Journal Article

Evolution of Tertiary Structure of Viral RNA Dependent Polymerases

Růžek, Daniel, Černá Bolfíková, Barbora, Černý, Jiří, Valdés, James J., Grubhoffer, Libor

2014

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Amino Acid Sequence / Amino acids / Analysis / Bayesian analysis / Binding Sites - genetics / Biological evolution / Biology and Life Sciences / Cladistic analysis / Crystal structure / Deoxyribonucleic acid / DNA / DNA polymerases / DNA viruses / DNA-directed DNA polymerase / Double-stranded RNA / Evolution / Evolution, Molecular / Kinases / Models, Molecular / Molecular Sequence Data / Nucleotide sequence / Phylogeny / Protein structure / Protein Structure, Secondary / Protein Structure, Tertiary / Replicating / Replication / Ribonucleic acid / RNA / RNA polymerase / RNA polymerases / RNA Replicase - chemistry / RNA Replicase - genetics / RNA viruses / RNA Viruses - classification / RNA Viruses - enzymology / RNA Viruses - genetics / Sequence Homology, Amino Acid / Similarity / Species Specificity / Tertiary structure / Viral Proteins - chemistry / Viral Proteins - genetics / Viruses