Multifarious Evolutionary Pathways of a Nuclear RNA Editing Factor: Disjunctions in Coevolution of DOT4 and Its Chloroplast Target rpoC1eU488SL

Abstract

Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 targeting ancient chloroplast editing sites in flowering plants. Here, we report on alternative evolutionary pathways for DOT4 addressing rpoC1eU488SL, a chloroplast editing site in the RNA polymerase β′ subunit mRNA. Upon loss of rpoC1eU488SL by C-to-T conversion, DOT4 got lost multiple times independently in angiosperm evolution with intermediate states of DOT4 orthologs in various stages of degeneration. Surprisingly, we now also observe degeneration and loss of DOT4 despite retention of a C in the editing position (in Carica, Coffea, Vicia, and Spirodela). We find that the cytidine remains unedited, proving that DOT4 was not replaced by another editing factor. Yet another pathway of DOT4 evolution is observed among the Poaceae. Although the rpoC1eU488SL edit has been lost through C-to-T conversion, DOT4 orthologs not only remain conserved but also have their array of PPRs extended by six additional repeats. Here, the loss of the ancient target has likely allowed DOT4 to adapt for a new function. We suggest rps3 antisense transcripts as previously demonstrated in barley (Hordeum vulgare) arising from promotor sequences newly emerging in the rpl16 intron of Poaceae as a new candidate target for the extended PPR stretch of DOT4. Altogether, DOT4 and its target show more flexible pathways for evolution than the previously explored editing factors CLB19, CRR28, and RARE1. Certain plant clades (e.g., Amaranthus, Vaccinium, Carica, the Poaceae, Fabales, and Caryophyllales) show pronounced dynamics in the evolution of editing sites and corresponding factors.

Towards a plant model for enigmatic U‐to‐C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis

“…Comparing plant lifestyles gives no reasonable clues as to why some plant lineages (like the Selaginellales) have lost reverse RNA editing altogether, may have never possessed it in the first place (possibly mosses and liverworts, depending on the ultimately true phylogeny of the bryophyte clades), or why U-to-C editing may even dominate over C-to-U editing in other lineages . Based on the working hypotheses presented here, the experimental approaches outlined herein will hopefully help to answer that puzzling evolutionary question or, for example, also why RNA editing evolves so dramatically fast in at least some genera, like Amaranthus or Silene among the angiosperms (Sloan et al, 2010;Hein et al, 2019), Selaginella among the lycophytes (Smith, 2019), Adiantum among ferns (Zumkeller et al, 2016), or, as also demonstrated here for U-to-C editing, in Anthoceros among the hornworts.…”

The study of organelle DNA variability in alloplasmic barley lines in the NGS era

“…Moreover, as revealed for DOT4 PPR protein -the loss of editing target site through C to T conversion allowed DOT4 in Poaceae to adapt for new function. Also some cases were described where the target sequences for editing exist, but no corresponding PPR is encoded by nucleus (Hein et al, 2019).…”

Integrated Transcriptome and Targeted Metabolite Analysis Reveal miRNA-mRNA Networks in Low-Light-Induced Lotus Flower Bud Abortion

“…Here, four PPR genes, including PPRDOT4 (LOC104586410), PPRAt1g56570 (LOC104607063), PPRat2g04860 (LOC104609601), and PPRAt1g69350 (LOC104598024), were significantly down-regulated, and the expression levels of their regulator miRNAs, miR156_2 , miR157d-3p , and miR6300 , increased, respectively ( Tables S3–S5 ). Among them, PPRDOT4 mediated chloroplast RNA editing [ 78 ]. It has been reported that RF-PPR592, which belongs to the PPR protein family, can restore the fertility of cytoplasmic male sterile plants [ 79 ].…”