Evolutionary Origin of RNA Editing

Abstract

The term "RNA editing" encompasses a wide variety of mechanistically and phylogenetically unrelated processes that change the nucleotide sequence of an RNA species relative to that of the encoding DNA. Two general classes of editing, substitution and insertion/deletion, have been described, with all major types of cellular RNA (messenger, ribosomal, and transfer) undergoing editing in different organisms. In cases where RNA editing is required for function (e.g., to generate a translatable open reading frame in a mRNA), editing is an obligatory step in the pathway of genetic information expression. How, when, and why individual RNA editing systems originated are intriguing biochemical and evolutionary questions. Here I review briefly what is known about the biochemistry, genetics, and phylogenetics of several very different RNA editing systems, emphasizing what we can deduce about their origin and evolution from the molecular machinery involved. An evolutionary model, centered on the concept of "constructive neutral evolution", is able to account in a general way for the origin of RNA editing systems. The model posits that the biochemical elements of an RNA editing system must be in place before there is an actual need for editing, and that RNA editing systems are inherently mutagenic because they allow potentially deleterious or lethal mutations to persist at the genome level, whereas they would otherwise be purged by purifying selection.

The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages

“…One such mechanism is DNA and RNA editing (Gray 2012). Since its discovery in trypanosomatids (Benne et al 1986), editing has been found in Drosophila (Rodriguez et al 2012), humans (Fritz et al 2013), and mice (Rosenberg et al 2011).…”

Azolla, a little fern with massive green potential

“…This persistence of start and stop codon edits suggests that their loss is selected against, that is, creating the translatable sequence by RNA editing has an advantage over having it encoded by the genome. This argues that these particular RNAediting events are not selectively neutral 29 and supports editing as a control mechanism for gene expression in fern organelles.…”

On the evolution of Boolean networks for computation: a guide RNA mechanism

“…RNA editing appears to serve many roles [6], including (organelle) mutation repair and defence against viruses. From a regulatory network perspective, editing such as that provided by guide RNA enables context sensitive structural dynamism.…”

“…RNA editing is widespread and appears to have evolved many times (eg, see [6]). For example, guide RNA (gRNA) are relatively small molecules that align themselves to complementary regions of messenger RNA (mRNA) and either insert or delete a base(s) thereby (typically) altering the structure of the protein specified in the expressed DNA.…”