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 |
|
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 |