{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T06:51:07Z","timestamp":1791528667753,"version":"4.3.4"},"reference-count":80,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T00:00:00Z","timestamp":1791504000000},"content-version":"vor","delay-in-days":17,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"French Agence Nationale de la Recherche","award":["ANR-22-CE44-0017"],"award-info":[{"award-number":["ANR-22-CE44-0017"]}],"id":[{"id":"https:\/\/ror.org\/00rbzpz17","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001677","name":"INSERM","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Rho-dependent transcription termination (RDTT) is crucial for bacterial gene regulation, fitness, and pathogenicity. RDTT relies on the ATP-dependent Rho helicase, which engages nascent transcripts at loosely defined, C\u00a0&amp;gt;\u00a0G-biased Rho utilization (Rut) sites to dismantle transcription complexes. In Mycobacterium tuberculosis, Rho features a unique, large N-terminal insertion domain (NID) of uncertain function. Using enzymatic Helicase-SELEX screening, we identified 1759 putative Rut sites across the M. tuberculosis genome with wild-type Rho (MtbRho) but only 47 with a NID-deleted variant (\u0394NID-MtbRho), demonstrating NID\u2019s importance for productive substrate recruitment. The selected Rut sites display an unusual composition and frequently occur upstream of or within coding regions, implying that MtbRho plays a broad role in conditional gene regulation. Integration with transcriptomics-defined RNA 3\u2032 ends further highlights the contribution of MtbRho to transcriptional plasticity, through both direct termination and downstream regulatory cascades. Complementary RDTT assays, affinity measurements, solution NMR, and cryogenic electron microscopy analyses show that the NID is intrinsically disordered, yet critical for engaging Rut sites with substantial secondary structure. Altogether, our findings provide the first genome-wide map and characterization of Rut sites in a GC-rich pathogen and define the NID as a model intrinsically disordered protein region with a critical mechanistic and functional role in mycobacterial gene expression<\/jats:p>","DOI":"10.1093\/nar\/gkag973","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T11:42:21Z","timestamp":1790682141000},"source":"Crossref","is-referenced-by-count":0,"title":["An intrinsically disordered domain of transcription terminator Rho governs genome-wide Rho utilization (\n                    <i>Rut<\/i>\n                    ) site selection in\n                    <i>Mycobacterium tuberculosis<\/i>"],"prefix":"10.1093","volume":"54","author":[{"given":"Thuy Duong","family":"Do","sequence":"first","affiliation":[{"name":"Centre de Biophysique Mol\u00e9culaire (CBM), CNRS UPR 4301, Orl\u00e9ans, affiliated with Universit\u00e9 d\u2019Orl\u00e9ans, rue Charles Sadron , 45071 Orl\u00e9ans cedex 2 ,","place":["France"]},{"name":"ED 549, Sciences Biologiques & Chimie du Vivant, Universit\u00e9 d\u2019Orl\u00e9ans , 450067 Orl\u00e9ans Cedex 2,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"Pino\u00a0Peco","sequence":"additional","affiliation":[{"name":"Institut de Recherche en Infectiologie de Montpellier (IRIM), Universit\u00e9 de Montpellier, CNRS , 34293 Montpellier Cedex 5,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Eveno","sequence":"additional","affiliation":[{"name":"Centre de Biophysique Mol\u00e9culaire (CBM), CNRS UPR 4301, Orl\u00e9ans, affiliated with Universit\u00e9 d\u2019Orl\u00e9ans, rue Charles Sadron , 45071 Orl\u00e9ans cedex 2 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charlotte","family":"Saint-Andr\u00e9","sequence":"additional","affiliation":[{"name":"Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U 1258, Universit\u00e9 de Strasbourg , 67404 Illkirch Cedex ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mildred","family":"Delaleau","sequence":"additional","affiliation":[{"name":"Centre de Biophysique Mol\u00e9culaire (CBM), CNRS UPR 4301, Orl\u00e9ans, affiliated with Universit\u00e9 d\u2019Orl\u00e9ans, rue Charles Sadron , 45071 Orl\u00e9ans cedex 2 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franck","family":"Coste","sequence":"additional","affiliation":[{"name":"Centre de Biophysique Mol\u00e9culaire (CBM), CNRS UPR 4301, Orl\u00e9ans, affiliated with Universit\u00e9 d\u2019Orl\u00e9ans, rue Charles Sadron , 45071 Orl\u00e9ans cedex 2 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Herv\u00e9","family":"Meudal","sequence":"additional","affiliation":[{"name":"Centre de Biophysique Mol\u00e9culaire (CBM), CNRS UPR 4301, Orl\u00e9ans, affiliated with Universit\u00e9 d\u2019Orl\u00e9ans, rue Charles Sadron , 45071 Orl\u00e9ans cedex 2 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Loth","sequence":"additional","affiliation":[{"name":"Centre de Biophysique Mol\u00e9culaire (CBM), CNRS UPR 4301, Orl\u00e9ans, affiliated with Universit\u00e9 d\u2019Orl\u00e9ans, rue Charles Sadron , 45071 Orl\u00e9ans cedex 2 ,","place":["France"]},{"name":"ED 549, Sciences Biologiques & Chimie du Vivant, Universit\u00e9 d\u2019Orl\u00e9ans , 450067 Orl\u00e9ans Cedex 2,","place":["France"]},{"name":"UFR Sciences et Technique, Universit\u00e9 d\u2019Orl\u00e9ans, 1 rue de Chartres , 450067 Orl\u00e9ans Cedex 2 ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert","family":"Weixlbaumer","sequence":"additional","affiliation":[{"name":"Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire (IGBMC), CNRS UMR 7104, Inserm U 1258, Universit\u00e9 de Strasbourg , 67404 Illkirch Cedex ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3124-7586","authenticated-orcid":false,"given":"Konstantin","family":"Brodolin","sequence":"additional","affiliation":[{"name":"Institut de Recherche en Infectiologie de Montpellier (IRIM), Universit\u00e9 de Montpellier, CNRS , 34293 Montpellier Cedex 5,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6398-9122","authenticated-orcid":false,"given":"Marc","family":"Boudvillain","sequence":"additional","affiliation":[{"name":"Centre de Biophysique Mol\u00e9culaire (CBM), CNRS UPR 4301, Orl\u00e9ans, affiliated with Universit\u00e9 d\u2019Orl\u00e9ans, rue Charles Sadron , 45071 Orl\u00e9ans cedex 2 ,","place":["France"]},{"name":"ED 549, Sciences Biologiques & Chimie du Vivant, Universit\u00e9 d\u2019Orl\u00e9ans , 450067 Orl\u00e9ans Cedex 2,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,9]]},"reference":[{"key":"2026100902313322700_B1","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1016\/0092-8674(91)90239-U","article-title":"A consensus motif common to all Rho-dependent prokaryotic transcription terminators","volume":"64","author":"Alifano","year":"1991","journal-title":"Cell"},{"key":"2026100902313322700_B2","doi-asserted-by":"publisher","first-page":"8245","DOI":"10.1093\/nar\/gky563","article-title":"A multivariate prediction model for Rho-dependent termination of transcription","volume":"46","author":"Nadiras","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B3","doi-asserted-by":"publisher","first-page":"e2209608119","DOI":"10.1073\/pnas.2209608119","article-title":"A scalable framework for the discovery of functional helicase substrates and helicase-driven regulatory switches","volume":"119","author":"Delaleau","year":"2022","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026100902313322700_B4","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1038\/s41586-022-05658-1","article-title":"Structural basis of Rho-dependent transcription termination","volume":"614","author":"Molodtsov","year":"2023","journal-title":"Nature"},{"key":"2026100902313322700_B5","doi-asserted-by":"publisher","first-page":"1401","DOI":"10.1073\/pnas.91.4.1401","article-title":"Evidence supporting a tethered tracking model for helicase activity of Escherichia coli Rho factor","volume":"91","author":"Steinmetz","year":"1994","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026100902313322700_B6","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/j.molcel.2020.11.013","article-title":"Pre-termination transcription complex: structure and function","volume":"81","author":"Hao","year":"2021","journal-title":"Mol Cell"},{"key":"2026100902313322700_B7","doi-asserted-by":"crossref","first-page":"eabd1673","DOI":"10.1126\/science.abd1673","article-title":"Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho","volume":"371","author":"Said","year":"2021","journal-title":"Science"},{"key":"2026100902313322700_B8","doi-asserted-by":"publisher","first-page":"1423","DOI":"10.1099\/mic.0.067462-0","article-title":"Phyletic distribution and conservation of the bacterial transcription termination factor Rho","volume":"159","author":"D\u2019Heygere","year":"2013","journal-title":"Microbiology"},{"key":"2026100902313322700_B9","doi-asserted-by":"publisher","first-page":"8979","DOI":"10.1093\/nar\/gkae582","article-title":"Diversification of the Rho transcription termination factor in bacteria","volume":"52","author":"Moreira","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B10","doi-asserted-by":"publisher","first-page":"eade7093","DOI":"10.1126\/sciadv.ade7093","article-title":"Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus","volume":"9","author":"Murayama","year":"2023","journal-title":"Sci Adv"},{"key":"2026100902313322700_B11","doi-asserted-by":"publisher","first-page":"1663","DOI":"10.1038\/s41467-022-29321-5","article-title":"Rho-dependent transcription termination proceeds via three routes","volume":"13","author":"Song","year":"2022","journal-title":"Nat Commun"},{"key":"2026100902313322700_B12","doi-asserted-by":"publisher","first-page":"2778","DOI":"10.1093\/nar\/gkad051","article-title":"Transcriptional pause extension benefits the stand-by rather than catch-up Rho-dependent termination","volume":"51","author":"Song","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B13","doi-asserted-by":"publisher","first-page":"e1008425","DOI":"10.1371\/journal.pgen.1008425","article-title":"NusG prevents transcriptional invasion of H-NS-silenced genes","volume":"15","author":"Bossi","year":"2019","journal-title":"PLoS Genet"},{"key":"2026100902313322700_B14","doi-asserted-by":"publisher","first-page":"9677","DOI":"10.1093\/nar\/gku690","article-title":"Redundancy of primary RNA-binding functions of the bacterial transcription terminator Rho","volume":"42","author":"Shashni","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B15","doi-asserted-by":"publisher","first-page":"1207","DOI":"10.1261\/rna.080486.125","article-title":"Rho-dependent transcription termination: mechanisms and roles in bacterial fitness and adaptation to environmental changes","volume":"31","author":"Do","year":"2025","journal-title":"RNA"},{"key":"2026100902313322700_B16","doi-asserted-by":"publisher","first-page":"14731","DOI":"10.1038\/ncomms14731","article-title":"Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death","volume":"8","author":"Botella","year":"2017","journal-title":"Nat Commun"},{"key":"2026100902313322700_B17","doi-asserted-by":"publisher","first-page":"935","DOI":"10.1126\/science.1152763","article-title":"Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli","volume":"320","author":"Cardinale","year":"2008","journal-title":"Science"},{"key":"2026100902313322700_B18","doi-asserted-by":"publisher","first-page":"106465","DOI":"10.1016\/j.isci.2023.106465","article-title":"Premature termination of transcription is shaped by Rho and translated uORFS in Mycobacterium tuberculosis","volume":"26","author":"D\u2019Halluin","year":"2023","journal-title":"iScience"},{"key":"2026100902313322700_B19","doi-asserted-by":"publisher","first-page":"2621","DOI":"10.1101\/gad.196741.112","article-title":"Rho and NusG suppress pervasive antisense transcription in Escherichia coli","volume":"26","author":"Peters","year":"2012","journal-title":"Genes Dev"},{"key":"2026100902313322700_B20","doi-asserted-by":"publisher","first-page":"3931","DOI":"10.1038\/s41467-023-39576-1","article-title":"Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi","volume":"14","author":"Petroni","year":"2023","journal-title":"Nat Commun"},{"key":"2026100902313322700_B21","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1042\/BCJ20253089","article-title":"The bacterial transcription terminator, Rho, functions as an RNA:DNA hybrid (RDH) helicase in vivo","volume":"482","author":"Bhosale","year":"2025","journal-title":"Biochem J"},{"key":"2026100902313322700_B22","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1073\/pnas.1213123110","article-title":"Rho-dependent transcription termination is essential to prevent excessive genome-wide R-loops in Escherichia coli","volume":"110","author":"Leela","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026100902313322700_B23","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1016\/j.cell.2011.07.034","article-title":"Linking RNA polymerase backtracking to genome instability in E. coli","volume":"146","author":"Dutta","year":"2011","journal-title":"Cell"},{"key":"2026100902313322700_B24","doi-asserted-by":"publisher","first-page":"1702","DOI":"10.1038\/s41467-022-28871-y","article-title":"Pervasive transcription-coupled DNA repair in E. coli","volume":"13","author":"Martinez","year":"2022","journal-title":"Nat Commun"},{"key":"2026100902313322700_B25","doi-asserted-by":"publisher","first-page":"2347","DOI":"10.1038\/s41564-019-0543-1","article-title":"Disruption of transcription-translation coordination in Escherichia coli leads to premature transcriptional termination","volume":"4","author":"Zhu","year":"2019","journal-title":"Nat Microbiol"},{"key":"2026100902313322700_B26","doi-asserted-by":"publisher","first-page":"194501","DOI":"10.1016\/j.bbagrm.2020.194501","article-title":"Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins","volume":"1863","author":"Bedard","year":"2020","journal-title":"Biochim Biophys Acta"},{"key":"2026100902313322700_B27","doi-asserted-by":"publisher","first-page":"194546","DOI":"10.1016\/j.bbagrm.2020.194546","article-title":"Regulatory interplay between small RNAs and transcription termination factor Rho","volume":"1863","author":"Bossi","year":"2020","journal-title":"Biochim Biophys Acta"},{"key":"2026100902313322700_B28","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1016\/j.tibs.2016.05.012","article-title":"Learning from the leaders: gene regulation by the transcription termination factor Rho","volume":"41","author":"Kriner","year":"2016","journal-title":"Trends Biochem Sci"},{"key":"2026100902313322700_B29","doi-asserted-by":"publisher","first-page":"3482","DOI":"10.1016\/j.molcel.2024.07.034","article-title":"Rho-dependent transcriptional switches regulate the bacterial response to cold shock","volume":"84","author":"Delaleau","year":"2024","journal-title":"Mol Cell"},{"key":"2026100902313322700_B30","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1101\/gad.240192.114","article-title":"RNA remodeling by bacterial global regulator CsrA promotes Rho-dependent transcription termination","volume":"28","author":"Figueroa-Bossi","year":"2014","journal-title":"Genes Dev"},{"key":"2026100902313322700_B31","doi-asserted-by":"publisher","first-page":"e1010618","DOI":"10.1371\/journal.pgen.1010618","article-title":"Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase","volume":"19","author":"Bidnenko","year":"2023","journal-title":"PLoS Genet"},{"key":"2026100902313322700_B32","doi-asserted-by":"publisher","first-page":"6797","DOI":"10.1093\/nar\/gky274","article-title":"High-resolution RNA 3'-ends mapping of bacterial Rho-dependent transcripts","volume":"46","author":"Dar","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B33","doi-asserted-by":"publisher","first-page":"gkaf765","DOI":"10.1093\/nar\/gkaf765","article-title":"Comprehensive mapping of transcription terminator Rho utilization (Rut) sites across the Bacillus subtilis genome","volume":"53","author":"Delaleau","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B34","doi-asserted-by":"publisher","first-page":"4440","DOI":"10.1073\/pnas.1813181116","article-title":"Processing generates 3' ends of RNA masking transcription termination events in prokaryotes","volume":"116","author":"Wang","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026100902313322700_B35","first-page":"1516","article-title":"The Rho termination factor of Clostridium botulinum contains a prion-like domain with a highly amyloidogenic core","volume":"6","author":"Pallares","year":"2015","journal-title":"Front Microbiol"},{"key":"2026100902313322700_B36","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1126\/science.abn7229","article-title":"Bacteria require phase separation for fitness in the mammalian gut","volume":"379","author":"Krypotou","year":"2023","journal-title":"Science"},{"key":"2026100902313322700_B37","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s42003-022-03069-6","article-title":"Cryo-EM structure of transcription termination factor Rho from Mycobacterium tuberculosis reveals bicyclomycin resistance mechanism","volume":"5","author":"Saridakis","year":"2022","journal-title":"Commun Biol"},{"key":"2026100902313322700_B38","doi-asserted-by":"publisher","first-page":"6099","DOI":"10.1093\/nar\/gkv505","article-title":"ATP-dependent motor activity of the transcription termination factor Rho from Mycobacterium tuberculosis","volume":"43","author":"D\u2019Heygere","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B39","doi-asserted-by":"publisher","first-page":"167060","DOI":"10.1016\/j.jmb.2021.167060","article-title":"A large insertion domain in the Rho factor from a low G+C, Gram-negative bacterium is critical for RNA binding and transcription termination activity","volume":"433","author":"Simon","year":"2021","journal-title":"J Mol Biol"},{"key":"2026100902313322700_B40","doi-asserted-by":"publisher","first-page":"194923","DOI":"10.1016\/j.bbagrm.2023.194923","article-title":"Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis","volume":"1866","author":"Ahmad","year":"2023","journal-title":"Biochim Biophy Acta"},{"key":"2026100902313322700_B41","doi-asserted-by":"publisher","first-page":"e107474","DOI":"10.1371\/journal.pone.0107474","article-title":"Mycobacterium tuberculosis Rho is an NTPase with distinct kinetic properties and a novel RNA-binding subdomain","volume":"9","author":"Mitra","year":"2014","journal-title":"PLoS One"},{"key":"2026100902313322700_B42","doi-asserted-by":"publisher","first-page":"742","DOI":"10.1074\/jbc.271.2.742","article-title":"Characterization of an unusual Rho factor from the high G+C Gram-positive bacterium Micrococcus luteus","volume":"271","author":"Nowatzke","year":"1996","journal-title":"J Biol Chem"},{"key":"2026100902313322700_B43","doi-asserted-by":"publisher","first-page":"2207","DOI":"10.1074\/jbc.272.4.2207","article-title":"Function of the novel subdomain in the RNA binding domain of transcription termination factor Rho from Micrococcus luteus","volume":"272","author":"Nowatzke","year":"1997","journal-title":"J Biol Chem"},{"key":"2026100902313322700_B44","doi-asserted-by":"publisher","first-page":"3088","DOI":"10.1038\/s41467-024-47410-5","article-title":"Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis","volume":"15","author":"Bei","year":"2024","journal-title":"Nat Commun"},{"key":"2026100902313322700_B45","doi-asserted-by":"publisher","first-page":"5445","DOI":"10.1021\/jf070337l","article-title":"Prediction of molar extinction coefficients of proteins and peptides using UV absorption of the constituent amino acids at 214 nm to enable quantitative reverse phase high-performance liquid chromatography-mass spectrometry analysis","volume":"55","author":"Kuipers","year":"2007","journal-title":"J Agric Food Chem"},{"key":"2026100902313322700_B46","doi-asserted-by":"publisher","first-page":"10399","DOI":"10.1093\/nar\/gku742","article-title":"Mycobacterium RbpA cooperates with the stress-response sigmaB subunit of RNA polymerase in promoter DNA unwinding","volume":"42","author":"Hu","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B47","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1038\/s41467-023-36113-y","article-title":"Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization","volume":"14","author":"Morichaud","year":"2023","journal-title":"Nat Commun"},{"key":"2026100902313322700_B48","doi-asserted-by":"publisher","first-page":"6547","DOI":"10.1093\/nar\/gks346","article-title":"Mycobacterium tuberculosis RbpA protein is a new type of transcriptional activator that stabilizes the sigma A-containing RNA polymerase holoenzyme","volume":"40","author":"Hu","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B49","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/j.jmb.2004.07.026","article-title":"Influence of substrate composition on the helicase activity of transcription termination factor Rho: reduced processivity of Rho hexamers during unwinding of RNA\u2013DNA hybrid regions","volume":"342","author":"Walmacq","year":"2004","journal-title":"J Mol Biol"},{"key":"2026100902313322700_B50","doi-asserted-by":"publisher","first-page":"9270","DOI":"10.1093\/nar\/gku595","article-title":"The RNA-mediated, asymmetric ring regulatory mechanism of the transcription termination Rho helicase decrypted by time-resolved Nucleotide Analog Interference Probing (trNAIP)","volume":"42","author":"Soares","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B51","doi-asserted-by":"publisher","first-page":"5428","DOI":"10.1073\/pnas.90.12.5428","article-title":"A double-filter method for nitrocellulose-filter binding: application to protein-nucleic acid interactions","volume":"90","author":"Wong","year":"1993","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026100902313322700_B52","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nmeth.4169","article-title":"cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination","volume":"14","author":"Punjani","year":"2017","journal-title":"Nat Methods"},{"key":"2026100902313322700_B53","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2026100902313322700_B54","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1002\/pro.3235","article-title":"UCSF ChimeraX: meeting modern challenges in visualization and analysis","volume":"27","author":"Goddard","year":"2018","journal-title":"Protein Sci"},{"key":"2026100902313322700_B55","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"2026100902313322700_B56","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1107\/S2059798319011471","article-title":"Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix","volume":"75","author":"Liebschner","year":"2019","journal-title":"Acta Crystallogr D Struct Biol"},{"key":"2026100902313322700_B57","doi-asserted-by":"publisher","first-page":"966","DOI":"10.1016\/j.jmb.2009.12.022","article-title":"A bacterial transcription terminator with inefficient molecular motor action but with a robust transcription termination function","volume":"395","author":"Kalarickal","year":"2010","journal-title":"J Mol Biol"},{"key":"2026100902313322700_B58","unstructured":"Bischler T, F\u00f6rstner K, Maticzka D \u00a0et al. \u00a0v0.2.0 ed, Zenodo.org, 2021."},{"key":"2026100902313322700_B59","doi-asserted-by":"publisher","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B60","doi-asserted-by":"publisher","article-title":"The RpfB switch is a novel B12-sensing riboswitch regulating (non-replicating) persistence in Mycobacterium tuberculosis","author":"Kipkorir","DOI":"10.1101\/2024.07.19.603033"},{"key":"2026100902313322700_B61","doi-asserted-by":"publisher","first-page":"5837","DOI":"10.1093\/nar\/gky226","article-title":"Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis","volume":"46","author":"Schwenk","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B62","doi-asserted-by":"publisher","first-page":"5376","DOI":"10.1073\/pnas.1112211109","article-title":"Riboswitch control of Rho-dependent transcription termination","volume":"109","author":"Hollands","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"2026100902313322700_B63","doi-asserted-by":"publisher","first-page":"7474","DOI":"10.1093\/nar\/gkx434","article-title":"Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation","volume":"45","author":"Bastet","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B64","doi-asserted-by":"publisher","first-page":"10.1093\/femspd\/fty035","DOI":"10.1093\/femspd\/fty035","article-title":"Regulatory RNA in Mycobacterium tuberculosis, back to basics","volume":"76","author":"Schwenk","year":"2018","journal-title":"Pathog Dis"},{"key":"2026100902313322700_B65","doi-asserted-by":"publisher","first-page":"e1002342","DOI":"10.1371\/journal.ppat.1002342","article-title":"Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis","volume":"7","author":"Arnvig","year":"2011","journal-title":"PLoS Pathog"},{"key":"2026100902313322700_B66","doi-asserted-by":"publisher","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"Zuker","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B67","doi-asserted-by":"publisher","first-page":"109807","DOI":"10.1016\/j.isci.2024.109807","article-title":"Mycobacterial CpsA activates type I IFN signaling in macrophages via cGAS-mediated pathway","volume":"27","author":"Ding","year":"2024","journal-title":"iScience"},{"key":"2026100902313322700_B68","doi-asserted-by":"publisher","first-page":"113607","DOI":"10.1016\/j.celrep.2023.113607","article-title":"CpsA mediates infection of recruited lung myeloid cells by Mycobacterium tuberculosis","volume":"43","author":"Grigsby","year":"2024","journal-title":"Cell Rep"},{"key":"2026100902313322700_B69","doi-asserted-by":"publisher","first-page":"1918","DOI":"10.1038\/s41564-022-01240-7","article-title":"Comprehensive transcription terminator atlas for Bacillus subtilis","volume":"7","author":"Mandell","year":"2022","journal-title":"Nat Microbiol"},{"key":"2026100902313322700_B70","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1016\/j.molcel.2026.01.028","article-title":"Cell-free genomics reveals fundamental regulatory principles of the Mycobacterium tuberculosis transcription cycle","volume":"86","author":"Froom","year":"2026","journal-title":"Mol Cell"},{"key":"2026100902313322700_B71","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1002\/1873-3468.70023","article-title":"Unraveling Mycobacterium tuberculosis acid resistance and pH homeostasis mechanisms","volume":"599","author":"Laudouze","year":"2025","journal-title":"FEBS Lett"},{"key":"2026100902313322700_B72","first-page":"10106","article-title":"RbpA relaxes promoter selectivity of M. tuberculosis RNA polymerase","volume":"46","author":"Sudalaiyadum\u00a0Perumal","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B73","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1006\/jmbi.1993.1368","article-title":"Nucleation of RNA chain formation by Escherichia coli DNA-dependent RNA polymerase","volume":"232","author":"Metzger","year":"1993","journal-title":"J Mol Biol"},{"key":"2026100902313322700_B74","doi-asserted-by":"publisher","first-page":"10802","DOI":"10.3390\/molecules180910802","article-title":"Structural characterization of intrinsically disordered proteins by NMR spectroscopy","volume":"18","author":"Kosol","year":"2013","journal-title":"Molecules"},{"key":"2026100902313322700_B75","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/s41580-023-00673-0","article-title":"The molecular basis for cellular function of intrinsically disordered protein regions","volume":"25","author":"Holehouse","year":"2024","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2026100902313322700_B76","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/S1097-2765(00)80027-1","article-title":"Independent ligand-induced folding of the RNA-binding domain and two functionally distinct antitermination regions in the phage lambda N protein","volume":"1","author":"Mogridge","year":"1998","journal-title":"Mol Cell"},{"key":"2026100902313322700_B77","doi-asserted-by":"publisher","first-page":"2453","DOI":"10.1038\/s41467-019-10356-0","article-title":"Disordered RNA chaperones can enhance nucleic acid folding via local charge screening","volume":"10","author":"Holmstrom","year":"2019","journal-title":"Nat Commun"},{"key":"2026100902313322700_B78","doi-asserted-by":"publisher","first-page":"2609","DOI":"10.1093\/nar\/gkad1215","article-title":"The disordered N-terminal tail of SARS-CoV-2 nucleocapsid protein forms a dynamic complex with RNA","volume":"52","author":"Cubuk","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2026100902313322700_B79","doi-asserted-by":"crossref","article-title":"Phase separation of mycobacterial Rho factor is associated with acid stress","author":"Moreira","DOI":"10.1101\/2025.08.28.672908"},{"key":"2026100902313322700_B80","doi-asserted-by":"publisher","first-page":"107318","DOI":"10.1016\/j.jmr.2022.107318","article-title":"A call to order: examining structured domains in biomolecular condensates","volume":"346","author":"Tibble","year":"2023","journal-title":"J Magn Reson"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/18\/gkag973\/71753784\/gkag973.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/54\/18\/gkag973\/71753784\/gkag973.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T06:31:40Z","timestamp":1791527500000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkag973\/8892736"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,22]]},"references-count":80,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2026,9,22]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkag973","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10,14]]},"published":{"date-parts":[[2026,9,22]]},"article-number":"gkag973"}}