UC San Diego

Nine cyanobacteria and 14 genera of bacteria from six phyla, with fully sequenced genomes, were analyzed for genes encoding P-type ATPase catalytic alpha-subunits. These miscellaneous phylas are Aquificae, Chlamydia, Chlorobi, Chloroflexi, Deinococcus-Thermus and Thermotogae. In cyanobacteria 59 such proteins were identified, and in the miscellaneous phyla, a total of 31 ATPases were identified. The P-type ATPase representation in genomes of closely related species was greatly varied, suggesting a gain or loss of genes. Along with the examined phyla, an integrative approach was taken to examine the P-type ATPase representation across all the major kingdoms of life. The Clustal X and TreeView programs were used to construct multiple alignments and phylogenetic trees, respectively. The families of proteins identified were either functionally characterized or previously uncharacterized. The alignments of the families were then used to examine motif conservation. Novel toplogies were discovered for families unique to both the prokaryotes and the eukaryotes, while the known toplogoical types were reinforced by the integrative approach to the research. The constructed 16S rRNA trees were used along with the family trees to gain evidence for orthology, and further shed light on the evolutionary descendency of the proteins. The same approaches taken at the individual phyla level were then applied to the integrated data. Overall, these studies reveal the nature of cyanobacterial P-type ATPases, and the ATPases from the six miscellaneous phyla. The integrated approach was also used to reinforce known ideas about the proteins as they are represented across the major kindgoms of life, and also to reveal novel information about the P-type ATPase proteins in general