The Path from the RNA World

Abstract

We describe a sequential (step by step) Darwinian model for the evolution of life from the late stages of the RNA world through to the emergence of eukaryotes and prokaryotes. The starting point is our model, derived from current RNA activity, of the RNA world just prior to the advent of genetically-encoded protein synthesis. By focusing on the function of the protoribosome we develop a plausible model for the evolution of a protein-synthesizing ribosome from a high-fidelity RNA polymerase that incorporated triplets of oligonucleotides. With the standard assumption that during the evolution of enzymatic activity, catalysis is transferred from RNA --> RNP --> protein, the first proteins in the "breakthrough organism" (the first to have encoded protein synthesis) would be nonspecific chaperone-like proteins rather than catalytic. Moreover, because some RNA molecules that pre-date protein synthesis under this model now occur as introns in some of the very earliest proteins, the model predicts these particular introns are older than the exons surrounding them, the "introns-first" theory. Many features of the model for the genome organization in the final RNA world ribo-organism are more prevalent in the eukaryotic genome and we suggest that the prokaryotic genome organization (a single, circular genome with one center of replication) was derived from a "eukaryotic-like" genome organization (a fragmented linear genome with multiple centers of replication). The steps from the proposed ribo-organism RNA genome --> eukaryotic-like DNA genome --> prokaryotic-like DNA genome are all relatively straightforward, whereas the transition prokaryotic-like genome --> eukaryotic-like genome appears impossible under a Darwinian mechanism of evolution, given the assumption of the transition RNA --> RNP --> protein. A likely molecular mechanism, "plasmid transfer," is available for the origin of prokaryotic-type genomes from an eukaryotic-like architecture. Under this model prokaryotes are considered specialized and derived with reduced dependence on ssRNA biochemistry. A functional explanation is that prokaryote ancestors underwent selection for thermophily (high temperature) and/or for rapid reproduction (r selection) at least once in their history.

Universal Sharing Patterns in Proteomes and Evolution of Protein Fold Architecture and Life

“…These architectures appear functionally versatile, since folds at the base of the tree of architectures harbor many enzymatic functions (Caetano-Anolle´s and CaetanoAnolle´s 2003). Our view is consistent with a primitive proto-eukaryote (Glansdorff 2000;Poole et al 1998) responsible for ''crystallizing'' diversified life (Woese 2000). It is also consistent with a limited role of HGT (Glansdorff 2000).…”

Novel function of C5 protein as a metabolic stabilizer of M1 RNA

“…In addition, it has been speculated that some RNP complexes (e.g. RNase P, ribosomes, and spliceosomes) represent vestiges of the transition from a RNA-driven environment to the contemporary world of proteins [7,[39][40][41][42]. During this transition, proteins were thought to assist with the tasks performed by RNA molecules, as the protein components of contemporary RNP complexes function as cofactors, whereas catalytic activities are retained by some RNAs.…”

The rocky roots of the acetyl-CoA pathway

“…A continuous supply of monomeric components for life's polymeric constituents (nucleic acids and proteins) is essential because, for any system to replicate at the origin of life, it must regularly double its total mass of organic material [12]. Ample concentrations of monomers must be therefore in continuous supply -a perhaps obvious, but in our view seemingly insurmountable, problem underlying the organic soup and surface metabolism theories.…”