Structural insights into transcription regulation of the global virulence factor PhoP from Mycobacterium tuberculosis

Structural insights into transcription regulation of the global virulence factor PhoP from Mycobacterium tuberculosis | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Structural insights into transcription regulation of the global virulence factor PhoP from Mycobacterium tuberculosis Jing Shi, Qian Song, Zhenzhen Feng, Aijia Wen, Tianyu Liu, Liqiao Xu, and 9 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4428360/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 13 Feb, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Abstract Mycobacterium tuberculosis (Mtb), remaining as the leading cause of the worldwide threat Tuberculosis, relies heavily on its transcriptional reprogramming of diverse stress genes to swiftly adapt to adverse environments and ensure infections. The global virulence factor PhoP plays a pivotal role in coordinating transcription activation or repression of the essential phosphate-nitrogen metabolic remodeling genes. However, what defines PhoP to deferentially act as an activator or a repressor remains largely unexplored. Here, we determine one cryo-EM structure of Mtb RNAP-promoter open complex, three cryo-EM structures of PhoP-dependent transcription activation complexes (PhoP-TACs) consisting of Mtb RNA polymerase (RNAP), different number of PhoP molecules binding to different types of well-characterized consensus promoters, and one cryo-EM structure of Mtb PhoP-dependent transcription repression complex (PhoP-TRC) comprising of Mtb RNAP, PhoP, the nitrogen metabolism regulator GlnR and their co-regulated promoter. Structural comparisons reveal phosphorylation of PhoP is required for stabilization of PhoP-TACs, PhoP specifically recognizes promoters as novel tandem dimers and recruits RNAP through extensively interacting with its conserved β flap and σAR4 domains. Strikingly, the distinct promoter spacer length and PhoP-GlnR interactions in PhoP-TRC constrain the upstream DNA into a distinct topology and retain PhoP in a novel ‘dragging repression mode’. Collectively, these data highlight the dual regulatory mechanisms of PhoP-dependent transcription regulation in governing stress adaptation. These findings provide structural basis for developing potential anti-tuberculosis drugs and/or interventions. Health sciences/Pathogenesis/Infection Biological sciences/Microbiology/Pathogens Biological sciences/Microbiology/Microbial genetics/Bacterial genes Biological sciences/Molecular biology/Transcription/Transcriptional regulatory elements Biological sciences/Drug discovery/Target identification Mycobacterium tuberculosis PhoP cryo-EM structure PhoP-TACs PhoP-TRC Full Text Additional Declarations There is NO Competing Interest. Table 1 is available in the Supplementary Files section. Supplementary Files Table.pdf RPoPDBvalidationreport8XED.pdf Dataset 1 2PhoPTACvalidationreport8XEC.pdf Dataset 2 4PhoPTACvalidationreport8XEB.pdf Dataset 3 6PhoPTACvalidationreport8X8B.pdf Dataset 4 PhoPTRCvalidationreport8X8D.pdf Dataset 5 20240516Supplementaryinformation.docx Cite Share Download PDF Status: Published Journal Publication published 13 Feb, 2025 Read the published version in Nature Communications → Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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PhoP-TRC","lastPublishedDoi":"10.21203/rs.3.rs-4428360/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4428360/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Mycobacterium tuberculosis (Mtb), remaining as the leading cause of the worldwide threat Tuberculosis, relies heavily on its transcriptional reprogramming of diverse stress genes to swiftly adapt to adverse environments and ensure infections. The global virulence factor PhoP plays a pivotal role in coordinating transcription activation or repression of the essential phosphate-nitrogen metabolic remodeling genes. However, what defines PhoP to deferentially act as an activator or a repressor remains largely unexplored. Here, we determine one cryo-EM structure of Mtb RNAP-promoter open complex, three cryo-EM structures of PhoP-dependent transcription activation complexes (PhoP-TACs) consisting of Mtb RNA polymerase (RNAP), different number of PhoP molecules binding to different types of well-characterized consensus promoters, and one cryo-EM structure of Mtb PhoP-dependent transcription repression complex (PhoP-TRC) comprising of Mtb RNAP, PhoP, the nitrogen metabolism regulator GlnR and their co-regulated promoter. Structural comparisons reveal phosphorylation of PhoP is required for stabilization of PhoP-TACs, PhoP specifically recognizes promoters as novel tandem dimers and recruits RNAP through extensively interacting with its conserved β flap and σAR4 domains. Strikingly, the distinct promoter spacer length and PhoP-GlnR interactions in PhoP-TRC constrain the upstream DNA into a distinct topology and retain PhoP in a novel ‘dragging repression mode’. Collectively, these data highlight the dual regulatory mechanisms of PhoP-dependent transcription regulation in governing stress adaptation. These findings provide structural basis for developing potential anti-tuberculosis drugs and/or interventions.","manuscriptTitle":"Structural insights into transcription regulation of the global virulence factor PhoP from Mycobacterium tuberculosis","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-05-24 04:36:27","doi":"10.21203/rs.3.rs-4428360/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"25326e5f-f4e7-4f59-bbac-f255b2a73501","owner":[],"postedDate":"May 24th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":32319725,"name":"Health sciences/Pathogenesis/Infection"},{"id":32319726,"name":"Biological sciences/Microbiology/Pathogens"},{"id":32319727,"name":"Biological sciences/Microbiology/Microbial genetics/Bacterial genes"},{"id":32319728,"name":"Biological sciences/Molecular biology/Transcription/Transcriptional regulatory elements"},{"id":32319729,"name":"Biological sciences/Drug discovery/Target identification"}],"tags":[],"updatedAt":"2025-02-14T08:05:23+00:00","versionOfRecord":{"articleIdentity":"rs-4428360","link":"https://doi.org/10.1038/s41467-025-56697-x","journal":{"identity":"nature-communications","isVorOnly":false,"title":"Nature Communications"},"publishedOn":"2025-02-13 05:00:00","publishedOnDateReadable":"February 13th, 2025"},"versionCreatedAt":"2024-05-24 04:36:27","video":"","vorDoi":"10.1038/s41467-025-56697-x","vorDoiUrl":"https://doi.org/10.1038/s41467-025-56697-x","workflowStages":[]},"version":"v1","identity":"rs-4428360","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4428360","identity":"rs-4428360","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}