Protein Structure-Guided Hidden Markov Models (HMMs) as A Powerful Method in the Detection of Ancestral Endogenous Viral Elements

Clicks: 316
ID: 266297
2019
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Abstract
It has been believed for a long time that the transfer and fixation of genetic material from RNA viruses to eukaryote genomes is very unlikely. However, during the last decade, there have been several cases in which “virus-to-host” gene transfer from various viral families into various eukaryotic phyla have been described. These transfers have been identified by sequence similarity, which may disappear very quickly, especially in the case of RNA viruses. However, compared to sequences, protein structure is known to be more conserved. Applying protein structure-guided protein domain-specific Hidden Markov Models, we detected homologues of the Virgaviridae capsid protein in Schizophora flies. Further data analysis supported “virus-to-host” transfer into Schizophora ancestors as a single transfer event. This transfer was not identifiable by BLAST or by other methods we applied. Our data show that structure-guided Hidden Markov Models should be used to detect ancestral virus-to-host transfers.
Reference Key
kirsip2019virusesprotein Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Heleri Kirsip;Aare Abroi;Kirsip, Heleri;Abroi, Aare;
Journal Viruses
Year 2019
DOI
10.3390/v11040320
URL
https://doi.org/10.3390/v11040320
Keywords
bioinformatics drosophila horizontal gene transfer tobacco mosaic virus hmm endogenous viral elements virus-to-host gene transfer capsid protein

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