Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses.
The origin and evolution of viruses is a subject of ongoing debate. In this study, we provide a full account of the evolutionary relationships between proteins of significant sequence and structural similarity found in viruses that belong to different classes according to the Baltimore classification. We show that such proteins can be found in viruses from all Baltimore classes. For protein families that include these proteins, we observe two patterns of the taxonomic spread. In the first pattern, they can be found in a large number of viruses from all implicated Baltimore classes. In the other pattern, the instances of the corresponding protein in species from each Baltimore class are restricted to a few compact clades. Proteins with the first pattern of distribution are products of so-called viral hallmark genes reported previously. Additionally, this pattern is displayed by the envelope glycoproteins from Flaviviridae and Bunyaviridae and helicases of superfamilies 1 and 2 that have homologs in cellular organisms. The second pattern can often be explained by horizontal gene transfer from the host or between viruses, an example being Orthomyxoviridae and Coronaviridae hemagglutinin esterases. Another facet of horizontal gene transfer comprises multiple independent introduction events of genes from cellular organisms into otherwise unrelated viruses.
Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany. scaprari@mpi-inf.mpg.de.
Silvia
S
Caprari
Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany. smetzler@mpi-inf.mpg.de.|Saarbrücken Graduate School of Computer Science, University of Saarland, Campus E1 3, 66123 Saarbrücken, Germany. smetzler@mpi-inf.mpg.de.
Saskia
S
Metzler
Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany. lengauer@mpi-inf.mpg.de.
Thomas
T
Lengauer
Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany. kalinina@mpi-inf.mpg.de.
Olga V
OV
Kalinina
D000818:Animals; D019295:Computational Biology; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D005814:Genes, Viral; D054884:Host-Pathogen Interactions; D006801:Humans; D012328:RNA Viruses / Q000235:genetics*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA
hemagglutinin esterase; horizontal gene transfer; structure comparison; viral evolution; viral hallmark genes