Transfer RNA and Origins of RNA Interference

Abstract

Almost 30 years ago the first microRNA (miRNA) was detected (Lee et al., 1993), later put in mechanistical context by the discovery of the RNA interference (RNAi) and RNA-induced silencing complex (RISC). miRNA is the variable RISC element (guide) that recognizes messenger RNA (mRNA) targets in the RNAi process facilitated by Argonaute (Ago) proteins, the fixed key players in RISC. Alas, poetically sounding Argonautes were named not after the adventurers from Greek mythology but octopus-shaped leaves of an Arabidopsis thaliana mutant (Bohmert et al., 1998). Production of miRNAs is performed by a sophisticated orchestra of players with even groovier names, like Drosha, Pasha or Dicer. While roles of miRNA in post-transcriptional regulation have been established, its evolution has been typically described as expansion of new miRNA genes from the existing ones, not their first appearance (Berezikov, 2011). The emergence of RNAi has been attributed to its defense against pathogens, which involves other participants, e.g., double-stranded RNA binding proteins (dsRBPs). But details of such emergence are lacking. This is a short opinion piece, not a full review, so I apologetically skip some of these players and hundreds of relevant miRNA/RNAi citations (and those for subsections below). The complexity of the RISC is bewildering. Intricate steps of miRNA production in the nucleus are followed by unequal strand loading to Ago, and finally resulting in cytoplasmic events, sometimes involving “slashing” of mRNA. All that (for simplicity, ignoring nuclear events upon Ago transport from cytoplasm) is based on weak and imperfect binding of short “seeds” (5′ 6-8 nucleotides in length in animals) to targets and on weak outcomes of slight tuning of target translation. How can such weak binding be a driving force for emergence and evolution of this complicated system and its parts, acting in concert in different cellular compartments? Plant RNAi requires full-length small RNA hybridization, significantly limiting the number of target genes, yet the system appears even more complex (four Dicers, seven dsRBPs versus a single Dicer/couple of dsRBPs in humans). Further, the miRNA generation machineries are not entirely homologous, mature miRNAs are produced and modified in the plant nucleus, but these processes are divided between the nucleus and cytoplasm in animals. How would these different processes evolve in parallel with creating the elaborate and divergent Ago functionalities (four different Agos in humans, ten in A. thaliana, 26 in Caenorhabditis elegans), able to utilize these precisely cut miRNAs for mRNA regulation? This scenario would require a small RNA already acting together with some Ago prototypic protein. Compatible with this view, the last common ancestor of eukaryotes likely appeared after the RNAi functional principles (and some components, except for miRNA) had been invented (Cerutti and Casas-Mollano, 2006). And many prokaryotes do not have miRNAs but possess Ago protein homologs.