Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids

Molecular Microbiology

Volumn 53, Issue 2, 2004, Pages 599-611

  Shivers, Robert P ^a   Sonenshein, Abraham L ^a  

^a TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; BRANCHED CHAIN AMINO ACID; DEOXYRIBONUCLEASE I; DNA; GUANOSINE TRIPHOSPHATE; PROTEIN CODY; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; BINDING AFFINITY; CONTROLLED STUDY; GEL MOBILITY SHIFT ASSAY; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN DNA BINDING; PROTEIN INTERACTION; PROTEIN TARGETING; REGULATORY MECHANISM;

ADAPTATION, PHYSIOLOGICAL; AMINO ACIDS, BRANCHED-CHAIN; ARTIFICIAL GENE FUSION; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BASE SEQUENCE; BETA-GALACTOSIDASE; DNA FOOTPRINTING; DNA-BINDING PROTEINS; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ENZYME ACTIVATORS; GENE EXPRESSION REGULATION, BACTERIAL; GENES, REPORTER; GUANOSINE TRIPHOSPHATE; ISOLEUCINE; LAC OPERON; MOLECULAR SEQUENCE DATA; OPERON; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; REPRESSOR PROTEINS; VALINE;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); POSIBACTERIA;

EID: 3242880574     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2004.04135.x     Document Type: Article

References (42)

1. Atkinson, M.R., Wray, L.V., Jr, and Fisher, S.H. (1990) Regulation of histidine and proline degradation enzymes by amino acid availability in Bacillus subtilis. J Bacteriol 172: 4758-4765.
2. Atkinson, M.R., Wray, L.V., Jr, and Fisher, S.H. (1993) Activation of the Bacillus subtilis hut operon at the onset of stationary growth phase in nutrient sporulation medium results primarily from the relief of amino acid repression of histidine transport. J Bacteriol 175: 4282-4289.
3. Belitsky, B.R. (2002) Biosynthesis of amino acids of the glutamate and aspartate families, alanine, and polyamines. In Bacillus subtilis and its Closest Relatives: from Genes to Cells. Sonenshein, A.L., Hoch, J.A., and Losick, R. (eds). Washington, DC: American Society for Microbiology Press, pp. 203-232.
4. Bergara, F., Ibarra, C., Iwamasa, J., Patarroyo, J.C., Aguilera, R., and Marquez-Magana, L.M. (2003) CodY is a nutritional repressor of flagellar gene expression in Bacillus subtilis. J Bacteriol 185: 3118-3126.
5. Calvo, J.M., and Matthews, R.G. (1994) The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol Rev 58: 466-490.
6. Chambellon, E., and Yvon, M. (2003) CodY-regulated aminotransferases AraT and BcaT play a major role in the growth of Lactococcus lactis in milk by regulating the intracellular pool of amino acids. Appl Environ Microbiol 69: 3061-3068.
7. Debarbouille, M., Gardan, R., Arnaud, M., and Rapoport, G. (1999) Role of bkdR, a transcriptional activator of the sigL-dependent isoleucine and valine degradation pathway in Bacillus subtilis. J Bacteriol 181: 2059-2066.
8. Deutscher, J., Galinier, A., and Martin-Verstraete, I. (2002) Carbohydrate uptake and metabolism. In Bacillus subtilis and its Closest Relatives: from Genes to Cells. Sonenshein, A.L., Hoch, J.A., and Losick, R. (eds). Washington, DC: American Society for Microbiology Press, pp. 129-150.
9. Epelbaum, S., LaRossa, R.A., VanDyk, T.K., Elkayam, T., Chipman, D.M., and Barak, Z. (1998) Branched-chain amino acid biosynthesis in Salmonella typhimurium: a quantitative analysis. J Bacteriol 180: 4056-4067.
10. Ferson, A.E., Wray, L.V., Jr, and Fisher, S.H. (1996) Expression of the Bacillus subtilis gabP gene is regulated independently in response to nitrogen and amino acid availability. Mol Microbiol 22: 693-701.
11. Fink, P.S. (1993) Biosynthesis of the branched-chain amino acids. In Bacillus subtilis and its Closest Relatives: from Genes to Cells. Sonenshein, A.L., Hoch, J.A., and Losick, R. (eds). Washington, DC: American Society for Microbiology Press, pp. 307-317.
12. Fisher, S.H., Rohrer, K., and Ferson, A.E. (1996) Role of CodY in regulation of the Bacillus subtilis hut operon. J Bacteriol 178: 3779-3784.
13. Fouet, A., and Sonenshein, A.L. (1990) A target for carbon source-dependent negative regulation of the citB promoter of Bacillus subtilis. J Bacteriol 172: 835-844.
14. Freese, E., Heinze, J.E., and Galliers, E.M. (1979) Partial purine deprivation causes sporulation of Bacillus subtilis in the presence of excess ammonia, glucose and phosphate. J Gen Microbiol 115: 193-205.
15. Grandoni, J.A., Zahler, S.A., and Calvo, J.M. (1992) Transcriptional regulation of the ilv-leu operon of Bacillus subtilis. J Bacteriol 174: 3212-3219.
16. Grandoni, J.A., Fulmer, S.B., Brizzio, V., Zahler, S.A., and Calvo, J.M. (1993) Regions of the Bacillus subtilis ilv-leu operon involved in regulation by leucine. J Bacteriol 175: 7581-7593.
17. Guédon, E., Serror, P., Ehrlich, S.D., Renault, P., and Delorme, C. (2001) Pleiotropic transcriptional repressor CodY senses the intracellular pool of branched-chain amino acids in Lactococcus lactis. Mol Microbiol 40: 1227-1239.
18. Haney, S.A., Platko, J.V., Oxender, D.L., and Calvo, J.M. (1992) Lrp, a leucine-responsive protein, regulates branched-chain amino acid transport genes in Escherichia coli. J Bacteriol 174: 108-115.
19. Henkin, T.M. (1994) tRNA-directed transcription antitermination. Mol Microbiol 13: 381-387.
20. Henkin, T.M. (1996) Control of transcription termination in prokaryotes. Annu Rev Genet 30: 35-57.
21. Inaoka, T., and Ochi, K. (2002) RelA protein is involved in induction of genetic competence in certain Bacillus subtilis strains by moderating the level of intracellular GTP. J Bacteriol 184: 3923-3930.
22. Inaoka, T., Takahashi, K., Ohnishi-Kameyama, M., Yoshida, M., and Ochi, K. (2003) Guanine nucleotides guanosine 5′-diphosphate 3′-diphosphate and GTP co-operatively regulate the production of an antibiotic bacilysin in Bacillus subtilis. J Biol Chem 278: 2169-2176.
23. Kim, H.-J., Roux, A., and Sonenshein, A.L. (2002) Direct and indirect roles of CcpA in regulation of Bacillus subtilis Krebs cycle genes. Mol Microbiol 45: 179-190.
24. Kim, H.-J., Kim, S.-I., Ratnayake-Lecamwasam, M., Tachikawa, K., Sonenshein, A.L., and Strauch, M. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J Bacteriol 185: 1672-1680.
25. Lopez, J.M., Marks, C.L., and Freese, E. (1979) The decrease of guanine nucleotides initiates sporulation of Bacillus subtilis. Biochim Biophys Acta 587: 238-252.
26. Lopez, J.M., Dromerick, A., and Freese, E. (1981) Response of guanosine 5′-triphosphate concentration to nutritional changes and its significance for Bacillus subtilis sporulation. J Bacteriol 146: 605-613.
27. Mäder, U., Henning, S., Hecker, M., and Homuth, G. (2004) Transcriptional organization and post-transcriptional regulation of the Bacillus subtilis branched-chain amino acids biosynthesis genes. J Bacteriol 186: 2240-2252.
28. Marta, P.T., Ladner, R.D., and Grandoni, J.A. (1996) A CUC triplet confers leucine-dependent regulation of the Bacillus subtilis ilv-leu operon. J Bacteriol 178: 2150-2153.
29. de Mendoza, D., Schujman, G.E., and Aguilar, P.S. (2002) Biosynthesis and function of membrane lipids. In Bacillus subtilis and its Closest Relatives: from Genes to Cells. Sonenshein, A.L., Hoch, J.A., and Losick, R. (eds). Washington, DC: American Society for Microbiology Press, pp. 43-56.
30. Mirel, D.B., Estacio, W.F., Mathieu, M., Olmsted, E., Ramirez, J., and Marquez-Magana, L.M. (2000) Environmental regulation of Bacillus subtilis sigma (D)-dependent gene expression. J Bacteriol 182: 3055-3062.
31. Molle, V., Nakaura, Y., Shivers, R.P., Yamaguchi, H., Losick, R., Fujita, Y., and Sonenshein, A.L. (2003) Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol 185: 1911-1922.
32. Petranovic, D., Guédon, E., Sperandio, B., Delorme, C., Ehrlich, D., and Renault, P. (2004) Intracellular effectors regulating the activity of the Lactococcus lactis CodY pleiotropic transcription regulator. Mol Microbiol doi:10.1111/j.1365-2958.2004.04136.x.
33. Ratnayake-Lecamwasam, M., Serror, P., Wong, K.W., and Sonenshein, A.L. (2001) Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev 15: 1093-1103.
34. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
35. Serror, P., and Sonenshein, A.L. (1996a) Interaction of CodY, a novel Bacillus subtilis DNA-binding protein, with the dpp promoter region. Mol Microbiol 20: 843-852.
36. Serror, P., and Sonenshein, A.L. (1996b) CodY is required for nutritional repression of Bacillus subtilis genetic competence. J Bacteriol 178: 5910-5915.
37. Slack, F.J., Mueller, J.P., and Sonenshein, A.L. (1993) Mutations that relieve nutritional repression of the Bacillus subtilis dipeptide permease operon. J Bacteriol 175: 4605-4614.
38. Slack, F.J., Serror, P., Joyce, E., and Sonenshein, A.L. (1995) A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon. Mol Microbiol 15: 689-702.
39. Tani, T.H., Khodursky, A., Blumenthal, R.M., Brown, P.O., and Matthews, R.G. (2002) Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis. Proc Natl Acad Sci USA 99: 13471-13476.
40. Willins, D.A., Ryan, C.W., Platko, J.V., and Calvo, J.M. (1991) Characterization of Lrp, and Escherichia coli regulatory protein that mediates a global response to leucine. J Biol Chem 266: 10768-10774.
41. Wray, L.V., Jr, and Fisher, S.H. (1994) Analysis of Bacillus subtilis hut operon expression indicates that histidine-dependent induction is mediated primarily by transcriptional antitermination and that amino acid repression is mediated by two mechanisms: regulation of transcription initiation and inhibition of histidine transport. J Bacteriol 176: 5466-5473.
42. Wray, L.V., Jr, Person, A.E., and Fisher, S.H. (1997) Expression of the Bacillus subtilis ureABC operon is controlled by multiple regulatory factors including CodY, GlnR, TnrA, and Spo0H. J Bacteriol 179: 5494-5501.