CURE-chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Du, Pufeng ^a   Jia, Liyan ^a   Li, Yanda ^a  

^a TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CHLOROPLAST GENOME; IN-VIVO; ON-LINE SERVICE; PLANT MITOCHONDRIA; POST-TRANSCRIPTIONAL MODIFICATION; RNA EDITING; SEED PLANTS; TRANSCRIPTOMES;

ALGORITHMS; CURING; FORECASTING; MITOCHONDRIA; RNA;

SEED;

MITOCHONDRIAL RNA; CHLOROPLAST RNA; PLANT RNA;

ACCURACY; ALGORITHM; ARTICLE; CHLOROPLAST; COMPUTER PROGRAM; GENE SEQUENCE; INTERNET; ONLINE SYSTEM; PLANT GENE; PLANT SEED; PREDICTION; RNA ANALYSIS; RNA EDITING; SENSITIVITY AND SPECIFICITY; CHEMISTRY; GENETIC DATABASE; GENETICS; METABOLISM; MITOCHONDRION; PLANT;

SPERMATOPHYTA;

ALGORITHMS; DATABASES, GENETIC; MITOCHONDRIA; PLANTS; RNA EDITING; RNA, CHLOROPLAST; RNA, PLANT; SEEDS;

EID: 66449105849     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-135     Document Type: Article

References (46)

1. Mulligan RM Williams MA Shanahan MT RNA editing site recognition in higher plant mitochondria J Hered 1999, 90(3):338-344 10.1093/jhered/ 90.3.338 10355119
2. Rajasekhar VK Mulligan RM RNA Editing in Plant Mitochondria: [alpha]-Phosphate Is Retained during C-to-U Conversion in mRNAs Plant Cell 1993, 5(12):1843-1852 160409 12271058 10.1105/tpc.5.12.1843
3. Yu W Schuster W Evidence for a site-specific cytidine deamination reaction involved in C to U RNA editing of plant mitochondria J Biol Chem 1995, 270(31):18227-18233 10.1074/jbc.270.31.18227 7629140
4. Giege P Brennicke A RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs Proc Natl Acad Sci USA 1999, 96(26):15324-15329 24818 10611383 10.1073/pnas.96.26.15324
5. Handa H The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): Comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana Nucleic Acids Res 2003, 31(20):5907-5916 219474 14530439 10.1093/nar/gkg795
6. Notsu Y Masood S Nishikawa T Kubo N Akiduki G Nakazono M Hirai A Kadowaki K 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 2002, 268(4):434-445 10.1007/s00438-002-0767-1 12471441
7. Mower JP Palmer JD Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris Mol Genet Genomics 2006, 276(3):285-293 10.1007/ s00438-006-0139-3 16862402
8. Maier RM Neckermann K Igloi GL Kossel H Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing J Mol Biol 1995, 251(5):614-628 10.1006/jmbi.1995.0460 7666415
9. Wakasugi T Hirose T Horihata M Tsudzuki T Kossel H Sugiura M 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 USA 1996, 93(16):8766-8770 38748 8710946 10.1073/pnas.93.16.8766
10. Hirose T Kusumegi T Tsudzuki T Sugiura M RNA editing sites in tobacco chloroplast transcripts: Editing as a possible regulator of chloroplast RNA polymerase activity Mol Gen Genet 1999, 262(3):462-467 10.1007/ s004380051106 10589833
11. Schmitz-Linneweber C Regel R Du TG Hupfer H Herrmann RG Maier RM 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 2002, 19(9):1602-1612 12200487
12. Tillich M Funk HT Schmitz-Linneweber C Poltnigg P Sabater B Martin M Maier RM Editing of plastid RNA in Arabidopsis thaliana ecotypes Plant J 2005, 43(5):708-715 10.1111/j.1365-313X.2005.02484.x 16115067
13. Covello PS Gray MW RNA editing in plant mitochondria Nature 1989, 341(6243):662-666 10.1038/341662a0 2552326
14. Gualberto JM Lamattina L Bonnard G Weil JH Grienenberger JM RNA editing in wheat mitochondria results in the conservation of protein sequences Nature 1989, 341(6243):660-662 10.1038/341660a0 2552325
15. Hiesel R Wissinger B Schuster W Brennicke A RNA editing in plant mitochondria Science 1989, 246(4937):1632-1634 10.1126/science.2480644 2480644
16. Schuster W Brennicke A RNA editing makes mistakes in plant mitochondria: editing loses sense in transcripts of a rps19 pseudogene and in creating stop codons in coxI and rps3 mRNAs of Oenothera Nucleic Acids Res 1991, 19(24):6923-6928 329329 1762921 10.1093/nar/19.24.6923
17. Shikanai T RNA editing in plant organelles: Machinery, physiological function and evolution Cell Mol Life Sci 2006, 63(6):698-708 10.1007/ s00018-005-5449-9 16465445
18. Heller WP Hayes ML Hanson MR Cross-competition in editing of chloroplast RNA transcripts in vitro implicates sharing of trans-factors between different C targets J Biol Chem 2008, 283(12):7314-7319 2276328 18192271 10.1074/jbc.M709595200
19. Hayes ML Hanson MR Identification of a sequence motif critical for editing of a tobacco chloroplast transcript RNA 2007, 13(2):281-288 1781371 17158709 10.1261/rna.295607
20. Hayes ML Reed ML Hegeman CE Hanson MR Sequence elements critical for efficient RNA editing of a tobacco chloroplast transcript in vivo and in vitro Nucleic Acids Res 2006, 34(13):3742-3754 1557790 16893957 10.1093/ nar/gkl490
21. Chateigner-Boutin AL Hanson MR Developmental co-variation of RNA editing extent of plastid editing sites exhibiting similar cis-elements Nucleic Acids Res 2003, 31(10):2586-2594 156036 12736308 10.1093/nar/gkg354
22. Chateigner-Boutin AL Hanson MR Cross-competition in transgenic chloroplasts expressing single editing sites reveals shared cis elements Mol Cell Biol 2002, 22(24):8448-8456 139884 12446765 10.1128/ MCB.22.24.8448-8456.2002
23. Okuda K Myouga F Motohashi R Shinozaki K Shikanai T Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing Proc Natl Acad Sci USA 2007, 104(19):8178-8183 1876591 17483454 10.1073/pnas.0700865104
24. Kotera E Tasaka M Shikanai T A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts Nature 2005, 433(7023):326-330 10.1038/nature03229 15662426
25. de Longevialle AF Meyer EH Andres C Taylor NL Lurin C Millar AH Small ID The pentatricopeptide repeat gene OTP43 is required for trans-splicing of the mitochondrial nad1 Intron 1 in Arabidopsis thaliana Plant Cell 2007, 19(10):3256-3265 2174710 17965268 10.1105/tpc.107.054841
26. Rudinger M Polsakiewicz M Knoop V Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts Mol Biol Evol 2008, 25(7):1405-1414 10.1093/molbev/msn084 18400790
27. Miyamoto T Obokata J Sugiura M A site-specific factor interacts directly with its cognate RNA editing site in chloroplast transcripts Proc Natl Acad Sci USA 2004, 101(1):48-52 314136 14694196 10.1073/pnas.0307163101
28. Hirose T Sugiura M Involvement of a site-specific trans-acting factor and a common RNA-binding protein in the editing of chloroplast mRNAs: development of a chloroplast in vitro RNA editing system EMBO J 2001, 20(5):1144-1152 145495 11230137 10.1093/emboj/20.5.1144
29. Cummings MP Myers DS Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA BMC Bioinformatics 2004, 5:132 521485 15373947 10.1186/1471-2105-5-132
30. Thompson J Gopal S Correction: Genetic algorithm learning as a robust approach to RNA editing site prediction BMC Bioinformatics 2006, 7:406 1569880 16956416 10.1186/1471-2105-7-406
31. Thompson J Gopal S Genetic algorithm learning as a robust approach to RNA editing site prediction BMC Bioinformatics 2006, 7:145 1459874 16542417 10.1186/1471-2105-7-145
32. Mower JP PREP-Mt: Predictive RNA editor for plant mitochondrial genes BMC Bioinformatics 2005, 6:96 1087475 15826309 10.1186/1471-2105-6-96
33. Du P Li Y Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information J Theor Biol 2008, 253(3):579-586 10.1016/j.jtbi.2008.04.006 18511083
34. Yura K Miyata Y Arikawa T Higuchi M Sugita M Characteristics and prediction of RNA editing sites in transcripts of the Moss Takakia lepidozioides chloroplast DNA Res 2008, 15(5):309-321 2575889 18650260 10.1093/dnares/dsn016
35. Corneille S Lutz K Maliga P Conservation of RNA editing between rice and maize plastids: Are most editing events dispensable? Mol Gen Genet 2000, 264(4):419-424 10.1007/s004380000295 11129045
36. Calsa Junior T Carraro DM Benatti MR Barbosa AC Kitajima JP Carrer H Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome Curr Genet 2004, 46(6):366-373 10.1007/s00294-004-0542-4 15526204
37. Inada M Sasaki T Yukawa M Tsudzuki T Sugiura M 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 2004, 45(11):1615-1622 10.1093/pcp/pch191 15574837
38. Zeng WH Liao SC Chang CC Identification of RNA editing sites in chloroplast transcripts of Phalaenopsis aphrodite and comparative analysis with those of other seed plants Plant Cell Physiol 2007, 48(2):362-368 10.1093/pcp/pcl058 17169923
39. He T Du P Li Y dbRES: A web-oriented database for annotated RNA editing sites Nucleic Acids Res 2007, 35 Database D141-144 1781157 17088288 10.1093/nar/gkl815
40. Picardi E Regina TM Brennicke A Quagliariello C REDIdb: The RNA editing database Nucleic Acids Res 2007, 35 Database D173-177 1781140 17175530 10.1093/nar/gkl793
41. Hung J-H Wang W-C Huang H-D Systematic Identification and Repository of RNA Editing Site in Human Genome International Computer Symposium 2007:1386-1391
42. Blanchette M Kent WJ Riemer C Elnitski L Smit AF Roskin KM Baertsch R Rosenbloom K Clawson H Green ED et al Aligning multiple genomic sequences with the threaded blockset aligner Genome Res 2004, 14(4):708-715 383317 15060014 10.1101/gr.1933104
43. Funk HT Berg S Krupinska K Maier UG Krause K Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii BMC Plant Biol 2007, 7:45 2089061 17714582 10.1186/1471-2229-7-45
44. Wolf PG Rowe CA Hasebe M High levels of RNA editing in a vascular plant chloroplast genome: Analysis of transcripts from the fern Adiantum capillus-veneris Gene 2004, 339:89-97 10.1016/j.gene.2004.06.018 15363849
45. Kugita M Yamamoto Y Fujikawa T Matsumoto T Yoshinaga K RNA editing in hornwort chloroplasts makes more than half the genes functional Nucleic Acids Res 2003, 31(9):2417-2423 154213 12711687 10.1093/nar/gkg327
46. Tillich M Lehwark P Morton BR Maier UG The evolution of chloroplast RNA editing Mol Biol Evol 2006, 23(10):1912-1921 10.1093/molbev/msl054 16835291