Abstract
Cytidine to uridine (C-to-U) RNA editing is an important type of substitutional RNA modification and is almost omnipresent in plant chloroplasts and mitochondria. In rice mitochondria, 491 C-to-U editing sites have been identified previously, and case studies have elucidated the function of several C-to-U editing sites in rice, but the functional consequence of most C-to-U alterations needs to be investigated further. Here, by means of Sanger sequencing and publicly available RNA-seq data, we identified a total of 569 C-to-U editing sites in rice mitochondria-encoded open reading frames (ORFs), 85.41% of these editing sites were observed on the first or the second base of a codon, resulting in the alteration of encoded amino acid. Moreover, we found some novel editing sites and several inaccurately annotated sites which may be functionally important, based on the highly conserved amino acids encoded by these edited codons. Finally, we annotated all 569 C-to-U RNA editing sites in their biological context. More precise information about C-to-U editing sites in rice mitochondria-encoded ORFs will facilitate our investigation on the function of C-to-U editing events in rice and also provide a valid benchmark from rice for the analysis of mitochondria C-to-U editing in other plant species.
Highlights
RNA editing is an essential post-transcriptional biological process that changes the nucleotide sequence of a primary transcript, making the genetic information in RNA different from that of the DNA template
Cytidine to uridine (C-to-U) editing sites in the rice mitochondria-encoded open reading frames (ORFs) were first detected in rice leaves by Sanger sequencing
RNA editing was first identified as C-to-U conversions in mitochondrial mRNA for
Summary
RNA editing is an essential post-transcriptional biological process that changes the nucleotide sequence of a primary transcript, making the genetic information in RNA different from that of the DNA template. The term RNA editing was introduced for the first time in 1986 to describe the addition and deletion of uridine nucleotides to and from mRNAs in the kinetoplast, the specialized mitochondrion of trypanosomes [1]. RNA editing has been found in a wide range of organisms, including basal eukaryotes, land plants, vertebrates, fungi, and viruses as well [2]. RNA modifications due to RNA editing comprise nucleotide insertions/deletions or substitutions that can occur in the nucleus, in the cytoplasm, as well as in organelles (plastids and mitochondria) [3]. RNA editing in plant organelles occurs mainly in the form of cytidine to uridine (C-to-U). Conversion, other types of RNA editing including the opposite U-to-C alteration has been seen especially in chloroplasts RNAs of some taxa of land plants [4].
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