Roadblock repression of transcription by Bacillus subtilis CodY

Journal of Molecular Biology

Volumn 411, Issue 4, 2011, Pages 729-743

  Belitsky, Boris R ^a   Sonenshein, Abraham L ^a  

^a TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Bacillus subtilis; branched chain aminotransferase; CodY binding sites; gene expression; roadblock repression

Indexed keywords

BACTERIAL PROTEIN; CODY PROTEIN; DEOXYRIBONUCLEASE I; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; BINDING SITE; COUPLING FACTOR; GENE EXPRESSION; GENE REPRESSION; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; SYNTHESIS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

BACILLUS SUBTILIS;

EID: 80051668431     PISSN: 00222836     EISSN: 10898638     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.06.012     Document Type: Article

References (57)

1. Slack F.J., Serror P., Joyce E., and Sonenshein A.L. A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon Mol. Microbiol. 15 1995 689 702
2. Molle V., Nakaura Y., Shivers R.P., Yamaguchi H., Losick R., Fujita Y., and Sonenshein A.L. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis J. Bacteriol. 185 2003 1911 1922 (Pubitemid 36297891)
3. Sonenshein A.L. CodY, a global regulator of stationary phase and virulence in Gram-positive bacteria Curr. Opin. Microbiol. 8 2005 203 207 (Pubitemid 40417963)
4. Sonenshein A.L. Control of key metabolic intersections in Bacillus subtilis Nat. Rev., Microbiol. 5 2007 917 927 (Pubitemid 350131180)
5. Fisher S.H. Regulation of nitrogen metabolism in Bacillus subtilis: vive la difference! Mol. Microbiol. 32 1999 223 232 (Pubitemid 29178690)
6. Luong T.T., Sau K., Roux C., Sau S., Dunman P.M., and Lee C.Y. Staphylococcus aureus ClpC divergently regulates capsule via sae and codY in strain Newman but activates capsule via codY in strain UAMS-1 and in strain Newman with repaired saeS J. Bacteriol. 193 2011 686 694
7. Caymaris S., Bootsma H.J., Martin B., Hermans P.W., Prudhomme M., and Claverys J.P. The global nutritional regulator CodY is an essential protein in the human pathogen Streptococcus pneumoniae Mol. Microbiol. 78 2010 344 360
8. Dineen S.S., McBride S.M., and Sonenshein A.L. Integration of metabolism and virulence by Clostridium difficile CodY J. Bacteriol. 192 2010 5350 5362
9. Majerczyk C.D., Dunman P.M., Luong T.T., Lee C.Y., Sadykov M.R., and Somerville G.A. Direct targets of CodY in Staphylococcus aureus J. Bacteriol. 192 2010 2861 2877
10. Serror P., and Sonenshein A.L. Interaction of CodY, a novel Bacillus subtilis DNA-binding protein, with the dpp promoter region Mol. Microbiol. 20 1996 843 852 (Pubitemid 26173810)
11. Levdikov V.M., Blagova E., Joseph P., Sonenshein A.L., and Wilkinson A.J. The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in gram-positive bacteria J. Biol. Chem. 281 2006 11366 11373 (Pubitemid 43855561)
12. Joseph P., Ratnayake-Lecamwasam M., and Sonenshein A.L. A region of Bacillus subtilis CodY protein required for interaction with DNA J. Bacteriol. 187 2005 4127 4139 (Pubitemid 40827796)
13. Guedon E., Sperandio B., Pons N., Ehrlich S.D., and Renault P. Overall control of nitrogen metabolism in Lactococcus lactis by CodY, and possible models for CodY regulation in Firmicutes Microbiology 151 2005 3895 3909 (Pubitemid 41829970)
14. den Hengst C.D., van Hijum S.A., Geurts J.M., Nauta A., Kok J., and Kuipers O.P. The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element J. Biol. Chem. 280 2005 34332 34342 (Pubitemid 41443159)
15. Belitsky B.R., and Sonenshein A.L. Genetic and biochemical analysis of CodY-binding sites in Bacillus subtilis J. Bacteriol. 190 2008 1224 1236 (Pubitemid 351215003)
16. Guedon E., Serror P., Ehrlich S.D., Renault P., and Delorme C. Pleiotropic transcriptional repressor CodY senses the intracellular pool of branched-chain amino acids in Lactococcus lactis Mol. Microbiol. 40 2001 1227 1239 (Pubitemid 32574988)
17. Petranovic D., Guedon E., Sperandio B., Delorme C., Ehrlich D., and Renault P. Intracellular effectors regulating the activity of the Lactococcus lactis CodY pleiotropic transcription regulator Mol. Microbiol. 53 2004 613 621 (Pubitemid 38998179)
18. Shivers R.P., and Sonenshein A.L. Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids Mol. Microbiol. 53 2004 599 611 (Pubitemid 38998178)
19. den Hengst C.D., Curley P., Larsen R., Buist G., Nauta A., and van Sinderen D. Probing direct interactions between CodY and the oppD promoter of Lactococcus lactis J. Bacteriol. 187 2005 512 521 (Pubitemid 40096240)
20. Ratnayake-Lecamwasam M., Serror P., Wong K.W., and Sonenshein A.L. Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels Genes Dev. 15 2001 1093 1103 (Pubitemid 32417302)
21. Handke L.D., Shivers R.P., and Sonenshein A.L. Interaction of Bacillus subtilis CodY with GTP J. Bacteriol. 190 2008 798 806 (Pubitemid 351170922)
22. Atkinson M.R., Wray L.V. Jr., and Fisher S.H. Regulation of histidine and proline degradation enzymes by amino acid availability in Bacillus subtilis J. Bacteriol. 172 1990 4758 4765 (Pubitemid 20281919)
23. Slack F.J., Mueller J.P., Strauch M.A., Mathiopoulos C., and Sonenshein A.L. Transcriptional regulation of a Bacillus subtilis dipeptide transport operon Mol. Microbiol. 5 1991 1915 1925 (Pubitemid 21896223)
24. Fisher S.H., Rohrer K., and Ferson A.E. Role of CodY in regulation of the Bacillus subtilis hut operon J. Bacteriol. 178 1996 3779 3784 (Pubitemid 26227192)
25. Lopez J.M. GTP pool expansion is necessary for the growth rate increase occurring in Bacillus subtilis after amino acids shift-up Arch. Microbiol. 131 1982 247 251 (Pubitemid 12066930)
26. Lopez J.M., Dromerick A., and Freese E. Response of guanosine 5′-triphosphate concentration to nutritional changes and its significance for Bacillus subtilis sporulation J. Bacteriol. 146 1981 605 613 (Pubitemid 11078245)
27. Soga T., Ohashi Y., Ueno Y., Naraoka H., Tomita M., and Nishioka T. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry J. Proteome Res. 2 2003 488 494 (Pubitemid 37376843)
28. Mader U., Hennig S., Hecker M., and Homuth G. Transcriptional organization and posttranscriptional regulation of the Bacillus subtilis branched-chain amino acid biosynthesis genes J. Bacteriol. 186 2004 2240 2252 (Pubitemid 38451826)
29. Shivers R.P., and Sonenshein A.L. Bacillus subtilis ilvB operon: an intersection of global regulons Mol. Microbiol. 56 2005 1549 1559 (Pubitemid 40780650)
30. Tojo S., Satomura T., Morisaki K., Deutscher J., Hirooka K., and Fujita Y. Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA Mol. Microbiol. 56 2005 1560 1573 (Pubitemid 40780651)
31. Berger B.J., English S., Chan G., and Knodel M.H. Methionine regeneration and aminotransferases in Bacillus subtilis, Bacillus cereus, and Bacillus anthracis J. Bacteriol. 185 2003 2418 2431 (Pubitemid 36417965)
32. Thomaides H.B., Davison E.J., Burston L., Johnson H., Brown D.R., and Hunt A.C. Essential bacterial functions encoded by gene pairs J. Bacteriol. 189 2007 591 602 (Pubitemid 46106391)
33. Brinsmade S.R., Kleijn R.J., Sauer U., and Sonenshein A.L. Regulation of CodY activity through modulation of intracellular branched-chain amino acid pools J. Bacteriol. 192 2010 6357 6368
34. Daniel R.A., Haiech J., Denizot F., and Errington J. Isolation and characterization of the lacA gene encoding beta-galactosidase in Bacillus subtilis and a regulator gene, lacR J. Bacteriol. 179 1997 5636 5638 (Pubitemid 27387645)
35. Belitsky B.R., and Sonenshein A.L. Contributions of multiple binding sites and effector-independent binding to CodY-mediated regulation in Bacillus subtilis J. Bacteriol. 193 2011 473 484
36. Meijer W.J.J., and Salas M. Relevance of UP elements for three strong Bacillus subtilis phage phi29 promoters Nucleic Acids Res. 32 2004 1166 1176 (Pubitemid 38854719)
37. Helmann J.D. Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA Nucleic Acids Res. 23 1995 2351 2360
38. Lee S., Belitsky B.R., Brinker J.P., Kerstein K.O., Brown D.W., and Clements J.D. Development of a Bacillus subtilis-based rotavirus vaccine Clin. Vaccine Immunol. 17 2010 1647 1655
39. Belitsky B.R., and Sonenshein A.L. Role and regulation of Bacillus subtilis glutamate dehydrogenase genes J. Bacteriol. 180 1998 6298 6305 (Pubitemid 28544262)
40. Srivastava D.B., and Darst S.A. Derepression of bacterial transcription-repair coupling factor is associated with a profound conformational change J. Mol. Biol. 406 2011 275 284
41. Selby C.P., and Sancar A. Molecular mechanism of transcription-repair coupling Science 260 1993 53 58 (Pubitemid 23122744)
42. Washburn R.S., Wang Y., and Gottesman M.E. Role of E. coli transcription-repair coupling factor Mfd in Nun-mediated transcription termination J. Mol. Biol. 329 2003 655 662 (Pubitemid 36629361)
43. Chambers A.L., Smith A.J., and Savery N.J. A DNA translocation motif in the bacterial transcription-repair coupling factor, Mfd Nucleic Acids Res. 31 2003 6409 6418 (Pubitemid 37508744)
44. Selby C.P., and Sancar A. Structure and function of transcription-repair coupling factor. II. Catalytic properties J. Biol. Chem. 270 1995 4890 4895
45. Zalieckas J.M., Wray L.V. Jr., Ferson A.E., and Fisher S.H. Transcription-repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons Mol. Microbiol. 27 1998 1031 1038 (Pubitemid 28254952)
46. Shivers R.P., Dineen S.S., and Sonenshein A.L. Positive regulation of Bacillus subtilis ackA by CodY and CcpA: establishing a potential hierarchy in carbon flow Mol. Microbiol. 62 2006 811 822 (Pubitemid 44571604)
47. Zalieckas J.M., Wray L.V. Jr., and Fisher S.H. Expression of the Bacillus subtilis acsA gene: position and sequence context affect cre-mediated carbon catabolite repression J. Bacteriol. 180 1998 6649 6654 (Pubitemid 29006080)
48. Park J.S., Marr M.T., and Roberts J.W. E. coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation Cell 109 2002 757 767 (Pubitemid 34722270)
49. Zeng X., Galinier A., and Saxild H.H. Catabolite repression of dra-nupC-pdp operon expression in Bacillus subtilis Microbiology 146 2000 2901 2908
50. Grandoni J.A., Zahler S.A., and Calvo J.M. Transcriptional regulation of the ilv-leu operon of Bacillus subtilis J. Bacteriol. 174 1992 3212 3219
51. Zeigler D.R., Pragai Z., Rodriguez S., Chevreux B., Muffler A., and Albert T. The origins of 168, W23, and other Bacillus subtilis legacy strains J. Bacteriol. 190 2008 6983 6995
52. Steinmetz M., and Richter R. Plasmids designed to alter the antibiotic resistance expressed by insertion mutations in Bacillus subtilis, through in vivo recombination Gene 142 1994 79 83 (Pubitemid 24147353)
53. Yanisch-Perron C., Vieira J., and Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors Gene 33 1985 103 119 (Pubitemid 15122816)
54. Sambrook J., Fritsch E.F., and Maniatis T.J. Molecular Cloning: A Laboratory Manual 2nd edit. 1989 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
55. Belitsky B.R., Gustafsson M.C., Sonenshein A.L., and Von Wachenfeldt C. An lrp-like gene of Bacillus subtilis involved in branched-chain amino acid transport J. Bacteriol. 179 1997 5448 5457 (Pubitemid 27387615)
56. Qi Y., and Hulett F.M. PhoP-P and RNA polymerase sigmaA holoenzyme are sufficient for transcription of Pho regulon promoters in Bacillus subtilis: PhoP-P activator sites within the coding region stimulate transcription in vitro Mol. Microbiol. 28 1998 1187 1197 (Pubitemid 28293542)
57. Helmann J.D. Purification of Bacillus subtilis RNA polymerase and associated factors Methods Enzymol. 370 2003 10 24 (Pubitemid 37542765)