Molecular palaeontology as a new tool to study the evolution of ribosomal RNA

Abstract

The ribosome is a large RNA-protein complex that performs the synthesis of proteins in all living organisms. The emergence of the ribosome has been a pivotal step in the evolution of life on earth. It is generally accepted that the ribosome emerged almost four billion years ago from the RNA world, in which the primordial chemical reactions of life were catalyzed by RNA (Crick, 1968; Gilbert, 1986). Correspondingly, the ancient ribosome represented an RNA body, while proteins were added to its structure later, when the ribosome became effective enough to synthesize them. The original ribosomal RNA (rRNA) is believed to have been a rather small molecule, which gradually expanded to the modern size through addition of new elements (Noller, 2004; Hury et al., 2006; Smith et al., 2008). In order to understand details of this evolutionary process, one cannot use the standard approach of aligning available nucleotide sequences of ribosomal RNA and constructing phylogenetic trees. Due to the nature of that approach, its ability to elucidate evolutionary events in the past is limited by the moment when all branches of the phylogenetic tree come together, which corresponds to the so-called Last Universal Common Ancestor (LUCA). On the other hand, because in all presently living organisms the ribosome core has essentially the same structure (Gutell et al., 1994; Doudna and Rath, 2002), it should have formed before the split of the tree of life in three major domains, i. e. before LUCA. This discrepancy makes the standard approach inapplicable to the problem of early ribosome evolution and necessitates the development of alternative approaches.