Author: Malik, Shahana S.; Azem-e-Zahra, Syeda; Kim, Kyung Mo; Caetano-Anollés, Gustavo; Nasir, Arshan
Title: Do Viruses Exchange Genes across Superkingdoms of Life? Document date: 2017_10_31
ID: 12dee0lv_3
Snippet: Here we take a comparative genomic approach to revisit virus-cell interactions by identifying the repertoires of protein structural domains (proteomes) in 3,440 viruses categorized into archaeoviruses, bacterioviruses, and eukaryoviruses and tracing their spread in the proteomes of 1,620 "hosts" from Archaea, Bacteria, and Eukarya. Protein domains were grouped into fold superfamilies (FSFs), as defined by the structural classification of proteins.....
Document: Here we take a comparative genomic approach to revisit virus-cell interactions by identifying the repertoires of protein structural domains (proteomes) in 3,440 viruses categorized into archaeoviruses, bacterioviruses, and eukaryoviruses and tracing their spread in the proteomes of 1,620 "hosts" from Archaea, Bacteria, and Eukarya. Protein domains were grouped into fold superfamilies (FSFs), as defined by the structural classification of proteins (SCOP) database (Andreeva et al., 2008; Fox et al., 2014) to include distantly related domains that show negligible sequence identity (can be < 15%) but recognizable common three-dimensional (3D) cores and biochemical functions that are likely indicative of shared ancestry. The evolutionary conservation of FSFs makes them useful molecular characters for inferring long-term viral evolutionary patterns, especially since fast mutational rates of viral gene sequences (Sanjuán et al., 2010) sometimes prohibit meaningful global evolutionary analyses (Abroi and Gough, 2011; Caetano-Anollés and Nasir, 2012; Nasir and Caetano-Anollés, 2015) .
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