Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

Abstract

BackgroundGene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encoded in the organelle genomes. Predicting and analyzing RNA editing, which ranges from only few sites in some species to thousands in other taxa, is bioinformatically demanding.ResultsHere, we present major enhancements and extensions of PREPACT, a WWW-based service for analysing, predicting and cataloguing plant-type RNA editing. New features in PREPACT’s core include direct GenBank accession query input and options to restrict searches to candidate U-to-C editing or to sites where editing has been documented previously in the references. The reference database has been extended by 20 new organelle editomes. PREPACT 3.0 features new modules “EdiFacts” and “TargetScan”. EdiFacts integrates information on pentatricopeptide repeat (PPR) proteins characterized as site-specific RNA editing factors. PREPACT’s editome references connect into EdiFacts, linking editing events to specific co-factors where known. TargetScan allows position-weighted querying for sequence motifs in the organelle references, optionally restricted to coding regions or sequences around editing sites, or in queries uploaded by the user. TargetScan is mainly intended to evaluate and further refine the proposed PPR-RNA recognition code but may be handy for other tasks as well. We present an analysis for the immediate sequence environment of more than 15,000 documented editing sites finding strong and different bias in the editome data sets.ConclusionsWe exemplarily present the novel features of PREPACT 3.0 aimed to enhance the analyses of plant-type RNA editing, including its new modules EdiFacts integrating information on characterized editing factors and TargetScan aimed to analyse RNA editing site recognition specificities.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2244-9) contains supplementary material, which is available to authorized users.

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

“…The chloroplast editome includes 67 editing sites in 5′ and 3′ untranslated regions (UTRs), 27 editing sites in introns, and 124 silent edits in coding regions that could not be predicted. No case of silent editing in either direction of pyrimidine exchange was observed in AGY serine, CGY arginine, GGY glycine, or UGY cysteine codons, fully matching previous observations of only very rare RNA editing immediately downstream of a guanidine (Lenz et al , ). Many silent sites and those outside of coding regions are edited to much lower degrees than those in codon‐changing positions (Table S1).…”

“…Most events of RNA editing in plant organelles serve to reconstitute conserved amino acid identities in protein coding sequences. We predicted 1371 candidate sites of RNA editing using the 12 nonangiosperm chloroplast references available with the latest update of P repact and the default ‘commons’ threshold level of 70% (Lenz et al , ). Analysing the transcriptome data, we ultimately identified 1549 sites of chloroplast RNA editing (636 C‐to‐U and 913 U‐to‐C edits) in the A. agrestis chloroplast (Supporting Information Table S1).…”

“…Silent editing sites are shown in green font and codons affected by multiple editing in purple. The output is based on the complementary DNA analysis function in PREPACT (Lenz et al, 2018). Some 50% of A. agrestis edits are shared with lycophytes Isoetes engelmannii and/or Selaginella moellendorffii included in the PREPACT 3.0 editome references.…”

“…In contrast to C‐to‐U editing, we have no idea yet about the mechanisms of reverse U‐to‐C RNA editing. The main reason is that the editomes of the aforementioned model systems and those of other flowering plants seem to be entirely devoid of U‐to‐C RNA editing (Edera et al , ; Lenz et al , ). We could not corroborate occasional reports of reverse RNA editing in angiosperms (P. Gerke, V. Knoop, unpublished findings) and consider it likely that U‐to‐C RNA editing is phylogenetically restricted to hornworts, lycophytes, and ferns.…”

“…The mechanism of C-to-U-type RNA editing is reasonably well understood, mainly owing to the characterization of many RNA editing factors in model systems such as the flowering plants Arabidopsis thaliana and Oryza sativa and in the moss model system Physcomitrella patens (Barkan & Small, 2014;Ichinose et al, 2014;Schallenberg-R€ udinger & Knoop, 2016). By now, c. 80 site-specific RNA editing factors have been characterized, recently summarized in the database EdiFacts, an addition to the PREPACT service for the analysis of plant-type RNA editing (Lenz et al, 2018). These site-specific RNA editing factors are unique RNAbinding pentatricopeptide repeat (PPR) proteins featuring additional carboxyterminal domains called E1, E2, and DYW (Cheng et al, 2016).…”