{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T18:46:05Z","timestamp":1787856365003,"version":"build-2784847793"},"reference-count":100,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T00:00:00Z","timestamp":1739923200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Netherlands Food Safety and Consumer Product Safety Authority"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Bacteria can quickly adapt to sub-lethal concentrations of antibiotics. Several stress and DNA repair genes contribute to this adaptation process. However, the pathways leading to adaptation by acquisition of <jats:italic>de novo<\/jats:italic> mutations remain poorly understood. This study explored the roles of DNA polymerase IV (<jats:italic>dinB<\/jats:italic>) and catalase HP2 (<jats:italic>katE<\/jats:italic>) in <jats:italic>E<\/jats:italic>. <jats:italic>coli<\/jats:italic>\u2019s adaptation to amoxicillin. These genes are thought to play essential roles in beta-lactam resistance\u2014<jats:italic>dinB<\/jats:italic> in increasing mutation rates and <jats:italic>katE<\/jats:italic> in managing oxidative stress. By comparing the adaptation rates, transcriptomic profiles, and genetic changes of wild-type and knockout strains, we aimed to clarify the contributions of these genes to beta-lactam resistance. While all strains exhibited similar adaptation rates and mutations in the <jats:italic>frdD<\/jats:italic> gene and <jats:italic>ampC<\/jats:italic> operon, several unique mutations were acquired in the \u0394<jats:italic>katE<\/jats:italic> and \u0394<jats:italic>dinB<\/jats:italic> strains. Overall, this study distinguishes the contributions of general stress-related genes on the one hand, and <jats:italic>dinB<\/jats:italic>, and <jats:italic>katE<\/jats:italic> on the other hand, in development of beta-lactam resistance.<\/jats:p>","DOI":"10.1371\/journal.pone.0312223","type":"journal-article","created":{"date-parts":[[2025,2,19]],"date-time":"2025-02-19T18:23:11Z","timestamp":1739989391000},"page":"e0312223","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Genetic adaptation to amoxicillin in Escherichia coli: The limited role of dinB and katE"],"prefix":"10.1371","volume":"20","author":[{"given":"Lisa","family":"Teichmann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus","family":"Wenne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sam","family":"Luitwieler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gaurav","family":"Dugar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan","family":"Bengtsson-Palme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8523-8135","authenticated-orcid":true,"given":"Benno","family":"ter Kuile","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,2,19]]},"reference":[{"issue":"8","key":"pone.0312223.ref001","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/s41579-023-00877-3","article-title":"Bacterial defences: mechanisms, evolution and antimicrobial resistance","volume":"21","author":"WPJ Smith","year":"2023","journal-title":"Nat Rev Microbiol"},{"issue":"7","key":"pone.0312223.ref002","doi-asserted-by":"crossref","first-page":"2248","DOI":"10.1128\/JB.01726-08","article-title":"The molecular alarmone (p)ppGpp mediates stress responses, vancomycin tolerance, and virulence in Enterococcus faecalis","volume":"191","author":"J Abranches","year":"2009","journal-title":"J Bacteriol"},{"issue":"31","key":"pone.0312223.ref003","doi-asserted-by":"crossref","first-page":"11685","DOI":"10.1074\/jbc.REV119.005593","article-title":"Trouble is coming: Signaling pathways that regulate general stress responses in bacteria","volume":"294","author":"S. 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