Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein

Molecular Microbiology

Volumn 64, Issue 2, 2007, Pages 368-381

  Smits, Wiep Klaas ^a   Hoa, Tran Thu ^b,c   Hamoen, Leendert W ^a,d   Kuipers, Oscar P ^a   Dubnau, David ^b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b PUBLIC HEALTH RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF MEDICINE AND PHARMACY AT HO CHI MINH CITY   (Viet Nam)

^d NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CODY PROTEIN; COMK PROTEIN; DEGU PROTEIN; DNA BINDING PROTEIN; REPRESSOR PROTEIN; ROK PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; BINDING AFFINITY; DEFENSE MECHANISM; DNA HELIX; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; REVERSE TRANSCRIPTION; TRANSCRIPTION INITIATION;

BACTERIAL PROTEINS; BINDING SITES; CHROMOMYCINS; DNA, BACTERIAL; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; METHYL GREEN; MODELS, GENETIC; MUTATION; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; REPRESSOR PROTEINS; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION FACTORS;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); OCTODON DEGUS;

EID: 34247383232     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2007.05662.x     Document Type: Article

References (48)

1. Albano, M., Hahn, J. Dubnau, D. (1987) Expression of competence genes in Bacillus subtilis. J Bacteriol 169: 3110 3117.
2. Albano, M., Smits, W.K., Ho, L.T.Y., Kraigher, B., Mandic-Mulec, I., Kuipers, O.P. Dubnau, D. (2005) The Rok protein of Bacillus subtilis represses genes for cell surface and extracellular functions. J Bacteriol 187: 1 10.
3. Bai, U., Mandic-Mulec, I. Smith, I. (1993) SinI modulates the activity of SinR, a developmental switch protein of Bacillus subtilis, by protein-protein interaction. Genes Dev 7: 139 148.
4. Berka, R.M., Hahn, J., Albano, M., Draskovic, I., Persuh, M., Cui, X., et al. (2002) Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK. Mol Microbiol 43: 1331 1345.
5. Bewley, C.A., Gronenborn, A.M. Clore, G.M. (1998) Minor groove-binding architectural proteins: structure, function, and DNA recognition. Annu Rev Biophys Biomol Struct 27: 105 131.
6. Blattner, F.R., Plunkett, G., III, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453 1474.
7. Browning, D.F., Cole, J.A. Busby, S.J. (2004) Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter. Mol Microbiol 53: 203 215.
8. Browning, D.F., Grainger, D.C., Beatty, C.M., Wolfe, A.J., Cole, J.A. Busby, S.J. (2005) Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression. Mol Microbiol 57: 496 510.
9. Browning, D.F., Lee, D.J., Wolfe, A.J., Cole, J.A. Busby, S.J. (2006) The Escherichia coli K-12 NarL and NarP proteins insulate the nrf promoter from the effects of integration host factor. J Bacteriol 188: 7449 7456.
10. Carey, M. (1998) The enhanceosome and transcriptional synergy. Cell 92: 5 8.
11. Fujita, M. Sadaie, Y. (1998) Feedback loops involving Spo0A and AbrB in in vitro transcription of the genes involved in the initiation of sporulation in Bacillus subtilis. J Biochem (Tokyo) 124: 98 104.
12. Fujita, M., Gonzalez-Pastor, J.E. Losick, R. (2005) High- and low-threshold genes in the Spo0A regulon of Bacillus subtilis. J Bacteriol 187: 1357 1368.
13. Goodrich, J.A., Schwartz, M.L. McClure, W.R. (1990) Searching for and predicting the activity of sites for DNA binding proteins. compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res 18: 4993 5000.
14. Hahn, J., Roggiani, M. Dubnau, D. (1995) The major role of Spo0A in genetic competence is to downregulate abrB, an essential competence gene. J Bacteriol 177: 3601 3605.
15. Hahn, J., Luttinger, A. Dubnau, D. (1996) Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis. Mol Microbiol 21: 763 775.
16. Haijema, B.J., Hahn, J., Haynes, J. Dubnau, D. (2001) A ComGA-dependent checkpoint limits growth during the escape from competence. Mol Microbiol 40: 52 64.
17. Hamoen, L.W., Van Werkhoven, A.F., Bijlsma, J.J., Dubnau, D. Venema, G. (1998) The competence transcription factor of Bacillus subtilis recognizes short A/T-rich sequences arranged in a unique, flexible pattern along the DNA helix. Genes Dev 12: 1539 1550.
18. Hamoen, L.W., Van Werkhoven, A.F., Venema, G. Dubnau, D. (2000) The pleiotropic response regulator DegU functions as a priming protein in competence development in Bacillus subtilis. Proc Natl Acad Sci USA 97: 9246 9251.
19. Hamoen, L.W., Haijema, B., Bijlsma, J.J., Venema, G. Lovett, C.M. (2001) The Bacillus subtilis competence transcription factor, ComK, overrides LexA-imposed transcriptional inhibition without physically displacing LexA. J Biol Chem 276: 42901 42907.
20. Hamoen, L.W., Smits, W.K., de Jong, A., Holsappel, S. Kuipers, O.P. (2002) Improving the predictive value of the competence transcription factor (ComK) binding site in Bacillus subtilis using a genomic approach. Nucleic Acids Res 30: 5517 5528.
21. Hamoen, L.W., Kausche, D., Marahiel, M.A., van Sinderen, D., Venema, G. Serror, P. (2003) The Bacillus subtilis transition state regulator AbrB binds to the -35 promoter region of comK. FEMS Microbiol Lett 218: 299 304.
22. Hayashi, K., Kensuke, T., Kobayashi, K., Ogasawara, N. Ogura, M. (2006) Bacillus subtilis RghR (YvaN) represses rapG and rapH, which encode inhibitors of expression of the srfA operon. Mol Microbiol 59: 1714 1729.
23. Hoa, T.T., Tortosa, P., Albano, M. Dubnau, D. (2002) Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK. Mol Microbiol 43: 15 26.
24. Horcajadas, J.A., Monsalve, M., Rojo, F. Salas, M. (1999) The switch from early to late transcription in phage GA-1: characterization of the regulatory protein p4G. J Mol Biol 290: 917 928.
25. Kim, H.J., Kim, S.I., Ratnayake-Lecamwasam, M., Tachikawa, K., Sonenshein, A.L. Strauch, M. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J Bacteriol 185: 1672 1680.
26. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390: 249 256.
27. Levdikov, V.M., Blagova, E., Joseph, P., Sonenshein, A.L. Wilkinson, A.J. (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.
28. Lewis, P.J. Marston, A.L. (1999) GFP vectors for controlled expression and dual labelling of protein fusions in Bacillus subtilis. Gene 227: 101 110.
29. Maamar, H. Dubnau, D. (2005) Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol 56: 615 624.
30. Ogura, M., Yamaguchi, H., Kobayashi, K., Ogasawara, N., Fujita, Y. Tanaka, T. (2002) Whole-genome analysis of genes regulated by the Bacillus subtilis competence transcription factor ComK. J Bacteriol 184: 2344 2351.
31. Perez-Martin, J., Rojo, F. de Lorenzo, V. (1994) Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol Rev 58: 268 290.
32. Predich, M., Nair, G. Smith, I. (1992) Bacillus subtilis early sporulation genes kinA, spo0F, and spo0A are transcribed by the RNA polymerase containing sigma H. J Bacteriol 174: 2771 2778.
33. Ratnayake-Lecamwasam, M., Serror, P., Wong, K.W. Sonenshein, A.L. (2001) Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev 15: 1093 1103.
34. Resnik, E., Pan, B., Ramani, N., Freundlich, M. LaPorte, D.C. (1996) Integration host factor amplifies the induction of the aceBAK operon of Escherichia coli by relieving IclR repression. J Bacteriol 178: 2715 2717.
35. Rojo, F. (2001) Mechanisms of transcriptional repression. Curr Opin Microbiol 4: 145 151.
36. Serror, P. Sonenshein, A.L. (1996) CodY is required for nutritional repression of Bacillus subtilis genetic competence. J Bacteriol 178: 5910 5915.
37. Shen, A., Kamp, H.D., Grundling, A. Higgins, D.E. (2006) A bifunctional O-GlcNAc transferase governs flagellar motility through anti-repression. Genes Dev 20: 3283 3295.
38. Shivers, R.P. Sonenshein, A.L. (2004) Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids. Mol Microbiol 53: 599 611.
39. Shivers, R.P. Sonenshein, A.L. (2005) Bacillus subtilis ilvB operon: an intersection of global regulons. Mol Microbiol 56: 1549 1559.
40. van Sinderen, D. Venema, G. (1994) comK acts as an autoregulatory control switch in the signal transduction route to competence in Bacillus subtilis. J Bacteriol 176: 5762 5770.
41. van Sinderen, D., ten Berge, A., Hayema, B.J., Hamoen, L. Venema, G. (1994) Molecular cloning and sequence of comK, a gene required for genetic competence in Bacillus subtilis. Mol Microbiol 11: 695 703.
42. van Sinderen, D., Luttinger, A., Kong, L., Dubnau, D., Venema, G. Hamoen, L. (1995) comK encodes the competence transcription factor, the key regulatory protein for competence development in Bacillus subtilis. Mol Microbiol 15: 455 462.
43. Sun, D., Hurley, L.H. Harshey, R.M. (1996) Structural distortions induced by integration host factor (IHF) at the H' site of phage lambda probed by (+)-CC-1065, pluramycin, and KMnO4 and by DNA cyclization studies. Biochemistry 35: 10815 10827.
44. Susanna, K.A., van der Werff, A.F., den Hengst, C.D., Calles, B., Salas, M., Venema, G., et al. (2004) Mechanism of transcription activation at the comG promoter by the competence transcription factor ComK of Bacillus subtilis. J Bacteriol 186: 1120 1128.
45. Susanna, K.A., Fusetti, F., Thunnissen, A.M., Hamoen, L.W. Kuipers, O.P. (2006) Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants. Microbiology 152: 473 483.
46. Turgay, K., Hamoen, L.W., Venema, G. Dubnau, D. (1997) Biochemical characterization of a molecular switch involving the heat shock protein ClpC, which controls the activity of ComK, the competence transcription factor of Bacillus subtilis. Genes Dev 11: 119 128.
47. Turgay, K., Hahn, J., Burghoorn, J. Dubnau, D. (1998) Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. EMBO J 17: 6730 6738.
48. Yang, C.C. Nash, H.A. (1989) The interaction of E. coli IHF protein with its specific binding sites. Cell 57: 869 880.