Skip to main content
Genetics logoLink to Genetics
. 1988 Apr;118(4):649–663. doi: 10.1093/genetics/118.4.649

Drosophila Melanogaster Mitochondrial DNA: Gene Organization and Evolutionary Considerations

R Garesse 1
PMCID: PMC1203320  PMID: 3130291

Abstract

The sequence of a 8351-nucleotide mitochondrial DNA (mtDNA) fragment has been obtained extending the knowledge of the Drosophila melanogaster mitochondrial genome to 90% of its coding region. The sequence encodes seven polypeptides, 12 tRNAs and the 3' end of the 16S rRNA and CO III genes. The gene organization is strictly conserved with respect to the Drosophila yakuba mitochondrial genome, and different from that found in mammals and Xenopus. The high A + T content of D. melanogaster mitochondrial DNA is reflected in a reiterative codon usage, with more than 90% of the codons ending in T or A, G + C rich codons being practically absent. The average level of homology between the D. melanogaster and D. yakuba sequences is very high (roughly 94%), although insertion and deletions have been detected in protein, tRNA and large ribosomal genes. The analysis of nucleotide changes reveals a similar frequency for transitions and transversions, and reflects a strong bias against G+C on both strands. The predominant type of transition is strand specific.

Full Text

The Full Text of this article is available as a PDF (1.4 MB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. doi: 10.1038/290457a0. [DOI] [PubMed] [Google Scholar]
  2. Anderson S., de Bruijn M. H., Coulson A. R., Eperon I. C., Sanger F., Young I. G. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol. 1982 Apr 25;156(4):683–717. doi: 10.1016/0022-2836(82)90137-1. [DOI] [PubMed] [Google Scholar]
  3. Berthier F., Renaud M., Alziari S., Durand R. RNA mapping on Drosophila mitochondrial DNA: precursors and template strands. Nucleic Acids Res. 1986 Jun 11;14(11):4519–4533. doi: 10.1093/nar/14.11.4519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bhat K. S., Bhat N. K., Kulkarni G. R., Iyengar A., Avadhani N. G. Expression of the cytochrome b-URF6-URF5 region of the mouse mitochondrial genome. Biochemistry. 1985 Oct 8;24(21):5818–5825. doi: 10.1021/bi00342a020. [DOI] [PubMed] [Google Scholar]
  5. Bibb M. J., Van Etten R. A., Wright C. T., Walberg M. W., Clayton D. A. Sequence and gene organization of mouse mitochondrial DNA. Cell. 1981 Oct;26(2 Pt 2):167–180. doi: 10.1016/0092-8674(81)90300-7. [DOI] [PubMed] [Google Scholar]
  6. Brown G. G., DesRosiers L. J. Rat mitochondrial DNA polymorphism: sequence analysis of a hypervariable site for insertions/deletions. Nucleic Acids Res. 1983 Oct 11;11(19):6699–6708. doi: 10.1093/nar/11.19.6699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brown W. M. Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3605–3609. doi: 10.1073/pnas.77.6.3605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Brown W. M., Prager E. M., Wang A., Wilson A. C. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol. 1982;18(4):225–239. doi: 10.1007/BF01734101. [DOI] [PubMed] [Google Scholar]
  9. Chomyn A., Mariottini P., Cleeter M. W., Ragan C. I., Matsuno-Yagi A., Hatefi Y., Doolittle R. F., Attardi G. Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory-chain NADH dehydrogenase. Nature. 1985 Apr 18;314(6012):592–597. doi: 10.1038/314592a0. [DOI] [PubMed] [Google Scholar]
  10. Clary D. O., Goddard J. M., Martin S. C., Fauron C. M., Wolstenholme D. R. Drosophila mitochondrial DNA: a novel gene order. Nucleic Acids Res. 1982 Nov 11;10(21):6619–6637. doi: 10.1093/nar/10.21.6619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Clary D. O., Wahleithner J. A., Wolstenholme D. R. Transfer RNA genes in Drosophila mitochondrial DNA: related 5' flanking sequences and comparisons to mammalian mitochondrial tRNA genes. Nucleic Acids Res. 1983 Apr 25;11(8):2411–2425. doi: 10.1093/nar/11.8.2411. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Clary D. O., Wolstenholme D. R. A cluster of six tRNA genes in Drosophila mitochondrial DNA that includes a gene for an unusual tRNAserAGY. Nucleic Acids Res. 1984 Mar 12;12(5):2367–2379. doi: 10.1093/nar/12.5.2367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Clary D. O., Wolstenholme D. R. Genes for cytochrome c oxidase subunit I, URF2, and three tRNAs in Drosophila mitochondrial DNA. Nucleic Acids Res. 1983 Oct 11;11(19):6859–6872. doi: 10.1093/nar/11.19.6859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Clary D. O., Wolstenholme D. R. Nucleotide sequence of a segment of Drosophila mitochondrial DNA that contains the genes for cytochrome c oxidase subunits II and III and ATPase subunit 6. Nucleic Acids Res. 1983 Jun 25;11(12):4211–4227. doi: 10.1093/nar/11.12.4211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Clary D. O., Wolstenholme D. R. The ribosomal RNA genes of Drosophila mitochondrial DNA. Nucleic Acids Res. 1985 Jun 11;13(11):4029–4045. doi: 10.1093/nar/13.11.4029. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Clayton D. A. Transcription of the mammalian mitochondrial genome. Annu Rev Biochem. 1984;53:573–594. doi: 10.1146/annurev.bi.53.070184.003041. [DOI] [PubMed] [Google Scholar]
  17. Doersen C. J., Guerrier-Takada C., Altman S., Attardi G. Characterization of an RNase P activity from HeLa cell mitochondria. Comparison with the cytosol RNase P activity. J Biol Chem. 1985 May 25;260(10):5942–5949. [PubMed] [Google Scholar]
  18. Eckerman D. J., Symons R. H. Sequence at the site of attachment of an affinity-label derivative of puromycin on 23-S ribosomal RNA of Escherichia coli ribosomes. Eur J Biochem. 1978 Jan 2;82(1):225–234. doi: 10.1111/j.1432-1033.1978.tb12015.x. [DOI] [PubMed] [Google Scholar]
  19. Eperon I. C., Anderson S., Nierlich D. P. Distinctive sequence of human mitochondrial ribosomal RNA genes. Nature. 1980 Jul 31;286(5772):460–467. doi: 10.1038/286460a0. [DOI] [PubMed] [Google Scholar]
  20. Ferris S. D., Sage R. D., Prager E. M., Ritte U., Wilson A. C. Mitochondrial DNA evolution in mice. Genetics. 1983 Nov;105(3):681–721. doi: 10.1093/genetics/105.3.681. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. HsuChen C. C., Kotin R. M., Dubin D. T. Sequences of the coding and flanking regions of the large ribosomal subunit RNA gene of mosquito mitochondria. Nucleic Acids Res. 1984 Oct 25;12(20):7771–7785. doi: 10.1093/nar/12.20.7771. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Merten S. H., Pardue M. L. Mitochondrial DNA in Drosophila. An analysis of genome organization and transcription in Drosophila melanogaster and Drosophila virilis. J Mol Biol. 1981 Nov 25;153(1):1–21. doi: 10.1016/0022-2836(81)90523-4. [DOI] [PubMed] [Google Scholar]
  23. Ojala D., Montoya J., Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981 Apr 9;290(5806):470–474. doi: 10.1038/290470a0. [DOI] [PubMed] [Google Scholar]
  24. Powell J. R., Caccone A., Amato G. D., Yoon C. Rates of nucleotide substitution in Drosophila mitochondrial DNA and nuclear DNA are similar. Proc Natl Acad Sci U S A. 1986 Dec;83(23):9090–9093. doi: 10.1073/pnas.83.23.9090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Roberts J. W., Grula J. W., Posakony J. W., Hudspeth R., Davidson E. H., Britten R. J. Comparison of sea urchin and human mtDNA: evolutionary rearrangement. Proc Natl Acad Sci U S A. 1983 Aug;80(15):4614–4618. doi: 10.1073/pnas.80.15.4614. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Roe B. A., Ma D. P., Wilson R. K., Wong J. F. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J Biol Chem. 1985 Aug 15;260(17):9759–9774. [PubMed] [Google Scholar]
  27. Solignac M., Monnerot M., Mounolou J. C. Mitochondrial DNA evolution in the melanogaster species subgroup of Drosophila. J Mol Evol. 1986;23(1):31–40. doi: 10.1007/BF02100996. [DOI] [PubMed] [Google Scholar]
  28. Staden R. A new computer method for the storage and manipulation of DNA gel reading data. Nucleic Acids Res. 1980 Aug 25;8(16):3673–3694. doi: 10.1093/nar/8.16.3673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Staden R. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Res. 1982 May 11;10(9):2951–2961. doi: 10.1093/nar/10.9.2951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Staden R. An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences. Nucleic Acids Res. 1982 May 11;10(9):2951–2961. doi: 10.1093/nar/10.9.2951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Staden R. Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res. 1982 Aug 11;10(15):4731–4751. doi: 10.1093/nar/10.15.4731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Steward R., Gehring W. J. A hybrid plasmid containing Drosophila melanogaster DNA sequences complementary to the large mitochondrial ribosomal RNA. Gene. 1981 Jun-Jul;14(1-2):131–135. doi: 10.1016/0378-1119(81)90155-4. [DOI] [PubMed] [Google Scholar]
  33. Wilson A. C., Carlson S. S., White T. J. Biochemical evolution. Annu Rev Biochem. 1977;46:573–639. doi: 10.1146/annurev.bi.46.070177.003041. [DOI] [PubMed] [Google Scholar]
  34. Wolstenholme D. R., Clary D. O. Sequence evolution of Drosophila mitochondrial DNA. Genetics. 1985 Apr;109(4):725–744. doi: 10.1093/genetics/109.4.725. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES