Modeling sites of RNA editing as a fifth nucleotide state reveals progressive loss of edited sites from Angiosperm mitochondria

Molecular Biology and Evolution

Volumn 25, Issue 1, 2008, Pages 52-61

  Mower, Jeffrey P ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

Angiosperm mitochondria; Fifth state; Maximum likelihood; Nonreversible model; RNA editing; Substitution rate

Indexed keywords

NUCLEOTIDE; RNA; THYMIDINE;

ANGIOSPERM; ARTICLE; EVOLUTION; GENE SEQUENCE; MITOCHONDRIAL GENE; MITOCHONDRION; NONHUMAN; PROTEIN MODIFICATION; RNA EDITING;

ANGIOSPERMS; MITOCHONDRIA; MODELS, GENETIC; PLASTIDS; RNA EDITING; RNA, PLANT;

EUKARYOTA; MAGNOLIOPHYTA;

EID: 38349192613     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msm226     Document Type: Article

References (50)

1. Angiosperm Phylogeny Group. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc. 141:399-436.
2. Bowe LM, dePamphilis CW. 1996. Effects of RNA editing and gene processing on phylogenetic reconstruction. Mol Biol Evol. 13:1159-1166.
3. Brennicke A, Marchfelder A, Binder S. 1999. RNA editing. FEMS Microbiol Rev. 23:297-316.
4. Burnham KP, Anderson DR. 2002. Model selection and multimodel inference: a practical information-theoretic approach. 2nd ed. New York: Springer.
5. Cho Y, Mower JP, Qiu YL, Palmer JD. 2004. Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants. Proc Natl Acad Sci USA. 101:17741-17746.
6. Choury D, Farre JC, Jordana X, Araya A. 2004. Different patterns in the recognition of editing sites in plant mitochondria. Nucleic Acids Res. 32:6397-6406.
7. Covello PS, Gray MW. 1989. RNA editing in plant mitochondria. Nature. 341:662-666.
8. Covello PS, Gray MW. 1993. On the evolution of RNA editing. Trends Genet. 9:265-268.
9. Cummings MP, Myers DS. 2004. Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA. BMC Bioinformatics. 5:132.
10. Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.
11. Fey J, Weil JH, Tomita K, Cosset A, Dietrich A, Small I, Marechal-Drouard L. 2001. Editing of plant mitochondrial transfer RNAs. Acta Biochim Pol. 48:383-389.
12. Geiss KT, Abbas GM, Makaroff CA. 1994. Intron loss from the NADH dehydrogenase subunit 4 gene of lettuce mitochondrial DNA: evidence for homologous recombination of a cDNA intermediate. Mol Gen Genet. 243:97-105.
13. Giege P, Brennicke A. 1999. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci USA. 96:15324-15329.
14. Glaubitz JC, Carlson JE. 1992. RNA editing in the mitochondria of a conifer. Curr Genet. 22:163-165.
15. Gott JM, Emeson RB. 2000. Functions and mechanisms of RNA editing. Annu Rev Genet. 34:499-531.
16. Gualberto JM, Lamattina L, Bonnard G, Weil JH, Grienenberger JM. 1989. RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature. 341:660-662.
17. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symp Ser. 41:95-98.
18. Handa H. 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.
19. Hiesel R, Combettes B, Brennicke A. 1994. Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta. Proc Natl Acad Sci USA. 91:629-633.
20. Hiesel R, Wissinger B, Schuster W, Brennicke A. 1989. RNA editing in plant mitochondria. Science. 246:1632-1634.
21. Karpinska B, Karpinski S, Hillgren JE. 1995. The genes encoding subunit 3 of NADH dehydrogenase and ribosomal protein S12 are co-transcribed and edited in Pinus sylvestris (L.) mitochondria. Curr Genet. 28:423-428.
22. Kosakovsky Pond SL, Frost SDW, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 21:676-679.
23. Kotera E, Tasaka M, Shikanai T. 2005. A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts. Nature. 433:326-330.
24. Lopez L, Picardi E, Quagliariello C. 2007. RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales. Biochimie. 89:159-167.
25. Lu MZ, Szmidt AE, Wang XR. 1998. RNA editing in gymnosperms and its impact on the evolution of the mitochondrial coxI gene. Plant Mol Biol. 37:225-234.
26. Lurin C, Andres C, Aubourg S, et al. 2004. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell. 16:2089-2103 (19 co-authors).
27. Lynch M, Koskella B, Schaack S. 2006. Mutation pressure and the evolution of organelle genomic architecture. Science. 311:1727-1730.
28. Mower JP. 2005. PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics. 6:96.
29. Mower JP, Palmer JD. 2006. Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genomics. 276:285-293.
30. Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD. 2007. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol. 7:135.
31. Mulligan RM, Chang KL, Chou CC. 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.
32. Neuwirt J, Takenaka M, van der Merwe JA, Brennicke A. 2005. An in vitro RNA editing system from cauliflower mitochondria: editing site recognition parameters can vary in different plant species. RNA. 11:1563-1570.
33. Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K. 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 Genomics. 268:434-445.
34. Okuda K, Nakamura T, Sugita M, Shimizu T, Shikanai T. 2006. A pentatricopeptide repeat protein is a site recognition factor in chloroplast RNA editing. J Biol Chem. 281:37661-37667.
35. Parkinson CL, Mower JP, Qiu YL, Shirk AJ, Song K, Young ND, dePamphilis CW, Palmer JD. 2005. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol Biol. 5:73.
36. Perrotta G, Malek O, Heiser V, Brennicke A, Grohmann L, Quagliariello C. 1996. RNA editing in the cox3 mRNA of Magnolia is more extensive than in other dicot or monocot plants. Biochim Biophys Acta. 1307:254-258.
37. Petersen G, Seberg O, Davis JI, Stevenson DW. 2006. RNA editing and phylogenetic reconstruction in two monocot mitochondrial genes. Taxon. 55:871-886.
38. Picardi E, Quagliariello C. 2006. EdiPy: a resource to simulate the evolution of plant mitochondrial genes under the RNA editing. Comput Biol Chem. 30:77-80.
39. Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817-818.
40. Qiu YL, Li L, Hendry TA, Li R, Taylor DW, Issa MJ, Ronen AJ, Vekaria ML, White AM. 2006. Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes. Taxon. 55:837-856.
41. Regina TM, Lopez L, Picardi E, Quagliariello C. 2002. Striking differences in RNA editing requirements to express the rps4 gene in magnolia and sunflower mitochondria. Gene. 286:33-41.
42. Salone V, Rudinger M, Polsakiewicz M, Hoffmann B, Groth-Malonek M, Szurek B, Small I, Knoop V, Lurin C. 2007. A hypothesis on the identification of the editing enzyme in plant organelles. FEBS Lett. 581:4132-4138.
43. Schuster W, Ternes R, Knoop V, Hiesel R, Wissinger B, Brennicke A. 1991. Distribution of RNA editing sites in Oenothera mitochondrial mRNAs and rRNAs. Curr Genet. 20:397-404.
44. Shields DC, Wolfe KH. 1997. Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts. Mol Biol Evol. 14:344-349.
45. Shikanai T. 2006. RNA editing in plant organelles: machinery, physiological function and evolution. Cell Mol Life Sci. 63:698-708.
46. Small ID, Peeters N. 2000. The PPR motif - a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci. 25:46-47.
47. Soltis PS, Soltis DE, Chase MW. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature. 402:402-404.
48. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
49. Vangerow S, Teerkorn T, Knoop V. 1999. Phylogenetic information in the mitochondrial nad5 gene of pteridophytes: RNA editing and intron sequences. Plant Biol. 1:235-243.
50. Wikstrom N, Savolainen V, Chase MW. 2001. Evolution of the angiosperms: calibrating the family tree. Proc R Soc Lond B Biol Sci. 268:2211-2220.