PREPACT 2.0: Predicting C-to-U and U-to-C RNA editing in organelle genome sequences with multiple references and curated RNA editing annotation

Bioinformatics and Biology Insights

Volumn 7, Issue , 2013, Pages

  Lenz, Henning ^a   Knoop, Volker ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

Blastx; Chloroplast DNA; Mitochondrial DNA; Plants; Protists; Pyrimidine substitutions; RNA editing prediction

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; BIOINFORMATICS; CELL ORGANELLE; CHLOROPLAST GENOME; COMPUTER PREDICTION; COMPUTER PROGRAM; DATA BASE; DNA SEQUENCE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MITOCHONDRIAL GENOME; NUCLEOTIDE SEQUENCE; PLANT GENOME; REFERENCE DATABASE; RNA EDITING; RNA SEQUENCE; STOP CODON;

PROTISTA; VASCONCELLEA CANDICANS;

EID: 84872537549     PISSN: 11779322     EISSN: None     Source Type: Journal    
DOI: 10.4137/BBI.S11059     Document Type: Article

References (53)

1. Benne R, Van Den Burg J, Brakenhoff JP, Sloof P, Van Boom JH, Tromp MC. Major transcript of the frameshifted coxII gene from trypanosome mitochon- dria contains four nucleotides that are not encoded in the DNA. Cell. 1986; 46(6):819-826.
2. Knoop V. When you can't trust the DNA: RNA editing changes transcript sequences. Cell Mol Life Sci. 2011;68(4):567-586.
3. Bundschuh R, Altmüller J, Becker C, Nürnberg P, Gott JM. Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA. Nucleic Acids Res. 2011; 39(14):6044-6055.
4. Hecht J, Grewe F, Knoop V. Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffi mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes. Genome Biol Evol. 2011;3:344-358.
5. Grewe F, Herres S, Viehöver P, Polsakiewicz M, Weisshaar B, Knoop V. A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucl Acids Res. 2011;39(7):2890-2902.
6. Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, Yoshinaga K. RNA edit- ing in hornwort chloroplasts makes more than half the genes functional. Nucl Acids Res. 2003;31(9):2417-2423.
7. Rüdinger M, Fritz-Laylin L, Polsakiewicz M, Knoop V. Plant-type mito- chondrial RNA editing in the protist Naegleria gruberi. RNA. 2011;17(12): 2058-2062.
8. Knoop V, Rüdinger M. DYW-type PPR proteins in a heterolobosean protist: plant RNA editing factors involved in an ancient horizontal gene transfer? FEBS Lett. 2010;584(20):4287-4291.
9. Lenz H, Rüdinger M, Volkmar U, et al. Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature. Curr Genet. 2010;56(2):189-201.
10. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local align- ment search tool. J Mol Biol. 1990;215(3):403-410.
11. Altschul SF, Madden TL, Schaffer AA, et al. Gapped BLAST and PSI- BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-3402.
12. Rüdinger M, Funk HT, Rensing SA, Maier UG, Knoop V. RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Mol Genet Genom. 2009;281(5):473-481.
13. Picardi E, Regina TM, Verbitskiy D, Brennicke A, Quagliariello C. REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites. Mito- chondrion. 2011;11(2):360-365.
14. Knoop V. The mitochondrial DNA of land plants: peculiarities in phyloge- netic perspective. Curr Genet. 2004;46(3):123-139.
15. Lang BF, Burger G, O'Kelly CJ, Cedergren R, Golding GB, Lemieux C, et al. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature. 1997;387(6632):493-497.
16. Wakasugi T, Hirose T, Horihata M, Tsudzuki T, Kössel 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 U S A. 1996;93(16): 8766-8770.
17. Salmans ML, Chaw SM, Lin CP, Shih AC, Wu YW, Mulligan RM. Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes. Curr Genet. 2010;56(5): 439-446.
18. Fang Y, Wu H, Zhang T, et al. A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS One. 2012;7(5):e37164.
19. Liu Y, Xue JY, Wang B, Li L, Qiu YL. The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: dynamic and conservative evolution. PLoS One. 2011;6(10):e25836.
20. Groth-Malonek M, Wahrmund U, Polsakiewicz M, Knoop V. Evolution of a pseudogene: exclusive survival of a functional mitochondrial nad7 gene supports Haplomitrium as the earliest liverwort lineage and proposes a sec- ondary loss of RNA editing in Marchantiidae. Mol Biol Evol. 2007;24(4): 1068-1074.
21. Rüdinger M, Volkmar U, Lenz H, Groth-Malonek M, Knoop V. Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria. J Mol Evol. 2012;74(1-2): 37-51.
22. Miyata Y, Sugiura C, Kobayashi Y, Hagiwara M, Sugita M. Chloroplast ribosomal S14 protein transcript is edited to create a translation initiation codon in the moss Physcomitrella patens. Biochim Biophys Acta. 2002; 1576(3):346-349.
23. Miyata Y, Sugita M. Tissue- and stage-specifc RNA editing of rps14 transcripts in moss (Physcomitrella patens) chloroplasts. J Plant Physiol. 2004;161(1):113-115.
24. Gray MW. Evolutionary origin of RNA editing. Biochemistry. 2012; 51(26):5235-5242.
25. Kotera E, Tasaka M, Shikanai T. A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature. 2005;433(7023):326-330.
26. Zehrmann A, Verbitskiy D, van der Merwe JA, Brennicke A, Takenaka M. A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana. Plant Cell. 2009;21(2):558-567.
27. Salone V, Rüdinger M, Polsakiewicz M, et al. A hypothesis on the identif- cation of the editing enzyme in plant organelles. FEBS Lett. 2007;581(22): 4132-4138.
28. Barkan A, Rojas M, Fujii S, et al. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet. 2012;8(8): e1002910.
29. Mower JP. PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics. 2005;6:96.
30. Du P, Jia L, Li Y. CURE-Chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics. 2009;10:135.
31. Thompson J, Gopal S. Genetic algorithm learning as a robust approach to RNA editing site prediction. BMC Bioinformatics. 2006;7:145.
32. Du P, He T, Li Y. Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features. Biochem Biophys Res Commun. 2007;358(1):336-341.
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.
34. Cummings MP, Myers DS. Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC Bioinformatics. 2004;5:132.
35. Picardi E, Regina TM, Brennicke A, Quagliariello C. REDIdb: the RNA editing database. Nucl Acids Res. 2007;35(Database issue):D173-D177.
36. Mower JP. The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defned alignments. Nucl Acids Res. 2009;37(Web Server issue):W253-W259.
37. Schmitz-Linneweber C, Regel R, Du TG, Hupfer H, Herrmann RG, Maier RM. The plastid chromosome of Atropa belladonna and its compari- son 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.
38. Giegé 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.
39. Mower JP, Palmer JD. Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genom. 2006;276(3):285-293.
40. 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. Nucl Acids Res. 2003;31(20):5907-5916.
41. Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, Palmer JD. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol. 2010;27(6):1436-1448.
42. Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, et al. The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of fowering plants. Mol Genet Genom. 2002;268(4):434-445.
43. Sloan DB, MacQueen AH, Alverson AJ, Palmer JD, Taylor DR. Extensive loss of RNA editing sites in rapidly evolving silene mitochondrial genomes: selection vs. retroprocessing as the driving force. Genetics. 2010; 185(4):1369-1380.
44. Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G. Large- scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucl Acids Res. 2010;38(14):4755-4767.
45. 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.
46. Tillich M, Funk HT, Schmitz-Linneweber C, Poltnigg P, Sabater B, Martin M, et al. Editing of plastid RNA in Arabidopsis thaliana ecotypes. Plant J. 2005;43(5):708-715.
47. Tangphatsornruang S, Uthaipaisanwong P, Sangsrakru D, Chanprasert J, Yoocha T, Jomchai N et al. Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships. Gene. 2011;475(2):104-112.
48. Sasaki T, Yukawa Y, Miyamoto T, Obokata J, Sugiura M. Identifcation 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. 2003;20(7):1028-1035.
49. 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.
50. Inada M, Sasaki T, Yukawa M, Tsudzuki T, Sugiura M. A systematic search for RNA editing sites in pea chloroplasts: an editing event causes diversifcation from the evolutionarily conserved amino acid sequence. Plant Cell Physiol. 2004;45(11):1615-1622.
51. 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.
52. Tsudzuki T, Wakasugi T, Sugiura M. Comparative analysis of RNA editing sites in higher plant chloroplasts. J Mol Evol. 2001;53(4-5):327-332.
53. Maier RM, Zeltz P, Kössel H, Bonnard G, Gualberto JM, Grienenberger JM. RNA editing in plant mitochondria and chloroplasts. Plant Mol Biol. 1996;32(1-2):343-365.