Recommended nomenclature for the vertebrate alcohol dehydrogenase gene family

Biochemical Pharmacology

Volumn 58, Issue 3, 1999, Pages 389-395

  Duester, Gregg ^{a,b,c,d,e,f,g}   Farrés, Jaume ^a   Felder, Michael R ^b   Holmes, Roger S ^c   Höög, Jan Olov ^d   Parés, Xavier ^e   Plapp, Bryce V ^f   Yin, Shih Jiun ^g   Jörnvally, Hans ^a  

^a BURNHAM INSTITUTE   (United States)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c UNIVERSITY OF SOUTH CAROLINA   (United States)

^d UNIVERSITY OF NEWCASTLE   (Australia)

^e KAROLINSKA INSTITUTE   (Sweden)

^f UNIVERSITY OF IOWA   (United States)

^g NATIONAL DEFENSE MEDICAL CENTER   (Taiwan)

Author keywords

Alcohol dehydrogenase; Nomenclature; Vertebrate

Indexed keywords

ALCOHOL DEHYDROGENASE;

ANIMAL; ARTICLE; CLASSIFICATION; GENETIC POLYMORPHISM; GENETICS; HUMAN; MULTIGENE FAMILY; NOMENCLATURE; SPECIES DIFFERENCE; VERTEBRATE;

ALCOHOL DEHYDROGENASE; ANIMALS; HUMANS; MULTIGENE FAMILY; POLYMORPHISM, GENETIC; SPECIES SPECIFICITY; TERMINOLOGY; VERTEBRATES;

EID: 0033173362     PISSN: 00062952     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-2952(99)00065-9     Document Type: Article

References (90)

1. Vallee BL and Bazzone TJ, Isozymes of human liver alcohol dehydrogenase. Curr Top Biol Med Res 8: 219-244, 1983.
2. Persson B, Zigler JS Jr and Jörnvall H, A super-family of medium-chain dehydrogenases/reductases (MDR)-Sub-lines including ζ-crystallin, alcohol and polyol dehydrogenases, quinone oxidoreductases, enoyl reductases, VAT-1 and other proteins. Eur J Biochem 226: 15-22, 1994.
3. Jez JM, Flynn TG and Penning TM, A new nomenclature for the aldo-keto reductase superfamily. Biochem Pharmacol 54: 639-647, 1997.
4. Persson B, Krook M and Jörnvall H, Short-chain dehydrogenases/reductases. Adv Exp Med Biol 372: 383-395, 1995.
5. Hempel J, Nicholas H and Lindahl R, Aldehyde dehydroge-nases: Widespread structural and functional diversity within a shared framework. Protein Sci 2: 1890-1900, 1993.
6. Jörnvall H, Shafqat J, el-Ahmad M, Hjelmqvist L, Persson B and Danielsson O, Alcohol dehydrogenase variability. Evolutionary and functional conclusions from characterization of further variants. Adv Exp Med Biol 414: 281-289, 1997.
7. Duester G, Deltour L and Ang HL, Evidence that class IV alcohol dehydrogenase may function in embryonic retinoic acid synthesis. Adv Exp Med Biol 414: 357-364, 1997.
8. Hoffmann I, Ang HL and Duester G, Alcohol dehydrogenases in Xenopus development: Conserved expression of ADH1 and ADH4 in epithelial retinoid target tissues. Dev Dyn 213: 261-270, 1998.
9. Žgombić-Knight M, Ang HL, Foglio MH and Duester G, Cloning of the mouse class IV alcohol dehydrogenase (retinol dehydrogenase) cDNA and tissue-specific expression patterns of the murine ADH gene family. J Biol Chem 270: 10868-10877, 1995.
10. Höög J-O and Brandt M, Mammalian class VI alcohol dehydrogenase: Novel types of the rodent enzymes. Adv Exp Med Biol 372: 355-364, 1995.
11. Zheng Y-W, Bey M, Liu H and Felder MR, Molecular basis of the alcohol dehydrogenase-negative deer mouse. Evidence for deletion of the gene for class I enzyme and identification of a possible new enzyme class. J Biol Chem 268: 24933-24939, 1993.
12. Kedishvili NY, Gough WH, Chernoff EAG, Hurley TD, Stone CL, Bowman KD, Popov KM, Bosron WE and Li TK, cDNA sequence and catalytic properties of a chick embryo alcohol dehydrogenase that oxidizes retinol and 3β,5α-hydroxysteroids. J Biol Chem 272: 7494-7500, 1997.
13. Cederlund E, Peralba JM, Parés X and Jörnvall H, Amphibian alcohol dehydrogenase, the major frog liver enzyme. Relationships to other forms and assessment of an early gene duplication separating vertebrate class I and class III alcohol dehydrogenases. Biochemistry 30: 2811-2816, 1991.
14. Sun H-W and Plapp BV, Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family. J Mol Evol 34: 522-535, 1992.
15. Danielsson O, Atrian S, Luque T, Hjelmqvist L, GonzàlezDuarte R and Jörnvall H, Fundamental molecular differences between alcohol dehydrogenase classes. Proc Natl Acad Sci USA 91: 4980-4984, 1994.
16. Danielsson O and Jörnvall H, "Enzymogenesis": Classical liver alcohol dehydrogenase origin from the glutathione-dependent formaldehyde dehydrogenase line. Proc Natl Acad Sci USA 89: 9247-9251, 1992.
17. Koivusalo M, Baumann M and Uotila L, Evidence for the identity of glutathione-dependent formaldehyde dehydrogenase and class III alcohol dehydrogenase. FEBS Lett 257: 105-109, 1989.
18. Holmquist B and Vallee BL, Human liver class III alcohol and glutathione dependent formaldehyde dehydrogenase are the same enzyme. Biochem Biophys Res Commun 178: 1371-1377, 1991.
19. Beisswenger TB, Holmquist B and Vallee BL, χ-ADH is the sole alcohol dehydrogenase isozyme of mammalian brains: Implications and inferences. Proc Natl Acad Sci USA 82: 8369-8373, 1985.
20. Li T-K, Enzymology of human alcohol metabolism. Adv Enzymol 45: 427-483, 1977.
21. Day CP, Bashir R, James OFW, Bassendine MF, Crabb DW, Thomasson HR, Li T-K and Edenberg HJ, Investigation of the role of polymorphisms at the alcohol and aldehyde dehydrogenase loci in genetic predisposition to alcohol-related endorgan damage. Hepatology 14: 798-801, 1991.
22. Chao Y-C, Liou S-R, Chung Y-Y, Tang H-S, Hsu C-T, Li T-K and Yin S-J, Polymorphism of alcohol and aldehyde dehydro-genase genes and alcoholic cirrhosis in Chinese patients. Hepatology 19: 360-366, 1994.
23. Thomasson HR, Beard JD and Li TK, ADH2 gene polymorphisms are determinants of alcohol pharmacokinetics. Alcohol Clin Exp Res 19: 1494-1499, 1995.
24. Boleda MD, Saubi N, Farrés J and Parés X, Physiological substrates for rat alcohol dehydrogenase classes: Aldehydes of lipid peroxidation, ω-hydroxyfatty acids, and retinoids. Arch Biochem Biophys 307: 85-90, 1993.
25. Yang Z-N, Davis GJ, Hurley TD, Stone CL, Li T-K and Bosron WF, Catalytic efficiency of human alcohol dehydrogenases for retinol oxidation and retinal reduction. Alcohol Clin Exp Res 18: 587-591, 1994.
26. Ang HL, Deltour L, Hayamizu TF, Žgombić-Knight M and Duester G, Retinoic acid synthesis in mouse embryos during gastrulation and craniofacial development linked to class IV alcohol dehydrogenase gene expression. J Biol Chem 271: 9526-9534, 1996.
27. Ang HL, Deltour L, Žgombić-Knight M, Wagner MA and Duester G, Expression patterns of class I and class IV alcohol dehydrogenase genes in developing epithelia suggest a role for alcohol dehydrogenase in local retinoic acid synthesis. Alcohol Clin Exp Res 20: 1050-1064, 1996.
28. 2-receptor antagonists as pharmacological inhibitors, of human class IV alcohol dehydrogenase. FEBS Lett 426: 362-366, 1998.
29. Han CL, Liao CS, Wu CW, Hwong CL, Lee AR and Yin SJ, Contribution to first-pass metabolism of ethanol and inhibition by ethanol for retinol oxidation in human alcohol dehydrogenase family - Implications for etiology of fetal alcohol syndrome and alcohol-related diseases. Eur J Biochem 254: 25-31, 1998.
30. McEvily AJ, Holmquist B, Auld DS and Vallée BL, 3βHydroxy-5β-steroid dehydrogenase activity of human liver alcohol dehydrogenase is specific to γ-subunits. Biochemistry 27: 4284-4288, 1988.
31. Sellin S, Holmquist B, Mannervik B and Vallée BL, Oxidation and reduction of 4-hydroxyalkenals catalyzed by isozymes of human alcohol dehydrogenase. Biochemistry 30: 2514 2518, 1991.
32. Mårdh G and Vallee BL, Human class I alcohol dehydrogenases catalyze the interconversion of alcohols and aldehydes in the metabolism of dopamine. Biochemistry 25: 7279-7282, 1986.
33. Mårdh G, Dingley AL, Auld DS and Vallée BL, Human class II (IT) alcohol dehydrogenase has a redox-specific function in norepinephrine metabolism. Proc Natl Acad Sci USA 83: 8908-8912, 1986.
34. Pietruszko R and Ringold HJ, Antibody studies with the multiple enzymes of horse liver alcohol dehydrogenase. I. Biochem Biophys Res Commun 33: 497-502, 1968.
35. Pietruszko R, Ringold HJ, Li T-K, Vallée BL, Akeson A and Theorell H, Structure and function relationships in isoenzymes of horse liver alcohol dehydrogenase. Nature 221: 440-443, 1969.
36. 3. Ann Hum Genet 37: 49-67, 1973.
37. Holmes RS, The genetics of α-hydroxyacid oxidase and alcohol dehydrogenase in the mouse: Evidence for multiple gene loci and linkage between Hao-2 and Adh-3. Genetics 87: 709-716, 1977.
38. Julià P, Farrés J and Parés X, Characterization of three isoenzymes of rat alcohol dehydrogenase: Tissue distribution and physical and enzymatic properties. Eur J Biochem 162: 179-189, 1987.
39. Jörnvall H and Höög J-O, Nomenclature of alcohol dehydrogenases. Alcohol Alcohol 30: 153-161, 1995.
40. Blake JA, Davisson MT, Eppig JT, Maltais LJ, Povey S, White JA and Womack JE, A report on the international nomenclature workshop held May 1997 at The Jackson Laboratory, Bar Harbor, Maine, U.S.A. Genomics 45: 464-468, 1997.
41. White JA, McAlpine PJ, Antonarakis S, Cann H, Eppig JT, Frazer K, Frezal J, Lancet D, Nahmias J, Pearson P, Peters J, Scott A, Scott H, Spurr N and Talbot C Jr, Guidelines for human gene nomenclature (1997). Genomics 45: 468-471, 1997.
42. Maltais LJ, Blake JA, Eppig JT and Davisson MT, Rules and guidelines for mouse gene nomenclature: A condensed version. Genomics 45: 471-476, 1997.
43. Svensson S, Hedberg JJ and Höög JO, Structural and functional divergence of class II alcohol dehydrogenase - Cloning and characterisation of rabbit liver isoforms of the enzyme. Eur J Biochem 251: 236-243, 1998.
44. Matsuo Y and Yokoyama S, Cloning and sequencing of a processed pseudogene derived from a human class III alcohol dehydrogenase gene. Am J Hum Genet 46: 85-91, 1990.
45. Foglio MH and Duester G, Characterization of the functional gene encoding mouse class III alcohol dehydrogenase (glutathione-dependent formaldehyde dehydrogenase) and an unexpressed processed pseudogene with an intact open reading frame. Eur J Biochem 237: 496-504, 1996.
46. Zheng YW and Felder MR, Genetic mapping of a possible new alcohol dehydrogenase sequence to mouse chromosome 3 at the Adh-l/Adh-3 complex. Biochem Genet 35: 105-117, 1997.
47. Duester G, Hatfield GW, Buhler R, Hempel J, Jörnvall H and Smith M, Molecular cloning and characterization of a cDNA for the β subunit of human alcohol dehydrogenase. Proc Natl Acad Sci USA 81: 4055-4059, 1984.
48. Duester G, Smith M, Bilanchone V and Hatfield GW, Molecular analysis of the human class I alcohol dehydrogenase gene family and nucleotide sequence of the gene encoding the βsubunit. J Biol Chem 261: 2027-2033, 1986.
49. von Bahr-Lindström H, Höög J-O, Hedén L-O, Kaiser R, Fleetwood L, Larsson K, Lake M, Holmquist B, Holmgren A, Hempel J, Vallee BL and Jörnvall H, cDNA and protein structure for the a subunit of human liver alcohol dehydrogenase. Biochemistry 25: 2465-2470, 1986.
50. Hedén L-O, Ḧög J-O, Larsson K, Lake M, Lagerholm E, Holmgren A, Vallee BL, Jörnvall H and von Bahr-Lindström H, cDNA clones coding for the β-subunit of human liver alcohol dehydrogenase have differently sized 3′-noncoding regions. FEBS Lett 194: 327-332, 1986.
51. 2 subunits of human liver alcohol dehydrogenase. cDNA structures, two amino acid replacements, and compatibility with changes in the enzymatic properties. Eur J Biochem 159: 215-218, 1986.
52. Höög J-O, von Bahr-Lindström H, Hedén L-O, Holmquist B, Larsson K, Hempel J, Vallee BL and Jörnvall H, Structure of the class II enzyme of human liver alcohol dehydrogenase: Combined cDNA and protein sequence determination of the π subunit. Biochemistry 26: 1926-1932, 1987.
53. Giri PR, Krug JF, Kozak C, Moretti T, O'Brien SJ, Seuanez HN and Goldman D, Cloning and comparative mapping of a human class III (Χ) alcohol dehydrogenase cDNA. Biochem Biophys Res Commun 164: 453-460, 1989.
54. Sharma CP, Fox EA, Holmquist B, Jörnvall H and Vallee BL, cDNA sequence of human class III alcohol dehydrogenase. Biochem Biophys Res Commun 164: 631-637, 1989.
55. Satre MA, Žgombić-Knight M and Duester G, The complete structure of human class IV alcohol dehydrogenase (retinol dehydrogenase) determined from the ADH7 gene. J Biol Chem 269: 15606-15612, 1994.
56. Farrés J, Moreno A, Crosas B, Peralba JM, Allali-Hassani A, Hjelmqvist L, Jörnvall H and Parés X, Alcohol dehydrogenase of class IV (σσ-ADH) from human stomach. cDNA sequence and structure/function relationships. Eur J Biochem 224: 549-557, 1994.
57. Yokoyama H, Baraona E and Lieber CS, Molecular cloning of human class IV alcohol dehydrogenase cDNA. Biochem Biophys Res Commun 203: 219-224, 1994.
58. Yokoyama S, Matsuo Y, Ramsbotham R and Yokoyama R, Molecular characterization of a class IV human alcohol dehydrogenase gene (ADH7). FEBS Lett 351: 411-415, 1994.
59. Kedishvili NY, Bosron WF, Stone CL, Hurley TD, Peggs CF, Thomasson HR, Popov KM, Carr LG, Edenberg HJ and Li T-K, Expression and kinetic characterization of recombinant human stomach alcohol dehydrogenase. Active-site amino acid sequence explains substrate specificity compared with liver isozymes. J Biol Chem 270: 3625-3630, 1995.
60. Yasunami M, Chen C-S, Yoshida A, A human alcohol dehydrogenase gene (ADH6) encoding an additional class of isozyme. Proc Natl Acad Sci USA 88: 7610-7614, 1991.
61. Edenberg HJ, Zhang K, Fong K, Bosron WF and Li T-K, Cloning and sequencing of cDNA encoding the complete mouse liver alcohol dehydrogenase. Proc Natl Acad Sci USA 82: 2262-2266, 1985.
62. Ceci JD, Lawther R, Duester G, Hatfield GW, Smith M, O'Malley MP and Felder MR, Androgen induction of alcohol dehydrogenase in mouse kidney: Studies with a cDNA probe confirmed by nucleotide sequence analysis. Gene 41: 217-224, 1986.
63. 2 cDNA: Nucleotide sequences of the class III ADH genes evolve slowly even for silent substitutions. DNA Seq-J DNA Seq Map 3: 167-175, 1992.
64. Crabb DW and Edenberg HJ, Complete amino acid sequence of rat liver alcohol dehydrogenase deduced from the cDNA sequence. Gene 48: 287-291, 1986.
65. Höög J-O, Cloning and characterization of a novel rat alcohol dehydrogenase of class II type. FEBS Lett 368: 445-448, 1995.
66. Julià P, Parés X and Jo̊rnvall H, Rat liver alcohol dehydrogenase of class III: Primary structure, functional consequences and relationships to other alcohol dehydrogenases. Eur J Biochem 172: 73-83, 1988.
67. Parés X, Cederlund E, Moreno A, Hjelmqvist L, Farrés J and Jörnvall H, Mammalian class IV alcohol dehydrogenase (stomach alcohol dehydrogenase): Structure, origin, and correlation with enzymology. Proc Natl Acad Sci USA 91: 1893-1897, 1994.
68. Jörnvall H, Horse liver alcohol dehydrogenase: On the primary structures of the isoenzymes. Eur J Biochem 16: 41-49, 1970.
69. Park D-H, Plapp BV, Isoenzymes of horse liver alcohol dehydrogenase active on ethanol and steroids. cDNA cloning, expression, and comparison of active sites. J Biol Chem 266: 13296-13302, 1991.
70. Trezise AEO, Godfrey EA, Holmes RS and Beacham IR, Cloning and sequencing of cDNA encoding baboon liver alcohol dehydrogenase: Evidence for a common ancestral lineage with the human alcohol dehydrogenase βsubunit and for class I ADH gene duplications predating primate radiation. Proc Natl Acad Sci USA 86: 5454-5458, 1989.
71. Light DR, Dennis MS, Forsythe IJ, Liu C-C, Green DW, Kratzer DA and Plapp BV, α-Isoenzyme of alcohol dehydro-genase from monkey liver. Cloning, expression, mechanism, coenzyme, and substrate specificity. J Biol Chem 267: 12592-12599, 1992.
72. Höög J-O, Vagelopoulos N, Yip P-K, Keung WM and Jörnvall H, Isozyme developments in mammalian class-I alcohol dehydrogenase - cDNA cloning, functional correlations, and lack of evidence for genetic isozymes in rabbit. Eur J Biochem 213: 31-38, 1993.
73. Bradley RD, Bull JJ, Johnson AD and Hillis DM, Origin of a novel allele in a mammalian hybrid zone. Proc Natl Acad Sci USA 90: 8939-8941, 1993.
74. Estonius M, Karlsson C, Fox EA, Höög J-O, Holmquist B, Vallee BL, Davidson WS and Jörnvall H, Avian alcohol dehydrogenase: The chicken liver enzyme - Primary structure, cDNA-cloning, and relationships to other alcohol dehydrogenases. Eur J Bioche 194: 593-602, 1990.
75. Kedishvili NY, Stone CL, Popov KM and Chernoff EAG, Role of alcohol dehydrogenases in steroid and retinoid metabolism. Adv Exp Med Biol 414: 321-329, 1997.
76. Kaiser R, Nussrallah B, Dam R, Wagner FW and Jörnvall H, Avian alcohol dehydrogenase. Characterization of the quail enzyme, functional interpretations, and relationships to the different classes of mammalian alcohol dehydrogenase. Biochemistry 29: 8365-8371, 1990.
77. Estonius M, Hjelmqvist L and Jörnvall H, Diversity of vertebrate class I alcohol dehydrogenase. Mammalian and non-mammalian enzyme functions correlated through the structure of a ratite enzyme. Eur J Biochem 224: 373-378, 1994.
78. Hjelmqvist L, Estonius M and Jörnvall H, The vertebrate alcohol dehydrogenase system: Variable class II type form elucidates separate stages of enzymogenesis. Proc Natl Acad Sci USA 92: 10904-10908, 1995.
79. Hjelmqvist L, Metsis M, Persson H, Höög J-O, McLennan J and Jörnvall H, Alcohol dehydrogenase of class I: Kiwi liver enzyme, parallel evolution in separate vertebrate lines, and correlation with 12S rRNA patterns. FEBS Lett 367: 306-310, 1995.
80. Persson B, Bergman T, Keung WM, Waldenström U, Holmquist B, Vallee BL and Jörnvall H, Basic features of class-I alcohol dehydrogenase: Variable and constant segments coordinated by inter-class and intra-class variability -Conclusions from characterization of the alligator enzyme. Eur J Biochem 216: 49-56, 1993.
81. Shafqat J, Hjelmqvist L and Jörnvall H, Liver class-I alcohol dehydrogenase isozyme relationships and constant patterns in a variable basic structure. Distinctions from characterization of an ethanol dehydrogenase in cobra, Naja naja. EUT J Biochem 236: 571-578, 1996.
82. Hjelmqvist L, Shafqat J, Siddiqi AR and Jörnvall H, Linking of isozyme and class variability patterns in the emergence of novel alcohol dehydrogenase functions. Characterization of isozymes in Uromastix hardwickii. Eur J Biochem 236: 563-570, 1996.
83. Hjelmqvist L, Shafqat J, Siddiqi AR and Jörnvall H, Alcohol dehydrogenase of class III: Consistent patterns of structural and functional conservation in relation to class I and other proteins. FEBS Lett 373: 212-216, 1995.
84. Danielsson O, Eklund H and Jörnvall H, The major piscine liver alcohol dehydrogenase has class-mixed properties in relation to mammalian alcohol dehydrogenases of classes I and III. Biochemistry 31: 3751-3759, 1992.
85. Danielsson O, Shafqat J, Estonius M, El-Ahmad M and Jörnvall H, Isozyme multiplicity with anomalous dimer patterns in a class III alcohol dehydrogenase. Effects on the activity and quaternary structure of residue exchanges at "nonfunctional" sites in a native protein. Biochemistry 35: 14561-14568, 1996.
86. Hjelmqvist L, Hackett M, Shafqat J, Danielsson O, Iida J, Hendrickson RC, Michel H, Shabanowitz J, Hunt DF and Jörnvall H, Multiplicity of N-terminal structures of mediumchain alcohol dehydrogenases: Mass-spectrometric analysis of plant, lower vertebrate and higher vertebrate class I, II, and III forms of the enzyme. FEBS Lett 367: 237-240, 1995.
87. Danielsson O, Shafqat J, Estonius M and Jörnvall H, Alcohol dehydrogenase class III contrasted to class I. Characterization of the cyclostome enzyme, the existence of multiple forms as for the human enzyme, and distant cross-species hybridization. Eur J Biochem 225: 1081-1088, 1994.
88. 2 Oriental isozyme explains functional properties, establishes an active site structure, and parallels mutational exchanges in the yeast enzyme. Proc Natl Acad Sci USA 81: 3024-3028, 1984.
89. 1 by a Cys for Arg-369 substitution which decreases NAD(H) binding. Biochem Biophys Res Commun 146: 1227-1233, 1987.
90. Cheung B, Holmes RS, Easteal S and Beacham IR, Evolution of class I alcohol dehydrogenase genes in catarrhine primates: Gene conversion, substitution rates, and gene regulation. Mol Biol Evol 16: 23-36, 1999.