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To illuminate how this regulator controls expression of various target genes, we applied ChIP-seq and DNase I-seq technologies. Vibrio alginolyticus LuxR controls expression of \u223c280 genes that contain either symmetric palindrome (repDNA) or asymmetric (actDNA) binding motifs with different binding profiles. The median number of LuxR binding sites for activated genes are nearly double for that of repressed genes. Crystal structures of LuxR in complex with the respective repDNA and actDNA motifs revealed a new mode of LuxR DNA binding that involves contacts of its N-terminal extension to the minor groove. The N-terminal contacts mediated by Arginine-9 and Arginine-11 differ when LuxR binds to repDNA vs actDNA, leading to higher binding affinity at repressed targets. Moreover, modification of LuxR binding sites, binding profiles, and N-terminal extension have important consequences on QS-regulated phenotypes. These results facilitate fundamental understanding of the high flexibility of mechanisms of LuxR control of gene activation and repression in Vibrio QS, which may facilitate to design QS inhibiting chemicals that interfere with LuxR regulation to effectively control pathogens.<\/jats:p>","DOI":"10.1093\/nar\/gkab150","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T12:30:59Z","timestamp":1614083459000},"page":"3274-3293","source":"Crossref","is-referenced-by-count":39,"title":["Binding site profiles and N-terminal minor groove interactions of the master quorum-sensing regulator LuxR enable flexible control of gene activation and repression"],"prefix":"10.1093","volume":"49","author":[{"given":"Jun","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Liu","sequence":"additional","affiliation":[{"name":"Institut de Biotecnologia i Biomedicina, Dept. de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona, 08193 Bellaterra, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Gu","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory of Zoonosis\/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Hao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mo","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Ma","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohui","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT 06269, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Reverter","sequence":"additional","affiliation":[{"name":"Institut de Biotecnologia i Biomedicina, Dept. de Bioqu\u00edmica i Biologia Molecular, Universitat Aut\u00f2noma de Barcelona, 08193 Bellaterra, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanxing","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China"},{"name":"Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), 519000\u00a0Zhuhai, China"},{"name":"Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7494-0869","authenticated-orcid":false,"given":"Qiyao","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China"},{"name":"Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China"},{"name":"Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,3,8]]},"reference":[{"key":"2021040616380338600_B1","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1038\/nrmicro.2016.89","article-title":"Quorum sensing signal-response systems in Gram-negative bacteria","volume":"14","author":"Papenfort","year":"2016","journal-title":"Nat. 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