title: Evolution of tertiary structure of viral RNA dependent polymerases.
abstract: 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.
authors.affiliation: Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Černý
authors.affiliation: Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic.
authors.forename: Barbora
authors.initials: B
authors.lastname: Černá Bolfíková
authors.affiliation: Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic.
authors.forename: James J
authors.initials: JJ
authors.lastname: Valdés
authors.affiliation: Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic.
authors.forename: Libor
authors.initials: L
authors.lastname: Grubhoffer
authors.affiliation: Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic; Veterinary Research Institute, Brno, Czech Republic.
authors.forename: Daniel
authors.initials: D
authors.lastname: Růžek
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites / Q000235:genetics; D019143:Evolution, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012328:RNA Viruses / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry* / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase