Extreme RNA Editing in Coding Islands and Abundant Microsatellites in Repeat Sequences of Selaginella moellendorffii Mitochondria: The Root of Frequent Plant mtDNA Recombination in Early Tracheophytes

Abstract Using an independent fosmid cloning approach and comprehensive transcriptome analysis to complement data from the Selaginella moellendorffii genome project, we determined the complete mitochondrial genome structure of this spikemoss. Numerous recombination events mediated mainly via long sequence repeats extending up to 7kbp result in a complex mtDNA network structure. Peculiar features associated with the repeat sequences are more than 80 different microsatellite sites (predominantly trinucleotide motifs). The S. moellendorffii mtDNA encodes a plant-typical core set of a twin-arginine translocase (tatC), 17 respiratory chain subunits, and 2 rRNAs but lacks atp4 and any tRNA genes. As a further novelty among plant chondromes, the nad4L gene is encoded within an intron of the nad1 gene. A total of 37 introns occupying the 20 mitochondrial genes (four of which are disrupted into trans-splicing arrangements including two novel instances of trans-splicing introns) make the S. moellendorffii chondrome the intron-richest and gene-poorest plant mtDNA known. Our parallel transcriptome analyses demonstrates functional splicing of all 37 introns and reveals a new record amount of plant organelle RNA editing with a total of 2,139 sites in mRNAs and 13 sites in the two rRNAs, all of which are exclusively of the C-to-U type.

[1]  Andrew J. Alverson,et al.  Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selection vs. Retroprocessing as the Driving Force , 2010, Genetics.

[2]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[3]  A. J. Bendich.  Reaching for the ring: the study of mitochondrial genome structure , 1993, Current Genetics.

[4]  Yu-Wei Wu,et al.  The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. , 2008, Molecular biology and evolution.

[5]  Jeffrey P. Mower,et al.  Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris , 2006, Molecular Genetics and Genomics.

[6]  L. Marechal-Drouard,et al.  Import of RNAs into Plant Mitochondria , 2011 .

[7]  Y. Qiu,et al.  The Complete Mitochondrial Genome Sequence of the Hornwort Megacerosaenigmaticus Shows a Mixed Mode of Conservative Yet Dynamic Evolution in Early Land Plant Mitochondrial Genomes , 2009, Journal of Molecular Evolution.

[8]  Volker Knoop,et al.  A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii , 2010, Nucleic acids research.

[9]  Y. Sekine,et al.  The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. , 2006, Molecular biology and evolution.

[10]  Jeffrey D. Palmer,et al.  Widespread horizontal transfer of mitochondrial genes in flowering plants , 2003, Nature.

[11]  Volker Knoop,et al.  DYW‐type PPR proteins in a heterolobosean protist: Plant RNA editing factors involved in an ancient horizontal gene transfer? , 2010, FEBS letters.

[12]  A. Brennicke,et al.  Mitochondrial DNA variations and nuclear RFLPs reflect different genetic similarities among 23 Arabidopsis thaliana ecotypes , 2004, Plant Molecular Biology.

[13]  Andrew J. Alverson,et al.  Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). , 2010, Molecular biology and evolution.

[14]  V. Knoop.  The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective , 2004, Current Genetics.

[15]  A. J. Bendich,et al.  The mitochondrial genome is large and variable in a family of plants (Cucurbitaceae) , 1981, Cell.

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

[17]  A. Brennicke,et al.  RNA editing in bryophytes and a molecular phylogeny of land plants. , 1996, The EMBO journal.

[18]  K. Oda,et al.  Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. , 1992, Journal of molecular biology.

[19]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[20]  D. Spencer,et al.  Identification and Structural Characterization of Nucleus-encoded Transfer RNAs Imported into Wheat Mitochondria* , 2001, The Journal of Biological Chemistry.

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

[22]  Karri M. Haen,et al.  Parallel loss of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases and mtDNA-encoded tRNAs in Cnidaria. , 2010, Molecular biology and evolution.

[23]  J. Palmer,et al.  Inaugural Article: Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution , 2002 .

[24]  Y. Qiu,et al.  Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications. , 2004, Molecular phylogenetics and evolution.

[25]  V. Knoop,et al.  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. , 2007, Molecular biology and evolution.

[26]  Felix Grewe,et al.  A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii , 2009, Nucleic acids research.

[27]  Ian Small,et al.  A hypothesis on the identification of the editing enzyme in plant organelles , 2007, FEBS letters.

[28]  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.

[29]  S. Bowman,et al.  Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP 644 ( Cryptophyceae ) , 2008 .

[30]  D. Smith.  Unparalleled GC content in the plastid DNA of Selaginella , 2009, Plant Molecular Biology.

[31]  Joel Dudley,et al.  MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences , 2008, Briefings Bioinform..

[32]  Sunggil Kim,et al.  Comparison of mitochondrial and chloroplast genome segments from three onion (Allium cepa L.) cytoplasm types and identification of a trans-splicing intron of cox2 , 2010, Current Genetics.

[33]  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.

[34]  J. Weng,et al.  Convergent Evolution of Syringyl Lignin Biosynthesis via Distinct Pathways in the Lycophyte Selaginella and Flowering Plants[C][W] , 2010, Plant Cell.

[35]  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.

[36]  A. Christensen,et al.  Plant Mitochondrial Recombination Surveillance Requires Unusual RecA and MutS Homologs[OA] , 2007, The Plant Cell Online.

[37]  I. Capesius,et al.  Plant Mitochondrial RNA Editing , 1999, Journal of Molecular Evolution.

[38]  Andrew J. Alverson,et al.  Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia , 2010, BMC Evolutionary Biology.

[39]  A. Brennicke,et al.  RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[40]  M. N. Schnare,et al.  Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA. , 2003, RNA.

[41]  James O. Allen,et al.  Comparisons Among Two Fertile and Three Male-Sterile Mitochondrial Genomes of Maize , 2007, Genetics.

[42]  Henning Lenz,et al.  Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature , 2010, Current Genetics.

[43]  B. Lang,et al.  A 5 S rRNA gene is present in the mitochondrial genome of the protist Reclinomonas americana but is absent from red algal mitochondrial DNA. , 1996, Journal of molecular biology.

[44]  J. Tohme,et al.  Tracing evolutionary and developmental implications of mitochondrial stoichiometric shifting in the common bean. , 2001, Genetics.

[45]  L. Marechal-Drouard,et al.  Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria , 2009, Current Genetics.

[46]  Kenneth Stuart,et al.  Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei , 1988, Cell.

[47]  Felix Grewe,et al.  Mitochondrial Genome Evolution in the Plant Lineage , 2011 .

[48]  S. Mackenzie,et al.  Plant Mitochondrial Genomes and Recombination , 2011 .

[49]  Y. Qiu,et al.  The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts , 2009, Current Genetics.

[50]  A. Elo,et al.  Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Y. Qiu,et al.  The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts , 2010, Current Genetics.

[52]  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.

[53]  Volker Knoop,et al.  When you can’t trust the DNA: RNA editing changes transcript sequences , 2011, Cellular and Molecular Life Sciences.

[54]  V. Knoop,et al.  Trans-splicing group II introns in plant mitochondria: the complete set of cis-arranged homologs in ferns, fern allies, and a hornwort. , 1998, RNA.

[55]  D. Smith,et al.  Mitochondrial genome of the colorless green alga Polytomella capuana: a linear molecule with an unprecedented GC content. , 2008, Molecular biology and evolution.

[56]  S. Bowman,et al.  Complete Sequence and Analysis of the Mitochondrial Genome of Hemiselmis andersenii CCMP644 (Cryptophyceae) , 2008, BMC Genomics.

[57]  B. Nielsen,et al.  DNA recombination activity in soybean mitochondria. , 2006, Journal of molecular biology.

[58]  B. Steffens,et al.  ABP1: an auxin receptor for fast responses at the plasma membrane. , 2010, Plant signaling & behavior.

[59]  J. Banks.  Selaginella and 400 million years of separation. , 2009, Annual review of plant biology.

[60]  Ralph Bock,et al.  OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes , 2007, Current Genetics.