Functional analysis of the carboxy-terminal region of Bacillus subtilis TnrA, a MerR family protein

Journal of Bacteriology

Volumn 189, Issue 1, 2007, Pages 20-27

  Wray Jr , Lewis V ^a   Fisher, Susan H ^a  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO ACID MIXTURE; ARGININE; ASPARAGINE; BACTERIAL PROTEIN; DNA; GLUTAMATE AMMONIA LIGASE; GLUTAMINE; GLYCINE; HISTIDINE; LEUCINE; MERR PROTEIN; METHIONINE; MUTANT PROTEIN; NITROGEN; PHENYLALANINE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR TNRA; TYROSINE; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; AMTB GENE; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIUM CULTURE; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; CONTROLLED STUDY; CROSS LINKING; CULTURE MEDIUM; DIMERIZATION; DNA BINDING MOTIF; ENZYME INHIBITION; ENZYME REGULATION; FUNCTIONAL PROTEOMICS; GEL FILTRATION; GENE EXPRESSION REGULATION; GENE MUTATION; IN VITRO STUDY; MUTAGENESIS; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; TNRA GENE;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; CULTURE MEDIA; DNA-BINDING PROTEINS; FEEDBACK; GENE EXPRESSION REGULATION, BACTERIAL; GLUTAMATE-AMMONIA LIGASE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NITROGEN; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; REPRESSOR PROTEINS; SEQUENCE ALIGNMENT; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION FACTORS;

BACILLUS SUBTILIS;

EID: 33845928570     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01238-06     Document Type: Article

References (53)

1. Atkinson, M. R., L. V. Wray, Jr., and S. H. Fisher. 1990. Regulation of histidine and proline degradation enzymes by amino acid availability in Bacillus subtilis. J. Bacteriol. 172:4758-4765.
2. Belitsky, B. R., L. V. Wray, Jr., S. H. Fisher, D. E. Bohannon, and A. L. Sonenshein. 2000. Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression. J. Bacteriol. 182:5939-5947.
3. Brown, N. L., J. V. Stoyanov, S. P. Kidd, and J. L. Hobman. 2003. The MerR family of transcriptional regulators. FEMS Microbiol. Rev. 27:145-163.
4. Buckle, A. M., P. Cramer, and A. R. Fersht. 1996. Structural and energetic responses to cavity-creating mutations in Hydrophobic cores: observation of a buried water molecule and the hydrophilic nature of such hydrophobic cavities. Biochemistry 35:4298-4305.
5. Burkhard, P., J. Stetefeld, and S. V. Strelkov. 2001. Coiled coils: a highly versatile protein folding motif. Trends Cell Biol. 11:82-88.
6. Caguiat, J. J., A. L. Watson, and A. O. Summers. 1999. Cd(II)-responsive and constitutive mutants implicate a novel domain in MerR. J. Bacteriol. 181:3462-3471.
7. Changela, A., K. Chen, Y. Xue, J. Holschen, C. E. Outten, T. V. O'Halloran, and A. Mondragon. 2003. Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR. Science 301:1383-1387.
8. Chasin, L. A., and B. Magasanik. 1968. Induction and repression of the histidine-degrading enzymes of Bacillus subtilis. J. Bacteriol. 178:4778-4786.
9. Chiu, M. L., P. H. Viollier, T. Katoh, J. J. Ramsden, and C. J. Thompson. 2001. Ligand-induced changes in the Streptomyces lividans TipAL protein imply an alternative mechanism of transcriptional activation for MerR-like proteins. Biochemistry 40:12950-12958.
10. Dall'Acqua, W., E. R. Goldman, W. Lin, C. Teng, D. Tsuchiya, H. Li, X. Ysern, B. C. Braden, Y. Li, S. J. Smith-Gill, and R. A. Mariuzza. 1998. A mutational analysis of binding interactions in an antigen-antibody protein-protein complex. Biochemistry 37:7981-7991.
11. Deul, T. F., and S. Prusiner. 1974. Regulation of glutamine synthetase from Bacillus subtilis by divalent cations, feedback inhibitors, and L-glutamine. J. Biol. Chem. 249:257-264.
12. Eriksson, A. E., W. A. Baase, X. J. Zhang, D. W. Heinz, M. Blaber, E. P. Baldwin, and B. W. Matthews. 1992. Response of a protein to cavity-creating mutations and its relation to the hydrophobic effect. Science 255:178-183.
13. Person, A. E., L. V. Wray, Jr., and S. H. Fisher. 1996. Expression of the Bacillus subtilis gabP gene is regulated independently in response to nitrogen and amino acid availability. Mol. Microbiol. 22:693-701.
14. Filée, P., C. Vreuls, R. Herman, I. Thamm, T. Aerts, P. P. De Deyn, J.-M. Frère, and B. Joris. 2003. Dimerization and DNA binding properties of the Bacillus licheniformis 749/1 BlaI repressor. J. Biol. Chem. 278:16482-16487.
15. Fisher, S. H., J. L. Brandenburg, and L. V. Wray, Jr. 2002. Mutations in Bacillus subtilis glutamine synthetase that block its interaction with transcription factor TnrA. Mol. Microbiol. 45:627-635.
16. Fisher, S. H., and A. L. Sonenshein. 1984. Bacillus subtilis glutamine synthetase mutants pleiotropically altered in glucose catabolite repression. J. Bacteriol. 157:612-621.
17. Fisher, S. H., and L. V. Wray, Jr. 2002. Bacillus subtilis 168 contains two differentially regulated genes encoding L-asparaginase. J. Bacteriol. 184: 2148-2154.
18. Frantz, B., and T. V. O'Halloran. 1990. DNA distortion accompanies transcriptional activation by the metal-responsive gene-regulatory protein MerR. Biochemistry 29:4747-4751.
19. Godsey, M. H., N. N. Baranova, A. A. Neyfakh, and R. G. Brennan. 2001. Crystal structure of MtaN, a global multidrug transporter gene activator. J. Biol. Chem. 276:47178-47184.
20. Guérout-Fleury, A.-M., N. Frandsen, and P. Stragier. 1996. Plasmids for ectopic integration in Bacillus subtilis. Gene 180:57-61.
21. Heldwein, E. E. Z., and R. G. Brennan. 2001. Crystal structure of the transcription activator BmrR bound to DNA and a drug. Nature 409:378-382.
22. Jones, D. T. 1999. Protein secondary structure prediction based on position-specific matrices. J. Mol. Biol. 292:195-202.
23. Kahmann, J. D., H. J. Sass, M. G. Allan, H. Seto, C. J. Thompson, and S. Grzesiek. 2003. Structural basis for antibiotic recognition by the TipA class of multidrug-resistance transcriptional regulators. EMBO J. 22:1824-1834.
24. Kammann, M., J. Laufs, J. Schell, and B. Gronenbom. 1989. Rapid insertional mutagenesis of DNA by polymerase chain reaction (PCR). Nucleic Acids Res. 17:5404.
25. Kidd, S. P., A. J. Potter, M. A. Apicella, M. P. Jennings, and A. G. McEwan. 2005. NmIR of Neisseria gonorrhoeae: a novel redox responsive transcription factor from the MerR family. Mol. Microbiol. 57:1676-1689.
26. Kloczkowski, A., K. L. Ting, R. L. Jemigan, and J. Garnier. 2002. Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins 49:154-166.
27. Lupas, A., M. Van Dyke, and J. Stock. 1991. Predicting coiled coils from protein sequences. Science 252:1162-1164.
28. Marchler-Bauer, A., J. B. Anderson, P. F. Cherukuri, C. DeWeese-Scott, L. Y. Geer, M. Gwadz, S. He, D. I. Hurwitz, J. D. Jackson, Z. Ke, C. J. Lanczycki, C. A. Liebert, C. Liu, F. Lu, G. H. Marchler, M. Mullokandov, B. A. Shoemaker, V. Simonyan, J. S. Song, P. A. Thiessen, R. A. Yamashita, J. J. Yin, D. Zhang, and S. H. Bryant. 2005. CDD: a conserved domain database for protein classification. Nucleic Acids Res. 33:D192-D196.
29. McCuffin, L. J., K. Bryson, and D. T. Jones. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16:404-405.
30. Miller, J. H. 1992. A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria, p. 439. Cold Spring Harbor Laboratory Press, Plainview, NY.
31. Nakano, M. M., T. Hoffmann, Y. Zhu, and D. Jahn. 1998. Nitrogen and oxygen regulation of Bacillus subtilis nasDEF encoding NADH-dependent nitrite reductase by TnrA and ResDE. J. Bacteriol. 180:5344-5350.
32. Nakano, M. M., F. Yang, P. Hardin, and P. Zuber. 1995. Nitrogen regulation of nasA and nasB operon, which encode genes required for nitrate assimilation in Bacillus subtilis. J. Bacteriol. 177:573-579.
33. Neidhardt, F. C., P. L. Bloch, and D. F. Smith. 1974. Culture medium for enterobacteria. J. Bacteriol. 119:736-747.
34. Newberry, K. J., and R. G. Brennan. 2004. The structural mechanism for transcription activation by MerR family member multidrug transporter activation, N terminus. J. Biol. Chem. 279:20356-20362.
35. Outten, C. E., F. W. Outten, and T. V. O'Halloran. 1999. DNA distortion mechanism for transcriptional activation by ZntR, a Zn(II)-responsive MerR homologue in Escherichia coli. J. Biol. Chem. 274:37517- 37524.
36. Pace, C. N., F. Vajdos, L. Fee, G. Grimsley, and T. Gray. 1995. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4:2411-2423.
37. Pettersen, E. F., T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin. 2004. UCSF Chimera: a visualization system for exploratory research and analysis. J. Comput. Chem. 25:1605-1612.
38. Schwede, T., J. Koop, N. Guex, and M. Peitsch. 2003. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31:3381-3385.
39. Sen, T. Z., R. L. Jemigan, J. Garnier, and A. Kloczkowski. 2005. GOR V server for protein secondary structure prediction. Bioinformatics 21:2787-2788.
40. Steinmetzer, K., J. Behlke, and S. Brantl. 1998. Plasmid pIP501 encoded transcriptional represser CopR binds to its target DNA as a dimer. J. Mol. Biol. 283:595-603.
41. Steinmetzer, K., and S. Brantl. 1997. Plasmid pIP501 encoded transcriptional represser CopR binds asymmetrically at two consecutive major grooves of the DNA. J. Mol. Biol. 269:684-693.
42. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
43. Vaughan, C. K., A. M. Buckle, and A. R. Fersht. 1999. Structural response to mutation at a protein-protein interface. J. Mol. Biol. 286:1487-1506.
44. Wray, L. V., Jr., M. R. Atkinson, and S. H. Fisher. 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.
45. Wray, L. V., Jr., A. E. Person, K. Rohrer, and S. H. Fisher. 1996. TnrA, a transcriptional factor required for global nitrogen regulation in Bacillus subtilis. Proc. Natl. Acad. Sci. USA 93:8841-8845.
46. Wray, L. V., Jr., and S. H. Fisher. 2005. A feedback-resistant mutant of Bacillus subtilis glutamine synthetase with pleiotropic defects in nitrogen-regulated gene expression. J. Biol. Chem. 280:33298-33304.
47. Wray, L. V., Jr., J. M. Zalieckas, and S. H. Fisher. 2000. Purification and in vitro activities of the Bacillus subtilis TnrA transcription factor. J. Mol. Biol. 300:29-10.
48. Wray, L. V., Jr., J. M. Zalieckas, and S. H. Fisher. 2001. Bacillus subtilis glutamine synthetase controls gene expression through a protein-protein interaction with transcription factor TnrA. Cell 107:427-435.
49. Wu, T. D., and D. L. Brutlag. 1996. Discovering empirically conserved amino acid substitution groups in databases of protein families. Proc. Int. Conf. Intell. Syst. Mol. Biol. 4:230-240.
50. Yoshida, K., H. Yamaguchi, M. Kinehara, Y. Ohki Y. Nakaura, and Y. Fujita. 2003. Identification of additional TnrA-regulated genes of Bacillus sublilis associated with a TnrA box. Mol. Microbiol. 49:157-165.
51. Youn, H., R. L. Kerby, M. Conrad, and G. P. Roberts. 2006. Study of highly constitutively active mutants suggests how cAMP activates cAMP receptor protein. J. Biol. Chem. 281:1119-1127.
52. Zalieckas, J. M., L. V. Wray, Jr., and S. H. Fisher. 2006. Cross-regulation of the Bacillus sublilis glnRA and lnrA genes provides evidence for DNA binding site discrimination by GInR and TnrA. J. Bacteriol. 188:2578-2585.
53. Zeng, Q., C. Stålhandske, M. C. Anderson, R. A. Scott, and A. O. Summers. 1998. The core metal-recognition domain of MerR. Biochemistry 37:15885-15895.