Evolution of class I alcohol dehydrogenase genes in catarrhine primates: Gene conversion, substitution rates, and gene regulation

Molecular Biology and Evolution

Volumn 16, Issue 1, 1999, Pages 23-36

  Cheung, Brenda ^b   Holmes, Roger S ^a   Easteal, Simon ^b   Beacham, Ifor R ^b  

^a SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

^b NONE

Author keywords

Alcohol dehydrogenase; Gene conversion; Gene duplication; Gene regulation; Molecular evolution; Papio hamadryas

Indexed keywords

ALCOHOL DEHYDROGENASE;

ARTICLE; CATALYSIS; CODING; GENE CONVERSION; GENE DUPLICATION; GENETIC ANALYSIS; GENETIC REGULATION; MOLECULAR CLONING; MOLECULAR EVOLUTION; MONKEY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIMATE; TRANSCRIPTION REGULATION;

CERCOPITHECIDAE; HAMADRYAS; MACACA MULATTA; MAMMALIA; PAPIO; PAPIO HAMADRYAS; PRIMATES;

EID: 0032931170     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026035     Document Type: Article

References (63)

1. BAILEY, W. J., D. H. A. FITCH, D. A. TAGLE, J. CZELUSNIAK, J. L. SLIGHTOM, and M. GOODMAN. 1991. Molecular evolution of the ψη-globin gene locus: gibbon phylogeny and the hominoid slowdown. Mol. Biol. Evol. 8:155-184.
2. BENVENISTE, R. E. 1985. The contributions of retroviruses to the study of mammalian evolution. Pp. 359-417 in R. J. MCINTYRE, ed. Molecular evolutionary genetics. Plenum Press, New York.
3. BERGER, S. L., and C. S. BIRKENMEIER. 1979. Inhibition of intractable nucleases with ribonucleoside-vanadyl complexes: isolation of messenger ribonucleic acid from resting lymphocytes. Biochemistry 18:5143-5149.
4. BOSRON, W. F., and T.-K. LI. 1986. Genetic polymorphism of human liver alcohol and aldehyde dehydrogenases, and their relationship to alcohol metabolism and alcoholism. Hepatology 6:502-510.
5. BROWN, C. J., K. A. BALTZ, and H. J. EDENBERG. 1992. Expression of the human ADH2 gene: an unusual Spl-binding site in the promoter of a gene expressed at high levels in liver. Gene 121:313-320.
6. CARR, L. G., and H. J. EDENBERG. 1990. Cis-acting sequences involved in protein binding and in-vitro transcription of the human alcohol dehydrogenase gene ADH2. J. Biol. Chem. 265:1658-1664.
7. CRABB, D. W., P. M. STEIN, K. M. DIPPLE, J. B. HITTLE, R. SIDHU, M. QULALI, K. ZHANG, and H. J. EDENBERG. 1989. Structure and expression of the rat class I alcohol dehydrogenase gene. Genomics 5:906-914.
8. DEUSTER, G. 1991. Human liver alcohol dehydrogenase gene expression. Pp. 375-402 in R. R. WATSON, ed. Drug and alcohol abuse reviews, Vol 2. Liver pathology and alcohol. Humana Press, Totowa, N.J.
9. EASTEAL, S. 1991. The relative rate of DNA evolution in primates. Mol. Biol. Evol. 8:115-127.
10. EASTEAL, S., C. C. COLLET, and D. J. BETTY. 1995. The mammalian molecular clock. Springer-Verlag and R. D. Landes, Austin.
11. EASTEAL, S., and G. HERBERT. 1997. Molecular evidence from the nuclear genome for the time frame of human evolution. J. Mol. Evol. 448:121-132.
12. EDENBERG, H. J. 1991. Molecular biological approaches to studies of alcohol metabolizing enzymes. Pp. 165-223 in J. C. CRABBE JR. and R. A. HARRIS, eds. The genetic basis of alcohol and drug actions. Plenum Press, New York.
13. EDENBERG, H. J., and C. BROWN. 1992. Regulation of human alcohol dehydrogenase genes. Pharmacogenetics 2:185-196.
14. EDENBERG, H. J., K. ZHANG, K. FONG, W. S. BOSRON, and T.-K. LI. 1985. Cloning and sequencing of a cDNA encoding the complete mouse liver alcohol dehydrogenase. Proc. Natl. Acad. Sci. USA 82:2262-2266.
15. ELLSWORTH, D. L., D. HEWETT-EMMETT, and W.-H. LI. 1993. Insulin-like growth factor II intron sequences support the hominoid rate-slowdown hypothesis. Mol. Phylogenet. Evol. 2:315-321.
16. FELSENSTEIN, J. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
17. FROHMAN, M. A., M. K. DUSH, and G. R. MARTIN. 1988. Rapid production of full-length cDNAs from rare transcripts: Amplification using a single gene-specific oligonucleotide primer. Proc. Natl. Acad. Sci. USA 85:8998-9002.
18. HEMPEL, J., R. BUHLER, R. KAISER, B. HOLMQUIST, C. DE ZALENSKI, J.-P. VON WARTBURG, B. VALLEE, and H. JORNVALL. 1984. Human liver alcohol dehydrogenase I. The primary structure of the betal isozyme. Eur. J. Biochem. 145: 437-445.
19. HEMPEL, J., B. HOLMQUIST, L. FLEETWOOD, R. KAISER, J. BARROS-SODERLING, R. BUHLER, B. L. VALLEE, and H. JORNVALL. 1985. Structural relationships among class I isozymes of human liver alcohol dehydrogenase. Biochemistry 24: 5303-5307.
20. HERBERT, G., and S. EASTEAL. 1996. The relative rates of DNA evolution in human and Old World monkey lineages. Mol. Biol. Evol. 13:1054-1057.
21. HOLMES, R. S. 1993. Alcohol dehydrogenases: gene multiplicity and differential functions of five classes of isozymes. Drug Alcohol Rev. 12:99-110.
22. HOLMES, R. S., Y. R. COURTNEY, and J. L. VANDEBERG. 1986. Alcohol dehydrogenase isozymes in baboons: tissue distribution, catalytic properties and variant phenotypes in liver, kidney, stomach and testis. Alcohol. Clin. Exp. Res. 10: 623-630.
23. HOLMES, R. S., J. A. DULEY, and J. N. BURNELL. 1983. The alcohol dehydrogenase gene complex on chromosome 3 of the mouse. Pp. 155-174 in M. C. RATTAZZI, J. G. SCANUALIOS, and G. S. WHITT, eds. Isozymes: current topics in biological and medical research. Vol. 8. Alan R. Liss, New York.
24. HOLMES, R. S., J. L. MEYER, and J. L. VANDEBERG. 1990. Baboon alcohol dehydrogenase isozymes: purification and properties of liver class I ADH. Moderate alcohol consumption reduces liver class I and II activities. Pp. 819-841 in C. L. MARKERT, ed. Isozymes: structure, function and use in biology and medicine. Wiley-Liss, New York.
25. HOOG, J.-O., L.-O. HEDEN, K. LARSSON, H. JORNVALL, and H. VON BAHR-LINDSTROM. 1986. The gammal and gamma2 subunits human liver alcohol dehydrogenase cDNA structures, two amino acid replacements and compatibility with changes in enzymatic properties. Eur. J. Biochem. 159:215-218.
26. IKUTA, T., T. FUJIYOSHI, K. KURACHI, and A. YOSHIDA. 1985. Molecular cloning of a full length cDNA for human alcohol dehydrogenase. Proc. Natl. Acad. Sci. USA 82:2703-2707.
27. IKUTA, T., S. SZETO, and A. YOSHIDA. 1986. Three human alcohol dehydrogenase subunits: cDNA structure and molecular and evolutionary divergence. Proc. Natl. Acad. Sci. USA 83:634-638.
28. JAKOBSEN, I. B., and S. EASTEAL. 1996. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput. Appl. Biosci. 12:291-295.
29. JAKOBSEN, I. B., S. R. WILSON, and S. EASTEAL. 1997. The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments. Mol. Biol. Evol. 14: 474-484.
30. JENNINGS, M. P., and I. R. BEACHAM. 1989. MacConkey agar as an alternative to Xgal in the detection of recombinant plasmids. Biotechniques 7:1082.
31. JORNVALL, H., J. HEMPEL, H. VON BAHR-LINDSTROM, J.-O. HOOG, and B. L. VALLEE. 1987. Alcohol and aldehyde dehydrogenases: structures of the human liver enzymes, functional properties and evolutionary aspects. Alcohol Alcohol. Suppl. 1:13-23.
32. JULIA, P., J. FERRES, and X. PARES. 1987. Characterization of three isoenzymes of rat alcohol dehydrogenases. Eur. J. Biochem. 43:139-147.
33. KADONAGA, J. T., K. A. JONES, and R. TIJAN. 1986. Promoter-specific activation of RNA polymerase II transcription by Spl. Trends Biochem. Sci. 11:20-24.
34. KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
35. LI, W.-H. 1993. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36: 96-99.
36. LI, W.-H., D. L. ELLSWORTH, J. KRUSHKAL, B. H.-J. CHANG, and D. HEWET-EMMETT. 1996. Rates of substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol. 5:182-187.
37. LI, W.-H., M. TANIMURA, and P. M. SHARP. 1987. An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J. Mol. Evol. 25:330-342.
38. LIGHT, D. R., M. S. DENNIS, I. J. FORSYTHE, C.-C. LIU, D. W. GREEN, D. A. KRATZER, and B. V. PLAPP. 1992. α-Isoenzyme of alcohol dehydrogenase from monkey liver. Cloning, expression, mechanism, coenzyme and substrate specificity. J. Biol. Chem. 267:12592-12599.
39. NOYES, B. E., M. MEVARECH, R. STEIN, and K. L. AGARWAL. 1979. Detection and partial sequence analysis of gastric mRNA by using an oligodeoxynucleotide probe. Proc. Natl. Acad. Sci. USA 76:1770-1774.
40. PAJOVIC, S., V. E. JONES, K. R. PROWSE, F. G. BERGER, and H. BAUMANN. 1994. Species-specific changes in regulatory elements of mouse haptoglobin genes. J. Biol. Chem. 269: 2215-2224.
41. PARES, X., E. CEDERLUND, A. MORENO, N. SAUBI, J.-O. HOOG, and H. JORNVALL. 1992. Class IV alcohol dehydrogenase (the gastric enzyme). Structural analysis of human σσ-ADH reveals class IV to be variable and confirms the presence of a fifth mammalian alcohol dehydrogenase class. FEBS Lett. 303:69-72.
42. PARK, D.-H., and B. V. PLAPP. 1991. Isoenzymes of horse liver alcohol dehydrogenase active on ethanol and steroids. J. Biol. Chem. 266:13296-13302.
43. PIETRUSZKO, R., and H. THEORELL. 1969. Subunit composition of horse liver alcohol dehydrogenase. Arch. Biochem. Biophys. 131:288-298.
44. SEINO, S., G. I. BELL, and W.-H. LI. 1992. Sequences of primate insulin genes support the hypothesis of a slower rate of molecular evolution in humans and apes than in monkeys. Mol. Biol. Evol. 9:193-203.
45. SMITH, M., D. A. HOPKINSON, and H. HARRIS. 1971. Developmental changes and polymorphism in human alcohol dehydrogenase. Ann. Hum. Genet. 34:251-271.
46. SMITH, S. W., R. OVERBEEK, C. R. WOESE, W. GILBERT, and P. M. GILLEVET. 1994. The genetic data environment, an expandable GUI for multiple sequence analysis. CABIOS 10:671-675.
47. SNEATH, P. H. A., M. J. SACKIN, and R. P. AMBLER. 1975. Detecting evolutionary incompatibilities from protein sequences. Syst. Zool. 24:311-332.
48. STEWART, M. J., M. S. MCBRIDE, L. A. WINTER, and G. DEUSTER. 1990. Promoters for the human alcohol dehydrogenase genes ADH1, ADH2 and ADH3: interaction of CCAAT/ enhancer binding protein and elements flanking the ADH2 TATA box. Gene 90:271-279.
49. STEWART, M. J., M. L. SHEAN, B. W. PAEPER, and G. DEUSTER. 1991. The role of CCAAT/enhancer-binding protein in the differential transcriptional regulation of a family of human liver alcohol dehydrogenase genes. J. Biol. Chem. 266: 11594-11603.
50. STONE, C. L., H. R. THOMASSON, W. F. BOSRON, and T-K. LI. 1993. Purification and partial amino acid sequence of a high-activity human alcohol dehydrogenase. Alcohol. Clin. Exp. Res. 17:911-918.
51. SUN, H.-W., and B. V. PLAPP. 1992. Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family. J. Mol. Evol. 34:522-535.
52. TAGLE, D. A., B. F. KOOP, M. GOODMAN, J. L. SLIGHTOM, D. L. HESS, and R. T. JONES. 1988. Embryonic ∈ and γ globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203:439-455.
53. THOMPSON, J. D., D. G. HIGGINS, and T. J. GIBSON. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
54. TREZISE, A. E. O., B. CHEUNG, R. S. HOLMES, and I. R. BEACHAM. 1991. Evidence for three genes encoding class-I alcohol dehydrogenase subunits in baboon and analysis of the 5́ region of the gene encoding the ADH beta subunit. Gene 103:211-218.
55. TREZISE, A. E. O., E. A. GODFREY, R. S. HOLMES, and I. R. BEACHAM. 1989. Cloning and sequencing of cDNA encoding baboon liver alcohol dehydrogenase: evidence for a common ancestral lineage with the human alcohol dehydrogenase beta subunit and for class-I ADH gene duplications predating primate radiation. Proc. Natl. Acad. Sci. USA 86: 5454-5458.
56. VON BAHR-LINDSTROM, H., J.-O. HOOG, L. O. HEDEN et al. (12 co-authors). 1986. cDNA and protein structure for the alpha subunit of human liver alcohol dehydrogenase. Biochemistry 25:2465-2470.
57. WEINBERG, R. A., S. O. WARNAAR, and E. WINOCAUR. 1972. Isolation and characterization of Simian virus 40 ribonucleic acid. J. Virol. 10:193-201.
58. WU, C.-I., and W.-H. LI. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA 82:1741-1745
59. YASUNAMI, M., C. S. CHEN, and A. YOSHIDA. 1990. Multiplication of the class I alcohol dehydrogenase locus in mammalian evolution. Biochem. Genet. 28:591-599.
60. _. 1991. A human alcohol dehydrogenase gene (ADH6) encoding an additional class of isozyme. Proc. Natl. Acad. Sci. USA 88:7610-7614.
61. YOKOYAMA, S., and D. E. HARRY. 1993. Molecular phylogeny and evolutionary rates of alcohol dehydrogenase in vertebrates and plants. Mol. Biol. Evol. 10:1215-1226.
62. YOKOYAMA, S., and R. YOKOYAMA. 1987. Molecular evolution of mammalian class I alcohol dehydrogenase. Mol. Biol. Evol. 4:504-513.
63. YOKOYAMA, S., R. YOKOYAMA, C. S. KINLAW, and D. E. HARRY. 1990. Molecular evolution of the zinc-containing long chain alcohol dehydrogenase genes. Mol. Biol. Evol. 7:143-154.