RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria

0582831 - MBÚ 2025 RIV US eng J - Článek v odborném periodiku
Vaňková Hausnerová, Viola - Shoman, Mahmoud - Kumar, Dilip - Schwarz, Marek - Modrák, Martin - Jirát Matějčková, Jitka - Mikesková, Eliška - Neva, Silva - Herrmannová, Anna - Šiková, Michaela - Halada, Petr - Novotná, I. - Pajer, J. - Valášek, Leoš Shivaya - Převorovský, M. - Krásný, Libor - Hnilicová, Jarmila
RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria.
Nucleic Acids Research. Roč. 52, May 8 (2024), s. 4604-4626. ISSN 0305-1048. E-ISSN 1362-4962
Grant CEP: GA ČR(CZ) GA20-07473S; GA MŠMT(CZ) LX22NPO5103; GA MŠMT(CZ) EF18_046/0015974; GA ČR(CZ) GA23-05622S
Grant ostatní: AV ČR(CZ) Premium Academiae of the Academy of Sciences of the Czech Republic
Program: Akademická prémie - Praemium Academiae
Institucionální podpora: RVO:61388971
Klíčová slova: RIP-seq reveals * RNA polymerase * 6S RNA * Ms1 RNA
Obor OECD: Microbiology
Impakt faktor: 14.9, rok: 2022
Způsob publikování: Open access
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae081/7606967?login=true

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.
Trvalý link: https://hdl.handle.net/11104/0350882