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Table 3 Proteins encoded by hallmark viral genes

From: The ancient Virus World and evolution of cells

Protein Function Virus groups Homologs in cellular life forms Comments References
Jelly-roll capsid protein (JRC) Main capsid subunit of icosahedral virions Picornaviruses, comoviruses, carmoviruses, dsRNA phage, NCLDV, herpesviruses, adenoviruses, papovaviruses, parvoviruses, icosahedral DNA phages and archaeal viruses Distinct jelly-roll domains are seen in eukaryotic nucleoplasmins and in protein-protein interaction domains of certain enzymes Certain icosahedral viruses, such as ssRNA phages and alphaviruses, have unrelated capsid proteins. In poxviruses, the JRC is not a virion protein but forms intermediate structures during virion morphogenesis [13–15, 53, 54, 109–111]
Superfamily 3 helicase (S3H) Initiation and elongation of genome replication Picornaviruses, comoviruses, eukaryotic RCR viruses, NCLDV, baculoviruses, some phages (e.g., P4), plasmids, particularly, archaeal ones S3H is a distinct, deep-branching family of the AAA+ ATPase class Characteristic fusion with primase in DNA viruses and plasmids [16, 112]
Archaeo-eukaryotic DNA primase Initiation of genome replication NCLDV, herpesviruses, baculoviruses, some phages All viral primases appear to form a clade within the archaeo-eukaryotic primase family Characteristic fusion with S3H in most NCLDV, some phages, and archaeal plasmids [18]
UL9-like superfamily 2 helicase Initiation and elongation of genome replication Herpesviruses, some NCLDV, some phages Viral UL9-like helicases form a distinct branch in the vast superfamily of DNA and RNA helicases Fusion with primase in asfarviruses, mimiviruses [53]
Rolling-circle replication initiation endonuclease (RCRE)/origin-binding protein Initiation of genome replication Small eukaryotic DNA viruses (parvo-, gemini-, circo-, papova), phages, plasmids, and eukaryotic helitron transposons No cellular RCRE or papovavirus-type origin-binding protein; however, these proteins have a derived form of the palm domain that is found in the majority of cellular DNA polymerases Papovaviruses have an inactivated form of RCRE that functions as origin-binding protein [17–20]
Packaging ATPase of the FtsK family DNA packaging into the virion NCLDV, adenoviruses, polydnaviruses, some phages (e.g., P9, M13), nematode transposons A distinct clade in the FtsK/HerA superfamily of P-loop NTPases that includes DNA-pumping ATPases of bacteria and archaea   [113]
ATPase subunit of terminase DNA packaging into the virion Herpesviruses, tailed phages The terminases comprise a derived family of P-loop NTPases that is distantly related to Superfamily I/II helicases and AAA+ ATPases   [109, 114]
RNA-dependent RNA polymerase (RdRp)/reverse transcriptase (RT) Replication of RNA genomes Positive-strand RNA viruses, dsRNA viruses, retroid viruses/elements, possibly, negative-strand RNA viruses Another major group of palm domains that are distinct from those in DNA polymerases The RdRps of dsRNA viruses are homologs of positive-strand RNA virus polymerases. The provenance of negative-strand RNA virus RdRp remains uncertain although sequence motif and, especially, structural analysis suggests their derivation from positive-strand RNA virus RdRps [23–25, 28, 87, 115]
  1. Abbreviations: NCLDV, Nucleo-Cytoplasmic Large DNA Viruses