|V-type ATPase beta subunit
ATPases are multimeric enzymes that synthesize ATP from ADP and phosphate, or inversely hydrolyze ATP to obtain energy for the transport of ions against a gradient (for reviews, see e.g. [1-3]). The V-type ATPase beta subunit is a component of the commonly vacuolar ATPase synthase of eukaryotes. The subunit consists of three domains: the N-terminal beta-barrel domain, the central nucleotide-binding domain and a conserved C-terminal domain (Pfam  domains: PF02874, PF00006, PF00306).
Seven gene duplication events are observed for the V-type ATPase beta subunit (Figure S3-1), one in vertebrates, one in Caenorhabditis, four in plants and one in Trypanosoma. Competing evolutionary scenarios for the evolution of genes from teleostei and Physcomitrella patens could not be resolved satisfactorily. The vertebrate species analyzed all possess two gene copies, but it remains unclear whether these vertebrate genes form two orthologous groups (the most parsimonious explanation), whether the two teleostei genes are co-orthologous to the tetrapod VATB2 gene (loss of VATB1 and lineage-specific gene duplication in teleostei), or whether the tetrapod VATB1 is an outparalog to VATB2, and tetrapod VATB2 is ortholog to one of the teleostei genes (two gene duplications prior to divergence of teleostei and tetrapods, followed by the loss of teleostei VATB1, and loss of one of the two tetrapod VATB2 gene copies). For the three very similar paralogs of moss it was not possible to obtain statistically significant support for one of the two possible tree topologies. The genes were retained in the example to demonstrate species variety in phylogenomic databases, but they have been removed from the reference tree that we provide. Compara predicts an additional gene duplication within the vertebrate VATB2 branch, resulting in the Xenopus gene being paralogous to those of amniotes. InParanoid shows similar results as in previous examples with a high number of accurate predictions (972 predicted gene relationships, 5 false positive relations, 68 false negatives). The multiple duplications lead OMA to present several groups which each include evolutionary distant species; for example the largest ortholog group includes the vertebrate VATB2 genes, a few other animal genes and all, save one, of the fungal genes. For OrthoDB, the data was mapped to all three database sections, vertebrates, arthropods and fungi. For vertebrates, the hierarchical groups include 1:1 orthologs only for primates, Glires and Euteleostomi, and as no gene duplication event occurred in the gene history of arthropods and fungi, corresponding groups contain 1:1 orthologs already from their root nodes. At the mammalian level, eggNOG distinguishes between the paralog groups VATB1 and VATB2, but misclassifies rat VATB1 at the rodent level. The Panther tree includes 27 relevant genes and two differences relative to the reference tree. These are the divergence of Xenopus genes prior to the gene duplication in amniotes and the lineage-specific gene duplication in the two Caenorhabditis species. One HOGENOM family contains 27 members, and its phylogenetic tree differs in one speciation node from the reference tree, with no implications on the orthology and paralogy assignments.
Figure S3-1. Reference tree for the V-type ATPase beta subunit subfamily and corresponding ortholog predictions from seven phylogenomic databases. Color codes: OMA: 2=52259, 3=128844, 4=51542, 5=50841, 6=81984, 7=49077, 8=48781, 9=61689 and 56303; InParanoid: 1=human paralogs, 7=predicted orthologs to human VATB1, 8=predicted orthologs to human VATB2; Compara: Ortholog hierarchies derived from the gene tree of ENSFM00250000001461; OrthoDB, largest groups consisting of 1:1 orthologs: 1=EOG9FBMFF, EOG9KH324 and EOG9R7WTC, 7=EOG9H4BMF and EOG9G7HQR, 8=EOG94BGHH and EOG98H1TZ; groups in gray scale concern speciation events (not listed); eggNOG, largest groups consisting of 1:1 orthologs: 1=KOG1351, 7=maNOG17736, 8=maNOG09631 and roNOG17349; groups in gray scale concern speciation events (not listed); Panther: 1=PTHR15184:SF11; HOGENOM: 1= HBG565875. Black horizontal bars separates groups of the same hierarchical level within the same column, for OrthoDB the black bar also separates the three taxonomic sections of the database (VeRTebrate, ARThropods, FUNgi). Red triangles mark gene duplication events.
We sought to use this family to widen the taxonomic range (see Figure S3-2). Indeed, ATPases are present in all the three major taxonomic super-kingdoms and it has been suggested that several of their subunits are derived from a common ancestor . F-type ATPases (containing the regulatory subunit atpA and the catalytic subunit atpB) are found in bacteria and organelles, and the eukaryotic nuclear encoded genes are most likely organelle-derived. The eukaryotic homologs are named V-type ATPases (containing the catalytic subunit VATA and the regulatory subunit VATB), which refers to the commonly vacuolar location of the protein complexes. The A-type ATPase is the homolog protein complex of archaea, and A-type ATPases found in bacteria are likely to be derived by horizontal gene transfer (HGT) . These proteins generally share the three conserved domains. Both subunits contain an ATP binding site, but only the F-type ATPase beta subunits and the V-type ATPase alpha subunits are catalytic, in contrast to their paralogs which have a regulatory function. In eukaryotes, the mitochondrial F-type ATPase alpha and beta subunits are often coded in the nuclear genome, although the F-type alpha subunit is found in the mitochondrial genome of many plants and amoeba. Plants additionally hold a chloroplast ATPase, and the two genes for the alpha and beta subunits are located on the plastid genome. A schematic summary of probable evolutionary events in the history of this gene family is illustrated below.
Figure S3-2. Schematic presentation of a possible evolutionary scenario for the F/A/V-type ATPase alpha and beta subunit subfamilies. Orthologs are the bacterial atpA and archaeal/eukaryotic VATB regulatory subunits, and the bacterial atpB and archaeal/eukaryotic VATA catalytic subunits. GD=Gene Duplication, HGT=Horizontal Gene Transfer, EGT=Endosymbiont Gene Transfer, LUCA = Last Universal Common Ancestor.
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