Intriguing phylogenetic arrangement of tailed bacteriophages based on putative DNA polymerase sequences

Abstract

VHS1 (Vibrio harveyi siphoviridae like) is a newly described bacteriophage that has been tentatively placed in the family Siphoviridae based on its morphology by transmission electron microscopy. However, there are examples among emergent viruses where morphological characteristics do not correspond with genomic properties. Thus we attempted to verify the phylogenetic relationship of VHS 1 to other tailed phages on the basis of its putative DNA polymerase. Although we found no clear support for placement of VHS1 in any tailed-phage family, we did discover that a general phylogenetic tree based on all putative tailed-phage sequences was not compatible with relationships based on phage morphology. However, construction of individual putative DNA polymerase trees for traditional morphological phage families revealed a clear tendency for grouping of putative DNA polymerase A and B types into either Gram negative or Gram positive bacteria hosts in a manner that varied with phage family. Based on these results, we propose that early branching of an ancestral DNA polymerase into polymerase A and B types may have accompanied phage specialization for Gram negative and Gram positive hosts. Whether this proposal is correct or not, the study suggests that comparisons based on major genes such as polymerases can constitute additional criteria for evaluation of DNA phage relationships and that genome comparisons may complement morphology in devising a more natural taxonomy.