UC San Diego

P-type ATPases are a class of cation transporting proteins located within the membranes of cells, both eukaryotic and prokaryotic. While much has been elucidated regarding the nature and function of eukaryotic P-type ATPases, much less in known about the prokaryotic enzymes. This study focuses upon the analysis of these enzymes from the Proteobacterial, Bacteroidetes and Fusobacterial phyla. 47 P-type ATPases were found in the Bacteroides, Flavobacterium, and Fusobacterium genuses while 218 members comprised the Protoebacterial phylum. Genomic searches of organisms with fully sequenced genomes revealed many such enzymes, which were then combined with known standards of P-type ATPases from the nine functionally characterized as well as 32 functionally uncharacterized ATPases to classify them phylogenetically. Familial representation of these proteins varied, with Bacteroides, Flavobacterium, and Fusobacterium genuses having homologues of Families 2, 4-7, 29, 30 and 32, and the Proteobacterial phylum having homologues of Families 1 -7, 25, 27-32. In addition, 16S rRNA trees were constructed; showing largely orthologous relationships among the proteins from Bacteroides, Flavobacterium, and Fusobacterium genuses with no evidence for horizontal gene transfer, but Proteobacteria exhibited high frequencies of horizontal gene transfer. Motif analyses were conducted in order to further classify the proteins. All proteins showed conservation at the crucial phosphorylation site required for P-type ATPase activity, and varying degrees of motif conservation for eight other motifs analyzed. Topological analyses classified the P-type ATPases according to hydropathy profiles, and a novel topological type, Type VII, was discovered.