Updating Mass and Composition of Archaeal and Bacterial Ribosomes. Archaeal-like Features of Ribosomes from the Deep-Branching Bacterium Aquifex pyrophilus

By using buoyant density methods, we have determined the mass and composition of ribosomal subunits from members of the green non-sulfur bacteria (Chloroflexus aurantiacus), the Thermotogales (Thermotoga maritima, Thermosypho africanus, Fervidobacterium islandicum) the Aquifex-Hydrogenobacter lineage, and from archaea belonging to both Crenarchaeota (Staphylothermus marinus) and Euryarchaeota (Pyrococcus species, Archaeoglobus fulgidus, Methanothermus fervidus). The principal result is the evidence that "low-density" ribosomes, richer in protein than those of the more recently evolved bacterial phyla, and comparable to those of most Archaea, exist in the deepest (eu)bacterial branching represented by Aquifex pyrophilus and the related VF5 strain. Also, among the archaea, protein-rich ribosomes, similar to those of sulfur-dependent thermophiles, Thermoplasmales and Methanococcales, are found in organisms (M. fervidus, A fulgidus) belonging to taxa (Methanobacteriales, Methanomicrobiales-extreme halophiles) that were previously assumed to harbor only "high density" ribosomes resembling those of most Bacteria. From the distribution, and the phylogenetic depth, of the low and high density ribosomes we argue that the protein-richer particles of Aquifex and of most Archaea are ancestral, and that the leaner (high-density) ribosomes of most Bacteria and of certain late-branching Euryarchaeaotes arose more than once from this protein-richer antecedent as a result of independently evolved (streamlining) events. It is surmised that the low-density version of prokaryotic ribosomes seen in Aquifex and in most Archaea represents an intermediate in the evolution of the miniaturized 70 S ribosome from an archaic particle resembling present-day 80 S ribosomes.