Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 Oct 11;11(19):6859–6872. doi: 10.1093/nar/11.19.6859

Genes for cytochrome c oxidase subunit I, URF2, and three tRNAs in Drosophila mitochondrial DNA.

D O Clary, D R Wolstenholme
PMCID: PMC326419  PMID: 6314262

Abstract

Genes for URF2, tRNAtrp, tRNAcys, tRNAtyr and cytochrome c oxidase subunit I (COI) have been identified within a sequenced segment of the Drosophila yakuba mtDNA molecule. The five genes are arranged in the order given. Transcription of the tRNAcys and tRNAtyr genes is in the same direction as replication, while transcription of the URF2, tRNAtrp and COI genes is in the opposite direction. A similar arrangement of these genes is found in mammalian mtDNA except that in the latter, the tRNAala and tRNAasn genes are located between the tRNAtrp and tRNAcys genes. Also, a sequence found between the tRNAasn and tRNAcys genes in mammalian mtDNA, which is associated with the initiation of second strand DNA synthesis, is not found in this region of the D. yakuba mtDNA molecule. As the D. yakuba COI gene lacks a standard translation initiation codon, we consider the possibility that the quadruplet ATAA may serve this function. As in other D. yakuba mitochondrial polypeptide genes, AGA codons in the URF2 and COI genes do not correspond in position to arginine-specifying codons in the equivalent genes of mouse and yeast mtDNAs, but do most frequently correspond to serine-specifying codons.

Full text

PDF
6859

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. Barrell B. G., Anderson S., Bankier A. T., de Bruijn M. H., Chen E., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A. Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3164–3166. doi: 10.1073/pnas.77.6.3164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beremand M. N., Blumenthal T. Overlapping genes in RNA phage: a new protein implicated in lysis. Cell. 1979 Oct;18(2):257–266. doi: 10.1016/0092-8674(79)90045-x. [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. Bonitz S. G., Berlani R., Coruzzi G., Li M., Macino G., Nobrega F. G., Nobrega M. P., Thalenfeld B. E., Tzagoloff A. Codon recognition rules in yeast mitochondria. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3167–3170. doi: 10.1073/pnas.77.6.3167. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bossi L., Roth J. R. Four-base codons ACCA, ACCU and ACCC are recognized by frameshift suppressor sufJ. Cell. 1981 Aug;25(2):489–496. doi: 10.1016/0092-8674(81)90067-2. [DOI] [PubMed] [Google Scholar]
  8. Bossi L., Ruth J. R. The influence of codon context on genetic code translation. Nature. 1980 Jul 10;286(5769):123–127. doi: 10.1038/286123a0. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. 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]
  11. 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]
  12. Clayton D. A. Replication of animal mitochondrial DNA. Cell. 1982 Apr;28(4):693–705. doi: 10.1016/0092-8674(82)90049-6. [DOI] [PubMed] [Google Scholar]
  13. Coruzzi G., Tzagoloff A. Assembly of the mitochondrial membrane system. DNA sequence of subunit 2 of yeast cytochrome oxidase. J Biol Chem. 1979 Sep 25;254(18):9324–9330. [PubMed] [Google Scholar]
  14. Cummins C. M., Donahue T. F., Culbertson M. R. Nucleotide sequence of the SUF2 frameshift suppressor gene of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1982 Jun;79(11):3565–3569. doi: 10.1073/pnas.79.11.3565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fiers W., Contreras R., Duerinck F., Haegmean G., Merregaert J., Jou W. M., Raeymakers A., Volckaert G., Ysebaert M., Van de Kerckhove J. A-protein gene of bacteriophage MS2. Nature. 1975 Jul 24;256(5515):273–278. doi: 10.1038/256273a0. [DOI] [PubMed] [Google Scholar]
  16. Fox T. D. Five TGA "stop" codons occur within the translated sequence of the yeast mitochondrial gene for cytochrome c oxidase subunit II. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6534–6538. doi: 10.1073/pnas.76.12.6534. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fox T. D., Leaver C. J. The Zea mays mitochondrial gene coding cytochrome oxidase subunit II has an intervening sequence and does not contain TGA codons. Cell. 1981 Nov;26(3 Pt 1):315–323. doi: 10.1016/0092-8674(81)90200-2. [DOI] [PubMed] [Google Scholar]
  18. Fox T. D., Weiss-Brummer B. Leaky +1 and -1 frameshift mutations at the same site in a yeast mitochondrial gene. Nature. 1980 Nov 6;288(5786):60–63. doi: 10.1038/288060a0. [DOI] [PubMed] [Google Scholar]
  19. Gauss D. H., Sprinzl M. Compilation of sequences of tRNA genes. Nucleic Acids Res. 1983 Jan 11;11(1):r55–103. [PMC free article] [PubMed] [Google Scholar]
  20. Gauss D. H., Sprinzl M. Compilation of tRNA sequences. Nucleic Acids Res. 1983 Jan 11;11(1):r1–53. [PMC free article] [PubMed] [Google Scholar]
  21. Gay N. J., Walker J. E. The atp operon: nucleotide sequence of the promoter and the genes for the membrane proteins, and the delta subunit of Escherichia coli ATP-synthase. Nucleic Acids Res. 1981 Aug 25;9(16):3919–3926. doi: 10.1093/nar/9.16.3919. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Goddard J. M., Wolstenholme D. R. Origin and direction of replication in mitochondrial DNA molecules from Drosophila melanogaster. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3886–3890. doi: 10.1073/pnas.75.8.3886. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Goddard J. M., Wolstenholme D. R. Origin and direction of replication in mitochondrial DNA molecules from the genus Drosophila. Nucleic Acids Res. 1980 Feb 25;8(4):741–757. [PMC free article] [PubMed] [Google Scholar]
  24. Heckman J. E., Sarnoff J., Alzner-DeWeerd B., Yin S., RajBhandary U. L. Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3159–3163. doi: 10.1073/pnas.77.6.3159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Kasamatsu H., Vinograd J. Replication of circular DNA in eukaryotic cells. Annu Rev Biochem. 1974;43(0):695–719. doi: 10.1146/annurev.bi.43.070174.003403. [DOI] [PubMed] [Google Scholar]
  26. Kastelein R. A., Remaut E., Fiers W., van Duin J. Lysis gene expression of RNA phage MS2 depends on a frameshift during translation of the overlapping coat protein gene. Nature. 1982 Jan 7;295(5844):35–41. doi: 10.1038/295035a0. [DOI] [PubMed] [Google Scholar]
  27. Macino G., Tzagoloff A. Assembly of the mitochondrial membrane system: sequence analysis of a yeast mitochondrial ATPase gene containing the oli-2 and oli-4 loci. Cell. 1980 Jun;20(2):507–517. doi: 10.1016/0092-8674(80)90637-6. [DOI] [PubMed] [Google Scholar]
  28. Martens P. A., Clayton D. A. Mechanism of mitochondrial DNA replication in mouse L-cells: localization and sequence of the light-strand origin of replication. J Mol Biol. 1979 Dec 5;135(2):327–351. doi: 10.1016/0022-2836(79)90440-6. [DOI] [PubMed] [Google Scholar]
  29. 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]
  30. Nass M. M. Pulse-label analysis and mapping of the two terminal regions of asynchronous complementary strand replication of mitochondrial DNA in transformed hamster cells. J Mol Biol. 1980 Jun 25;140(2):257–281. doi: 10.1016/0022-2836(80)90105-9. [DOI] [PubMed] [Google Scholar]
  31. Netzker R., Köchel H. G., Basak N., Küntzel H. Nucleotide sequence of Aspergillus nidulans mitochondrial genes coding for ATPase subunit 6, cytochrome oxidase subunit 3, seven unidentified proteins, four tRNAs and L-rRNA. Nucleic Acids Res. 1982 Aug 11;10(15):4783–4794. doi: 10.1093/nar/10.15.4783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. 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]
  33. Riddle D. L., Carbon J. Frameshift suppression: a nucleotide addition in the anticodon of a glycine transfer RNA. Nat New Biol. 1973 Apr 25;242(121):230–234. doi: 10.1038/newbio242230a0. [DOI] [PubMed] [Google Scholar]
  34. Robberson D. L., Kasamatsu H., Vinograd J. Replication of mitochondrial DNA. Circular replicative intermediates in mouse L cells. Proc Natl Acad Sci U S A. 1972 Mar;69(3):737–741. doi: 10.1073/pnas.69.3.737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Taira M., Yoshida E., Kobayashi M., Yaginuma K., Koike K. Tumor-associated mutations of rat mitochondrial transfer RNA genes. Nucleic Acids Res. 1983 Mar 25;11(6):1635–1643. doi: 10.1093/nar/11.6.1635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Tapper D. P., Clayton D. A. Mechanism of replication of human mitochondrial DNA. Localization of the 5' ends of nascent daughter strands. J Biol Chem. 1981 May 25;256(10):5109–5115. [PubMed] [Google Scholar]
  38. Thalenfeld B. E., Tzagoloff A. Assembly of the mitochondrial membrane system. Sequence of the oxi 2 gene of yeast mitochondrial DNA. J Biol Chem. 1980 Jul 10;255(13):6173–6180. [PubMed] [Google Scholar]
  39. Wolstenholme D. R., Koike K., Cochran-Fouts P. Single strand-containing replicating molecules of circular mitochondrial DNA. J Cell Biol. 1973 Jan;56(1):230–245. doi: 10.1083/jcb.56.1.230. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES