Identification of RNA editing sites in cotton (Gossypium hirsutum) chloroplasts and editing events that affect secondary and three-dimensional protein structures

Genetics and Molecular Research

Volumn 11, Issue 2, 2012, Pages 987-1001

  Jiang, Y ^a   Fan, S L ^b   Song, M Z ^b   Yu, J N ^a   Yu, S X ^b  

^a SHAANXI NORMAL UNIVERSITY   (China)

^b Cotton Research Institute of the Chinese Academy of Agricultural Sciences ^*  (China)

Author keywords

Chloroplast; Gossypium hirsutum (cotton); Protein structures; RESOPS; RNA editing

Indexed keywords

ARTICLE; CHLOROPLAST; CODON; GOSSYPIUM HIRSUTUM; HYDROPHILICITY; HYDROPHOBICITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; RNA EDITING; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; SPECIES COMPARISON;

EID: 84930486118     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: 10.4238/2012.April.19.4     Document Type: Article

References (40)

1. Bock R (2000). Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing. Biochimie 82: 549-557.
2. Bock R (2001). RNA Editing in Plant Mitochondria and Chloroplasts. In: RNA Editing (Bass BL, ed.). Oxford University Press, Oxford, 38-60.
3. 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.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. Gray MW and Covello PS (1993). RNA editing in plant mitochondria and chloroplasts. FASEB J. 7: 64-71.
10. 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.
11. 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.
12. Häder DP and Sinha RP (2005). Solar ultraviolet radiation-induced DNA damage in aquatic organisms: potential environmental impact. Mutat. Res. 571: 221-233.
13. 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.
14. 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.
15. Jiang Y, Yu J, Yao Y, Song M, et al. (2010). Research progress of cotton chloroplast genome. Cotton Sci. 22: 495-500.
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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.
22. 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.
23. 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.
24. 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.
25. 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.
26. 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.
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. Shikanai T (2006). RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol. Life Sci. 63: 698-708.
33. 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.
34. 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.
35. 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.
36. 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.
37. 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.
38. 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.
39. 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.
40. 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.