{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T02:41:41Z","timestamp":1792550501719,"version":"4.5.0"},"reference-count":51,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2015,12,4]],"date-time":"2015-12-04T00:00:00Z","timestamp":1449187200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1005317","type":"journal-article","created":{"date-parts":[[2015,12,4]],"date-time":"2015-12-04T18:42:24Z","timestamp":1449254544000},"page":"e1005317","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":28,"title":["The Extraintestinal Pathogenic Escherichia coli Factor RqlI Constrains the Genotoxic Effects of the RecQ-Like Helicase RqlH"],"prefix":"10.1371","volume":"11","author":[{"given":"Colin W.","family":"Russell","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew A.","family":"Mulvey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2015,12,4]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1093\/cid\/cit284","article-title":"Urinary tract infections: current and emerging management strategies","volume":"57","author":"AE Barber","year":"2013","journal-title":"Clin Infect Dis"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.yexmp.2008.03.007","article-title":"Origins and virulence mechanisms of uropathogenic Escherichia coli","volume":"85","author":"TJ Wiles","year":"2008","journal-title":"Exp Mol Pathol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/S1047-2797(00)00072-7","article-title":"Urinary tract infection: self-reported incidence and associated costs","volume":"10","author":"B Foxman","year":"2000","journal-title":"Ann Epidemiol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1038\/nrurol.2010.190","article-title":"The epidemiology of urinary tract infection","volume":"7","author":"B Foxman","year":"2010","journal-title":"Nat Rev Urol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1111\/1469-0691.12144","article-title":"Incidence of bloodstream infection: a review of population-based studies","volume":"19","author":"KB Laupland","year":"2013","journal-title":"Clin Microbiol Infect"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1086\/344649","article-title":"Epidemiology of bloodstream infection in nursing home residents: evaluation in a large cohort from multiple homes","volume":"35","author":"JM Mylotte","year":"2002","journal-title":"Clin Infect Dis"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1086\/339809","article-title":"Reappraisal of community-acquired bacteremia: a proposal of a new classification for the spectrum of acquisition of bacteremia","volume":"34","author":"Y Siegman-Igra","year":"2002","journal-title":"Clin Infect Dis"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"3983","DOI":"10.1128\/IAI.68.7.3983-3989.2000","article-title":"Prevalence of virulence genes and clonality in Escherichia coli strains that cause bacteremia in cancer patients","volume":"68","author":"F Hilali","year":"2000","journal-title":"Infect Immun"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1128\/CMR.00031-13","article-title":"Early-onset neonatal sepsis","volume":"27","author":"KA Simonsen","year":"2014","journal-title":"Clin Microbiol Rev"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1128\/CMR.00125-13","article-title":"Escherichia coli ST131, an intriguing clonal group","volume":"27","author":"MH Nicolas-Chanoine","year":"2014","journal-title":"Clin Microbiol Rev"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1101\/gr.180190.114","article-title":"Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains","volume":"25","author":"SJ Salipante","year":"2015","journal-title":"Genome Res"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"6881","DOI":"10.1128\/JB.00619-08","article-title":"The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates","volume":"190","author":"DA Rasko","year":"2008","journal-title":"J Bacteriol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1E 3 1","DOI":"10.1002\/9780471729259.mc01e03s36","article-title":"Genome-Wide Fitness and Genetic Interactions Determined by Tn-seq, a High-Throughput Massively Parallel Sequencing Method for Microorganisms","volume":"36","author":"T van Opijnen","year":"2015","journal-title":"Curr Protoc Microbiol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"e1003716","DOI":"10.1371\/journal.pgen.1003716","article-title":"Combining quantitative genetic footprinting and trait enrichment analysis to identify fitness determinants of a bacterial pathogen","volume":"9","author":"TJ Wiles","year":"2013","journal-title":"PLoS Genet"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e1000605","DOI":"10.1371\/journal.pcbi.1000605","article-title":"Annotation error in public databases: misannotation of molecular function in enzyme superfamilies","volume":"5","author":"AM Schnoes","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"2541","DOI":"10.1101\/gr.137430.112","article-title":"A fine scale phenotype-genotype virulence map of a bacterial pathogen","volume":"22","author":"T van Opijnen","year":"2012","journal-title":"Genome Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"3643","DOI":"10.1128\/JB.01836-14","article-title":"Towards an informative mutant phenotype for every bacterial gene","volume":"196","author":"A Deutschbauer","year":"2014","journal-title":"J Bacteriol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1146\/annurev.biochem.66.1.233","article-title":"Molybdenum-cofactor-containing enzymes: structure and mechanism","volume":"66","author":"C Kisker","year":"1997","journal-title":"Annu Rev Biochem"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"3235","DOI":"10.1128\/jb.177.11.3235-3240.1995","article-title":"DNA sequence and characterization of Haemophilus influenzae dprA+, a gene required for chromosomal but not plasmid DNA transformation","volume":"177","author":"S Karudapuram","year":"1995","journal-title":"J Bacteriol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"338","DOI":"10.7150\/ijbs.4.338","article-title":"Inducible SOS response system of DNA repair and mutagenesis in Escherichia coli","volume":"4","author":"C Janion","year":"2008","journal-title":"Int J Biol Sci"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"4604","DOI":"10.1093\/nar\/gks046","article-title":"Mycobacterium smegmatis RqlH defines a novel clade of bacterial RecQ-like DNA helicases with ATP-dependent 3&apos;-5&apos; translocase and duplex unwinding activities","volume":"40","author":"H Ordonez","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1093\/genetics\/28.6.491","article-title":"Mutations of Bacteria from Virus Sensitivity to Virus Resistance","volume":"28","author":"SE Luria","year":"1943","journal-title":"Genetics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1100","DOI":"10.1128\/JB.164.3.1100-1109.1985","article-title":"Transcription of the Escherichia coli fumarate reductase genes (frdABCD) and their coordinate regulation by oxygen, nitrate, and fumarate","volume":"164","author":"HM Jones","year":"1985","journal-title":"J Bacteriol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1459","DOI":"10.1534\/genetics.104.039107","article-title":"The exchangeability of amino acids in proteins","volume":"170","author":"LY Yampolsky","year":"2005","journal-title":"Genetics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"4080","DOI":"10.4161\/cc.9.20.13667","article-title":"Helicase-inactivating mutations as a basis for dominant negative phenotypes","volume":"9","author":"Y Wu","year":"2010","journal-title":"Cell Cycle"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1053\/j.gastro.2014.07.020","article-title":"Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota","volume":"147","author":"L Albenberg","year":"2014","journal-title":"Gastroenterology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"e1001187","DOI":"10.1371\/journal.ppat.1001187","article-title":"Escherichia coli global gene expression in urine from women with urinary tract infection","volume":"6","author":"EC Hagan","year":"2010","journal-title":"PLoS Pathog"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1146\/annurev-biochem-060713-035428","article-title":"Human RecQ helicases in DNA repair, recombination, and replication","volume":"83","author":"DL Croteau","year":"2014","journal-title":"Annu Rev Biochem"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"11070","DOI":"10.1073\/pnas.0504978102","article-title":"Obesity alters gut microbial ecology","volume":"102","author":"RE Ley","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e62578","DOI":"10.1371\/journal.pone.0062578","article-title":"Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome","volume":"8","author":"L Krych","year":"2013","journal-title":"PLoS One"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1128\/JB.126.3.1141-1148.1976","article-title":"Escherichia coli mutants deficient in guanine-xanthine phosphoribosyltransferase","volume":"126","author":"JA Holden","year":"1976","journal-title":"J Bacteriol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1016\/j.cell.2007.07.038","article-title":"A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA","volume":"130","author":"I Mortier-Barriere","year":"2007","journal-title":"Cell"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1111\/j.1574-6968.2006.00423.x","article-title":"Functional characterization of the competence protein DprA\/Smf in Escherichia coli","volume":"263","author":"LC Smeets","year":"2006","journal-title":"FEMS Microbiol Lett"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1111\/j.1365-2958.1993.tb01674.x","article-title":"comF, a Bacillus subtilis late competence locus, encodes a protein similar to ATP-dependent RNA\/DNA helicases","volume":"9","author":"JA Londono-Vallejo","year":"1993","journal-title":"Mol Microbiol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0378-1119(91)90457-M","article-title":"Nucleotide sequence of a cluster of genes involved in the transformation of Haemophilus influenzae Rd","volume":"104","author":"JF Tomb","year":"1991","journal-title":"Gene"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e16355","DOI":"10.1371\/journal.pone.0016355","article-title":"Cell-to-cell transformation in Escherichia coli: a novel type of natural transformation involving cell-derived DNA and a putative promoting pheromone","volume":"6","author":"R Etchuuya","year":"2011","journal-title":"PLoS One"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1111\/j.1574-6968.2006.00503.x","article-title":"Escherichia coli is naturally transformable in a novel transformation system","volume":"265","author":"D Sun","year":"2006","journal-title":"FEMS Microbiol Lett"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"e35620","DOI":"10.1371\/journal.pone.0035620","article-title":"Natural DNA uptake by Escherichia coli","volume":"7","author":"S Sinha","year":"2012","journal-title":"PLoS One"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"e26219","DOI":"10.4161\/mge.26219","article-title":"Toxin-antitoxin systems: Biology, identification, and application","volume":"3","author":"SJ Unterholzner","year":"2013","journal-title":"Mob Genet Elements"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e1002954","DOI":"10.1371\/journal.ppat.1002954","article-title":"Toxin-antitoxin systems are important for niche-specific colonization and stress resistance of uropathogenic Escherichia coli","volume":"8","author":"JP Norton","year":"2012","journal-title":"PLoS Pathog"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.molcel.2013.02.002","article-title":"Discovery of functional toxin\/antitoxin systems in bacteria by shotgun cloning","volume":"50","author":"H Sberro","year":"2013","journal-title":"Mol Cell"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1471-2199-4-11","article-title":"Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli","volume":"4","author":"KC Murphy","year":"2003","journal-title":"BMC Mol Biol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"e204","DOI":"10.1093\/nar\/gkt1075","article-title":"Positive and negative selection using the tetA-sacB cassette: recombineering and P1 transduction in Escherichia coli","volume":"41","author":"XT Li","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1073\/pnas.120163297","article-title":"One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products","volume":"97","author":"KA Datsenko","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"15623","DOI":"10.1073\/pnas.0506040102","article-title":"Insights into the organization and dynamics of bacterial chemoreceptor clusters through in vivo crosslinking studies","volume":"102","author":"CA Studdert","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1128\/jb.177.14.4121-4130.1995","article-title":"Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter","volume":"177","author":"LM Guzman","year":"1995","journal-title":"J Bacteriol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/978-1-62703-625-2_4","article-title":"Overlap extension PCR cloning","volume":"1073","author":"A Bryksin","year":"2013","journal-title":"Methods Mol Biol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH Image to ImageJ: 25 years of image analysis","volume":"9","author":"CA Schneider","year":"2012","journal-title":"Nat Methods"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"11181","DOI":"10.1074\/jbc.270.19.11181","article-title":"Control of the Escherichia coli rrnB P1 promoter strength by ppGpp","volume":"270","author":"X Zhang","year":"1995","journal-title":"J Biol Chem"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1093\/bioinformatics\/btp253","article-title":"Fluctuation analysis CalculatOR: a web tool for the determination of mutation rate using Luria-Delbruck fluctuation analysis","volume":"25","author":"BM Hall","year":"2009","journal-title":"Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"PJ Cock","year":"2009","journal-title":"Bioinformatics"}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1005317","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,28]],"date-time":"2022-05-28T10:04:00Z","timestamp":1653732240000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1005317"}},"subtitle":[],"editor":[{"given":"Tomoko","family":"Kubori","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2015,12,4]]},"references-count":51,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2015,12,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1005317","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,12,4]]}}}