Bacteria have evolved structured RNAs that can associate with RNA polymerase (RNAP). Two of them have been known so far-6S RNA and Ms1 RNA but it is unclear if any other types of RNAs binding to RNAP exist in bacteria. To identify all RNAs interacting with RNAP and the primary σ factors, we have established and performed native RIP-seq in Bacillus subtilis, Corynebacterium glutamicum, Streptomyces coelicolor, Mycobacterium smegmatis and the pathogenic Mycobacterium tuberculosis. Besides known 6S RNAs in B. subtilis and Ms1 in M. smegmatis, we detected MTS2823, a homologue of Ms1, on RNAP in M. tuberculosis. In C. glutamicum, we discovered novel types of structured RNAs that associate with RNAP. Furthermore, we identified other species-specific RNAs including full-length mRNAs, revealing a previously unknown landscape of RNAs interacting with the bacterial transcription machinery.

Department of Bioinformatics 2nd Faculty of Medicine Charles University Prague150 06 Czech Republic

Department of Cell Biology Faculty of Science Charles University Prague128 00 Czech Republic

Laboratory of Bioinformatics Institute of Microbiology of the Czech Academy of Sciences Prague142 20 Czech Republic

Laboratory of Microbial Genetics and Gene Expression Institute of Microbiology of the Czech Academy of Sciences Prague142 20 Czech Republic

Laboratory of Regulation of Gene Expression Institute of Microbiology of the Czech Academy of Sciences Prague142 20 Czech Republic

Laboratory of Regulatory RNAs Faculty of Science Charles University Prague128 44 Czech Republic

Laboratory of Structural Biology and Cell Signaling Institute of Microbiology of the Czech Academy of Sciences Vestec252 50 Czech Republic

Military Health Institute Military Medical Agency Prague169 02 Czech Republic

Zobrazit více v PubMed

Sensi P. History of the development of rifampin. Rev. Infect. Dis. 1983; 5:S402–S406. PubMed

Chen J., Boyaci H., Campbell E.A.. Diverse and unified mechanisms of transcription initiation in bacteria. Nat. Rev. Micro. 2021; 19:95–109. PubMed PMC

Gomez M., Doukhan L., Nair G., Smith I.. sigA is an essential gene in Mycobacterium smegmatis. Mol. Microbiol. 1998; 29:617–628. PubMed

Brown K.L., Wood S., Buttner M.J.. Isolation and characterization of the major vegetative RNA polymerase of Streptomyces coelicolor A3(2); renaturation of a sigma subunit using GroEL. Mol. Microbiol. 1992; 6:1133–1139. PubMed

Browning D.F., Busby S.J.. Local and global regulation of transcription initiation in bacteria. Nat. Rev. Micro. 2016; 14:638–650. PubMed

Wassarman K.M. 6S RNA, a global regulator of transcription. Microbiol. Spectr. 2018; 6:355–367. PubMed PMC

Steuten B., Hoch P.G., Damm K., Schneider S., Köhler K., Wagner R., Hartmann R.K.. Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems. RNA Biol. 2014; 11:508–521. PubMed PMC

Trotochaud A.E., Wassarman K.M.. A highly conserved 6S RNA structure is required for regulation of transcription. Nat. Struct. Mol. Biol. 2005; 12:313–319. PubMed

Wassarman K.M., Storz G.. 6S RNA regulates E. coli RNA polymerase activity. Cell. 2000; 101:613–623. PubMed

Hindley J. Fractionation of 32P-labelled ribonucleic acids on polyacrylamide gels and their characterization by fingerprinting. J. Mol. Biol. 1967; 30:125–136. PubMed

Burenina O.Y., Elkina D.A., Hartmann R.K., Oretskaya T.S., Kubareva E.A.. Small noncoding 6S RNAs of bacteria. Biochemistry. 2015; 80:1429–1446. PubMed

Neusser T., Polen T., Geissen R., Wagner R.. Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery. Bmc Genomics [Electronic Resource]. 2010; 11:165. PubMed PMC

Cavanagh A.T., Chandrangsu P., Wassarman K.M.. 6S RNA regulation of relA alters ppGpp levels in early stationary phase. Microbiology. 2010; 156:3791–3800. PubMed PMC

Cavanagh A.T., Klocko A.D., Liu X., Wassarman K.M.. Promoter specificity for 6S RNA regulation of transcription is determined by core promoter sequences and competition for region 4.2 of sigma70. Mol. Microbiol. 2008; 67:1242–1256. PubMed

Trotochaud A.E., Wassarman K.M.. 6S RNA function enhances long-term cell survival. J. Bacteriol. 2004; 186:4978–4985. PubMed PMC

Trotochaud A.E., Wassarman K.M.. 6S RNA regulation of pspF transcription leads to altered cell survival at high pH. J. Bacteriol. 2006; 188:3936–3943. PubMed PMC

Klocko A.D., Wassarman K.M.. 6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2. Mol. Microbiol. 2009; 73:152–164. PubMed PMC

Chen J., Wassarman K.M., Feng S., Leon K., Feklistov A., Winkelman J.T., Li Z., Walz T., Campbell E.A., Darst S.A.. 6S RNA mimics B-form DNA to regulate Escherichia coli RNA polymerase. Mol. Cell. 2017; 68:388–397. PubMed PMC

Steuten B., Setny P., Zacharias M., Wagner R.. Mapping the spatial neighborhood of the regulatory 6S RNA bound to Escherichia coli RNA polymerase holoenzyme. J. Mol. Biol. 2013; 425:3649–3661. PubMed

Cavanagh A.T., Sperger J.M., Wassarman K.M.. Regulation of 6S RNA by pRNA synthesis is required for efficient recovery from stationary phase in E. coli and B. subtilis. Nucleic Acids Res. 2012; 40:2234–2246. PubMed PMC

Wassarman K.M., Saecker R.M.. Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science. 2006; 314:1601–1603. PubMed

Beckmann B.M., Burenina O.Y., Hoch P.G., Kubareva E.A., Sharma C.M., Hartmann R.K.. In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis. RNA Biol. 2011; 8:839–849. PubMed

Hoch P.G., Schlereth J., Lechner M., Hartmann R.K.. Bacillus subtilis 6S-2 RNA serves as a template for short transcripts in vivo. RNA. 2016; 22:614–622. PubMed PMC

Beckmann B.M., Hoch P.G., Marz M., Willkomm D.K., Salas M., Hartmann R.K.. A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis. EMBO J. 2012; 31:1727–1738. PubMed PMC

Panchapakesan S.S., Unrau P.J.. E. coli 6S RNA release from RNA polymerase requires σ70 ejection by scrunching and is orchestrated by a conserved RNA hairpin. RNA. 2012; 18:2251–2259. PubMed PMC

Wurm R., Neusser T., Wagner R.. 6S RNA-dependent inhibition of RNA polymerase is released by RNA-dependent synthesis of small de novo products. Biol. Chem. 2010; 391:187–196. PubMed

Gildehaus N., Neusser T., Wurm R., Wagner R.. Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts. Nucleic Acids Res. 2007; 35:1885–1896. PubMed PMC

Barrick J.E., Sudarsan N., Weinberg Z., Ruzzo W.L., Breaker R.R.. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA. 2005; 11:774–784. PubMed PMC

Wehner S., Damm K., Hartmann R.K., Marz M.. Dissemination of 6S RNA among bacteria. RNA Biol. 2014; 11:1467–1478. PubMed PMC

Bobek J., Mikulová A., Šetinová D., Elliot M., Čihák M.. 6S-Like scr3559 RNA affects development and antibiotic production in Streptomyces coelicolor. Microorganisms. 2021; 9:2004. PubMed PMC

Mikulík K., Bobek J., Zídková J., Felsberg J.. 6S RNA modulates growth and antibiotic production in Streptomyces coelicolor. Appl. Microbiol. Biotechnol. 2014; 98:7185–7197. PubMed

Pánek J., Krásny L., Bobek J., Jezková E., Korelusová J., Vohradsky J.. The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures. Nucleic Acids Res. 2011; 39:3418–3426. PubMed PMC

Hnilicová J., Jirát Matějčková J., Šiková M., Pospíšil J., Halada P., Pánek J., Krásný L.. Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria. Nucleic Acids Res. 2014; 42:11763–11776. PubMed PMC

Šiková M., Janoušková M., Ramaniuk O., Páleníková P., Pospíšil J., Bartl P., Suder A., Pajer P., Kubičková P., Pavliš O.et al. .. Ms1 RNA increases the amount of RNA polymerase in mycobacterium smegmatis. Mol. Microbiol. 2019; 111:354–372. PubMed

Arnvig K.B., Comas I., Thomson N.R., Houghton J., Boshoff H.I., Croucher N.J., Rose G., Perkins T.T., Parkhill J., Dougan G.et al. .. Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of mycobacterium tuberculosis. PLoS Pathog. 2011; 7:e1002342. PubMed PMC

Behra P.R.K., Pettersson B.M.F., Das S., Dasgupta S., Kirsebom L.A.. Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA. BMC Evol. Biol. 2019; 19:124. PubMed PMC

Vaňková Hausnerová V., Marvalová O., Šiková M., Shoman M., Havelková J., Kambová M., Janoušková M., Kumar D., Halada P., Schwarz M.et al. .. Ms1 RNA interacts with the RNA polymerase core in streptomyces coelicolor and was identified in majority of actinobacteria using a linguistic gene synteny search. Front. Microbiol. 2022; 13:848536. PubMed PMC

Šmídová K., Ziková A., Pospíšil J., Schwarz M., Bobek J., Vohradsky J.. DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor. Nucleic Acids Res. 2019; 47:621–633. PubMed PMC

Moody M.J., Young R.A., Jones S.E., Elliot M.A.. Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria. Bmc Genomics [Electronic Resource]. 2013; 14:558. PubMed PMC

Bolger A.M., Lohse M., Usadel B.. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30:2114–2120. PubMed PMC

Kim D., Langmead B., Salzberg S.L.. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods. 2015; 12:357–360. PubMed PMC

Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R., Subgroup G.P.D.P.. The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25:2078–2079. PubMed PMC

Bonfield J.K., Marshall J., Danecek P., Li H., Ohan V., Whitwham A., Keane T., Davies R.M.. HTSlib: c library for reading/writing high-throughput sequencing data. Gigascience. 2021; 10:giab007. PubMed PMC

Ramírez F., Ryan D.P., Grüning B., Bhardwaj V., Kilpert F., Richter A.S., Heyne S., Dündar F., Manke T.. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016; 44:W160–W165. PubMed PMC

Zhang Y., Liu T., Meyer C.A., Eeckhoute J., Johnson D.S., Bernstein B.E., Nusbaum C., Myers R.M., Brown M., Li W.et al. .. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9:R137. PubMed PMC

Quinn T.P., Erb I., Richardson M.F., Crowley T.M.. Understanding sequencing data as compositions: an outlook and review. Bioinformatics. 2018; 34:2870–2878. PubMed PMC

Love M.I., Huber W., Anders S.. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15:550. PubMed PMC

Benjamini Y., Hochberg Y.. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Series B Stat. Methodol. 1995; 57:289–300.

Hofacker I.L., Priwitzer B., Stadler P.F.. Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics. 2004; 20:186–190. PubMed

Gruber A.R., Lorenz R., Bernhart S.H., Neuböck R., Hofacker I.L.. The Vienna RNA websuite. Nucleic Acids Res. 2008; 36:W70–W74. PubMed PMC

Lorenz R., Bernhart S.H., Höner Zu Siederdissen C., Tafer H., Flamm C., Stadler P.F., Hofacker I.L.. ViennaRNA package 2.0. Algorithms Mol. Biol. 2011; 6:26. PubMed PMC

Kouba T., Koval' T., Sudzinová P., Pospíšil J., Brezovská B., Hnilicová J., Šanderová H., Janoušková M., Šiková M., Halada Pet al. .. Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase. Nat. Commun. 2020; 11:6419. PubMed PMC

Hör J., Garriss G., Di Giorgio S., Hack L.M., Vanselow J.T., Förstner K.U., Schlosser A., Henriques-Normark B., Vogel J.. Grad-seq in a gram-positive bacterium reveals exonucleolytic sRNA activation in competence control. EMBO J. 2020; 39:e103852. PubMed PMC

Hu Y., Morichaud Z., Perumal A.S., Roquet-Baneres F., Brodolin K.. Mycobacterium RbpA cooperates with the stress-response σb subunit of RNA polymerase in promoter DNA unwinding. Nucleic Acids Res. 2014; 42:10399–10408. PubMed PMC

Lee J.H., Karakousis P.C., Bishai W.R.. Roles of SigB and SigF in the mycobacterium tuberculosis sigma factor network. J. Bacteriol. 2008; 190:699–707. PubMed PMC

Hurst-Hess K., Biswas R., Yang Y., Rudra P., Lasek-Nesselquist E., Ghosh P.. Mycobacterial SigA and SigB cotranscribe essential housekeeping genes during exponential growth. mBio. 2019; 10:e00273-19. PubMed PMC

Moore S.D., Sauer R.T.. The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 2007; 76:101–124. PubMed

Valle M., Gillet R., Kaur S., Henne A., Ramakrishnan V., Frank J.. Visualizing tmRNA entry into a stalled ribosome. Science. 2003; 300:127–130. PubMed

Kapopoulou A., Lew J.M., Cole S.T.. The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes. Tuberculosis (Edinb.). 2011; 91:8–13. PubMed

Robinson J.T., Thorvaldsdottir H., Turner D., Mesirov J.P.. igv.Js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics. 2023; 39:btac830. PubMed PMC

Dronkert M.L., Kanaar R.. Repair of DNA interstrand cross-links. Mutat. Res. 2001; 486:217–247. PubMed

IYER V.N., SZYBALSKI W.. Mitomycins and porfiromycin: chemical mechanism of activation and cross-linking of dna. Science. 1964; 145:55–58. PubMed

Flynn J.L., Chan J.. Immunology of tuberculosis. Annu. Rev. Immunol. 2001; 19:93–129. PubMed

Manganelli R., Voskuil M.I., Schoolnik G.K., Dubnau E., Gomez M., Smith I.. Role of the extracytoplasmic-function sigma factor sigma(H) in mycobacterium tuberculosis global gene expression. Mol. Microbiol. 2002; 45:365–374. PubMed

Hu Y., Coates A.R.. Transcription of two sigma 70 homologue genes, sigA and sigB, in stationary-phase mycobacterium tuberculosis. J. Bacteriol. 1999; 181:469–476. PubMed PMC

Manganelli R., Dubnau E., Tyagi S., Kramer F.R., Smith I.. Differential expression of 10 sigma factor genes in mycobacterium tuberculosis. Mol. Microbiol. 1999; 31:715–724. PubMed

Müller A.U., Imkamp F., Weber-Ban E.. The mycobacterial LexA/RecA-independent DNA damage response is controlled by PafBC and the pup-proteasome system. Cell Rep. 2018; 23:3551–3564. PubMed

Ofer N., Wishkautzan M., Meijler M., Wang Y., Speer A., Niederweis M., Gur E.. Ectoine biosynthesis in Mycobacterium smegmatis. Appl. Environ. Microb. 2012; 78:7483–7486. PubMed PMC

Fudrini Olivencia B., Müller A.U., Roschitzki B., Burger S., Weber-Ban E., Imkamp F.. Mycobacterium smegmatis PafBC is involved in regulation of DNA damage response. Sci. Rep. 2017; 7:13987. PubMed PMC

Morichaud Z., Trapani S., Vishwakarma R.K., Chaloin L., Lionne C., Lai-Kee-Him J., Bron P., Brodolin K.. Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization. Nat. Commun. 2023; 14:484. PubMed PMC

Swiercz J.P., Hindra Bobek J., Haiser H.J., Di Berardo C., Tjaden B., Elliot M.A. Small non-coding RNAs in Streptomyces coelicolor. Nucleic Acids Res. 2008; 36:7240–7251. PubMed PMC

Köhler K., Duchardt-Ferner E., Lechner M., Damm K., Hoch P.G., Salas M., Hartmann R.K.. Structural and mechanistic characterization of 6S RNA from the hyperthermophilic bacterium Aquifex aeolicus. Biochimie. 2015; 117:72–86. PubMed

Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J.. Basic local alignment search tool. J. Mol. Biol. 1990; 215:403–410. PubMed

Schwarz M., Vohradský J., Pánek J.. rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output. Bioinformatics. 2021; 37:2755–2756. PubMed

Ruwe M., Persicke M., Busche T., Müller B., Kalinowski J.. Physiology and transcriptional analysis of (p)ppGpp-related regulatory effects in Corynebacterium glutamicum. Front. Microbiol. 2019; 10:2769. PubMed PMC

Graf M., Haas T., Teleki A., Feith A., Cerff M., Wiechert W., Nöh K., Busche T., Kalinowski J., Takors R.. Revisiting the growth modulon of of Corynebacterium glutamicum under glucose limited chemostat conditions. Front. Bioeng. Biotechnol. 2020; 8:584614. PubMed PMC

Haas T., Graf M., Nieß A., Busche T., Kalinowski J., Blombach B., Takors R.. Identifying the growth modulon of Corynebacterium glutamicum. Front. Microbiol. 2019; 10:974. PubMed PMC

Taniguchi H., Busche T., Patschkowski T., Niehaus K., Pátek M., Kalinowski J., Wendisch V.F.. Physiological roles of sigma factor SigD in Corynebacterium glutamicum. BMC Microbiol. 2017; 17:158. PubMed PMC

Franco E.F., Rana P., Queiroz Cavalcante A.L., da Silva A.L., Cybelle Pinto Gomide A., Carneiro Folador A.R., Azevedo V., Ghosh P., T J Ramos R.. Co-expression networks for causal gene identification based on RNA-seq data ofCorynebacterium pseudotuberculosis. Genes (Basel). 2020; 11:794. PubMed PMC

Ibraim I.C., Parise M.T.D., Parise D., Sfeir M.Z.T., de Paula Castro T.L., Wattam A.R., Ghosh P., Barh D., Souza E.M., Góes-Neto A.et al. .. Transcriptome profile of Corynebacterium pseudotuberculosis in response to iron limitation. Bmc Genomics [Electronic Resource]. 2019; 20:663. PubMed PMC

Luong T.T., Nguyen M.T., Chen Y.W., Chang C., Lee J.H., Wittchen M., Ton-That H., Cruz M., Garsin D.A., Das A.et al. .. Ribonuclease J-mediated mRNA turnover modulates cell shape, metabolism and virulence in Corynebacterium diphtheriae. Microorganisms. 2021; 9:389. PubMed PMC

Hamabata T., Senoh M., Iwaki M., Nishiyama A., Yamamoto A., Shibayama K.. Induction and resuscitation of viable but nonculturable Corynebacterium diphtheriae. Microorganisms. 2021; 9:927. PubMed PMC

Burenina O.Y., Hoch P.G., Damm K., Salas M., Zatsepin T.S., Lechner M., Oretskaya T.S., Kubareva E.A., Hartmann R.K.. Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs–commonalities and differences. RNA. 2014; 20:348–359. PubMed PMC

Cavanagh A.T., Wassarman K.M.. 6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond. Annu. Rev. Microbiol. 2014; 68:45–60. PubMed

Thüring M., Ganapathy S., Schlüter M.A.C., Lechner M., Hartmann R.K.. 6S-2 RNA deletion in the undomesticated B. subtilis strain NCIB 3610 causes a biofilm derepression phenotype. RNA Biol. 2021; 18:79–92. PubMed PMC

Delumeau O., Lecointe F., Muntel J., Guillot A., Guédon E., Monnet V., Hecker M., Becher D., Polard P., Noirot P.. The dynamic protein partnership of RNA polymerase in Bacillus subtilis. Proteomics. 2011; 11:2992–3001. PubMed

Shahbabian K., Jamalli A., Zig L., Putzer H.. RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis. EMBO J. 2009; 28:3523–3533. PubMed PMC

Benda M., Woelfel S., Faßhauer P., Gunka K., Klumpp S., Poehlein A., Kálalová D., Šanderová H., Daniel R., Krásný L.et al. .. Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis. Nucleic Acids Res. 2021; 49:7088–7102. PubMed PMC

Lee C.A., Fournier M.J., Beckwith J.. Escherichia coli 6S RNA is not essential for growth or protein secretion. J. Bacteriol. 1985; 161:1156–1161. PubMed PMC

Faucher S.P., Friedlander G., Livny J., Margalit H., Shuman H.A.. Legionella pneumophila 6S RNA optimizes intracellular multiplication. Proc. Natl. Acad. Sci. U.S.A. 2010; 107:7533–7538. PubMed PMC

Hoch P.G., Burenina O.Y., Weber M.H., Elkina D.A., Nesterchuk M.V., Sergiev P.V., Hartmann R.K., Kubareva E.A.. Phenotypic characterization and complementation analysis of Bacillus subtilis 6S RNA single and double deletion mutants. Biochimie. 2015; 117:87–99. PubMed

Cavanagh A.T., Wassarman K.M.. 6S-1 RNA function leads to a delay in sporulation in Bacillus subtilis. J. Bacteriol. 2013; 195:2079–2086. PubMed PMC

Thüring M., Ganapathy S., Schlüter M.A.C., Lechner M., Hartmann R.K.. 6S-2 RNA deletion in the undomesticated. RNA Biol. 2021; 18:79–92. PubMed PMC

Nguyen V.T., Kiss T., Michels A.A., Bensaude O.. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature. 2001; 414:322–325. PubMed

Yang Z., Zhu Q., Luo K., Zhou Q.. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature. 2001; 414:317–322. PubMed

Michels A.A., Fraldi A., Li Q., Adamson T.E., Bonnet F., Nguyen V.T., Sedore S.C., Price J.P., Price D.H., Lania L.et al. .. Binding of the 7SK snRNA turns the HEXIM1 protein into a P-TEFb (CDK9/cyclin T) inhibitor. EMBO J. 2004; 23:2608–2619. PubMed PMC

Müller A.U., Leibundgut M., Ban N., Weber-Ban E.. Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC. Nat. Commun. 2019; 10:4653. PubMed PMC

Dey A., Verma A.K., Chatterji D. Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin. Microbiology. 2010; 156:873–883. PubMed

Hubin E.A., Fay A., Xu C., Bean J.M., Saecker R.M., Glickman M.S., Darst S.A., Campbell E.A.. Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA. eLife. 2017; 6:e22520. PubMed PMC

MoaB2, a newly identified transcription factor, binds to σA in Mycobacterium smegmatis