Taxonomic distribution of proteins containing B3_4 domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing B3_4 domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Evolution of aminoacyl-tRNA synthetases--analysis of unique domainarchitectures and phylogenetic trees reveals a complex history ofhorizontal gene transfer events.

Wolf YI, Aravind L, Grishin NV, Koonin EV
Genome Res. 1999; 9: 689-710

Phylogenetic analysis of aminoacyl-tRNA synthetases (aaRSs) of all 20specificities from completely sequenced bacterial, archaeal, andeukaryotic genomes reveals a complex evolutionary picture. Detailedexamination of the domain architecture of aaRSs using sequence profilesearches delineated a network of partially conserved domains that is evenmore elaborate than previously suspected. Several unexpected evolutionaryconnections were identified, including the apparent origin of thebeta-subunit of bacterial GlyRS from the HD superfamily of hydrolases, adomain shared by bacterial AspRS and the B subunit of archaealglutamyl-tRNA amidotransferases, and another previously undetected domainthat is conserved in a subset of ThrRS, guanosine polyphosphate hydrolasesand synthetases, and a family of GTPases. Comparison of domainarchitectures and multiple alignments resulted in the delineation ofsynapomorphies-shared derived characters, such as extra domains orinserts-for most of the aaRSs specificities. These synapomorphiespartition sets of aaRSs with the same specificity into two or moredistinct and apparently monophyletic groups. In conjunction with clusteranalysis and a modification of the midpoint-rooting procedure, thispartitioning was used to infer the likely root position in phylogenetictrees. The topologies of the resulting rooted trees for most of the aaRSsspecificities are compatible with the evolutionary "standard model"whereby the earliest radiation event separated bacteria from the commonancestor of archaea and eukaryotes as opposed to the two other possibleevolutionary scenarios for the three major divisions of life. For almostall aaRSs specificities, however, this simple scheme is confounded bydisplacement of some of the bacterial aaRSs by their eukaryotic or, lessfrequently, archaeal counterparts. Displacement of ancestral eukaryoticaaRS genes by bacterial ones, presumably of mitochondrial origin, wasobserved for three aaRSs. In contrast, there was no convincing evidence ofdisplacement of archaeal aaRSs by bacterial ones. Displacement of aaRSgenes by eukaryotic counterparts is most common among parasitic andsymbiotic bacteria, particularly the spirochaetes, in which 10 of the 19aaRSs seem to have been displaced by the respective eukaryotic genes andtwo by the archaeal counterpart. Unlike the primary radiation eventsbetween the three main divisions of life, that were readily traceablethrough the phylogenetic analysis of aaRSs, no consistent large-scalebacterial phylogeny could be established. In part, this may be due toadditional gene displacement events among bacterial lineages. Argument ispresented that, although lineage-specific gene loss might have contributedto the evolution of some of the aaRSs, this is not a viable alternative tohorizontal gene transfer as the principal evolutionary phenomenon in thisgene class.