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A role for oxidized guanine residues was observed, but the mechanisms of this induction remained unclear. To select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen that renders induction of SOS lethal. We identified genes involved in this pathway using two strategies, inactivation by transposition and gene overexpression. Interestingly, we obtained mutants inactivated for the expression of proteins known to destabilize the RNA polymerase complex. Reconstruction of the corresponding mutants confirmed their specific involvement in induction of SOS by low aminoglycoside concentrations. We propose that DNA lesions formed on aminoglycoside treatment are repaired through the formation of single-stranded DNA intermediates, inducing SOS. Inactivation of functions that dislodge RNA polymerase leads to prolonged stalling on these lesions, which hampers SOS induction and repair and reduces viability under antibiotic stress. The importance of these mechanisms is illustrated by a reduction of aminoglycoside sub-MIC. Our results point to a central role for transcription blocking at DNA lesions in SOS induction, so far underestimated.<\/jats:p>","DOI":"10.1093\/nar\/gkt1259","type":"journal-article","created":{"date-parts":[[2013,12,7]],"date-time":"2013-12-07T04:12:02Z","timestamp":1386389522000},"page":"2366-2379","source":"Crossref","is-referenced-by-count":40,"title":["Identification of genes involved in low aminoglycoside-induced SOS response in<i>Vibrio cholerae<\/i>: a role for transcription stalling and Mfd helicase"],"prefix":"10.1093","volume":"42","author":[{"given":"Zeynep","family":"Baharoglu","sequence":"first","affiliation":[{"name":"D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Unit\u00e9 Plasticit\u00e9 du G\u00e9nome Bact\u00e9rien, Institut Pasteur, 75015 Paris, France and 2Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France"},{"name":"D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Unit\u00e9 Plasticit\u00e9 du G\u00e9nome Bact\u00e9rien, Institut Pasteur, 75015 Paris, France and 2Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anamaria","family":"Babosan","sequence":"additional","affiliation":[{"name":"D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Unit\u00e9 Plasticit\u00e9 du G\u00e9nome Bact\u00e9rien, Institut Pasteur, 75015 Paris, France and 2Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France"},{"name":"D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Unit\u00e9 Plasticit\u00e9 du G\u00e9nome Bact\u00e9rien, Institut Pasteur, 75015 Paris, France and 2Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Didier","family":"Mazel","sequence":"additional","affiliation":[{"name":"D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Unit\u00e9 Plasticit\u00e9 du G\u00e9nome Bact\u00e9rien, Institut Pasteur, 75015 Paris, France and 2Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France"},{"name":"D\u00e9partement G\u00e9nomes et G\u00e9n\u00e9tique, Unit\u00e9 Plasticit\u00e9 du G\u00e9nome Bact\u00e9rien, Institut Pasteur, 75015 Paris, France and 2Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,12,5]]},"reference":[{"key":"2020112408364441800_gkt1259-B1","first-page":"1400","article-title":"The SOS Response of Escherichia coli","volume-title":"Escherichia coli and Salmonella","author":"Walker","year":"1996"},{"key":"2020112408364441800_gkt1259-B2","doi-asserted-by":"crossref","first-page":"e1001165","DOI":"10.1371\/journal.pgen.1001165","article-title":"Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation","volume":"6","author":"Baharoglu","year":"2010","journal-title":"PLoS Genet."},{"key":"2020112408364441800_gkt1259-B3","doi-asserted-by":"crossref","first-page":"1659","DOI":"10.1128\/JB.05982-11","article-title":"Transformation-induced SOS regulation and carbon catabolite control of the V. cholerae integron integrase: connecting environment and genome plasticity","volume":"194","author":"Baharoglu","year":"2012","journal-title":"J. Bacteriol."},{"key":"2020112408364441800_gkt1259-B4","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.watres.2010.08.019","article-title":"Environmental toxicology and risk assessment of pharmaceuticals from hospital wastewater","volume":"45","author":"Escher","year":"2011","journal-title":"Water Res."},{"key":"2020112408364441800_gkt1259-B5","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.envint.2012.03.008","article-title":"Consumption-based approach for assessing the contribution of hospitals towards the load of pharmaceutical residues in municipal wastewater","volume":"45","author":"Le Corre","year":"2012","journal-title":"Environ. 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Sci."},{"key":"2020112408364441800_gkt1259-B34","doi-asserted-by":"crossref","first-page":"3353","DOI":"10.1073\/pnas.1115105109","article-title":"Nucleotide excision repair (NER) machinery recruitment by the transcription-repair coupling factor involves unmasking of a conserved intramolecular interface","volume":"109","author":"Deaconescu","year":"2012","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2020112408364441800_gkt1259-B35","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1146\/annurev.bi.65.070196.000355","article-title":"DNA excision repair","volume":"65","author":"Sancar","year":"1996","journal-title":"Annu. Rev. Biochem."},{"key":"2020112408364441800_gkt1259-B36","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1111\/j.1365-2958.2010.07208.x","article-title":"RNA polymerase mutations that facilitate replication progression in the rep uvrD recF mutant lacking two accessory replicative helicases","volume":"77","author":"Baharoglu","year":"2010","journal-title":"Mol. Microbiol."},{"key":"2020112408364441800_gkt1259-B37","doi-asserted-by":"crossref","first-page":"6713","DOI":"10.1093\/nar\/20.24.6713","article-title":"Bound Lac repressor protein differentially inhibits the unwinding reactions catalyzed by DNA helicases","volume":"20","author":"Yancey-Wrona","year":"1992","journal-title":"Nucleic Acids Res."},{"key":"2020112408364441800_gkt1259-B38","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/emboj.2009.308","article-title":"The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo","volume":"29","author":"Boubakri","year":"2010","journal-title":"EMBO J."},{"key":"2020112408364441800_gkt1259-B39","doi-asserted-by":"crossref","first-page":"e1002622","DOI":"10.1371\/journal.pgen.1002622","article-title":"Replication fork reversal after replication-transcription collision","volume":"8","author":"De Septenville","year":"2012","journal-title":"PLoS Genet."},{"key":"2020112408364441800_gkt1259-B40","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1016\/j.molcel.2011.12.003","article-title":"R we there yet? R-loop hazards to finishing the journey","volume":"44","author":"Potenski","year":"2011","journal-title":"Mol. Cell"},{"key":"2020112408364441800_gkt1259-B41","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1126\/science.1172914","article-title":"The SOS response controls integron recombination","volume":"324","author":"Guerin","year":"2009","journal-title":"Science"},{"key":"2020112408364441800_gkt1259-B42","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1128\/AEM.02147-06","article-title":"Construction of a Vibrio splendidus mutant lacking the metalloprotease gene vsm by use of a novel counterselectable suicide vector","volume":"73","author":"Le Roux","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"2020112408364441800_gkt1259-B43","doi-asserted-by":"crossref","first-page":"e1000201","DOI":"10.1371\/journal.pgen.1000201","article-title":"FtsK-dependent dimer resolution on multiple chromosomes in the pathogen Vibrio cholerae","volume":"4","author":"Val","year":"2008","journal-title":"PLoS Genet."},{"key":"2020112408364441800_gkt1259-B44","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/S0378-1119(02)00856-9","article-title":"Construction of a mariner-based transposon for epitope-tagging and genomic targeting","volume":"296","author":"Chiang","year":"2002","journal-title":"Gene"},{"key":"2020112408364441800_gkt1259-B45","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1006\/jmbi.1996.0835","article-title":"A survey of polypeptide deformylase function throughout the eubacterial lineage","volume":"266","author":"Mazel","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2020112408364441800_gkt1259-B46","doi-asserted-by":"crossref","first-page":"6418","DOI":"10.1128\/JB.00621-10","article-title":"Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery","volume":"192","author":"Ferrieres","year":"2010","journal-title":"J. Bacteriol."},{"key":"2020112408364441800_gkt1259-B47","doi-asserted-by":"crossref","first-page":"e1000012","DOI":"10.1371\/journal.pgen.1000012","article-title":"ruvA Mutants that resolve Holliday junctions but do not reverse replication forks","volume":"4","author":"Baharoglu","year":"2008","journal-title":"PLoS Genet."},{"key":"2020112408364441800_gkt1259-B48","doi-asserted-by":"crossref","first-page":"4882","DOI":"10.1074\/jbc.270.9.4882","article-title":"Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties","volume":"270","author":"Selby","year":"1995","journal-title":"J. Biol. Chem."},{"key":"2020112408364441800_gkt1259-B49","doi-asserted-by":"crossref","first-page":"4596","DOI":"10.1073\/pnas.92.10.4596","article-title":"Intrinsic transcript cleavage activity of RNA polymerase","volume":"92","author":"Orlova","year":"1995","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2020112408364441800_gkt1259-B50","doi-asserted-by":"crossref","first-page":"8899","DOI":"10.1073\/pnas.89.19.8899","article-title":"GreA protein: a transcription elongation factor from Escherichia coli","volume":"89","author":"Borukhov","year":"1992","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2020112408364441800_gkt1259-B51","doi-asserted-by":"crossref","first-page":"6853","DOI":"10.1093\/emboj\/19.24.6853","article-title":"GreA and GreB proteins revive backtracked RNA polymerase in vivo by promoting transcript trimming","volume":"19","author":"Toulme","year":"2000","journal-title":"EMBO J."},{"key":"2020112408364441800_gkt1259-B52","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1002\/j.1460-2075.1983.tb01445.x","article-title":"The origin of replication, oriC, and the dnaA protein are dispensable in stable DNA replication (sdrA) mutants of Escherichia coli K-12","volume":"2","author":"Kogoma","year":"1983","journal-title":"EMBO J."},{"key":"2020112408364441800_gkt1259-B53","doi-asserted-by":"crossref","first-page":"7247","DOI":"10.1128\/JB.175.22.7247-7253.1993","article-title":"DNA-polymerase-I and the bypassing of reca dependence of constitutive stable DNA-replication in Escherichia-Coli Rnha mutants","volume":"175","author":"Cao","year":"1993","journal-title":"J. Bacteriol."},{"key":"2020112408364441800_gkt1259-B54","doi-asserted-by":"crossref","first-page":"2637","DOI":"10.1128\/JB.06725-11","article-title":"Mfd is required for rapid recovery of transcription following UV-induced DNA damage but not oxidative DNA damage in Escherichia coli","volume":"194","author":"Schalow","year":"2012","journal-title":"J. Bacteriol."},{"key":"2020112408364441800_gkt1259-B55","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1016\/j.dnarep.2005.03.006","article-title":"Cisplatin induces DNA double-strand break formation in Escherichia coli dam mutants","volume":"4","author":"Nowosielska","year":"2005","journal-title":"DNA Repair"},{"key":"2020112408364441800_gkt1259-B56","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1073\/pnas.93.3.1292","article-title":"Products of DNA mismatch repair genes mutS and mutL are required for transcription-coupled nucleotide-excision repair of the lactose operon in Escherichia coli","volume":"93","author":"Mellon","year":"1996","journal-title":"Proc. Natl Acad. Sci. 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Microbiol."},{"key":"2020112408364441800_gkt1259-B58","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1126\/science.1179595","article-title":"Direct restart of a replication fork stalled by a head-on RNA polymerase","volume":"327","author":"Pomerantz","year":"2010","journal-title":"Science"},{"key":"2020112408364441800_gkt1259-B59","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1093\/nar\/gkp1247","article-title":"Oxidative stress triggers the preferential assembly of base excision repair complexes on open chromatin regions","volume":"38","author":"Amouroux","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2020112408364441800_gkt1259-B60","doi-asserted-by":"crossref","first-page":"483","DOI":"10.1016\/j.dnarep.2004.01.003","article-title":"Effect of 8-oxoguanine on transcription elongation by T7 RNA polymerase and mammalian RNA polymerase II","volume":"3","author":"Tornaletti","year":"2004","journal-title":"DNA Repair"},{"key":"2020112408364441800_gkt1259-B61","doi-asserted-by":"crossref","first-page":"724","DOI":"10.1093\/emboj\/cdg043","article-title":"A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins","volume":"22","author":"Mahdi","year":"2003","journal-title":"EMBO J."},{"key":"2020112408364441800_gkt1259-B62","doi-asserted-by":"crossref","first-page":"21330","DOI":"10.1016\/S0021-9258(17)45364-6","article-title":"Transcription preferentially inhibits nucleotide excision repair of the template DNA strand in vitro","volume":"265","author":"Selby","year":"1990","journal-title":"J. Biol. Chem."},{"key":"2020112408364441800_gkt1259-B63","doi-asserted-by":"crossref","first-page":"6601","DOI":"10.1073\/pnas.90.14.6601","article-title":"Effects of abasic sites and DNA single-strand breaks on prokaryotic RNA polymerases","volume":"90","author":"Zhou","year":"1993","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2020112408364441800_gkt1259-B64","doi-asserted-by":"crossref","first-page":"21276","DOI":"10.1074\/jbc.273.33.21276","article-title":"Effects of nonbulky DNA base damages on Escherichia coli RNA polymerase-mediated elongation and promoter clearance","volume":"273","author":"Viswanathan","year":"1998","journal-title":"J. Biol. Chem."},{"key":"2020112408364441800_gkt1259-B65","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1006\/jmbi.1996.0087","article-title":"The Mfd protein of Bacillus subtilis 168 is involved in both transcription-coupled DNA repair and DNA recombination","volume":"256","author":"Ayora","year":"1996","journal-title":"J. Mol. Biol."},{"key":"2020112408364441800_gkt1259-B66","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1016\/j.diagmicrobio.2009.08.007","article-title":"The Helicobacter pylori Mfd protein is important for antibiotic resistance and DNA repair","volume":"65","author":"Lee","year":"2009","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"2020112408364441800_gkt1259-B67","doi-asserted-by":"crossref","first-page":"e1000083","DOI":"10.1371\/journal.ppat.1000083","article-title":"Key role of Mfd in the development of fluoroquinolone resistance in Campylobacter jejuni","volume":"4","author":"Han","year":"2008","journal-title":"PLoS Pathog."},{"key":"2020112408364441800_gkt1259-B68","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1159\/000332751","article-title":"Transcriptional de-repression and Mfd are mutagenic in stressed Bacillus subtilis cells","volume":"21","author":"Martin","year":"2011","journal-title":"J. Mol. Microbiol. 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Bacteriol."},{"key":"2020112408364441800_gkt1259-B84","doi-asserted-by":"crossref","first-page":"13738","DOI":"10.1073\/pnas.0703078104","article-title":"Yeast aconitase binds and provides metabolically coupled protection to mitochondrial DNA","volume":"104","author":"Chen","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2020112408364441800_gkt1259-B85","doi-asserted-by":"crossref","first-page":"43728","DOI":"10.1074\/jbc.M304484200","article-title":"YodA from Escherichia coli is a metal-binding, lipocalin-like protein","volume":"278","author":"David","year":"2003","journal-title":"J. Biol. Chem."},{"key":"2020112408364441800_gkt1259-B86","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1111\/j.1574-6968.2007.01011.x","article-title":"Diversity and distribution of hemerythrin-like proteins in prokaryotes","volume":"279","author":"French","year":"2008","journal-title":"FEMS Microbiol. Lett."},{"key":"2020112408364441800_gkt1259-B87","doi-asserted-by":"crossref","first-page":"168","DOI":"10.1046\/j.1365-2958.2000.01984.x","article-title":"Novel effects of a transposon insertion in the Vibrio fischeri glnD gene: defects in iron uptake and symbiotic persistence in addition to nitrogen utilization","volume":"37","author":"Graf","year":"2000","journal-title":"Mol. Microbiol."},{"key":"2020112408364441800_gkt1259-B88","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.jsb.2003.10.010","article-title":"Evolutionary history and higher order classification of AAA+ ATPases","volume":"146","author":"Iyer","year":"2004","journal-title":"J. Struct. Biol."},{"key":"2020112408364441800_gkt1259-B89","doi-asserted-by":"crossref","first-page":"24434","DOI":"10.1074\/jbc.M111.243535","article-title":"Structure of the PilM-PilN inner membrane type IV pilus biogenesis complex from Thermus thermophilus","volume":"286","author":"Karuppiah","year":"2011","journal-title":"J. Biol. Chem."},{"key":"2020112408364441800_gkt1259-B90","doi-asserted-by":"crossref","first-page":"2065","DOI":"10.1128\/JB.01740-07","article-title":"The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance","volume":"190","author":"Laubacher","year":"2008","journal-title":"J. Bacteriol."},{"key":"2020112408364441800_gkt1259-B91","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1111\/j.1365-2958.2006.05106.x","article-title":"Cyclic-diGMP signal transduction systems in Vibrio cholerae: modulation of rugosity and biofilm formation","volume":"60","author":"Lim","year":"2006","journal-title":"Mol. 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