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Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems
Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a comp...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736814/ https://www.ncbi.nlm.nih.gov/pubmed/33275130 http://dx.doi.org/10.1093/nar/gkaa1149 |
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author | Mestre, Mario Rodríguez González-Delgado, Alejandro Gutiérrez-Rus, Luis I Martínez-Abarca, Francisco Toro, Nicolás |
author_facet | Mestre, Mario Rodríguez González-Delgado, Alejandro Gutiérrez-Rus, Luis I Martínez-Abarca, Francisco Toro, Nicolás |
author_sort | Mestre, Mario Rodríguez |
collection | PubMed |
description | Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications. |
format | Online Article Text |
id | pubmed-7736814 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-77368142020-12-17 Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems Mestre, Mario Rodríguez González-Delgado, Alejandro Gutiérrez-Rus, Luis I Martínez-Abarca, Francisco Toro, Nicolás Nucleic Acids Res Data Resources and Analyses Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications. Oxford University Press 2020-12-04 /pmc/articles/PMC7736814/ /pubmed/33275130 http://dx.doi.org/10.1093/nar/gkaa1149 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Data Resources and Analyses Mestre, Mario Rodríguez González-Delgado, Alejandro Gutiérrez-Rus, Luis I Martínez-Abarca, Francisco Toro, Nicolás Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems |
title | Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems |
title_full | Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems |
title_fullStr | Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems |
title_full_unstemmed | Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems |
title_short | Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems |
title_sort | systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems |
topic | Data Resources and Analyses |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736814/ https://www.ncbi.nlm.nih.gov/pubmed/33275130 http://dx.doi.org/10.1093/nar/gkaa1149 |
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