Mitochondrial genomes: Anything goes

Trends in Genetics

Volumn 19, Issue 12, 2003, Pages 709-716

  Burger, Gertraud ^a   Gray, Michael W ^b   Lang, B Franz ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

EUKARYOTE EVOLUTION; GENE EXPRESSION; GENE STRUCTURE; GENE TRANSFER; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME; MITOCHONDRIAL GENETICS; MITOCHONDRIAL RESPIRATION; MITOCHONDRION; NONHUMAN; OXIDATIVE PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN TRANSPORT; REVIEW; RNA TRANSLATION;

EUKARYOTA; PROTEOBACTERIA;

EID: 0344861878     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2003.10.012     Document Type: Review

References (84)

1. Saraste M. Oxidative phosphorylation at the fin de siecle. Science. 283:1999;1488-1493.
2. Herrmann J.M. Converting bacteria to organelles: evolution of mitochondrial protein sorting. Trends Microbiol. 11:2003;74-79.
3. Embley T.M., et al. Mitochondria and hydrogenosomes are two forms of the same fundamental organelle. Philos. Trans. R. Soc. Lond. B Biol. Sci. 358:2003;191-201.
4. Roger A.J., Silberman J.D. Cell evolution: mitochondria in hiding. Nature. 418:2002;827-829.
5. Gray M.W., et al. Mitochondrial evolution. Science. 283:1999;1476-1481.
6. Lang B.F., et al. Mitochondrial genome evolution and the origin of eukaryotes. Annu. Rev. Genet. 33:1999;351-397.
7. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 27:1999;1767-1780.
8. Bendich A.J. Reaching for the ring: the study of mitochondrial genome structure. Curr. Genet. 24:1993;279-290.
9. Bendich A.J. Structural analysis of mitochondrial DNA molecules from fungi and plants using moving pictures and pulsed-field gel electrophoresis. J. Mol. Biol. 255:1996;564-588.
10. Nosek, J. and Tomaska, L. Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy. Curr. Genet. (in press).
11. Burger G., Lang B.F. Parallels in genome evolution in mitochondria and bacterial symbionts. IUBMB Life. 55:2003;205-212.
12. Armstrong M.R., et al. A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics. 154:2000;181-192.
13. Watanabe K.I., et al. Mitochondrial genes are found on minicircle DNA molecules in the mesozoan animal Dicyema. J. Mol. Biol. 286:1999;645-650.
14. Lang B.F., et al. The closest unicellular relatives of animals. Curr. Biol. 12:2002;1773-1778.
15. Burger G., et al. Unique mitochondrial genome architecture in unicellular relatives of animals. Proc. Natl. Acad. Sci. U. S. A. 100:2003;892-897.
16. Morris J.C., et al. Replication of kinetoplast DNA: an update for the new millennium. Int. J. Parasitol. 31:2001;453-458.
17. Feagin J.E. Mitochondrial genome diversity in parasites. Int. J. Parasitol. 30:2000;371-390.
18. Notsu Y., et al. 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.
19. Ward B.L., et al. The mitochondrial genome is large and variable in a family of plants (cucurbitaceae). Cell. 25:1981;793-803.
20. Lang B.F., et al. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature. 387:1997;493-497.
21. Turmel M., et al. The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae. Plant Cell. 11:1999;1717-1730.
22. Lunt D.H., et al. Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology. Molec. Ecol. 7:1998;1441-1455.
23. Paquin B., Lang B.F. The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus. J. Mol. Biol. 255:1996;688-701.
24. Paquin B., et al. Double-hairpin elements in the mitochondrial DNA of Allomyces: evidence for mobility. Mol. Biol. Evol. 17:2000;1760-1768.
25. Andre C., et al. Small repeated sequences and the structure of plant mitochondrial genomes. Trends Genet. 8:1992;128-132.
26. Cummings D.J., et al. The complete DNA sequence of the mitochondrial genome of Podospora anserina. Curr. Genet. 17:1990;375-402.
27. Burger G., et al. The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: complete sequence, gene content and genome organization. J. Mol. Biol. 245:1995;522-537.
28. Ogawa S., et al. The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization. Mol. Gen. Genet. 263:2000;514-519.
29. Lonergan K.M., Gray M.W. Expression of a continuous open reading frame encoding subunits 1 and 2 of cytochrome c oxidase in the mitochondrial DNA of Acanthamoeba castellanii. J. Mol. Biol. 257:1996;1019-1030.
30. Hanson M.R. Plant mitochondrial mutations and male sterility. Annu. Rev. Genet. 25:1991;461-486.
31. Oudot-Le Secq M.P., et al. The complete sequence of a brown algal mitochondrial genome, the ectocarpale Pylaiella littoralis (L.) Kjellm. J. Mol. Evol. 53:2001;80-88.
32. Bullerwell C.E., et al. A novel motif for identifying rps3 homologs in fungal mitochondrial genomes. Trends Biochem. Sci. 25:2000;363-365.
33. Heinonen T.Y., et al. Rearranged coding segments, separated by a transfer RNA gene, specify the two parts of a discontinuous large subunit ribosomal RNA in Tetrahymena pyriformis mitochondria. J. Biol. Chem. 262:1987;2879-2887.
34. Schnare M., et al. A discontinuous subunit ribosomal RNA in Tetrahymena pyriformis mitochondria. J. Biol. Chem. 261:1986;5187-5193.
35. Boer P.H., Gray M.W. Scrambled ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA. Cell. 55:1988;399-411.
36. Gillespie D.E., et al. The fragmented mitochondrial ribosomal RNAs of Plasmodium falciparum have short A tails. Nucleic Acids Res. 27:1999;2416-2422.
37. Edqvist J., et al. Expression of mitochondrial protein-coding genes in Tetrahymena pyriformis. J. Mol. Biol. 297:2000;381-393.
38. Nedelcu A.M., et al. The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome. Genome Res. 10:2000;819-831.
39. Perez-Martinez X., et al. Subunit II of cytochrome c oxidase in chlamydomonad algae is a heterodimer encoded by two independent nuclear genes. J. Biol. Chem. 276:2001;11302-11309.
40. Adams K.L., et al. Mitochondrial gene transfer in pieces: fission of the ribosomal protein gene rpl2 and partial or complete gene transfer to the nucleus. Mol. Biol. Evol. 18:2001;2289-2297.
41. Gray M.W., et al. Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res. 26:1998;865-878.
42. Seif E.R., et al. Mitochondrial RNase P RNAs in ascomycete fungi: lineage-specific variations in RNA secondary structure. RNA. 9:2003;1073-1083.
43. Bullerwell C.E., et al. Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences. Nucleic Acids Res. 31:2003;1614-1623.
44. Kennell, J.C. and Cohen, S.M. In Handbook of Fungal Biotechnology (Arora, D., ed.), Marcel Dekker (in press).
45. Schardl C.L., et al. Mitochondrial DNA rearrangements associated with fertile revertants of S-type male-sterile maize. Cell. 43:1985;361-368.
46. Chesnick J.M., et al. The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization. Nucleic Acids Res. 28:2000;2512-2518.
47. Forget L., et al. Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi. Mol. Biol. Evol. 19:2002;310-319.
48. Bullerwell C.E., et al. A comparison of three fission yeast mitochondrial genomes. Nucleic Acids Res. 31:2003;759-768.
49. Marienfeld J., et al. The mitochondrial genome of Arabidopsis is composed of both native and immigrant information. Trends Plant Sci. 4:1999;495-502.
50. Koulintchenko M., et al. Plant mitochondria actively import DNA via the permeability transition pore complex. EMBO J. 22:2003;1245-1254.
51. Adams K.L., et al. Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature. 408:2000;354-357.
52. Adams K.L., et al. Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution. Genetics. 158:2001;1289-1300.
53. Adams K.L., et al. Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc. Natl. Acad. Sci. U. S. A. 99:2002;9905-9912.
54. Chomyn A., Attardi G. MtDNA mutations in aging and apoptosis. Biochem. Biophys. Res. Commun. 304:2003;519-529.
55. Wei Y.H., Lee H.C. Oxidative stress, mitochondrial DNA mutation, and impairment of antioxidant enzymes in aging. Exp. Biol. Med. (Maywood). 227:2002;671-682.
56. Lonergan K.M., Gray M.W. The ribosomal RNA gene region in Acanthamoeba castellanii mitochondrial DNA. A case of evolutionary transfer of introns between mitochondria and plastids? J. Mol. Biol. 239:1994;476-499.
57. Turmel M., et al. Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion). Mol. Biol. Evol. 12:1995;533-545.
58. Burger G., et al. Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea. Cyanobacterial introns and shared ancestry of red and green algae. Plant Cell. 11:1999;1675-1694.
59. Lang B.F. The mitochondrial genome of the fission yeast Schizosaccharomyces pombe: highly homologous introns are inserted at the same position of the otherwise less conserved cox1 genes in Schizosaccharomyces pombe and Aspergillus nidulans. EMBO J. 3:1984;2129-2136.
60. Cho Y., et al. Explosive invasion of plant mitochondria by a group I intron. Proc. Natl. Acad. Sci. U. S. A. 95:1998;14244-14249.
61. Cho Y., Palmer J.D. Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial cox1 gene during evolution of the Araceae family. Mol. Biol. Evol. 16:1999;1155-1165.
62. Paquin B., et al. Interspecific transfer of mitochondrial genes in fungi and creation of a homologous hybrid gene. Proc. Natl. Acad. Sci. U. S. A. 91:1994;11807-11810.
63. Bergthorsson U., et al. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature. 424:2003;197-201.
64. Hanson M.R., Folkerts O. Structure and function of the higher plant mitochondrial genome. Int. J. Cytol. 141:1992;129-172.
65. Anderson S., et al. Sequence and organization of the human mitochondrial genome. Nature. 290:1981;457-465.
66. Lander E.S., et al. Initial sequencing and analysis of the human genome. Nature. 409:2001;860-921.
67. Venter J.C., et al. The sequence of the human genome. Science. 291:2001;1304-1351.
68. Foury F., et al. The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 440:1998;325-331.
69. Giaever G., et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418:2002;387-391.
70. Elmerot C., et al. The mitochondrial genome of the pufferfish, Fugu rubripes, and ordinal teleostean relationships. Gene. 295:2002;163-172.
71. Aparicio S., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 297:2002;1301-1310.
72. Thorsness P.E., Fox T.D. Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae. Nature. 346:1990;376-379.
73. Woischnik M., Moraes C.T. Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Res. 12:2002;885-893.
74. Wolff G., et al. Complete sequence of the mitochondrial DNA of the chlorophyte alga Prototheca wickerhamii. Gene content and genome organization. J. Mol. Biol. 237:1994;75-86.
75. Kuck U., et al. DNA sequence analysis of the complete mitochondrial genome of the green alga Scenedesmu obliquus: evidence for UAG being a leucine and UCA being a non-sense codon. Gene. 253:2000;13-18.
76. Gray M.W., Boer P.H. Organization and expression of algal (Chlamydomonas reinhardtii) mitochondrial DNA. Philos. Trans. R. Soc. Lond. B Biol. Sci. 319:1988;135-147.
77. Tessier L.H., et al. The cox1 gene from Euglena gracilis: a protist mitochondrial gene without introns and genetic code modifications. Curr. Genet. 31:1997;208-213.
78. Covello P.S., 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.
79. Gabaldon T., Huynen M.A. Reconstruction of the proto-mitochondrial metabolism. Science. 301:2003;609.
80. Rasmusson A.G., et al. Homologues of yeast and bacterial rotenone-insensitive NADH dehydrogenases in higher eukaryotes: two enzymes are present in potato mitochondria. Plant J. 20:1999;79-87.
81. Baldauf S.L. The deep roots of eukaryotes. Science. 300:2003;1703-1706.
82. Cavalier-Smith T. A 6-kingdom classification and a unified phylogeny. Schwemmler W., Schenk H.E.A. Endocytobiology II. 1983;1027-1034 De Gruyter.
83. Martin W., Müller M. The hydrogen hypothesis for the first eukaryote. Nature. 392:1998;37-41.
84. Cermakian N., et al. On the evolution of the single-subunit RNA polymerases. J. Mol. Evol. 45:1997;671-681.