The LexA regulated genes of the Clostridium difficile

BMC Microbiology

Volumn 14, Issue 1, 2014, Pages

  Walter, Beata M ^a   Rupnik, Maja ^a,b,c   Hodnik, Vesna ^d   Anderluh, Gregor ^d,e   Dupuy, Bruno ^f   Paulič, Nejc ^d   Žgur Bertok, Darja ^d   Butala, Matej ^d  

^a Centre for Microbiology   (Slovenia)

^b UNIVERSITY OF MARIBOR   (Slovenia)

^c Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins   (Slovenia)

^d UNIVERSITY OF LJUBLJANA   (Slovenia)

^e NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

^f INSTITUT PASTEUR   (France)

Author keywords

Antibiotic resistance; Clostridium difficile; LexA repressor; SOS system; Surface plasmon resonance; Toxin regulation

Indexed keywords

LEXA PROTEIN;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BINDING SITE; CLOSTRIDIUM DIFFICILE; COMPUTER MODEL; DNA REPAIR; GENE LOCUS; GENE REGULATORY NETWORK; GENETIC VARIABILITY; HOUSEKEEPING GENE; LEX A GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; PROTEIN BINDING; RECA GENE; REGULATOR GENE; REGULON; RUVCA GENE; SPOROGENESIS; SURFACE PLASMON RESONANCE; UVRBA GENE;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM DIFFICILE;

BACTERIAL PROTEINS; BINDING SITES; CLOSTRIDIUM DIFFICILE; COMPUTER SIMULATION; DNA, BACTERIAL; GENE EXPRESSION REGULATION, BACTERIAL; REGULON; SERINE ENDOPEPTIDASES; SURFACE PLASMON RESONANCE;

EID: 84898822661     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-14-88     Document Type: Article

References (34)

1. Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli. Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC, Genetics 2001 158 41 64 11333217
2. Aeons of distress: an evolutionary perspective on the bacterial SOS response. Erill I, Campoy S, Barbe J, FEMS Microbiol Rev 2007 31 637 656 10.1111/j.1574-6976.2007.00082.x 17883408
3. Reconstruction of the evolutionary history of the LexA-binding sequence. Mazon G, Erill I, Campoy S, Cortes P, Forano E, Barbe J, Microbiology 2004 150 3783 3795 10.1099/mic.0.27315-0 15528664
4. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Wade JT, Reppas NB, Church GM, Struhl K, Genes Dev 2005 19 2619 2630 10.1101/gad.1355605 16264194
5. Genetic composition of the Bacillus subtilis SOS system. Au N, Kuester-Schoeck E, Mandava V, Bothwell LE, Canny SP, Chachu K, Colavito SA, Fuller SN, Groban ES, Hensley LA, O'Brien TC, Shah A, Tierney JT, Tomm LL, O'Gara TM, Goranov AI, Grossman AD, Lovett CM, J Bacteriol 2005 187 7655 7666 10.1128/JB.187.22.7655-7666.2005 16267290
6. Double locking of an Escherichia coli promoter by two repressors prevents premature colicin expression and cell lysis. Butala M, Sonjak S, Kamensek S, Hodoscek M, Browning DF, Zgur-Bertok D, Busby SJ, Mol Microbiol 2012 86 129 139 10.1111/j.1365-2958.2012.08179.x 22812562
7. LexA cleavage is required for CTX prophage induction. Quinones M, Kimsey HH, Waldor MK, Mol Cell 2005 17 291 300 10.1016/j.molcel.2004.11.046 15664197
8. The SOS response promotes qnrB quinolone-resistance determinant expression. Da Re S, Garnier F, Guerin E, Campoy S, Denis F, Ploy MC, EMBO Rep 2009 10 929 933 10.1038/embor.2009.99 19556999
9. The SOS response controls integron recombination. Guerin E, Cambray G, Sanchez-Alberola N, Campoy S, Erill I, Da Re S, Gonzalez-Zorn B, Barbe J, Ploy MC, Mazel D, Science 2009 324 1034 10.1126/science.1172914 19460999
10. Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci. Ubeda C, Maiques E, Knecht E, Lasa I, Novick RP, Penades JR, Mol Microbiol 2005 56 836 844 10.1111/j.1365-2958.2005.04584.x 15819636
11. SOS response promotes horizontal dissemination of antibiotic resistance genes. Beaber JW, Hochhut B, Waldor MK, Nature 2004 427 72 74 10.1038/nature02241 14688795
12. Characterization of the global transcriptional responses to different types of DNA damage and disruption of replication in Bacillus subtilis. Goranov AI, Kuester-Schoeck E, Wang JD, Grossman AD, J Bacteriol 2006 188 5595 5605 10.1128/JB.00342-06 16855250
13. Clostridium difficile infection: new developments in epidemiology and pathogenesis. Rupnik M, Wilcox MH, Gerding DN, Nat Rev Microbiol 2009 7 526 536 10.1038/nrmicro2164 19528959
14. Novel high-molecular-weight, R-type bacteriocins of Clostridium difficile. Gebhart D, Williams SR, Bishop-Lilly KA, Govoni GR, Willner KM, Butani A, Sozhamannan S, Martin D, Fortier LC, Scholl D, J Bacteriol 2012 194 6240 6247 10.1128/JB.01272-12 22984261
15. The recA gene from Clostridium perfringens is induced by methyl methanesulphonate and contains an upstream Cheo box. Johnston JL, Sloan J, Fyfe JA, Davies JK, Rood JI, Microbiology 1997 143 Pt 3 885 890 9084172
16. Insertion or deletion of the Cheo box modifies radiation inducibility of Clostridium promoters. Nuyts S, Van Mellaert L, Barbe S, Lammertyn E, Theys J, Landuyt W, Bosmans E, Lambin P, Anne J, Appl Environ Microbiol 2001 67 4464 4470 10.1128/AEM.67.10.4464-4470.2001 11571144
17. Inference of self-regulated transcriptional networks by comparative genomics. Cornish JP, Matthews F, Thomas JR, Erill I, Evol Bioinform Online 2012 8 449 461 23032607
18. Relationship between bacterial strain type, host biomarkers, and mortality in Clostridium difficile infection. Walker AS, Eyre DW, Wyllie DH, Dingle KE, Griffiths D, Shine B, Oakley S, O'Connor L, Finney J, Vaughan A, Crook DW, Wilcox MH, Peto TE, Clin Infect Dis 2013 56 1589 1600 10.1093/cid/cit127 23463640
19. Heterogeneity of large clostridial toxins: importance of Clostridium difficile toxinotypes. Rupnik M, FEMS Microbiol Rev 2008 32 541 555 10.1111/j.1574-6976.2008.00110.x 18397287
20. Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile. Marsden GL, Davis IJ, Wright VJ, Sebaihia M, Kuijper EJ, Minton NP, BMC Genomics 2010 11 389 10.1186/1471-2164-11-389 20565959
21. Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Stabler RA, He M, Dawson L, Martin M, Valiente E, Corton C, Lawley TD, Sebaihia M, Quail MA, Rose G, Gerding DN, Gibert M, Popoff MR, Parkhill J, Dougan G, Wren BW, Genome Biol 2009 10 102 10.1186/gb-2009-10-9-r102 19781061
22. Macro and micro diversity of Clostridium difficile isolates from diverse sources and geographical locations. Stabler RA, Dawson LF, Valiente E, Cairns MD, Martin MJ, Donahue EH, Riley TV, Songer JG, Kuijper EJ, Dingle KE, Wren BW, PLoS One 2012 7 31559 10.1371/journal.pone.0031559 22396735
23. Genetic markers for Clostridium difficile lineages linked to hypervirulence. Knetsch CW, Hensgens MP, Harmanus C, van der Bijl MW, Savelkoul PH, Kuijper EJ, Corver J, Van Leeuwen HC, Microbiology 2011 157 3113 3123 10.1099/mic.0.051953-0 21873406
24. A reexamination of information theory-based methods for DNA-binding site identification. Erill I, O'Neill MC, BMC Bioinformatics 2009 10 57 10.1186/1471-2105-10-57 19210776
25. Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response. Butala M, Klose D, Hodnik V, Rems A, Podlesek Z, Klare JP, Anderluh G, Busby SJ, Steinhoff HJ, Zgur-Bertok D, Nucleic Acids Res 2011 39 6546 6557 10.1093/nar/gkr265 21576225
26. Characterization of the SigD Regulon of C. difficile and Its Positive Control of Toxin Production through the Regulation of tcdR. El Meouche I, Peltier J, Monot M, Soutourina O, Pestel-Caron M, Dupuy B, Pons JL, PLoS One 2013 8 83748 10.1371/journal.pone.0083748 24358307
27. Effects of ciprofloxacin on the expression and production of exotoxins by Clostridium difficile. Aldape MJ, Packham AE, Nute DW, Bryant AE, Stevens DL, J Med Microbiol 2013 62 741 747 10.1099/jmm.0.056218-0 23429695
28. The bacterial LexA transcriptional repressor. Butala M, Zgur-Bertok D, Busby SJ, Cell Mol Life Sci 2009 66 82 93 10.1007/s00018-008-8378-6 18726173
29. Comparison of responses to double-strand breaks between Escherichia coli and Bacillus subtilis reveals different requirements for SOS induction. Simmons LA, Goranov AI, Kobayashi H, Davies BW, Yuan DS, Grossman AD, Walker GC, J Bacteriol 2009 191 1152 1161 10.1128/JB.01292-08 19060143
30. The NCBI BioSystems database. Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH, Nucleic Acids Res 2010 38 492 496 10.1093/nar/gkp858 19854944
31. Reannotation of the genome sequence of Clostridium difficile strain 630. Monot M, Boursaux-Eude C, Thibonnier M, Vallenet D, Moszer I, Medigue C, Martin-Verstraete I, Dupuy B, J Med Microbiol 2011 60 1193 1199 10.1099/jmm.0.030452-0 21349987
32. Dendroscope: an interactive viewer for large phylogenetic trees. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R, BMC Bioinformatics 2007 8 460 10.1186/1471-2105-8-460 18034891
33. MEME SUITE: tools for motif discovery and searching. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS, Nucleic Acids Res 2009 37 202 208 10.1093/nar/gkp335 19458158
34. RecA-Dependent Cleavage of LexA Dimers. Giese KC, Michalowski CB, Little JW, J Mol Biol 2008 377 148 161 10.1016/j.jmb.2007.12.025 18234215