Targeted gene disruption identifies three PPR-DYW proteins involved in RNA editing for five editing sites of the moss mitochondrial transcripts.

In plant organelles, RNA editing frequently occurs in many transcripts, but little is known about its molecular mechanism. Eleven RNA editing sites are present in the moss Physcomitrella patens mitochondria. Recently PpPPR_71, one member of 10 DYW-subclass pentatricopeptide repeat (PPR-DYW) proteins, has been identified as a site-specific recognition factor for RNA editing in the mitochondrial transcript. In this study, we disrupted three genes encoding a PPR-DYW protein-PpPPR_56, PpPPR_77, and PpPPR_91-to investigate whether they are involved in RNA editing. Transient expression of an N-terminal amino acid sequence fused to the green fluorescent protein (GFP) suggests that the three PPR-DYW proteins are targeted to mitochondria. Disruption of each gene by homologous recombination revealed that PpPPR_56 was involved in RNA editing at the nad3 and nad4 sites, PpPPR_77 at the cox2 and cox3 sites, and PpPPR_91 at the nad5-2 site in the mitochondrial transcripts. The nucleotide sequences surrounding the two editing sites targeted by a single PPR-DYW protein share 42 to 56% of their identities. Thus, moss PPR-DYW proteins seem to be site-specific factors for RNA editing in mitochondrial transcripts.

[1]  M. Sugita,et al.  The moss Physcomitrella patens, a model plant for the study of RNA editing in plant organelles , 2010, Plant signaling & behavior.

[2]  Giorgio Valle,et al.  Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing , 2010, Nucleic acids research.

[3]  Mamoru Sugita,et al.  The moss pentatricopeptide repeat protein with a DYW domain is responsible for RNA editing of mitochondrial ccmFc transcript. , 2010, The Plant journal : for cell and molecular biology.

[4]  S. Hsu,et al.  Editing of accD and ndhF chloroplast transcripts is partially affected in the Arabidopsisvanilla cream1 mutant , 2010, Plant Molecular Biology.

[5]  Masashi Suzuki,et al.  The mitochondrial PPR protein LOVASTATIN INSENSITIVE 1 plays regulatory roles in cytosolic and plastidial isoprenoid biosynthesis through RNA editing. , 2010, The Plant journal : for cell and molecular biology.

[6]  A. Brennicke,et al.  The PPR protein encoded by the LOVASTATIN INSENSITIVE 1 gene is involved in RNA editing at three sites in mitochondria of Arabidopsis thaliana. , 2010, The Plant journal : for cell and molecular biology.

[7]  Sandra K. Tanz,et al.  The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. , 2009, The Plant journal : for cell and molecular biology.

[8]  M. Takenaka.  MEF9, an E-Subclass Pentatricopeptide Repeat Protein, Is Required for an RNA Editing Event in the nad7 Transcript in Mitochondria of Arabidopsis1[C][OA] , 2009, Plant Physiology.

[9]  Sandra K. Tanz,et al.  A Study of New Arabidopsis Chloroplast RNA Editing Mutants Reveals General Features of Editing Factors and Their Target Sites[W][OA] , 2009, The Plant Cell Online.

[10]  K. Chong,et al.  AtECB2, a pentatricopeptide repeat protein, is required for chloroplast transcript accD RNA editing and early chloroplast biogenesis in Arabidopsis thaliana. , 2009, The Plant journal : for cell and molecular biology.

[11]  Gynheung An,et al.  Rice OGR1 encodes a pentatricopeptide repeat-DYW protein and is essential for RNA editing in mitochondria. , 2009, The Plant journal : for cell and molecular biology.

[12]  M. Hanson,et al.  A comparative genomics approach identifies a PPR-DYW protein that is essential for C-to-U editing of the Arabidopsis chloroplast accD transcript. , 2009, RNA.

[13]  Congming Lu,et al.  LPA66 Is Required for Editing psbF Chloroplast Transcripts in Arabidopsis1[W][OA] , 2009, Plant Physiology.

[14]  Yuxiang Cheng,et al.  The Arabidopsis gene YS1 encoding a DYW protein is required for editing of rpoB transcripts and the rapid development of chloroplasts during early growth. , 2009, The Plant journal : for cell and molecular biology.

[15]  Axel Brennicke,et al.  A DYW Domain–Containing Pentatricopeptide Repeat Protein Is Required for RNA Editing at Multiple Sites in Mitochondria of Arabidopsis thaliana[W] , 2009, The Plant Cell Online.

[16]  Stefan A. Rensing,et al.  RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal , 2009, Molecular Genetics and Genomics.

[17]  F. Myouga,et al.  Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts[W] , 2009, The Plant Cell Online.

[18]  Takahiro J. Nakamura,et al.  A conserved DYW domain of the pentatricopeptide repeat protein possesses a novel endoribonuclease activity , 2008, FEBS letters.

[19]  I. Small,et al.  Pentatricopeptide repeat proteins: a socket set for organelle gene expression. , 2008, Trends in plant science.

[20]  P. León,et al.  CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts. , 2008, The Plant journal : for cell and molecular biology.

[21]  S. Rensing,et al.  Complex chloroplast RNA metabolism: just debugging the genetic programme? , 2008, BMC Biology.

[22]  Volker Knoop,et al.  Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts. , 2008, Molecular biology and evolution.

[23]  Ian Small,et al.  On the expansion of the pentatricopeptide repeat gene family in plants. , 2008, Molecular biology and evolution.

[24]  S. Bentolila,et al.  Genetic Architecture of Mitochondrial Editing in Arabidopsis thaliana , 2008, Genetics.

[25]  J. Bennetzen,et al.  The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants , 2008, Science.

[26]  A. Brennicke,et al.  The process of RNA editing in plant mitochondria. , 2008, Mitochondrion.

[27]  Y. Kobayashi,et al.  Transcription of plastid genes is modulated by two nuclear-encoded alpha subunits of plastid RNA polymerase in the moss Physcomitrella patens. , 2007, The Plant journal : for cell and molecular biology.

[28]  Kazuo Shinozaki,et al.  Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing , 2007, Proceedings of the National Academy of Sciences.

[29]  M. Sugita,et al.  A Pentatricopeptide Repeat Protein Is Required for RNA Processing of clpP Pre-mRNA in Moss Chloroplasts* , 2007, Journal of Biological Chemistry.

[30]  Toshiyuki Shimizu,et al.  A Pentatricopeptide Repeat Protein Is a Site Recognition Factor in Chloroplast RNA Editing*♦ , 2006, Journal of Biological Chemistry.

[31]  A. Brennicke,et al.  RNA editing sites in plant mitochondria can share cis‐elements , 2006, FEBS letters.

[32]  R. Bock,et al.  Sequence of the Tomato Chloroplast DNA and Evolutionary Comparison of Solanaceous Plastid Genomes , 2006, Journal of Molecular Evolution.

[33]  T. Shikanai,et al.  RNA editing in plant organelles: machinery, physiological function and evolution , 2006, Cellular and Molecular Life Sciences CMLS.

[34]  A. Brennicke,et al.  An in vitro RNA editing system from cauliflower mitochondria: editing site recognition parameters can vary in different plant species. , 2005, RNA.

[35]  T. Shikanai,et al.  A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts , 2005, Nature.

[36]  M. Hasebe,et al.  Identification and characterization of cDNAs encoding pentatricopeptide repeat proteins in the basal land plant, the moss Physcomitrella patens. , 2004, Gene.

[37]  Frédérique Bitton,et al.  Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis , 2004, The Plant Cell Online.

[38]  F. Legeai,et al.  Predotar: A tool for rapidly screening proteomes for N‐terminal targeting sequences , 2004, Proteomics.

[39]  Axel Brennicke,et al.  Complex cis-elements determine an RNA editing site in pea mitochondria. , 2004, Nucleic acids research.

[40]  M. Sugita,et al.  Tissue- and stage-specific RNA editing of rps 14 transcripts in moss (Physcomitrella patens) chloroplasts. , 2004, Journal of plant physiology.

[41]  Gilles Peltier,et al.  A nucleus-encoded factor, CRR2, is essential for the expression of chloroplast ndhB in Arabidopsis. , 2003, The Plant journal : for cell and molecular biology.

[42]  H. Handa,et al.  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. , 2003, Nucleic acids research.

[43]  S. Aoki,et al.  Complete chloroplast DNA sequence of the moss Physcomitrella patens: evidence for the loss and relocation of rpoA from the chloroplast to the nucleus. , 2003, Nucleic acids research.

[44]  Y. Notsu,et al.  The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants , 2002, Molecular Genetics and Genomics.

[45]  J. Farré,et al.  cis Recognition Elements in Plant Mitochondrion RNA Editing , 2001, Molecular and Cellular Biology.

[46]  M. Sugiura,et al.  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 , 2001, The EMBO journal.

[47]  S. Aoki,et al.  Cloning and characterization of the cDNA for a plastid σ factor from the moss Physcomitrella patens , 2001 .

[48]  S. Brunak,et al.  Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. , 2000, Journal of molecular biology.

[49]  M. Shimizu,et al.  Non-invasive quantitative detection and applications of non-toxic, S65T-type green fluorescent protein in living plants. , 1999, The Plant journal : for cell and molecular biology.

[50]  P. Maliga,et al.  Sequences directing C to U editing of the plastid psbL mRNA are located within a 22 nucleotide segment spanning the editing site. , 1996, The EMBO journal.

[51]  Takanori Hirano,et al.  Engineered GFP as a vital reporter in plants , 1996, Current Biology.

[52]  H. Carrer,et al.  Site‐specific factor involved in the editing of the psbL mRNA in tobacco plastids. , 1995, The EMBO journal.