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Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds to the RNA polymerase (RNAP) core and affects the intracellular level of this essential enzyme. Ms1 is structurally related to 6S RNA that binds to a different form of RNAP, the holoenzyme bearing th...

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Autores principales: Vaňková Hausnerová, Viola, Marvalová, Olga, Šiková, Michaela, Shoman, Mahmoud, Havelková, Jarmila, Kambová, Milada, Janoušková, Martina, Kumar, Dilip, Halada, Petr, Schwarz, Marek, Krásný, Libor, Hnilicová, Jarmila, Pánek, Josef
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9130861/
https://www.ncbi.nlm.nih.gov/pubmed/35633709
http://dx.doi.org/10.3389/fmicb.2022.848536
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author Vaňková Hausnerová, Viola
Marvalová, Olga
Šiková, Michaela
Shoman, Mahmoud
Havelková, Jarmila
Kambová, Milada
Janoušková, Martina
Kumar, Dilip
Halada, Petr
Schwarz, Marek
Krásný, Libor
Hnilicová, Jarmila
Pánek, Josef
author_facet Vaňková Hausnerová, Viola
Marvalová, Olga
Šiková, Michaela
Shoman, Mahmoud
Havelková, Jarmila
Kambová, Milada
Janoušková, Martina
Kumar, Dilip
Halada, Petr
Schwarz, Marek
Krásný, Libor
Hnilicová, Jarmila
Pánek, Josef
author_sort Vaňková Hausnerová, Viola
collection PubMed
description Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds to the RNA polymerase (RNAP) core and affects the intracellular level of this essential enzyme. Ms1 is structurally related to 6S RNA that binds to a different form of RNAP, the holoenzyme bearing the primary sigma factor. 6S RNAs are widespread in the bacterial kingdom except for the industrially and medicinally important Actinobacteria. While Ms1 RNA was identified in Mycobacterium, it is not clear whether Ms1 RNA is present also in other Actinobacteria species. Here, using a computational search based on secondary structure similarities combined with a linguistic gene synteny approach, we identified Ms1 RNA in Streptomyces. In S. coelicolor, Ms1 RNA overlaps with the previously annotated scr3559 sRNA with an unknown function. We experimentally confirmed that Ms1 RNA/scr3559 associates with the RNAP core without the primary sigma factor HrdB in vivo. Subsequently, we applied the computational approach to other Actinobacteria and identified Ms1 RNA candidates in 824 Actinobacteria species, revealing Ms1 RNA as a widespread class of RNAP binding sRNAs, and demonstrating the ability of our multifactorial computational approach to identify weakly conserved sRNAs in evolutionarily distant genomes.
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spelling pubmed-91308612022-05-26 Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search Vaňková Hausnerová, Viola Marvalová, Olga Šiková, Michaela Shoman, Mahmoud Havelková, Jarmila Kambová, Milada Janoušková, Martina Kumar, Dilip Halada, Petr Schwarz, Marek Krásný, Libor Hnilicová, Jarmila Pánek, Josef Front Microbiol Microbiology Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds to the RNA polymerase (RNAP) core and affects the intracellular level of this essential enzyme. Ms1 is structurally related to 6S RNA that binds to a different form of RNAP, the holoenzyme bearing the primary sigma factor. 6S RNAs are widespread in the bacterial kingdom except for the industrially and medicinally important Actinobacteria. While Ms1 RNA was identified in Mycobacterium, it is not clear whether Ms1 RNA is present also in other Actinobacteria species. Here, using a computational search based on secondary structure similarities combined with a linguistic gene synteny approach, we identified Ms1 RNA in Streptomyces. In S. coelicolor, Ms1 RNA overlaps with the previously annotated scr3559 sRNA with an unknown function. We experimentally confirmed that Ms1 RNA/scr3559 associates with the RNAP core without the primary sigma factor HrdB in vivo. Subsequently, we applied the computational approach to other Actinobacteria and identified Ms1 RNA candidates in 824 Actinobacteria species, revealing Ms1 RNA as a widespread class of RNAP binding sRNAs, and demonstrating the ability of our multifactorial computational approach to identify weakly conserved sRNAs in evolutionarily distant genomes. Frontiers Media S.A. 2022-05-11 /pmc/articles/PMC9130861/ /pubmed/35633709 http://dx.doi.org/10.3389/fmicb.2022.848536 Text en Copyright © 2022 Vaňková Hausnerová, Marvalová, Šiková, Shoman, Havelková, Kambová, Janoušková, Kumar, Halada, Schwarz, Krásný, Hnilicová and Pánek. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Vaňková Hausnerová, Viola
Marvalová, Olga
Šiková, Michaela
Shoman, Mahmoud
Havelková, Jarmila
Kambová, Milada
Janoušková, Martina
Kumar, Dilip
Halada, Petr
Schwarz, Marek
Krásný, Libor
Hnilicová, Jarmila
Pánek, Josef
Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
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
title_full Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
title_fullStr Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
title_full_unstemmed Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
title_short Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search
title_sort ms1 rna interacts with the rna polymerase core in streptomyces coelicolor and was identified in majority of actinobacteria using a linguistic gene synteny search
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9130861/
https://www.ncbi.nlm.nih.gov/pubmed/35633709
http://dx.doi.org/10.3389/fmicb.2022.848536
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