Comparative studies of vertebrate aldehyde dehydrogenase 3: Sequences, structures, phylogeny and evolution. Evidence for a mammalian origin for the ALDH3A1 gene

Chemico-Biological Interactions

Volumn 191, Issue 1-3, 2011, Pages 113-121

  Holmes, Roger S ^a   Hempel, John ^b  

^a GRIFFITH UNIVERSITY   (Australia)

^b UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Aldehyde dehydrogenase; Aldehyde metabolism; ALDH3; Enzyme structure; Evolution; Gene duplication

Indexed keywords

ALDEHYDE DEHYDROGENASE; ALDEHYDE DEHYDROGENASE 3; UNCLASSIFIED DRUG;

ALDH3A1 GENE; ALDH3A2 GENE; ALDH3B1 GENE; ALDH3B2 GENE; AMINO ACID SEQUENCE; ANIMAL CELL; ANIMAL TISSUE; BONY FISH; CATALYSIS; CHICKEN; CONFERENCE PAPER; CONTROLLED STUDY; ENZYME BINDING; ENZYME STRUCTURE; EYE; FILTRATION; GENE; GENE DUPLICATION; GENE FUNCTION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CONSERVATION; GENOME; HUMAN; HUMAN CELL; MAMMAL; NONHUMAN; OPOSSUM; PHYLOGENY; PLATYPUS; RAT; ULTRAVIOLET RADIATION; XENOPUS; ZEBRA FISH;

ALDEHYDE DEHYDROGENASE; ALDEHYDE OXIDOREDUCTASES; AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; EXONS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

DANIO RERIO; DIDELPHIDAE; MAMMALIA; OSTEICHTHYES; RATTUS; VERTEBRATA;

EID: 79957547123     PISSN: 00092797     EISSN: 18727786     Source Type: Journal    
DOI: 10.1016/j.cbi.2011.01.014     Document Type: Conference Paper

References (53)

1. V. Vasiliou, D.W. Nebert, Analysis and update of the human aldehyde dehydrogenase (ALDH) gene family, Hum. Genomics 2 (2005) 138-145.
2. N.A. Sophos, W.J. Black, V. Vasiliou, An update of the ALDH gene family, in: H. Weiner, B. Plapp, R. Lindahl, E. Maser (Eds.), Enzymology and Molecular Biology of Carbonyl Metabolism, vol. 12, Purdue University Press, Indiana, 2006, pp. 3-7.
3. G.P. Timms, R.S. Holmes, Genetics and ontogeny of aldehyde dehydrogenase isozymes in the mouse; evidence for a locus controlling the inducibility of the liver microsomal isozymes, Biochem. Genet. 19 (1981) 122-336.
4. D.E. Jones, M.D. Brennan, J. Hempel, R. Lindahl, Cloning and complete nucleotide sequence of a full-length cDNA encoding a catalytically functional tumor-associated aldehyde dehydrogenase, Proc. Natl. Acad. Sci. U.S.A. 85 (1988) 1782-1786. (Pubitemid 24315766)
5. R.S. Holmes, R.A. Popp, J.L. VandeBerg, Genetics of ocular NAD-dependent alcohol dehydrogenase and aldehyde dehydrogenase in the mouse: evidence for genetic identity with stomach isozymes and localization of Ahd-4 on chromosome 11 near Trembler, Biochem. Genet. 26 (1988) 191-205.
6. J.S. Boesch, C. Lee, R.G. Lindahl, Constitutive expression of class 3 aldehyde dehydrogenase in cultured rat corneal epithelium, J. Biol. Chem. 271 (1996) 5150-5157.
7. M. Abedinia, T. Pain, E.M. Algar, R.S. Holmes, Bovine corneal aldehyde dehydrogenase: the major soluble protein with a possible dual protective role for the eye, Exp. Eye Res. 51 (1990) 419-426.
8. N. Lassen, J.B. Bateman, T. Estev, J.R. Kuszak, D.W. Nees, J. Piatigorsky, G. Deuster, B.J. Day, J. Huang, L.M. Hines, V. Vasiliou, Multiple and additive functions of ALDH3A1 and ALDH1A1: cataract phenotype and ocular oxidative damage in aldh3a1(-/-)/aldh1a1(-/-) knockout mice, J. Biol. Chem. 282 (2007) 25668-25676.
9. K. Miyauchi, R. Masaki, S. Taketani, A. Yamamoto, M. Akayama, Y. Tashiro, Molecular cloning, sequencing and expression of cDNA for rat liver microsomal aldehyde dehydrogenase, J. Biol. Chem. 266 (1991) 19536-19542. (Pubitemid 21908263)
10. G.R. Rogers, N.G. Marlova, V. De Laurenzi, W.B. Rizzo, J.G. Compton, Genomic organization and expression of the fatty aldehyde dehydrogenase gene (FALDH), Genomics 39 (1997) 127-135. (Pubitemid 27069210)
11. V. De Laurenzi, G.R. Rogers, D.J. Hamrock, L.N. Marekov, P.M. Steinhart, J.N. Compton, N. Markova, W.B. Rizzo, Sjogren-Larsson syndrome is caused by mutations in the fatty aldehyde dehydrogenase gene, Nat. Genet. 12 (1996) 52-57.
12. L.C. Hsu, W.C. Chang, L. Hiraoka, C.L. Hsieh, Molecular cloning, genomic organization and chromosomal localization of an additional human aldehyde dehydrogenase, ALDH6, Genomics 24 (1994) 333-341.
13. L. Hsu, W.-C. Chang, A. Yoshida, Sequencing and expression of the human ALDH8 encoding a new member of the aldehyde dehydrogenase family, Gene 151 (1994) 285-289.
14. L. Hsu, W.C. Chang, A. Yoshida, Human aldehyde dehydrogenase genes ALDH7 and ALDH8: genomic organization and gene structure comparison, Gene 189 (1997) 89-94. (Pubitemid 27183178)
15. R.S. Holmes, Opossum aldehyde dehydrogenases. Evidence for four ALDH1A1-like genes on chromosome 6 and ALDH1A2 and ALDH1A3 genes on chromosome 1, Biochem. Genet. 47 (2009) 609-624.
16. R.S. Holmes, Biochemical genetics of opossum aldehyde dehydrogenase 3: evidence for three ALDH3A-like genes and an ALDH3B-like gene, Biochem. Genet. 48 (2010) 287-303.
17. S.F. Altschul, W. Gish, W. Miller, E.W.Myers, D.J. Lipman, Basic local alignment search tool, J. Mol. Biol. 215 (1990) 403-410.
18. W.J. Kent, C.W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, A.M. Zahler, D. Haussler, The human genome browser at UCSC, Genome Res. 12 (2003) 994-1006.
19. W.C. Warren, L.W. Hillier, J.A. Marshall Graves, E. Birney, C.P. Ponting, F. Grützner, K. Belov, W. Miller, L. Clarke, A.T. Chinwalla, S.P. Yang, A. Heger, D.P. Locke, P. Miethke, P.D. Waters, F. Veyrunes, L. Fulton, B. Fulton, T. Graves, J. Wallis, X.S. Puente, C. López-Otín, G.R. Ordóñez, E.E. Eichler, L. Chen, Z. Cheng, J.E. Deakin, A. Alsop, K. Thompson, P. Kirby, A.T. Papenfuss, M.J. Wakefield, T. Olender, D. Lancet, G.A. Huttley, A.F. Smit, A. Pask, P. Temple-Smith, M.A. Batzer, J.A. Walker, M.K. Konkel, R.S. Harris, C.M.Whittington, E.S. Wong, N.J. Gemmell, E. Buschiazzo, I.M. Vargas Jentzsch, A. Merkel, J. Schmitz, A. Zemann, G. Churakov, J.O. Kriegs, J. Brosius, E.P. Murchison, R. Sachidanandam,C. Smith, G.J. Hannon, E. Tsend-Ayush, D. McMillan, R. Attenborough, W. Rens, M. Ferguson-Smith, C.M. Lefèvre, J.A. Sharp, K.R. Nicholas, D.A. Ray, M. Kube, R. Reinhardt, T.H. Pringle, J. Taylor, R.C. Jones, B. Nixon, J.L. Dacheux, H. Niwa, Y. Sekita, X. Huang, A. Stark, P. Kheradpour, M. Kellis, P. Flicek, Y. Chen, C. Webber, R. Hardison, J. Nelson, K. Hallsworth-Pepin, K. Delehaunty, C. Markovic, P. Minx, Y. Feng, C. Kremitzki, M. Mitreva, J. Glasscock, T. Wylie, P. Wohldmann, P. Thiru, M.N. Nhan, C.S. Pohl, S.M. Smith, S. Hou, M. Nefedov, P.J. de Jong, M.B. Renfree, E.R. Mardis, R.K. Wilson, Genome analysis of the platypus reveals unique signatures of evolution, Nature 453 (2008) 175-183. (Pubitemid 351667983)
20. The International Chicken Genome Sequencing Consortium, Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature 432 (2004) 695-716.
21. U. Hellsten, R.M. Harland, M.J. Gilchrist, D. Hendrix, J. Jurka, V. Kapitonov, I. Ovcharenko, N.H. Putnam, S. Shu, L. Taher, I.L. Blitz, B. Blumberg, D.S. Dichmann, I. Dubchak, E. Amaya, J.C. Detter, R. Fletcher, D.S. Gerhard, D. Goodstein, T. Graves, I.V. Grigoriev, J. Grimwood, T. Kawashima, E. Lindquist, S.M. Lucas, P.E. Mead, T. Mitros, H. Ogino, Y. Ohta, A.V. Poliakov, N. Pollet, J. Robert, A. Salamov, A.K. Sater, J. Schmutz, A. Terry, P.D. Vize, W.C. Warren, D. Wells, A. Wills, R.K. Wilson, L.B. Zimmerman, A.M. Zorn, R. Grainger, T. Grammer, M.K. Khokha, P.M. Richardson, D.S. Rokhsar, The Genome of the Western Clawed Frog Xenopus tropicalis, Science 328 (2010) 633-636.
22. The Danio rerio Sequencing Project, 2008, http://www.sanger.ac.uk/ Projects/D-rerio/Zv8-assembly information.shtml.
23. L.C. Hsu, W.-C. Chang, A. Shibuya, A. Yoshida, Human stomach aldehyde dehydrogenase cDNA and genomic cloning, primary structure, and expression in Escherichia coli, J. Biol. Chem. 267 (1992) 3030-3037.
24. R. Chenna, H. Sugawara, T. Koike, R. Lopez, T.J. Gibson, D.G. Higgins, J.D. Thompson, Multiple sequence alignment with the Clustal series of programs, Nucleic Acids Res. 31 (2003) 3497-3500. (Pubitemid 37442184)
25. L.J. McGuffin, K. Bryson, D.T. Jones, The PSIPRED protein structure prediction server, Bioinformatics 16 (2000) 404-405. (Pubitemid 30417087)
26. T. Schwede, J. Kopp, N. Guex, M.C. Peitsch, SWISS-MODEL: an automated protein homology-modelling server, Nucleic Acids Res. 31 (2003) 3383-3385.
27. Z.-J. Liu, Y.J. Sun, J.P. Rose, Y.-J. Chung, C.D. Hsiao, W.-R. Chang, I. Kuo, J. Perozich, R. Lindahl, J. Hempel, B.-C. Wang, The first structure of an aldehyde dehydrogenase reveals novel interactions between NAD and the Rossmann fold, Nat. Struct. Biol. 4 (1997) 317-326. (Pubitemid 27157205)
28. T.A. Hall, BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser. 41 (1999) 95-98.
29. M. Kimura, The Neutral Theory of Molecular Evolution, Cambridge University Press, Cambridge, 1983.
30. Y. Van De Peer, R. de Wachter, TreeCon for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment, Comput. Appl. Sci. 10 (1994) 569-570.
31. N. Saitou, M. Nei, The neighbour-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol. 4 (1987) 406-425.
32. J. Felsenstein, Confidence limits on phylogenies: an approach using the bootstrap, Evolution 39 (1985) 783-791.
33. J. Hempel, I. Kuo, J. Perozich, B.-C. Wang, R. Lindahl, H. Nicholas, ALDH: maintaining critical active site geometry at motif 8 in the class 3 enzyme, Eur. J. Biochem. 268 (2001) 722-726.
34. T. Wymore, J. Hempel, S.S. Cho, A.D. MacKerell Jr., H.B. Nicholas Jr., D.W. Deerfield II, Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophilic activation, Proteins: Struct. Funct. Bioinformat. 57 (2004) 758-771. (Pubitemid 39626997)
35. J. Hempel, S. Stanley, J. Perozich, T. Wymore, H.B. Nicholas Jr., Residue conservations in aldehyde dehydrogenase gene fusion products reemphasize functional interpretations, in: H. Weiner, B. Plapp, R. Lindahl, E. Maser (Eds.), Enzymology and Molecular Biology of Carbonyl Metabolism, vol. 12, Purdue University Press, Lafayette, IN, 2006, pp. 8-14.
36. J.V. Jester, T. Moller-Pedersen, J. Huang, C.M. Sax, W.T. Kays, H.D. Cavangh, W.M. Petroll, J. Piatigorsky, The cellular basis of corneal transparency: evidence for 'corneal crystallins', J. Cell Sci. 112 (1999) 613-622.
37. V. Vasiliou, S.F. Reuter, S. Williams, A. Puga, D.W. Nebert, Mouse cytosolic class 3 aldehyde dehydrogenase (Aldh1a1): gene structure and regulation of constitutive and dioxine-inducible expression, Pharmacogenetics 9 (1999) 569-580.
38. Mammalian Gene Collection Team, The status, quality and expansion of the NIH full-length cDNA project: the mammalian gene collection, Genome Res. 14 (2004) 2121-2127.
39. R.B. Caldwell, A.M. Kierzek, H. Arakawa, Y. Bezzubov, J. Zaim, P. Fiedler, S. Kutter, A. Blagodatski, D. Kostovska, M. Koter, J. Plachy, P. Carninci, Y. Hayashizaki, J.M. Buerstedde, Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis, Genome Biol. 6 (2005) R6-R16.
40. S. Kumar, S.B. Hedges, A molecular timescale for vertebrate evolution, Nature 392 (1998) 917-920. (Pubitemid 28232061)
41. E.M. Algar, R.S. Holmes, Purification and properties of mouse stomach aldehyde dehydrogenase. Evidence for a role in the oxidation of peroxidic and aromatic aldehydes, Biochim. Biophys. Acta 995 (1989) 168-173. (Pubitemid 19088373)
42. S. Evces, R. Lindahl, Characterization of rat cornea aldehyde dehydrogenase, Arch. Biochem. Biophys. 274 (1989) 518-524. (Pubitemid 19261143)
43. T. Shiao, P. Tran, D. Siegel, J. Lee, V. Vasiliou, Four amino acid changes are associated with the Aldh3a1 locus polymorphism in mice which may be responsible for corneal sensitivity to ultraviolet light, Pharmacogenetics 9 (1999) 145-153. (Pubitemid 29358996)
44. G. King, R.S. Holmes, Human ocular aldehyde dehydrogenase isozymes: distribution and properties as major soluble proteins in cornea and lens, J. Exp. Zool. 282 (1998) 12-17.
45. A. Pappa, T. Estey, R. Manzer, D. Brown, V. Vasiliou, Human aldehyde dehydrogenase 3A1 (ALDH3A1): biochemical characterization and immunohistochemical localization in the cornea, Biochem. J. 376 (2003) 615-623. (Pubitemid 38063115)
46. A. Pappa, D. Brown, Y. Koutalos, J. DeGregory, C. White, V. Vasilou, Human aldehyde dehydrogenase 3A1 inhibits proliferation and promotes survival of human corneal epithelial cells, J. Biol. Chem. 280 (2005) 27998-28006.
47. N.E. Sladek,Humanaldehyde dehydrogenases: potential pathological, pharmacological and toxicological impact, J. Biochem. Mol. Toxicol. 17 (2003) 7-23.
48. J.S. Moreb, H.V. Baker, L.-J. Chang, M. Amaya, M.C. Lopez, B. Ostmark, Chou W, ALDH isozymes downregulation affects cell growth, cell motility and gene expression in lung cancer cells, Mol. Cancer 7 (2008) 87, doi:10.1186/1476- 4598r-r7-87.
49. A.I. Su, T. Wiltshire, S. Batalov, H. Lapp, K.R. Ching, D. Block, J. Zhang, R. Soden, M. Hayakawa, G. Kreiman, M.P. Cooke, J.R. Walker, J.B. Hogenesch, A gene atlas of the human and mouse protein encoding transcriptomes, Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 6062-6067. (Pubitemid 38520528)
50. J. Hempel, A. Kraut, T. Wymore, Gamma glutamyl semialdehyde dehydrogenase: simulations on native and mutant forms support the importance of outer shell lysines, Chem. Biol. Interact. 178 (2009) 75-78.
51. J. Perozich, H. Nicholas, B.C. Wang, R. Lindahl, J. Hempel, Relationships within the aldehyde dehydrogenase extended family, Protein Sci. 8 (1999) 137-146. (Pubitemid 29035527)
52. J.E. Downes, RS Holmes, Differential corneal sensitivity to ultraviolet light among inbred strains of mice, Cornea 13 (1994) 67-72.
53. V. Vasiliou, A. Pappa, D.R. Petersen, Role of aldehyde dehydrogenases in endogenous and xenobiotic metabolism, Chem. Biol. Interact. 129 (2000) 1-19. (Pubitemid 32061051)