Table 1 Evolutionary provenance of the genes of the three well-characterized virophages
Gene/protein | Domain architecture | Predicted activity/function | Phylogenetic spread and affinity | Representation in environmental sequences |
|---|---|---|---|---|
Proteins (domains) conserved in all three virophages | ||||
V9, OLV7, MV16 | C5-family cysteine protease | Protease, probably involved in capsid protein maturation | Only distantly related to other proteases from NCLDV, adenoviruses, eukaryotes and some bacteria | No obvious homologs |
V3, OLV4, MV15 | P-loop ATPase, FtsK-like family | Packaging ATPase | Only distantly related to other ATPases of the FtsK-like family: NCLDV, adenoviruses, diverse phages, bacteria and archaea (DNA pumping during cell division and conjugation) | Abundant moderately conserved homologs |
V20, OLV9, MV18 | Predicted distorted jelly-roll domain | Major capsid protein | No homologs beyond virophages | None |
V18-19, OLV8, MV17 | No detectable domains | Minor capsid protein | No homologs beyond virophages | None |
V14, V4, MV06 (C-terminal), OLV1 (C-terminal), | C2H2 Zn-ribbon; N-terminal GIY-YIG endonuclease domain in MV06 and OLV1 | Unknown | Homologs in transpovirons (closest to V14, Zn-ribbon only), Phytophtora and Dictyostelium polintons, P.globosa virus | Moderately conserved homologs, mostly containing GIY-YIG nuclease domain |
V13 (C-terminal), OLV25 (C-terminal), MV01 | S3H helicase; N-terminal TVpol in V13 and OLV25 | primase-helicase | Sputnik helicase is most similar to bacterial and bacteriophage homologs; the MV01 helicase is most similar to the NCLDV homolog; the OLV helicase is most similar to homologs from bacteriophages and polintons | Numerous conserved homologs including proteins with both TVpol and helicase domains |
Proteins (domains) shared between Sputnik and OLV | ||||
V13 (N-terminal), OLV25 (N-terminal) | TVpol | Primase and DNA polymerase ([22]) | Related to Micromonas pusilla and different bacteria | Numerous conserved homologs including proteins with both TVpol and helicase domains |
V21, OLV5 | No detectable domains | Unknown | No other homologs | None |
V6(part), V7(part) OLV13 (part), OLV19 (part), OLV20 (part) | Collagen-like repeats | Adsorbtion on host virus? | V6 is highly similar to mimiviruses, OLV13 - to bacteria; OLV19 has regions similar to OLPV, T.vaginalis (phage protein) | Abundant homologs mostly containing collagen domain |
Proteins (domains) shared between OLV and Mavirus | ||||
OLV1 (N-terminal), OLV24 and MV06 (N- terminal | GIY-YIG endonuclease, fused to C2H2 Zn-ribbon in OLV1 and MV06 | Unknown | Close homologs in Phytophtora polintons and P. globosa virus | Moderately conserved homologs |
OLV12 (C- terminal), MV13 (C- terminal) | Lipase 3 domain | Unknown | Homologs in all cellular organisms; Mavirus closest homolog is a Physcomitrella patens protein; OLV12 is close to bacterial proteins | Few moderately conserved homologs for each of the proteins |
Proteins (domains) shared between Sputnik and Mavirus | ||||
V10, MV02 | Integrase | Â | Mavirus interase is related to Polintons, Sputnik - to archaeal and bacterial proviruses | Very few homologs |
Sputnik genes with homologs outside virophages | ||||
V17 | Transposase, DNA-binding domain | DNA-binding protein | Closest homologs in transpovirons | Numerous moderately conserved homologs |
V16 | No detectable domains | Unknown | Homologs in moumouvirus: mv_L1152 | none |
V12 | No detectable domains | Unknown | Highly conserved homologs in Mimiviridae | none |
V10 | XerD family integrase | Integrase | Closest homologs in archaeal proviruses | Only distant integrases |
OLV genes with homologs outside virophages | ||||
OLV23 | N6 A-specific methylase | DNA methylase | Numerous bacterial homolog | Numerous homologs |
OLV16, OLV21 | Proline-rich, mucien –like repeats | Unknown (adsorption on virus host?) | Similar repeats in bacteria and eukaryotes | Numerous similar repeats |
OLV18, OLV19 | Phage Tail Collar Domain | Unknown (adsorption on virus host?) | Closely related to a family of OLPV proteins | Numerous close homologs |
OLV2 | Uncharacterized domain | Unknown | Homologs in many phycodnaviruses and in Tlr1 element (6Fp) | Abundant homologs with wide range of similarity including very close ones |
OLV22 | Uncharacterized domain | Unknown | Highly similar to OLPV2, GI:322510937 | A few close homologs |
OLV12(N-terminal) | Uncharacterized domain fused to Lipase 3 | Unknown | Highly similar to Chloroviruses | Numerous close homologs |
Mavirus genes with homologs outside virophages | ||||
MV20 | FNIP repeats | Unknown | Closely related homologs in mimiviruses | Numerous moderately similar homologs |
MV04 | C2H2 Zn finger | Unknown | No close homologs | None |
MV02 | RVE family integrase | Integration of Mavirus genome into the virus host genome? | Numerous homologs, closest in Polintons | Numerous moderately similar homologs |
MV19, M09 | S74 family peptidase (C-terminal), N-terminal glycosylase (?); MV09 has only the N-terminal domain | Unknown | Numerous homologs in phages and bacteria (prophages?); homologs in Marseillevirus, Lausannevirus, Paramecium virus, and Polintons (N-terminal only). | Numerous moderately similar homologs |
MV13 | Lipase (a/b hydrolase superfamily) | Unknown | Homologs in all cellular organisms, closest in plants | Several moderately similar homologs |
MV03 | B family DNA polymerase | Genome replication | Homologs in all cellular organisms and numerous viruses, the closest homologs in Polintons | No close homologs |