The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures

Pánek, Josef; Krásný, Libor; Bobek, Jan; Ježková, Edita; Korelusová, Jana; Vohradský, Jiřı́

doi:10.1093/nar/gkq1186

Cited by 32 publications

(36 citation statements)

References 19 publications

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“…29 The presence of 6S RNAs in Actinobacteria has been previously addressed. Pan ek et al 31 used suboptimal structures to find 6S RNAs and reported candidates in Streptomyces and Mycobacterium. The candidate 6S RNA of M. smegmatis did not bind to the s 70 -RNAP homolog of this bacterium, as inferred from co-immunoprecipitation experiments.…”

Section: Resultsmentioning

confidence: 99%

Dissemination of 6S RNA among Bacteria

et al. 2014

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6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis.

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Section: Resultsmentioning

confidence: 99%

Dissemination of 6S RNA among Bacteria

et al. 2014

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“…At least one RNA identified based on its structural similarity to 6S RNA (Ms1 RNA in Mycobacterium smegmatis ) does not bind to the holoenzyme form of RNA polymerase, although it does interact with core RNA polymerase (60, 61). This example serves as a cautionary tale in relying too heavily on secondary structure as the predictor of 6S RNA candidates, but also raises the intriguing possibility that there are additional classes of sRNAs that function through interaction with RNA polymerase using different mechanisms.…”

Section: S Rnas Are Widespread Throughout the Bacterial Kingdommentioning

confidence: 99%

6S RNA, a Global Regulator of Transcription

Wassarman

2018

Microbiol Spectr

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6S RNA is a small RNA regulator of RNA polymerase that is present broadly throughout the bacterial kingdom. Initial functional studies in Escherichia coli revealed that 6S RNA forms a complex with RNA polymerase resulting in regulation of transcription, and cells lacking 6S RNA have altered survival phenotypes. The last decade has focused on deepening the understanding of several aspects of 6S RNA activity including: 1. Addressing questions of how broadly conserved 6S RNAs are in diverse organisms through continued identification and initial characterization of divergent 6S RNAs; 2. The nature of the 6S RNA-RNA polymerase interaction through examination of variant proteins and mutant RNAs, crosslinking approaches, and ultimately a cryo-EM structure; 3. The physiological consequences of 6S RNA function through identification of the 6S RNA-regulon and promoter features that determine 6S RNA sensitivity; 4. The mechanism and cellular impact of 6S RNA-directed synthesis of pRNAs (i.e. pRNA synthesis). Much has been learned about this unusual RNA, its mechanism of action and how it is regulated; yet, much still remains to be investigated, especially regarding potential differences in behavior of 6S RNAs in diverse bacteria.

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“…A bioinformatics search based on matching for energetically suboptimal structures recently identified the M. smegmatis homolog of MTS2823 as a potential 6S RNA candidate, but lack of binding to RNA polymerase led the authors to conclude that it is not a genuine 6S RNA, 86 and so far no 6S RNA homolog has been identified in mycobacteria. It remains to be determined if MTS2823 is a conventional sRNA that acts via base-pairing with specific mRNA targets or with protein or whether its mode of action differs entirely from other sRNAs.…”

Section: Tuberculosis Intergenic Srnas and Stressmentioning

confidence: 99%

Non-coding RNA and its potential role in Mycobacterium tuberculosis pathogenesis

2012

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It is estimated that one third of the human population is infected with Mycobacterium tuberculosis. Efforts to understand the molecular basis of its gene regulation have been focused on identification of protein encoding genes and regulons implicated in pathogenesis. Recently, a number of studies have described the identification of several non-coding RNAs that are likely to contribute significantly to the regulatory networks responsible for adaptation and virulence in M. tuberculosis. We have reviewed emerging information on the presence and abundance of different types of non-coding RNA in M. tuberculosis and consider their potential contribution to the adaptive responses that underlie disease pathogenesis.

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The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures

Cited by 32 publications

References 19 publications

Dissemination of 6S RNA among Bacteria

Dissemination of 6S RNA among Bacteria

6S RNA, a Global Regulator of Transcription

Non-coding RNA and its potential role in Mycobacterium tuberculosis pathogenesis

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