Evolution of tertiary structure of viral RNA dependent polymerases.

Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evoluti...

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Autores principales:	Jiří Černý, Barbora Černá Bolfíková, James J Valdés, Libor Grubhoffer, Daniel Růžek
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/b695d498de1946d0943aa48e3d58a4c4
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spelling	oai:doaj.org-article:b695d498de1946d0943aa48e3d58a4c42021-11-18T08:19:57ZEvolution of tertiary structure of viral RNA dependent polymerases.1932-620310.1371/journal.pone.0096070https://doaj.org/article/b695d498de1946d0943aa48e3d58a4c42014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24816789/?tool=EBIhttps://doaj.org/toc/1932-6203Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evolutionary history. The major strength of this work is in unifying sequence and structural data into a single quantitative phylogenetic analysis, using powerful a Bayesian approach. The resulting phylogram of vRdPs demonstrates that RNA-dependent DNA polymerases (RdDPs) of viruses within Retroviridae family cluster in a clearly separated group of vRdPs, while RNA-dependent RNA polymerases (RdRPs) of dsRNA and +ssRNA viruses are mixed together. This evidence supports the hypothesis that RdRPs replicating +ssRNA viruses evolved multiple times from RdRPs replicating +dsRNA viruses, and vice versa. Moreover, our phylogram may be presented as a scheme for RNA virus evolution. The results are in concordance with the actual concept of RNA virus evolution. Finally, the methods used in our work provide a new direction for studying ancient virus evolution.Jiří ČernýBarbora Černá BolfíkováJames J ValdésLibor GrubhofferDaniel RůžekPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 5, p e96070 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jiří Černý Barbora Černá Bolfíková James J Valdés Libor Grubhoffer Daniel Růžek Evolution of tertiary structure of viral RNA dependent polymerases.
description	Viral RNA dependent polymerases (vRdPs) are present in all RNA viruses; unfortunately, their sequence similarity is too low for phylogenetic studies. Nevertheless, vRdP protein structures are remarkably conserved. In this study, we used the structural similarity of vRdPs to reconstruct their evolutionary history. The major strength of this work is in unifying sequence and structural data into a single quantitative phylogenetic analysis, using powerful a Bayesian approach. The resulting phylogram of vRdPs demonstrates that RNA-dependent DNA polymerases (RdDPs) of viruses within Retroviridae family cluster in a clearly separated group of vRdPs, while RNA-dependent RNA polymerases (RdRPs) of dsRNA and +ssRNA viruses are mixed together. This evidence supports the hypothesis that RdRPs replicating +ssRNA viruses evolved multiple times from RdRPs replicating +dsRNA viruses, and vice versa. Moreover, our phylogram may be presented as a scheme for RNA virus evolution. The results are in concordance with the actual concept of RNA virus evolution. Finally, the methods used in our work provide a new direction for studying ancient virus evolution.
format	article
author	Jiří Černý Barbora Černá Bolfíková James J Valdés Libor Grubhoffer Daniel Růžek
author_facet	Jiří Černý Barbora Černá Bolfíková James J Valdés Libor Grubhoffer Daniel Růžek
author_sort	Jiří Černý
title	Evolution of tertiary structure of viral RNA dependent polymerases.
title_short	Evolution of tertiary structure of viral RNA dependent polymerases.
title_full	Evolution of tertiary structure of viral RNA dependent polymerases.
title_fullStr	Evolution of tertiary structure of viral RNA dependent polymerases.
title_full_unstemmed	Evolution of tertiary structure of viral RNA dependent polymerases.
title_sort	evolution of tertiary structure of viral rna dependent polymerases.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/b695d498de1946d0943aa48e3d58a4c4
work_keys_str_mv	AT jiricerny evolutionoftertiarystructureofviralrnadependentpolymerases AT barboracernabolfikova evolutionoftertiarystructureofviralrnadependentpolymerases AT jamesjvaldes evolutionoftertiarystructureofviralrnadependentpolymerases AT liborgrubhoffer evolutionoftertiarystructureofviralrnadependentpolymerases AT danielruzek evolutionoftertiarystructureofviralrnadependentpolymerases
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Evolution of tertiary structure of viral RNA dependent polymerases.

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