{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,20]],"date-time":"2026-04-20T22:59:21Z","timestamp":1776725961264,"version":"3.51.2"},"reference-count":49,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T00:00:00Z","timestamp":1712707200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec><jats:title>Introduction\/objective<\/jats:title><jats:p>Suppression of the SOS response in combination with drugs damaging DNA has been proposed as a potential target to tackle antimicrobial resistance. The SOS response is the pathway used to repair bacterial DNA damage induced by antimicrobials such as quinolones. The extent of <jats:italic>lexA<\/jats:italic>-regulated protein expression and other associated systems under pressure of agents that damage bacterial DNA in clinical isolates remains unclear. The aim of this study was to assess the impact of this strategy consisting on suppression of the SOS response in combination with quinolones on the proteome profile of <jats:italic>Escherichia coli<\/jats:italic> clinical strains.<\/jats:p><\/jats:sec><jats:sec><jats:title>Materials and methods<\/jats:title><jats:p>Five clinical isolates of <jats:italic>E. coli<\/jats:italic> carrying different chromosomally- and\/or plasmid-mediated quinolone resistance mechanisms with different phenotypes were selected, with <jats:italic>E. coli<\/jats:italic> ATCC 25922 as control strain. In addition, from each clinical isolate and control, a second strain was created, in which the SOS response was suppressed by deletion of the <jats:italic>recA<\/jats:italic> gene. Bacterial inocula from all 12 strains were then exposed to 1xMIC ciprofloxacin treatment (relative to the wild-type phenotype for each isogenic pair) for 1\u2009h. Cell pellets were collected, and proteins were digested into peptides using trypsin. Protein identification and label-free quantification were done by liquid chromatography-mass spectrometry (LC\u2013MS) in order to identify proteins that were differentially expressed upon deletion of <jats:italic>recA<\/jats:italic> in each strain. Data analysis and statistical analysis were performed using the MaxQuant and Perseus software.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The proteins with the lowest expression levels were: RecA (as control), AphA, CysP, DinG, DinI, GarL, PriS, PsuG, PsuK, RpsQ, UgpB and YebG; those with the highest expression levels were: Hpf, IbpB, TufB and RpmH. Most of these expression alterations were strain-dependent and involved DNA repair processes and nucleotide, protein and carbohydrate metabolism, and transport. In isolates with suppressed SOS response, the number of underexpressed proteins was higher than overexpressed proteins.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>High genomic and proteomic variability was observed among clinical isolates and was not associated with a specific resistant phenotype. This study provides an interesting approach to identify new potential targets to combat antimicrobial resistance.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmicb.2024.1379534","type":"journal-article","created":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T04:43:16Z","timestamp":1712724196000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["Impact of suppression of the SOS response on protein expression in clinical isolates of Escherichia coli under antimicrobial pressure of ciprofloxacin"],"prefix":"10.3389","volume":"15","author":[{"given":"Esther","family":"Recacha","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benno","family":"Kuropka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sara","family":"D\u00edaz-D\u00edaz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Garc\u00eda-Montaner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enrique","family":"Gonz\u00e1lez-Tortuero","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fernando","family":"Docobo-P\u00e9rez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandro","family":"Rodr\u00edguez-Rojas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jose Manuel","family":"Rodr\u00edguez-Mart\u00ednez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2024,4,10]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1126","DOI":"10.1111\/1574-6976.12077","article-title":"SOS, the formidable strategy of bacteria against aggressions","volume":"38","author":"Baharoglu","year":"2014","journal-title":"FEMS Microbiol. Rev."},{"key":"ref9001","doi-asserted-by":"publisher","first-page":"4382","DOI":"10.1128\/JCM.43.9.4382-4390.2005","article-title":"Development of a multilocus sequence typing scheme for characterization of clinical isolates of Acinetobacter baumannii","volume":"43","author":"Bartual","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1016\/j.ijantimicag.2011.12.009","article-title":"Prevalence of plasmid-mediated quinolone resistance determinants qnr and aac(6\u2032)-Ib-cr in Escherichia coli and Klebsiella pneumoniae producing extended-spectrum \u03b2-lactamases in Spain","volume":"39","author":"Briales","year":"2012","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1128\/JB.01464-06","article-title":"Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin","volume":"189","author":"Cirz","year":"2007","journal-title":"J. Bacteriol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"7101","DOI":"10.1128\/JB.00807-06","article-title":"Defining the Pseudomonas aeruginosa SOS response and its role in the global response to the antibiotic ciprofloxacin","volume":"188","author":"Cirz","year":"2006","journal-title":"J. Bacteriol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1093\/genetics\/158.1.41","article-title":"Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli","volume":"158","author":"Courcelle","year":"2001","journal-title":"Genetics"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e1007405","DOI":"10.1371\/journal.pgen.1007405","article-title":"Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network","volume":"14","author":"Culyba","year":"2018","journal-title":"PLoS Genet."},{"key":"ref9","doi-asserted-by":"publisher","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":"Datsenko","year":"2000","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"Emms","year":"2015","journal-title":"Genome Biol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1046\/j.1365-2958.2000.01826.x","article-title":"Identification of additional genes belonging to the LexA regulon in Escherichia coli","volume":"35","author":"Fern\u00e1ndez De Henestrosa","year":"2000","journal-title":"Mol. Microbiol."},{"key":"ref9002","doi-asserted-by":"publisher","first-page":"770","DOI":"10.1128\/JCM.01796-09","article-title":"Multilocus sequence typing of Clostridium difficile","volume":"48","author":"Griffiths","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"ref9003","doi-asserted-by":"publisher","first-page":"D192","DOI":"10.1093\/nar\/gkaa1047","article-title":"Rfam 14: expanded coverage of metagenomic, viral and microRNA families","volume":"49","author":"Kalvari","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1146\/annurev-micro-092412-155708","article-title":"Mechanisms of acid resistance in Escherichia coli","volume":"67","author":"Kanjee","year":"2013","journal-title":"Annu. Rev. Microbiol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"2018","DOI":"10.1128\/ecosalplus.ESP-0006-2018","article-title":"The EcoCyc database","volume":"8","author":"Karp","year":"2018","journal-title":"EcoSal Plus"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1146\/annurev.micro.59.030804.121255","article-title":"Interplay between DNA replication and recombination in prokaryotes","volume":"59","author":"Kreuzer","year":"2005","journal-title":"Annu. Rev. Microbiol."},{"key":"ref9004","doi-asserted-by":"publisher","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus sequence typing of total-genome-sequenced bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J Clin Microbiol"},{"key":"ref9005","doi-asserted-by":"publisher","first-page":"2609","DOI":"10.1128\/JCM.42.6.2609-2617.2004","article-title":"Multilocus sequence typing analysis of human and animal Clostridium difficile isolates of various toxigenic types","volume":"42","author":"Lemee","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1111\/j.1574-6968.1997.tb12715.x","article-title":"Identification of yebG as a DNA damage-inducible Escherichia coli gene","volume":"156","author":"Lomba","year":"1997","journal-title":"FEMS Microbiol. Lett."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1126\/science.aba0862","article-title":"Clinically relevant mutations in core metabolic genes confer antibiotic resistance","volume":"371","author":"Lopatkin","year":"2021","journal-title":"Science"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.eimc.2012.09.005","article-title":"Escherichia coli O25b:H4\/ST131 are prevalent in Spain and are often not associated with ESBL or quinolone resistance","volume":"31","author":"L\u00f3pez-Cerero","year":"2013","journal-title":"Enferm. Infecc. Microbiol. Clin."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1370","DOI":"10.3389\/fmicb.2017.01370","article-title":"Cellular response to ciprofloxacin in low-level quinolone-resistant Escherichia coli","volume":"8","author":"Machuca","year":"2017","journal-title":"Front. Microbiol."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1093\/jac\/dkaa448","article-title":"Effect of RecA inactivation on quinolone susceptibility and the evolution of resistance in clinical isolates of Escherichia coli","volume":"76","author":"Machuca","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1128\/CMR.00116-14","article-title":"The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae","volume":"28","author":"Mathers","year":"2015","journal-title":"Clin. Microbiol. Rev."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"15025","DOI":"10.1016\/S0021-9258(17)42508-7","article-title":"Comparison of the basic Escherichia coli antizyme 1 and antizyme 2 with the ribosomal proteins S20\/L26 and L34","volume":"259","author":"Panagiotidis","year":"1984","journal-title":"J. Biol. Chem."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences","volume":"50","author":"Perez-Riverol","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"167054","DOI":"10.1016\/j.jmb.2021.167054","article-title":"Two bacterial small heat shock proteins, IbpA and IbpB, form a functional heterodimer","volume":"433","author":"Pir\u00f3g","year":"2021","journal-title":"J. Mol. Biol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"195","DOI":"10.12688\/f1000research.10609.1","article-title":"Escherichia coli ST131: a multidrug-resistant clone primed for global domination","volume":"6","author":"Pitout","year":"2017","journal-title":"F1000Res"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"25238","DOI":"10.1074\/jbc.M804122200","article-title":"Molecular identification of pseudouridine-metabolizing enzymes","volume":"283","author":"Preumont","year":"2008","journal-title":"J. Biol. Chem."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.1038\/nprot.2007.261","article-title":"Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips","volume":"2","author":"Rappsilber","year":"2007","journal-title":"Nat. Protoc."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1128\/mBio.00971-17","article-title":"Quinolone resistance reversion by targeting the SOS response","volume":"8","author":"Recacha","year":"2017","journal-title":"MBio"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1093\/jac\/dky407","article-title":"Suppression of the SOS response modifies spatiotemporal evolution, post-antibiotic effect, bacterial fitness and biofilm formation in quinolone-resistant Escherichia coli","volume":"74","author":"Recacha","year":"2019","journal-title":"J. Antimicrob. Chemother."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1093\/jac\/dkv392","article-title":"Assessment of a phenotypic algorithm to detect plasmid-mediated quinolone resistance in Enterobacteriaceae","volume":"71","author":"Rodr\u00edguez-Mart\u00ednez","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref9006","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.bbrc.2020.01.102","article-title":"ppGpp ribosome dimerization model for bacterial persister formation and resuscitation","volume":"523","author":"Song","year":"2020","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"2301","DOI":"10.1038\/nprot.2016.136","article-title":"The MaxQuant computational platform for mass spectrometry-based shotgun proteomics","volume":"11","author":"Tyanova","year":"","journal-title":"Nat. Protoc."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1038\/nmeth.3901","article-title":"The Perseus computational platform for comprehensive analysis of (prote)omics data","volume":"13","author":"Tyanova","year":"","journal-title":"Nat. Methods"},{"key":"ref902","doi-asserted-by":"publisher","first-page":"2699","DOI":"10.1093\/nar\/gky092","article-title":"UniProt: the universal protein knowledgebase","volume":"46","author":"The UniProt Consortium","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1146\/annurev.micro.62.081307.162938","article-title":"Regulation and function of Ag43 (flu)","volume":"62","author":"van der Woude","year":"2008","journal-title":"Annu. Rev. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1111\/j.1365-2958.1992.tb01516.x","article-title":"Elongation factor Tu: a molecular switch in protein biosynthesis","volume":"6","author":"Weijland","year":"1992","journal-title":"Mol. Microbiol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"736","DOI":"10.1111\/j.1574-6976.2011.00268.x","article-title":"Multiresistant gram-negative bacteria: the role of high-risk clones in the dissemination of antibiotic resistance","volume":"35","author":"Woodford","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1046\/j.1365-2958.2001.02345.x","article-title":"CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli","volume":"39","author":"Yamanaka","year":"2001","journal-title":"Mol. Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"3207","DOI":"10.1093\/emboj\/17.11.3207","article-title":"Inhibition of Escherichia coli RecA coprotease activities by DinI","volume":"17","author":"Yasuda","year":"1998","journal-title":"EMBO J."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1038\/s41579-021-00539-2","article-title":"A new general mechanism of AMR","volume":"19","author":"York","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1126\/science.abf7922","article-title":"The genetic underground of antibiotic resistance","volume":"371","author":"Zampieri","year":"2021","journal-title":"Science"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"2764","DOI":"10.1093\/jac\/dkx217","article-title":"PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens","volume":"72","author":"Zankari","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1379534\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T04:43:20Z","timestamp":1712724200000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2024.1379534\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4,10]]},"references-count":49,"alternative-id":["10.3389\/fmicb.2024.1379534"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2024.1379534","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,4,10]]},"article-number":"1379534"}}