Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris
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RNA editing is a process that modifies the information in transcripts of almost all angiosperm mitochondrial protein-coding genes. In order to determine the frequency and distribution of mitochondrial RNA editing in Beta vulgaris, cDNAs were sequenced and compared to the published genome sequence. 357 C to U conversions were identified across the 31 known protein genes and pseudogenes in Beta, the fewest so far for a plant mitochondrial genome. Editing patterns in the putative gene orf518 indicate that it is most likely a functional ccmC homolog, indicating that patterns of editing can be a useful determinant of gene functionality. orf518 also contains a triplicated repeat region whose members are nearly identical yet differentially edited, most likely due to differences in the sequence context of the editing sites. In addition, we show that partial editing in Beta is common at silent editing sites but rare at nonsilent editing sites, extending previous observations to a complete plant mitochondrial genome. Finally, the degree of partial editing observed for certain genes was dependent on the choice of primers used, demonstrating that care must be taken when designing primers for use in editing studies.
KeywordsBeta vulgaris Plant mitochondria RNA editing Partial editing
We wish to thank the National Agricultural Research Center for Hokkaido Region (Hokkaido, Japan) for providing the seeds used in this study. This research was supported by NIH Grant R01-GM-70612 to JDP.
- Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K (2002) The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Genet Genomics 268:434–445PubMedCrossRefGoogle Scholar
- Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T, Ohyama K (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA: a primitive form of plant mitochondrial genome. J Mol Biol 223:1–7PubMedCrossRefGoogle Scholar
- Ohyama K, Oda K, Ohta E, Takemura M (1993) Gene organization and evolution of introns of a liverwort, Marchantia polymorpha, mitochondrial genome. In: Brennicke A, Kuck U (eds) Plant mitochondria. Verlag Chemie, Weinheim, pp 115–129Google Scholar
- Onodera Y, Yamamoto MP, Kubo T, Mikami T (1999) Heterogeneity of the atp6 presequences in normal and different sources of male-sterile cytoplasms of sugar beet. J Plant Physiol 155:656–660Google Scholar
- Satoh M, Kubo T, Nishizawa S, Estiati A, Itchoda N, Mikami T (2004) The cytoplasmic male-sterile type and normal type mitochondrial genomes of sugar beet share the same complement of genes of known function but differ in the content of expressed ORFs. Mol Genet Genomics 272:247–256PubMedCrossRefGoogle Scholar
- Siqueira SF, Dias SM, Hardouin P, Pereira FR, Lejeune B, de Souza AP (2002) Transcription of succinate dehydrogenase subunit 4 (sdh4) gene in potato: detection of extensive RNA editing and co-transcription with cytochrome oxidase subunit III (cox3) gene. Curr Genet 41:282–289PubMedCrossRefGoogle Scholar
- Sugiyama Y, Watase Y, Nagase M, Makita N, Yagura S, Hirai A, Sugiura M (2005) The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol Genet Genomics 272:603–615PubMedCrossRefGoogle Scholar
- Thomson MC, Macfarlane JL, Beagley CT, Wolstenholme DR (1994) RNA editing of mat-r transcripts in maize and soybean increases similarity of the encoded protein to fungal and bryophyte group II intron maturases: evidence that mat-r encodes a functional protein. Nucleic Acids Res 22:5745–5752PubMedCrossRefGoogle Scholar