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Genome-wide discovery of structured noncoding RNAs in bacteria
BACKGROUND: Structured noncoding RNAs (ncRNAs) play essential roles in many biological processes such as gene regulation, signaling, RNA processing, and protein synthesis. Among the most common groups of ncRNAs in bacteria are riboswitches. These cis-regulatory, metabolite-binding RNAs are present i...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429828/ https://www.ncbi.nlm.nih.gov/pubmed/30902049 http://dx.doi.org/10.1186/s12866-019-1433-7 |
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author | Stav, Shira Atilho, Ruben M. Mirihana Arachchilage, Gayan Nguyen, Giahoa Higgs, Gadareth Breaker, Ronald R. |
author_facet | Stav, Shira Atilho, Ruben M. Mirihana Arachchilage, Gayan Nguyen, Giahoa Higgs, Gadareth Breaker, Ronald R. |
author_sort | Stav, Shira |
collection | PubMed |
description | BACKGROUND: Structured noncoding RNAs (ncRNAs) play essential roles in many biological processes such as gene regulation, signaling, RNA processing, and protein synthesis. Among the most common groups of ncRNAs in bacteria are riboswitches. These cis-regulatory, metabolite-binding RNAs are present in many species where they regulate various metabolic and signaling pathways. Collectively, there are likely to be hundreds of novel riboswitch classes that remain hidden in the bacterial genomes that have already been sequenced, and potentially thousands of classes distributed among various other species in the biosphere. The vast majority of these undiscovered classes are proposed to be exceedingly rare, and so current bioinformatics search techniques are reaching their limits for differentiating between true riboswitch candidates and false positives. RESULTS: Herein, we exploit a computational search pipeline that can efficiently identify intergenic regions most likely to encode structured ncRNAs. Application of this method to five bacterial genomes yielded nearly 70 novel genetic elements including 30 novel candidate ncRNA motifs. Among the riboswitch candidates identified is an RNA motif involved in the regulation of thiamin biosynthesis. CONCLUSIONS: Analysis of other genomes will undoubtedly lead to the discovery of many additional novel structured ncRNAs, and provide insight into the range of riboswitches and other kinds of ncRNAs remaining to be discovered in bacteria and archaea. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12866-019-1433-7) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6429828 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-64298282019-04-04 Genome-wide discovery of structured noncoding RNAs in bacteria Stav, Shira Atilho, Ruben M. Mirihana Arachchilage, Gayan Nguyen, Giahoa Higgs, Gadareth Breaker, Ronald R. BMC Microbiol Research Article BACKGROUND: Structured noncoding RNAs (ncRNAs) play essential roles in many biological processes such as gene regulation, signaling, RNA processing, and protein synthesis. Among the most common groups of ncRNAs in bacteria are riboswitches. These cis-regulatory, metabolite-binding RNAs are present in many species where they regulate various metabolic and signaling pathways. Collectively, there are likely to be hundreds of novel riboswitch classes that remain hidden in the bacterial genomes that have already been sequenced, and potentially thousands of classes distributed among various other species in the biosphere. The vast majority of these undiscovered classes are proposed to be exceedingly rare, and so current bioinformatics search techniques are reaching their limits for differentiating between true riboswitch candidates and false positives. RESULTS: Herein, we exploit a computational search pipeline that can efficiently identify intergenic regions most likely to encode structured ncRNAs. Application of this method to five bacterial genomes yielded nearly 70 novel genetic elements including 30 novel candidate ncRNA motifs. Among the riboswitch candidates identified is an RNA motif involved in the regulation of thiamin biosynthesis. CONCLUSIONS: Analysis of other genomes will undoubtedly lead to the discovery of many additional novel structured ncRNAs, and provide insight into the range of riboswitches and other kinds of ncRNAs remaining to be discovered in bacteria and archaea. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12866-019-1433-7) contains supplementary material, which is available to authorized users. BioMed Central 2019-03-22 /pmc/articles/PMC6429828/ /pubmed/30902049 http://dx.doi.org/10.1186/s12866-019-1433-7 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Stav, Shira Atilho, Ruben M. Mirihana Arachchilage, Gayan Nguyen, Giahoa Higgs, Gadareth Breaker, Ronald R. Genome-wide discovery of structured noncoding RNAs in bacteria |
title | Genome-wide discovery of structured noncoding RNAs in bacteria |
title_full | Genome-wide discovery of structured noncoding RNAs in bacteria |
title_fullStr | Genome-wide discovery of structured noncoding RNAs in bacteria |
title_full_unstemmed | Genome-wide discovery of structured noncoding RNAs in bacteria |
title_short | Genome-wide discovery of structured noncoding RNAs in bacteria |
title_sort | genome-wide discovery of structured noncoding rnas in bacteria |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429828/ https://www.ncbi.nlm.nih.gov/pubmed/30902049 http://dx.doi.org/10.1186/s12866-019-1433-7 |
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