The mitochondrial DNA molecule ofDrosophila yakuba: Nucleotide sequence, gene organization, and genetic code (original) (raw)

• Altman PL, Katz DD (eds) (1976) Biological handbooks I: cell biology. Federation of American Societies for Experimental Biology, Bethesda, Maryland, pp 217–219
  Google Scholar
• Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465
  Article PubMed Google Scholar
• Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1982a) Comparison of the human and bovine mitochondrial genomes. In: Slonimski P, Borst P, Attardi G (eds) Mitochondrial genes. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 5–43
  Google Scholar
• Anderson S, de Bruijn MHL, Coulson AR, Eperon IC, Sanger F, Young IG (1982b) The complete sequence of bovine mitochondrial DNA: conserved features of the mammalian mitochondrial genome. J Mol Biol 156:683–717
  Article PubMed Google Scholar
• Arcari P, Brownlee GG (1980) The nucleotide sequence of a small (3S) seryl-tRNA (anticodon GCU) from beef heart mitochondria. Nucleic Acids Res 8:5207–5212
  PubMed Google Scholar
• Barrell BG, Bankier AT, Drouin J (1979) A different genetic code in human mitochondria. Nature 282: 189–194
  Article PubMed Google Scholar
• Barrell BG, Anderson S, Bankier AT de Bruijn MHL, Chen E, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1980) Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc Natl Acad Sci USA 77:3164–3166
  PubMed Google Scholar
• Battey J, Rubenstein JLR, Clayton DA (1979) Transcription patterns of_Drosophila melanogaster_ mitochondrial DNA. In: Cummings DJ, Dawid IB, Borst P, Weissman SM, Fox CF (eds) Extrachromosomal DNA. Academic Press, New York, pp 427–442 (ICN-UCLA symposia on molecular and cellular biology, vol XV)
  Google Scholar
• Bibb MJ, Van Etten RA, Wright CT, Walberg MW, Clayton DA (1981) Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167–180
  Article PubMed Google Scholar
• Bogenhagen DF, Applegate EF, Yoza BK (1984) Identification of a promoter for transcription of the heavy strand of human mtDNA:in vitro transcription and deletion mutagenesis. Cell 36:1105–1113
  Article PubMed Google Scholar
• Bonitz SG, Berlani R, Coruzzi G, Li M, Macino G, Nobrega FG, Nobrega MP, Thalenfeld BE, Tzagoloff A (1980) Codon recognition rules in yeast mitochondria. Proc Natl Acad Sci USA 77:3167–3170
  PubMed Google Scholar
• Bonner JJ, Berninger M, Pardue ML (1978) Transcription of polytene chromosomes and of the mitochondrial genome in_Drosophila melanogaster_. Cold Spring Harbor Symp Quant Biol 42:803–814
  PubMed Google Scholar
• Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences in primates: tempo and mode of evolution. J Mol Evol 18:225–239
  PubMed Google Scholar
• Brutlag DL, Clayton J, Frieland P, Kedes LH (1982) SEQ: a nucleotide sequence analysis and recombination system. Nucleic Acids Res 10:279–304
  PubMed Google Scholar
• Bultmann H, Laird CD (1973) Mitochondrial DNA from_Drosophila melanogaster_. Biochim Biophys Acta 299:196–209
  PubMed Google Scholar
• Chan Y-L, Olvera J, Wood IG (1983) The structure of rat 28S ribosomal ribonucleic acid inferred from the sequence of nucleotides in a gene. Nucleic Acids Res 11:7819–7830
  PubMed Google Scholar
• Chang DD, Clayton DA (1984) Precise identification of mitochondrial promoters for transcription of each strand of human mitochondrial DNA. Cell 36:635–643
  Article PubMed Google Scholar
• Chomyn A, Mariottini P, Gonzalez-Cadavid N, Attardi G, Strong DD, Trovato D, Riley M, Doolittle R (1983) Identification of the polypeptides encoded in the ATPase 6 gene and in the unassigned reading frames 1 and 3 of human mtDNA. Proc Natl Acad Sci USA 80:5535–5539
  PubMed Google Scholar
• Clark CG, Tague BW, Ware VC, Gerbi SA (1984)Xenopus laevis 28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications. Nucleic Acids Res 12:6197–6220
  PubMed Google Scholar
• Clary DO, Wolstenholme DR (1983a) 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 11:4211–4227
  PubMed Google Scholar
• Clary DO, Wolstenholme DR (1983b) Genes for cytochrome_c_ oxidase subunit I, URF2 and three tRNAs in_Drosophila_ mitochondrial DNA. Nucleic Acids Res 11:6859–6872
  PubMed Google Scholar
• Clary DO, Wolstenholme DR (1984a) A cluster of six tRNA genes in_Drosophila_ mitochondrial DNA that includes a gene for an unusual tRNA serAGY . Nucleic Acids Res 12:2367–2379
  PubMed Google Scholar
• Clary DO, Wolstenholme DR (1984b) The_Drosophila_ mitochondrial genome. In: Maclean N (ed) Oxford surveys on eukaryotic genes, vol 1. Oxford University Press, Oxford, pp 1–35
  Google Scholar
• Clary DO, Wolstenholme DR (1985) The ribosomal genes of_Drosophila_ mitochondrial DNA. Nucleic Acids Res 113:4029–4045
  Google Scholar
• Clary DO, Goddard JM, Martin SC, Fauron CMR, Wolstenholme DR (1982)Drosophila mitochondrial DNA: a novel gene order. Nucleic Acids Res 10:6619–6637
  PubMed Google Scholar
• Clary DO, Wahleithner JA, Wolstenholme DR (1983) Transfer RNA genes in_Drosophila_ mitochondrial DNA: related 5′ flanking sequences and comparisons to mammalian mitochondrial tRNA genes. Nucleic Acids Res 11:2411–2425
  PubMed Google Scholar
• Clary DO, Wahleithner JA, Wolstenholme DR (1984) Sequence and arrangement of the genes for cytochrome b, URF1, URF4L, URF4, URF5, URF6 and five tRNAs in_Drosophila_ mitochondrial DNA. Nucleic Acids Res 12:3747–3762
  PubMed Google Scholar
• Clayton DA (1982) Replication of animal mitochondrial DNA. Cell 28:693–705
  Article PubMed Google Scholar
• Crews S, Attardi G (1980) The sequences of the small ribosomal RNA gene and the phenylalanine tRNA gene are joined end to end in human mitochondrial DNA. Cell 19:775–784
  PubMed Google Scholar
• de Bruijn MHL (1983)Drosophila melanogaster mitochondrial DNA: a novel organization and genetic code. Nature 304:234–241
  Article PubMed Google Scholar
• de Bruijn MHL, Klug A (1983) A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire dihydrouridine loop and stem. EMBO J 2:1309–1321
  PubMed Google Scholar
• de Bruijn MHL, Schreier PH, Eperon IC, Barrell BG, Chen EY, Armstrong PW, Wong JFH, Roe BA (1980) A mammalian mitochondrial serine transfer RNA lacking the “dihydrouridine” loop and stem. Nucleic Acids Res 8:5213–5222
  PubMed Google Scholar
• Doolittle RF (1981) Similar amino acid sequences: chance or common ancestry. Science 214:149–159
  PubMed Google Scholar
• Dubin DT, HsuChen CC (1984) Sequence and structure of a methionine transfer RNA from mosquito mitochondria. Nucleic Acids Res 12:4185–4189
  PubMed Google Scholar
• Dubin DT, HsuChen CC, Timko KD, Azzolina TM, Prince DL, Ranzini JL (1982) 3′ termini of mammalian and insect mitochondrial rRNAs. In: Slonimski P, Borst P, Attardi G (eds) Mitochondrial genes. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 89–98
  Google Scholar
• Dubin DT, HsuChen CC, Cleaves GR, Timko KD (1984) Sequence and structure of a serine transfer RNA with GCU anticodon from mosquito mitochondria. J Mol Biol 176:251–260
  Article PubMed Google Scholar
• Fauron CMR, Wolstenholme DR (1976) Structural heterogeneity of mitochondrial DNA molecules within the genus_Drosophila_. Proc Natl Acad Sci USA 73:3623–3627
  PubMed Google Scholar
• Fauron CMR, Wolstenholme DR (1980) Extensive diversity among_Drosophila_ species with respect to nucleotide sequences within the adenine + thymine-rich region of mitochondrial DNA molecules. Nucleic Acids Res 8:2439–2452
  PubMed Google Scholar
• Fox TD (1979) Five TGA “stop” codons occur within th translated sequence of the yeast mitochondrial gene for cytochrome_c_ oxidase subunit II. Proc Natl Acad Sci USA 76:6534–6538
  PubMed Google Scholar
• Glotz C, Zweib C, Brimacombe R (1981) Secondary structure of the large subunit ribosomal RNA from_Escherichia coli, Zea mays_ chloroplast, and human and mouse mitochondrial ribosomes. Nucleic Acids Res 9:3287–3306
  PubMed Google Scholar
• Goddard JM, Wolstenholme DR (1978) Origin and direction of replication in mitochondrial DNA molecules from_Drosophila melanogaster_. Proc Natl Acad Sci USA 75:3886–3890
  PubMed Google Scholar
• Goddard JM, Wolstenholme DR (1980) Origin and direction of replication in mitochondrial DNA molecules from the genus_Drosophila_. Nucleic Acids Res 8:741–757
  PubMed Google Scholar
• Gray MW, Sankoff D, Cedergren RJ (1984) 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 12:5837–5852
  PubMed Google Scholar
• Gronenborn B, Messing J (1978) Methylation of single stranded DNA_in vitro_ introduces new restriction endonuclease cleavage sites. Nature 272:375–377
  Article PubMed Google Scholar
• Grosskopf R, Feldmann H (1981) Analysis of a DNA segment from rat liver mitochondria containing the genes for cytochrome oxidase subunits I, II and III, ATPase6 and several tRNA genes. Curr Genet 4:151–158
  Article Google Scholar
• Heckman JE, Sarnoff J, Alzner-De Weerd B, Yin S, RajBhandary UL (1980) Novel features in the genetic code and codon reading patterns in_Neurospora crassa_ mitochondria based on sequences of six mitochondrial tRNAs. Proc Natl Acad Sci USA 77:3159–3163
  PubMed Google Scholar
• Hong GF (1982) A systematic DNA sequencing strategy. J Mol Biol 158:539–549
  PubMed Google Scholar
• HsuChen CC, Cleaves GR, Dubin DT (1983a) Sequences of three transfer RNAs from mosquito mitochondria. Plasmid 10:55–65
  Article PubMed Google Scholar
• HsuChen CC, Cleaves GR, Dubin DT (1983b) A major lysine tRNA with a CUU anticodon in insect mitochondria. Nucleic Acids Res 11:8659–8662
  PubMed Google Scholar
• HsuChen CC, Kotin RM, Dubin DT (1984) Sequence of the coding and flanking regions of the large ribosomal subunit RNA gene of mosquito mitochondria. Nucleic Acids Res 12:7771–7785
  PubMed Google Scholar
• Hudspeth MES, Ainley WM, Shumard DS, Butow RA, Grossman LI (1982) Location and structure of the varl gene of yeast mitochondrial DNA: nucleotide sequence of the 40.0 allele. Cell 30:617–626
  Article PubMed Google Scholar
• Jue RA, Woodbury NW, Doolittle RF (1980) Sequence homologies among_E. coli_ ribosomal proteins: evidence for evolutionarily related groupings and internal duplications. J Mol Evol 15:129–148
  Article PubMed Google Scholar
• Kasamatsu H, Vinograd J (1974) Replication of circular DNA in eukaryotic cells. Annu Rev Biochem 43:695–719
  Article PubMed Google Scholar
• Kim SH (1979) Crystal structure of yeast tRNAphe and general structural features of other tRNAs. In: Schimmel PR, Soll D, Abelson JN (eds) Transfer RNA: structure, properties and recognition. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 83–100
  Google Scholar
• Klukas CK, Dawid IB (1976) Characterization and mapping of mitochondrial ribsomal RNA and mitochondrial DNA in_Drosophila melanogaster_. Cell 9:615–625
  Article PubMed Google Scholar
• Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:333–348
  Article Google Scholar
• Lagerkvist U (1981) Unorthodox codon reading and the evolution of the genetic code. Cell 23:305–306
  Article PubMed Google Scholar
• Macreadie IG, Novitski CE, Maxwell RJ, John LL, Goi B-G, McMullan L, Lukins HB, Linnane AW, Nagley P (1983) Biogenesis of mitochondria: the mitochondrial gene (aapl) coding for mitochondrial ATPase subunit 8 in_Saccharomyces cerevisiae_. Nucleic Acids Res 11:4435–4451
  PubMed Google Scholar
• Mariottini P, Chomyn A, Attardi G (1983) Antibodies against synthetic peptides reveal that the unidentified reading frame A6L, overlapping the ATPase 6 gene, is expressed in human mitochondria. Cell 32:1269–1277
  Article PubMed Google Scholar
• Merten SH, Pardue ML (1981) Mitochondrial DNA in_Drosophila_. An analysis of genome organization and transcription in_Drosophila melanogaster_ and_Drosophila virilis_. J Mol Biol 153:1–23
  PubMed Google Scholar
• Messing J, Vieira J (1982) A new pair of M13 vectors for selecting either DNA strand of double digest restriction fragments. Gene 19:269–276
  Article PubMed Google Scholar
• Michael NL, Rothbard JB, Shiurba RA, Linke HK, Schoolnik GK, Clayton DA (1984) All eight unassigned reading frames of mouse mitochondrial DNA are expressed. EMBO J 3:3165–3175
  PubMed Google Scholar
• Montoya J, Ojala D, Attardi G (1981) Distictive features of the 5′ terminal sequences of the human mitochondrial mRNAs. Nature 290:465–470
  Article PubMed Google Scholar
• Montoya J, Christianson T, Levens D, Rabinowitz M, Attardi G (1982) Identification of initiation sites for heavy-strand and light-strand transcription in human mitochondrial DNA. Proc Natl Acad Sci USA 79:7195–7199
  PubMed Google Scholar
• Montoya J, Gaines GL, Attardi G (1983) The pattern of transcription of the human mitochondrial rRNA genes reveals two overlapping transcription units. Cell 34:151–159
  Article PubMed Google Scholar
• Nass MMK (1980) Pulse-label analysis and mapping of the two terminal regions of asynchronous complementary strand replication of mitochondrial DNA in transformed hamster cells. J Mol Biol 140:257–281
  Article PubMed Google Scholar
• Noller HF (1984) Structure of ribosomal RNA. Annu Rev Biochem 53:119–162
  Article PubMed Google Scholar
• Ohi S, Ramirez JL, Upholt WB, Dawid IB (1978) Mapping of mitochondrial 4S RNA genes in_Xenopus laevis_ by electron microscopy. J Mol Biol 121:299–310
  Article PubMed Google Scholar
• Ojala D, Merkel C, Gelfand R, Attardi G (1980) The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA. Cell 22:393–403
  Article PubMed Google Scholar
• Ojala D, Montoya J, Attardi G (1981) tRNA punctuation model of RNA processing in human mitochondria. Nature 290:470–474
  Article PubMed Google Scholar
• Peacock WJ, Brutlag D, Goldring E, Appels R, Hinton CW, Lindsley DL (1974) The organization of highly repeated DNA sequences in_Drosophila melanogaster_ chromosomes. Cold Spring Harbor Symp Quant Biol 38:405–416
  PubMed Google Scholar
• Pepe G, Holtrop M, Gadaleta G, Kroon AM, Cantatore P, Gallerani R, De Benedetto C, Quagliariello E, Sbisa E, Saccone C (1983) Non random patterns of nucleotide substitutions and codon strategy in the mammalian mitochondrial genes coding for identified and unidentified reading frames. Biochem Int 6:553–563
  PubMed Google Scholar
• Polan ML, Friedman S, Gall JG, Gehring W (1973) Isolation and characterization of mitochondrial DNA from_Drosophila melanogaster_. J Cell Biol 56:580–589
  Article PubMed Google Scholar
• Rajput B, Duncan L, DeMille D, Miller RC Jr, Spiegelman G (1982) Transcription of cloned transfer RNA genes from_Drosophila melanogaster_ in a homologous cell free extract. Nucleic Acids Res 10:6541–6550
  PubMed Google Scholar
• Ramirez JL, Dawid IB (1978) Mapping of mitochondrial DNA in_Xenopus laevis_ and_X. borealis_: the positions of ribosomal genes and D-loops. J Mol Biol 119:133–146
  Article PubMed Google Scholar
• Rastl E, Dawid IB (1978) Expression of the mitochondrial genome in_Xenopus laevis_: a map of transcripts. Cell 18:501–510
  Article Google Scholar
• Robberson DL, Kasamatsu H, Vinograd J (1972) Replication of mitochondrial DNA. Circular replicative intermediates in mouse L cells. Proc Natl Acad Sci USA 69:737–741
  PubMed Google Scholar
• Roe BA, Wong JFH, Chen EY, Armstrong PW, Stankiewicz A, Ma DP, McDonough J (1982) Mammalian mitochondrial tRNAs: A modified nucleotide 3′ to the anticodon may modulate their codon response. In: Slonimski P, Borst P, Attardi G (eds) Mitochondrial genes. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 45–49
  Google Scholar
• Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
  PubMed Google Scholar
• Spradling A, Pardue ML, Penman S (1977) Messenger RNA in heat-shocked_Drosophila_ cells. J Mol Biol 109:559–587
  PubMed Google Scholar
• Sprinzl M, Gauss DH (1984a) Compilation of tRNA sequences. Nucleic Acids Res 12:r1-r57
  PubMed Google Scholar
• Sprinzl M, Gauss DH (1984b) Compilation of sequences of tRNA genes. Nucleic Acids Res 12:r59-r131
  PubMed Google Scholar
• Staden R (1980) A computer program to search for tRNA genes. Nucleic Acids Res 8:817–825
  PubMed Google Scholar
• Staden R (1982) Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res 10:4731–4751
  PubMed Google Scholar
• Stormo GD, Schneider TD, Gold LM (1982) Characterization of translation initiation sites in_E. coli_. Nucleic Acids Res 10:2971–2996
  PubMed Google Scholar
• Taira M, Yoshida E, Kobayashi M, Yaginuma K, Koike K (1983) Tumor-associated mutations of rat mitochondrial transfer RNA genes. Nucleic Acids Res 11:1635–1643
  PubMed Google Scholar
• Van Etten RA, Walberg MW, Clayton DA (1980) Precise localization and nucleotide sequence of the two mouse mitochondrial rRNA genes and three immediately adjacent novel tRNA genes. Cell 22:157–170
  Article PubMed Google Scholar
• Van Etten RA, Michael NL, Bibb MJ, Brennicke A, Clayton DA (1982) Expression of the mouse mitochondrial DNA genome. In: Slonimski P, Borst P, Attardi G (eds) Mitochondrial genes. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 73–88
  Google Scholar
• Ware VC, Tague BW, Clark CG, Gourse RL, Brand RC, Gerbi SA (1983) Sequence analysis of 28S ribosomal DNA from the amphibian_Xenopus laevis_. Nucleic Acids Res 11:7795–7817
  PubMed Google Scholar
• Woese CR, Gutnell R, Gupta R, Noller HF (1983) Detailed analysis of the higher order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev 47:621–669
  PubMed Google Scholar
• Wolstenholme DR, Clary DO (1985) Sequence evolution of_Drosophila_ mitochondrial DNA. Genetics 109:725–744
  PubMed Google Scholar
• Wolstenholme DR, Koike K, Cochran-Fouts P (1974) Replication of mitochondrial DNA: replicative forms of molecules from rat tissues and evidence for discontinuous replication. Cold Spring Harbor Symp Quant Biol 38:267–280
  PubMed Google Scholar
• Wong JFH, Ma DP, Wilson RK, Roe BA (1983) DNA sequence of the_Xenopus laevis_ mitochondrial heavy and light strand replication origins and flanking tRNA genes. Nucleic Acids Res 11:4977–4995
  PubMed Google Scholar
• Zweib C, Glotz C, Brimacombe R (1981) Secondary structure comparison between small subunit ribosomal RNA molecules from six different species. Nucleic Acids Res 9:3621–3640
  PubMed Google Scholar