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Mutations in the mitochondrial split gene COXI are preferentially located in exons: a mapping study of 170 mutants

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Abstract

We have analysed the precise location of a large number (170) of mutations affecting the structural gene for subunit 1 of the cytochrome c oxidase complex. This gene, COXI, is 12.9 kb long and the major part of the sequence (i.e. 11.3 kb) is composed of introns. Several conclusions can be drawn from this study: (1) A significant proportion (84/170) of the mutations cannot be assigned to a single position within the gene by deletion mapping, in spite of clearly being located in it. These mutations are probably large deletions or multiple mutations. (2) Four mutants carry distant double mutations, which have been individually localized. (3) Eighty-two mutants have lesions that are restricted to very short regions of the gene and we therefore conclude that they are most probably due to single hits; amongst these single mutations, 41 are unambiguously located in exons and 28 in introns. This result implies that, at least in this particular split gene, the probability of selection of a mutant phenotype in an exon is, on the average, 13.3 times greater than in an intron, in spite of the existence, within most of these introns, of open reading frames specifying intronic proteins. The evolutionary significance and biological implications of these results are discussed.

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References

  • Banroques J, Delahodde A, Jacq C (1986) A mitochondrial RNA maturase gene transferred to the yeast nucleus can control mitochondrial mRNA splicing. Cell 46:837–844

    Google Scholar 

  • Belfort M, Chandry PS, Pedersen-Lane J (1987) Genetic delineation of functional components of the group I intron in the phage T4 td gene. Cold Spring Harbor Symp Quant Biol 52:181–192

    Google Scholar 

  • Bonitz SG, Coruzzi G, Thalenfeld BE, Tzagoloff A, Macino G (1980) Assembly of the mitochondrial membrane system: physical map of the oxi3 locus of yeast mitochondrial DNA. J Biol Chem 255:11927–11941

    Google Scholar 

  • Calder KM, McEwen JE (1990) Nucleotide sequence of the gene encoding cytochrome c oxidase subunit VII from Saccharomyces cerevisiae. Nucleic Acids Res 18:1632

    Google Scholar 

  • Carignani G, Dujardin G, Slonimski P (1979) Petite deletion map of the mitochondrial oxi3 region in S. cerevisiae. Mol Gen Genet 167:301–308

    Google Scholar 

  • Carignani G, Groudinsky O, Frezza D, Schiavon E, Bergantino E, Slonimski P (1983) An mRNA maturase is encoded by the first intron of the mitochondrial gene for the subunit I of cytochrome oxidase in S. cerevisiae. Cell 35:733–742

    Google Scholar 

  • Carignani G, Netter P, Bergantino E, Robineau S (1986) Expression of the mitochondrial split gene coding for cytochrome oxidase subunit I in S. cerevisiae: RNA splicing pathway. Curr Genet 11:55–63

    Google Scholar 

  • Cech TR (1990) Self-splicing of group I introns. Annu Rev Biochem 59:543–568

    Google Scholar 

  • Coruzzi G, Tzagoloff A (1979) Assembly of the mitochondrial membrane system: DNA sequence of subunit 2 of yeast cytochrome oxidase. J Biol Chem 254:9324–9330

    Google Scholar 

  • Couture S, Ellington A, Gerber A, Cherry M, Doudna J, Green R, Hanna M, Pace U, Rajapogal J, Szostak J (1990) Mutational analysis of conserved nucleotides in a self-splicing group I intron. J Mol Biol 215:345–358

    Google Scholar 

  • Cumsky MG, Trueblood CE, Ko C, Poyton RO (1987) Structural analysis of two genes encoding divergent forms of yeast cytochrome c oxidase subunit V. Mol Cell Biol 7:3511–3519

    Google Scholar 

  • Davies RW, Waring RB, Ray JA, Brown TA, Scazzocchio C (1982) Making ends meet: a model for RNA splicing in fungal mitochondria. Nature 300:719–724

    Google Scholar 

  • De La Salle H, Jacq C, Slonimski PP (1982) Critical sequences within mitochondrial introns: pleiotropic mRNA maturase and cis-dominant signals of the box intron controlling reductase and oxidase. Cell 28:721–732

    Google Scholar 

  • Degli Esposti M, De Vries S, Crimi M, Ghelli A, Patarnello T, Meyer A. (1993) Mitochondrial cytochrome b: evolution and structure of the protein. Biochim Biophys Acta 1143:243–271

    Google Scholar 

  • Dujardin G, Jacq C, Slonimski PP (1982) Single base substitution in an intron of oxidase gene compensates splicing defects of the cytochrome b gene. Nature 298:628–632

    Google Scholar 

  • Dujardin G, Pajot P, Groudinsky O, Slonimski PP (1980) Long range control circuits within mitochondria and between nucleus and mitochondria. I. Methodology and phenomenology of suppressors. Mol Gen Genet 179:469–482

    Google Scholar 

  • Garriga G, Lambowitz AM (1984) RNA splicing in Neurospora mitochondria: self-splicing of a mitochondrial intron in vitro. Cell 39:631–641

    Google Scholar 

  • Goguel V, Bailone A, Devoret R, Jacq C (1989) The bI4 RNA mitochondrial maturase of S. cerevisiae can stimulate intrachromosomal recombination in E. coli. Mol Gen Genet 216:70–74

    Google Scholar 

  • Haltia T, Puustinen A, Finel M (1988) The Paracoccus denitrificans cytochrome aa3 has a third subunit. Eur J Biochem 172:543–546

    Google Scholar 

  • Hensgens LAM, Bonen L, de Haan M, Horst G, Grivell L (1983) Two intron sequences in yeast mitochondrial COX I gene: homology among URF containing introns and strain dependant variation in flanking exons. Cell 32:379–389

    Google Scholar 

  • Hosler J, Fetter J, Tecklenburg M, Espe M, Lerma C, Ferguson-Miller S (1992) Cytochrome aa3 of Rhodobacter sphaeroides as a model for mitochondrial cytochrome c oxidase. J Biol Chem 267:24264–24272

    Google Scholar 

  • Jacq C, Pajot P, Lazowska J, Dujardin G, Claisse M, Groudinsky O, De La Salle H, Grandchamps C, Labouesse M, Gargouri A, Guiard B, Spiridakis A, Dreyfus M, Slonimski P (1982) Role of introns in the yeast cytochrome b gene: cis- and trans-acting signal, intron manipulation, expression and intergenic communications. In: Slonimski P, Borst P, Attardi G (eds) Mitochondrial genes. (Cold Spring Harbour Symposium on Mitochondrial Genes) Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, pp 155–183

    Google Scholar 

  • Kennell JC, Moran JV, Perlman PS, Butow RA, Lambowitz AM (1993) Reverse transcriptase activity associated with maturase-encoding group II introns in yeast mitochondria. Cell 73:133–146

    Google Scholar 

  • Kotylak Z, Slonimski PP (1977) Mitochondrial mutants isolated by a new method based upon the use of the nuclear mutation op1. In: Bandlow W, Schweyen RJ, Wolf K, Kandewitz F (eds) Mitochondria 1977. de Gruyter, Berlin. pp 83–89

    Google Scholar 

  • Kotylak Z, Lazowska J, Hawthorne DC, Slonimski PP (1985) Intron encoded proteins in mitochondria: key elements of gene expression and genomic evolution. In: Quagliarello E, Slater EC, Palmieri F, Saconne C, Kroon AM (eds) Achievements and perspectives in mitochondrial research, vol 2. Elseiner Amsterdam, pp 1–20

    Google Scholar 

  • Kruszewska A, Slonimski P (1984) Mitochondrial and nuclear mitoribosomal suppressors that enable misreading of ochre codons in yeast mitochondria. Curr Genet 9:11–19

    Google Scholar 

  • Lamarche AEP, Abate MI, Chan SHP, Trumpower BL (1992) Isolation and characterization of COX12, the nuclear gene for a previously unrecognized subunit of Saccharomyces cerevisiae cytochrome-c oxidase. J Biol Chem 267:22473–22480

    Google Scholar 

  • Lambowitz AM, Belfort M (1993) Introns as mobile elements. Annu Rev Biochem 62:587–622

    Google Scholar 

  • Lazowska J, Jacq C, Slonimski PP (1980) Sequence of introns and flanking exons in wild-type and box3 mutants of cytochrome b reveals an interlaced splicing protein coded by an intron. Cell 22:333–348

    Google Scholar 

  • Lemarre P, Robineau S, Colson AM, Netter P (1994) Sequence analysis of three deficient mutants of cytochrome oxidase subunit I of S. cerevisiae and their revertants. Curr Genet 26(5–6):546–552

    Google Scholar 

  • Lewin A, Morimoto R, Rabinowitz M, Fukuhara H (1978) Restriction enzyme analysis of mitochondrial DNAs of petite mutants of yeast. Mol Gen Genet 163:257–275

    Google Scholar 

  • Maarse AC, Van LA, Riezman H, Gregor I, Schatz G, Grivell LA (1984) Subunit IV of yeast cytochrome c oxidase: cloning and nucleotide sequencing of the gene and partial amino acid sequencing of the mature protein. EMBO J 3:2831–2837

    Google Scholar 

  • Meunier B, Coster F, Lemarre P, Colson AM (1993) Insight into topological and functional relationships of cytochrome-c oxidase subunit I of S. cerevisiae by means of intragenic complementation. FEBS Lett 321:159–162

    Google Scholar 

  • Michel F, Dujon B (1983) Conservation of RNA secondary structures in two intron families including mitochondrial-, chloroplast- and nuclear encoded members. EMBO J 2:33–38

    Google Scholar 

  • Michel F, Lang BF (1985) Mitochondrial class II introns encode proteins related to the reverse transcriptases of retroviruses. Nature 316:641–643

    Google Scholar 

  • Michel F, Umesono K, Okesi H (1989a) Comparative and functional anatomy of group II catalytic introns — a review. Gene 82:5–30

    Google Scholar 

  • Michel F, Hanna M, Green R, Bartel D, Szostak J (1989b) The guanosine binding site of Tetrahymena ribozyme. Nature 23:391–395

    Google Scholar 

  • Moran JV, Wernette CM, Mecklenburg KL, Butow RA, Perlman PS (1992) Intron 5 alpha of the COXI gene of yeast mitochondrial DNA is a mobile group I intron. Nucleic Acids Res 20:4069–4076

    Google Scholar 

  • Netter P, Carignani G, Jacq C, Groudinsky O, Clavillier L, Slonimski PP (1982a) The cytochrome oxidase subunit I split gene in Saccharomyces cerevisiae: genetic and physical studies of the mtDNA segment encompassing the ‘cytochrome b-homologous’ intron. Mol Gen Genet 188:551–559

    Google Scholar 

  • Netter P, Jacq C, Carignam G, Slonimski PP (1982b) Critical sequences within mitochondrial introns: cis-dominant mutations of the “cytochrome-b-like” intron of the oxidase gene. Cell 28:733–738

    Google Scholar 

  • Netter P, Robineau S, Sirand-Pugnet P, Fauvarque MO (1992) The unusual reversion properties of a mitochondrial mutation in the structural gene of subunit I of cytochrome oxidase of Saccharomyces cerevisiae reveal a probable histidine ligand of the redox center. Curr Genet 21:147–151

    Google Scholar 

  • Patterson TE, Poyton RO (1986) COX8, the structural gene for yeast cytochrome c oxidase subunit VIII. DNA sequence and gene disruption indicate that subunit VIII is required for maximal levels of cellular respiration and is derived from a precursor which is extended at both its NH2 and COOH termini. J Biol Chem 261:17192–17197

    Google Scholar 

  • Peebles CL, Perlman PS, Mecklenburg KL, Petrillo ML, Tabor JH, Jarrell KA, Cheng HL (1986) A self-splicing RNA excises an intron lariat. Cell 44:213–223

    Google Scholar 

  • Perea J, Jacq C (1985) Role of the 5′ hairpin structure in the splicing accuracy of the fourth intron of the yeast cob-box gene. EMBO J 4:3281–3288

    Google Scholar 

  • Rao JKM, Argos P (1986) A conformational preference parameter to predict helices in integral membrane proteins. Biochim Biophys Acta 869:197–214

    Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York

    Google Scholar 

  • Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467

    Google Scholar 

  • Sargueil B, Delahodde A, Hatat D, Tian GL, Lazowska J, Jacq C (1991) A new specific DNA endonuclease activity in yeast mitochondria. Mol Gen Genet 225:340–341

    Google Scholar 

  • Schapira M, Desdouets C, Jacq C, Perea J (1993) I-SceIII an intron-encoded DNA endonuclease from yeast mitochondria. Asymmetrical DNA binding properties and cleavage reaction. Nucleic Acids Res 21:3683–3689

    Google Scholar 

  • Schmelzer C, Schweyen RJ (1986) Self-splicing of group II introns in vitro: mapping of the branch point and mutational inhibition of lariat formation. Cell 46:557–565

    Google Scholar 

  • Seraphin B, Simon M, Faye G (1985) Primary structure of a gene for subunit 5 of the cytochrome oxidase from S. cerevisiae. Curr Genet 9:435–439

    Google Scholar 

  • Slonimski P, Tzagoloff A (1976) Localization in yeast mitochondrial DNA of mutations expressed in a deficiency of cytochrome oxidase and/or coenzyme QH2-cytochrome c reductase. Eur J Biochim 61:27–41

    Google Scholar 

  • Szczepanek T, Macadre C, Meunier B, Lazowska J (1994) Two homologous introns from related Saccharomyces species differ in their mobility. Gene 139:1–7

    Google Scholar 

  • Taanman JW, Capaldi RA (1992) Purification of yeast cytochrome c oxidase with a subunit composition resembling the mammalian enzyme. J Biol Chem 267:224–815

    Google Scholar 

  • Taanman JW, Capaldi RA (1993) Subunit VIa of yeast cytochrome c oxidase is not necessary for assembly of the enzyme complex but modulates the enzyme activity. Isolation and characterization of the nuclear-coded gene. J Biol Chem 268:18754–18761

    Google Scholar 

  • Thalenfeld BE, Tzagoloff A (1980) Assembly of the mitochondrial membrane system. Sequence of the oxi 2 gene of yeast mitochondrial DNA. J Biol Chem 255:6173–6180

    Google Scholar 

  • van der Horst G, Tabak HF (1985) Self-splicing of yeast mitochondrial ribosomal and messenger RNA precursors. Cell 40:759–766

    Google Scholar 

  • van der Veen R, Arnberg AC, van der Horst G, Bonen L, Tabak HF, Grivell LA (1986) Excised group II introns in yeast mitochondria are lariats and can be formed by self-splicing in vitro. Cell 44:225–234

    Google Scholar 

  • Weiss-Brummer B, Rodel G, Schweyen R, Kaudewitz F (1982) Expression of the split gene cob in yeast: evidence for a precursor of a maturase protein translated from intron 4 and preceding exons. Cell 29:527–536

    Google Scholar 

  • Wright RM, Dircks LK, Poyton RO (1986) Characterization of COX9, the nuclear gene encoding the yeast mitochondrial protein cytochrome c oxidase subunit VIIa. Subunit VIIa lacks a leader peptide and is an essential component of the holoenzyme. J Biol Chem 261:17183–17191

    Google Scholar 

  • Wright RM, KO C, Cumsky MG, Poyton RO (1984) Isolation and sequence of the structural gene for cytochrome c oxidase subunit 6 from S. cerevisiae. J Biol Chem 259:15401–15407

    Google Scholar 

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  1. Centre de Génétique Moléculaire du CNRS, Laboratoire associé à l'Université Pierre et Marie Curie, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France

    Pierre Netter, Sylviane Robineau & Claire Lemaire

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  1. Pierre Netter
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  2. Sylviane Robineau
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  3. Claire Lemaire
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Communicated by A. Kondorosi

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Netter, P., Robineau, S. & Lemaire, C. Mutations in the mitochondrial split gene COXI are preferentially located in exons: a mapping study of 170 mutants. Molec. Gen. Genet. 246, 445–454 (1995). https://doi.org/10.1007/BF00290448

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