Evolution of the mammalian mitochondrial control region - Comparisons of control region sequences between monotreme and therian mammals

Molecular Biology and Evolution

Volumn 13, Issue 6, 1996, Pages 798-808

  Gemmell, Neil J ^a,b   Western, Patrick S ^a   Watson, Jaclyn M ^a   A Marshall Graves, Jennifer ^a  

^a LA TROBE UNIVERSITY   (Australia)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

control region; D loop; evolution; length variation; mitochondrial DNA; platypus; polymerase chain reaction (PCR)

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; EVOLUTION; GENE CONTROL; GENETIC CONSERVATION; GENETIC VARIABILITY; MONOTREMATE; NONHUMAN; OPOSSUM;

ANIMALIA; DIDELPHIDAE; MAMMALIA; MONOTREMATA; THERIA;

EID: 0030008957     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025640     Document Type: Article

References (62)

1. ANDERSON, S., A. T. BANKIER, B. G. BARRELL et al. (14 co-authors). 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
2. ANDERSON, S., M. H. L. DEBRUIJN, A. R. COULSON, I. C. EPERON, R. SANGER, and I. G. YOUNG. 1982. Complete sequence of bovine mitochondrial DNA. J. Mol. Biol. 156: 683-717.
3. ARNASON, U., and E. JOHNSSON. 1992. The complete mitochondrial DNA sequence of the Harbour Seal. Phoca vitulina. J. Mol. Evol. 34:493-505.
4. BIBB, M. J., R. A. VAN ETTEN, C. T. WRIGHT, M. W. WALBERG, and R. A. CLAYTON. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167-180.
5. BOGENHAGEN, D. E. and B. K. YOZA, 1986. Accurate in vitro transcription of Xenopus laevis mitochondrial DNA from two bidirectional promoters. Mol. Cell. Biol. 6:2543-2550.
6. BROWN, G. G., G. GADALETA, G. PEPE, C. SACCONE, and E. SBISÁ. 1986. Structural conservation and variation in the D-loop containing region of vertebrate mitochondrial DNA. J. Mol. Biol. 192:503-511.
7. BUROKER, N. E., J. R. BROWN, T. A. GILBERT, P. J. O'HARA, A. T. BECKENBACH, W. K. THOMAS, and M. J. SMITH. 1990. Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model. Genetics 124:157-163.
8. CAIRNS, S. S., and D. F. BOGENHAGEN. 1986. Mapping of the displacement loop within the nucleotide-sequence of Xenopus laevis mtDNA. J. Biol. Chem 261:8481-8487.
9. CANTATORE, P., and C. SACCONE. 1987. Organization, structure, and evolution of mammalian mitochondrial genes. Int. Rev. Cytol. 108:149-208.
10. CHANG, D. D., and D. A. CLAYTON. 1984. Precise identification of individual promoters for transcription of each strand of human mitochondrial DNA. Cell 36:635-643.
11. _. 1985. Priming of human mitochondrial DNA replication occurs at the light strand promoter. Proc. Natl. Acad. Sci. USA 82:351-355.
12. _. 1987. A mammalian mitochondrial RNA processing activity contains nucleus-encoded RNA. Science 235:1178-1184.
13. CLAYTON, D. A. 1991. Nuclear gadgets in mitochondrial DNA replication and transcription. Trends Biol. Sci. 16:107-111.
14. COTÉ, J., and A. C. RUIZ-CARRILLO. 1993. Primers for mitochondrial DNA replication generated by endonuclease G. Science 261:765-769.
15. DESJARDINS, P., and R. MORAIS. 1990. Sequence and gene organization of the chicken mitochondrial genome. J. Mol. Biol. 212:599-634.
16. DILLON, M. C., and J. M. WRIGHT. 1993. Nucleotide-sequence of the D-loop region of the sperm whale (Physeter macrocephalus) mitochondrial genome. Mol. Biol. Evol. 10:296-305.
17. DODA, J. N., D. T. WRIGHT, and D. A. CLAYTON. 1981. Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc. Natl. Acad. Sci. USA 78:6116-6120.
18. DUNON-BLUTEAU, D. C., and G. M. BRUN. 1987. Mapping at the nucleotide level of Xenopus laevis mitochondrial D-loop H strand: structural features of the 3′ region. Biochem. Int. 14:643-657.
19. DUNON-BLUTEAL, D. C., M. VOLOVITCH, and G. M. BRUN. 1985. Nucleotide sequence of a Xenopus laevis mitochondrial DNA fragment containing the D-loop, flanking tRNA genes and the apocytochrome b gene. Gene 36:65-78.
20. FICKETT, J. W. 1982. Recognition of protein coding regions in DNA sequences. Nucleic Acids Res. 10:5303-5318.
21. FISCHER, R. P., J. N. TOPPER, and D. A. CLAYTON. 1987. Promoter selection in human mitochondria involves binding of a transcription factor to orientation-independent upstream regulatory elements. Cell 50:247-258.
22. FORAN, D. R., J. E. HIXSON, and W. M. BROWN. 1988. Comparisons of ape and human sequences that regulate mitochondrial DNA transcription and D-loop DNA synthesis. Nucleic Acids Res. 16:5841-5861.
23. GADALETA, G., G. PEPE, G. DE CANDIA, C. QUAGLIARIELLO, E. SBISÁ, and C. SACCONE. 1989. The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. J. Mol. Evol. 28:497-516.
24. GEMMELL, N. J., A. JANKE, P. W. WESTERN, J. M. WATSON, S. PAABO, and J. A. MARSHALL GRAVES. 1994. Cloning and characterisation of the platypus mitochondrial genome. J. Mol. Evol. 39:200-205.
25. GEMMELL, N. J., P. W. WESTERN, J. WALMSLEY, J. M. WATSON. N. D. MURRAY, and J. A. MARSHALL GRAVES. 1995. Determining platypus relationships. Aust. J. Zool. 43:283-291.
26. GHIVIZZANI, S. C., S. L. D. MACKAY, C. S. MADSEN, P. J. LAIPIS, and W. W. HAUSWIRTH. 1993. Transcribed heteroplasmic repeated sequences in the porcine mitochondrial DNA D-loop region. J Mol. Evol. 37:36-47.
27. GILBERT, D. G. 1992. Loopdloop, A Macintosh program for visualizing RNA secondary structure. Published electronically on the internet and available via anonymous ftp to iubio.bio.indiana.edu.
28. HAYASAKA, K., T. ISHIDA, and S. HORAI. 1991. Heteroplasmy and polymorphism in the major noncoding region of mitochondrial DNA in Japanese monkeys - association with tandemly repeated sequences. Mol. Biol. Evol. 8:399-415.
29. HAYASHI, J. I., Y. TAGASHIRA, and M. C. YOSHIDA. 1985. Absence of extensive recombination between inter- and intraspecies mitochondrial DNA in mammalian cells. Exp. Cell Res. 160:387-395.
30. HIGGINS, D., and P. M. SHARP. 1988. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244.
31. HOELZEL, A. R., J. M. HANCOCK, and G. A. DOVER. 1991. Evolution of the cetacean mitochondrial D-loop region. Mol. Biol. Evol. 8:475-493.
32. _. 1993. Generation of VNTRs and heteroplasmy by sequence turnover in the mitochondrial control region of two elephant seal species. J. Mol. Evol. 37:190-197.
33. HOELZEL, A. R., J. V. LOPEZ, G. A. DOVER, and S. J. O'BRIEN, 1994. Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores. J. Mol. Evol. 39:191-199.
34. JAEGER, J. A., D. H. TURNER, and M. ZUKER. 1989a. Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. USA 86:7706-7710.
35. _. 1989b. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 183:281-306.
36. JANKE, A., G. FELDMAIER-FUCHS, W. K. THOMAS, A. VON HAESELER, and S. PAABO. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243-256.
37. JANKE, A., N. J. GEMMELL, G. FELDMAIER-FUCHS, A. VON HAESELER, and S. PAABO. 1996. The mitochondrial genome of a monotreme - the platypus (Ornithorhychus anatinus). J. Mol. Evol. 42:153-159.
38. JOHANSEN, S., P. H. GUDDAL, and T. JOHANSEN. 1990. Organization of the mitochondrial genome of Atlantic cod, Gadus morhua. Nucleic Acids Res. 18:411-419.
39. JOHANSEN, S., and T. JOHANSEN. 1994. Sequence-analysis of 12 structural genes and a novel noncoding region from mitochondrial DNA of Atlantic cod, Gadus morhua. Biochim. Biophys. Acta 1218:213-217.
40. L'ABBé. D., J. F. DUHAIME, B. F. LANG, and R. MORAIS. 1991. The transcription of DNA in chicken mitochondria initiates from one major bidirectional promoter. J. Biol. Chem. 266: 10844-10850.
41. LEVINSON, G., and G. A. GUTMAN. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:203-221.
42. Low, R. L., J. M. BUZAN, and C. L. COUPER. 1987. The preference of the mitochondrial endonuclease for a conserved sequence block in mitochondrial DNA is conserved during mammalian evolution. Nucleic Acids Res. 14:6427-6445.
43. Low, R. L., O. W. CUMMINGS, and T. C. KING. 1988. The bovine mitochondrial endonuclease prefers a conserved sequence in the displacement loop region of mitochondrial DNA. J. Biol. Chem. 262:16164-16170.
44. MACKAY, S. L. D., P. D. OLIVO, P. J. LAIPIS, and W. W. HAUSWIRTH. 1986. Template-directed arrest of mammalian mitochondrial DNA synthesis. Mol. Cell. Biol. 6:1261-1267.
45. MADSEN, C. S., S. C. GHIVIZZANI, and W. W. HAUSWIRTH, 1993. In vivo and in vitro evidence for slipped mispairing in mammalian mitochondria. Proc. Natl. Acad. Sci. USA 90:7671-7675.
46. MIGNOTTE, B., M. BARAT, and J.-C. MOUNOLOU. 1985. Characterisation of a mitochondrial protein binding to single-stranded DNA. Nucleic Acids Res. 13:1703-1716.
47. MIGNOTTE, B., D. DUNON-BLUTEAU, C. REISS, and J.-C. MOUNOLOU. 1987. Sequence deduced physical properties in the D-loop region common to five vertebrate mitochondrial DNAs. J. Theor. Biol. 124:57-69.
48. MIGNOTTE, F., M. GUERIDE, A. M. CHAMPAGNE, and J.-C. MOUNOLOU. 1990. Direct repeats in the non-coding region of rabbit mitochondrial DNA: involvement in the generation of intra- and inter-individual heterogeneity. Eur. J. Biochem. 194:561-571.
49. MORITZ, C., and W. M. BROWN. 1987. Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards. Proc. Natl. Acad. Sci. USA 84: 7183-7187.
50. QUINN, T. W., and A. C. WILSON. 1993. Sequence evolution in and around the mitochondrial control region in birds. J. Mol. Evol. 37:36-47.
51. RAND, D. M. 1993. Endotherms, ectotherms, and mitochondrial genome-size variation. J. Mol. Evol. 37:281-295.
52. RAND, D. M., and R. G. HARRISON. 1989. Molecular population genetics of mtDNA size variation in crickets. Genetics 121:551-569.
53. ROE, B. A., D. MA, R. K. WILSON, and J. F. WONG. 1985. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260:9759-9774.
54. SACCONE, C., M. ATTIMONELLI, and E. SBISÁ. 1987. Structural elements highly preserved during the evolution of the D-loop containins region in venebrate mitochondrial DNA. J. Mol. Evol. 26:205-211.
55. SACCONE, C., G. PESOLE, and E. SBISÁ. 1991. The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. J. Mol. Evol. 33:83-91.
56. SOUTHERN, S. O., P. J. SOUTHERN, and A. E. DIZON. 1988. Molecular characterization of a cloned dolphin mitochondrial genome. J. Mol. Evol. 28:32-42.
57. UPHOLT, W. B., and I. B. DAWID. 1977. Mapping of mitochondrial DNA of individual sheep and goats: rapid evolution in the D-loop region. Cell 11:571-583.
58. WALBERG, M. W., and D. A. CLAYTON. 1981. Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res. 9:5411-5421.
59. WALLACE, D. C. 1989. Mitochondrial DNA mutations and neuromuscular disease. Trends Genet. 5:9-13
60. WILKINSON, G. S., and A. M. CHAPMAN. 1991. Length and sequence variation in evening bat D-loop mtDNA. Genetics 128:607-617.
61. ZEVERINO, C. E., C. MORITZ, A. HEIDMAN, R. A. STURM. 1992. Parallel origins of duplications and the formation of pseudogenes in mitochondrial DNA from parthenogenetic lizards (Heteronotia binoei; Gekkonidae). J. Mol. Evol. 33: 431-441.
62. ZUKER, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.