Organellar RNA editing

Wiley Interdisciplinary Reviews: RNA

Volumn 2, Issue 4, 2011, Pages 493-506

  Chateigner Boutin, Anne Laure ^a   Small, Ian ^b  

^a INRA   (France)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA; RIBOSOME RNA; RNA; PLANT RNA; PROTOZOAL RNA; RNA, MITOCHONDRIAL;

ARCHAEPLASTIDA; CELL ORGANELLE; DINOFLAGELLATE; EUKARYOTE; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; INDEL MUTATION; KINETOPLAST; KINETOPLASTIDA; METAZOON; MITOCHONDRIAL GENOME; MYXOGASTRIA; NONHUMAN; PHYLOGENY; PLANT GENOME; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN SYNTHESIS; REVIEW; RNA EDITING; BIOLOGICAL MODEL; GENETICS; METABOLISM; MUTATION; PHYSIOLOGY; PLANT;

EUKARYOTA;

DINOFLAGELLIDA; DNA; MODELS, BIOLOGICAL; MUTATION; MYXOMYCETES; ORGANELLES; PHYLOGENY; PLANTS; RNA; RNA EDITING; RNA, MESSENGER; RNA, PLANT; RNA, PROTOZOAN; RNA, RIBOSOMAL; TRYPANOSOMATINA;

EID: 84857734312     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.72     Document Type: Review

References (133)

1. Gray MW. Evolution of organellar genomes. Curr Opin Genet Dev 1999, 9:678-687.
2. Gray MW, Burger G, Lang BF. Mitochondrial evolution. Science 1999, 283:1476-1481.
3. Lang BF, Gray MW, Burger G. Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 1999, 33:351-397.
4. Dyall SD, Brown MT, Johnson PJ. Ancient invasions: from endosymbionts to organelles. Science 2004, 304:253-257.
5. Andersson SG, Zomorodipour A, Andersson JO, Sicheritz-Ponten T, Alsmark UC, Podowski RM, Näslund AK, Eriksson AS, Winkler HH, Kurland CG. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 1998, 396:133-140.
6. Tovar J, Leon-Avila G, Sanchez LB, Sutak R, Tachezy J, van der Giezen M, Hernández M, Müller M, Lucocq JM. Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 2003, 426:172-176.
7. Lill R, Muhlenhoff U. Maturation of iron-sulfur proteins in eukaryotes: mechanisms, connected processes, and diseases. Annu Rev Biochem 2008, 77:669-700.
8. Goldberg AV, Molik S, Tsaousis AD, Neumann K, Kuhnke G, Delbac F, Vivares CP, Hirt RP, Lill R, Embley TM. Localization and functionality of microsporidian iron-sulphur cluster assembly proteins. Nature 2008, 452:624-628.
9. Schneider A, Marechal-Drouard L. Mitochondrial tRNA import: are there distinct mechanisms? Trends Cell Biol 2000, 10:509-513.
10. Salinas T, Duchene AM, Marechal-Drouard L. Recent advances in tRNA mitochondrial import. Trends Biochem Sci 2008, 33:320-329.
11. Adams KL, Palmer JD. Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 2003, 29:380-395.
12. Lindmark DG, Muller M. Hydrogenosome, a cytoplasmic organelle of the anaerobic flagellate Tritrichomonas foetus, and its role in pyruvate metabolism. J Biol Chem 1973, 248:7724-7728.
13. Mai Z, Ghosh S, Frisardi M, Rosenthal B, Rogers R, Samuelson J. Hsp60 is targeted to a cryptic mitochondrion-derived organelle ( "crypton") in the microaerophilic protozoan parasite Entamoeba histolytica. Mol Cell Biol 1999, 19:2198-2205.
14. Gott JM, Emeson RB. Functions and mechanisms of RNA editing. Annu Rev Genet 2000, 34:499-531.
15. Ohman M. A-to-I editing challenger or ally to the microRNA process. Biochimie 2007, 89:1171-1176.
16. Agris PF. Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep 2008, 9:629-635.
17. Motorin Y, Helm M. tRNA stabilization by modified nucleotides. Biochemistry 2010, 49:4934-4944.
18. Leigh J, Lang BF. Mitochondrial 3′ tRNA editing in the jakobid Seculamonas ecuadoriensis: a novel mechanism and implications for tRNA processing. RNA 2004, 10:615-621.
19. Laforest MJ, Bullerwell CE, Forget L, Lang BF. Origin, evolution, and mechanism of 5′ tRNA editing in chytridiomycete fungi. RNA 2004, 10:1191-1199.
20. Gott JM, Somerlot BH, Gray MW. Two forms of RNA editing are required for tRNA maturation in Physarum mitochondria. RNA 2010, 16:482-488.
21. Cavalier-Smith T. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Microbiol 1999, 46:347-366.
22. Keeling PJ. Chromalveolates and the evolution of plastids by secondary endosymbiosis. J Eukaryot Microbiol 2009, 56:1-8.
23. Waller RF, Jackson CJ. Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology. Bioessays 2009, 31:237-245.
24. Nash EA, Barbrook AC, Edwards-Stuart RK, Bernhardt K, Howe CJ, Nisbet RE. Organization of the mitochondrial genome in the dinoflagellate Amphidinium carterae. Mol Biol Evol 2007, 24:1528-1536.
25. Nash EA, Nisbet RE, Barbrook AC, Howe CJ. Dinoflagellates: a mitochondrial genome all at sea. Trends Genet 2008, 24:328-335.
26. Howe CJ, Nisbet RE, Barbrook AC. The remarkable chloroplast genome of dinoflagellates. J Exp Bot 2008, 59:1035-1045.
27. Wang Y, Morse D. Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium. Nucleic Acids Res 2006, 34:613-619.
28. Lin S, Zhang H, Spencer DF, Norman JE, Gray MW. Widespread and extensive editing of mitochondrial mRNAS in dinoflagellates. J Mol Biol 2002, 320:727-739.
29. Lin S, Zhang H, Gray MW. RNA Editing in Dinoflagellates and its Implications for the Evolutionary History of the Editing Machinery. New York: Wiley Press; 2008.
30. Dang Y, Green BR. Substitutional editing of Heterocapsa triquetra chloroplast transcripts and a folding model for its divergent chloroplast 16S rRNA. Gene 2009, 442:73-80.
31. Zauner S, Greilinger D, Laatsch T, Kowallik KV, Maier UG. Substitutional editing of transcripts from genes of cyanobacterial origin in the dinoflagellate Ceratium horridum. FEBS Lett 2004, 577:535-538.
32. Jackson CJ, Norman JE, Schnare MN, Gray MW, Keeling PJ, Waller RF. Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria. BMC Biol 2007, 5:41.
33. Leander BS. Did trypanosomatid parasites have photosynthetic ancestors? Trends Microbiol 2004, 12:251-258.
34. Shapiro TA, Englund PT. The structure and replication of kinetoplast DNA. Annu Rev Microbiol 1995, 49:117-143.
35. Benne R, Van den Burg J, Brakenhoff JP, Sloof P, Van Boom JH, Tromp MC. Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 1986, 46:819-826.
36. Lukes J, Leander BS, Keeling PJ. Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci U S A 2009, 106(suppl 1):9963-9970.
37. Takano H, Abe T, Sakurai R, Moriyama Y, Miyazawa Y, Nozaki H, Kawano S, Sasaki N, Kuroiwa T. The complete DNA sequence of the mitochondrial genome of Physarum polycephalum. Mol Gen Genet 2001, 264:539-545.
38. Gott JM, Parimi N, Bundschuh R. Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs. Nucleic Acids Res 2005, 33:5063-5072.
39. Traphagen SJ, Dimarco MJ, Silliker ME. RNA editing of 10 Didymium iridis mitochondrial genes and comparison with the homologous genes in Physarum polycephalum. RNA 2010, 16:828-838.
40. Gott JM, Visomirski LM, Hunter JL. Substitutional and insertional RNA editing of the cytochrome c oxidase subunit 1 mRNA of Physarum polycephalum. J Biol Chem 1993, 268:25483-25486.
41. Mahendran R, Spottswood MR, Miller DL. RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature 1991, 349:434-438.
42. Miller D, Mahendran R, Spottswood M, Costandy H, Wang S, Ling ML, Yang N. Insertional editing in mitochondria of Physarum. Semin Cell Biol 1993, 4:261-266.
43. Beargie C, Liu T, Corriveau M, Lee HY, Gott J, Bundschuh R. Genome annotation in the presence of insertional RNA editing. Bioinformatics 2008, 24:2571-2578.
44. Gissi C, Iannelli F, Pesole G. Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species. Heredity 2008, 101:301-320.
45. Dellaporta SL, Xu A, Sagasser S, Jakob W, Moreno MA, Buss LW, Schierwater B. Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum. Proc Natl Acad Sci U S A 2006, 103:8751-8756.
46. Yokobori SI, Paabo S. tRNA editing in metazoans. Nature 1995, 377:490.
47. Anant S, Davidson NO. Molecular mechanisms of apolipoprotein B mRNA editing. Curr Opin Lipidol 2001, 12:159-165.
48. Daniel C, Ohman M. RNA editing and its impact on GABAA receptor function. Biochem Soc Trans 2009, 37(Pt 6):1399-1403.
49. Burger G, Yan Y, Javadi P, Lang BF. Group I-intron trans-splicing and mRNA editing in the mitochondria of placozoan animals. Trends Genet 2009, 25:381-386.
50. Freyer R, Kiefer-Meyer MC, Kossel H. Occurrence of plastid RNA editing in all major lineages of land plants. Proc Natl Acad Sci U S A 1997, 94:6285-6290.
51. Steinhauser S, Beckert S, Capesius I, Malek O, Knoop V. Plant mitochondrial RNA editing. J Mol Evol 1999, 48:303-312.
52. Tillich M, Lehwark P, Morton BR, Maier UG. The evolution of chloroplast RNA editing. Mol Biol Evol 2006, 23:1912-1921.
53. Maier UG, Bozarth A, Funk HT, Zauner S, Rensing SA, Schmitz-Linneweber C, Börner T, Tillich M. Complex chloroplast RNA metabolism: just debugging the genetic programme? BMC Biol 2008, 6:36.
54. Groth-Malonek M, Wahrmund U, Polsakiewicz M, Knoop V. 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. Mol Biol Evol 2007, 24:1068-1074.
55. Giege P, Brennicke A. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci U S A 1999, 96:15324-15329.
56. Chateigner-Boutin AL, Small I. A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res 2007, 35:e114.
57. Grewe F, Viehoever P, Weisshaar B, Knoop V. A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii. Nucleic Acids Res 2009, 37:5093-5104.
58. Kugita M, Yamamoto Y, Fujikawa T, Matsumoto T, Yoshinaga K. RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Res 2003, 31:2417-2423.
59. Stuart KD, Schnaufer A, Ernst NL, Panigrahi AK. Complex management: RNA editing in trypanosomes. Trends Biochem Sci 2005, 30:97-105.
60. Golden DE, Hajduk SL. The 3′-untranslated region of cytochrome oxidase II mRNA functions in RNA editing of African trypanosomes exclusively as a cis guide RNA. RNA 2005, 11:29-37.
61. Blum B, Bakalara N, Simpson L. A model for RNA editing in kinetoplastid mitochondria: "guide" RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 1990, 60:189-198.
62. Niemann M, Kaibel H, Schluter E, Weitzel K, Brecht M, Goringer HU. Kinetoplastid RNA editing involves a 3′ nucleotidyl phosphatase activity. Nucleic Acids Res 2009, 37:1897-1906.
63. Worthey EA, Schnaufer A, Mian IS, Stuart K, Salavati R. Comparative analysis of editosome proteins in trypanosomatids. Nucleic Acids Res 2003, 31:6392-6408.
64. Panigrahi AK, Ernst NL, Domingo GJ, Fleck M, Salavati R, Stuart KD. Compositionally and functionally distinct editosomes in Trypanosoma brucei. RNA 2006, 12:1038-1049.
65. Ringpis GE, Aphasizheva I, Wang X, Huang L, Lathrop RH, Hatfield GW, Aphasizhev R. Mechanism of U-insertion RNA editing in trypanosome mitochondria: the bimodal TUTase activity of the core complex. J Mol Biol 2010, 399:680-695.
66. Blum B, Simpson L. Guide RNAs in kinetoplastid mitochondria have a nonencoded 3′ oligo(U) tail involved in recognition of the preedited region. Cell 1990, 62:391-397.
67. Koslowsky DJ, Reifur L, Yu LE, Chen W. Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing. RNA Biol 2004, 1:28-34.
68. Connell GJ, Byrne EM, Simpson L. Guide RNA-independent and guide RNA-dependent uridine insertion into cytochrome b mRNA in a mitochondrial lysate from Leishmania tarentolae. Role of RNA secondary structure. J Biol Chem 1997, 272:4212-4218.
69. Frech GC, Bakalara N, Simpson L, Simpson AM. In vitro RNA editing-like activity in a mitochondrial extract from Leishmania tarentolae. EMBO J 1995, 14:178-187.
70. Peris M, Simpson AM, Grunstein J, Liliental JE, Frech GC, Simpson L. Native gel analysis of ribonucleoprotein complexes from a Leishmania tarentolae mitochondrial extract. Mol Biochem Parasitol 1997, 85:9-24.
71. Aphasizhev R, Aphasizheva I, Nelson RE, Gao G, Simpson AM, Kang X, Falick AM, Sbicego S, Simpson L. Isolation of a U-insertion/deletion editing complex from Leishmania tarentolae mitochondria. EMBO J 2003, 22:913-924.
72. Li F, Ge P, Hui WH, Atanasov I, Rogers K, Guo Q, Osato D, Falick AM, Zhou ZH, Simpson L. Structure of the core editing complex (L-complex) involved in uridine insertion/deletion RNA editing in trypanosomatid mitochondria. Proc Natl Acad Sci U S A 2009, 106:12306-12310.
73. Drozdz M, Palazzo SS, Salavati R, O'Rear J, Clayton C, Stuart K. TbMP81 is required for RNA editing in Trypanosoma brucei. EMBO J 2002, 21:1791-1799.
74. Kang X, Rogers K, Gao G, Falick AM, Zhou S, Simpson L. Reconstitution of uridine-deletion precleaved RNA editing with two recombinant enzymes. Proc Natl Acad Sci U S A 2005, 102:1017-1022.
75. Schnaufer A, Wu M, Park YJ, Nakai T, Deng J, Proff R, Hol WG, Stuart KD. A protein-protein interaction map of trypanosome ~20S editosomes. J Biol Chem 2010, 285:5282-5295.
76. Carnes J, Trotter JR, Peltan A, Fleck M, Stuart K. RNA editing in Trypanosoma brucei requires three different editosomes. Mol Cell Biol 2008, 28:122-130.
77. Pelletier M, Read LK. RBP16 is a multifunctional gene regulatory protein involved in editing and stabilization of specific mitochondrial mRNAs in Trypanosoma brucei. RNA 2003, 9:457-468.
78. Vondrusková E, van den Burg J, Zíková A, Ernst NL, Stuart K, Benne R, Lukes J. RNA interference analyses suggest a transcript-specific regulatory role for mitochondrial RNA-binding proteins MRP1 and MRP2 in RNA editing and other RNA processing in Trypanosoma brucei. J Biol Chem 2005, 280:2429-2438.
79. Miller MM, Halbig K, Cruz-Reyes J, Read LK. RBP16 stimulates trypanosome RNA editing in vitro at an early step in the editing reaction. RNA 2006, 12:1292-1303.
80. Sprehe M, Fisk JC, McEvoy SM, Read LK, Schumacher MA. Structure of the Trypanosoma brucei p22 protein, a cytochrome oxidase subunit II-specific RNA-editing accessory factor. J Biol Chem 2010, 285:18899-18908.
81. Fisk JC, Ammerman ML, Presnyak V, Read LK. TbRGG2, an essential RNA editing accessory factor in two Trypanosoma brucei life cycle stages. J Biol Chem 2008, 283:23016-23025.
82. Visomirski-Robic LM, Gott JM. Insertional editing in isolated Physarum mitochondria is linked to RNA synthesis. RNA 1997, 3:821-837.
83. Visomirski-Robic LM, Gott JM. Insertional editing of nascent mitochondrial RNAs in Physarum. Proc Natl Acad Sci U S A 1997, 94:4324-4329.
84. Kao C, Zheng M, Rudisser S. A simple and efficient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase. RNA 1999, 5:1268-1272.
85. Miller ML, Antes TJ, Qian F, Miller DL. Identification of a putative mitochondrial RNA polymerase from Physarum polycephalum: characterization, expression, purification, and transcription in vitro. Curr Genet 2006, 49:259-271.
86. Miller ML, Miller DL. Non-DNA-templated addition of nucleotides to the 3′ end of RNAs by the mitochondrial RNA polymerase of Physarum polycephalum. Mol Cell Biol 2008, 28:5795-5802.
87. Byrne EM, Gott JM. Cotranscriptional editing of Physarum mitochondrial RNA requires local features of the native template. RNA 2002, 8:1174-1185.
88. Rhee AC, Somerlot BH, Parimi N, Gott JM. Distinct roles for sequences upstream of and downstream from Physarum editing sites. RNA 2009, 15:1753-1765.
89. Shikanai T. RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol Life Sci 2006, 63:698-708.
90. Okuda K, Myouga F, Motohashi R, Shinozaki K, Shikanai T. Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing. Proc Natl Acad Sci U S A 2007, 104:8178-8183.
91. Okuda K, Chateigner-Boutin AL, Nakamura T, Delannoy E, Sugita M, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T. Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts. Plant Cell 2009, 21:146-156.
92. Salone V, Rudinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M, Szurek B, Small I, Knoop V, Lurin C. A hypothesis on the identification of the editing enzyme in plant organelles. FEBS Lett 2007, 581:4132-4138.
93. Hirose T, Sugiura M. 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. EMBO J 2001, 20:1144-1152.
94. Zeltz P, Hess WR, Neckermann K, Borner T, Kossel H. Editing of the chloroplast rpoB transcript is independent of chloroplast translation and shows different patterns in barley and maize. EMBO J 1993, 12:4291-4296.
95. Chateigner-Boutin AL, Small I. Plant RNA editing. RNA Biol 2010, 7:213-219.
96. Kotera E, Tasaka M, Shikanai T. A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature 2005, 433:326-330.
97. Tasaki E, Hattori M, Sugita M. The moss pentatricopeptide repeat protein with a DYW domain is responsible for RNA editing of mitochondrial ccmFc transcript. Plant J 2010, 62:560-570.
98. Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 2004, 16:2089-2103.
99. Schmitz-Linneweber C, Small I. Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 2008, 13:663-670.
100. Okuda K, Nakamura T, Sugita M, Shimizu T, Shikanai T. A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing. J Biol Chem 2006, 281:37661-37667.
101. Hammani K, Okuda K, Tanz SK, Chateigner-Boutin AL, Shikanai T, Small I. General features of chloroplast RNA editing factors and their target sites gained from a study of new Arabidopsis editing mutants. Plant Cell 2009, 21:3686-3689.
102. Rajasekhar VK, Mulligan RM. RNA editing in plant mitochondria: [α]-phosphate is retained during C-to-U conversion in mRNAs. Plant Cell 1993, 5:1843-1852.
103. Blanc V, Litvak S, Araya A. RNA editing in wheat mitochondria proceeds by a deamination mechanism. FEBS Lett 1995, 373:56-60.
104. Takenaka M, Brennicke A. In vitro RNA editing in pea mitochondria requires NTP or dNTP, suggesting involvement of an RNA helicase. J Biol Chem 2003, 278:47526-47533.
105. Faivre-Nitschke SE, Grienenberger JM, Gualberto JM. A prokaryotic-type cytidine deaminase from Arabidopsis thaliana gene expression and functional characterization. Eur J Biochem 1999, 263:896-903.
106. Muller HJ. The relation of recombination to mutational advance. Mutat Res 1964, 1:2-9.
107. Barr CM, Neiman M, Taylor DR. Inheritance and recombination of mitochondrial genomes in plants, fungi and animals. New Phytol 2005, 168:39-50.
108. Hauswirth WW, Laipis PJ. Mitochondrial DNA polymorphism in a maternal lineage of Holstein cows. Proc Natl Acad Sci U S A 1982, 79:4686-4690.
109. Chinnery PF, Thorburn DR, Samuels DC, White SL, Dahl HM, Turnbull DM, Lightowlers RN, Howell N. The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both? Trends Genet 2000, 16:500-505.
110. Fan W, Waymire KG, Narula N, Li P, Rocher C, Coskun PE, Vannan MA, Narula J, Macgregor GR, Wallace DC. A mouse model of mitochondrial disease reveals germline selection against severe mtDNA mutations. Science 2008, 319:958-962.
111. Tuppen HA, Blakely EL, Turnbull DM, Taylor RW. Mitochondrial DNA mutations and human disease. Biochim Biophys Acta 2010, 1797:113-128.
112. Hanson MR, Bentolila S. Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 2004, 16(suppl):S154-S169.
113. Morton BR. The role of context-dependent mutations in generating compositional and codon usage bias in grass chloroplast DNA. J Mol Evol 2003, 56:616-629.
114. Parkinson CL, Mower JP, Qiu YL, Shirk AJ, Song K, Young ND, DePamphilis CW, Palmer JD. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol Biol 2005, 5:73.
115. Smith DR. Unparalleled GC content in the plastid DNA of Selaginella. Plant Mol Biol 2009, 71:627-639.
116. Malek O, Lattig K, Hiesel R, Brennicke A, Knoop V. RNA editing in bryophytes and a molecular phylogeny of land plants. EMBO J 1996, 15:1403-1411.
117. Schmitz-Linneweber C, Kushnir S, Babiychuk E, Poltnigg P, Herrmann RG, Maier RM. Pigment deficiency in nightshade/tobacco cybrids is caused by the failure to edit the plastid ATPase α-subunit mRNA. Plant Cell 2005, 17:1815-1828.
118. Englund PT, Hajduk SL, Marini JC. The molecular biology of trypanosomes. Annu Rev Biochem 1982, 51:695-726.
119. Feagin JE, Jasmer DP, Stuart K. Developmentally regulated addition of nucleotides within apocytochrome b transcripts in Trypanosoma brucei. Cell 1987, 49:337-345.
120. Souza AE, Myler PJ, Stuart K. Maxicircle CR1 transcripts of Trypanosoma brucei are edited and developmentally regulated and encode a putative iron-sulfur protein homologous to an NADH dehydrogenase subunit. Mol Cell Biol 1992, 12:2100-2107.
121. Lu B, Hanson MR. A single nuclear gene specifies the abundance and extent of RNA editing of a plant mitochondrial transcript. Nucleic Acids Res 1992, 20:5699-5703.
122. Okuda K, Hammani K, Tanz SK, Peng L, Fukao Y, Myouga F, Motohashi R, Shinozaki K, Small I, Shikanai T. The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. Plant J 2010, 61:339-349.
123. Lu B, Hanson MR. Fully edited and partially edited nad9 transcripts differ in size and both are associated with polysomes in potato mitochondria. Nucleic Acids Res 1996, 24:1369-1374.
124. Phreaner CG, Williams MA, Mulligan RM. Incomplete editing of rps12 transcripts results in the synthesis of polymorphic polypeptides in plant mitochondria. Plant Cell 1996, 8:107-117.
125. Peeters NM, Hanson MR. Transcript abundance supercedes editing efficiency as a factor in developmental variation of chloroplast gene expression. RNA 2002, 8:497-511.
126. Chateigner-Boutin AL, Hanson MR. Developmental co-variation of RNA editing extent of plastid editing sites exhibiting similar cis-elements. Nucleic Acids Res 2003, 31:2586-2594.
127. Karcher D, Bock R. Site-selective inhibition of plastid RNA editing by heat shock and antibiotics: a role for plastid translation in RNA editing. Nucleic Acids Res 1998, 26:1185-1190.
128. Nakajima Y, Mulligan RM. Heat stress results in incomplete C-to-U editing of maize chloroplast mRNAs and correlates with changes in chloroplast transcription rate. Curr Genet 2001, 40:209-213.
129. Blanc V, Davidson NO. C-to-U RNA editing: mechanisms leading to genetic diversity. J Biol Chem 2003, 278:1395-1398.
130. Ochsenreiter T, Hajduk SL. Alternative editing of cytochrome c oxidase III mRNA in trypanosome mitochondria generates protein diversity. EMBO Rep 2006, 7:1128-1133.
131. Ochsenreiter T, Anderson S, Wood ZA, Hajduk SL. Alternative RNA editing produces a novel protein involved in mitochondrial DNA maintenance in trypanosomes. Mol Cell Biol 2008, 28:5595-5604.
132. Conticello SG. The AID/APOBEC family of nucleic acid mutators. Genome Biol 2008, 9:229.
133. Hegeman CE, Hayes ML, Hanson MR. Substrate and cofactor requirements for RNA editing of chloroplast transcripts in Arabidopsis in vitro. Plant J 2005, 42:124-132.