October 2010, Volume 56, Issue 5, pp 439-446,
Open Access This content is freely available online to anyone, anywhere at any time.
Date: 09 Jul 2010
Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes
Sequence analysis of organelle genomes and comprehensive analysis of C-to-U editing sites from flowering and non-flowering plants have provided extensive sequence information from diverse taxa. This study includes the first comprehensive analysis of RNA editing sites from a gymnosperm mitochondrial genome, and utilizes informatics analyses to determine conserved features in the RNA sequence context around editing sites. We have identified 565 editing sites in 21 full-length and 4 partial cDNAs of the 39 protein-coding genes identified from the mitochondrial genome of Cycas taitungensis. The information profiles and RNA sequence context of C-to-U editing sites in the Cycas genome exhibit similarity in the immediate flanking nucleotides. Relative entropy analyses indicate that similar regions in the 5′ flanking 20 nucleotides have information content compared to angiosperm mitochondrial genomes. These results suggest that evolutionary constraints exist on the nucleotide sequences immediately adjacent to C-to-U editing sites, and similar regions are utilized in editing site recognition.
Communicated by R. Bock.
Cummings MP, Myers DS (2004) Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC Bioinform 5:132CrossRef
Mower JP (2005) PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinform 6:96CrossRef
Mower JP, Palmer JD (2006) Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genom 276:285–293CrossRef
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 Genom 268:434–445CrossRef
Okuda K, Chateigner-Boutin AL, Nakamura T, Delannoy E, Sugita M, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T (2009) Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts. Plant Cell 21:146–156CrossRefPubMed
Okuda K, Hammani K, Tanz SK, Peng L, Fukao Y, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T (2010) The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. Plant J 61:339–349
Palmer JD, Soltis DE, Chase MW (2004) The plant tree of life: an overview and some points of view. Am J Bot 91:1437–1445CrossRef
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049PubMed
- Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes
- Open Access
- Available under Open Access This content is freely available online to anyone, anywhere at any time.
Volume 56, Issue 5 , pp 439-446
- Cover Date
- Print ISSN
- Online ISSN
- Additional Links
- RNA editing
- Relative entropy
- Organelle evolution
- Industry Sectors
- Author Affiliations
- 1. Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697-2300, USA
- 2. Biodiversity Research Center, Academia Sinica, 128 Academy Road, Section 2, Taipei, 115, Taiwan
- 3. Institute of Information Science, Academia Sinica, 128 Academy Road, Section 2, Taipei, 115, Taiwan
- 4. School of Informatics and Computing, Indiana University, Bloomington, IN, 47405-7000, USA