Taxonomic distribution of proteins containing PINc domains

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

PIN domains in nonsense-mediated mRNA decay and RNAi.

Clissold PM, Ponting CP
Curr Biol. 2000; 10: 88890-88890

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.