Genome-wide discovery of structured noncoding RNAs in bacteria
Abstract 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 p...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-03-01
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| Series: | BMC Microbiology |
| Online Access: | http://link.springer.com/article/10.1186/s12866-019-1433-7 |
| _version_ | 1819010688450822144 |
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| author | Shira Stav Ruben M. Atilho Gayan Mirihana Arachchilage Giahoa Nguyen Gadareth Higgs Ronald R. Breaker |
| author_facet | Shira Stav Ruben M. Atilho Gayan Mirihana Arachchilage Giahoa Nguyen Gadareth Higgs Ronald R. Breaker |
| author_sort | Shira Stav |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-21T01:16:14Z |
| format | Article |
| id | doaj.art-2bf074d99d144bed80388b1d94009858 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-12-21T01:16:14Z |
| publishDate | 2019-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-2bf074d99d144bed80388b1d940098582022-12-21T19:20:47ZengBMCBMC Microbiology1471-21802019-03-0119111810.1186/s12866-019-1433-7Genome-wide discovery of structured noncoding RNAs in bacteriaShira Stav0Ruben M. Atilho1Gayan Mirihana Arachchilage2Giahoa Nguyen3Gadareth Higgs4Ronald R. Breaker5Department of Molecular, Cellular and Developmental Biology, Yale UniversityDepartment of Molecular Biophysics and Biochemistry, Yale UniversityHoward Hughes Medical Institute, Yale UniversityDepartment of Molecular, Cellular and Developmental Biology, Yale UniversityDepartment of Molecular, Cellular and Developmental Biology, Yale UniversityDepartment of Molecular, Cellular and Developmental Biology, Yale UniversityAbstract 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.http://link.springer.com/article/10.1186/s12866-019-1433-7 |
| spellingShingle | Shira Stav Ruben M. Atilho Gayan Mirihana Arachchilage Giahoa Nguyen Gadareth Higgs Ronald R. Breaker Genome-wide discovery of structured noncoding RNAs in bacteria BMC Microbiology |
| 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 |
| url | http://link.springer.com/article/10.1186/s12866-019-1433-7 |
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