{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T05:08:17Z","timestamp":1789189697230,"version":"build-2803163510"},"reference-count":50,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T00:00:00Z","timestamp":1789084800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SCHN371\/11\u20101"],"award-info":[{"award-number":["SCHN371\/11\u20101"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Microbiology"],"abstract":"ABSTRACT<\/jats:title>\n \n YdcI, a LysR\u2010type transcription regulator, has been associated with various phenotypes related to stress response and metabolic adaptation in\n \n Escherichia coli<\/jats:styled-content>\n and\n Salmonella enterica<\/jats:styled-content>\n <\/jats:italic>\n . This work addresses regulation of specific target loci by YdcI as well as regulation of\n ydcI<\/jats:italic>\n expression and YdcI synthesis in\n \n E. coli<\/jats:italic>\n <\/jats:styled-content>\n . DNA binding of YdcI to loci previously identified through ChIP\u2010exo analysis in\n \n E. coli<\/jats:italic>\n <\/jats:styled-content>\n K12 was validated for 10 loci by electrophoretic mobility shift assays. Two of these loci,\n iraP<\/jats:italic>\n and\n mqo<\/jats:italic>\n , are regulated by YdcI as shown using promoter\n lacZ<\/jats:italic>\n fusions, while regulation of the other loci is marginal, at least under the conditions tested. Our data suggest that YdcI acts as an H\u2010NS antagonist at the H\u2010NS repressed and (p)ppGpp\u2010dependent stress\u2010induced\n iraP<\/jats:italic>\n promoter. Gene\n iraP<\/jats:italic>\n encodes the RssB anti\u2010adaptor protein IraP that prevents RssB\u2010mediated targeting of RpoS for degradation.\n Gene mqo<\/jats:italic>\n , which is repressed by YdcI, encodes the TCA cycle enzyme malate: quinone oxidoreductase. Other YdcI bound loci encode enzymes involved in the TCA cycle, as well as membrane transport proteins. Furthermore, the transcription of the\n ydcI<\/jats:italic>\n gene itself is induced by the alarmone (p)ppGpp under phosphate stress conditions; it is not autoregulated, and a significant increase in YdcI protein levels occurs upon entry from early to mid\u2010exponential growth phase. Taken together, aspects of regulation by YdcI and of\n ydcI<\/jats:italic>\n expression as well as YdcI synthesis are presented that relate to its potential role in the response to abiotic stresses and control of metabolism in\n \n E. coli<\/jats:styled-content>\n <\/jats:italic>\n .\n <\/jats:p>","DOI":"10.1111\/mmi.70110","type":"journal-article","created":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T04:32:51Z","timestamp":1789187571000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Regulation by the Transcriptional Regulator\n YdcI<\/scp>\n in\n \n E. coli<\/i>\n <\/scp>\n and (p)\n ppGpp<\/scp>\n \u2010Dependent Activation of\n \n ydcI<\/i>\n <\/scp>\n Expression"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-4227-5336","authenticated-orcid":false,"given":"Ria Basu","family":"Roy","sequence":"first","affiliation":[{"name":"Department of Biology, Faculty of Mathematics and Natural Sciences, Institute for Genetics University of Cologne Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4693-6202","authenticated-orcid":false,"given":"Karin","family":"Schnetz","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Mathematics and Natural Sciences, Institute for Genetics University of Cologne Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,11]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The Galaxy Platform for Accessible, Reproducible and Collaborative Biomedical Analyses: 2016 Update","volume":"44","author":"Afgan E.","year":"2016","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_11_3_1","doi-asserted-by":"crossref","first-page":"2997","DOI":"10.1128\/JB.02013-07","article-title":"Dual Role of LldR in Regulation of the lldPRD Operon, Involved in L\u2010Lactate Metabolism in \n Escherichia coli","volume":"190","author":"Aguilera L.","year":"2008","journal-title":"Journal of Bacteriology"},{"key":"e_1_2_11_4_1","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2014A Python Framework to Work With High\u2010Throughput Sequencing Data","volume":"31","author":"Anders S.","year":"2014","journal-title":"Bioinformatics"},{"key":"e_1_2_11_5_1","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"Bailey T. 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