Three human alcohol dehydrogenase subunits: cDNA structure and molecular and evolutionary divergence

The natural history of class I primate alcohol dehydrogenases includes gene duplication, gene loss, and gene conversion

BACKGROUND

Gene duplication is a source of molecular innovation throughout evolution. However, even with massive amounts of genome sequence data, correlating gene duplication with speciation and other events in natural history can be difficult. This is especially true in its most interesting cases, where rapid and multiple duplications are likely to reflect adaptation to rapidly changing environments and life styles. This may be so for Class I of alcohol dehydrogenases (ADH1s), where multiple duplications occurred in primate lineages in Old and New World monkeys (OWMs and NWMs) and hominoids.

METHODOLOGY/PRINCIPAL FINDINGS

To build a preferred model for the natural history of ADH1s, we determined the sequences of nine new ADH1 genes, finding for the first time multiple paralogs in various prosimians (lemurs, strepsirhines). Database mining then identified novel ADH1 paralogs in both macaque (an OWM) and marmoset (a NWM). These were used with the previously identified human paralogs to resolve controversies relating to dates of duplication and gene conversion in the ADH1 family. Central to these controversies are differences in the topologies of trees generated from exonic (coding) sequences and intronic sequences.

CONCLUSIONS/SIGNIFICANCE

We provide evidence that gene conversions are the primary source of difference, using molecular clock dating of duplications and analyses of microinsertions and deletions (micro-indels). The tree topology inferred from intron sequences appear to more correctly represent the natural history of ADH1s, with the ADH1 paralogs in platyrrhines (NWMs) and catarrhines (OWMs and hominoids) having arisen by duplications shortly predating the divergence of OWMs and NWMs. We also conclude that paralogs in lemurs arose independently. Finally, we identify errors in database interpretation as the source of controversies concerning gene conversion. These analyses provide a model for the natural history of ADH1s that posits four ADH1 paralogs in the ancestor of Catarrhine and Platyrrhine primates, followed by the loss of an ADH1 paralog in the human lineage.

Alcohol dehydrogenases: gene multiplicity and differential functions of five classes of isozymes

Mammalian alcohol dehydrogenases (ADHs) constitute an enzyme family of multiple forms (isozymes) which are differentially distributed throughout the body. Subunit types alpha, beta and gamma in dimeric combinations constitute the isozymes of human liver class I ADH, and are >94% homologous in structure. Human pi and chi subunits form homodimeric Class II and III ADH isozymes. pi-ADH is liver specific whereas chi-ADH is widely distributed throughout the body. A sixth human ADH subunit (designated mu or sigma), forming a new dimeric human stomach ADH, has been recently reported as Class IV ADH. Evidence for a seventh human ADH subunit has also been described, designated as Class V, the transcripts having been reported in the stomach and liver. All five classes of ADH represent isozymes which are homologous but exhibit at least 30% sequence differences in primary srtructure. Kinetic analyses of four of these classes of ADH indicated differential functions, serving either in the oxidative or reductive mode. Studies from various laboratories indicate the following respective functions: oxidation of aliphatic and aromatic alcohols-liver Class I and Class II, and stomach Class IV ADHs; reduction of peroxidic aldehydes-Classes I, II and IV; 'biogenic' alcohol oxidation-Classes I and II; and glutathione-dependent formaldehyde dehydrogenase-Class III.

Origin and dispersal of atypical aldehyde dehydrogenase ALDH2487Lys

The East Asian respond with a marked facial flushing and mild to moderate symptoms of intoxication after drinking the amounts of alcohol that has no detectable effect on European. The alcohol sensitivity in Orientals is due to a delayed oxidation of acetaldehyde by an atypical aldehyde dehydrogenase ALDH2487Lys, which is resulted from a structural mutation in gene ALDH2. The atypical ALDH2487Lys allele has been associated with various phenotypic statuses, such as protective against alcohol dependence and the risk of alcohol-related digestive tract cancers. Here, we have examined this SNP, adjacent four non-coding SNPs, and one downstream STRP on ALDH2 gene, in total of 1072 unrelated healthy individuals from 14 Chinese populations and 130 Indian individuals. Five major haplotypes based on five SNPs across the ALDH2 gene 40 kb were found in all East Asian populations. The frequencies of the ancestral haplotype GCCTG and the East Asian special haplotype GCCTA containing the atypical ALDH2487Lys allele were 44.8% and 14.9%, respectively. The frequency of the atypical ALDH2487Lys allele or the East Asian specific haplotype GCCTA is high in Yunnan, South coastal, east coastal of China, and decreased gradually toward inland China, West, Northwest and North China. Combined with demographic history in East Asian, our results showed that the presence of ALDH2487Lys allele in peripheral regions of China might be the results of historical migration events from China to these regions. The origin of ALDH2487Lys could be possibly traced back to ancient Pai-Yuei tribe in South China.

Opossum alcohol dehydrogenases: Sequences, structures, phylogeny and evolution: evidence for the tandem location of ADH genes on opossum chromosome 5

BLAT (BLAST-Like Alignment Tool) analyses and interrogations of the recently published opossum genome were undertaken using previously reported rat ADH amino acid sequences. Evidence is presented for six opossum ADH genes localized on chromosome 5 and organized in a comparable ADH gene cluster to that reported for human and rat ADH genes. The predicted amino acid sequences and secondary structures for the opossum ADH subunits and the intron-exon boundaries for opossum ADH genes showed a high degree of similarity with other mammalian ADHs, and four opossum ADH classes were identified, namely ADH1, ADH3, ADH6 and ADH4 (for which three genes were observed: ADH4A, ADH4B and ADH4C). Previous biochemical analyses of opossum ADHs have reported the tissue distribution and properties for these enzymes: ADH1, the major liver enzyme; ADH3, widely distributed in opossum tissues with similar kinetic properties to mammalian class 3 ADHs; and ADH4, for which several forms were localized in extrahepatic tissues, especially in the digestive system and in the eye. These ADHs are likely to perform similar functions to those reported for other mammalian ADHs in the metabolism of ingested and endogenous alcohols and aldehydes. Phylogenetic analyses examined opossum, human, rat, chicken and cod ADHs, and supported the proposed designation of opossum ADHs as class I (ADH1), class III (ADH3), class IV (ADH4A, ADH4B and ADH4C) and class VI (ADH6). Percentage substitution rates were examined for ADHs during vertebrate evolution which indicated that ADH3 is evolving at a much slower rate to that of the other ADH classes.

Polymorphism in ADH and MTHFR genes in oral squamous cell carcinoma of Indians

OBJECTIVES

Alcohol consumption is known to increase the risk for several cellular disorders like oral cancer. The risk may be reinforced by polymorphism in genes like alcohol dehydrogenase. Therefore, this study is designed to asses the polymorphic status in ADH1B (formerly ADH2), ADH1C (formerly ADH3) and MTHFR genes in order to correlate the susceptibility to oral squamous cell carcinoma (OSCC).

SUBJECTS AND METHODS

DNA from 126 OSCC samples were amplified using primers for ADH1B, ADH1C and MTHFR genes. The amplicons were analyzed for ADH1B*1, ADH1C*2 and MTHFR C677T allelic polymorphism by restriction digestion using appropriate enzymes.

RESULTS

ADH1B*1/*1 genotype in cancer patients who were heavy drinkers showed a negligible risk association with an odds ratio of 1.62; 95% CI = 1.08-2.14. In OSCC patients, ADH1C*2/*2 genotypes showed a relatively higher risk (odds ratio 2.65; 95% CI = 1.78-3.53) in heavy drinkers and a less significant risk (1.6; 95% CI = 1.15-2.03) in moderate drinkers and negligible risk in light drinkers (1.23; 95% CI = 0.77-1.63). In contrast, MTHFR 677TT genotype showed a high risk association for OSCC in heavy drinkers (odds ratio 3.0; 95% CI = 2.02-4.0). Interestingly, the combination of ADH1B*1/*1/ MTHFR 677TT genotypes in alcoholic cancer patients showed a high risk (odds ratio 4.16; 95% CI = 2.78-5.53). A similar risk (odds ratio 4.16; 95% CI = 1.18-5.53) was shown by ADH1B*1/*2/*2/*2MTHFR 677TT genotype combination. The ADH1C*2/*2 /MTHFR 677TT genotype combination showed the maximum risk (odds ratio 20; 95% CI = 13.45-26.64) in the heavy drinker group. This combination showed a high risk in moderate drinkers (odds ratio 5.88; 95% CI = 4.24-7.50) and relatively lower risk in light drinkers (odds ratio 2.77; 95% CI = 1.74-3.68).

CONCLUSIONS

The ADH1C*2/*2/MTHFR 677TT genotype combination appears to be more susceptible for OSCC, since it showed a 20-fold increase in risk in heavy drinkers and a 5.9- and 2.8-fold increase in risk respectively in moderate drinkers and light drinkers. This study suggests the association of ADH1C*2/*2/MTHFR 677TT genotype combination as a risk factor for OSCC in alcoholics.

Identification of human liver diacetyl reductases by nano-liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry

Several forms of diacetyl-reducing enzyme were found to exist in the human liver cytosol. Three (DAR-2, DAR-5, and DAR-7) of them were purified as a single band on SDS-PAGE by a combination of a few kinds of column chromatographies. The in-gel tryptic digests of the purified enzymes were analyzed by nano-liquid chromatography (LC)/Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), which provided peptide masses at a ppm-level accuracy. The enzymes, DAR-2, DAR-5, and DAR-7, were identified as alcohol dehydrogenase beta subunit (ADH2), carbonyl reductase (CBR1), and aldehyde reductase (AKR1A1), respectively, by peptide mass fingerprinting. In addition, an alternating-scan acquisition of nano-LC/FT ICR mass spectra, i.e., switching of normal acquisition conditions and in-source fragmentation conditions scan by scan, provided sets of parent and fragment ion masses of many of the tryptic peptides in a single LC/MS run. The peptide sequence-tag information at the ppm-level accuracy was used to further confirm the protein identities. It was demonstrated that nano-LC/FT ICR MS can be used for rigorous protein identification at a subpicomole level as an alternative technique to nano-LC/MS/MS.

Effects of worldwide population subdivision on ALDH2 linkage disequilibrium

The effect of human population subdivision on linkage disequilibrium has previously been studied for unlinked genes. However, no study has focused on closely linked polymorphisms or formally partitioned linkage disequilibrium within and among worldwide populations. With an emphasis on population subdivision, the goal of this paper is to investigate the causes of linkage disequilibrium in ALDH2, the gene that encodes aldehyde dehydrogenase 2. Haplotypes for 756 people from 17 populations across five continents were estimated by maximum-likelihood from genotypes at six closely linked ALDH2 nucleotide substitutions. Linkage disequilibrium was partitioned into three components: within populations, among populations within continents, and among continents. It was found that population subdivision among continents had a larger and more disparate effect on linkage disequilibrium than subdivision among local populations. Further, linkage disequilibrium did not increase with population divergence as predicted by a simple model. Rather, the patterns of linkage disequilibrium were complicated because of the interplay of a near absence of recombination, the linkage disequilibrium that existed prior to the divergence of modern humans, subsequent mutation, population subdivision, random genetic drift, and perhaps natural selection. These results suggest that simple models may not well predict patterns of linkage disequilibrium in human populations.

Linkage disequilibrium at the ADH2 and ADH3 loci and risk of alcoholism

Two of the three class I alcohol dehydrogenase (ADH) genes (ADH2 and ADH3) encode known functional variants that act on alcohol with different efficiencies. Variants at both these genes have been implicated in alcoholism in some populations because allele frequencies differ between alcoholics and controls. Specifically, controls have higher frequencies of the variants with higher Vmax (ADH2*2 and ADH3*1). In samples both of alcoholics and of controls from three Taiwanese populations (Chinese, Ami, and Atayal) we found significant pairwise disequilibrium for all comparisons of the two functional polymorphisms and a third, presumably neutral, intronic polymorphism in ADH2. The class I ADH genes all lie within 80 kb on chromosome 4; thus, variants are not inherited independently, and haplotypes must be analyzed when evaluating the risk of alcoholism. In the Taiwanese Chinese we found that, only among those chromosomes containing the ADH3*1 variant (high Vmax), the proportions of chromosomes with ADH2*1 (low Vmax) and those with ADH2*2 (high Vmax) are significantly different between alcoholics and controls (P<10-5). The proportions of chromosomes with ADH3*1 and those with ADH3*2 are not significantly different between alcoholics and controls, on a constant ADH2 background (with ADH2*1, P=.83; with ADH2*2, P=.53). Thus, the observed differences in the frequency of the functional polymorphism at ADH3, between alcoholics and controls, can be accounted for by the disequilibrium with ADH2 in this population.

Simultaneous genotyping of alcohol dehydrogenase 2 (ADH2) and aldehyde dehydrogenase 2 (ALDH2) loci by amplified product length polymorphism (APLP) analysis

Genotyping of the alcohol dehydrogenase 2 (ADH2) and aldehyde dehydrogenase 2 (ALDH2) loci is important in alcohol studies. We describe a method for simultaneous genotyping of ADH2 and ALDH2 based on amplified product length polymorphism (APLP) analysis. Two polymerase chain reaction (PCR) fragments for ADH2 (57 bp, 53 bp) and two for ALDH2 (78 bp, 73 bp) are simultaneously amplified. Nine banding patterns reflecting the genotypes of the ADH2 and ALDH2 loci are clearly and unambiguously distinguished. The APLP method seems to be particularly suited for large-scale population studies of ADH2 and ALDH2 loci because it is simple and rapid.

Polymorphism of alcohol dehydrogenase genes in alcoholic and nonalcoholic individuals from Valencia (Spain)

Polymorphisms in the two variable ADH loci (ADH2 and ADH3) were analyzed in two groups (alcoholics and nonalcoholics) from a Spanish population. The frequencies were similar to those reported for other Causcasian groups. ADH2-1 and ADH3-1 genotypes were more frequent in alcoholics than in nonalcoholics, but the differences were not significant.

The contribution of polymorphism in the alcohol dehydrogenase beta subunit to alcohol sensitivity in a Japanese population

In humans, ingested alcohol is mainly metabolized by the combination of class I alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH). In Orientals, there are highly frequent polymorphisms both in the class I ADH beta subunit (ADH2) and in the low Km ALDH (ALDH2). We characterized the three genotypes of ALDH2 in a Japanese population. In the present study, we evaluated the effects of the ADH2 polymorphism in the same population (424 males and 100 females) controlling for the effects of the ALDH2 polymorphism. In the ALDH2(1)/ALDH2(2) group, the frequency of facial flushing with one glass of beer was significantly higher in the ADH2(1)/ADH2(2) and ADH2(2)/ADH2(2) genotype than in the ADH2(1)/ADH2(1) genotype. Likewise, the proportion of persons with positive results for ethanol-induced cutaneous erythema differed significantly depending on the ADH2 genotype in both the ALDH2(1)/ALDH2(1) and ALDH2(1)/ALDH2(2) genotypes. However, drinking habits were not significantly associated with the ADH2 genotype, suggesting that the ADH2 genotype influences the metabolism of ethanol only in the peripheral tissues.

Purification and partial amino acid sequence of a high-activity human stomach alcohol dehydrogenase

To understand the relative importance of alcohol dehydrogenase (ADH) isoenzymes in gastric ethanol metabolism, a stomach-specific ADH (sigma-ADH) was purified to homogeneity from human transplant donor and surgical tissues, and its activity for ethanol oxidation was examined. The enzyme from these tissues had a specific activity at pH 10 of approximately 70 units/mg, about 10 times that reported by Moreno and Parés (J. Biol. Chem. 266:1128-1133, 1991). The enzyme exhibited a high Km for ethanol at pH 7.5 and 10 (29 and 5.2 mM, respectively). This high-activity sigma-ADH isoenzyme migrated on starch and isoelectric focusing gels to a position slightly anodic to the liver pi pi isoenzyme. It was subjected to digestion by endoproteinases, and approximately 40% of the protein was sequenced. The sigma-ADH exhibited 75%, 68%, and 62% sequence identity to the human class I (beta 1), II (pi), and III (chi) isoenzymes, respectively, and 61% identity to the deduced ADH6 amino acid sequence. Phylogenetic analysis indicated that precursors to this high-activity sigma-ADH and the class I isoenzymes diverged more recently than precursors to the class II and III isoenzymes, after reptilian and avian divergence. The high-activity sigma-ADH isoenzyme therefore represents a distinct class of ADH (class IV), more closely related in evolution to the class I isoenzymes than to the other known human isoenzymes.

Purification and characterization of a primary-secondary alcohol dehydrogenase from two strains of Clostridium beijerinckii

Two primary alcohols (1-butanol and ethanol) are major fermentation products of several clostridial species. In addition to these two alcohols, the secondary alcohol 2-propanol is produced to a concentration of about 100 mM by some strains of Clostridium beijerinckii. An alcohol dehydrogenase (ADH) has been purified to homogeneity from two strains (NRRL B593 and NESTE 255) of 2-propanol-producing C. beijerinckii. When exposed to air, the purified ADH was stable, whereas the partially purified ADH was inactivated. The ADHs from the two strains had similar structural and kinetic properties. Each had a native M(r) of between 90,000 and 100,000 and a subunit M(r) of between 38,000 and 40,000. The ADHs were NADP(H) dependent, but a low level of NAD(+)-linked activity was detected. They were equally active in reducing aldehydes and 2-ketones, but a much lower oxidizing activity was obtained with primary alcohols than with secondary alcohols. The kcat/Km value for the alcohol-forming reaction appears to be a function of the size of the larger alkyl substituent on the carbonyl group. ADH activities measured in the presence of both acetone and butyraldehyde did not exceed activities measured with either substrate present alone, indicating a common active site for both substrates. There was no similarity in the N-terminal amino acid sequence between that of the ADH and those of fungi and several other bacteria. However, the N-terminal sequence had 67% identity with those of two other anaerobes, Thermoanaerobium brockii and Methanobacterium palustre. Furthermore, conserved glycine and tryptophan residues are present in ADHs of these three anaerobic bacteria and ADHs of mammals and green plants.

Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family

Sequences of 47 members of the Zn-containing alcohol dehydrogenase (ADH) family were aligned progressively, and an evolutionary tree with detailed branch order and branch lengths was produced. The alignment shows that only 9 amino acid residues (of 374 in the horse liver ADH sequence) are conserved in this family; these include eight Gly and one Val with structural roles. Three residues that bind the catalytic Zn and modulate its electrostatic environment are conserved in 45 members. Asp 223, which determines specificity for NAD, is found in all but the two NADP-dependent enzymes, which have Gly or Ala. Ser or Thr 48, which makes a hydrogen bond to the substrate, is present in 46 members. The four Cys ligands for the structural zinc are conserved except in zeta-crystallin, the sorbitol dehydrogenases, and two bacterial enzymes. Analysis of the evolutionary tree gives estimates of the times of divergence for different animal ADHs. The human class II (pi) and class III (chi) ADHs probably diverged about 630 million years ago, and the newly identified human ADH6 appeared about 520 million years ago, implying that these classes of enzymes may exist or have existed in all vertebrates. The human class I ADH isoenzymes (alpha, beta, and gamma) diverged about 80 million years ago, suggesting that these isoenzymes may exist or have existed in all primates. Analysis of branch lengths shows that these plant ADHs are more conserved than the animal ones and that class III ADHs are more conserved than class I ADHs. The rate of acceptance of point mutations (PAM units) shows that selection pressure has existed for ADHs, implying that these enzymes play definite metabolic roles.

Biochemical genetics of alcohol dehydrogenase isozymes in the gray short-tailed opossum (Monodelphis domestica)

Polyacrylamide gel-isoelectric focusing (PAGE-IEF) methods were used to examine the multiplicity, tissue distribution, and biochemical genetics of alcohol dehydrogenase (ADH) isozymes among gray short-tailed opossums (Monodelphis domestica). Seven ADH isozymes were resolved and distinguished on the basis of their isoelectric points, tissue distributions, and substrate and inhibitor specificities. ADH1 and ADH2 exhibited Class I properties and were observed in liver (and intestine) extracts. ADH3, ADH4, and ADH5 showed "high-Km" (possibly Class IV) properties, with ADH3 and ADH4 exhibiting high activity in cornea, ear, stomach, and esophagus extracts. ADH6 and ADH7 exhibited Class III properties, including activities as formaldehyde dehydrogenases, with each showing different tissue distribution characteristics; ADH6 was widely distributed, and ADH7 was restricted to prostate extracts. An additional form of formaldehyde dehydrogenase (FDH) was observed, which was inactive with hexenol and ethanol as substrates. Isoelectric point variants were observed for ADH3 (three forms) and for ADH4 (two forms), and the inheritance of ADH3 was studied in 15 families of M. domestica. The data were consistent with codominant inheritance of two alleles (ADH3*A and ADH3*B) at a single autosomal locus (designated ADH3) and with a model involving a dimeric ADH isozyme: ADH3 (gamma 2 isozyme, forming three dimers designated gamma 1(2), gamma 1 gamma 2, and gamma 2(2) in heterozygous individuals).

Molecular structure of the human alcohol dehydrogenase 3 gene

The structure and nucleotide sequence of an ADH3(1) allele, which encodes the ADH gamma 1 subunit, have been determined. The intron positions of the ADH3 gene are identical to those of the other class I and class II ADH genes. The level of nucleotide variation at the ADH3 locus is somewhat higher than those at the ADH1 and ADH2 loci.

A human alcohol dehydrogenase gene (ADH6) encoding an additional class of isozyme

The human alcohol dehydrogenase (ADH; alcohol:NAD+ oxidoreductase, EC 1.1.1.1) gene family consists of five known loci (ADH1-ADH5), which have been mapped close together on chromosome 4 (4q21-25). ADH isozymes encoded by these genes are grouped in three distinct classes in terms of their enzymological properties. A moderate structural similarity is observed between the members of different classes. We isolated an additional member of the ADH gene family by means of cross-hybridization with the ADH2 (class I) cDNA probe. cDNA clones corresponding to this gene were derived from PCR-amplified libraries as well. The coding sequence of a 368-amino-acid-long open reading frame was interrupted by introns into eight exons and spanned approximately 17 kilobases on the genome. The gene contains a glucocorticoid response element at the 5' region. The transcript was detected in the stomach and liver. The deduced amino acid sequence of the open reading frame showed about 60% positional identity with known human ADHs. This extent of homology is comparable to interclass similarity in the human ADH family. Thus, the newly identified gene, which is designated ADH6, governs the synthesis of an enzyme that belongs to another class of ADHs presumably with a distinct physiological role.

Multiplication of the class I alcohol dehydrogenase locus in mammalian evolution

Chromosomal DNA samples derived from various primates and other mammals (horse, sheep, rabbit, and mouse) were digested with restriction endonuclease and hybridized with a probe of the sixth exon of the human ADH gene, which is highly conserved in the class I alcohol dehydrogenase of these mammalian species. The copy number of the class I ADH gene in each species was estimated from the number of hybridized bands. Primate DNA samples showed three distinct bands in the blots of PstI digest and DraI digest. Moreover, most of the bands from primate DNA showed a similarity in size so as to allow us to assign the ADH1, ADH2, and ADH3 homologues in each species. In contrast, mouse has only one gene, and rabbit, sheep, and horse seem to have only two genes, for the class I ADH, which showed divergent hybridization bands. These results are consistent with the view that the human class I ADH gene cluster has been generated through gene multiplication events which occurred before the Catarrhini branch point in the course of primate evolution.

Cloning of the Zymomonas mobilis structural gene encoding alcohol dehydrogenase I (adhA): sequence comparison and expression in Escherichia coli

Zymomonas mobilis ferments sugars to produce ethanol with two biochemically distinct isoenzymes of alcohol dehydrogenase. The adhA gene encoding alcohol dehydrogenase I has now been sequenced and compared with the adhB gene, which encodes the second isoenzyme. The deduced amino acid sequences for these gene products exhibited no apparent homology. Alcohol dehydrogenase I contained 337 amino acids, with a subunit molecular weight of 36,096. Based on comparisons of primary amino acid sequences, this enzyme belongs to the family of zinc alcohol dehydrogenases which have been described primarily in eucaryotes. Nearly all of the 22 strictly conserved amino acids in this group were also conserved in Z. mobilis alcohol dehydrogenase I. Alcohol dehydrogenase I is an abundant protein, although adhA lacked many of the features previously reported in four other highly expressed genes from Z. mobilis. Codon usage in adhA is not highly biased and includes many codons which were unused by pdc, adhB, gap, and pgk. The ribosomal binding region of adhA lacked the canonical Shine-Dalgarno sequence found in the other highly expressed genes from Z. mobilis. Although these features may facilitate the expression of high enzyme levels, they do not appear to be essential for the expression of Z. mobilis adhA.

Cloning and sequencing of a processed pseudogene derived from a human class III alcohol dehydrogenase gene

Current information on the molecular structure of human alcohol dehydrogenase (ADH) genes is fragmentary. To characterize all ADH genes, we have isolated 63 ADH clones from human genomic libraries made from one individual. Fifty-nine clones have been classified into five previously known loci: ADH1 (18 clones), ADH2 (20 clones), and ADH3 class I (16 clones), ADH4 class II (4 clones), and ADH5 class III (1 clone). Sequencing of one of the remaining four unclassified clones, SY lambda ADHE38, about 1.1 kb in length, shows no introns and three frameshift mutations in the coding region, with a total of 10 internal termination codons. When its deduced amino acid sequence was compared with those of the class I, class II, and class III ADHs, the proportions of identical amino acids were 56.7%, 55.5%, and 88.7%, respectively, suggesting that the processed pseudogene was derived from an ADH5 gene. The duplication event seems to have occurred about 3.5 million years ago, and the pseudogene has undergone a rapid change since then.

The genes for human alcohol dehydrogenases beta 1 and beta 2 differ by only one nucleotide

Allelic differences at the alcohol dehydrogenase (ADH) and aldehyde dehydrogenase loci may have an important role in an individual's alcohol sensitivity. We have cloned and sequenced all nine exons of an ADH2(2) allele which codes for an 'atypical' ADH, ADH beta 2. Our sequence data shows that the histidine at residue 47 of ADH beta 2 is encoded by CAC. Surprisingly, no silent substitution was found between the coding regions of ADH2(1) [Duester, G., Smith, M., Bilanchone, V. & Hatfield, G. W. (1986) J. Biol. Chem. 261, 2027-2033.] and ADH2(2) alleles over the 1122 nucleotide sites.

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

The baboon has at least five alcohol dehydrogenases (ADH; alcohol:NAD+ oxidoreductase, EC 1.1.1.1) and has distinct liver and kidney class I isozymes. A rat liver class I ADH partial cDNA was used to screen a baboon liver cDNA library. A cDNA clone was isolated and sequenced and found to contain the entire coding region for baboon liver ADH, 12 nucleotides of the 5' noncoding region, and 256 nucleotides of the 3' noncoding region. The amino acid sequence deduced from this cDNA most closely resembles that of human liver ADH beta subunit (ADH-beta): 363 of 374 residues were identical. This suggested that baboon liver class I ADH is of the same ancestral lineage as the human ADH-beta. In contrast to human liver, only a single ADH-beta transcript is observed in baboon liver. A comparison of human and baboon ADH 3' noncoding regions suggests that a single nucleotide change in a polyadenylylation signal consensus sequence may, in part, be responsible for the generation of ADH-beta transcripts with variable-length 3' ends in human liver. A nucleotide substitution rate of 0.5 x 10(-9) substitutions per site per year for primate class I ADH genes was deduced from the data, which suggests that the alpha-beta gamma separation of human ADH genes occurred about 60 million years ago, and that primate class I ADH gene duplications predated primate radiation.

Molecular structure of the human alcohol dehydrogenase 1 gene

The structure and nucleotide sequence of an allele at the ADH1 locus have been determined. The nucleotide sequence of this allele is identical to that of a cDNA clone [(1986) Biochemistry 25, 2465-2470] and the intron positions of the ADH1 gene are identical to that of the ADH2 gene [(1986) J. Biol. Chem. 261, 2027-2033].

Direct determination of usual (Caucasian-type) and atypical (Oriental-type) alleles of the class I human alcohol dehydrogenase-2 locus

Two types of alleles exist in the human alcohol dehydrogenase-2 (ADH2) locus. The usual ADH12 allele is common in Caucasians, while the atypical ADH22 allele is predominant in Orientals. The ADH22 produces the beta 2 subunit, which is catalytically far more active than the beta 1 subunit produced by the ADH12 gene. The racial difference in alcohol-related problems could be related to the genetic differences in ADH and other ethanol-metabolizing enzymes. In order to examine the possibility, a method for determining ADH2 genotypes was developed. Two 21-base synthetic oligonucleotides, one complementary to the usual ADH12 allele and the other complementary to the atypical ADH22 allele, were used as specific probes for in-gel hybridization analysis of human genomic DNA from peripheral blood. Under appropriate hybridization conditions, these two probes can hybridize to their specific complementary alleles and, thus, allow the genotyping of the ADH2 locus. Genotypes of the ADH2 locus of 49 unrelated Japanese individuals were determined. The frequency of the atypical ADH22 gene was found to be 0.71 in the Japanese population examined.

cDNA sequence of the beta 2-subunit of human liver alcohol dehydrogenase

A cDNA library of mRNA from a human liver expressing the beta 2-subunit of alcohol dehydrogenase was constructed in lambda gt11. One clone coding for 352 of a total of 374 amino acid residues of the beta 2-subunit was isolated. The sequence differed from that of the beta 1-subunit at one nucleotide position resulting in an Arg/His exchange at position 47 of the peptide chain, in agreement with data from protein sequence analysis [(1984) FEBS Lett. 173, 360-366].

Human stomach alcohol and aldehyde dehydrogenases (ALDH): a genetic model proposed for ALDH III isozymes

Isozyme phenotypes of alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) from human gastroendoscopic as well as surgical gastric biopsies were determined by starch gel electrophoresis and agarose isoelectric focusing. gamma gamma ADH isozymes were expressed predominantly in the mucosal layer of the stomach, whereas beta beta isozymes were in the muscular layer. In the 56 gastroendoscopic mucosal biopsies examined, the homozygous ADH3 1-1 phenotype was found in 75% of the samples, and the heterozygous ADH3 2-1 phenotype in 25%. Accordingly, the gene frequencies of the alleles ADH1/3 and ADH2/3 were calculated to be 0.88 and 0.12, respectively. Using a modified agarose isoelectric focusing procedure, gastric ALDH I, ALDH II, and up to five ALDH III forms could be clearly resolved. The ALDH III isozymes accounted for more than 80% of the total ALDH activities in gastric mucosa and exhibited Km values in the millimolar range for propionaldehyde at pH 9.0. Forty-five percent of the 55 gastroendoscopic biopsies studied lacked ALDH I isozyme. The complex gastric ALDH III isozyme phenotypes seen in these biopsies fall into three patterns. They can be interpreted by a genetic hypothesis, based on a dimeric molecule, in which there are two separate genes, ALDH3a and ALDH3b, with the ALDH3b locus exhibiting polymorphism. The homozygous phenotypes ALDH3b 1-1 and ALDH3b 2-2 were found to be 4 and 76%, respectively, and the heterozygous ALDH3b 2-1 phenotype 20%, of the total. Therefore, the allele frequencies for ALDH1/3b and ALDH2/3b were calculated to be 0.14 and 0.86, respectively. Several lines of biochemical evidence consistent with this genetic model are discussed.

H8Zn(c)2 and Zn(c)2Co(n)2 human liver alcohol dehydrogenase

The zinc ion in the noncatalytic site of human beta 1 beta 1 and beta 1 gamma 1 isozymes of class I alcohol dehydrogenases (EC 1.1.1.1) was specifically replaced by Co(II) ion. The absorption and CD spectra prove that these derivatives contain cobalt bound at the noncatalytic site to the same ligands and in the same coordination geometry as in the corresponding species obtained from the horse liver EE isozyme. These Zn(c)2Co(n)2 human liver alcohol dehydrogenases could be obtained in two ways: (a) by exchange dialysis, (b) by removal of the noncatalytic zinc and subsequent insertion of cobalt(II) ion into the empty site. The human isozymes differ from the horse liver EE enzyme in the possibility of forming stable species lacking the noncatalytic zinc ion. This difference in chemical reactivity of the noncatalytic zinc atom may be related to amino acid changes in the human isozymes, compared to horse liver alcohol dehydrogenase.

Purification and characterization of three forms of class III alcohol dehydrogenase

We have resolved and characterized three forms of human and rat hepatic class III alcohol dehydrogenase. Separations were carried out in narrow immobilized pH gradients. Both in humans and rats the three forms were visualized by enzyme staining with cinnamol, but not with ethanol. They were insensitive to the inhibitory effect of pyrazole. The isoelectric points were approximately from 6.3-6.4, from 5.9-6.0 and 5.6. Each electroeluted enzyme extract, purified further by analytical isoelectric focusing over the pH range from 5-6 or 6-7, revealed a single band by enzyme and silver staining and by Western blotting followed by avidin-biotin staining. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate of each extract revealed a single molecular mass species corresponding to class III alcohol dehydrogenase (ADH). All forms of class III alcohol dehydrogenase were recognized by antisera raised against total class III ADH.

Computer-graphics interpretations of residue exchanges between the alpha, beta and gamma subunits of human-liver alcohol dehydrogenase class I isozymes

Three-dimensional models of human alcohol dehydrogenase subunits have been constructed, based on the homologous horse enzyme, with computer graphics. All types of class I subunits (alpha, beta, and gamma) and the major allelic variants (beta 1/beta 2 and gamma 1/gamma 2) have been studied. Residue differences between the E-type subunit of the horse enzyme and any of the subunits of the human isozymes occur at 64 positions, about half of which are isozyme-specific. About two thirds of the substitutions are at the surface and all differences can be accommodated in highly conserved three-dimensional structures. The model of the gamma isozyme is most similar to the crystallographically analyzed horse liver E-type alcohol dehydrogenase, and has all the functional residues identical to those of the E subunit except for one which is slightly smaller: Val-141 in the substrate pocket. The residues involved in coenzyme binding are generally conserved between the horse enzyme and the alpha, beta, and gamma types of the human enzyme. In contrast, single exchanges of these residues are the ones involved in the major allelic differences (beta 1 versus beta 2 and gamma 1 versus gamma 2), which affects the overall rate of alcohol oxidation since NADH dissociation is the rate-determining step. Residue 47 is His in beta 2 and Arg in the beta 1, gamma 1, and gamma 2 subunits, and in horse liver alcohol dehydrogenase. Both His and Arg can make a hydrogen bond to a phosphate oxygen atom of NAD; hence the lower turnover rate of beta 1 apparently derives from a charge effect. The substitution to Gly in the alpha subunit results in one less hydrogen bond in NAD binding, and consequently in rapid dissociation. This may explain why the overall rate is an order of magnitude faster than that of beta 1. The important difference between gamma 1 and gamma 2 is an exchange at position 271 from Arg to Gln which can give a hydrogen bond from Gln in gamma 2 to the adenine of NAD. The tighter binding to gamma 2 can account for the slower overall catalytic rate in this isozyme. The kinetics and interactions of cyclohexanol and benzyl alcohol with the isozymes were judged by docking experiments using an interactive fitting program.(ABSTRACT TRUNCATED AT 400 WORDS)

Characteristics of alcohol/polyol dehydrogenases. The zinc-containing long-chain alcohol dehydrogenases

Sixteen characterized alcohol dehydrogenases and one sorbitol dehydrogenase have been aligned. The proteins represent two formally different enzyme activities (EC 1.1.1.1 and EC 1.1.1.14), three different types of molecule (dimeric alcohol dehydrogenase, tetrameric alcohol dehydrogenase, tetrameric sorbitol dehydrogenase), metalloproteins with different zinc contents (1 or 2 atoms per subunit), and polypeptide chains from different kingdoms and orders (mammals, higher plants, fungus, yeasts). Present comparisons utilizing all 17 forms reveal extensive variations in alcohol dehydrogenase, but with evolutionary changes that are of the same order in different branches and at different times. They emphasize the general importance of particular residues, suggesting related overall functional constraints in the molecules. The comparisons also define a few coincidences between intron positions in the genes and gap positions in the gene products. Only 22 residues are strictly conserved; half of these are Gly, and most of the remaining ones are Pro or acidic residues. No basic residue, no straight-chain hydrophobic residues, no aromatic residues, and essentially no branched-chain or polar neutral residues are invariable. Tentative consensus sequences were calculated, defining 13 additional residues likely to be typical of but not invariant among the alcohol dehydrogenases. These show a predominance of Val, charged residues, and Gly. Combined, the comparisons, which are particularly relevant to the data base for protein engineering, illustrate the requirements for functionally important binding interactions, and the extent of space restrictions in proteins with related overall conformations and functions.

Mammalian alcohol dehydrogenases of separate classes: intermediates between different enzymes and intraclass isozymes

A comparison of the structure of class II human liver alcohol dehydrogenase (alcohol:NAD+ oxidoreductase, EC 1.1.1.1) (containing pi subunits) with those of the human class I isozymes (containing alpha, beta, and gamma subunits) reveals differences at about 40% of all positions. Variations are large for active-site regions, the segment around the second zinc atom, and for segments involved in subunit interactions. The two classes of alcohol dehydrogenase have diverged to exhibit structural differences to about half the extent of those between alcohol and polyol dehydrogenases. Hence, the two classes of alcohol dehydrogenase represent steps in enzyme rather than isozyme divergence. An evolutionary scheme that relates different types of zinc-containing mammalian dehydrogenases to one another encompasses at least three levels of gene duplication subsequent to the early step(s) of assembly of building unit(s). The first level of duplication results in the formation of now clearly different enzymes. The second level concerns the various classes of alcohol dehydrogenase, forming steps between typical enzymes and isozymes. The third level encompasses recent and multiple duplications in isozyme evolution of alcohol dehydrogenases. This scheme, linking zinc-containing dehydrogenases at different levels, resembles that in other protein families and reflects general patterns in protein relationships.

Human glucose-6-phosphate dehydrogenase: primary structure and cDNA cloning

The X-chromosome-linked glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate:NADP+ oxidoreductase, EC 1.1.1.49) of humans and other mammals consists of a subunit with a molecular weight of about 58,000. The enzyme plays a key role in the generation of NADPH, particularly in matured erythrocytes, and the genetic deficiency of the enzyme is associated with chronic and drug- or food-induced hemolytic anemia in humans. The enzyme was purified to homogeneity from human erythrocytes. The complete amino acid sequence of the subunit, consisting of 531 amino acid residues, was determined by automated and manual Edman degradation of tryptic, chymotryptic, thermolytic, and cyanogen bromide peptides obtained from the enzyme. Based on the amino acid sequence data thus obtained, a 41-mer oligonucleotide with unique sequence was prepared. Two cDNA libraries constructed in phage lambda gt11--i.e., a human liver cDNA library and a human hepatoma Li-7 cDNA library--were screened with the synthetic nucleotide probe. Two positive clones, lambda G6PD-19 and lambda G6PD-25, were obtained from the hepatoma library. lambda G6PD-19 contained an insertion of 2.0 kilobase pairs (kbp), and encoded 204 amino acid residues that were completely compatible with the COOH-terminal portion of the enzyme. The insertion of the clone had a 3' noncoding region of 1.36 kbp. The other clone, lambda G6PD-25, had an insertion of 1.8 kbp and encoded 362 amino acid residues of G6PD. Southern blot analysis of DNA samples obtained from cells with and without the human X chromosome indicated that the cDNA hybridizes with a sequence in the X chromosome.

Multiple mRNAs for human alcohol dehydrogenase (ADH): developmental and tissue specific differences

Human class I alcohol dehydrogenase (ADH) genes show developmental and tissue specific differences in expression at the polypeptide level. In these studies ADH expression was investigated at the RNA level. Northern blot analysis of total and poly (A) RNA from adult liver using pADH12 probe demonstrated multiple RNA size classes of 2.6, 2.2, 1.9 and 1.6kb. In contrast, fetal liver, and fetal intestine contained only 2.6 and 1.6kb mRNA while fetal lung showed only 2.6kb mRNA. All of these tissues showed a relative reduction in the amount of ADH mRNA present when compared to adult liver. Immunoprecipitation of in vitro translation products of adult liver RNA by polyclonal ADH antibody revealed a single polypeptide of 40,000 daltons. This result points out the homogeneity of size of class I ADH polypeptides despite mRNA size diversity. Variation in length of the 3' untranslated region probably contributes to the multiple size classes of ADH mRNA observed.