Current Genetics

, Volume 56, Issue 2, pp 189–201 | Cite as

Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature

  • Henning Lenz
  • Mareike Rüdinger
  • Ute Volkmar
  • Simon Fischer
  • Stefan Herres
  • Felix Grewe
  • Volker Knoop
Technical Note


Transcripts in mitochondria and chloroplasts of land plants are modified through RNA editing, the exchanges of pyrimidines—a post-transcriptional process that may affect more than 1,000 sites in the mitochondrial transcriptomes of some plant species. RNA editing mainly acts as a correcting mechanism to re-create evolutionary conserved coding sequences on mRNA level and can be reasonably well predicted in new plant organelle gene sequence data. Identification and annotation of RNA editing sites is cumbersome and error-prone for larger data sets or organelle sequences subject to highly frequent RNA editing. We here present PREPACT, WWW-accessible at, which allows prediction, analysis, annotation and graphical display of RNA editing sites for both directions of pyrimidine exchanges, using the recently proposed RNA editing nomenclature. PREPACT offers prediction of RNA editing, analysis of partial editing in cDNA pools and a BLASTX mode for simultaneous prediction of genes and RNA editing sites in novel sequences. Output options include (i) lists and annotations of RNA editing sites, (ii) sequence alignments with user-controlled color highlighting of editings, (iii) graphical displays of RNA editing in sequences and alignments. Finally, binary matrices of editing positions can be produced that may be used for downstream (e.g. phylogenetic) analyses.


RNA editing Pyrimidine exchanges Sequence analysis Plant organelles Mitochondria Chloroplasts 



We are very grateful to our colleagues of the Fachgruppe Informatik—Mike Follwerk, Rainer Manthey and Armin B. Cremers—for support with the computer infrastructure.


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402CrossRefPubMedGoogle Scholar
  3. Carrillo C, Bonen L (1997) RNA editing status of nad7 intron domains in wheat mitochondria. Nucleic Acids Res 25:403–409CrossRefPubMedGoogle Scholar
  4. Chaw SM, Chun-Chieh SA, Wang D, Wu YW, Liu SM, Chou TY (2008) The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. Mol Biol Evol 25:603–615CrossRefPubMedGoogle Scholar
  5. Covello PS, Gray MW (1989) RNA editing in plant mitochondria. Nature 341:662–666CrossRefPubMedGoogle Scholar
  6. Du P, Li Y (2008) Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information. J Theor Biol 253:579–586CrossRefPubMedGoogle Scholar
  7. Freyer R, Kiefer-Meyer M-C, Kössel H (1997) Occurrence of plastid RNA editing in all major lineages of land plants. Proc Natl Acad Sci USA 94:6285–6290CrossRefPubMedGoogle Scholar
  8. Giegé P, Brennicke A (1999) RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci USA 96:15324–15329CrossRefPubMedGoogle Scholar
  9. Grewe F, Viehoever P, Weisshaar B, Knoop V (2009) A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii. Nucleic Acids Res 37:5093–5104CrossRefPubMedGoogle Scholar
  10. Groth-Malonek M, Wahrmund U, Polsakiewicz M, Knoop V (2007) Evolution of a pseudogene: exclusive survival of a functional mitochondrial nad7 gene supports Haplomitrium as the earliest liverwort lineage and proposes a secondary loss of RNA editing in Marchantiidae. Mol Biol Evol 24:1068–1074CrossRefPubMedGoogle Scholar
  11. Gualberto JM, Lamattina L, Bonnard G, Weil JH, Grienenberger JM (1989) RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature 341:660–662CrossRefPubMedGoogle Scholar
  12. Gualberto JM, Weil JH, Grienenberger JM (1990) Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites. Nucleic Acids Res 18:3771–3776CrossRefPubMedGoogle Scholar
  13. Hammani K, Okuda K, Tanz SK, Chateigner-Boutin AL, Shikanai T, Small I (2009) A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites. Plant Cell. doi: 10.1105/tpc.109.071472
  14. Handa H (2003) 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 31:5907–5916CrossRefPubMedGoogle Scholar
  15. Hiesel R, Wissinger B, Schuster W, Brennicke A (1989) RNA editing in plant mitochondria. Science 246:1632–1634CrossRefPubMedGoogle Scholar
  16. Hoch B, Maier RM, Appel K, Igloi GL, Kössel H (1991) Editing of a chloroplast mRNA by creation of an initiation codon. Nature 353:178–180CrossRefPubMedGoogle Scholar
  17. Kim SR, Yang JI, Moon S, Ryu CH, An K, Kim KM, Yim J, An G (2009) Rice OGR1 encodes a pentatricopeptide repeat-DYW protein and is essential for RNA editing in mitochondria. Pl J 59:738–749CrossRefGoogle Scholar
  18. Kotera E, Tasaka M, Shikanai T (2005) A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 433:326–330CrossRefPubMedGoogle Scholar
  19. Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, Yoshinaga K (2003) RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res 31:2417–2423CrossRefPubMedGoogle Scholar
  20. Lamattina L, Weil JH, Grienenberger JM (1989) RNA editing at a splicing site of NADH dehydrogenase subunit IV gene transcript in wheat mitochondria. FEBS Lett 258:79–83CrossRefPubMedGoogle Scholar
  21. Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, Szurek B, Taconnat L, Small I (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16:2089–2103CrossRefPubMedGoogle Scholar
  22. Malek O, Lättig K, Hiesel R, Brennicke A, Knoop V (1996) RNA editing in bryophytes and a molecular phylogeny of land plants. EMBO J 15:1403–1411PubMedGoogle Scholar
  23. Mower JP (2005) PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinform 6:96CrossRefGoogle Scholar
  24. Mower JP (2009) The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic Acids Res 37:W253–W259CrossRefPubMedGoogle Scholar
  25. Mower JP, Palmer JD (2006) Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genom 276:285–293CrossRefGoogle Scholar
  26. Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T, Ohyama K (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J Mol Biol 223:1–7CrossRefPubMedGoogle Scholar
  27. Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S, Inokuchi H, Ozeki H (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572–574CrossRefGoogle Scholar
  28. Picardi E, Quagliariello C (2006) EdiPy: a resource to simulate the evolution of plant mitochondrial genes under the RNA editing. Comput Biol Chem 30:77–80CrossRefPubMedGoogle Scholar
  29. Picardi E, Regina TM, Brennicke A, Quagliariello C (2007) REDIdb: the RNA editing database. Nucleic Acids Res 35:D173–D177CrossRefPubMedGoogle Scholar
  30. Rüdinger M, Polsakiewicz M, Knoop V (2008) Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat (PPR) proteins in jungermanniid but not in marchantiid liverworts. Mol Biol Evol 25:1405–1414CrossRefPubMedGoogle Scholar
  31. Rüdinger M, Funk HT, Rensing SA, Maier UG, Knoop V (2009) RNA editing: 11 sites only in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Mol Genet Genom 281:473–481CrossRefGoogle Scholar
  32. Salone V, Rüdinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M, Szurek B, Small I, Knoop V, Lurin C (2007) A hypothesis on the identification of the editing enzyme in plant organelles. FEBS Lett 581:4132–4138CrossRefPubMedGoogle Scholar
  33. Schuster W, Brennicke A (1991) 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 19:6923–6928CrossRefPubMedGoogle Scholar
  34. Schuster W, Hiesel R, Wissinger B, Brennicke A (1990) RNA editing in the cytochrome b locus of the higher plant Oenothera berteriana includes a U-to-C transition. Mol Cell Biol 10:2428–2431PubMedGoogle Scholar
  35. Small ID, Peeters N (2000) The PPR motif—a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 25:46–47CrossRefPubMedGoogle Scholar
  36. Steinhauser S, Beckert S, Capesius I, Malek O, Knoop V (1999) Plant mitochondrial RNA editing: extreme in hornworts and dividing the liverworts? J Mol Evol 48:303–312CrossRefPubMedGoogle Scholar
  37. Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, Fujiwara M, Sato N (2006) The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol Biol Evol 24:699–709CrossRefPubMedGoogle Scholar
  38. Turmel M, Otis C, Lemieux C (2002) The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc Natl Acad Sci USA 99:11275–11280CrossRefPubMedGoogle Scholar
  39. Turmel M, Otis C, Lemieux C (2003) The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants. Plant Cell 15:1888–1903CrossRefPubMedGoogle Scholar
  40. Turmel M, Otis C, Lemieux C (2006) The chloroplast genome sequence of Chara vulgaris sheds new light into the closest green algal relatives of land plants. Mol Biol Evol 23:1324–1338CrossRefPubMedGoogle Scholar
  41. Vangerow S, Teerkorn T, Knoop V (1999) Phylogenetic information in the mitochondrial nad5 gene of pteridophytes: RNA editing and intron sequences. Plant Biol 1:235–243CrossRefGoogle Scholar
  42. Verbitskiy D, Zehrmann A, van der Merwe JA, BrennickeA, Takenaka M (2009) The PPR-protein encoded by the LOVASTATIN INSENSITIVE 1 gene is involved in RNA editing at three sites in mitochondria of Arabidopsis thaliana. Plant J. doi: 10.1111/j.1365-313X.2009.04076.x
  43. Wolf PG, Rowe CA, Hasebe M (2004) High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris. Gene 339:89–97CrossRefPubMedGoogle Scholar
  44. Yoshinaga K, Iinuma H, Masuzawa T, Uedal K (1996) Extensive RNA editing of U to C in addition to C to U substitution in the rbcL transcripts of hornwort chloroplasts and the origin of RNA editing in green plants. Nucleic Acids Res 24:1008–1014CrossRefPubMedGoogle Scholar
  45. Zehrmann A, van der Merwe JA, Verbitskiy D, Brennicke A, Takenaka M (2008) Seven large variations in the extent of RNA editing in plant mitochondria between three ecotypes of Arabidopsis thaliana. Mitochondrion 8:319–327CrossRefPubMedGoogle Scholar
  46. Zehrmann A, Verbitskiy D, van der Merwe JA, Brennicke A, Takenaka M (2009) A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana. Plant Cell 21:558–567CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Henning Lenz
    • 1
  • Mareike Rüdinger
    • 1
  • Ute Volkmar
    • 1
  • Simon Fischer
    • 1
  • Stefan Herres
    • 1
  • Felix Grewe
    • 1
  • Volker Knoop
    • 1
  1. 1.Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik (IZMB)Universität BonnBonnGermany

Personalised recommendations