• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of geneticsGeneticsCurrent IssueInformation for AuthorsEditorial BoardSubscribeSubmit a Manuscript
Genetics. Mar 1998; 148(3): 1091–1108.
PMCID: PMC1460033

The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code.

Abstract

The circular, 17,443 nucleotide-pair mitochondrial (mt) DNA molecule of the sea anemone, Metridium senile (class Anthozoa, phylum Cnidaria) is presented. This molecule contains genes for 13 energy pathway proteins and two ribosomal (r) RNAs but, relative to other metazoan mtDNAs, has two unique features: only two transfer RNAs (tRNA(f-Met) and tRNA(Trp)) are encoded, and the cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 5 (ND5) genes each include a group I intron. The COI intron encodes a putative homing endonuclease, and the ND5 intron contains the molecule's ND1 and ND3 genes. Most of the unusual characteristics of other metazoan mtDNAs are not found in M. senile mtDNA: unorthodox translation initiation codons and partial translation termination codons are absent, the use of TGA to specify tryptophan is the only genetic code modification, and both encoded tRNAs have primary and secondary structures closely resembling those of standard tRNAs. Also, with regard to size and secondary structure potential, the mt-s-rRNA and mt-1-rRNA have the least deviation from Escherichia coli 16S and 23S rRNAs of all known metazoan mt-rRNAs. These observations indicate that most of the genetic variations previously reported in metazoan mtDNAs developed after Cnidaria diverged from the common ancestral line of all other Metazoa.

Full Text

The Full Text of this article is available as a PDF (782K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Model Alfred. Five Years of General Practice. Br Med J. 1958 Jan 11;1(5062):d101–102. [PMC free article]
  • Arnason U, Xu X, Gullberg A. Comparison between the complete mitochondrial DNA sequences of Homo and the common chimpanzee based on nonchimeric sequences. J Mol Evol. 1996 Feb;42(2):145–152. [PubMed]
  • Asakawa S, Himeno H, Miura K, Watanabe K. Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome. Genetics. 1995 Jul;140(3):1047–1060. [PMC free article] [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]
  • Beagley CT, Okada NA, Wolstenholme DR. Two mitochondrial group I introns in a metazoan, the sea anemone Metridium senile: one intron contains genes for subunits 1 and 3 of NADH dehydrogenase. Proc Natl Acad Sci U S A. 1996 May 28;93(11):5619–5623. [PMC free article] [PubMed]
  • Bessho Y, Ohama T, Osawa S. Planarian mitochondria. II. The unique genetic code as deduced from cytochrome c oxidase subunit I gene sequences. J Mol Evol. 1992 Apr;34(4):331–335. [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]
  • Boer PH, Gray MW. Transfer RNA genes and the genetic code in Chlamydomonas reinhardtii mitochondria. Curr Genet. 1988 Dec;14(6):583–590. [PubMed]
  • Boore JL, Brown WM. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics. 1994 Oct;138(2):423–443. [PMC free article] [PubMed]
  • Boore JL, Brown WM. Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics. 1995 Sep;141(1):305–319. [PMC free article] [PubMed]
  • Bridge D, Cunningham CW, Schierwater B, DeSalle R, Buss LW. Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8750–8753. [PMC free article] [PubMed]
  • Burger G, Plante I, Lonergan KM, Gray MW. The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: complete sequence, gene content and genome organization. J Mol Biol. 1995 Feb 3;245(5):522–537. [PubMed]
  • Buzzo K, Fouts DL, Wolstenholme DR. EcoRI cleavage site variants of mitochondrial DNA molecules from rats. Proc Natl Acad Sci U S A. 1978 Feb;75(2):909–913. [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]
  • Hatzoglou E, Rodakis GC, Lecanidou R. Complete sequence and gene organization of the mitochondrial genome of the land snail Albinaria coerulea. Genetics. 1995 Aug;140(4):1353–1366. [PMC free article] [PubMed]
  • Hayashi J, Takemitsu M, Goto Y, Nonaka I. Human mitochondria and mitochondrial genome function as a single dynamic cellular unit. J Cell Biol. 1994 Apr;125(1):43–50. [PMC free article] [PubMed]
  • Chomyn A, Hunkapiller MW, Attardi G. Alignment of the amino terminal amino acid sequence of human cytochrome c oxidase subunits I and II with the sequence of their putative mRNAs. Nucleic Acids Res. 1981 Feb 25;9(4):867–877. [PMC free article] [PubMed]
  • Hoffmann RJ, Boore JL, Brown WM. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics. 1992 Jun;131(2):397–412. [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]
  • 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]
  • 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]
  • Krettek A, Gullberg A, Arnason U. Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of the Lipotyphla. J Mol Evol. 1995 Dec;41(6):952–957. [PubMed]
  • Clayton DA. Replication and transcription of vertebrate mitochondrial DNA. Annu Rev Cell Biol. 1991;7:453–478. [PubMed]
  • Lambowitz AM, Belfort M. Introns as mobile genetic elements. Annu Rev Biochem. 1993;62:587–622. [PubMed]
  • Clayton DA. Transcription and replication of animal mitochondrial DNAs. Int Rev Cytol. 1992;141:217–232. [PubMed]
  • Colleaux L, D'Auriol L, Galibert F, Dujon B. Recognition and cleavage site of the intron-encoded omega transposase. Proc Natl Acad Sci U S A. 1988 Aug;85(16):6022–6026. [PMC free article] [PubMed]
  • Crozier RH, Crozier YC. The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics. 1993 Jan;133(1):97–117. [PMC free article] [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]
  • Nugent JM, Palmer JD. RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell. 1991 Aug 9;66(3):473–481. [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]
  • de Bruijn MH, Schreier PH, Eperon IC, Barrell BG, Chen EY, Armstrong PW, Wong JF, Roe BA. A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem. Nucleic Acids Res. 1980 Nov 25;8(22):5213–5222. [PMC free article] [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]
  • Dietrich A, Weil JH, Maréchal-Drouard L. Nuclear-encoded transfer RNAs in plant mitochondria. Annu Rev Cell Biol. 1992;8:115–131. [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]
  • Okimoto R, Macfarlane JL, Clary DO, Wolstenholme DR. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics. 1992 Mar;130(3):471–498. [PMC free article] [PubMed]
  • Doolittle RF. The comings and goings of homing endonucleases and mobile introns. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5379–5381. [PMC free article] [PubMed]
  • Fauron CM, Wolstenholme DR. Extensive diversity among Drosophila species with respect to nucleotide sequences within the adenine + thymine-rich region of mitochondrial DNA molecules. Nucleic Acids Res. 1980 Jun 11;8(11):2439–2452. [PMC free article] [PubMed]
  • Pont-Kingdon GA, Beagley CT, Okimoto R, Wolstenholme DR. Mitochondrial DNA of the sea anemone, Metridium senile (Cnidaria): prokaryote-like genes for tRNA(f-Met) and small-subunit ribosomal RNA, and standard genetic code specificities for AGR and ATA codons. J Mol Evol. 1994 Oct;39(4):387–399. [PubMed]
  • Flook PK, Rowell CH, Gellissen G. The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome. J Mol Evol. 1995 Dec;41(6):928–941. [PubMed]
  • Pont-Kingdon GA, Okada NA, Macfarlane JL, Beagley CT, Wolstenholme DR, Cavalier-Smith T, Clark-Walker GD. A coral mitochondrial mutS gene. Nature. 1995 May 11;375(6527):109–111. [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]
  • Pritchard AE, Seilhamer JJ, Mahalingam R, Sable CL, Venuti SE, Cummings DJ. Nucleotide sequence of the mitochondrial genome of Paramecium. Nucleic Acids Res. 1990 Jan 11;18(1):173–180. [PMC free article] [PubMed]
  • Gutell RR, Gray MW, Schnare MN. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. Nucleic Acids Res. 1993 Jul 1;21(13):3055–3074. [PMC free article] [PubMed]
  • Hancock K, Hajduk SL. The mitochondrial tRNAs of Trypanosoma brucei are nuclear encoded. J Biol Chem. 1990 Nov 5;265(31):19208–19215. [PubMed]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [PMC free article] [PubMed]
  • Sargueil B, Hatat D, Delahodde A, Jacq C. In vivo and in vitro analyses of an intron-encoded DNA endonuclease from yeast mitochondria. Recognition site by site-directed mutagenesis. Nucleic Acids Res. 1990 Oct 11;18(19):5659–5665. [PMC free article] [PubMed]
  • Ramón Valverde J, Batuecas B, Moratilla C, Marco R, Garesse R. The complete mitochondrial DNA sequence of the crustacean Artemia franciscana. J Mol Evol. 1994 Oct;39(4):400–408. [PubMed]
  • Wallace DC. Maternal genes: mitochondrial diseases. Birth Defects Orig Artic Ser. 1987;23(3):137–190. [PubMed]
  • Schneider A, Martin J, Agabian N. A nuclear encoded tRNA of Trypanosoma brucei is imported into mitochondria. Mol Cell Biol. 1994 Apr;14(4):2317–2322. [PMC free article] [PubMed]
  • Simpson AM, Suyama Y, Dewes H, Campbell DA, Simpson L. Kinetoplastid mitochondria contain functional tRNAs which are encoded in nuclear DNA and also contain small minicircle and maxicircle transcripts of unknown function. Nucleic Acids Res. 1989 Jul 25;17(14):5427–5445. [PMC free article] [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]
  • Wolstenholme DR. Genetic novelties in mitochondrial genomes of multicellular animals. Curr Opin Genet Dev. 1992 Dec;2(6):918–925. [PubMed]
  • Small I, Maréchal-Drouard L, Masson J, Pelletier G, Cosset A, Weil JH, Dietrich A. In vivo import of a normal or mutagenized heterologous transfer RNA into the mitochondria of transgenic plants: towards novel ways of influencing mitochondrial gene expression? EMBO J. 1992 Apr;11(4):1291–1296. [PMC free article] [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]
  • 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]
  • 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]
  • Suyama Y. Two dimensional polyacrylamide gel electrophoresis analysis of Tetrahymena mitochondrial tRNA. Curr Genet. 1986;10(5):411–420. [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]
  • Wolstenholme DR, Okimoto R, Macfarlane JL. Nucleotide correlations that suggest tertiary interactions in the TV-replacement loop-containing mitochondrial tRNAs of the nematodes, Caenorhabditis elegans and Ascaris suum. Nucleic Acids Res. 1994 Oct 11;22(20):4300–4306. [PMC free article] [PubMed]
  • Tarassov IA, Entelis NS. Mitochondrially-imported cytoplasmic tRNA(Lys)(CUU) of Saccharomyces cerevisiae: in vivo and in vitro targetting systems. Nucleic Acids Res. 1992 Mar 25;20(6):1277–1281. [PMC free article] [PubMed]

Articles from Genetics are provided here courtesy of Genetics Society of America

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...