Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts

Abstract

Adar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome in a flexible manner. It has been a challenging task to identify beneficial editing sites from the sea of total editing events. The functional Ser>Gly auto-recoding site in insect Adar gene has uneditable Ser codons in ancestral nodes, indicating the selective advantage to having an editable status. Here, we extended this case study to more metazoan species, and also looked for all Drosophila recoding events with potential uneditable synonymous codons. Interestingly, in D. melanogaster, the abundant nonsynonymous editing is enriched in the codons that have uneditable counterparts, but the Adar Ser>Gly case suggests that the editable orthologous codons in other species are not necessarily edited. The use of editable versus ancestral uneditable codon is a smart way to infer the selective advantage of RNA editing, and priority might be given to these editing sites for functional studies due to the feasibility to construct an uneditable allele. Our study proposes an idea to narrow down the candidates of beneficial recoding sites. Meanwhile, we stress that the matched transcriptomes are needed to verify the conservation of editing events during evolution.

Keywords: A-to-I RNA editing; Adar; auto-recoding; beneficial; editable; metazoan.

Figure 1.

A-to-I RNA editing and the evolution of Adar auto-recoding sites in insects. (a) A-to-I RNA editing mediated by ADAR. I is recognized as G. (b) Prediction of adaptive RNA editing theory. The relative fitness of A- and G-alleles under different conditions is considered. (c) Drosophila Adar has an auto-recoding site that forms a negative feedback loop. (d) Evolution of Adar S>G (site1) and I>M (site2) sites in insects. “edSer”: editable serine codon; “unSer”: uneditable serine codon; “edIle”: editable isoleucine codon; “unIle”: uneditable isoleucine codon.

Figure 2.

Observed and expected numbers/proportions of AA changes caused by nonsynonymous RNA editing. Total numbers of expected mutations were obtained by changing all adenosines to guanosines in the reference genome of D. melanogaster. The expected proportions of each AA change were estimated by the proportions of observed AA changes caused by nonsynonymous RNA editing. The 3-mer motif preferred by Adar is also considered. p values of the enrichments were calculated using one-tailed Fisher’s exact tests for each AA change. *, p < 0.05; ***, p < 0.001.

Figure 3.

Enrichment of each type of AA change. (a) SNPs in global population of D. melanogaster. (b) Nonsynonymous editing sites in humans. (c) SNPs in global human populations.

Figure 4.

Hypotheses raised to explain the enrichment of Ile>Met, Ser>Gly, Arg>Gly recoding sites in Drosophila RNA editome. (a) the “uneditable-to-editable is beneficial” hypothesis. Editable is fitter than uneditable, but the benefit can either be diversifying or restorative. (b) The “deleterious editing replaced with uneditable codons” hypothesis. Since the editable ile, ser, and arg codons have another choice to mutate to uneditable ones, the observed editing after purifying selection shows enrichment on those codons.

Figure 5.

The orthologous codons of Adar S>G (site1) and I>M (site2) auto-recoding sites in metazoan species with systematic RNA editing study. “#” means that although the codon itself is editable, no RNA editing events were reported by the original study. The phylogenetic tree is unscaled.

Figure 6.

Horizontal and vertical comparison of editing sites. (a) the fraction of edited adenosines was very low in D. melanogaster genome. (b) Orthologous adenosine sites in three species. Two sites are known editing sites. The probability of the third species being edited should be high but the exact probability depends on the divergence.

Figure 7.

It is unexpected to observe the absence of editing at the edIle codon in ant A. echinatior. the top panel shows the phylogeny of three Drosophila species. The bottom panel shows the phylogeny of honeybee, bumblebee, and leaf-cutting ant.