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.
Highlights
Gene expression in plant chloroplasts and mitochondria is affected by RNA editing
The 14 chloroplast editomes of the flowering plants Amborella trichopoda [40], Aegilops tauschii [41], coconut Cocos nucifera [42], cucumber Cucumis sativus [40, 43], cotton Gossypium hirsutum [44], the orchid Phalaenopsis aphrodite [45], the duckweed Spirodela polyrhiza [46] and the mung bean Vigna radiata [47], the gymnosperm Ginkgo biloba [48], the liverwort Apopellia endiviifolia [49], the lycophyte Selaginella uncinata [36], the horsetail Equisetum hyemale [50] and the ferns Ophioglossum californicum and Psilotum nudum [51] have been added to the plastome references previously included in PREPACT 2.0 [39]
Over the recent years, research on plant-type RNA editing has extended to the characterization of the specific, RNA-binding pentatricopeptide repeat (PPR) protein factors addressing individual editing sites in the endosymbiotic organelles
Summary
Gene 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. PPR proteins characterized as editing factors carry carboxyterminal protein domain additions, minimally “E” (extension) domains, frequently followed by the so-called “DYW” domain. The latter in particular is of fundamental interest owing to its significant similarity to cytidine deaminases, which likely provides the biochemical activity for C-to-U conversion [20,21,22,23]. DYW-type PPR proteins that were previously believed to be plant-specific, have recently been identified in very distant evolutionary lineages of eukaryotes where their presence likewise seems to be connected to mitochondrial RNA editing of the C-to-U type [24,25,26,27]
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