Expression of a continuous open reading frame encoding subunits 1 and 2 of cytochrome c oxidase in the mitochondrial DNA of Acanthamoeba castellanii

Journal of Molecular Biology

Volumn 257, Issue 5, 1996, Pages 1019-1030

  Lonergan, Kim M ^a,b   Gray, Michael W ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

Acanthamoeba castellanii; Continuous open reading frame; cox1 and cox2; Cytochrome oxidase; Mitochondrial DNA

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA; RIBOSOME RNA;

ACANTHAMOEBA CASTELLANII; ARTICLE; ENZYME SUBUNIT; IMMUNOBLOTTING; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN PROCESSING; RNA PROCESSING; STOP CODON;

ACANTHAMOEBA CASTELLANII; SACCHAROMYCES CEREVISIAE;

EID: 0029968249     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0220     Document Type: Article

References (67)

1. Attardi, G. (1985). Animal mitochondrial DNA: an extreme example of genetic economy. Int. Rev. Cytol. 93, 93-145.
2. Bégu, D., Graves, P.-V., Domec, C., Arselin, G., Litvak, S. & Araya, A. (1990). RNA editing of wheat mitochondrial ATP synthase subunit 9: direct protein and cDNA sequencing. Plant Cell, 2, 1283-1290.
3. Boer, P. H. & Gray, M. W. (1986). The URF 5 gene of Chlamydomonas reinhardtii mitochondria: DNA sequence and mode of transcription. EMBO J. 5, 21-28.
4. Boer, P. H. & Gray, M. W. (1988). Genes encoding a subunit of respiratory NADH dehydrogenase (ND1) and a reverse transcriptase-like protein (RTL) are linked to ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA. EMBO J. 7, 3501-3508.
5. Bonen, L., Boer, P. H. & Gray, M. W. (1984). The wheat cytochrome oxidase subunit II gene has an intron insert and three radical amino acid changes relative to maize. EMBO J. 3, 2531-2536.
6. Bonen, L., Boer, P. H., McIntosh, J. E. & Gray, M. W. (1987). Nucleotide sequence of the wheat mitochondrial gene for subunit I of cytochrome oxidase. Nucl. Acids Res. 15, 6734.
7. Bonitz, S. G., Coruzzi, G., Thalenfeld, B. E., Tzagoloff, A. & Macino, G. (1980). Assembly of the mitochondrial membrane system. Structure and nucleotide sequence of the gene coding for subunit 1 of yeast cytochrome oxidase. J. Biol. Chem. 255, 11927-11941.
8. 3, branch of the Bradyrhizobium japonicum respiratory chain. Mol. Microbiol. 4, 2147-2157.
9. Brown, T. A., Waring, R. B., Scazzocchio, C. & Davies, R. W. (1985). The Aspergillus nidulans mitochondrial genome. Curr. Genet. 9, 113-117.
10. Burger, G., Plante, I., Lonergan, K. M. & Gray, M. W. (1995). The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: complete sequence, gene content and genome organization. J. Mol. Biol. 245, 522-537.
11. Chang, D. D., Fisher, R. P. & Clayton, D. A. (1987). Roles for a promoter and RNA processing in the synthesis of mitochondrial displacement-loop strands. Biochim. Biophys. Acta, 909, 85-91.
12. Chen, S. H., Habib, G., Yang, C.-Y., Gu, Z.-W., Lee, B. R., Weng, S.-a., Silberman, S. R., Cai, S.-J., Deslypere, J. P., Rosseneu, M., Goto, A. M. Jr, Li, W. H. & Chan, L. (1987). Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science, 238, 363-366.
13. Clary, D. O. & Wolstenholme, D. R. (1983). Nucleotide sequence of a segment of Drosophila mitochondrial DNA that contains genes for cytochrome c oxidase subunits II and III and ATPase subunit 6. Nucl. Acids Res. 11, 4211-4227.
14. Clayton, D. A. (1984). Transcription of the mammalian mitochondrial genome. Annu. Rev. Biochem. 53, 573-594.
15. Clayton, D. A. (1991). Nuclear gadgets in mitochondrial DNA replication and transcription. Trends Biochem. Sci. 16, 107-111.
16. Clayton, D. A. (1992). Transcription and replication of animal mitochondrial DNAs. Int. Rev. Cytol. 141, 217-232.
17. Coruzzi, G. & Tzagoloff, A. (1979). Assembly of the mitochondrial membrane system. DNA sequence of subunit 2 of yeast cytochrome oxidase. J. Biol. Chem. 254, 9324-9330.
18. Covello, P. S. & Gray, M. W. (1990). Differences in editing at homologous sites in messenger RNAs from angiosperm mitochondria. Nucl. Acids Res. 18, 5189-5196.
19. Covello, P. S. & Gray, M. W. (1992). 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, 3815-3820.
20. Darley-Usmar, V. M., Capaldi, R. A., Takamiya, S., Millett, F., Wilson, M. T., Malatesta, F. & Sarti, P. (1987). Reconstitution and molecular analysis of the respiratory chain. In Mitochondria: A Practical Approach (Darley-Usmar, V. M., Rickwood, D. & Wilson, M. T., eds), pp. 113-152, IRL Press Limited, Eynsham, Oxford, England.
21. Dyson, N. J., Brown, T. A., Ray, J. A., Waring, R. B., Scazzocchio, C. & Davies, R. W. (1989). Processing of mitochondrial RNA in Aspergillus nidulans. J. Mol. Biol. 208, 587-599.
22. Field, D. J., Sommerfield, A., Saville, B. J. & Collins, R. A. (1989). A group II intron in the Neurospora mitochondrial coI gene: nucleotide sequence and implications for splicing and molecular evolution. Nucl. Acids Res. 17, 9087-9099.
23. Geliebter, J. (1987). Dideoxynucleotide sequencing of RNA and uncloned cDNA. Focus, 9(1), 5-8.
24. Gonzalez, D. H., Bonnard, G. & Grienenberger, J.-M. (1993). A gene involved in the biogenesis of c-type cytochromes is co-transcribed with a ribosomal protein gene in wheat mitochondria. Curr. Genet. 24, 248-255.
25. Gray, M. W. (1989). Origin and evolution of mitochondrial DNA. Annu. Rev. Cell. Biol. 5, 25-50.
26. Gray, M. W. (1992). The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141, 233-357.
27. Gray, M. W. (1993). Origin and evolution of organelle genomes. Curr. Opin. Genet. Dev. 3, 884-890.
28. Gray, M. W. & Boer, P. H. (1988). Organization and expression of algal (Chlamydomonas reinhardtii) mitochondrial DNA. Phil. Trans. Roy. Soc. Lond. 319, 135-147.
29. Gray, M. W., Hanic-Joyce, P. J. & Covello, P. S. (1992). Transcription, processing and editing in plant mitochondria. Annu. Rev. Plant Physiol. Plant Mol. Biol. 43, 145-175.
30. Gualberto, J. M., Bonnard, G., Lamattina, L. & Grienenberger, J. M. (1991). Expression of the wheat mitochondrial nad3-rps12 transcription unit: correlation between editing and mRNA maturation. Plant Cell, 3, 1109-1120.
31. Haouazine, N., Takvorian, A., Jubier, M.-F., Michel, F. & Lejeune, B (1993). The nad6 gene and the exon d of nad1 are co-transcribed in wheat mitochondria. Curr. Genet. 24, 533-538.
32. Henikoff, S. (1984). Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene, 28, 351-359.
33. Higgins, D. G., Bleasby, A. J. & Fuchs, R. (1992). Clustal V: improved software for multiple sequence alignment. Comput. Appl. Biosci. 8, 189-191.
34. Holm, L., Saraste, M. & Wikström, M. (1987). Structural models of the redox centres in cytochrome oxidase. EMBO J. 6, 2819-2823.
35. Kelly, M., Lappalainen, P., Talbo, G., Haltia, T., van der Oost, J. & Saraste, M. (1993). Two cysteines, two histidines, and one methionine are ligands of a binuclear purple copper center. J. Biol. Chem. 268, 16781-16787.
36. Laemmli, U. K. (1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature, 227, 680-685.
37. Liu, A. W., Narayanan, K. K., André, C. P., Kaleikau, E. K. & Walbot, V. (1992). Co-transcription of orf25 and coxIII in rice mitochondria. Curr. Genet. 21, 507-513.
38. Lonergan, K. M. (1993). PhD thesis, Dalhousie University, Halifax, Nova Scotia, Canada.
39. Lonergan, K. M. & Gray, M. W. (1993). Editing of transfer RNAs in Acanthamoeba castellanii mitochondria. Science, 259, 812-816.
40. Lonergan, K. M. & Gray, M. W. (1994). The ribosomal RNA gene region in Acanthamoeba castellanii mitochondrial DNA. A case of evolutionary transfer of introns between mitochondria and plastids? J. Mol. Biol. 239, 476-499.
41. Maniatis, T., Fritsch, E. F. & Sambrook, J. (1982). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
42. Marck, C. (1989). Service de Biochimie, Département de Biologie, Institut de Recherche Fondamentale, CEA, France.
43. Neff, R. J., Ray, S. A., Benton, W. F. & Wilborn, M. (1964). Induction of synchronous encystment (differentiation) in Acanthamoeba sp. Methods Cell Physiol. 1, 55-83.
44. Newton, K. J. (1988). Plant mitochondrial genomes: organization, expression and variation. Annu. Rev. Plant Physiol. Plant Mol. Biol. 39, 503-532.
45. Nozato, N., Oda, K., Yamato, K., Ohta, E., Takemura, M., Akashi, K., Fukuzawa, H. & Ohyama K. (1993). Cotranscriptional expression of mitochondrial genes for subunits of NADH dehydrogenase, nad5, nod4, nad2, in Marchantia polymorpha. Mol. Gen. Genet. 237, 343-350.
46. Ojala, D., Montoya, J. & Attardi, G. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature, 290, 470-474.
47. Osinga, K. A., De Vries, E., Van der Horst, G. & Tabak, H. F. (1984). Processing of yeast mitochondrial messenger RNAs at a conserved dodecamer sequence. EMBO J. 3, 829-834.
48. Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
49. Perler, F. B., Davis, E. O., Dean, G. E., Gimble, F. S., Jack, W. E., Neff, N., Noren, C. J., Thorner, J. & Belfort, M. (1994). Protein splicing elements: inteins and exteins - a definition of terms and recommended nomenclature. Nucl. Acids Res. 22, 1125-1127.
50. Pietrokovski, S. (1994). Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Sci. 3, 2340-2350.
51. Pratje, E., Mannhaupt, G., Michaelis, G. & Beyreuther, K. (1983). A nuclear mutation prevents processing of a mitochondrially encoded membrane protein in Saccharomyces cerevisiae. EMBO J. 2, 1049-1054.
52. Raitio, M., Jalli, T. & Saraste, M. (1987). Isolation and analysis of the genes for cytochrome c oxidase in Paracoccus denitrificans. EMBO J. 6, 2825-2833.
53. Satta, Y. & Takahata, N. (1990). Evolution of Drosophila mitochondrial DNA and the history of the melanogaster subgroup. Proc. Natl Acad. Sci. USA, 87, 9558-9562.
54. Schinkel, A. H. & Tabak, H. F. (1989). Mitochondrial RNA polymerase: dual role in transcription and replication. Trends Genet. 5, 149-154.
55. Schuster, W. (1993). Ribosomal protein gene rpl5 is cotranscribed with the nad3 gene in Oenothera mitochondria. Mol. Gen. Genet. 240, 445-449.
56. Schuster, W. & Brennicke, A. (1994). The plant mitochondrial genome: physical structure, information content, RNA editing, and gene migration to the nucleus. Annu. Rev. Plant Physiol. Plant Mol. Biol. 45, 61-78.
57. Shang, J. & Clayton, D. A. (1994). Human mitochondrial transcription termination exhibits RNA polymerase independence and biased polarity in vitro. J. Biol. Chem. 269, 29112-29120.
58. 3-type cytochrome c oxidase of Rhodobacter sphaeroides. Mol. Microbiol. 6, 635-642.
59. Simon, M. & Faye, G. (1984). Organization and processing of the mitochondrial oxi3/oli2 multigenic transcript in yeast. Mol. Gen. Genet. 196, 266-274.
60. Stuart, K. (1991). RNA editing in mitochondrial mRNA of trypanosomatids. Trends Biochem. Sci. 16, 68-72.
61. Tabak, H. F., Grivell, L. A. & Borst, P. (1983). Transcription of mitochondrial DNA. CRC Crit. Rev. Biochem. 14, 297-317.
62. Tzagoloff, A. & Myers, A. M. (1986). Genetics of mitochondrial biogenesis. Annu. Rev. Biochem. 55, 249-285.
63. Wallace, C. J. A. (1993). The curious case of protein splicing: mechanistic insights suggested by protein semisynthesis. Protein Sci. 2, 697-705.
64. Wolstenholme, D. R. (1992). Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141, 173-216.
65. Xu, M.-Q., Comb, D. G., Paulus, H., Noren, C. J., Shao, Y. & Perler, F. B. (1994). Protein splicing: an analysis of the branched intermediate and its resolution by succinimide formation. EMBO J. 13, 5517-5522.
66. Young, I. G. & Anderson, S. (1980). The genetic code in bovine mitochondria: sequence of genes for the cytochrome oxidase subunit II and two mRNAs. Gene, 12, 257-265.
67. Zeff, R. A. & Geliebter, J. (1987). Oligonucleotide probes for genomic DNA blots. Focus, 9(2), 1-2.