Evolution of the F0F1 ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes
Figure 2
Phylogenetic reconstruction of ATPF0A.
The tree shown is the best Bayesian topology, based on 215 sequences and 232 amino acid positions (length after trimming; median sequence length before trimming: 254). Numerical values at the nodes of the tree (x/y/z) indicate statistical support by MrBayes, PhyML and RAxML (posterior probability, bootstrap and bootstrap, respectively). Values for highly supported nodes have been replaced by symbols, as indicated. Species names are colour-coded based on their bioenergetic mode as in Figure 1. Full details and accession numbers for all protein sequences used are given in Table S1. The tree is rooted at the N-ATPase clade, previously reported to be the result of horizontal gene transfer in a variety of species, all of which also contain a canonical ATPF0F1 (apart from the two Methanosarcina species shown, which also have a canonical ATPV). The tree confidently separates the major bacterial taxonomic lineages, but with limited support for their branching order: strong support is provided for a subgroup containing the verrucomicrobia and chloroflexi, while another subgroup containing the alpha-proteobacteria, actinobacteria, chlorobi, bacteroidetes and planctomycetes also has reasonable support. This group also includes the spirochaete Leptospira interrogans and the gemmatimonadete Gemmatimonas aurantiaca, as well as Candidatus Nitrospira defluvii which groups with the alpha-proteobacteria. Reasonable support is also provided for the grouping of dictyoglomi and cyanobacteria, and for a subgroup containing the fusobacteria, firmicutes, tenericutes, thermotogae, and beta-gamma-proteobacteria. Two species-specific duplications (in Saccharopolyspora erythraea and Pelobacter carbinolicus) are highlighted with a red “>”. Two further duplications are highlighted with a red “-” after the species name; in Photobacterium profundum the duplication either occurred before the split from other closely-related species or represents HGT from other gamma-proteobacteria; the duplication in Desulfococcus oleovorans possibly represents HGT from thermotogae (also see Figures S1 and S2).