The origin of RNA interference: Adaptive or neutral evolution?

Abstract

The origin of RNA interference (RNAi) is usually explained by a defense-based hypothesis, in which RNAi evolved as a defense against transposable elements (TEs) and RNA viruses and was already present in the last eukaryotic common ancestor (LECA). However, since RNA antisense regulation and double-stranded RNAs (dsRNAs) are ancient and widespread phenomena, the origin of defensive RNAi should have occurred in parallel with its regulative functions to avoid imbalances in gene regulation. Thus, we propose a neutral evolutionary hypothesis for the origin of RNAi in which qualitative system drift from a prokaryotic antisense RNA gene regulation mechanism leads to the formation of RNAi through constructive neutral evolution (CNE). We argue that RNAi was already present in the ancestor of LECA before the need for a new defense system arose and that its presence helped to shape eukaryotic genomic architecture and stability.

Fig 1. Evolution from prokaryotic RNA-mediated gene regulation to eukaryotic RNAi.

We propose that the evolutionary journey from prokaryotic RNA-mediated gene regulation to eukaryotic RNAi comprised 2 distinct evolutionary process. The first involved changes in the molecular machinery without changes in the final outcomes of the process (qualitative system drift). The second involved a ratcheting cascade caused by the suppressive role of RNAi on the deleterious effects of TEs, as postulated by CNE. asRNA, antisense RNA; CNE, constructive neutral evolution; LECA, last common eukaryotic ancestor; RNAi, RNA interference; sRNA, small RNA; TE, transposable element.

Fig 2. General examples of CNE.

(a) Multifunctionality evolution through CNE. (1) α is a generic noncoding RNA that mediates RNA silencing on its target mRNA (red), and β is an enzyme that participates in cellular metabolism. (2) By chance, α and β may interact in the cellular environment creating an ephemeral complex. (3) Excess capacity in β results in the stabilization of the α–mRNA complex and then exerts a suppressive effect on mutations in α, which are now no longer deleterious [19,114]. (4) At this stage, α is reliant on interaction with β to exert its activity, while β has gained a new function in becoming a chaperone for α. (b) Increasing molecular complexity by CNE. (1) Mutations that inhibit the catalytic function of β (black arrow) or compromise α–β interactions (red arrow) are dangerous for the organism and would be eliminated by purifying selection. (2) In the case of gene duplication of β (represented by β1 and β2), there is now an excess capacity in the system that can exert a presuppressive activity [19,113]. (3) Mutations that compromise the stability of α–β interactions in β1 and the enzymatic activity in β2 are no longer deleterious since that function can be carried out by the other protein. (4) β1 and β2 can now evolve as 2 different proteins, without adaptive evolution. CNE, constructive neutral evolution.

Fig 3. An example of qualitative system drift during binary fission.

Mitochondria in the protist Dictyostelium, retain the bacterial protein FtsZ together with the eukaryotic Drp1, whereas in mitochondria in higher eukaryotes, only Drp1 is present, indicating a shift in the molecular effector for binary fission during evolution.

Fig 4. Hypothetical transition from bacterial asRNA gene regulation to eukaryotic RNAi due to CNE.

(a) asRNAs (not in figure) or sRNAs may lead to the production of short dsRNAs. (b) Prior to degradation, the short dsRNAs may interact with cellular proteins such as Ago and become guide RNAs. The slicer activity of Ago may cause an amplification of the interference effect that triggers the down-regulation of the asRNA or sRNA by dosage compensation. (c) Mutations that reduce the expression or functionality of the asRNA or sRNA are now likely to appear and accumulate owing to the suppressive effect of Ago, causing irreversibility to this process. Ago, Argonaute; asRNA, antisense RNA; CNE, constructive neutral evolution; dsRNA, double-stranded RNA; RNAi, RNA interference; sRNA, small RNA.