Table 3 Proteins encoded by hallmark viral genes

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]