RNA Editing Sites Exist in Protein-coding Genes in the Chloroplast Genome of Cycas taitungensis

• Published in: Journal of integrative plant biology 2011-12, Vol.53 (12), p.961-970
• Main Authors: Chen, Haiyan, Deng, Likun, Jiang, Yuan, Lu, Ping, Yu, Jianing
• Format: Article
• Language: English
• Subjects: Amino Acids - metabolism; Base Sequence; chloroplasts; codons; Cycas; Cycas - genetics; Cycas taitungensis; embryophytes; evolution; genes; Genes, Chloroplast - genetics; Genes, Plant - genetics; Genome, Chloroplast - genetics; Hydrophobic and Hydrophilic Interactions; mitochondria; Mitochondria - genetics; Mitochondrial Proteins - genetics; ndh genes; Open Reading Frames - genetics; post-transcriptional modification; prediction; proline; protein structure; ribonucleotides; RNA editing; RNA Editing - genetics; RNA编辑; serine; Species Specificity; 台东苏铁; 叶绿体基因组; 密码子; 种子植物; 站点; 线粒体蛋白质; 蛋白编码基因
• ISSN: 1672-9072; 1744-7909
• DOI: 10.1111/j.1744-7909.2011.01082.x

RNA editing is a post‐transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C‐to‐U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein‐coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position. ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein‐coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed.