Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes

Current Genetics

Volumn 56, Issue 5, 2010, Pages 439-446

  Salmans, Michael Lee ^a   Chaw, Shu Miaw ^b   Lin, Ching Ping ^b   Shih, Arthur Chun Chieh ^c   Wu, Yu Wei ^d   Mulligan, R Michael ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BIODIVERSITY RESEARCH CENTER   (Taiwan)

^c INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^d INDIANA UNIVERSITY   (United States)

Author keywords

Organelle evolution; Relative entropy; RNA editing

Indexed keywords

COMPLEMENTARY DNA; CYTOSINE; URACIL;

ANGIOSPERM; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; CYCAS; CYCAS TAITUNGENSIS; DNA FLANKING REGION; ENTROPY; FLOWERING; GENE IDENTIFICATION; GENETIC CODE; GENETIC CONSERVATION; GENETIC SIMILARITY; GYMNOSPERM; MITOCHONDRIAL GENOME; MOLECULAR RECOGNITION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PRIORITY JOURNAL; RNA EDITING; RNA SEQUENCE; SEQUENCE ANALYSIS;

ANGIOSPERMS; BASE SEQUENCE; CYCAS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, MITOCHONDRIAL; GENES, PLANT; GENOME, MITOCHONDRIAL; GENOME, PLANT; GYMNOSPERMS; MITOCHONDRIA; ORGANELLES; RNA EDITING; RNA, PLANT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA;

CYCAS; CYCAS TAITUNGENSIS; GYMNOSPERMAE; MAGNOLIOPHYTA;

EID: 77957692936     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-010-0312-4     Document Type: Article

References (34)

1. AL Chateigner-Boutin MR Hanson 2002 Cross-competition in transgenic chloroplasts expressing single editing sites reveals shared cis elements Mol Cell Biol 22 8448 8456 1:CAS:528:DC%2BD38XptlGrsL4%3D 10.1128/MCB.22.24.8448- 8456.2002 12446765 (Pubitemid 35397161)
2. AL Chateigner-Boutin M Ramos-Vega A Guevara-Garcia C Andres M de la Luz Gutierrez-Nava A Cantero E Delannoy LF Jimenez C Lurin I Small P Leon 2008 CLB19, a pentatricopeptide repeat protein required for editing of rpoA and clpP chloroplast transcripts Plant J 56 590 602 1:CAS:528:DC%2BD1cXhsFSnsLnI 10.1111/j.1365-313X.2008.03634.x 18657233
3. SM Chaw AC Shih D Wang YW Wu SM Liu TY Chou 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 25 603 615 1:CAS:528:DC%2BD1cXjt1Cltbs%3D 10.1093/molbev/msn009 18192697 (Pubitemid 351301916)
4. MP Cummings DS Myers 2004 Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA BMC Bioinform 5 132 10.1186/1471-2105-5-132 (Pubitemid 40195374)
5. P Giege A Brennicke 1999 RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs Proc Natl Acad Sci USA 96 15324 15329 1:CAS:528:DC%2BD3cXhtFehsQ%3D%3D 10.1073/pnas.96.26.15324 10611383 (Pubitemid 30019810)
6. K Hammani K Okuda SK Tanz AL Chateigner-Boutin T Shikanai I Small 2009 A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites Plant Cell 21 3686 3699 1:CAS:528:DC%2BC3cXovVajsw%3D%3D 10.1105/tpc.109.071472 19934379
7. H Handa 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 5916 1:CAS:528:DC%2BD3sXotVCltr0%3D 10.1093/nar/gkg795 14530439 (Pubitemid 37442317)
8. ML Hayes MR Hanson 2008 High conservation of a 5' element required for RNA editing of a C target in chloroplast psbE transcripts J Mol Evol 67 233 245 1:CAS:528:DC%2BD1cXhtV2isr3M 10.1007/s00239-008-9101-9 18696032
9. RW Jobson YL Qiu 2008 Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Biol Direct 3 43 10.1186/1745-6150-3-43 18939975
10. Y Kobayashi M Matsuo K Sakamoto T Wakasugi K Yamada J Obokata 2008 Two RNA editing sites with cis-acting elements of moderate sequence identity are recognized by an identical site-recognition protein in tobacco chloroplasts Nucleic Acids Res 36 311 318 1:CAS:528:DC%2BD1cXpt12ksw%3D%3D 10.1093/nar/gkm1026 18032432
11. T Kubo S Nishizawa A Sugawara N Itchoda A Estiati T Mikami 2000 The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA) Nucleic Acids Res 28 2571 2576 1:CAS:528:DC%2BD3cXlvFWqsLg%3D 10.1093/nar/28.13.2571 10871408
12. M Kugita A Kaneko Y Yamamoto Y Takeya T Matsumoto K Yoshinaga 2003 The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants Nucleic Acids Res 31 716 721 1:CAS:528:DC%2BD3sXitlCnsrw%3D 10.1093/nar/gkg155 12527781 (Pubitemid 36175962)
13. M Kugita Y Yamamoto T Fujikawa T Matsumoto K Yoshinaga 2003 RNA editing in hornwort chloroplasts makes more than half the genes functional Nucleic Acids Res 31 2417 2423 1:CAS:528:DC%2BD3sXjt1Ogtrc%3D 10.1093/nar/gkg327 12711687 (Pubitemid 37442110)
14. RM Maier K Neckermann GL Igloi H Kossel 1995 Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing J Mol Biol 251 614 628 1:CAS:528:DyaK2MXotVWitbo%3D 10.1006/jmbi.1995.0460 7666415
15. JP Mower 2005 PREP-Mt: predictive RNA editor for plant mitochondrial genes BMC Bioinform 6 96 10.1186/1471-2105-6-96 (Pubitemid 41357921)
16. JP Mower JD Palmer 2006 Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris Mol Genet Genom 276 285 293 1:CAS:528: DC%2BD28Xotlajurc%3D 10.1007/s00438-006-0139-3 (Pubitemid 44268038)
17. RM Mulligan KL Chang CC Chou 2007 Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites Mol Biol Evol 24 1971 1981 1:CAS:528:DC%2BD2sXhtFSjsLbK 10.1093/molbev/msm125 17591603
18. Y Notsu S Masood T Nishikawa N Kubo G Akiduki M Nakazono A Hirai K Kadowaki 2002 The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants Mol Genet Genom 268 434 445 1:CAS:528:DC%2BD38XptlWltb0%3D 10.1007/s00438-002-0767-1 (Pubitemid 35435847)
19. K Oda K Yamato E Ohta Y Nakamura M Takemura N Nozato K Akashi T Kanegae Y Ogura T Kohchi, et al. 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 7 1:CAS:528:DyaK3sXhvVCls7s%3D 10.1016/0022-2836(92)90708-R 1731062
20. K Okuda T Nakamura M Sugita T Shimizu T Shikanai 2006 A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing J Biol Chem 281 37661 37667 1:CAS:528:DC%2BD28Xht1KitrbE 10.1074/jbc.M608184200 17015439 (Pubitemid 46042069)
21. K Okuda AL Chateigner-Boutin T Nakamura E Delannoy M Sugita F Myouga R Motohashi K Shinozaki I Small T Shikanai 2009 Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts Plant Cell 21 146 156 1:CAS:528: DC%2BD1MXlsFCitrc%3D 10.1105/tpc.108.064667 19182104
22. Okuda K, Hammani K, Tanz SK, Peng L, Fukao Y, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T (2010) The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. Plant J 61:339-349
23. JD Palmer DE Soltis MW Chase 2004 The plant tree of life: an overview and some points of view Am J Bot 91 1437 1445 10.3732/ajb.91.10.1437
24. T Shikanai 2006 RNA editing in plant organelles: machinery, physiological function and evolution Cell Mol Life Sci 63 698 708 1:CAS:528: DC%2BD28Xjs1Omsro%3D 10.1007/s00018-005-5449-9 16465445
25. K Shinozaki M Ohme M Tanaka T Wakasugi N Hayashida T Matsubayashi N Zaita J Chunwongse J Obokata K Yamaguchi-Shinozaki C Ohto K Torazawa BY Meng M Sugita H Deno T Kamogashira K Yamada J Kusuda F Takaiwa A Kato N Tohdoh H Shimada M Sugiura 1986 The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression EMBO J 5 2043 2049 1:CAS:528: DyaL28Xls1Kjt7o%3D 16453699
26. M Takenaka J Neuwirt A Brennicke 2004 Complex cis-elements determine an RNA editing site in pea mitochondria Nucleic Acids Res 32 4137 4144 1:CAS:528:DC%2BD2cXntFansLc%3D 10.1093/nar/gkh763 15295040 (Pubitemid 39232286)
27. M Tillich P Lehwark BR Morton UG Maier 2006 The evolution of chloroplast RNA editing Mol Biol Evol 23 1912 1921 1:CAS:528:DC%2BD28XhtVWgs7rN 10.1093/molbev/msl054 16835291 (Pubitemid 44412877)
28. T Tsudzuki T Wakasugi M Sugiura 2001 Comparative analysis of RNA editing sites in higher plant chloroplasts J Mol Evol 53 327 332 1:CAS:528: DC%2BD3MXotVaiu78%3D 10.1007/s002390010222 11675592 (Pubitemid 32889540)
29. JA van der Merwe M Takenaka J Neuwirt D Verbitskiy A Brennicke 2006 RNA editing sites in plant mitochondria can share cis-elements FEBS Lett 580 268 272 10.1016/j.febslet.2005.12.011 16364306 (Pubitemid 43005348)
30. T Wakasugi T Tsudzuki M Sugiura 2001 The genomics of land plant chloroplasts: gene content and alteration of genomic information by RNA editing Photosynth Res 70 107 118 1:CAS:528:DC%2BD38Xht1Wgt7s%3D 10.1023/A:1013892009589 16228365 (Pubitemid 34133281)
31. PG Wolf CA Rowe RB Sinclair M Hasebe 2003 Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L DNA Res 10 59 65 1:CAS:528:DC%2BD3sXjsFCqsLo%3D 10.1093/dnares/10.2.59 12755170 (Pubitemid 36612723)
32. PG Wolf CA Rowe M Hasebe 2004 High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris Gene 339 89 97 1:CAS:528:DC%2BD2cXnsVKjtbc%3D 10.1016/j.gene.2004.06.018 15363849 (Pubitemid 39201131)
33. K Yura Y Miyata T Arikawa M Higuchi M Sugita 2008 Characteristics and prediction of RNA editing sites in transcripts of the moss Takakia lepidozioides chloroplast DNA Res 15 309 321 1:CAS:528:DC%2BD1cXhtlyqtrvP 10.1093/dnares/dsn016 18650260
34. A Zehrmann D Verbitskiy JA van der Merwe A Brennicke M Takenaka 2009 A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana Plant Cell 21 558 567 1:CAS:528:DC%2BD1MXksVKrtrc%3D 10.1105/tpc.108.064535 19252080