Tuesday, November 25, 2008

One protein family, many insights: The TV-pol story

Using sensitive sequence analysis methods, we recently discovered and characterized a divergent member of the DNA polymerase I superfamily /Superfamily A DNA polymerase that we denote the Transposon-Virus polymerase (TV-Pol) family. These proteins are found in a wide range of bacteria and their prophages, phages, the chloroplast of the alga Nephroselmis, and in the Sputnik virus (virophage of Mimivirus).

Using gene neighborhood analysis we show that the TV-pol genes are components of mobile elements and might be involved in replicative transposition. As evidence, we detected a recent transposition event in Brucella melitensis 16M, of a transposon with a direct repeat that contains the TV-Pol gene, and a γδ-resolvase.More specifically, based on their frequent fusion to D5-helicases (e.g. V13 of the Sputnik virus) we speculate that TV-Pol proteins are primase-polymerases (primpols), like some members of the archaeo-eukaryotic primases (To learn more about AEP-like primpols click here).

Additional interesting insights
  • Superfamily A DNA polymerases contain a HTH domain.Upon defining the structural core of the DNA polymerase I superfamily, we noted that these proteins are distinguished by the presence of a HTH-domain within the fingers of the RRM-like palm domain. This HTH contains the highly conserved RxxxK motif characteristic of this superfamily, and potentially interacts with the elongating daughter strand.
  • The thumb, palm and fingers probably existed as independent polypeptides at an early point in the evolution of the superfamily A polymerases. Given the presence of distinct globular folds in the fingers (HTH) and palm domain (RRM) and also the displacement of the coiled coil thumb by a distinct globular domain in a TV-Pol of Gemmata obscuriglobus, an early stage in the evolution of this superfamily can be conceived where these three units were present on different polypeptides and then fused to give the Superfamily A DNA polymerases.
  • The predicted primpol activity of the TV-Pols throws light on the origins of the T7-like RNA polymerases. The T7-like DNA-dependent RNA polymerases are members of the superfamily A DNA polymerases. Their origins can now be understood in light of the discovery of TV-pols, where a primpol ancestor that had both DNA and RNA polymerase activity might have possibly contributed to the T7-like RNA polymerases. This view is also supported by experimental studies that have shown some members of the T7-like RNA polymerases to function as primases.
  • The Sputnik virophage could have evolved from a mobile element. Based on the gene contexts of the TV-Pol gene in the Sputnik virophage, we speculate that the virus may have arose from a a TV-Pol containing transposase, which subsequently acquired a DNA-packaging HerA-FtsK ATPase and virion proteins from a distinct viral source.
You can read the open access version of this study by clicking here.