Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors

Abstract

BackgroundRNA editing by cytidine-to-uridine conversions is an essential step of RNA maturation in plant organelles. Some 30–50 sites of C-to-U RNA editing exist in chloroplasts of flowering plant models like Arabidopsis, rice or tobacco. We now predicted significantly more RNA editing in chloroplasts of early-branching angiosperm genera like Amborella, Calycanthus, Ceratophyllum, Chloranthus, Illicium, Liriodendron, Magnolia, Nuphar and Zingiber. Nuclear-encoded RNA-binding pentatricopeptide repeat (PPR) proteins are key editing factors expected to coevolve with their cognate RNA editing sites in the organelles.ResultsWith an extensive chloroplast transcriptome study we identified 138 sites of RNA editing in Amborella trichopoda, approximately the 3- to 4-fold of cp editing in Arabidopsis thaliana or Oryza sativa. Selected cDNA studies in the other early-branching flowering plant taxa furthermore reveal a high diversity of early angiosperm RNA editomes. Many of the now identified editing sites in Amborella have orthologues in ferns, lycophytes or hornworts. We investigated the evolution of CRR28 and RARE1, two known Arabidopsis RNA editing factors responsible for cp editing events ndhBeU467PL, ndhDeU878SL and accDeU794SL, respectively, all of which we now found conserved in Amborella. In a phylogenetically wide sampling of 65 angiosperm genomes we find evidence for only one single loss of CRR28 in chickpea but several independent losses of RARE1, perfectly congruent with the presence of their cognate editing sites in the respective cpDNAs.ConclusionChloroplast RNA editing is much more abundant in early-branching than in widely investigated model flowering plants. RNA editing specificity factors can be traced back for more than 120 million years of angiosperm evolution and show highly divergent patterns of evolutionary losses, matching the presence of their target editing events.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0589-0) contains supplementary material, which is available to authorized users.

Establishment of a Heterologous RNA Editing Event in Chloroplasts

“…Due to their high binding specificity for particular RNA sequences, PPR-type editing factors strictly coevolve with their target ciselement(s) and, in this way, with the corresponding RNA editing site(s). Therefore, the loss of a chloroplast editing site often correlates with the degeneration of the gene for the corresponding PPR protein in the nucleus (Hayes et al, 2012;Hein et al, 2016; this study), especially in those cases where the PPR protein only serves a single editing site. It, therefore, seemed reasonable to suspect the lack of editing at heterologous sites is due to the lack of the required PPR factor.…”

“…Because of their high specificity, PPRs are thought to tightly coevolve with their target site(s). It is, therefore, assumed that the loss of an editing site is often accompanied by the loss or degeneration of the corresponding PPR gene in the nuclear genome (Hayes et al, 2012;Hein et al, 2016), consistent with the lack of editing at heterologous sites introduced into the plastid genome.…”

Plant organellar RNA editing: what 30 years of research has revealed

“…Welwitschia , however, has massively lost editing sites in both organelles, most likely to have been caused by retroprocessing (Fan et al , ). A gradual decrease in organellar RNA editing is apparent during the evolution of angiosperms (Freyer et al , ; Shields and Wolfe, ; Tillich et al , ; Mower, ; Cuenca et al , ; Sloan et al , ; Fujii and Small, ; Richardson et al , ; Hein et al , ; Ishibashi et al , ).…”

Gaining comprehensive biological insight into chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis

“…However, no instance of RNA editing has yet been reported in Marchantiidae and algae, suggesting that RNA editing may have evolved only after the plants established themselves on the land, [13]. Excellent studies in different plants have recently appeared and describe their mechanistic and functional aspects [14][15][16]. The frequency of organellar RNA editing varies from zero to thousands of sites across plant kingdom, among land plants, early-diverging lineages show the highest numbers of editing sites compared with higher plants that undergoing an extensive loss of editing sites through the substitution of genomic editable cytidines to thymidines [17].…”