Abstract
RNA editing is a post-transcriptional process of modifying genetic information on RNA molecules, which provides cells an additional level of gene expression regulation. Unlike mammals, in land plants, RNA editing converts C-to-U residues in organelles. However, its potential roles in response to different stressors (heat, salt, and so on) remains unclear. Grape is one of the most popular and economically important fruits in the world, and its production, like other crops, must deal with abiotic and biotic stresses, which cause reductions in yield and fruit quality. In our study, we tested the influence of the environmental factor temperature on RNA editing process in the whole mRNA from grape organelle. In total, we identified 122 and 627 RNA editing sites in chloroplast and mitochondria respectively with the average editing efficiency nearly ~ 60%. The analyses revealed that number of non-synonymous editing sites were higher than that of synonymous editing sites, and the amino acid substitution type tends to be hydrophobic. Additionally, the overall editing level decreased with the temperature rises, especially for several gene transcripts in chloroplast and mitochondria (matK, ndhB, etc.). We also found that the expression level of most PPR genes decreased with the temperature rises, which may contribute to the decline of RNA editing efficiency at high temperature. Our findings suggested that the RNA editing events were very sensitive to heat stress; the changes of amino acid in RNA editing genes may contribute to the stress adaption for grape.
Highlights
RNA editing is a post-transcriptional process that could alter the nucleotide sequence of gene transcripts, potentially diversifies the transcriptome and proteomes beyond the genomic blueprint (Takenaka et al 2013b)
The growing of public RNA-seq data provides an excellent opportunity to investigate the effect of RNA editing on organelle function and evolution (Edera et al 2018; Smith 2013); a comprehensive picture of C-to-U RNA editing sites was described in angiosperm mitochondria, revealing that RNA editing sites are conserved across angiosperms but some species-specific sites still exist
Our study suggested that RNA editing was responsive to environmental inputs in the form of temperature alterations
Summary
RNA editing is a post-transcriptional process that could alter the nucleotide sequence of gene transcripts, potentially diversifies the transcriptome and proteomes beyond the genomic blueprint (Takenaka et al 2013b). RNA editing has various biological functions; recent studies reported that RNA editing plays important roles in various plant developmental processes and evolutionary adaptation, including organelle biogenesis, signal transduction, and adaptation to environmental changes (Fujii and Small 2011; Hammani and Giege 2014). Since the advent of next-generation sequencing technologies, RNA-seq data becomes a comprehensive, precise, and low-cost approach for transcriptome profiling and variant analysis; tens of thousands of editing sites have been identified in more and more plants (Edera et al 2018; Grimes et al 2014; Picardi et al 2010). The growing of public RNA-seq data provides an excellent opportunity to investigate the effect of RNA editing on organelle function and evolution (Edera et al 2018; Smith 2013); a comprehensive picture of C-to-U RNA editing sites was described in angiosperm mitochondria, revealing that RNA editing sites are conserved across angiosperms but some species-specific sites still exist
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