Taxonomic distribution of proteins containing DALR_2 domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing DALR_2 domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Comparative genomics of the Archaea (Euryarchaeota): evolution ofconserved protein families, the stable core, and the variable shell.

Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV
Genome Res. 1999; 9: 608-28

Comparative analysis of the protein sequences encoded in the foureuryarchaeal species whose genomes have been sequenced completely(Methanococcus jannaschii, Methanobacterium thermoautotrophicum,Archaeoglobus fulgidus, and Pyrococcus horikoshii) revealed 1326orthologous sets, of which 543 are represented in all four species. Theproteins that belong to these conserved euryarchaeal families comprise31%-35% of the gene complement and may be considered the evolutionarilystable core of the archaeal genomes. The core gene set includes the greatmajority of genes coding for proteins involved in genome replication andexpression, but only a relatively small subset of metabolic functions. Formany gene families that are conserved in all euryarchaea, previouslyundetected orthologs in bacteria and eukaryotes were identified. A numberof euryarchaeal synapomorphies (unique shared characters) were identified;these are protein families that possess sequence signatures or domainarchitectures that are conserved in all euryarchaea but are not found inbacteria or eukaryotes. In addition, euryarchaea-specific expansions ofseveral protein and domain families were detected. In terms of theirapparent phylogenetic affinities, the archaeal protein families split intobacterial and eukaryotic families. The majority of the proteins that haveonly eukaryotic orthologs or show the greatest similarity to theireukaryotic counterparts belong to the core set. The families ofeuryarchaeal genes that are conserved in only two or three speciesconstitute a relatively mobile component of the genomes whose evolutionshould have involved multiple events of lineage-specific gene loss andhorizontal gene transfer. Frequently these proteins have detectableorthologs only in bacteria or show the greatest similarity to thebacterial homologs, which might suggest a significant role of horizontalgene transfer from bacteria in the evolution of the euryarchaeota.

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.