Do Viruses Exchange Genes across Superkingdoms of Life?

Malik, Shahana S.; Azem-e-Zahra, Syeda; Kim, Kyung Mo; Caetano-Anollés, Gustavo; Nasir, Arshan

While the data of Figure 2 indicated significant levels of genetic exchange restricted between viruses and their known host superkingdoms, some bacterioviral and eukaryoviral FSFs were also shared with Eukarya and Bacteria, respectively (archaeoviruses shared no domains exclusively with either Bacteria or Eukarya) (Figure 2 , Tables S2-S4). For example, bacterioviruses shared 2 FSFs exclusively with Archaea (group A) and 6 with Eukarya (group E) (Table S3) . Interestingly, 4/6 E FSFs in bacterioviruses could be considered viral hallmark proteins such as FSFs b.121.2 (the "double jelly-roll" fold hallmark of capsid proteins of the PRD1/Adenoviruslike lineage) (Bamford, 2003; Abrescia et al., 2012) , b.121.5 (the "jelly-roll" fold in ssDNA viruses members of the Picornavirus-like lineage), d.85.1 (capsid/coat related fold in RNA bacteriophages), and a.251.1 (the phage replication organizer domain) ( Table S3) . Viruses have been recently (re)-classified into structure-based lineages based on 3D structural similarities in capsid/coat architectures or common principles of functional virion construction (Bamford, 2003; Abrescia et al., 2012; . Some of the lineages such as the PRD1/Adenovirus-like lineage (characterized by the so-called "double jelly-roll" fold) include member viruses infecting the three cellular superkingdoms (Bamford, 2003; Abrescia et al., 2012) . Thus, it is no surprise that bacterioviruses share capsid/coat related protein folds characteristic of eukaryoviruses. It is however indeed intriguing to note that these FSFs were present in eukaryotic proteomes, especially because the capsid is considered to be a virus hallmark (Benson et al., 2004; Abrescia et al., 2010) . Thus, rare occurrences of capsid/coat related genes in cellular proteomes are more likely due to virus-to-cell HGT or their utilization in the assembly of capsid-like architectures in cells (e.g., carboxysomes and protein microcompartments in prokaryotes, Yeates et al., 2007 Yeates et al., , 2011 that are hitherto believed to be rare in cells (Cheng and Brooks, 2013; .