Phylogeny of genes for secretion NTPases: Identification of the widespreadtadA subfamily and development of a diagnostic key for gene classification

Macromolecular transport systems in bacteria currently are classified by fu nction and sequence comparisons into five basic types. In this classificati on system, type II and type IV secretion systems both possess members of a superfamily of genes for putative NTP hydrolase (NTPase) proteins that are strikingly similar in structure, function, and sequence. These include VirB 11, TrbB, TraG, GspE, PiIB, PiIT, and ComG1. The predicted protein product of tadA, a recently discovered gene required for tenacious adherence of Act inobacillus actinomycetemcomitans, also has significant sequence similarity to members of this superfamily and to several unclassified and uncharacter ized gene products of both Archaea and Bacteria. To understand the relation ship of tadA and tadA-like genes to those encoding the putative NTPases of type II/IV secretion, we used a phylogenetic approach to obtain a genealogy of 148 NTPase genes and reconstruct a scenario of gene superfamily evoluti on. In this phylogeny, clear distinctions can be made between type II and t ype IV families and their constituent subfamilies. In addition, the subgrou p containing tadA constitutes a novel and extremely widespread subfamily of the family encompassing all putative NTPases of type IV secretion systems. We report diagnostic amino acid residue positions for each major monophyle tic family and subfamily in the phylogenetic tree, and we propose an easy m ethod for precisely classifying and naming putative NTPase genes based on p hylogeny. This molecular key-based method can be applied to other gene supe rfamilies and represents a valuable tool for genome analysis.