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PMID: 7672576 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome.

Genetics ·Vol. 140 ·No. 3 ·1995-07-00 ·Pages 1047-60

Asakawa S, Himeno H, Miura K, Watanabe K

Abstract

The 16,260-bp mitochondrial DNA (mtDNA) from the starfish Asterina pectinifera has been sequenced. The genes for 13 proteins, two rRNAs and 22 tRNAs are organized in an extremely economical fashion, similar to those of other animal mtDNAs, with some of the genes overlapping each other. The gene organization is the same as that for another echinoderm, sea urchin, except for the inversion of a 4.6-kb segment that contains genes for two proteins, 13 tRNAs and the 16S rRNA. Judging from the organization of the protein coding genes, mammalian mtDNAs resemble the sea urchin mtDNA more than that of the starfish. The region around the 3' end of the 12S rRNA gene of the starfish shows a high similarity with those for vertebrates. This region encodes a possible stem and loop structure; similar potential structures occur in this region of vertebrate mtDNAs and also in nonmitochondrial small subunit rRNA. A similar stem and loop structure is also found at the 3' end of the 16S rRNA genes in A. pectinifera, in another starfish Pisaster ochraceus, in vertebrates and in Drosophila, but not in sea urchins. The full sequence data confirm the presumption that AGA/AGG, AUA and AAA codons, respectively, code for serine, isoleucine, and asparagine in the starfish mitochondria, and that AGA/AGG codons are read by tRNA(GCUSer), which possesses a truncated dihydrouridine arm, that was previously suggested from a partial mtDNA sequence. The structural characteristics of tRNAs and possible mechanisms for the change in the mitochondrial genetic code are also discussed.

MeSH Terms
Amino Acid Sequence Animals Base Sequence Chromosome Inversion Codon DNA, Mitochondrial/chemistry,genetics Mammals/genetics Mitochondria/metabolism Molecular Sequence Data Nucleic Acid Conformation RNA, Ribosomal, 16S/genetics RNA, Transfer, Amino Acyl/chemistry,genetics Sea Urchins/genetics Species Specificity Starfish/genetics Vertebrates/genetics
Chemicals
Codon DNA, Mitochondrial RNA, Ribosomal, 16S RNA, Transfer, Amino Acyl
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Asakawa S
Department of Chemistry and Biotechnology, Faculty of Engineering, University of Tokyo, Japan.
Himeno H
Miura K
Watanabe K
References (82)
82 references, click to expand
  1. 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
  2. Translational efficiency of transfer RNA's: uses of an extended anticodon.
    Science. 1982 Nov 12;218(4573):646-52 PMID: 6753149
  3. Sequence and organization of the human mitochondrial genome.
    Nature. 1981 Apr 9;290(5806):457-65 PMID: 7219534
  4. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes.
    Nature. 1987 Oct 29-Nov 4;329(6142):853-5 PMID: 3670390
  5. Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species.
    Nucleic Acids Res. 1981 Aug 11;9(15):3621-40 PMID: 7024918
  6. Transfer RNA modification.
    Annu Rev Biochem. 1987;56:263-87 PMID: 3304135
  7. Sequence analysis and precise mapping of the 3' ends of HeLa cell mitochondrial ribosomal RNAs.
    J Mol Biol. 1982 May 5;157(1):1-19 PMID: 7108954
  8. Mitochondrial DNA sequences of primates: tempo and mode of evolution.
    J Mol Evol. 1982;18(4):225-39 PMID: 6284948
  9. Large scale isolation and some properties of AGY-specific serine tRNA from bovine heart mitochondria.
    J Biochem. 1985 Nov;98(5):1275-84 PMID: 3853562
  10. Gene arrangement in sea star mitochondrial DNA demonstrates a major inversion event during echinoderm evolution.
    Gene. 1989 Mar 15;76(1):181-5 PMID: 2744480
  11. Higher-order structure of bovine mitochondrial tRNA(Phe) lacking the 'conserved' GG and T psi CG sequences as inferred by enzymatic and chemical probing.
    Nucleic Acids Res. 1994 Feb 11;22(3):347-53 PMID: 7510390
  12. 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 PMID: 2329578
  13. Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition.
    Nucleic Acids Res. 1993 Apr 11;21(7):1523-5 PMID: 8479901
  14. A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem.
    Nucleic Acids Res. 1980 Nov 25;8(22):5213-22 PMID: 6906662
  15. 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
  16. Do ribosomes regulate mitochondrial RNA synthesis?
    Bioessays. 1989 Jul;11(1):27-34 PMID: 2476122
  17. Identification of two homologous mitochondrial DNA sequences, which bind strongly and specifically to a mitochondrial protein of Paracentrotus lividus.
    Nucleic Acids Res. 1991 Nov 25;19(22):6249-54 PMID: 1956785
  18. Different mitochondrial gene orders among insects: exchanged tRNA gene positions in the COII/COIII region between an orthopteran and a dipteran species.
    Curr Genet. 1988 Nov;14(5):471-6 PMID: 2852067
  19. Mechanisms of chain folding in nucleic acids. The (omega, omega) plot and its correlation to the nucleotide geometry in yeast tRNAPhe1.
    Nucleic Acids Res. 1976 Oct;3(10):2471-84 PMID: 792815
  20. Codon reassignment (codon capture) in evolution.
    J Mol Evol. 1989 Apr;28(4):271-8 PMID: 2499683
  21. 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
  22. Distinctive features of the 5'-terminal sequences of the human mitochondrial mRNAs.
    Nature. 1981 Apr 9;290(5806):465-70 PMID: 7219535
  23. The pattern of transcription of the human mitochondrial rRNA genes reveals two overlapping transcription units.
    Cell. 1983 Aug;34(1):151-9 PMID: 6883508
  24. Transcription of the mammalian mitochondrial genome.
    Annu Rev Biochem. 1984;53:573-94 PMID: 6383200
  25. A different genetic code in human mitochondria.
    Nature. 1979 Nov 8;282(5735):189-94 PMID: 226894
  26. New M13 vectors for cloning.
    Methods Enzymol. 1983;101:20-78 PMID: 6310323
  27. The complete mitochondrial DNA sequence of the crustacean Artemia franciscana.
    J Mol Evol. 1994 Oct;39(4):400-8 PMID: 7966370
  28. Sequence and structure of a serine transfer RNA with GCU anticodon from mosquito mitochondria.
    J Mol Biol. 1984 Jun 25;176(2):251-60 PMID: 6565045
  29. The aminoacylation of structurally variant phenylalanine tRNAs from mitochondria and various nonmitochondrial sources by bovine mitochondrial phenylalanyl-tRNA synthetase.
    J Biol Chem. 1989 Aug 5;264(22):13005-11 PMID: 2473985
  30. Rearrangements of mitochondrial transfer RNA genes in marsupials.
    J Mol Evol. 1991 Nov;33(5):426-30 PMID: 1720466
  31. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli.
    J Biol Chem. 1988 Jul 5;263(19):9261-7 PMID: 3132458
  32. Sequence and structure of a methionine transfer RNA from mosquito mitochondria.
    Nucleic Acids Res. 1984 May 25;12(10):4185-9 PMID: 6328414
  33. Clustering of tRNA genes in Paracentrotus lividus mitochondrial DNA.
    Curr Genet. 1988;13(1):91-6 PMID: 2834108
  34. Actions of the anticodon arm in translation on the phenotypes of RNA mutants.
    J Mol Biol. 1986 Nov 20;192(2):235-55 PMID: 2435916
  35. Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code.
    Nature. 1983 Jul 21-27;304(5923):234-41 PMID: 6408489
  36. 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):5837-52 PMID: 6462918
  37. Replication and transcription of vertebrate mitochondrial DNA.
    Annu Rev Cell Biol. 1991;7:453-78 PMID: 1809353
  38. Serine tRNA complementary to the nonuniversal serine codon CUG in Candida cylindracea: evolutionary implications.
    Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7408-11 PMID: 1502151
  39. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG.
    Nature. 1991 Jan 31;349(6308):431-4 PMID: 1992344
  40. Three-dimensional structure of Escherichia coli initiator tRNAfMet.
    Nature. 1980 Jul 24;286(5771):346-51 PMID: 6157105
  41. [The nucleotide sequences of the heavy and light strand replication origins of the Rana catesbeiana mitochondrial genome].
    Nihon Ika Daigaku Zasshi. 1987 Aug;54(4):429-40 PMID: 2444617
  42. Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA.
    Gene. 1987;56(2-3):219-30 PMID: 3678836
  43. The nucleotide sequence of a small (3S) seryl-tRNA (anticodon GCU) from beef heart mitochondria.
    Nucleic Acids Res. 1980 Nov 25;8(22):5207-12 PMID: 6906661
  44. Nucleotide sequence and gene organization of sea urchin mitochondrial DNA.
    J Mol Biol. 1988 Jul 20;202(2):185-217 PMID: 3172215
  45. 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
  46. Characterization of a high-affinity binding site for a DNA-binding protein from sea urchin embryo mitochondria.
    Nucleic Acids Res. 1993 Feb 25;21(4):811-6 PMID: 8383839
  47. Conserved tRNA gene cluster in starfish mitochondrial DNA.
    Curr Genet. 1989 Mar;15(3):193-206 PMID: 2766382
  48. Mapping and characterization of Paracentrotus lividus mitochondrial transcripts: multiple and overlapping transcription units.
    Curr Genet. 1990 Mar;17(3):235-45 PMID: 1692770
  49. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase.
    Science. 1988 Jan 29;239(4839):487-91 PMID: 2448875
  50. The molecular basis for the differential translation of TMV RNA in tobacco protoplasts and wheat germ extracts.
    EMBO J. 1984 May;3(5):1091-6 PMID: 16453524
  51. The functional role of ribosomal RNA in protein synthesis.
    Cell. 1989 May 19;57(4):525-9 PMID: 2655923
  52. The genetic code in mitochondria and chloroplasts.
    Experientia. 1990 Dec 1;46(11-12):1117-26 PMID: 2253709
  53. The phylogeny of echinoderm classes based on mitochondrial gene arrangements.
    J Mol Evol. 1993 Jun;36(6):545-54 PMID: 8350349
  54. Purification and characterization of two serine isoacceptor tRNAs from bovine mitochondria by using a hybridization assay method.
    Nucleic Acids Res. 1989 Apr 11;17(7):2623-38 PMID: 2717404
  55. Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes.
    J Mol Evol. 1991 Jun;32(6):511-20 PMID: 1908022
  56. pi turn is a conformational pattern in RNA loops and bends.
    Nature. 1976 Apr 15;260(5552):645-6 PMID: 772447
  57. 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
  58. The gene for serine tRNA having anticodon sequence CAG in a pathogenic yeast, Candida albicans.
    Nucleic Acids Res. 1993 Jan 25;21(2):356 PMID: 8441644
  59. Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards.
    Proc Natl Acad Sci U S A. 1987 Oct;84(20):7183-7 PMID: 3478691
  60. Sequence and gene organization of mouse mitochondrial DNA.
    Cell. 1981 Oct;26(2 Pt 2):167-80 PMID: 7332926
  61. The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization.
    Genetics. 1993 Jan;133(1):97-117 PMID: 8417993
  62. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome.
    J Biol Chem. 1985 Aug 15;260(17):9759-74 PMID: 4019494
  63. A novel cloverleaf structure found in mammalian mitochondrial tRNA(Ser) (UCN).
    Nucleic Acids Res. 1991 Nov 25;19(22):6101-5 PMID: 1840673
  64. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis.
    Genetics. 1992 Jun;131(2):397-412 PMID: 1386586
  65. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors.
    Gene. 1985;33(1):103-19 PMID: 2985470
  66. Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA.
    Science. 1986 Sep 26;233(4771):1425-7 PMID: 3018925
  67. 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):387-99 PMID: 7966369
  68. 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
  69. A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire 'dihydrouridine' loop and stem.
    EMBO J. 1983;2(8):1309-21 PMID: 10872325
  70. Comparative anatomy of 16-S-like ribosomal RNA.
    Prog Nucleic Acid Res Mol Biol. 1985;32:155-216 PMID: 3911275
  71. The sequence of a possible 5S RNA-equivalent in hamster mitochondria.
    Nucleic Acids Res. 1980 Aug 25;8(16):3603-10 PMID: 6159582
  72. The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code.
    J Mol Evol. 1985;22(3):252-71 PMID: 3001325
  73. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum.
    Genetics. 1992 Mar;130(3):471-98 PMID: 1551572
  74. Preclinical toxic effects of manganese in workers from a Mn salts and oxides producing plant.
    Sci Total Environ. 1985 Mar 15;42(1-2):201-6 PMID: 4012283
  75. 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
  76. Unidirectional digestion with exonuclease III in DNA sequence analysis.
    Methods Enzymol. 1987;155:156-65 PMID: 3323819
  77. 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
  78. Mutually exclusive synthetic pathways for sea urchin mitochondrial rRNA and mRNA.
    Mol Cell Biol. 1989 Mar;9(3):1069-82 PMID: 2471058
  79. The nucleotide sequence of the initiator tRNA from Drosophila melanogaster.
    Nucleic Acids Res. 1979 Feb;6(2):421-33 PMID: 106370
  80. Animal mitochondrial DNA: structure and evolution.
    Int Rev Cytol. 1992;141:173-216 PMID: 1452431
  81. Suppression and the code: beyond codons and anticodons.
    Experientia. 1990 Dec 1;46(11-12):1134-41 PMID: 2253711
  82. A major lysine tRNA with a CUU anticodon in insect mitochondria.
    Nucleic Acids Res. 1983 Dec 20;11(24):8659-62 PMID: 6561519
Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
DOI
10.1093/genetics/140.3.1047
Published
1995-07-00
Pages
1047-60
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC1206660
Subset
IM
External Links
PubMed source DOI: 10.1093/genetics/140.3.1047 PMC Full Text View journal details
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