A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii

Grewe F, Herres S, Viehöver P, Polsakiewicz M, Weisshaar B, Knoop V (2011)
Nucleic Acids Research 39(7): 2890-2902.

Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Autor
; ; ; ; ;
Abstract / Bemerkung
The analysis of the mitochondrial DNA of Isoetes engelmannii as a first representative of the lycophytes recently revealed very small introns and indications for extremely frequent RNA editing. To analyze functionality of intron splicing and the extent of RNA editing in I. engelmannii, we performed a comprehensive analysis of its mitochondrial transcriptome. All 30 groups I and II introns were found to be correctly removed, showing that intron size reduction does not impede splicing. We find that mRNA editing affects 1782 sites, which lead to a total of 1406 changes in codon meanings. This includes the removal of stop codons from 23 of the 25 mitochondrial protein encoding genes. Comprehensive sequence analysis of multiple cDNAs per locus allowed classification of partially edited sites as either inefficiently edited but relevant or as non-specifically edited at mostly low frequencies. Abundant RNA editing was also found to affect tRNAs in hitherto unseen frequency, taking place at 41 positions in tRNA-precursors, including the first identification of U-to-C exchanges in two tRNA species. We finally investigated the four group II introns of the nad7 gene and could identify 27 sites of editing, most of which improve base pairing for proper secondary structure formation.
Erscheinungsjahr
Zeitschriftentitel
Nucleic Acids Research
Band
39
Ausgabe
7
Seite(n)
2890-2902
ISSN
eISSN
PUB-ID

Zitieren

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. Nucleic Acids Research. 2011;39(7):2890-2902.
Grewe, F., Herres, S., Viehöver, P., Polsakiewicz, M., Weisshaar, B., & Knoop, V. (2011). A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Research, 39(7), 2890-2902. doi:10.1093/nar/gkq1227
Grewe, F., Herres, S., Viehöver, P., Polsakiewicz, M., Weisshaar, B., and Knoop, V. (2011). A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Research 39, 2890-2902.
Grewe, F., et al., 2011. A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Research, 39(7), p 2890-2902.
F. Grewe, et al., “A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii”, Nucleic Acids Research, vol. 39, 2011, pp. 2890-2902.
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. Nucleic Acids Research. 39, 2890-2902 (2011).
Grewe, Felix, Herres, Stefan, Viehöver, Prisca, Polsakiewicz, Monika, Weisshaar, Bernd, and Knoop, Volker. “A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii”. Nucleic Acids Research 39.7 (2011): 2890-2902.

38 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Transcriptional Dynamics of Grain Development in Barley (Hordeum vulgare L.).
Bian J, Deng P, Zhan H, Wu X, Nishantha MDLC, Yan Z, Du X, Nie X, Song W., Int J Mol Sci 20(4), 2019
PMID: 30813307
Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria.
Edera AA, Gandini CL, Sanchez-Puerta MV., Plant Mol Biol 97(3), 2018
PMID: 29761268
LNCediting: a database for functional effects of RNA editing in lncRNAs.
Gong J, Liu C, Liu W, Xiang Y, Diao L, Guo AY, Han L., Nucleic Acids Res 45(d1), 2017
PMID: 27651464
Comparative Analysis of Four Calypogeia Species Revealed Unexpected Change in Evolutionarily-Stable Liverwort Mitogenomes.
Ślipiko M, Myszczyński K, Buczkowska-Chmielewska K, Bączkiewicz A, Szczecińska M, Sawicki J., Genes (Basel) 8(12), 2017
PMID: 29257096
Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution.
Guo W, Grewe F, Fan W, Young GJ, Knoop V, Palmer JD, Mower JP., Mol Biol Evol 33(6), 2016
PMID: 26831941
Novel modes of RNA editing in mitochondria.
Moreira S, Valach M, Aoulad-Aissa M, Otto C, Burger G., Nucleic Acids Res 44(10), 2016
PMID: 27001515
Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome.
Cuenca A, Ross TG, Graham SW, Barrett CF, Davis JI, Seberg O, Petersen G., Genome Biol Evol 8(7), 2016
PMID: 27435795
RNA Editing and Its Molecular Mechanism in Plant Organelles.
Ichinose M, Sugita M., Genes (Basel) 8(1), 2016
PMID: 28025543
Selective homo- and heteromer interactions between the multiple organellar RNA editing factor (MORF) proteins in Arabidopsis thaliana.
Zehrmann A, Härtel B, Glass F, Bayer-Császár E, Obata T, Meyer E, Brennicke A, Takenaka M., J Biol Chem 290(10), 2015
PMID: 25583991
RNA editing in plant mitochondria—connecting RNA target sequences and acting proteins.
Takenaka M, Verbitskiy D, Zehrmann A, Härtel B, Bayer-Császár E, Glass F, Brennicke A., Mitochondrion 19 Pt B(), 2014
PMID: 24732437
Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea.
Grewe F, Edger PP, Keren I, Sultan L, Pires JC, Ostersetzer-Biran O, Mower JP., Mitochondrion 19 Pt B(), 2014
PMID: 24907441
Possible formation of mitochondrial-RNA containing chimeric or trimeric RNA implies a post-transcriptional and post-splicing mechanism for RNA fusion.
Yang W, Wu JM, Bi AD, Ou-Yang YC, Shen HH, Chirn GW, Zhou JH, Weiss E, Holman EP, Liao DJ., PLoS One 8(10), 2013
PMID: 24204722
Determinants of tRNA editing and modification: avoiding conundrums, affecting function.
Paris Z, Fleming IM, Alfonzo JD., Semin Cell Dev Biol 23(3), 2012
PMID: 22024020
Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates.
Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR., PLoS Biol 10(1), 2012
PMID: 22272183
Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria.
Rüdinger M, Volkmar U, Lenz H, Groth-Malonek M, Knoop V., J Mol Evol 74(1-2), 2012
PMID: 22302222
Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants.
Takenaka M, Zehrmann A, Verbitskiy D, Kugelmann M, Härtel B, Brennicke A., Proc Natl Acad Sci U S A 109(13), 2012
PMID: 22411807
The mitochondrial genome of the lycophyte Huperzia squarrosa: the most archaic form in vascular plants.
Liu Y, Wang B, Cui P, Li L, Xue JY, Yu J, Qiu YL., PLoS One 7(4), 2012
PMID: 22511984
Two related RNA-editing proteins target the same sites in mitochondria of Arabidopsis thaliana.
Verbitskiy D, Zehrmann A, Härtel B, Brennicke A, Takenaka M., J Biol Chem 287(45), 2012
PMID: 22977245
Plant-type mitochondrial RNA editing in the protist Naegleria gruberi.
Rüdinger M, Fritz-Laylin L, Polsakiewicz M, Knoop V., RNA 17(12), 2011
PMID: 22025737

57 References

Daten bereitgestellt von Europe PubMed Central.

RNA editing in wheat mitochondria results in the conservation of protein sequences.
Gualberto JM, Lamattina L, Bonnard G, Weil JH, Grienenberger JM., Nature 341(6243), 1989
PMID: 2552325
RNA editing in plant mitochondria.
Covello PS, Gray MW., Nature 341(6243), 1989
PMID: 2552326
RNA editing in plant mitochondria.
Hiesel R, Wissinger B, Schuster W, Brennicke A., Science 246(4937), 1989
PMID: 2480644
Editing of a chloroplast mRNA by creation of an initiation codon.
Hoch B, Maier RM, Appel K, Igloi GL, Kossel H., Nature 353(6340), 1991
PMID: 1653905
Ecotype allelic variation in C-to-U editing extent of a mitochondrial transcript identifies RNA-editing quantitative trait loci in Arabidopsis
Bentolila S, Chateigner-Boutin AL, Hanson MR., 2005
Seven large variations in the extent of RNA editing in plant mitochondria between three ecotypes of Arabidopsis thaliana.
Zehrmann A, van der Merwe JA, Verbitskiy D, Brennicke A, Takenaka M., Mitochondrion 8(4), 2008
PMID: 18678284
Tissue- and stage-specific modulation of RNA editing of the psbF and psbL transcript from spinach plastids - a new regulatory mechanism? Mol
Bock R, Hagemann R, Kössel H, Kudla J., 1993
Cell type-specific loss of atp6 RNA editing in cytoplasmic male sterile Sorghum bicolor.
Howad W, Kempken F., Proc. Natl. Acad. Sci. U.S.A. 94(20), 1997
PMID: 9380764
A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts.
Kotera E, Tasaka M, Shikanai T., Nature 433(7023), 2005
PMID: 15662426
A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana.
Zehrmann A, Verbitskiy D, van der Merwe JA, Brennicke A, Takenaka M., Plant Cell 21(2), 2009
PMID: 19252080
Plant RNA editing.
Chateigner-Boutin AL, Small I., RNA Biol 7(2), 2010
PMID: 20473038
Plant mitochondrial RNA editing: extreme in hornworts and dividing the liverworts? J
Steinhauser S, Beckert S, Capesius I, Malek O, Knoop V., 1999
RNA editing: 11 sites only in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal
Rüdinger M, Funk HT, Rensing SA, Maier UG, Knoop V., 2009
RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs.
Giege P, Brennicke A., Proc. Natl. Acad. Sci. U.S.A. 96(26), 1999
PMID: 10611383
The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants
Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K., 2002
Genetic architecture of mitochondrial editing in Arabidopsis thaliana.
Bentolila S, Elliott LE, Hanson MR., Genetics 178(3), 2007
PMID: 17565941
Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris
Mower JP, Palmer JD., 2006
Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing.
Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G., Nucleic Acids Res. 38(14), 2010
PMID: 20385587
RNA editing in wheat mitochondria proceeds by a deamination mechanism.
Blanc V, Litvak S, Araya A., FEBS Lett. 373(1), 1995
PMID: 7589434
RNA editing in the cytochrome b locus of the higher plant Oenothera berteriana includes a U-to-C transition.
Schuster W, Hiesel R, Wissinger B, Brennicke A., Mol. Cell. Biol. 10(5), 1990
PMID: 2325659
RNA editing in hornwort chloroplasts makes more than half the genes functional.
Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, Yoshinaga K., Nucleic Acids Res. 31(9), 2003
PMID: 12711687
Phylogenetic information in the mitochondrial nad5 gene of pteridophytes: RNA editing and intron sequences
Vangerow S, Teerkorn T, Knoop V., 1999
A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii.
Grewe F, Viehoever P, Weisshaar B, Knoop V., Nucleic Acids Res. 37(15), 2009
PMID: 19553190
Transcript end mapping and analysis of RNA editing in plant mitochondria.
Kempken F, Bolle N, Forner J, Binder S., Methods Mol. Biol. 372(), 2007
PMID: 18314726
Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature.
Lenz H, Rudinger M, Volkmar U, Fischer S, Herres S, Grewe F, Knoop V., Curr. Genet. 56(2), 2009
PMID: 20041252
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0.
Tamura K, Dudley J, Nei M, Kumar S., Mol. Biol. Evol. 24(8), 2007
PMID: 17488738
Intron RNA editing is essential for splicing in plant mitochondria.
Castandet B, Choury D, Begu D, Jordana X, Araya A., Nucleic Acids Res. 38(20), 2010
PMID: 20615898
Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes.
Salmans ML, Chaw SM, Lin CP, Shih AC, Wu YW, Mulligan RM., Curr. Genet. 56(5), 2010
PMID: 20617318
On the evolution of RNA editing.
Covello PS, Gray MW., Trends Genet. 9(8), 1993
PMID: 8379005
The evolution of chloroplast RNA editing.
Tillich M, Lehwark P, Morton BR, Maier UG., Mol. Biol. Evol. 23(10), 2006
PMID: 16835291
Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Biol
Jobson RW, Qiu YL., 2008
Complex chloroplast RNA metabolism: just debugging the genetic programme?
Maier UG, Bozarth A, Funk HT, Zauner S, Rensing SA, Schmitz-Linneweber C, Borner T, Tillich M., BMC Biol. 6(), 2008
PMID: 18755031
Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates.
Lukes J, Leander BS, Keeling PJ., Proc. Natl. Acad. Sci. U.S.A. 106 Suppl 1(), 2009
PMID: 19528647
When you can't trust the DNA: RNA editing changes transcript sequences
Knoop V., 2010
Gene organization and evolution of introns of a liverwort, Marchantia polymorpha, mitochondrial genome
Ohyama K, Oda K, Ohta E, Takemura M., 1993
RNA editing in bryophytes and a molecular phylogeny of land plants.
Malek O, Lattig K, Hiesel R, Brennicke A, Knoop V., EMBO J. 15(6), 1996
PMID: 8635473
The deepest divergences in land plants inferred from phylogenomic evidence.
Qiu YL, Li L, Wang B, Chen Z, Knoop V, Groth-Malonek M, Dombrovska O, Lee J, Kent L, Rest J, Estabrook GF, Hendry TA, Taylor DW, Testa CM, Ambros M, Crandall-Stotler B, Duff RJ, Stech M, Frey W, Quandt D, Davis CC., Proc. Natl. Acad. Sci. U.S.A. 103(42), 2006
PMID: 17030812
Phylogenetic relationships among group II intron ORFs.
Zimmerly S, Hausner G, Wu Xc ., Nucleic Acids Res. 29(5), 2001
PMID: 11222775
Structure and activities of group II introns.
Michel F, Ferat JL., Annu. Rev. Biochem. 64(), 1995
PMID: 7574489

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 21138958
PubMed | Europe PMC

Suchen in

Google Scholar