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Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons
To date only a handful of duplicated genes have been described in RNA viruses. This shortage can be attributed to different factors, including the RNA viruses with high mutation rate that would make a large genome more prone to acquire deleterious mutations. This may explain why sequence-based appro...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7967035/ https://www.ncbi.nlm.nih.gov/pubmed/33758672 http://dx.doi.org/10.1093/ve/veab019 |
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author | Cisneros-Martínez, Alejandro Miguel Becerra, Arturo Lazcano, Antonio |
author_facet | Cisneros-Martínez, Alejandro Miguel Becerra, Arturo Lazcano, Antonio |
author_sort | Cisneros-Martínez, Alejandro Miguel |
collection | PubMed |
description | To date only a handful of duplicated genes have been described in RNA viruses. This shortage can be attributed to different factors, including the RNA viruses with high mutation rate that would make a large genome more prone to acquire deleterious mutations. This may explain why sequence-based approaches have only found duplications in their most recent evolutionary history. To detect earlier duplications, we performed protein tertiary structure comparisons for every RNA virus family represented in the Protein Data Bank. We present a list of thirty pairs of possible paralogs with <30 per cent sequence identity. It is argued that these pairs are the outcome of six duplication events. These include the α and β subunits of the fungal toxin KP6 present in the dsRNA Ustilago maydis virus (family Totiviridae), the SARS-CoV (Coronaviridae) nsp3 domains SUD-N, SUD-M and X-domain, the Picornavirales (families Picornaviridae, Dicistroviridae, Iflaviridae and Secoviridae) capsid proteins VP1, VP2 and VP3, and the Enterovirus (family Picornaviridae) 3C and 2A cysteine-proteases. Protein tertiary structure comparisons may reveal more duplication events as more three-dimensional protein structures are determined and suggests that, although still rare, gene duplications may be more frequent in RNA viruses than previously thought. Keywords: gene duplications; RNA viruses. |
format | Online Article Text |
id | pubmed-7967035 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-79670352021-03-22 Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons Cisneros-Martínez, Alejandro Miguel Becerra, Arturo Lazcano, Antonio Virus Evol Research Article To date only a handful of duplicated genes have been described in RNA viruses. This shortage can be attributed to different factors, including the RNA viruses with high mutation rate that would make a large genome more prone to acquire deleterious mutations. This may explain why sequence-based approaches have only found duplications in their most recent evolutionary history. To detect earlier duplications, we performed protein tertiary structure comparisons for every RNA virus family represented in the Protein Data Bank. We present a list of thirty pairs of possible paralogs with <30 per cent sequence identity. It is argued that these pairs are the outcome of six duplication events. These include the α and β subunits of the fungal toxin KP6 present in the dsRNA Ustilago maydis virus (family Totiviridae), the SARS-CoV (Coronaviridae) nsp3 domains SUD-N, SUD-M and X-domain, the Picornavirales (families Picornaviridae, Dicistroviridae, Iflaviridae and Secoviridae) capsid proteins VP1, VP2 and VP3, and the Enterovirus (family Picornaviridae) 3C and 2A cysteine-proteases. Protein tertiary structure comparisons may reveal more duplication events as more three-dimensional protein structures are determined and suggests that, although still rare, gene duplications may be more frequent in RNA viruses than previously thought. Keywords: gene duplications; RNA viruses. Oxford University Press 2021-03-10 /pmc/articles/PMC7967035/ /pubmed/33758672 http://dx.doi.org/10.1093/ve/veab019 Text en © The Author(s) 2021. Published by Oxford University Press. 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 | Research Article Cisneros-Martínez, Alejandro Miguel Becerra, Arturo Lazcano, Antonio Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons |
title | Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons |
title_full | Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons |
title_fullStr | Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons |
title_full_unstemmed | Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons |
title_short | Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons |
title_sort | ancient gene duplications in rna viruses revealed by protein tertiary structure comparisons |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7967035/ https://www.ncbi.nlm.nih.gov/pubmed/33758672 http://dx.doi.org/10.1093/ve/veab019 |
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