{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T15:40:19Z","timestamp":1785426019587,"version":"3.56.0"},"reference-count":90,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32260233"],"award-info":[{"award-number":["32260233"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32260233"],"award-info":[{"award-number":["32260233"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015397","name":"Inner Mongolia Autonomous Region Science and Technology Plan Project","doi-asserted-by":"publisher","award":["2025KYPT0131"],"award-info":[{"award-number":["2025KYPT0131"]}],"id":[{"id":"10.13039\/501100015397","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: The \u03c3 factor of bacterial RNA polymerase (RNAP) directs promoter recognition, recruits RNAP to initiate transcription, and is released from the elongation complex to participate in subsequent rounds of initiation. However, the dynamic recycling mechanism of the primary \u03c3 factor, \u03c370 (RpoD), during transcription in Escherichia coli remains poorly understood. Methods: We employed in vivo and in vitro interaction assays to screen for \u03c370-interacting partners under different growth conditions. Protein localization studies were performed using fluorescence microscopy. The transcriptomic profile of \u0394clpB, \u0394dnaK, \u0394htpG, or \u0394yhgF mutant was assessed by RNA-seq. Results: The molecular chaperones ClpB, DnaK, HtpG, and the RNA-binding protein YhgF interacts with RpoD both in vivo and in vitro, and the interaction in vivo is growth medium-dependent (LB vs. ABTGcasa). During exponential growth, each of these proteins co-localizes with the nucleoid. The transcriptome profile in \u0394clpB, \u0394htpG or \u0394yhgF mutant is mutant-specific to some extent; differentially expressed genes (DEGs) associated with amino acid metabolism and lipopolysaccharide biosynthesis are down-regulated in \u0394clpB, \u0394htpG or \u0394yhgF mutant in a manner that is growth medium-dependent, in agreement with the medium-dependent interaction of RpoD with the chaperones and YhgF. In contrast, the absence of DnaK resulted in delays to initiation of replication with a slow growth, and decreases cell motility, accompanied by down-regulated flagellar assembly and up-regulated amino acid metabolism genes. In summary, ClpB, DnaK, HtpG, and YhgF may regulate transcription by directly interacting with \u03c370. The \u03c3 factor recycling guides global transcription to select genes for transcription and subsequently allows cells to cope with the changing environments by responding to the nutrient level as a signal.<\/jats:p>","DOI":"10.3390\/genes17060621","type":"journal-article","created":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T06:17:31Z","timestamp":1780467451000},"page":"621","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Roles of Molecular Chaperones Interacting with the \u03c370 Factor in Global Transcription of the Escherichia coli Genome"],"prefix":"10.3390","volume":"17","author":[{"given":"Jianlu","family":"Jiao","sequence":"first","affiliation":[{"name":"Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Wu","sequence":"additional","affiliation":[{"name":"Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China"},{"name":"Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoli","family":"Lv","sequence":"additional","affiliation":[{"name":"Department of Pharmacology of Pharmaceutical College, Inner Mongolia Medical University, Hohhot 010110, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morigen","family":"Morigen","sequence":"additional","affiliation":[{"name":"Inner Mongolia Key Laboratory for Molecular Regulation of the Cell, School of Life Sciences, Inner Mongolia University, Hohhot 010020, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"66","DOI":"10.4161\/trns.1.2.12791","article-title":"The interaction between bacterial transcription factors and RNA polymerase during the transition from initiation to elongation","volume":"1","author":"Yang","year":"2010","journal-title":"Transcription"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1139\/cjm-2016-0576","article-title":"The essential activities of the bacterial sigma factor","volume":"63","author":"Davis","year":"2017","journal-title":"Can. 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