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2012
Y. Jiang, Fan, S. L., Song, M. Z., Yu, J. N., and Yu, S. X., Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures, vol. 11, pp. 987-1001, 2012.
Bock R (2000). Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing. Biochimie 82: 549-557. http://dx.doi.org/10.1016/S0300-9084(00)00610-6 Bock R (2001). RNA Editing in Plant Mitochondria and Chloroplasts. In: RNA Editing (Bass BL, ed.). Oxford University Press, Oxford, 38-60. Cai W, Ji D, Peng L, Guo J, et al. (2009). LPA66 is required for editing psbF chloroplast transcripts in Arabidopsis. Plant Physiol. 150: 1260-1271. http://dx.doi.org/10.1104/pp.109.136812 PMid:19448041    PMCid:2705037 Calsa JT, Carraro DM, Benatti MR, Barbosa AC, et al. (2004). Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome. Curr. Genet. 46: 366-373. http://dx.doi.org/10.1007/s00294-004-0542-4 PMid:15526204 Chateigner-Boutin AL, Ramos-Vega M, Guevara-Garcia A, Andres C, et al. (2008). CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts. Plant J. 56: 590-602. http://dx.doi.org/10.1111/j.1365-313X.2008.03634.x PMid:18657233 Chou PY and Fasman GD (1978). Prediction of the secondary structure of proteins from their amino acid sequence. Adv. Enzymol. Relat. Areas Mol. Biol. 47: 45-148. PMid:364941 Corneille S, Lutz K and Maliga P (2000). Conservation of RNA editing between rice and maize plastids: are most editing events dispensable? Mol. Gen. Genet. 264: 419-424. http://dx.doi.org/10.1007/s004380000295 Fiebig A, Stegemann S and Bock R (2004). Rapid evolution of RNA editing sites in a small non-essential plastid gene. Nucleic Acids Res. 32: 3615-3622. http://dx.doi.org/10.1093/nar/gkh695 PMid:15240834    PMCid:484182 Gray MW and Covello PS (1993). RNA editing in plant mitochondria and chloroplasts. FASEB J. 7: 64-71. PMid:8422976 Guzowska-Nowowiejska M, Fiedorowicz E and Plader W (2009). Cucumber, melon, pumpkin, and squash: are rules of editing in flowering plants chloroplast genes so well known indeed? Gene 434: 1-8. http://dx.doi.org/10.1016/j.gene.2008.12.017 PMid:19162145 Hammani K, Okuda K, Tanz SK, Chateigner-Boutin AL, et al. (2009). A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites. Plant Cell 21: 3686-3699. http://dx.doi.org/10.1105/tpc.109.071472 PMid:19934379    PMCid:2798323 Häder DP and Sinha RP (2005). Solar ultraviolet radiation-induced DNA damage in aquatic organisms: potential environmental impact. Mutat. Res. 571: 221-233. http://dx.doi.org/10.1016/j.mrfmmm.2004.11.017 PMid:15748649 Hoch B, Maier RM, Appel K, Igloi GL, et al. (1991). Editing of a chloroplast mRNA by creation of an initiation codon. Nature 353: 178-180. http://dx.doi.org/10.1038/353178a0 PMid:1653905 Inada M, Sasaki T, Yukawa M, Tsudzuki T, et al. (2004). A systematic search for RNA editing sites in pea chloroplasts: an editing event causes diversification from the evolutionarily conserved amino acid sequence. Plant Cell Physiol. 45: 1615-1622. http://dx.doi.org/10.1093/pcp/pch191 PMid:15574837 Jiang Y, Yu J, Yao Y, Song M, et al. (2010). Research progress of cotton chloroplast genome. Cotton Sci. 22: 495-500. Kahlau S, Aspinall S, Gray JC and Bock R (2006). Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J. Mol. Evol. 63: 194-207. http://dx.doi.org/10.1007/s00239-005-0254-5 PMid:16830097 Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, et al. (2003). RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res. 31: 2417-2423. http://dx.doi.org/10.1093/nar/gkg327 PMid:12711687    PMCid:154213 Lee SB, Kaittanis C, Jansen RK, Hostetler JB, et al. (2006). The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7: 61. http://dx.doi.org/10.1186/1471-2164-7-61 PMid:16553962    PMCid:1513215 Lutz KA and Maliga P (2001). Lack of conservation of editing sites in mRNAs that encode subunits of the NAD(P)H dehydrogenase complex in plastids and mitochondria of Arabidopsis thaliana. Curr. Genet. 40: 214-219. http://dx.doi.org/10.1007/s002940100242 PMid:11727998 Maier RM, Neckermann K, Igloi GL and Kössel H (1995). Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251: 614- 628. http://dx.doi.org/10.1006/jmbi.1995.0460 PMid:7666415 Miyata Y and Sugita M (2004). Tissue- and stage-specific RNA editing of rps 14 transcripts in moss (Physcomitrella patens) chloroplasts. J. Plant Physiol. 161: 113-115. http://dx.doi.org/10.1078/0176-1617-01220 PMid:15002671 Okuda K, Myouga F, Motohashi R, Shinozaki K, et al. (2007). Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing. Proc. Natl. Acad. Sci. U. S. A. 104: 8178-8183. http://dx.doi.org/10.1073/pnas.0700865104 PMid:17483454    PMCid:1876591 Okuda K, Chateigner-Boutin AL, Nakamura T, Delannoy E, et al. (2009). Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts. Plant Cell 21: 146-156. http://dx.doi.org/10.1105/tpc.108.064667 PMid:19182104    PMCid:2648089 Okuda K, Hammani K, Tanz SK, Peng L, et al. (2010). The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. Plant J. 61: 339-349. http://dx.doi.org/10.1111/j.1365-313X.2009.04059.x PMid:19845878 Robbins JC, Heller WP and Hanson MR (2009). A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript. RNA 15: 1142-1153. http://dx.doi.org/10.1261/rna.1533909 PMid:19395655    PMCid:2685521 Sasaki T, Yukawa Y, Miyamoto T, Obokata J, et al. (2003). Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): comparative analysis shows the involvement of distinct trans-factors for ndhB editing. Mol. Biol. Evol. 20: 1028-1035. http://dx.doi.org/10.1093/molbev/msg098 PMid:12716996 Sasaki T, Yukawa Y, Wakasugi T, Yamada K, et al. (2006). A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcripts. Plant J. 47: 802-810. http://dx.doi.org/10.1111/j.1365-313X.2006.02825.x PMid:16856984 Sasaki Y and Nagano Y (2004). Plant acetyl-CoA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding. Biosci. Biotechnol. Biochem. 68: 1175-1184. http://dx.doi.org/10.1271/bbb.68.1175 PMid:15215578 Sasaki Y, Kozaki A, Ohmori A, Iguchi H, et al. (2001). Chloroplast RNA editing required for functional acetyl-CoA carboxylase in plants. J. Biol. Chem. 276: 3937-3940. http://dx.doi.org/10.1074/jbc.M008166200 PMid:11078738 Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, et al. (2002). The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol. Biol. Evol. 19: 1602-1612. http://dx.doi.org/10.1093/oxfordjournals.molbev.a004222 PMid:12200487 Schmitz-Linneweber C, Kushnir S, Babiychuk E, Poltnigg P, et al. (2005). Pigment deficiency in nightshade/tobacco cybrids is caused by the failure to edit the plastid ATPase alpha-subunit mRNA. Plant Cell 17: 1815-1828. http://dx.doi.org/10.1105/tpc.105.032474 PMid:15894714    PMCid:1143079 Shikanai T (2006). RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol. Life Sci. 63: 698-708. http://dx.doi.org/10.1007/s00018-005-5449-9 PMid:16465445 Wakasugi T, Hirose T, Horihata M, Tsudzuki T, et al. (1996). Creation of a novel protein-coding region at the RNA level in black pine chloroplasts: the pattern of RNA editing in the gymnosperm chloroplast is different from that in angiosperms. Proc. Natl. Acad. Sci. U. S. A. 93: 8766-8770. http://dx.doi.org/10.1073/pnas.93.16.8766 Wolf PG, Rowe CA and Hasebe M (2004). High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris. Gene 339: 89-97. http://dx.doi.org/10.1016/j.gene.2004.06.018 PMid:15363849 Yu QB, Jiang Y, Chong K and Yang ZN (2009). AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana. Plant J. 59: 1011-1023. http://dx.doi.org/10.1111/j.1365-313X.2009.03930.x PMid:19500301 Yura K and Go M (2008). Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles. BMC Plant Biol. 8: 79. http://dx.doi.org/10.1186/1471-2229-8-79 PMid:18631376    PMCid:2488346 Yura K, Sulaiman S, Hatta Y, Shionyu M, et al. (2009). RESOPS: A database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures. Plant Cell Physiol. 50: 1865-1873. http://dx.doi.org/10.1093/pcp/pcp132 PMid:19808808    PMCid:2775959 Zeng WH, Liao SC and Chang CC (2007). Identification of RNA editing sites in chloroplast transcripts of Phalaenopsis aphrodite and comparative analysis with those of other seed plants. Plant Cell Physiol. 48: 362-368. http://dx.doi.org/10.1093/pcp/pcl058 PMid:17169923 Zhou W, Cheng Y, Yap A, Chateigner-Boutin AL, et al. (2009). The Arabidopsis gene YS1 encoding a DYW protein is required for editing of rpoB transcripts and the rapid development of chloroplasts during early growth. Plant J. 58: 82-96. http://dx.doi.org/10.1111/j.1365-313X.2008.03766.x PMid:19054358 Zito F, Kuras R, Choquet Y, Koessel H, et al. (1997). Mutations of cytochrome b6 in Chlamydomonas reinhardtii disclose the functional significance for a proline to leucine conversion by petB editing in maize and tobacco. Plant Mol. Biol. 33: 79-86. http://dx.doi.org/10.1023/A:1005734809834 PMid:9037161