The vacuolar ATPase catalytic subunit as a phylogenetic marker: Reconstructing the paths of microbial evolution

Phylogenetic trees based on protein coding genes often differ in topology from those constructed from rRNA genes. Microsporidia, Trichomonads and Diplomonads consistently appear as a deep early branches of the eukaryoec lineage in small subunit rRNA trees. Vacuolar ATPases are ubiquitous in eukaryotes, and their phylogeny appears to reflect the evolution of the nucleocytoplasm. Complete sequences of the vacuolar ATPase catalytic subunit for Nosema locustae , a microsporidian, and Trichomonas vaginalis, a parabasalid were obtained and phylogenetic analyses show that Nosema is most closely related to fungi, while Trichomonas is an unresolved lineage within the eukaryotes. Analyses of rRNA tree topologies using maximum likelihood ratio tests suggest that the conflict in tree topology appears to be due to long branch artifacts in the construction of the rRNA trees. In the case of red algae, numerous mitochondrial and plastid genes support a monophyletic relationship among red algae, green algae and plants whereas the majority of nuclear markers that have been examined suggest that the red algae are not related to these groups. Using a PCR based approach employing degenerate primers designed against a variety of organisms, a partial sequence of the V-ATPase subunit was obtained from the red alga Lithophyllum . Analyses of the complete V-ATPase sequence from the red alga Cyanidium support the hypothesis that red algae share a common ancestor with green algae and plants while analyses of the partial sequence from Lithophyllum weakly support this grouping.^ An alternative explanation for conflicting tree topologies is horizontal gene transfer. Processes that involve the incorporation of foreign DNA into organisms play an important role in the evolution of prokaryotes. In a computer based analysis of the genomes of Borrelia burgdorferi and Treponema pallidum, the genes from the VATPase subunit A and B genes, as well as numerous tRNA synthetase genes are shown to be more closely related to genes from archaea or eukaryotes and were probably introduced into the spirochete lineage in many separate horizontal gene transfer events.