosynthetic enzyme acetolactate synthase in Salmonella typhimurium. J Bacteriol 169: 1372-1378, 1987.
35. Lees ND, Skaggs B, Kirsch DR, and Bard M. Cloning of the late genes in the ergosterol biosynthetic pathway of Saccharomyces cerevisiae: a review. Lipids 30: 221-226, 1995.
36. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, and Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680, 1996.
37. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE Jr, Hartwell LH, Brown PO, and Friend SH. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med 4: 1293-1301, 1998.
38. Matsuura A, Tsukada M, Wada Y, and Ohsumi Y. Apglp, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae. Gene 192: 245-250, 1997.
39. Measday V, Moore L, Retnakaran R, Lee J, Donoviel M, Neiman AM, and Andrews B. A family of cyclin-like proteins that interact with the Pho85 cyclin-dependent kinase. Mol Cell Biol 17: 1212-1223, 1997.
40. Mountain HA, Bystrom AS, Larsen JL, and Korch C. Four major transcriptional responses in the methionine/threonine biosynthetic pathway of Saccharomyces cerevisiae. Yeast 7: 781-791, 1991.
41. O'Farrell PH. High resolution two dimensional electrophoresis of proteins. J Biol Chem 250: 4007-4021, 1975.
42. Osmani AH, May GS, and Osmani SA. The extremely conserved pyroA gene of Aspergillus nidulans is required for pyridoxine synthesis and is required indirectly for resistance to photosensitizers. J Biol Chem 274: 23565-23569, 1999.
43. Padilla PA, Fuge EK, Crawford ME, Errett A, and Werner-Washburne M. The highly conserved, coregulated SNO and SNZ gene families in Saccharomyces cerevisiae respond to nutrient limitation. J Bacteriol 180: 5718-5726, 1998.
44. Paltauf F, Kohlwein SD, Henry SA. Regulation and compartmentalization of lipid synthesis in yeast. In: The Molecular and Cellular Biology of the Yeast Saccharomyces, edited by Jones EW, Pringle JR, and Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1992, p. 415-500.
45. Philippsen P, Stotz A, and Scherf C. DNA of Saccharomyces cerevisiae. Methods Enzymol 194: 169-182, 1991.
46. Ray TB. The mode of action of chlorsulfuron: the lack of direct inhibition of plant DNA synthesis. Pestic Biochem Physiol 18: 262-266, 1982.
47. Ray TB. Site of action of chlorsulfuron. Plant Physiol 75: 827-831, 1984.
48. Rolfes RJ and Hinnebusch AG. Translation of the yeast transcriptional activator GCN4 is stimulated by purine limitation: implications for activation of the protein kinase GCN2. Mol Cell Biol 13: 5099-5111, 1993.
49. Schena M, Shalon D, Davis RW, and Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470, 1995.
50. Sherman F, Hicks JB, and Fink GR. Methods of Yeast Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 1986.
51. Sikorski RS and Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122: 19-27, 1989.
52. Straub M, Bredschneider M, and Thumm M. AUT3, a serine/threonine kinase gene, is essential for autophagocytosis in Saccharomyces cerevisiae. J Bacteriol 179: 3875-3883, 1997.
53. Struhl K. Yeast transcriptional regulatory mechanisms. Annu Rev Genet 29: 651-674, 1995.
54. Umbarger HE. Biosynthesis of branched-chain amino acids. In: Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, edited by Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Magasanik B, Reznikoff WS, Riley M, Schaechter M, and Umbarger HE. Washington, DC: ASM, 1996, vol. 1, p. 442-457.
55. Van Dyk T, Ayers BL, Morgan RW, and LaRossa RA. Constricted flux through the branched-chain amino acid biosynthetic enzyme acetolactate synthase triggers elevated expression of genes regulated by rpoS and internal acidification. J Bacteriol 180: 785-792, 1998.
56. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE Jr, Hieter P, Vogelstein B, and Kinzler KW. Characterization of the yeast transcriptome. Cell 88: 243-251, 1997.
57. Wei Y, Lee JM, Richmond CS, Blattner FR, Rafalski JJA, and LaRossa RA. High-density microarray mediated gene expression profiling of Escherichia coli. Proc Natl Acad Sci USA In press.
58. Wodicka L, Dong H, Mittmann M, Ho MH, and Lockhart DJ. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol 15: 1359-1367, 1997.
59. Zaman Z, Bowman SB, Kornfeld GD, Brown AJP, and Dawes IW. Transcription factor GCN4 for control of amino acid biosynthesis also regulates the expression of the gene for lipoamide dehydrogenase. Biochem J 340: 855-862, 1999.