Bacillus subtilis CodY operators contain overlapping CodY binding sites

Journal of Bacteriology

Volumn 193, Issue 18, 2011, Pages 4841-4848

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

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; DEOXYRIBONUCLEASE I; ISOLEUCINE; REGULATOR PROTEIN; TRANSCRIPTION REGULATOR CODY; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DNA FOOTPRINTING; GEL MOBILITY SHIFT ASSAY; GENE DOSAGE; HUTPP GENE; MUTATIONAL ANALYSIS; NONHUMAN; PH; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN INDUCTION; TRANSCRIPTION REGULATION; UREAP3 GENE;

BACILLUS SUBTILIS; BINDING SITES; DNA FOOTPRINTING; DNA MUTATIONAL ANALYSIS; DNA, BACTERIAL; ELECTROPHORETIC MOBILITY SHIFT ASSAY; HYDROGEN-ION CONCENTRATION; OPERATOR REGIONS, GENETIC; PROTEIN BINDING; TRANSCRIPTION FACTORS;

BACILLUS SUBTILIS;

EID: 80052528894     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.05258-11     Document Type: Article

References (51)

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. Baichoo, N., and J. D. Helmann. 2002. Recognition of DNA by Fur: a reinterpretation of the Fur box consensus sequence. J. Bacteriol. 184:5826-5832.
3. Belitsky, B. R., and A. L. Sonenshein. 2008. Genetic and biochemical analysis of CodY-binding sites in Bacillus subtilis. J. Bacteriol. 190:1224-1236.
4. Belitsky, B. R., and A. L. Sonenshein. 2011. Contributions of multiple binding sites and effector-independent binding to CodY-mediated regulation in Bacillus subtilis. J. Bacteriol. 193:473-484.
5. Bennett, H., et al. 2007. Characterization of relA and codY mutants of Listeria monocytogenes: identification of the CodY regulon and its role in virulence. Mol. Microbiol. 63:1453-1467.
6. Bergara, F., et al. 2003. CodY is a nutritional repressor of flagellar gene expression in Bacillus subtilis. J. Bacteriol. 185:3118-3126.
7. Blagova, E. V., V. M. Levdikov, K. Tachikawa, A. L. Sonenshein, and A. J. Wilkinson. 2003. Crystallization of the GTP-dependent transcriptional regulator CodY from Bacillus subtilis. Acta Crystallogr. D Biol. Crystallogr. 59:155-157.
8. Calogero, S., et al. 1994. RocR, a novel regulatory protein controlling arginine utilization in Bacillus subtilis, belongs to the NtrC/NifA family of transcriptional activators. J. Bacteriol. 176:1234-1241.
9. Carey, J. 1988. Gel retardation at low pH resolves trp repressor-DNA complexes for quantitative study. Proc. Natl. Acad. Sci. U. S. A. 85:975-979.
10. Chen, J. D., and D. A. Morrison. 1988. Construction and properties of a new insertion vector, pJDC9, that is protected by transcriptional terminators and useful for cloning of DNA from Streptococcus pneumoniae. Gene 64:155-164.
11. Dahl, M. K., J. Degenkolb, and W. Hillen. 1994. Transcription of the xyl operon is controlled in Bacillus subtilis by tandem overlapping operators spaced by four base-pairs. J. Mol. Biol. 243:413-424.
12. de Lorenzo, V., S. Wee, M. Herrero, and J. B. Neilands. 1987. Operator sequences of the aerobactin operon of plasmid ColV-K30 binding the ferric uptake regulation (fur) repressor. J. Bacteriol. 169:2624-2630.
13. den Hengst, C. D., et al. 2005. The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element. J. Biol. Chem. 280:34332-34342.
14. den Hengst, C. D., et al. 2005. Probing direct interactions between CodY and the oppD promoter of Lactococcus lactis. J. Bacteriol. 187:512-521.
15. Dineen, S., A. Villapakkam, J. Nordman, and A. Sonenshein. 2007. Repression of Clostridium difficile toxin gene expression by CodY. Mol. Microbiol. 66:206-219.
16. Eda, S., T. Hoshino, and M. Oda. 2000. Role of the DNA sequence downstream of the Bacillus subtilis hut promoter in regulation of the hut operon. Biosci. Biotechnol. Biochem. 64:484-491.
17. Ferson, 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.
18. Fisher, S. H., K. Rohrer, and A. E. Ferson. 1996. Role of CodY in regulation of the Bacillus subtilis hut operon. J. Bacteriol. 178:377937-377984.
19. Guédon, E., P. Serror, S. D. Ehrlich, P. Renault, and C. Delorme. 2001. Pleiotropic transcriptional repressor CodY senses the intracellular pool of branched-chain amino acids in Lactococcus lactis. Mol. Microbiol. 40:1227-1239.
20. Guédon, E., B. Sperandio, N. Pons, S. D. Ehrlich, and P. Renault. 2005. Overall control of nitrogen metabolism in Lactococcus lactis by CodY, and possible models for CodY regulation in Firmicutes. Microbiology 151:3895-3909.
21. Handke, L. D., R. P. Shivers, and A. L. Sonenshein. 2008. Interaction of Bacillus subtilis CodY with GTP. J. Bacteriol. 190:798-806.
22. Ho, S. N., H. D. Hunt, R. M. Horton, J. K. Pullen, and L. R. Pease. 1989. Site-directed mutagenesis by overlap extension using the PCR. Gene 77:51-59.
23. Jeeves, M., P. D. Evans, R. A. Parslow, M. Jaseja, and E. I. Hyde. 1999. Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences. Eur. J. Biochem. 265:919-928.
24. Krell, T., et al. 2007. Optimization of the palindromic order of the TtgR operator enhances binding cooperativity. J. Mol. Biol. 369:1188-1199.
25. Lavrrar, J. L., C. A. Christoffersen, and M. A. McIntosh. 2002. Fur-DNA interactions at the bidirectional fepDGC-entS promoter region in Escherichia coli. J. Mol. Biol. 322:983-995.
26. Lavrrar, J. L., and M. A. McIntosh. 2003. Architecture of a Fur binding site: a comparative analysis. J. Bacteriol. 185:2194-2202.
27. Lawson, C. L., and J. Carey. 1993. Tandem binding in crystals of a trp repressor/operator half-site complex. Nature 366:178-182.
28. Lemos, J. A., M. M. Nascimento, V. K. Lin, J. Abranches, and R. A. Burne. 2008. Global regulation by (p)ppGpp and CodY in Streptococcus mutans. J. Bacteriol. 190:5291-5299.
29. Levdikov, V. M., E. Blagova, P. Joseph, A. L. Sonenshein, and A. J. Wilkinson. 2006. The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in Gram-positive bacteria. J. Biol. Chem. 281:11366-11373.
30. Liu, Q., X. Li, and S. S. Sommer. 1999. pK-matched running buffers for gel electrophoresis. Anal. Biochem. 270:112-122.
31. Liu, S.-T., and G. F. Hong. 1998. Three-minute G + A specific reaction for DNA sequencing. Anal. Biochem. 255:158-159.
32. Magill, N. G., et al. 1996. Analysis of the relationship between the decrease in pH and accumulation of 3-phosphoglyceric acid in developing forespores of Bacillus species. J. Bacteriol. 178:2204-2210.
33. Majerczyk, C. D., et al. 2010. Direct targets of CodY in Staphylococcus aureus. J. Bacteriol. 192:2861-2877.
34. Molle, V., et al. 2003. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J. Bacteriol. 185:1911-1922.
35. Morinaga, T., K. Kobayashi, H. Ashida, Y. Fujita, and K. Yoshida. 2010. Transcriptional regulation of the Bacillus subtilis asnH operon and role of the 5'-proximal long sequence triplication in RNA stabilization. Microbiology 156:1632-1641.
36. Neidhardt, F. C., P. L. Bloch, and D. F. Smith. 1974. Culture medium for enterobacteria. J. Bacteriol. 119:736-747.
37. 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.
38. Petranovic, D., et al. 2004. Intracellular effectors regulating the activity of the Lactococcus lactis CodY pleiotropic transcription regulator. Mol. Microbiol. 53:613-621.
39. Ratnayake-Lecamwasam, M., P. Serror, K. W. Wong, and A. L. Sonenshein. 2001. Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev. 15:1093-1103.
40. Rudner, D. Z., J. R. LeDeaux, K. Ireton, and A. D. Grossman. 1991. The spo0K locus of Bacillus subtilis is homologous to the oligopeptide permease locus and is required for sporulation and competence. J. Bacteriol. 173:1388-1398.
41. Schumacher, M. A., et al. 2002. Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein QacR. EMBO J. 21: 1210-1218.
42. Serror, P., and A. L. Sonenshein. 1996. CodY is required for nutritional repression of Bacillus subtilis genetic competence. J. Bacteriol. 178:5910-5915.
43. Serror, P., and A. L. Sonenshein. 1996. Interaction of CodY, a novel Bacillus subtilis DNA-binding protein, with the dpp promoter region. Mol. Microbiol. 20:843-852.
44. Shivers, R. P., and A. L. Sonenshein. 2004. Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids. Mol. Microbiol. 53:599-611.
45. Sonenshein, A. L. 2005. CodY, a global regulator of stationary phase and virulence in Gram-positive bacteria. Curr. Opin. Microbiol. 8:203-207.
46. Villapakkam, A. C., et al. 2009. Genetic and biochemical analysis of the interaction of Bacillus subtilis CodY with branched-chain amino acids. J. Bacteriol. 191:6865-6876.
47. White, A., D. Xiaochun, J. C. vanderSpek, J. R. Murphy, and D. Ringe. 1998. Structure of the metal-ion-activated diphtheria toxin repressor/tox operator complex. Nature 394:502-506.
48. Wray, L. V., Jr., A. E. Ferson, and S. H. Fisher. 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.
49. Wray, L. V., Jr., and S. H. Fisher. 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.
50. Wray, L. V., Jr., F. K. Pettengill, and S. H. Fisher. 1994. Catabolite repression of the Bacillus subtilis hut operon requires a cis-acting located downstream of the transcription initiation site. J. Bacteriol. 176:1894-1902.
51. Xu, H., M. Moraitis, R. J. Reedstrom, and K. S. Matthews. 1998. Kinetic and thermodynamic studies of purine repressor binding to corepressor and operator DNA. J. Biol. Chem. 273:8958-8964.