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Genetics. May 1994; 137(1): 233–241.
PMCID: PMC1205940

Sequences with the Potential to Form Stem-and-Loop Structures Are Associated with Coding-Region Duplications in Animal Mitochondrial DNA

Abstract

Tandem duplications of gene-encoding regions occur in the mitochondrial DNA (mt DNA) of some individuals belonging to several species of whiptail lizards (genus Cnemidophorus). All or part of the duplicated regions of the mtDNAs from five different species were sequenced. In all, the duplication endpoints were within or immediately adjacent to sequences in tRNA, rRNA or protein genes that are capable of forming energetically stable stem-and-loop structures. In two of these mtDNAs, the duplication endpoints were also associated with a direct sequence repeat of 13 bp. The consistent association of stem-and-loop structures with duplication endpoints suggests that these structures may play a role in the duplication process. These data, combined with the absence of direct or palindromic repeats at three of the pairs of duplication endpoints, also suggest the existence of a mechanism for generating de novo duplications that is qualitatively different from those previously modeled.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • 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]
  • Battey J, Clayton DA. The transcription map of human mitochondrial DNA implicates transfer RNA excision as a major processing event. J Biol Chem. 1980 Dec 10;255(23):11599–11606. [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]
  • Brown WM. Mechanisms of evolution in animal mitochondrial DNA. Ann N Y Acad Sci. 1981;361:119–134. [PubMed]
  • Calos MP, Miller JH. Transposable elements. Cell. 1980 Jul;20(3):579–595. [PubMed]
  • Cantatore P, Gadaleta MN, Roberti M, Saccone C, Wilson AC. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature. 329(6142):853–855. [PubMed]
  • Chalker DL, Sandmeyer SB. Transfer RNA genes are genomic targets for de Novo transposition of the yeast retrotransposon Ty3. Genetics. 1990 Dec;126(4):837–850. [PMC free article] [PubMed]
  • Degoul F, Nelson I, Amselem S, Romero N, Obermaier-Kusser B, Ponsot G, Marsac C, Lestienne P. Different mechanisms inferred from sequences of human mitochondrial DNA deletions in ocular myopathies. Nucleic Acids Res. 1991 Feb 11;19(3):493–496. [PMC free article] [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]
  • Desjardins P, Ramirez V, Morais R. Gene organization of the Peking duck mitochondrial genome. Curr Genet. 1990 Jun;17(6):515–518. [PubMed]
  • Glickman BW, Ripley LS. Structural intermediates of deletion mutagenesis: a role for palindromic DNA. Proc Natl Acad Sci U S A. 1984 Jan;81(2):512–516. [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]
  • Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. [PubMed]
  • Hattori M, Sakaki Y. Dideoxy sequencing method using denatured plasmid templates. Anal Biochem. 1986 Feb 1;152(2):232–238. [PubMed]
  • Hixson JE, Wong TW, Clayton DA. Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J Biol Chem. 1986 Feb 15;261(5):2384–2390. [PubMed]
  • Shoffner JM, Lott MT, Voljavec AS, Soueidan SA, Costigan DA, Wallace DC. Spontaneous Kearns-Sayre/chronic external ophthalmoplegia plus syndrome associated with a mitochondrial DNA deletion: a slip-replication model and metabolic therapy. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7952–7956. [PMC free article] [PubMed]
  • Howe CJ, Barker RF, Bowman CM, Dyer TA. Common features of three inversions in wheat chloroplast DNA. Curr Genet. 1988 Apr;13(4):343–349. [PubMed]
  • Johansen S, Guddal PH, Johansen T. Organization of the mitochondrial genome of Atlantic cod, Gadus morhua. Nucleic Acids Res. 1990 Feb 11;18(3):411–419. [PMC free article] [PubMed]
  • Klein RD, Selsing E, Wells RD. A rapid microscale technique for isolation of recombinant plasmid DNA suitable for restriction enzyme analysis. Plasmid. 1980 Jan;3(1):88–91. [PubMed]
  • Levinson G, Gutman GA. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol. 1987 May;4(3):203–221. [PubMed]
  • Marschalek R, Brechner T, Amon-Böhm E, Dingermann T. Transfer RNA genes: landmarks for integration of mobile genetic elements in Dictyostelium discoideum. Science. 1989 Jun 23;244(4911):1493–1496. [PubMed]
  • Moritz C. Evolutionary dynamics of mitochondrial DNA duplications in parthenogenetic geckos, Heteronotia binoei. Genetics. 1991 Sep;129(1):221–230. [PMC free article] [PubMed]
  • Moritz C, Brown WM. Tandem duplication of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science. 1986 Sep 26;233(4771):1425–1427. [PubMed]
  • Moritz C, Brown WM. 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):7183–7187. [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]
  • Quigley F, Weil JH. Organization and sequence of five tRNA genes and of an unidentified reading frame in the wheat chloroplast genome: evidence for gene rearrangements during the evolution of chloroplast genomes. Curr Genet. 1985;9(6):495–503. [PubMed]
  • Rand DM, Harrison RG. Molecular population genetics of mtDNA size variation in crickets. Genetics. 1989 Mar;121(3):551–569. [PMC free article] [PubMed]
  • Reiter WD, Palm P, Yeats S. Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements. Nucleic Acids Res. 1989 Mar 11;17(5):1907–1914. [PMC free article] [PubMed]
  • Ripley LS, Glickman BW. Unique self-complementarity of palindromic sequences provides DNA structural intermediates for mutation. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):851–861. [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]
  • Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. [PubMed]
  • Sandmeyer SB, Bilanchone VW, Clark DJ, Morcos P, Carle GF, Brodeur GM. Sigma elements are position-specific for many different yeast tRNA genes. Nucleic Acids Res. 1988 Feb 25;16(4):1499–1515. [PMC free article] [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]
  • Schon EA, Rizzuto R, Moraes CT, Nakase H, Zeviani M, DiMauro S. A direct repeat is a hotspot for large-scale deletion of human mitochondrial DNA. Science. 1989 Apr 21;244(4902):346–349. [PubMed]
  • Wallis GP. Mitochondrial DNA insertion polymorphism and germ line heteroplasmy in the Triturus cristatus complex. Heredity (Edinb) 1987 Apr;58(Pt 2):229–238. [PubMed]
  • Wolstenholme DR, Clary DO. Sequence evolution of Drosophila mitochondrial DNA. Genetics. 1985 Apr;109(4):725–744. [PMC free article] [PubMed]
  • Wong TW, Clayton DA. In vitro replication of human mitochondrial DNA: accurate initiation at the origin of light-strand synthesis. Cell. 1985 Oct;42(3):951–958. [PubMed]
  • Wong TW, Clayton DA. DNA primase of human mitochondria is associated with structural RNA that is essential for enzymatic activity. Cell. 1986 Jun 20;45(6):817–825. [PubMed]
  • Zevering CE, Moritz C, Heideman A, Sturm RA. Parallel origins of duplications and the formation of pseudogenes in mitochondrial DNA from parthenogenetic lizards (Heteronotia binoei; Gekkonidae). J Mol Evol. 1991 Nov;33(5):431–441. [PubMed]
  • Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 1989 Apr 7;244(4900):48–52. [PubMed]

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