Our investigation of the complete genomes from 66 different species allows us to gain insight into the conservation of r-proteins across the three primary domains of life and within each of them. Regarding the inter-domain distribution, 32 r-proteins are strictly conserved in all the bacterial, archaeal and eukaryotic studied genomes (BAE set) in agreement with structural comparison between prokaryotic and eukaryotic ribosomes (10
) which demonstrates the preservation of the core and global shape of ribosome. The high number of r-proteins conserved in all species of the wide phylogenetic range covered confirms the prevalence of r-proteins within the universal pool that may be present in the last universal common ancestor (63
The distribution of the other r-proteins shows a profound rupture in the protein component of the bacterial ribosome as opposed to the archaeal and eukaryotic ones. No r-proteins are specific to Bacteria and Eucarya (BE) or to Bacteria and Archaea (BA) while 33 are common to Archaea and Eucarya (AE) and 23 r-proteins are bacterial specific (B). Even if we cannot exclude that some of the proteins of the B and AE sets have in fact the same ancestral origin but have diverged beyond recognition, the importance of the two sets testifies to a specialization of bacterial versus archaeal/eukaryotic ribosomes. An appealing hypothesis is that the B and AE proteins are involved in the folding of lineage-specific rRNA extensions shown by comparison of rRNA sequences (65
). However, some of these r-proteins could also interact with domain-specific translation factors or be implicated in extra-ribosomal functions as frequently observed for r-proteins (66
The intra-domain distribution of r-proteins shows unforeseen differences between the three domains of life. In Bacteria, a relatively simple picture of conservation emerges since only four proteins are lost in the wide collection of bacterial species investigated in our study. Gene losses are restricted to a small number of divergent species or genera suggesting that gene disruptions occurred independently in these lineages. From a physiological point of view, there is a bias toward losses in intracellular pathogens with M.genitalium and M.pneumoniae lacking three of the four dispensable proteins. In addition to these losses, some small r-proteins are found in a restricted number of bacteria such as the Thx protein in Thermus species. It is therefore possible that additional r-proteins limited to a small phylogenetic spectrum are still unknown and could lead to a slightly more diverse picture of the bacterial ribosome than expected.
The distribution of r-proteins appears more complex in Eucarya and Archaea and reveals intricate evolutionary relationships between the two domains. In Eucarya, we observe a remarkable conservation of r-proteins in all investigated genomes except in E.cuniculi
that lacks at least four proteins. The homogeneous distribution of r-proteins in representatives of the eukaryotic crown group is noteworthy since rRNA exhibit numerous taxon-specific insertions in these groups (67
). Interpretation of gene absences in Microsporidia is complicated by both their intracellular parasitic lifestyle and their uncertain phylogenetic position but gene absences appear directly correlated to the extremely small size of the rRNA which is reduced to the universal core in this species (69
). The amitochondriate Microsporidia were first considered as one of the most basal eukaryotic lineages (70
) which diverged before the endosymbiotic event that led to mitochondria. According to this evolutionary scenario, the small size of rRNA and the absence of certain r-protein genes in E.cuniculi
could be considered as primitive characters. The appearance of eukaryotic-specific proteins after the emergence of the Microsporidia would be a trace of the eukaryotic ribosome enrichment in proteins in the course of evolution. However, according to a growing number of studies (reviewed in 72
), Microsporidia may be atypical fungi that secondarily lost mitochondria. If this later origin is confirmed, the reduction of rRNA size and the loss of some r-proteins would participate in the general process of genome compaction revealed by the genomic sequence (73
) which is probably linked to its intracellular parasitic lifestyle.
In Archaea, the pattern of r-protein conservation differs dramatically from those observed in Bacteria and Eucarya. In the archaeal domain, losses include 10 r-proteins while only four proteins appear dispensable in each of the two other domains, revealing a higher than expected plasticity in the archaeal ribosome. Moreover, the losses cannot be explained by an intracellular lifestyle as in the case of eukaryotes and, to a lesser extent, bacteria, since all archaeal species considered in our study are free-living organisms. On the contrary, the pattern of gene losses indicates a progressive elimination of r-protein genes in the course of archaeal evolution, with the deeply branched Crenarchaeota exhibiting up to 10 r-proteins more than the latest divergent representatives of Euryarchaeota. This ribosome ‘striptease’ is, to our knowledge, the first tangible example of reductive evolution observed at a primary domain scale. It is all the more remarkable since informational proteins involved in a macromolecular complex are concerned. The subsequent question is why these r-protein genes have been lost. One could imagine that the loss of r-proteins is functionally and/or structurally compensated by a rRNA enlargement. The inverse mechanism has been proposed in the case of mammalian mitochondrial ribosome where the deficit of rRNA relative to the bacterial one is balanced by a protein enrichment (74
). However, the situation seems more complex in Archaea since there is no indication of an rRNA shortening between the deeply branch Crenarchaeota and the later diverging Euryarchaeota. Thus, the ribosome of a Crenarchaeota, like A.pernix
, may be a rich target for structural studies aimed at understanding the fundamental mechanisms underlying the reductive evolution process.
From an evolutionary perspective, our results lead to troublesome conclusions. On one hand, it seems that, with the exception of LXa, the full complement of archaeal r-proteins was present at an early stage of evolution, i.e. in the cenancestor of Archaea and Eucarya and was progressively eroded. This is in agreement with the eukaryotic-rooting tree (75
) which proposes that prokaryotes would have evolved by simplification of an ancestral eukaryotic-like genome. On the other hand, the clear-cut opposition between bacterial and archaeal/eukaryotic r-protein complements is in agreement with the bacterial-rooting tree (77
) or the symbiosis hypothesis (discussed in 78
) which both explain the close relationships observed between Archaea and Eucarya. It even suggests that the ribosome specialization has been constitutive of the segregation of the bacterial lineage from the cenancestor(s) of Archaea and Eucarya, in agreement with Woese’s proposal that the translation apparatus ‘crystallizes’ first. Faced with these two opposite evolutionary scenarios, genome sequencing of early branching representatives of the three domains and comparative analyses of other macromolecular complexes will be essential in deciding whether the reductive evolution is a special trait of archaeal ribosomes or whether it constitutes a general trend in prokaryote evolution.