Virus Genes

, Volume 16, Issue 1, pp 47–58

Evolution of Viral DNA-Dependent DNA Polymerases

  • Charles W. Knopf
Article

DOI: 10.1023/A:1007997609122

Cite this article as:
Knopf, C.W. Virus Genes (1998) 16: 47. doi:10.1023/A:1007997609122

Abstract

DNA viruses as their host cells require a DNA-dependent DNA polymerase (Pol) to faithfully replicate their genomic information. Large eukaryotic DNA viruses as well as bacterial viruses encode a specific Pol equipped with a proofreading 3′-5′-exonuclease, and other replication proteins. All known viral Pol belong to family A and family B Pol. Common to all viral Pol is the conservation of the 3′-5′-exonuclease domain manifested by the three sequence motifs Exo I, Exo II, and Exo III. The polymerase domain of family A and B Pol is clearly distinguishable. Family A Pol share 9 distinct consensus sequences, only two of them are convincingly homologous to sequence motif B of family B Pol. The putative sequence motifs A, B, and C of the polymerase domain are located near the C-terminus in family A Pol and more central in family B Pol. Thus, family A Pol show a significant greater spacing between the Exo III motif and the Pol motif A that is especially extended in the case of the mitochondrial Pol γ. From each host and virus family whenever possible the consensus sequences of two distantly related polymerase species were aligned for assessment of phylogenetic trees, using both maximum parsimony and distance methods, and evaluated by bootstrap analysis. Three alternative methods yielded trees with identical major groupings. A subdivision of viral family B Pol was achieved resulting in a branch with Pol carrying out a protein-primed mechanism of DNA replication, including adenoviruses, bacteriophages and linear plasmids of plant and fungal origin. Archaebacterial Pol and cellular Pol ∈ were consistently found at the base of this branch. Another major branch comprised alpha- and delta-like viral Pol from mammalian herpesviruses, fish lymphocystis disease virus, insect ascovirus, and chlorella virus. Due to a lower branch integrity Pol of T-even bacteriophages, poxviruses, African swine fever virus, fish herpesvirus, and baculoviruses were not clearly resolved and placed in alternate groupings. A composite and rooted tree of family A and B Pol shows that viral Pol with a protein-priming requirement represent the oldest viral Pol species suggesting that the protein-primed mechanism is one of the earliest modes of viral DNA replication.

DNA virusesHerpesviridaeAdenoviridaeAscoviridaeBaculoviridaePhycodnaviridaecytoplasmic DNA virusesIridoviridaePoxviridaeAfrican swine fever virusfish lymphocystis disease virusvaccinia virusbacterial virusesbacteriophagesMyoviridaeSiphoviridaeMycoviridaePodoviridaeTectiviridaefamily A DNA polymerasesfamily B DNA polymerasesDNA polymerase αDNA polymerase βDNA polymerase δDNA polymerase ∈DNA polymerase γmitochondrial DNA polymeraseDNA-dependent DNA polymeraseprotein-primed mechanism of DNA replicationproofreading activityexonuclease domainpolymerase domainmolecular phylogeny

Copyright information

© Kluwer Academic Publishers 1998

Authors and Affiliations

  • Charles W. Knopf
    • 1
  1. 1.Forschungsschwerpunkt Genomforschung und Bioinformatik, Deutsches KrebsforschungszentrumHeidelbergFRG; E-Mail