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Genetics. Mar 1992; 130(3): 471–498.
PMCID: PMC1204866

The Mitochondrial Genomes of Two Nematodes, Caenorhabditis Elegans and Ascaris Suum

Abstract

The nucleotide sequences of the mitochondrial DNA (mtDNA) molecules of two nematodes, Caenorhabditis elegans [13,794 nucleotide pairs (ntp)], and Ascaris suum (14,284 ntp) are presented and compared. Each molecule contains the genes for two ribosomal RNAs (s-rRNA and l-rRNA), 22 transfer RNAs (tRNAs) and 12 proteins, all of which are transcribed in the same direction. The protein genes are the same as 12 of the 13 protein genes found in other metazoan mtDNAs: Cyt b, cytochrome b; COI-III, cytochrome c oxidase subunits I-III; ATPase6, F(o) ATPase subunit 6; ND1-6 and 4L, NADH dehydrogenase subunits 1-6 and 4L: a gene for ATPase subunit 8, common to other metazoan mtDNAs, has not been identified in nematode mtDNAs. The C. elegans and A. suum mtDNA molecules both include an apparently noncoding sequence that contains runs of AT dinucleotides, and direct and inverted repeats (the AT region: 466 and 886 ntp, respectively). A second, apparently noncoding sequence in the C. elegans and A. suum mtDNA molecules (109 and 117 ntp, respectively) includes a single, hairpin-forming structure. There are only 38 and 89 other intergenic nucleotides in the C. elegans and A. suum mtDNAs, and no introns. Gene arrangements are identical in the C. elegans and A. suum mtDNA molecules except that the AT regions have different relative locations. However, the arrangement of genes in the two nematode mtDNAs differs extensively from gene arrangements in all other sequenced metazoan mtDNAs. Unusual features regarding nematode mitochondrial tRNA genes and mitochondrial protein gene initiation codons, previously described by us, are reviewed. In the C. elegans and A. suum mt-genetic codes, AGA and AGG specify serine, TGA specifies tryptophan and ATA specifies methionine. From considerations of amino acid and nucleotide sequence similarities it appears likely that the C. elegans and A. suum ancestral lines diverged close to the time of divergence of the cow and human ancestral lines, about 80 million years ago.

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Selected References

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  • Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. [PubMed]
  • Anderson S, de Bruijn MH, Coulson AR, Eperon IC, Sanger F, Young IG. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol. 1982 Apr 25;156(4):683–717. [PubMed]
  • Barrell BG, Bankier AT, Drouin J. A different genetic code in human mitochondria. Nature. 1979 Nov 8;282(5735):189–194. [PubMed]
  • Barrell BG, Anderson S, Bankier AT, de Bruijn MH, Chen E, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, et al. Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3164–3166. [PMC free article] [PubMed]
  • Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA. Sequence and gene organization of mouse mitochondrial DNA. Cell. 1981 Oct;26(2 Pt 2):167–180. [PubMed]
  • Boyce TM, Zwick ME, Aquadro CF. Mitochondrial DNA in the bark weevils: size, structure and heteroplasmy. Genetics. 1989 Dec;123(4):825–836. [PMC free article] [PubMed]
  • Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974 May;77(1):71–94. [PMC free article] [PubMed]
  • Brutlag DL, Clayton J, Friedland P, Kedes LH. SEQ: a nucleotide sequence analysis and recombination system. Nucleic Acids Res. 1982 Jan 11;10(1):279–294. [PMC free article] [PubMed]
  • Cantatore P, Roberti M, Rainaldi G, Gadaleta MN, Saccone C. The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus. J Biol Chem. 1989 Jul 5;264(19):10965–10975. [PubMed]
  • Clary DO, Wolstenholme DR. 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. [PMC free article] [PubMed]
  • Clary DO, Wolstenholme DR. 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. [PMC free article] [PubMed]
  • Clary DO, Wolstenholme DR. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J Mol Evol. 1985;22(3):252–271. [PubMed]
  • Clary DO, Wolstenholme DR. Drosophila mitochondrial DNA: conserved sequences in the A + T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNA. J Mol Evol. 1987;25(2):116–125. [PubMed]
  • Clary DO, Goddard JM, Martin SC, Fauron CM, Wolstenholme DR. Drosophila mitochondrial DNA: a novel gene order. Nucleic Acids Res. 1982 Nov 11;10(21):6619–6637. [PMC free article] [PubMed]
  • Clayton DA. Replication of animal mitochondrial DNA. Cell. 1982 Apr;28(4):693–705. [PubMed]
  • Clayton DA. Transcription of the mammalian mitochondrial genome. Annu Rev Biochem. 1984;53:573–594. [PubMed]
  • Dahlberg AE. The functional role of ribosomal RNA in protein synthesis. Cell. 1989 May 19;57(4):525–529. [PubMed]
  • Dale RM, McClure BA, Houchins JP. A rapid single-stranded cloning strategy for producing a sequential series of overlapping clones for use in DNA sequencing: application to sequencing the corn mitochondrial 18 S rDNA. Plasmid. 1985 Jan;13(1):31–40. [PubMed]
  • de Bruijn MH. Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code. Nature. 1983 Jul 21;304(5923):234–241. [PubMed]
  • Desjardins P, Morais R. Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J Mol Biol. 1990 Apr 20;212(4):599–634. [PubMed]
  • Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH. Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci U S A. 1986 Dec;83(24):9373–9377. [PMC free article] [PubMed]
  • Glotz C, Zwieb C, Brimacombe R, Edwards K, Kössel H. Secondary structure of the large subunit ribosomal RNA from Escherichia coli, Zea mays chloroplast, and human and mouse mitochondrial ribosomes. Nucleic Acids Res. 1981 Jul 24;9(14):3287–3306. [PMC free article] [PubMed]
  • Gray MW, Sankoff D, Cedergren RJ. On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA. Nucleic Acids Res. 1984 Jul 25;12(14):5837–5852. [PMC free article] [PubMed]
  • Gutell RR, Fox GE. A compilation of large subunit RNA sequences presented in a structural format. Nucleic Acids Res. 1988;16 (Suppl):r175–r269. [PMC free article] [PubMed]
  • Gutell RR, Weiser B, Woese CR, Noller HF. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. [PubMed]
  • Himeno H, Masaki H, Kawai T, Ohta T, Kumagai I, Miura K, Watanabe K. Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA. Gene. 1987;56(2-3):219–230. [PubMed]
  • Jacobs HT, Elliott DJ, Math VB, Farquharson A. Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J Mol Biol. 1988 Jul 20;202(2):185–217. [PubMed]
  • Jue RA, Woodbury NW, Doolittle RF. Sequence homologies among E. coli ribosomal proteins: evidence for evolutionarily related groupings and internal duplications. J Mol Evol. 1980 May;15(2):129–148. [PubMed]
  • Moazed D, Noller HF. Interaction of tRNA with 23S rRNA in the ribosomal A, P, and E sites. Cell. 1989 May 19;57(4):585–597. [PubMed]
  • Montoya J, Christianson T, Levens D, Rabinowitz M, Attardi G. Identification of initiation sites for heavy-strand and light-strand transcription in human mitochondrial DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(23):7195–7199. [PMC free article] [PubMed]
  • Ojala D, Montoya J, Attardi G. tRNA punctuation model of RNA processing in human mitochondria. Nature. 1981 Apr 9;290(5806):470–474. [PubMed]
  • Ojala D, Merkel C, Gelfand R, Attardi G. The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell. 1980 Nov;22(2 Pt 2):393–403. [PubMed]
  • Okimoto R, Wolstenholme DR. A set of tRNAs that lack either the T psi C arm or the dihydrouridine arm: towards a minimal tRNA adaptor. EMBO J. 1990 Oct;9(10):3405–3411. [PMC free article] [PubMed]
  • Okimoto R, Macfarlane JL, Wolstenholme DR. Evidence for the frequent use of TTG as the translation initiation codon of mitochondrial protein genes in the nematodes, Ascaris suum and Caenorhabditis elegans. Nucleic Acids Res. 1990 Oct 25;18(20):6113–6118. [PMC free article] [PubMed]
  • Okimoto R, Chamberlin HM, Macfarlane JL, Wolstenholme DR. Repeated sequence sets in mitochondrial DNA molecules of root knot nematodes (Meloidogyne): nucleotide sequences, genome location and potential for host-race identification. Nucleic Acids Res. 1991 Apr 11;19(7):1619–1626. [PMC free article] [PubMed]
  • Roe BA, Ma DP, Wilson RK, Wong JF. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J Biol Chem. 1985 Aug 15;260(17):9759–9774. [PubMed]
  • Singhal RP, Fallis PA. Structure, function, and evolution of transfer RNAs (with appendix giving complete sequences of 178 tRNAs). Prog Nucleic Acid Res Mol Biol. 1979;23:227–290. [PubMed]
  • Sprinzl M, Hartmann T, Weber J, Blank J, Zeidler R. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 1989;17 (Suppl):r1–172. [PMC free article] [PubMed]
  • 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. [PMC free article] [PubMed]
  • Sulston JE, Brenner S. The DNA of Caenorhabditis elegans. Genetics. 1974 May;77(1):95–104. [PMC free article] [PubMed]
  • Wahleithner JA, Wolstenholme DR. Mitochondrial plasmid DNAs of broad bean: nucleotide sequences, complex secondary structures, and transcription. Curr Genet. 1987;12(1):55–67. [PubMed]
  • Wilson AC, Carlson SS, White TJ. Biochemical evolution. Annu Rev Biochem. 1977;46:573–639. [PubMed]
  • Wolstenholme DR, Fauron CM. A partial map of the circular mitochondrial genome of Drosophila melanogaster. Location of EcoRI-sensitive sites and the adenine-thymine-rich region. J Cell Biol. 1976 Nov;71(2):434–448. [PMC free article] [PubMed]
  • Wolstenholme DR, Macfarlane JL, Okimoto R, Clary DO, Wahleithner JA. Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proc Natl Acad Sci U S A. 1987 Mar;84(5):1324–1328. [PMC free article] [PubMed]

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