Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box

Molecular Microbiology

Volumn 49, Issue 1, 2003, Pages 157-165

  Yoshida, Ken Ichi ^a   Yamaguchi, Hirotake ^a   Kinehara, Masaki ^a   Ohki, Yo Hei ^a   Nakaura, Yoshiko ^a   Fujita, Yasutaro ^a  

^a FUKUYAMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID; AMMONIA; ASPARAGINASE; BACTERIAL PROTEIN; CARRIER PROTEIN; GLUTAMATE SYNTHASE; GUANINE DEAMINASE; NITRATE; PROTEIN ALST; PROTEIN GINQHMP; PROTEIN GLTAB; PROTEIN NASA; PROTEIN NASBCDEF; PROTEIN NASDEF; PROTEIN NRGAB; PROTEIN OPPABCDF; PROTEIN PEL; PROTEIN PUCJKLM; PROTEIN YODF; PROTEIN YTTA; PROTEIN YWDIJK; PROTEIN YWLFG; PROTEIN YWRD; PROTEIN YXKC; PROTEIN YYCCB; PURINE; UNCLASSIFIED DRUG; UREASE;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; CONSENSUS SEQUENCE; DNA HYBRIDIZATION; DNA MICROARRAY; DNA SEQUENCE; DNA STRUCTURE; GENE CONTROL; GENE FUNCTION; GENE IDENTIFICATION; GENE NRGAB; NONHUMAN; OPERON; PRIORITY JOURNAL; REGULON; SEQUENCE ANALYSIS; SRY GENE; TNRA BOX; TNRA GENE;

AMINO ACID MOTIFS; BACILLUS SUBTILIS; BACTERIAL PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULATORY SEQUENCES, NUCLEIC ACID; REPRESSOR PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); NASA; POSIBACTERIA;

EID: 0037709014     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2003.03567.x     Document Type: Article

References (30)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
2. Beier, L., Nygaard, P., Jarmer, H., and Saxild, H.H. (2002) Transcription analysis of the Bacillus subtilis PucR regulon and identification of a cis-acting sequence required for PucR-regulated expression of genes involved in purine catabolism. J Bacteriol 184: 3232-3241.
3. Belitsky, B.R., Wray, L.V., Jr, Fisher, S.H., Bohannon, D.E., and Sonenshein, A.L. (2000) Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression. J Bacteriol 182: 5939-5947.
4. Brandenburg, J.L., Wray, L.V., Jr, Beier, L., Jarmer, H., Saxild, H.H., and Fisher, S.H. (2002) Roles of pucR, glnR, and tnrA. regulating expression of the Bacillus subtilis ure P3 promoter. J Bacteriol 184: 6060-6064.
5. Brown, S.W., and Sonenshein, A.L. (1996) Autogenous regulation of the Bacillus subtilis glnRA operon. J Bacteriol 178: 2450-2454.
6. 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.
7. Fisher, S.H. (1999) Regulation of nitrogen metabolism in Bacillus subtilis: vive la difference! Mol Microbiol 32: 223-232.
8. Fisher, S.H., and Wray, L.V., Jr (2002) Bacillus subtilis 168 contains two differentially regulated genes encoding L-asparaginase. J Bacteriol 184: 2148-2154.
9. Higuchi, R. (1990) Recombinant PCR. In PCR Protocols: a Guide to Methods and Applications. Innis, M.A., Gelfand, D.H., Sninsky, J.J., and White, T.J. (eds). San Diego: Academic Press, pp. 177-183.
10. Kaempfer, R.O., and Magasanik, B. (1967) Effect of infection with T-even phage on the inducible synthesis of beta-galactosidase in Escherichia coli. J Mol Biol 27: 453-468.
11. 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.
12. Nakano, M.M., Yang, F., Hardin, P., and Zuber, P. (1995) Nitrogen regulation of nasA and the nasB operon, which encode genes required for nitrate assimilation in Bacillus subtilis. J Bacteriol 177: 573-579.
13. Nakano, M.M., Hoffmann, T., Zhu, Y., and Jahn, D. (1998) Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE. J Bacteriol 180: 5344-5350.
14. Nygaard, P., Bested, S.M., Andersen, K.A., and Saxild, H.H. (2002) Bacillus subtilis guanine deaminase is encoded by the yknA gene and is induced during growth with purines as the nitrogen source. Microbiology 146: 3061-3069.
15. Ogura, M., Yamaguchi, H., Yoshida, K., Fujita, Y., and Tanaka, T. (2001) DNA microarray analysis of Bacillus subtilis DegU, ComA and PhoP regulons: an approach to comprehensive analysis of B. subtilis two-component regulatory systems. Nucleic Acids Res 29: 3804-3813.
16. 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.
17. Robichon, D., Arnaud, M., Gardan, R., Pragai, Z., O'Reilly, M., Rapoport, G., and Debarbouille, M. (2000) Expression of a new operon from Bacillus subtilis, ykzB-ykoL, under the control of the TnrA and PhoP-phoR global regulators. J Bacteriol 182: 1226-1231.
18. Sambrook, J., and Russell, D.W. (2001) Molecular Cloning, a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
19. Schilling, C.H., Held, L., Torre, M., and Saier, M.H., Jr (2000) GRASP-DNA: a web application to screen prokaryotic genomes for specific DNA-binding sites and repeat motifs. J Mol Microbiol Biotechnol 2: 495-500.
20. Schultz, A.C., Nygaard, P., and Saxild, H.H. (2001) Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription activator. J Bacteriol 183: 3293-3302.
21. Wang, L., Grau, R., Perego, M., and Hoch, J.A. (1997) A novel histidine kinase inhibitor regulating development in Bacillus subtilis. Genes Dev 11: 2569-2579.
22. Wray, L.V., Jr, Atkinson, M.R., and Fisher, S.H. (1994) The nitrogen-regulated Bacillus subtilis nrgAB operon encodes a membrane protein and a protein highly similar to the Escherichia coli glnB-encoded PII protein. J Bacteriol 176: 108-114.
23. Wray, L.V., Jr, Ferson, A.E., Rohrer, K., and Fisher, S.H. (1996) TnrA, a transcription factor required for global nitrogen regulation in Bacillus subtilis. Proc Natl Acad Sci USA 93: 8841-8845.
24. Wray, L.V., Jr, Ferson, 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.
25. Wray, L.V., Jr, Zalieckas, J.M., and Fisher, S.H. (2000) Purification and in vitro activities of the Bacillus subtilis TnrA transcription factor. J Mol Biol 300: 29-40.
26. Wray, L.V., Jr, Zalieckas, J.M., and Fisher, S.H. (2001) Bacillus subtilis glutamine synthetase controls gene expression through a protein-protein interaction with transcription factor TnrA. Cell 107: 427-435.
27. Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Improved M13 phage cloning vectors and host strain: nucleotide sequences of M13mp18 and pUC19 vectors. Gene 33: 103-119.
28. Yoshida, K., Shibayama, T., Aoyama, D., and Fujita, Y. (1999) Interaction of a repressor and its binding sites for regulation of the Bacillus subtilis iol divergon. J Mol Biol 285: 917-929.
29. Yoshida, K., Ishio, I., Nagakawa, E., Yamamoto, Y., Yamamoto, M., and Fujita, Y. (2000) Systematic study of gene expression and transcription organization in the gntZ-ywaA region of the Bacillus subtilis genome. Microbiology 146: 573-579.
30. Yoshida, K., Kobayashi, K., Miwa, Y., Kang, C.-M., Matsunaga, M., Yamaguchi, H., et al. (2001) Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res 29: 683-692.