Cytochrome oxidase subunit III from Arbacia lixula: Detection of functional constraints by comparison with homologous sequences

References

• Anderson S., Bankier A. T., Barrell B. C., De Bruijn M. H.L., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F., Schreier P., Smith A. J.H., Staden R., Young I. G. Sequence and organization of the human mitochondrial genome. Nature 1981; 290: 457–465
   PubMed Web of Science ®Google Scholar
• Anderson S., De Bruijn M. H.L., Coulson A. R., Eperon I. C., Sanger F., Young I. G. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 1982; 156: 683–717
   PubMed Web of Science ®Google Scholar
• Arnason U., Gullberg A., Widegren B. The complete nucleotide sequence of the mitochondrial DNA of the fin whale Balaenoptera physalul. J. Mol. Evol. 1991; 33: 556–568
   PubMed Web of Science ®Google Scholar
• Bibb M. J., Van Etten R. A., Wright C. T., Walberg M. W., Clayton D. A. Sequence and gene organization of mouse mitochondrial DNA. Cell 1981; 26: 167–180
   PubMed Web of Science ®Google Scholar
• Bisson R., Schiavo G., Montecucco C. ATP induces conformational changes in mitochondrial cytochrome c oxidase. Jour. Biol. Chem. 1987; 262: 5992–5998
   Google Scholar
• Brown G. G., Simpson M. V. Novel features of animal mtDNA evolution as shown by sequences of two rat cytochrome oxidase subunit II genes. Proc. Natl. Acad. Sci. USA 1982; 79: 3246–3250
   PubMed Web of Science ®Google Scholar
• Brunori M., Antonini G., Malatesta F., Sarti P., Wilson M. T. Cytochrome c oxidase: subunit structure and proton pumping. Eur. J. Biochem. 1987; 169: 1–8
   PubMedGoogle Scholar
• Casey R. P., Thelen M., Azzi A. Dicyclohexyl-carbodiimide binds specifically and covalently to cytochrome c oxidase while inhibiting its H+-translocating activity. J. Biol. Chem. 1980; 255: 3994–4000
   PubMedGoogle Scholar
• Capaldi R. A., Darley-Usmar V., Fuller S., Millet F. Structural and functional features of the interaction of cytochrome c with complex III and cytochrome c oxidase. FEBS Letters 1982; 138: 1–7
   PubMed Web of Science ®Google Scholar
• Chen E. J., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA 1985; 4: 165–170
   PubMedGoogle Scholar
• Cantatore P., Roberti M., Rainaldi G., Cadaleta M. N., Saccone C. The complete nucleotide sequence, the gene organization and the genetic code of the mitochondrial genome of Paracentrotus lividus. J. Biol. Chem. 1989; 264: 10965–10975
   PubMed Web of Science ®Google Scholar
• De Ciorgi C., La Nave C., Musci M., Saccone C. Mitochondrial DNA in the sea urchin Arbacia lixula: Evolutionary inferences from nucleotide sequence analysis. Molecular Biology and Evolution 1990; 19: 515–529
   Google Scholar
• De Ciorgi C., De Luca F., Saccone C. Mitochondrial DNA in the sea urchin Arbacia lixula. Nucleotide differences between two polymorphic molecules indicate asimmetry of substitution. Gene 1991; 103: 249–252
   PubMedGoogle Scholar
• Elbein A. D. The tunicamycins. Useful tools for studies on glycoproteins. Trends Biochem. Sci. 1981; 6: 219–221
   Google Scholar
• Cadaleta C., Pepe G., De Candia G., Quagliariello C., Sbisa E., Saccone C. The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. J. Mol. Evol. 1989; 28: 497–516
   PubMedGoogle Scholar
• Grantham R., Gautier C., Gouy M., Mercier R., Pave A. Codon catalog and the genome hypothesis. Nucleic Acids Res. 1980; 8: r49–r62
   PubMed Web of Science ®Google Scholar
• Haltia T., Finel M., Harms M., Nakari T., Raitio M., Wikstrom M., Saraste M. Deletion of the gene for the subunit III leads to defective assembly of bacterial cytochrome oxidase. EMBO J. 1989; 8: 3571–3579
   PubMedGoogle Scholar
• Haltia T., Saraste M., Wikström M. Subunit III of cytochrome c oxidase is not involved in proton translocation: a site-directed mutagenesis study. EMBO J. 1991; 10: 2015–2021
   PubMedGoogle Scholar
• Jacobs H. T., Elliot D., Veerabhadracharya B. M., Farquharson A. Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J. Mol. Biol. 1988; 202: 185–217
   PubMed Web of Science ®Google Scholar
• Janin J., Wodak S., Levitt M., Maigret B. Conformation of amino acid side-chains in Proteins. J. Mol. Biol. 1978; 125: 357–386
   PubMed Web of Science ®Google Scholar
• Kyte J., Doolittle R. F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982; 157: 105–132
   PubMed Web of Science ®Google Scholar
• Lanave C., Preparata G., Saccone C., Serio G. A new method for calculating evolutionary substitution rate. J. Mol. Biol. 1984; 20: 86–93
   Google Scholar
• Pepe G., Holtrop M., Gadaleta G., Kroon A. M., Cantatore P., Gallerani R., De Bendetto C., Quagliariello C., Sbisa E., Saccone C. Non random patterns of nucleotide substitutions and codon strategy in the mammalian mitochondrial genes coding for identified and unidentified reading flames. Biochemistry International 1983; 6: 553–563
   PubMedGoogle Scholar
• Ronin C., Granier C., Caseti C., Bouchilloux S., Van Rietschoten J. Synthetic substrates for thyroid oligosaccharide transferase. Effects of peptide chain length and modifications in the-Asn-Xae-Thr-region. Eur. J. Biochem. 1981; 118: 159–164
   PubMedGoogle Scholar
• Saccone C., Lanave C, Pesole C., Preparata C. Influence of base composition on quantitative estimates of gene evolution. Methods in Enzymology 1990; 183: 570–583
   PubMed Web of Science ®Google Scholar
• Saccone C., Pesole G., Kadenbach B. Evolutionary analysis of the nucleus-encoded subunits of mammalian cytochrome c oxidase. Eur. J. Biochem. 1991; 195: 151–156
   PubMedGoogle Scholar
• Sanger F., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 1977; 74: 5463–5467
   PubMed Web of Science ®Google Scholar
• Saraste M. Structural features of cytochrome oxidase. Quarterly Reviews of Biophysics 1990; 23: 331–366
   PubMed Web of Science ®Google Scholar
• Schaaper R. M., Dunn R. L. Spectra of spontaneous mutation in Escherichia coli strain defective in mismatch correction: The nature of in vivo DNA replication errors. Proc. Natl. Acad. Sci. USA 1987; 84: 6220–6224
   PubMed Web of Science ®Google Scholar
• Sueoka N. On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. USA 1962; 48: 582–592
   PubMed Web of Science ®Google Scholar
• Suske G., Mengel T., Cordingley M., Kadenbach B. Molecular cloning and further characterization of cDNAs for rat nuclear-encoded cytochrome c oxidase subunit VIc and VII. Eur. J. Biochem. 1987; 168: 233–237
   PubMedGoogle Scholar
• Thomas W. K., Wilson A. C. Evolution by base substitution in animal mitochondrial DNA. International Rev. Cytology. 1992, in press
   Google Scholar
• Topal M. D., Fresco J. R. Complementary base pairing and the origin of substitution mutations. Nature 1976; 263: 285–289
   PubMed Web of Science ®Google Scholar
• Yanamura W., Zhang Y. Z., Takamiya S., Capaldi R. A. Tissue-specific differences between heart and liver cytochrome c oxidase. Biochemistry 1988; 27: 4909–4914
   PubMedGoogle Scholar