Phylogenomics of prokaryotic ribosomal proteins

Background

Archaeal and bacterial ribosomes contain more than 50 proteins. Thirty-four ribosomal proteins (r-proteins) are universally conserved in the three domains of cellular life (Bacteria, Archaea and Eukarya), and 33 r-proteins are shared between Archaea and Eukarya to the exclusion of Bacteria; there are also 23 Bacteria-specific, 1 Archaea-specific and 11 Eukarya-specific r-proteins [1]. Despite the high sequence conservation of r-proteins, the annotation of r-protein genes is often dificult because of their short lengths and biased sequence composition.

Methods

To perform a comprehensive survey of prokaryotic r-proteins, we developed an automated computational pipeline for the identification of r-protein genes and applied it to 995 completely sequenced bacterial genomes and 87 archaeal genomes available in the RefSeq database. The pipeline employs curated seed alignments of r-proteins to run position-specific scoring matrix (PSSM)-based BLAST searches against six-frame genome translations, thus overcoming possible gene annotation errors. Likely false positives are identified using comparisons against the original seed alignments.

Results

In the course of this analysis, we gained insight into the diversity of prokaryotic r-protein complements, such as missing and paralogous r-proteins and distributions of r-protein genes among chromosomal partitions. A phylogenetic tree was constructed from a concatenated alignment of 50 almost-ubiquitous bacterial r-proteins. The topology of the tree is generally compatible with the current high-level bacterial taxonomy, although we detected several inconsistencies, possibly indicating uncertain or erroneous classification of the respective bacteria. Similarly, a concatenated alignment of 57 ubiquitous archaeal proteins was used for an archaeal phylogenetic tree reconstruction. In both Bacteria and Archaea, the patterns of the presence/absence of non-ubiquitous r-proteins suggest several independent losses and/or gains of these proteins. According to parsimony reconstruction, three bacterial and five archaeal r-proteins do not appear to be ancestral. Remarkably, all five non-ancestral archaeal r-proteins are present in Eukarya.

Conclusions

Extended sets of prokaryotic r-proteins were created. Alignments of these sets may be used as new seed profiles for the identification of r-proteins in new genomes and for comparative genomics studies.