Home LiteratureArticle Details
PMID: 7966369 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

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.

Journal of molecular evolution ·Vol. 39 ·No. 4 ·1994-10-00 ·Pages 387-99

Pont-Kingdon GA, Beagley CT, Okimoto R, Wolstenholme DR

Abstract

The nucleotide sequence of a segment of the mitochondrial DNA (mtDNA) molecule of the sea anemone Metridium senile (phylum Cnidaria, class Anthozoa, order Actiniaria) has been determined, within which have been identified the genes for respiratory chain NADH dehydrogenase subunit 2 (ND2), the small-subunit rRNA (s-rRNA), cytochrome c oxidase subunit II (COII), ND4, ND6, cytochrome b (Cyt b), tRNA(f-Met), and the large-subunit rRNA (1-rRNA). The eight genes are arranged in the order given and are all transcribed from the same strand of the molecule. The overall order of the M. senile mt-genes differs from that of other metazoan mtDNAs. In M. senile mt-protein genes, AGA and AGG codons appear to have the standard genetic code specification of arginine, rather than serine as found for other invertebrate mt-genetic codes. Also, ATA has the standard genetic code specification of isoleucine. TGA occurs in three M. senile mt-protein genes and may specify tryptophan as in other metazoan, protozoan, and some fungal mt-genetic codes. The M. senile mt-rRNA(f-Met) gene has primary and secondary structure features closely resembling those of the Escherichia coli initiator tRNA, including standard dihydrouridine and T psi C loop sequences and a mismatch pair at the top of the aminoacyl stem. Determinations of the 5' and 3' end nucleotides of the M. senile mt-s-rRNAs indicated that these molecules have a homogenous size of 1,081 ntp, larger than any other known metazoan mt-s-rRNAs. Consistent with its larger size, the M. senile mt-s-rRNA can be folded into a secondary structure that more closely resembles that of the E. coli 16S rRNA than can any other metazoan mt-s-rRNA. These findings concerning M. senile mtDNA indicate that most of the unusual features regarding metazoan mt-genetic codes, rRNAs, and probably tRNAs developed after divergence of the Cnidarian line from the ancestral line common to other metazoa.

MeSH Terms
Amino Acid Sequence Animals Base Sequence Codon/genetics DNA, Mitochondrial Escherichia coli/genetics Gene Expression Regulation Genetic Code Models, Structural Molecular Conformation Molecular Sequence Data Oligonucleotides Polymerase Chain Reaction RNA, Ribosomal/genetics RNA, Transfer/genetics Sea Anemones/genetics Sequence Alignment
Chemicals
Codon DNA, Mitochondrial Oligonucleotides RNA, Ribosomal RNA, Transfer
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Pont-Kingdon G A
Department of Biology, University of Utah, Salt Lake City 84112.
Beagley C T
Okimoto R
Wolstenholme D R
References (44)
44 references, click to expand
  1. 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 PMID: 3991809
  2. Platyhelminth mitochondrial DNA: evidence for early evolutionary origin of a tRNA(serAGN) that contains a dihydrouridine arm replacement loop, and of serine-specifying AGA and AGG codons.
    J Mol Evol. 1989 May;28(5):374-87 PMID: 2545889
  3. The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates.
    J Mol Evol. 1989 Jun;28(6):497-516 PMID: 2504926
  4. Sequence and organization of the human mitochondrial genome.
    Nature. 1981 Apr 9;290(5806):457-65 PMID: 7219534
  5. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids.
    Cell. 1977 Nov;12(3):721-32 PMID: 922889
  6. A simple method for displaying the hydropathic character of a protein.
    J Mol Biol. 1982 May 5;157(1):105-32 PMID: 7108955
  7. Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms.
    Proc Natl Acad Sci U S A. 1987 Mar;84(5):1324-8 PMID: 3469671
  8. 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):434-48 PMID: 825520
  9. Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome.
    J Mol Evol. 1991 Feb;32(2):153-61 PMID: 1706782
  10. The ribosomal RNA genes of Drosophila mitochondrial DNA.
    Nucleic Acids Res. 1985 Jun 11;13(11):4029-45 PMID: 2989784
  11. Codons AGA and AGG are read as glycine in ascidian mitochondria.
    J Mol Evol. 1993 Jan;36(1):1-8 PMID: 8381878
  12. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome.
    J Mol Biol. 1982 Apr 25;156(4):683-717 PMID: 7120390
  13. Mitochondrial plasmid DNAs of broad bean: nucleotide sequences, complex secondary structures, and transcription.
    Curr Genet. 1987;12(1):55-67 PMID: 2835174
  14. The complete mitochondrial DNA sequence of the harbor seal, Phoca vitulina.
    J Mol Evol. 1992 Jun;34(6):493-505 PMID: 1593642
  15. Evolution of the mitochondrial genetic code. IV. AAA as an asparagine codon in some animal mitochondria.
    J Mol Evol. 1990 Apr;30(4):329-32 PMID: 2111847
  16. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  17. Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA.
    Gene. 1987;56(2-3):219-30 PMID: 3678836
  18. Nucleotide sequence and gene organization of sea urchin mitochondrial DNA.
    J Mol Biol. 1988 Jul 20;202(2):185-217 PMID: 3172215
  19. Genetic novelties in mitochondrial genomes of multicellular animals.
    Curr Opin Genet Dev. 1992 Dec;2(6):918-25 PMID: 1282405
  20. 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):6113-8 PMID: 2235493
  21. Compilation of tRNA sequences and sequences of tRNA genes.
    Nucleic Acids Res. 1989;17 Suppl:r1-172 PMID: 2470031
  22. Compilation of small ribosomal subunit RNA sequences.
    Nucleic Acids Res. 1988;16 Suppl:r87-173 PMID: 2453029
  23. The functional role of ribosomal RNA in protein synthesis.
    Cell. 1989 May 19;57(4):525-9 PMID: 2655923
  24. Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes.
    J Mol Evol. 1991 Jun;32(6):511-20 PMID: 1908022
  25. 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):3405-11 PMID: 2209550
  26. Structure, function, and evolution of transfer RNAs (with appendix giving complete sequences of 178 tRNAs).
    Prog Nucleic Acid Res Mol Biol. 1979;23:227-90 PMID: 549104
  27. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.
    Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342-6 PMID: 4598299
  28. Sequence and gene organization of mouse mitochondrial DNA.
    Cell. 1981 Oct;26(2 Pt 2):167-80 PMID: 7332926
  29. The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization.
    Genetics. 1993 Jan;133(1):97-117 PMID: 8417993
  30. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome.
    J Biol Chem. 1985 Aug 15;260(17):9759-74 PMID: 4019494
  31. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis.
    Genetics. 1992 Jun;131(2):397-412 PMID: 1386586
  32. The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus.
    J Mol Evol. 1991 Dec;33(6):556-68 PMID: 1779436
  33. Comparative anatomy of 16-S-like ribosomal RNA.
    Prog Nucleic Acid Res Mol Biol. 1985;32:155-216 PMID: 3911275
  34. Transfer RNA: molecular structure, sequence, and properties.
    Annu Rev Biochem. 1976;45:805-60 PMID: 60910
  35. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code.
    J Mol Evol. 1985;22(3):252-71 PMID: 3001325
  36. Planarian mitochondria. II. The unique genetic code as deduced from cytochrome c oxidase subunit I gene sequences.
    J Mol Evol. 1992 Apr;34(4):331-5 PMID: 1314909
  37. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum.
    Genetics. 1992 Mar;130(3):471-98 PMID: 1551572
  38. Recent evidence for evolution of the genetic code.
    Microbiol Rev. 1992 Mar;56(1):229-64 PMID: 1579111
  39. A systemic DNA sequencing strategy.
    J Mol Biol. 1982 Jul 5;158(3):539-49 PMID: 6290669
  40. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: conservation and variations among vertebrates.
    Nucleic Acids Res. 1992 Sep 25;20(18):4853-8 PMID: 1408800
  41. The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus.
    J Biol Chem. 1989 Jul 5;264(19):10965-75 PMID: 2544576
  42. Animal mitochondrial DNA: structure and evolution.
    Int Rev Cytol. 1992;141:173-216 PMID: 1452431
  43. tRNA punctuation model of RNA processing in human mitochondria.
    Nature. 1981 Apr 9;290(5806):470-4 PMID: 7219536
  44. Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure.
    Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8750-3 PMID: 1356268
Article Info
Journal
Journal of molecular evolution
Abbr.
J Mol Evol
ISSN
0022-2844
DOI
10.1007/BF00160271
Published
1994-10-00
Pages
387-99
Language
English
Region
Germany
NLM ID
0360051
Subset
IM
Grants
NIGMS NIH HHS · GM-18375 · United States
Databases
GENBANK
S75445
External Links
PubMed source DOI: 10.1007/BF00160271 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2