{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T10:24:42Z","timestamp":1765967082024,"version":"3.48.0"},"reference-count":162,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"publisher","award":["23-05622S J.Hn."],"award-info":[{"award-number":["23-05622S J.Hn."]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001824","name":"Czech Science Foundation","doi-asserted-by":"publisher","award":["22\u201312023S"],"award-info":[{"award-number":["22\u201312023S"]}],"id":[{"id":"10.13039\/501100001824","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007397","name":"Charles University","doi-asserted-by":"publisher","award":["275823"],"award-info":[{"award-number":["275823"]}],"id":[{"id":"10.13039\/100007397","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2014Next Generation EU, National Institute of Virology and Bacteriology","award":["EXCELES LX22NPO5103"],"award-info":[{"award-number":["EXCELES LX22NPO5103"]}]},{"DOI":"10.13039\/100009122","name":"Ministry of Education","doi-asserted-by":"publisher","award":["OPJAK"],"award-info":[{"award-number":["OPJAK"]}],"id":[{"id":"10.13039\/100009122","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009122","name":"Ministry of Education","doi-asserted-by":"publisher","award":["CZ.02.01.01\/00\/22_008\/0004597"],"award-info":[{"award-number":["CZ.02.01.01\/00\/22_008\/0004597"]}],"id":[{"id":"10.13039\/100009122","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009122","name":"Ministry of Education","doi-asserted-by":"publisher","award":["CZ.02.01.01\/00\/22_008\/0004575"],"award-info":[{"award-number":["CZ.02.01.01\/00\/22_008\/0004575"]}],"id":[{"id":"10.13039\/100009122","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ELIXIR CZ","award":["LM2023055"],"award-info":[{"award-number":["LM2023055"]}]},{"DOI":"10.13039\/100009647","name":"Ministry of Health","doi-asserted-by":"publisher","award":["75010330"],"award-info":[{"award-number":["75010330"]}],"id":[{"id":"10.13039\/100009647","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Bacterial transcription regulation is critical for adaptation and survival. CarD is an essential transcription factor in mycobacteria involved in the regulation of gene expression. We searched for CarD interaction partners in Mycobacterium smegmatis and identified a novel uncharacterized protein, named CrsL (MSMEG_5890). CrsL is a 5.7 kDa protein shown by NMR to be intrinsically disordered. CrsL homologs are present in actinobacteria, including pathogenic species such as Mycobacterium tuberculosis. CrsL interacts directly with CarD, adopting an ordered structure in the complex, and also binds RNAP, controlling CarD\u2013RNAP association. ChIP-seq showed that CrsL associates with the promoters of actively transcribed genes and \u223c75% of these regions are also associated with CarD. RNA-seq revealed \u223c50% and \u223c66% overlap in differentially expressed genes between CrsL and CarD knockdowns during the exponential and stationary phases, respectively. Among CrsL-regulated genes are DesA desaturase (MSMEG_5773) and DEAD\/DEAH-box RNA helicase MSMEG_1930, which contribute to cold stress adaptation. CrsL supports the growth of M. smegmatis at elevated temperature but limits growth in cold environments. In summary, these findings identify CrsL as a novel, conserved CarD-interacting protein playing a key role in mycobacterial stress responses by modulating CarD function.<\/jats:p>","DOI":"10.1093\/nar\/gkaf1342","type":"journal-article","created":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T13:07:57Z","timestamp":1762952877000},"source":"Crossref","is-referenced-by-count":0,"title":["Expanding the CarD interaction network: CrsL is a novel transcription regulator in actinobacteria"],"prefix":"10.1093","volume":"53","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-4510-3439","authenticated-orcid":false,"given":"Mahmoud","family":"Shoman","sequence":"first","affiliation":[{"name":"Laboratory of Regulatory RNAs, Faculty of Science, Charles University , Prague 12844 ,","place":["Czech Republic"]},{"name":"Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8231-9634","authenticated-orcid":false,"given":"Martin","family":"\u010cern\u00fd","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology (CEITEC), Masaryk University , Brno 62500 ,","place":["Czech Republic"]},{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno 62500 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6359-4817","authenticated-orcid":false,"given":"Jitka","family":"Jir\u00e1t\u00a0Mat\u011bj\u010dkov\u00e1","sequence":"additional","affiliation":[{"name":"Laboratory of Regulatory RNAs, Faculty of Science, Charles University , Prague 12844 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marek","family":"Schwarz","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1197-8237","authenticated-orcid":false,"given":"Nabajyoti","family":"Borah","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9261-4768","authenticated-orcid":false,"given":"Viola","family":"Va\u0148kov\u00e1\u00a0Hausnerov\u00e1","sequence":"additional","affiliation":[{"name":"Laboratory of Regulatory RNAs, Faculty of Science, Charles University , Prague 12844 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia","family":"Neva","sequence":"additional","affiliation":[{"name":"Laboratory of Regulatory RNAs, Faculty of Science, Charles University , Prague 12844 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michaela","family":"\u0160ikov\u00e1","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hana","family":"\u0160anderov\u00e1","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petr","family":"Halada","sequence":"additional","affiliation":[{"name":"Laboratory of Structural Biology and Cell Signaling, BIOCEV, Institute of Microbiology of the Czech Academy of Sciences , Vestec 25250 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Hub\u00e1lek","sequence":"additional","affiliation":[{"name":"Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Prague 16000 ,","place":["Czech Republic"]},{"name":"Military Health Institute, Military Medical Agency , Prague 16200 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"V\u011bra","family":"Dvo\u0159\u00e1kov\u00e1","sequence":"additional","affiliation":[{"name":"National Institute of Public Health , Prague 10000 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"P\u0159evorovsk\u00fd","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Faculty of Science, Charles University , Prague 12800 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jana","family":"Holubov\u00e1","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology of Bacterial Pathogen, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ond\u0159ej","family":"Stan\u011bk","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology of Bacterial Pathogen, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4120-4347","authenticated-orcid":false,"given":"Libor","family":"Kr\u00e1sn\u00fd","sequence":"additional","affiliation":[{"name":"Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8013-0336","authenticated-orcid":false,"given":"Luk\u00e1\u0161","family":"\u017d\u00eddek","sequence":"additional","affiliation":[{"name":"Central European Institute of Technology (CEITEC), Masaryk University , Brno 62500 ,","place":["Czech Republic"]},{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno 62500 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0953-491X","authenticated-orcid":false,"given":"Jarmila","family":"Hnilicov\u00e1","sequence":"additional","affiliation":[{"name":"Laboratory of Regulatory RNAs, Faculty of Science, Charles University , Prague 12844 ,","place":["Czech Republic"]},{"name":"Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences , Prague 14220 ,","place":["Czech Republic"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,12,17]]},"reference":[{"key":"2025121705163652500_B1","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1093\/cid\/civ198","article-title":"Prolonged outbreak of mycobacterium chimaera infection after open-chest heart surgery","volume":"61","author":"Sax","year":"2015","journal-title":"Clin Infect Dis"},{"key":"2025121705163652500_B2","doi-asserted-by":"publisher","first-page":"1008","DOI":"10.3201\/eid2206.160045","article-title":"Transmission of Mycobacterium chimaera from heater-cooler units during cardiac surgery despite an ultraclean air ventilation system","volume":"22","author":"Sommerstein","year":"2016","journal-title":"Emerg Infect Dis"},{"key":"2025121705163652500_B3","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/S0959-440X(02)00005-2","article-title":"Bacterial RNA polymerases: the wholo story","volume":"13","author":"Murakami","year":"2003","journal-title":"Curr Opin Struct Biol"},{"key":"2025121705163652500_B4","doi-asserted-by":"publisher","first-page":"1280","DOI":"10.1126\/science.1069594","article-title":"Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 \u00c5 resolution","volume":"296","author":"Murakami","year":"2002","journal-title":"Science"},{"key":"2025121705163652500_B5","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/s41579-020-00450-2","article-title":"Diverse and unified mechanisms of transcription initiation in bacteria","volume":"19","author":"Chen","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"2025121705163652500_B6","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nrmicro787","article-title":"The regulation of bacterial transcription initiation","volume":"2","author":"Browning","year":"2004","journal-title":"Nat Rev Microbiol"},{"key":"2025121705163652500_B7","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1111\/mmi.14309","article-title":"Where to begin? Sigma factors and the selectivity of transcription initiation in bacteria","volume":"112","author":"Helmann","year":"2019","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B8","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.3390\/biom5031245","article-title":"Bacterial sigma factors and anti-sigma factors: structure, function and distribution","volume":"5","author":"Paget","year":"2015","journal-title":"Biomolecules"},{"key":"2025121705163652500_B9","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1046\/j.1365-2958.1998.00960.x","article-title":"sigA is an essential gene in Mycobacterium smegmatis","volume":"29","author":"Gomez","year":"1998","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B10","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1111\/j.1574-6976.2006.00040.x","article-title":"The \u03c3 factors of Mycobacterium tuberculosis","volume":"30","author":"Rodrigue","year":"2006","journal-title":"FEMS Microbiol Rev"},{"key":"2025121705163652500_B11","doi-asserted-by":"publisher","first-page":"10399","DOI":"10.1093\/nar\/gku742","article-title":"Mycobacterium RbpA cooperates with the stress-response \u03c3B subunit of RNA polymerase in promoter DNA unwinding","volume":"42","author":"Hu","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B12","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1128\/JB.01273-07","article-title":"Roles of SigB and SigF in the Mycobacterium tuberculosis sigma factor network","volume":"190","author":"Lee","year":"2008","journal-title":"J Bacteriol"},{"key":"2025121705163652500_B13","doi-asserted-by":"crossref","first-page":"e00273","DOI":"10.1128\/mBio.00273-19","article-title":"Mycobacterial SigA and SigB cotranscribe essential housekeeping genes during exponential growth","volume":"10","author":"Hurst-Hess","year":"2019","journal-title":"mBio"},{"key":"2025121705163652500_B14","doi-asserted-by":"publisher","first-page":"102933","DOI":"10.1016\/j.jbc.2023.102933","article-title":"The unique N-terminal region of Mycobacterium tuberculosis sigma factor A plays a dominant role in the essential function of this protein","volume":"299","author":"Singha","year":"2023","journal-title":"J Biol Chem"},{"key":"2025121705163652500_B15","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1111\/j.1742-4658.2009.07479.x","article-title":"The sigma factors of Mycobacterium tuberculosis: regulation of the regulators","volume":"277","author":"Sachdeva","year":"2010","journal-title":"FEBS J"},{"key":"2025121705163652500_B16","doi-asserted-by":"publisher","first-page":"2790","DOI":"10.1073\/pnas.93.7.2790","article-title":"A stationary-phase stress-response sigma factor from Mycobacterium tuberculosis","volume":"93","author":"Demaio","year":"1996","journal-title":"Proc Natl Acad Sci"},{"key":"2025121705163652500_B17","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1016\/S0962-8479(97)90024-1","article-title":"Sigma factors of Mycobacterium tuberculosis","volume":"78","author":"Gomez","year":"1997","journal-title":"Tuber Lung Dis"},{"key":"2025121705163652500_B18","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1093\/nar\/gku1231","article-title":"Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD","volume":"43","author":"Davis","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B19","doi-asserted-by":"publisher","first-page":"3272","DOI":"10.1093\/nar\/gkv078","article-title":"CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism","volume":"43","author":"Rammohan","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B20","doi-asserted-by":"publisher","first-page":"14438","DOI":"10.1074\/jbc.M113.459883","article-title":"Mycobacterium tuberculosis RNA polymerase-binding protein A (RbpA) and its interactions with sigma factors","volume":"288","author":"Bortoluzzi","year":"2013","journal-title":"J Biol Chem"},{"key":"2025121705163652500_B21","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1016\/j.tube.2011.07.004","article-title":"Isolation of conditional expression mutants in Mycobacterium tuberculosis by transposon mutagenesis","volume":"91","author":"Forti","year":"2011","journal-title":"Tuberculosis"},{"key":"2025121705163652500_B22","doi-asserted-by":"publisher","first-page":"873","DOI":"10.1099\/mic.0.033670-0","article-title":"Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin","volume":"156","author":"Dey","year":"2010","journal-title":"Microbiology"},{"key":"2025121705163652500_B23","doi-asserted-by":"publisher","first-page":"e22520","DOI":"10.7554\/eLife.22520","article-title":"Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA","volume":"6","author":"Hubin","year":"2017","journal-title":"eLife"},{"key":"2025121705163652500_B24","doi-asserted-by":"publisher","first-page":"2018","DOI":"10.1099\/mic.0.079186-0","article-title":"Dual role of MsRbpA: transcription activation and rescue of transcription from the inhibitory effect of rifampicin","volume":"160","author":"Verma","year":"2014","journal-title":"Microbiology"},{"key":"2025121705163652500_B25","doi-asserted-by":"publisher","first-page":"7171","DOI":"10.1073\/pnas.1504942112","article-title":"Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA","volume":"112","author":"Hubin","year":"2015","journal-title":"Proc Natl Acad Sci"},{"key":"2025121705163652500_B26","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1080\/21541264.2019.1707612","article-title":"Transcription initiation in mycobacteria: a biophysical perspective","volume":"11","author":"Boyaci","year":"2020","journal-title":"Transcription"},{"key":"2025121705163652500_B27","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 \u03c3 A-containing RNA polymerase holoenzyme","volume":"40","author":"Hu","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B28","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1046\/j.1365-2958.2002.02779.x","article-title":"Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling","volume":"43","author":"Betts","year":"2002","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B29","doi-asserted-by":"publisher","first-page":"2056","DOI":"10.1099\/mic.0.047480-0","article-title":"Molecular insights into the mechanism of phenotypic tolerance to rifampicin conferred on mycobacterial RNA polymerase by MsRbpA","volume":"157","author":"Dey","year":"2011","journal-title":"Microbiology"},{"key":"2025121705163652500_B30","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1111\/j.1365-2958.2006.05116.x","article-title":"The RNA polymerase-binding protein RbpA confers basal levels of rifampicin resistance on Streptomyces coelicolor","volume":"60","author":"Newell","year":"2006","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B31","doi-asserted-by":"publisher","first-page":"1859","DOI":"10.1016\/j.str.2013.08.014","article-title":"Structure of the Mtb CarD\/RNAP \u03b2-lobes complex reveals the molecular basis of interaction and presents a distinct DNA-binding domain for Mtb CarD","volume":"21","author":"Gulten","year":"2013","journal-title":"Structure"},{"key":"2025121705163652500_B32","doi-asserted-by":"publisher","first-page":"104724","DOI":"10.1016\/j.jbc.2023.104724","article-title":"Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics","volume":"299","author":"Zhu","year":"2023","journal-title":"J Biol Chem"},{"key":"2025121705163652500_B33","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.cell.2009.04.041","article-title":"CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence","volume":"138","author":"Stallings","year":"2009","journal-title":"Cell"},{"key":"2025121705163652500_B34","doi-asserted-by":"publisher","first-page":"12619","DOI":"10.1073\/pnas.1308270110","article-title":"Structure and function of CarD, an essential mycobacterial transcription factor","volume":"110","author":"Srivastava","year":"2013","journal-title":"Proc Natl Acad Sci"},{"key":"2025121705163652500_B35","doi-asserted-by":"publisher","first-page":"13573","DOI":"10.1073\/pnas.1900176116","article-title":"CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis","volume":"116","author":"Zhu","year":"2019","journal-title":"Proc Natl Acad Sci"},{"key":"2025121705163652500_B36","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1111\/mmi.12681","article-title":"CarD integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria","volume":"93","author":"Garner","year":"2014","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B37","doi-asserted-by":"publisher","first-page":"e00698","DOI":"10.1128\/JB.00698-16","article-title":"Effects of increasing the affinity of CarD for RNA polymerase on Mycobacterium tuberculosis growth, rRNA transcription, and virulence","volume":"199","author":"Garner","year":"2017","journal-title":"J Bacteriol"},{"key":"2025121705163652500_B38","doi-asserted-by":"publisher","first-page":"e73347","DOI":"10.7554\/eLife.73347","article-title":"Clp protease and antisense RNA jointly regulate the global regulator CarD to mediate mycobacterial starvation response","volume":"11","author":"Li","year":"2022","journal-title":"eLife"},{"key":"2025121705163652500_B39","doi-asserted-by":"publisher","first-page":"3418","DOI":"10.1093\/nar\/gkq1186","article-title":"The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures","volume":"39","author":"Panek","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B40","doi-asserted-by":"publisher","first-page":"11763","DOI":"10.1093\/nar\/gku793","article-title":"Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria","volume":"42","author":"Hnilicov\u00e1","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B41","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1111\/mmi.14159","article-title":"Ms1 RNA increases the amount of RNA polymerase in Mycobacterium smegmatis","volume":"111","author":"\u0160ikov\u00e1","year":"2019","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B42","doi-asserted-by":"publisher","first-page":"848536","DOI":"10.3389\/fmicb.2022.848536","article-title":"Ms1 RNA interacts with the RNA polymerase core in Streptomyces coelicolor and was identified in majority of actinobacteria using a linguistic gene synteny search","volume":"13","author":"Va\u0148kov\u00e1\u00a0Hausnerov\u00e1","year":"2022","journal-title":"Front Microbiol"},{"key":"2025121705163652500_B43","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":"2025121705163652500_B44","doi-asserted-by":"publisher","first-page":"4604","DOI":"10.1093\/nar\/gkae081","article-title":"RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria","volume":"52","author":"Va\u0148kov\u00e1\u00a0Hausnerov\u00e1","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-020-20158-4","article-title":"Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase","volume":"11","author":"Kouba","year":"2020","journal-title":"Nat Commun"},{"key":"2025121705163652500_B46","doi-asserted-by":"crossref","article-title":"HelD is a global transcription factor enhancing gene expression in rapidly growing mycobacteria","author":"Va\u0148kov\u00e1\u00a0Hausnerov\u00e1","DOI":"10.1101\/2024.11.27.625628"},{"key":"2025121705163652500_B47","doi-asserted-by":"publisher","first-page":"e0006624","DOI":"10.1128\/jb.00066-24","article-title":"MoaB2, a newly identified transcription factor, binds to \u03c3 in Mycobacterium smegmatis","volume":"206","author":"Brezovsk\u00e1","year":"2024","journal-title":"J Bacteriol"},{"key":"2025121705163652500_B48","doi-asserted-by":"publisher","first-page":"3278","DOI":"10.1038\/nprot.2007.459","article-title":"Detecting protein\u2013protein interactions by far western blotting","volume":"2","author":"Wu","year":"2007","journal-title":"Nat Protoc"},{"key":"2025121705163652500_B49","first-page":"E12","volume-title":"Molecular Cloning. A Laboratory Manual","author":"Sambrook","year":"1987"},{"key":"2025121705163652500_B50","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1006\/jmra.1993.1098","article-title":"Gradient-tailored water suppression for 1H-15N HSQC experiments optimized to retain full sensitivity","volume":"102","author":"Sklenar","year":"1993","journal-title":"J Magn Res Ser A"},{"key":"2025121705163652500_B51","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/0009-2614(80)80041-8","article-title":"Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy","volume":"69","author":"Bodenhausen","year":"1980","journal-title":"Chem Phys Lett"},{"key":"2025121705163652500_B52","first-page":"496","article-title":"Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins","volume":"89","author":"Kay","year":"1990","journal-title":"J Magn Reson 1969"},{"key":"2025121705163652500_B53","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1007\/BF01874573","article-title":"An efficient 3D NMR technique for correlating the proton and15N backbone amide resonances with the \u03b1-carbon of the preceding residue in uniformly15N\/13C enriched proteins","volume":"1","author":"Bax","year":"1991","journal-title":"J Biomol NMR"},{"key":"2025121705163652500_B54","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1006\/jmrb.1993.1033","article-title":"HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha- and beta-carbon resonances in proteins","volume":"101","author":"Wittekind","year":"1993","journal-title":"J Magn Res Ser B"},{"key":"2025121705163652500_B55","doi-asserted-by":"publisher","first-page":"6291","DOI":"10.1021\/ja00042a003","article-title":"Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR","volume":"114","author":"Grzesiek","year":"1992","journal-title":"J Am Chem Soc"},{"key":"2025121705163652500_B56","doi-asserted-by":"publisher","first-page":"2387","DOI":"10.1021\/bi00432a008","article-title":"Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a","volume":"28","author":"Zuiderweg","year":"1989","journal-title":"Biochemistry"},{"key":"2025121705163652500_B57","doi-asserted-by":"publisher","first-page":"12366","DOI":"10.1073\/pnas.94.23.12366","article-title":"Attenuated T2 relaxation by mutual cancellation of dipole\u2013dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in\u2009solution","volume":"94","author":"Pervushin","year":"1997","journal-title":"Proc Natl Acad Sci"},{"key":"2025121705163652500_B58","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1007\/BF00197809","article-title":"NMRPipe: a multidimensional spectral processing system based on UNIX pipes","volume":"6","author":"Delaglio","year":"1995","journal-title":"J Biomol NMR"},{"key":"2025121705163652500_B59","doi-asserted-by":"publisher","first-page":"2795","DOI":"10.1110\/ps.062465306","article-title":"Sensitivity of secondary structure propensities to sequence differences between \u03b1-and \u03b3-synuclein: implications for fibrillation","volume":"15","author":"Marsh","year":"2006","journal-title":"Protein Sci"},{"key":"2025121705163652500_B60","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1007\/s10858-011-9508-2","article-title":"Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution","volume":"50","author":"Kjaergaard","year":"2011","journal-title":"J Biomol NMR"},{"key":"2025121705163652500_B61","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1007\/s10858-011-9472-x","article-title":"Random coil chemical shift for intrinsically disordered proteins: effects of temperature and pH","volume":"49","author":"Kjaergaard","year":"2011","journal-title":"J Biomol NMR"},{"key":"2025121705163652500_B62","doi-asserted-by":"publisher","first-page":"2970","DOI":"10.1021\/ja003760i","article-title":"Sequence-dependent correction of random coil NMR chemical shifts","volume":"123","author":"Schwarzinger","year":"2001","journal-title":"J Am Chem Soc"},{"key":"2025121705163652500_B63","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1042\/BST20120171","article-title":"Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins","volume":"40","author":"Tamiola","year":"2012","journal-title":"Biochem Soc Trans"},{"key":"2025121705163652500_B64","doi-asserted-by":"publisher","first-page":"18000","DOI":"10.1021\/ja105656t","article-title":"Sequence-specific random coil chemical shifts of intrinsically disordered proteins","volume":"132","author":"Tamiola","year":"2010","journal-title":"J Am Chem Soc"},{"key":"2025121705163652500_B65","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1007\/s10858-011-9478-4","article-title":"SHIFTX2: significantly improved protein chemical shift prediction","volume":"50","author":"Han","year":"2011","journal-title":"J Biomol NMR"},{"key":"2025121705163652500_B66","doi-asserted-by":"publisher","first-page":"3986","DOI":"10.1093\/nar\/26.17.3986","article-title":"Protein sequence similarity searches using patterns as seeds","volume":"26","author":"Zhang","year":"1998","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B67","doi-asserted-by":"publisher","first-page":"2105","DOI":"10.1093\/bioinformatics\/btz863","article-title":"DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins","volume":"36","author":"Zhang","year":"2020","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B68","doi-asserted-by":"publisher","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B69","doi-asserted-by":"publisher","first-page":"1166","DOI":"10.1093\/bioinformatics\/bts091","article-title":"Unipro UGENE: a unified bioinformatics toolkit","volume":"28","author":"Okonechnikov","year":"2012","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B70","doi-asserted-by":"publisher","first-page":"W320","DOI":"10.1093\/nar\/gku316","article-title":"Deciphering key features in protein structures with the new ENDscript server","volume":"42","author":"Robert","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B71","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"2025121705163652500_B72","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1093\/bioinformatics\/16.4.404","article-title":"The PSIPRED protein structure prediction server","volume":"16","author":"McGuffin","year":"2000","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B73","doi-asserted-by":"publisher","first-page":"W510","DOI":"10.1093\/nar\/gkac439","article-title":"accurate and fast prediction of protein structural features by protein language models and deep learning","volume":"50","author":"H\u00f8ie","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B74","doi-asserted-by":"publisher","first-page":"e99","DOI":"10.1002\/cpbi.99","article-title":"Analyzing protein disorder with IUPred2A","volume":"70","author":"Erd\u0151s","year":"2020","journal-title":"Curr Protoc Bioinform"},{"key":"2025121705163652500_B75","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1093\/bioinformatics\/btr682","article-title":"ESpritz: accurate and fast prediction of protein disorder","volume":"28","author":"Walsh","year":"2012","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B76","doi-asserted-by":"publisher","first-page":"4438","DOI":"10.1038\/s41467-021-24773-7","article-title":"flDPnn: accurate intrinsic disorder prediction with putative propensities of disorder functions","volume":"12","author":"Hu","year":"2021","journal-title":"Nat Commun"},{"key":"2025121705163652500_B77","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":"2025121705163652500_B78","doi-asserted-by":"publisher","DOI":"10.1101\/2021.10.04.463034","article-title":"Protein complex prediction with AlphaFold-Multimer","author":"Evans","journal-title":"bioRxiv"},{"key":"2025121705163652500_B79","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat Methods"},{"key":"2025121705163652500_B80","doi-asserted-by":"publisher","DOI":"10.1101\/496521","article-title":"Improved peak-calling with MACS2","author":"Gaspar","journal-title":"bioRxiv"},{"key":"2025121705163652500_B81","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-017-1708-7","article-title":"Intervene: a tool for intersection and visualization of multiple gene or genomic region sets","volume":"18","author":"Khan","year":"2017","journal-title":"BMC Bioinf"},{"key":"2025121705163652500_B83","doi-asserted-by":"publisher","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B84","doi-asserted-by":"publisher","first-page":"1841","DOI":"10.1093\/bioinformatics\/btp328","article-title":"rtracklayer: an R package for interfacing with genome browsers","volume":"25","author":"Lawrence","year":"2009","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B85","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: a 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput Sci Eng"},{"key":"2025121705163652500_B86","doi-asserted-by":"publisher","first-page":"3021","DOI":"10.21105\/joss.03021","article-title":"Seaborn: statistical data visualization","volume":"6","author":"Waskom","year":"2021","journal-title":"J Open Source Software"},{"key":"2025121705163652500_B87","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B88","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"Kim","year":"2015","journal-title":"Nat Methods"},{"key":"2025121705163652500_B89","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B90","doi-asserted-by":"crossref","unstructured":"Bonfield JK, Marshall J, Danecek P \u00a0et al. \u00a0HTSlib: c library for reading\/writing high-throughput sequencing data. Gigascience. 2021;10:giab007. 10.1093\/gigascience\/giab007.","DOI":"10.1093\/gigascience\/giab007"},{"key":"2025121705163652500_B91","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2025121705163652500_B92","doi-asserted-by":"publisher","first-page":"6267","DOI":"10.1038\/ncomms7267","article-title":"Gene silencing by CRISPR interference in mycobacteria","volume":"6","author":"Choudhary","year":"2015","journal-title":"Nat Commun"},{"key":"2025121705163652500_B93","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1146\/annurev.micro.57.030502.090913","article-title":"Multiple sigma subunits and the partitioning of bacterial transcription space","volume":"57","author":"Gruber","year":"2003","journal-title":"Annu Rev Microbiol"},{"key":"2025121705163652500_B94","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1111\/mmi.13952","article-title":"RbpA and \u03c3B association regulates polyphosphate levels to modulate mycobacterial isoniazid-tolerance","volume":"108","author":"Wang","year":"2018","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B95","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2022\/7475704","article-title":"Expression, purification, and in silico characterization of Mycobacterium smegmatis alternative sigma factor SigB","volume":"2022","author":"Singh","year":"2022","journal-title":"Dis Markers"},{"key":"2025121705163652500_B96","doi-asserted-by":"publisher","first-page":"e2220785120","DOI":"10.1073\/pnas.2220785120","article-title":"Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB","volume":"120","author":"Lilic","year":"2023","journal-title":"Proc Natl Acad Sci"},{"key":"2025121705163652500_B97","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1038\/24206","article-title":"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence","volume":"396","author":"Cole","year":"1998","journal-title":"Nature"},{"key":"2025121705163652500_B98","doi-asserted-by":"publisher","first-page":"M111.011445","DOI":"10.1074\/mcp.M111.011627","article-title":"Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry","volume":"10","author":"Kelkar","year":"2011","journal-title":"Mol Cell Proteomics"},{"key":"2025121705163652500_B99","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.tube.2010.09.006","article-title":"The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes","volume":"91","author":"Kapopoulou","year":"2011","journal-title":"Tuberculosis"},{"key":"2025121705163652500_B100","doi-asserted-by":"publisher","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the universal protein knowledgebase in 2023","volume":"51","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B101","doi-asserted-by":"publisher","first-page":"2603","DOI":"10.1128\/JB.00188-13","article-title":"The \u03b4 subunit of RNA polymerase is required for rapid changes in gene expression and competitive fitness of the cell","volume":"195","author":"Rabatinov\u00e1","year":"2013","journal-title":"J Bacteriol"},{"key":"2025121705163652500_B102","doi-asserted-by":"publisher","first-page":"16817","DOI":"10.1021\/jacs.9b07837","article-title":"Quantitative conformational analysis of functionally important electrostatic interactions in the intrinsically disordered region of delta subunit of bacterial RNA polymerase","volume":"141","author":"Kub\u00e1\u0148","year":"2019","journal-title":"J Am Chem Soc"},{"key":"2025121705163652500_B103","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/s41586-018-0840-5","article-title":"Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding","volume":"565","author":"Boyaci","year":"2019","journal-title":"Nature"},{"key":"2025121705163652500_B104","doi-asserted-by":"publisher","first-page":"e73347","DOI":"10.7554\/eLife.73347","article-title":"Clp protease and antisense RNA jointly regulate the global regulator CarD to mediate mycobacterial starvation response","volume":"11","author":"Li","year":"2022","journal-title":"eLife"},{"key":"2025121705163652500_B105","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":"2025121705163652500_B106","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/nmicrobiol.2016.274","article-title":"Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform","volume":"2","author":"Rock","year":"2017","journal-title":"Nat Microbiol"},{"key":"2025121705163652500_B107","doi-asserted-by":"publisher","first-page":"btac830","DOI":"10.1093\/bioinformatics\/btac830","article-title":"igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)","volume":"39","author":"Robinson","year":"2023","journal-title":"Bioinformatics"},{"key":"2025121705163652500_B108","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat Protoc"},{"key":"2025121705163652500_B109","doi-asserted-by":"publisher","first-page":"e0164253","DOI":"10.1371\/journal.pone.0164253","article-title":"Identification of a desaturase involved in mycolic acid biosynthesis in Mycobacterium smegmatis","volume":"11","author":"Singh","year":"2016","journal-title":"PLoS One"},{"key":"2025121705163652500_B110","doi-asserted-by":"publisher","first-page":"2194","DOI":"10.1128\/JB.180.8.2194-2200.1998","article-title":"A Bacillus subtilis gene induced by cold shock encodes a membrane phospholipid desaturase","volume":"180","author":"Aguilar","year":"1998","journal-title":"J Bacteriol"},{"key":"2025121705163652500_B111","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1016\/S1369-5274(02)00306-5","article-title":"Regulation of the desaturation of fatty acids and its role in tolerance to cold and salt stress","volume":"5","author":"Sakamoto","year":"2002","journal-title":"Curr Opin Microbiol"},{"key":"2025121705163652500_B112","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1042\/bj3080001","article-title":"Acyl-lipid desaturases and their importance in the tolerance and acclimatization to cold of cyanobacteria","volume":"308","author":"Murata","year":"1995","journal-title":"Biochem J"},{"key":"2025121705163652500_B113","doi-asserted-by":"publisher","first-page":"1321","DOI":"10.1111\/j.1365-2958.2001.02322.x","article-title":"Role of the Bacillus subtilis fatty acid desaturase in membrane adaptation during cold shock","volume":"39","author":"Weber","year":"2001","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B114","doi-asserted-by":"publisher","first-page":"1379","DOI":"10.1046\/j.1365-2958.2002.03103.x","article-title":"Mechanism of membrane fluidity optimization: isothermal control of the Bacillus subtilis acyl-lipid desaturase","volume":"45","author":"Cybulski","year":"2002","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B115","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1111\/mmi.12606","article-title":"Global effects of the DEAD-box RNA helicase DeaD (CsdA) on gene expression over a broad range of temperatures","volume":"92","author":"Vakulskas","year":"2014","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B116","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/j.mib.2016.01.002","article-title":"RNA helicases in bacteria","volume":"30","author":"Khemici","year":"2016","journal-title":"Curr Opin Microbiol"},{"key":"2025121705163652500_B117","doi-asserted-by":"publisher","first-page":"4189","DOI":"10.1093\/nar\/gkl500","article-title":"DEAD-box RNA helicases in Escherichia coli","volume":"34","author":"Iost","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B118","doi-asserted-by":"publisher","first-page":"e01934","DOI":"10.1128\/spectrum.01934-23","article-title":"The DEAD-box RNA helicase RhlB is required for efficient RNA processing at low temperature in Caulobacter","volume":"11","author":"de\u00a0Ara\u00fajo","year":"2023","journal-title":"Microbiol Spectr"},{"key":"2025121705163652500_B119","doi-asserted-by":"publisher","first-page":"394","DOI":"10.4161\/rna.8.3.14823","article-title":"Unwinding activity of cold shock proteins and RNA metabolism","volume":"8","author":"Phadtare","year":"2011","journal-title":"RNA Biol"},{"key":"2025121705163652500_B120","doi-asserted-by":"publisher","first-page":"2505","DOI":"10.3389\/fmicb.2017.02505","article-title":"Transcriptome landscape of Mycobacterium smegmatis","volume":"8","author":"Li","year":"2017","journal-title":"Front Microbiol"},{"key":"2025121705163652500_B121","doi-asserted-by":"publisher","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2025121705163652500_B122","doi-asserted-by":"publisher","first-page":"e71947","DOI":"10.7554\/eLife.71947","article-title":"Transposon mutagenesis in Mycobacterium abscessus identifies an essential penicillin-binding protein involved in septal peptidoglycan synthesis and antibiotic sensitivity","volume":"11","author":"Akusobi","year":"2022","journal-title":"eLife"},{"key":"2025121705163652500_B123","doi-asserted-by":"publisher","first-page":"4579","DOI":"10.1016\/j.cell.2021.06.033","article-title":"Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis","volume":"184","author":"Bosch","year":"2021","journal-title":"Cell"},{"key":"2025121705163652500_B124","doi-asserted-by":"publisher","first-page":"28835","DOI":"10.1074\/jbc.M313103200","article-title":"Trehalose is required for growth of Mycobacterium smegmatis","volume":"279","author":"Woodruff","year":"2004","journal-title":"J Biol Chem"},{"key":"2025121705163652500_B125","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1099\/00221287-146-1-199","article-title":"Three pathways for trehalose biosynthesis in mycobacteria","volume":"146","author":"De\u00a0Smet","year":"2000","journal-title":"Microbiology"},{"key":"2025121705163652500_B126","doi-asserted-by":"publisher","first-page":"14524","DOI":"10.1074\/jbc.M414232200","article-title":"The OtsAB pathway is essential for trehalose biosynthesis in Mycobacterium tuberculosis","volume":"280","author":"Murphy","year":"2005","journal-title":"J Biol Chem"},{"key":"2025121705163652500_B127","doi-asserted-by":"publisher","first-page":"e00070","DOI":"10.1128\/msystems.00070-00019","article-title":"Genomewide assessment of Mycobacterium tuberculosis conditionally essential metabolic pathways","volume":"4","author":"Minato","year":"2019","journal-title":"MSystems"},{"key":"2025121705163652500_B128","doi-asserted-by":"publisher","first-page":"e02133","DOI":"10.1128\/mbio.02133-16","article-title":"Comprehensive essentiality analysis of the Mycobacterium tuberculosis genome via saturating transposon mutagenesis","volume":"8","author":"DeJesus","year":"2017","journal-title":"mBio"},{"key":"2025121705163652500_B129","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1046\/j.1365-2958.2001.02684.x","article-title":"The Mycobacterium tuberculosis IdeR is a dual functional regulator that controls transcription of genes involved in iron acquisition, iron storage and survival in macrophages","volume":"42","author":"Gold","year":"2001","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B130","doi-asserted-by":"publisher","first-page":"2798","DOI":"10.1128\/AAC.02774-13","article-title":"Antimicrobial treatment improves mycobacterial survival in nonpermissive growth conditions","volume":"58","author":"Turapov","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"key":"2025121705163652500_B131","doi-asserted-by":"publisher","first-page":"1192","DOI":"10.1080\/21505594.2020.1809326","article-title":"Trehalose and bacterial virulence","volume":"11","author":"Vanaporn","year":"2020","journal-title":"Virulence"},{"key":"2025121705163652500_B132","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2180-12-207","article-title":"Role of trehalose in heat and desiccation tolerance in the soil bacterium Rhizobium etli","volume":"12","author":"Reina-Bueno","year":"2012","journal-title":"BMC Microbiol"},{"key":"2025121705163652500_B133","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0923-2508(02)01321-9","article-title":"Role of trehalose biosynthesis in environmental survival and virulence of Salmonella enterica serovar Typhimurium","volume":"153","author":"Howells","year":"2002","journal-title":"Res Microbiol"},{"key":"2025121705163652500_B134","doi-asserted-by":"publisher","first-page":"6943","DOI":"10.1038\/s41598-022-10589-y","article-title":"The mycobacterial desaturase DesA2 is associated with mycolic acid biosynthesis","volume":"12","author":"Bailo","year":"2022","journal-title":"Sci Rep"},{"key":"2025121705163652500_B135","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1007\/978-1-4614-7969-7","article-title":"Remodeling of membrane phospholipids by bacterial desaturases","volume-title":"Stearoyl-CoA Desaturase Genes Lipid Metab","author":"Altabe","year":"2013"},{"key":"2025121705163652500_B136","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/nrm3154","article-title":"From unwinding to clamping\u2014the DEAD box RNA helicase family","volume":"12","author":"Linder","year":"2011","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025121705163652500_B137","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1002\/wrna.50","article-title":"DEAD-box proteins as RNA helicases and chaperones","volume":"2","author":"Jarmoskaite","year":"2011","journal-title":"Wiley Interdiscip Rev"},{"key":"2025121705163652500_B138","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1016\/j.sbi.2007.05.007","article-title":"RNA helicases\u2014one fold for many functions","volume":"17","author":"Jankowsky","year":"2007","journal-title":"Curr Opin Struct Biol"},{"key":"2025121705163652500_B139","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1073\/pnas.93.1.76","article-title":"Cold shock induces a major ribosomal-associated protein that unwinds double-stranded RNA in Escherichia coli","volume":"93","author":"Jones","year":"1996","journal-title":"Proc Natl Acad Sci"},{"key":"2025121705163652500_B140","doi-asserted-by":"publisher","first-page":"6395","DOI":"10.1128\/JB.184.22.6395-6402.2002","article-title":"Genomewide transcriptional analysis of the cold shock response in Bacillus subtilis","volume":"184","author":"Beckering","year":"2002","journal-title":"J Bacteriol"},{"key":"2025121705163652500_B141","doi-asserted-by":"publisher","first-page":"12706","DOI":"10.3390\/ijms241612706","article-title":"Dynamic transcriptional landscape of Mycobacterium smegmatis under cold stress","volume":"24","author":"Grigorov","year":"2023","journal-title":"Int J Mol Sci"},{"key":"2025121705163652500_B142","doi-asserted-by":"publisher","first-page":"e1004516","DOI":"10.1371\/journal.pgen.1004516","article-title":"An essential nonredundant role for mycobacterial DnaK in native protein folding","volume":"10","author":"Fay","year":"2014","journal-title":"PLoS Genet"},{"key":"2025121705163652500_B143","doi-asserted-by":"publisher","first-page":"00123","DOI":"10.1128\/mbio.00123-21","article-title":"The DnaK Chaperone System Buffers the Fitness Cost of Antibiotic Resistance Mutations in Mycobacteria","volume":"12","author":"Fay","year":"2021","journal-title":"mBio"},{"key":"2025121705163652500_B144","doi-asserted-by":"publisher","first-page":"3129","DOI":"10.1099\/00221287-148-10-3129","article-title":"Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays","volume":"148","author":"Stewart","year":"2002","journal-title":"Microbiology (Reading)"},{"key":"2025121705163652500_B145","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/s42003-022-03542-2","article-title":"DnaK response to expression of protein mutants is dependent on translation rate and stability","volume":"5","author":"Christensen","year":"2022","journal-title":"Commun Biol"},{"key":"2025121705163652500_B146","doi-asserted-by":"publisher","first-page":"109166","DOI":"10.1016\/j.celrep.2021.109166","article-title":"Structural basis for aggregate dissolution and refolding by the Mycobacterium tuberculosis ClpB-DnaK bi-chaperone system","volume":"35","author":"Yin","year":"2021","journal-title":"Cell Rep"},{"key":"2025121705163652500_B147","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1038\/89113","article-title":"Overexpression of heat-shock proteins reduces survival of Mycobacterium tuberculosis in the chronic phase of infection","volume":"7","author":"Stewart","year":"2001","journal-title":"Nat Med"},{"key":"2025121705163652500_B148","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1111\/mmi.14615","article-title":"Nonredundant functions of Mycobacterium tuberculosis chaperones promote survival under stress","volume":"115","author":"Harnagel","year":"2021","journal-title":"Mol Microbiol"},{"key":"2025121705163652500_B149","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1093\/femsre\/fux015","article-title":"Regulation of heat-shock genes in bacteria: from signal sensing to gene expression output","volume":"41","author":"Roncarati","year":"2017","journal-title":"FEMS Microbiol Rev"},{"key":"2025121705163652500_B150","doi-asserted-by":"publisher","first-page":"4688","DOI":"10.1128\/JB.00415-12","article-title":"DnaK dependence of the mycobacterial stress-responsive regulator HspR is mediated through its hydrophobic C-terminal tail","volume":"194","author":"Bandyopadhyay","year":"2012","journal-title":"J Bacteriol"},{"key":"2025121705163652500_B151","doi-asserted-by":"publisher","first-page":"816","DOI":"10.1002\/iub.1438","article-title":"Role of DnaK in HspR\u2013HAIR interaction of Mycobacterium tuberculosis","volume":"67","author":"Parijat","year":"2015","journal-title":"IUBMB Life"},{"key":"2025121705163652500_B152","doi-asserted-by":"publisher","first-page":"3997","DOI":"10.1111\/febs.16792","article-title":"Crystal structure of FadA2 thiolase from Mycobacterium tuberculosis and prediction of its substrate specificity and membrane-anchoring properties","volume":"290","author":"Singh","year":"2023","journal-title":"FEBS J"},{"key":"2025121705163652500_B153","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nrm1589","article-title":"Intrinsically unstructured proteins and their functions","volume":"6","author":"Dyson","year":"2005","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025121705163652500_B154","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.pbiomolbio.2009.03.001","article-title":"The rules of disorder or why disorder rules","volume":"99","author":"Gsponer","year":"2009","journal-title":"Prog Biophys Mol Biol"},{"key":"2025121705163652500_B155","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1042\/BJ20130545","article-title":"Promiscuity as a functional trait: intrinsically disordered regions as central players of interactomes","volume":"454","author":"Cumberworth","year":"2013","journal-title":"Biochem J"},{"key":"2025121705163652500_B156","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.sbi.2008.12.003","article-title":"Linking folding and binding","volume":"19","author":"Wright","year":"2009","journal-title":"Curr Opin Struct Biol"},{"key":"2025121705163652500_B157","doi-asserted-by":"publisher","first-page":"1076","DOI":"10.1021\/bi971952t","article-title":"The C-terminal half of the anti-sigma factor FlgM contains a dynamic equilibrium solution structure favoring helical conformations","volume":"37","author":"Daughdrill","year":"1998","journal-title":"Biochemistry"},{"key":"2025121705163652500_B158","doi-asserted-by":"publisher","first-page":"3614","DOI":"10.3390\/ijms19113614","article-title":"Transient secondary structures as general target-binding motifs in intrinsically disordered proteins","volume":"19","author":"Kim","year":"2018","journal-title":"Int J Mol Sci"},{"key":"2025121705163652500_B159","doi-asserted-by":"publisher","first-page":"6418","DOI":"10.1038\/s41467-020-20159-3","article-title":"The \u03b4 subunit and NTPase HelD institute a two-pronged mechanism for RNA polymerase recycling","volume":"11","author":"Pei","year":"2020","journal-title":"Nat Commun"},{"key":"2025121705163652500_B160","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/j.sbi.2005.01.002","article-title":"Natively unfolded proteins","volume":"15","author":"Fink","year":"2005","journal-title":"Curr Opin Struct Biol"},{"key":"2025121705163652500_B161","doi-asserted-by":"publisher","first-page":"e1007186","DOI":"10.1371\/journal.pcbi.1007186","article-title":"Why do eukaryotic proteins contain more intrinsically disordered regions?","volume":"15","author":"Basile","year":"2019","journal-title":"PLoS Comput Biol"},{"key":"2025121705163652500_B162","doi-asserted-by":"publisher","first-page":"eadh4591","DOI":"10.1126\/sciadv.adh4591","article-title":"Functional regulation of an intrinsically disordered protein via a conformationally excited state","volume":"9","author":"Madhurima","year":"2023","journal-title":"Sci Adv"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/22\/gkaf1342\/65937259\/gkaf1342.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/53\/22\/gkaf1342\/65937259\/gkaf1342.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T10:17:08Z","timestamp":1765966628000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/doi\/10.1093\/nar\/gkaf1342\/8382376"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,26]]},"references-count":162,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2025,11,26]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaf1342","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,12,11]]},"published":{"date-parts":[[2025,11,26]]},"article-number":"gkaf1342"}}