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RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal

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Abstract

RNA editing in mitochondria and chloroplasts of land plants alters the coding content of transcripts through site-specific exchanges of cytidines into uridines and vice versa. The abundance of RNA editing in model plant species such as rice or Arabidopsis with some 500 affected sites in their organelle transcripts hinders straightforward approaches to elucidate its mechanisms. The moss Physcomitrella patens is increasingly being appreciated as an alternative plant model system, enhanced by the recent availability of its complete chloroplast, mitochondrial, and nuclear genome sequences. We here report the transcriptomic analysis of Physcomitrella mitochondrial mRNAs as a prerequisite for future studies of mitochondrial RNA editing in this moss. We find a strikingly low frequency of RNA editing affecting only eleven, albeit highly important, sites of C-to-U nucleotide modification in only nine mitochondrial genes. Partial editing was seen for two of these sites but no evidence for any silent editing sites (leaving the identity of the encoded amino acid unchanged) as commonly observed in vascular plants was found in Physcomitrella, indicating a compact and efficient organization of the editing machinery. Furthermore, we here wish to propose a unifying nomenclature to clearly identify and designate RNA editing positions and to facilitate future communication and database annotation.

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Acknowledgments

Research in the authors’ laboratories is supported by grants from the Deutsche Forschungsgemeinschaft DFG, in particular SFB-TR1 (Marburg), and BMBF FRISYS (Freiburg). We thank Andrew Bozarth for comments on the manuscript. H.T.F. thanks Christopher Grosche for skilful lab assistance. M.R. is grateful to Julia Dreistein for concentrated and helpful work during a laboratory practical training and to Judith Schleppenbäumer and Thomas Münster, MPI Cologne, who have kindly provided the P. patens Gransden strain. We wish to dedicate this publication to the memory of Rudolf Hiesel, colleague, friend and co-discoverer of RNA editing in plants, who passed away much too early.

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  1. Abteilung Molekulare Evolution, IZMB–Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Kirschallee 1, 53115, Bonn, Germany

    Mareike Rüdinger & Volker Knoop

  2. Fachbereich Biologie, Zellbiologie, Philipps-Universität Marburg, Karl-von-Frisch-Str., 35032, Marburg, Germany

    Helena T. Funk & Uwe G. Maier

  3. FRISYS, Faculty of Biology, University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany

    Stefan A. Rensing

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  1. Mareike Rüdinger
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  2. Helena T. Funk
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  3. Stefan A. Rensing
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  4. Uwe G. Maier
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  5. Volker Knoop
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Correspondence to Volker Knoop.

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Communicated by B. Franz Lang.

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Rüdinger, M., Funk, H.T., Rensing, S.A. et al. RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Mol Genet Genomics 281, 473–481 (2009). https://doi.org/10.1007/s00438-009-0424-z

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