RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales

Biochimie

Volumn 89, Issue 1, 2007, Pages 159-167

  Lopez, L ^a   Picardi, E ^a   Quagliariello, C ^a  

^a UNIVERSITY OF CALABRIA   (Italy)

Author keywords

Asparagales; cox3; Plant mitochondria; Retroprocessing events; RNA editing loss; rps13

Indexed keywords

MESSENGER RNA; MITOCHONDRIAL RNA;

AMARYLLIDACEAE; ARTICLE; ASPARAGALES; CCB2 GENE; COX3 GENE; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME ANALYSIS; HIGHER PLANT; IRIDACEAE; LILIALES; MITOCHONDRIAL GENE; MITOCHONDRIAL GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT GENETICS; REVERSE TRANSCRIPTION; RNA EDITING; RNA GENE; RNA SEQUENCE; RPS13; SEQUENCE ANALYSIS; TRANSCRIPTOMICS; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; DNA, MITOCHONDRIAL; ELECTRON TRANSPORT COMPLEX IV; LILIACEAE; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; POLYMERASE CHAIN REACTION; RIBOSOMAL PROTEINS; RNA EDITING; RNA, PLANT;

AMARYLLIDACEAE; ASPARAGALES; EMBRYOPHYTA; IRIDACEAE; LILIALES; LILIOPSIDA;

EID: 33845672553     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2006.09.011     Document Type: Article

References (43)

1. Sugiyama Y., Watase Y., Nagase M., Makita N., Yagura S., Hirai A., and Sugiura M. The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol. Gen. Genomics 272 (2005) 603-615
2. Millar A.H., Heazlewood J.L., Kristensen B.K., Braun H.P., and Moller I.M. The plant mitochondrial proteome. Trends Plant Sci. 10 (2005) 36-43
3. Binder S., and Brennicke A. Gene expression in plant mitochondria: transcriptional and post-transcriptional control. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 358 (2002) 181-188
4. Shikanai T. RNA editing in plant organelles: machinery, physiological function and evolution. Cell. Mol. Life Sci. 63 (2006) 698-708
5. Giegé P., and Brennicke A. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc. Natl. Acad. Sci. USA 96 (1999) 15324-15329
6. Ward G.C., and Levings III C.S. The protein-encoding gene T-urf13 is not edited in maize mitochondria. Plant Mol. Biol. 17 (1991) 1083-1088
7. 2-terminal protein sequencing. Plant Mol. Biol. 24 (1994) 129-141
8. Rankin C.T., Cutright M.T., and Makaroff C.A. Characterization of the radish mitochondrial nad3/rps12 locus: analysis of recombination repeats and RNA editing. Curr. Genet. 29 (1996) 564-571
9. Handa H. 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 (2003) 5907-5916
10. Steinhauser S., Beckert S., Capesius I., Malek O., and Knoop V. Plant mitochondrial RNA editing. J. Mol. Evol. 48 (1999) 303-312
11. Turmel M., Otis C., and Lemieux C. The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants. Plant Cell 15 (2003) 1888-1903
12. Turmel M., Otis C., and Lemieux C. The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc. Natl. Acad. Sci. USA 99 (2002) 11275-11280
13. Friis E.M., Pedersen K.R., and Crane P.R. Araceae from the Early Cretaceous of Portugal: Evidence on the emergence of monocotyledons. Proc. Natl. Acad. Sci. USA 101 (2004) 16565-16570
14. Angiosperm Phylogeny Group (APG). An ordinal classification for the families of flowering plants. Ann. Missouri Bot. Gard. 85 (1998) 531-533
15. Doyle J.J., and Doyle J.L. Isolation of plant DNA from fresh tissue. Focus 12 (1990) 13-15
16. Sambrook J., and Russel D.W. Molecular Cloning. A Laboratory Manual. third ed. (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
17. Thompson J.D., Higgins D.G., and Gibson T.J. 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 (1994) 4673-4680
18. Nicholas K.B., Nicholas Jr. H.B., and Deerfield II D.W. GeneDoc: Analysis and visualization of genetic variation. EMBNEW. NEWS 4 (1997) 14
19. Kumar S., Tamura K., and Nei M. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5 (2004) 150-163
20. Mower J.P. PREP-Mt: predictive RNA editor for plant mitochondrial genes. BMC Bioinformatics 6 (2005) 96
21. Quagliariello C., Saiardi A., and Gallerani R. The cytochrome oxidase subunit III gene in sunflower mitochondria is co-transcribed with an open reading frame conserved in higher plants. Curr. Genet. 18 (1990) 355-363
22. Regina T.M.R., Lopez L., Bruno R., and Quagliariello C. RNA editing of the ribosomal protein S13 transcripts in magnolia and sunflower mitochondria. Plant Cell Physiol. 42 (2001) 768-774
23. Oda K., Yamoto K., Ohta E., Nakamura Y., Takemura M., Nozato N., Akashi K., Kanegae T., Ogura Y., Kohchi T., and Ohyama K. Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. J. Mol. Biol. 223 (1992) 1-7
24. Sper-Whitis G.L., Moody J.L., and Vaughn J.C. Universality of mitochondrial RNA editing in cytochrome-c oxidase subunit I (coxI) among the land plants. Biochim. Biophys. Acta 1307 (1996) 301-308
25. Perrotta G., Malek O., Heiser V., Brennicke A., Grohmann L., and Quagliariello C. RNA editing in the cox3 mRNA of Magnolia is more extensive than in other dicot or monocot plants. Biochim. Biophys. Acta 1307 (1996) 254-258
26. Gualberto J.M., Weil J.H., and Grienenberger J.M. Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites. Nucleic Acids Res. 18 (1990) 3771-3776
27. Anderson S., Bankier A.T., Barrell B.G., De Bruijn M.H.L., Coulson A.R., Drouin J., Eperon I.C., Nierlich D.P., Roe B.A., Sanger F., Schreier P.H., Smith A.J.H., Staden R., and Young I.G. Sequence and organization of the human mitochondrial genome. Nature 290 (1981) 457-465
28. Takvorian A., Coville J.L., Haouazine-Takvorian N., Rode A., and Hartmann C. The wheat mitochondrial rps13 gene: RNA editing and co-transcription with the atp6 gene. Curr. Genet. 31 (1997) 497-502
29. Faivre-Nitschke S.E., Nazoa P., Gualberto J.M., Grienenberger J.-M., and Bonnard G. Wheat mitochondria ccmB encodes the membrane domain of a putative ABC transporter involved in cytochrome c biogenesis. Biochim. Biophys. Acta 1519 (2001) 199-208
30. Regina T.M., Picardi E., Lopez L., Pesole G., and Quagliariello C. A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms. J. Mol. Evol. 60 (2005) 196-206
31. Covello P.S., and Gray M.W. On the evolution of RNA editing. Trends Genet. 9 (1993) 265-268
32. Covello P.S., and Gray M.W. Silent mitochondrial and active nuclear genes for subunit 2 of cytochrome c oxidase (cox2) in soybean: evidence for RNA-mediated gene transfer. EMBO J. 11 (1992) 3815-3820
33. Laroche J., Li P., Maggia L., and Bousquet J. Molecular evolution of angiosperm mitochondrial introns and exons. Proc. Natl. Acad. Sci. USA 94 (1997) 5722-5727
34. Perez-Martinez X., Vazquez-Acevedo M., Tolkunova E., Funes S., Claros M.G., Davidson E., King M.P., and Gonzalez-Halphen D. Unusual location of a mitochondrial gene. Subunit III of cytochrome c oxidase is encoded in the nucleus of Chlamydomonad algae. J. Biol. Chem. 275 (2000) 30144-30152
35. Adams K.L., Daley D.O., Whelan J., and Palmer J.D. Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterpart. Plant Cell 14 (2002) 931-943
36. Mollier P., Hoffmann B., Debast C., and Small I. The gene encoding Arabidopsis thaliana mitochondrial ribosomal protein S13 is a recent duplication of the gene encoding plastid S13. Curr. Genet. 40 (2002) 405-409
37. Lu M.Z., Szmidt A.E., and Wang X.R. RNA editing in gymnosperms and its impact on the evolution of the mitochondrial cox1 gene. Plant Mol. Biol. 37 (1998) 225-234
38. Notsu Y., Masood S., Nishikawa T., Kubo N., Akiduki G., Nakazono M., Hirai A., and Kadowaki K. 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 (2002) 434-445
39. Geiss K.T., Abbas G.M., and Makaroff C.A. 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 (1994) 97-105
40. Itchoda N., Nishizawa S., Nagano H., Kubo T., and Mikami T. The sugar beet mitochondrial nad4 gene: an intron loss and its phylogenetic implication in the Caryophyllales. Theor. Appl. Genet. 104 (2002) 209-213
41. Parkinson C.L., Mower J.P., Qiu Y.L., Shirk A.J., Song K., Young N.D., dePamphilis C.W., and Palmer J.D. Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol. Biol. 5 (2005) 73
42. Shields D.C., and Wolfe K.H. Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts. Mol. Biol. Evol. 14 (1997) 344-349
43. Lindemann H., and Wittmann-Liebold B. Primary structure of protein S13 from the small subunit of Escherichia coli ribosomes, Hoppe Seylers Z. Physiol. Chem. 358 (1977) 843-863