Human liver alcohol dehydrogenase: ADHIndianapolis results from genetic polymorphism at the ADH 2 gene locus

New molecular forms of human liver alcohol dehydrogenase (ADH), collectively designated ADH_Indianapolis (ADH_Ind), were recently discovered in 29% of liver specimens from Black Americans [Bosron, W. F., Li, T.-K., and Vallee, B. L. (1981). Proc. Natl. Acad. Sci. USA 77:5784]. Three different ADH_Ind phenotypes have now been identified by starch gel electrophoresis, and four ADH_Ind enzyme forms isolated by affinity and ion-exchange chromatography. The most cathodic ADH_Ind form has a single pH optimum at 7.0 for ethanol oxidation and is a homodimer of a newly discovered subunit, as evidenced by dissociation-recombination studies. The remaining three purified ADH_Ind forms have dual pH optima for ethanol oxidation at 7.0 and 10.0 and generate two new bands on starch gel electrophoresis after dissociation-recombination. They appear to be heterodimers of this new subunit with the known subunits, , ₁, and ₁. Based on the occurrence of these four ADH_Ind isozymes and isozymes containing ₁ subunits in the homogenate supernatants of 135 livers, we conclude that ADH_Ind results from polymorphism at the ADH ₂locus, with the variant ADH ₂ ^Ind allele coding for the _Ind subunit. The frequency of ADH ₂ ^Ind was 0.16 in Black Americans, and this allele was not observed in any of the 63 livers from White Americans. The frequency of the ADH ₃ ¹ and ADH ₃ ² alleles also differed in these two populations.This study was supported by U.S. Public Health Service, Grant AA 02342.     

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. γγ ADH isozymes were expressed predominantly in the mucosal layer of the stomach, whereas ββ 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 allelesADH ₃ ¹ andADH ₃ ² 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 exhibitedK _m values in the millimolar range for propionaldehyde atpH 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,ALDH _3a andALDH _3b, with theALDH _3b locus exhibiting polymorphism. The homozygous phenotypes ALDH_3b 1-1 and ALDH_3b 2-2 were found to be 4 and 76%, respectively, and the heterozygous ALDH_3b 2-1 phenotype 20%, of the total. Therefore, the allele frequencies forALDH _3b ¹ andALDH _3b ² were calculated to be 0.14 and 0.86, respectively. Several lines of biochemical evidence consistent with this genetic model are discussed. This work was supported by grants from the National Science Council, Republic of China, and the Institute of Biomedical Sciences, Academia Sinica.     

Genotypes of alcohol dehydrogenase and aldehyde dehydrogenase loci in Japanese alcohol flushers and nonflushers

Summary A much higher incidence of alcohol flushing among Orientals in comparison to Caucasians, i.e., >50% vs 5%–10%, has been attributed to racial differences in alcohol-metabolizing enzymes. A large majority of Orientals are atypical in alcohol dehydrogenase-2 locus (ADH ₂ ), and their livers exhibit significantly higher ADH activity than the livers of most Caucasians. Approximately 50% of Orientals lack the mitochondrial aldehyde dehydrogenase (ALDH₂) activity, and elimination of acetaldehyde might be disturbed. We determined by means of hybridization of genomic DNA samples with allele specific oligonucleotide probes, genotypes of the ADH ₂ and ALDH ₂ loci in Japanese alcohol flushers and nonflushers. We found that all individuals with homozygous atypical ALDH ₂ ² /ALDH ₂ ² and most of those with heterozygous atypical ALDH ₁ ² /ALDH ₂ ² were alcohol flushers, while all subjects with homozygous usual ALDH ₁ ² /ALDH ₁ ² were nonflushers. Frequency of the atypical ADH ₂ ² was found to be higher in alcohol flushers than in nonflushers, but the statistical significance was not established in the sample size examined.     

Polymorphism of human liver alcohol dehydrogenase: Identification of ADH2 2-1 and ADH2 2-2 phenotypes in the Japanese by isoelectric focusing

Liver homogenate-supernatants from most Japanese exhibit an atypical pH optimum for ethanol oxidation at pH 8.8 instead of 10.5, the typical pH-activity optimum. It has been proposed that atypical livers contain alcohol dehydrogenase isozymes with ₂ subunits while typical livers contain isozymes with ₁ subunits, both produced by the ADH ₂ gene. Because it is difficult to differentiate the atypical ADH₂ 2-2 phenotype from the ADH₂ 2-1 phenotype by starch gel electrophoresis, an agarose isoelectric focusing procedure was developed that clearly separated the atypical Japanese livers into two groups, A1 and A2. The isozymes in A1 and A2 livers were purified. Type A1 livers contained a single isozyme with an atypical pH-rate profile; it was designated ₂₂. Three isozymes were isolated from A2 livers, two of which corresponded to ₁₁ and ₂₂. A third, absent from the typical and the atypical A1 livers, had an intermediate mobility; it was designated ₂₁. Type A1 livers are, therefore, the homozygous ADH₂ 2-2 phenotype, and type A2 livers, the heterozygous ADH₂ 2-1 phenotype. The ADH₂ 2-2 phenotype was found in 53% of 194 Japanese livers, and the ADH₂ 2-1 phenotype, in 31%. Accordingly, the frequency of ADH ₂ ² was 0.68.This study was supported by U.S. Public Health Service Grant AA 02342.     

The contribution of polymorphism in the alcohol dehydrogenase β 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 β subunit (ADH₂) and in the low K_m 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 ALDH2¹/ALDH2² 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 ALDH2¹/ALDH2¹ and ALDH2¹/ ALDH2² 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. Received: 25 April 1995 / Revised: 25 September 1995     

Genetic polymorphism and activities of human lung alcohol and aldehyde dehydrogenases: Implications for ethanol metabolism and cytotoxicity

Alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) exhibit genetic polymorphism and tissue specificity. ADH and ALDH isozyme phenotypes from 39 surgical Chinese lung specimens were identified by agarose isoelectric focusing. The identity of the lung β-ADHs was further demonstrated by their characteristic pH-activity profiles for ethanol oxidation,K _m values for NAD and ethanol, and inhibition by 4-methylpyrazole or 1,10-phenanthroline. The β₂ allele, coding for β₂ polypeptide, was found to be predominant in the lung specimens studied. The ADH activities in the lungs with the homozygous phenotype ADH₂ 2-2 (exhibiting β₂β₂) and ADH₂ 1-1 (exhibiting β₁β₁) and the heterozygous phenotype ADH₂ 2-1 (exhibiting β₂β₂, β₂β₁, and β₁β₁) were determined to be 999±77, 48±17, and 494±61 nmol/min/g tissue, respectively. Fifty-one percent of the specimens studied lacked the ALDH2 activity band on the isoelectric focusing gels. The activities in the lung tissues with the ALDH2-active phenotype and the inactive phenotype were determined to be 30±3 and 17±1 nmol/min/g tissue, respectively. These findings indicate that human pulmonary ethanol-metabolizing activities differ significantly with respect to genetic polymorphism at both theADH ₂ and theALDH ₂ loci. The results suggest that individuals with highV _max β₂-ADH and deficient in low-K _m mitochondrial ALDH2, accounting for approximately 45% of the Chinese population, may end up with acetaldehyde accumulation during alcohol consumption, rendering them vulnerable to tissue injury caused by this highly reactive and toxic metabolite. This work was supported by Grants NSC 77-0412-B016-58 and NSC 80-0412-B016-21 from the National Science Council, Republic of China.     

Orosomucoid (ORM) typing by isoelectric focusing: evidence for gene duplication of ORM1 and genetic polymorphism of ORM2

Summary It has been demonstrated that the genetic polymorphism of human serum orosomucoid (ORM) is controlled by polymorphic ORM1 and monomorphic ORM2 loci. In this study a Japanese family was encountered in which several members had puzzling electrophoretic patterns consisting of four bands. The ORM patterns were due to the products of a duplicated ORM1 locus haplotype (ORM1 ^* 2·1) or the products of new variant alleles at the ORM2 locus. The ORM1 ^* 2·1 haplotype is very common in the Japanese population, occurring at an allele frequency of 0.16. The increased occurrence of ORM1 2-1 and the heterogeneity in band intensity among ORM1 2-1 phenotypes could be explained in terms of a duplicated gene ORM1 ^* 2·1. The ORM2 locus proved to be polymorphic, with six alleles in the Japanese population. Dedicated to Professor Dr. K. Nishigami on the occasion of his 60th birthday     

Dissemination of soybeans (Glycine max): Seed protein electrophoresis profiles among Japanese cultivars

Seed protein extracts from 477 Japanese soybean cultivars were analyzed by polyaery lamide gel electrophoresis to determine the distribution of the alleles of the Ti (Ti ^a,Ti ^b,Ti ^c) and Sp₁ (Sp ₁ ^a,Sp ₁ ^b loci with respect to maturity group and district of adaptation of each cultivar. About 60 percent of the soybean cultivars had theTi ^a allele. The frequency of theTi ^b allele was found to be highest in the southeast district and lowest in the northeast district. TheTi ^c allele discovered in 6 cultivars was traced to two possible sources adapted in the Tohoku District. TheSp _l ^a, allele was found in 26 cultivars ranging from Maturity Group II through VIII. The summer season type cultivars adapted to the Kyushu District having the genotypeTi ^b Sp_l ^b probably played a major role in the peculiar accumulation of theTi ^ub allele and the decrease of theSp _l ^a allele in the Japanese soybean cultivar population.     

Super-suppressor induced interallelic complementation

Summary In yeast the dominant super-suppressorS ₅ has a distinct expression in heterozygotes depending on the particular combination of alleles at thead ₁ orad ₂ loci. If thead ₁ combination is represented by two suppressible alleles, the phenotype of diploid is wild. If thead ₁ combination consists of a suppressible and a non-suppressible allele the phenotype of the diploid is partially mutant. Such a difference in the manifestation of suppressor depending on the combination of alleles is more pronounced in the case ofad ₂ mutations. In the case when bothad ₂ alleles are suppressible, the diploid is prototrophic, but when only one allele is suppressible, the diploid is an adenineless auxotroph as a rule.This type ofS ₅-effect gave us the possibility to study interallelic complementation atad ₂ locus in presence of the super-suppressor. It was shown that some combinations of noncomplementing alleles do complement as a result of suppression.Comparison of the two complementation maps with and without suppressor is made for thead ₂ locus. The mechanisms of the phenomena and of super-suppression are discussed.     

Chromosomal location of the gene encoding the murine acute-phase protein serum amyloid P-component (SAP)

A full-length cDNA clone, pmSAP3, encoding the serum P component (SAP), has been used to search for DNA fragment length variation among mouse strains previously analyzed for differences in endogenous SAP levels. Three alleles were found usingEcoRI-digested DNA. The finding of a single 5.4-kb fragment, alleled, in DNA from DBA/2J mice suggests the presence of a singleSap locus. Segregation of DNA fragment associated withSap ^b andSap ^d alleles was analyzed in three sets of recombinant inbred (RI) strains. The strain distribution pattern found for theSap alleles was identical to that of alleles ofLy-9 in 43 individual RI strains, suggesting tight linkage withLy-9 on mouse chromosome 1. In the BXD RI strains, the SDP of theSap locus, defined by the difference in the endogenous SAP level, is also identical to the SDP of the DNA fragments. We propose to redesignate theSap locus to include both the structural element defined by the DNA polymorphism and the regulatory element involved in the regulation of SAP synthesis. TheSap locus is the major genetic element contributing to the regulation of SAP production. Other genetic factors are also involved, as shown by the presence of nonparental phenotypes in the individual BXH RI strains. This study was performed through special Coordination Funds of the Science and Technology Agency of the Japanese Government and PHS Grant GM24464 to R.W.E.     

Allelic variation at high-molecular-weight glutenin subunit loci in <Emphasis Type="Italic">Aegilops biuncialis</Emphasis> Vis.

Alleles at the high-molecular-weight glutenin subunit loci Glu-U1 and Glu-M ^b 1 were analyzed in the tetraploid species Aegilops biuncialis (UUM^bM^b). The material for the investigation included the collection of 39 accessions of Ae. biuncialis from Ukraine (the Crimea), one Hellenic accession, one accession of unknown origin, F₂ seeds from different crosses, as well as samples from natural populations from the Crimea. Ae. umbellulata and Ae. comosa accessions were used to allocate components of the HMW glutenin subunit patterns of Ae. biuncialis to U or M ^b genomes. Eight alleles were identified at the Glu-U1 locus and ten alleles were revealed at the Glu-M ^b 1 locus. Among alleles at the Glu-M ^b 1 locus of Ae. biuncialis there were two alleles controlling the y-type subunit only and one allele encoding the x-subunit only.     

DNA sequence variation of the human ABO-secretor locus (FUT2) in New Guinean populations: possible early human migration from Africa

We have investigated the allelic polymorphism of the human ABO-secretor locus (FUT2) in 90 unrelated Papuan-speaking New Guineans (Dani group), 101 admixed New Guineans from Irian Jaya, Indonesia, and 32 New Guineans from Papua New Guinea by DNA sequencing analysis. Whereas the total frequency of various nonfunctional alleles at the FUT2 locus in the worldwide populations so far examined is around 0.5, we have found only one individual heterozygous for a nonfunctional allele in the 90 Dani group members and a frequency of nonfunctional alleles of 0.1–0.2 in the admixed New Guineans. Admixed New Guineans had the Asian-specific null allele se³⁸⁵ and the characteristic nonfunctional allele se^del2 found in Polynesians. In addition, both New Guinean populations had unique functional alleles (Se³⁷⁵ and Se⁴⁰⁰) with high frequencies (0.11–0.37); these are absent in other populations of the world except for African and Samoan populations. The Se³⁷⁵ allele had G and C at positions 1009 and 1011 of the 3' untranslated region, respectively, whereas all other FUT2 alleles found so far in the world, except for se⁴²⁸, have 1009A and 1011T. The Se³⁷⁵ allele found in Africans has 1009G and 1011T, or 1009A and 1011T. Corresponding positions of nonhuman primates have G and C, suggesting that the Se³⁷⁵ allele is one of the ancestral alleles, reflecting the early human migration from Africa to New Guinea and the long isolation of Dani populations from neighboring populations.     

Human alcohol dehydrogenase ADH2 and ADH3 polymorphisms in ethnic Chinese and Indians of West Malaysia

Summary Human alcohol dehydrogenase ADH₂ and ADH₃ were investigated in liver and stomach specimens of Chinese and Indians from West Malaysia. Eight-nine percent of the Chinese carry the atypical ADH₂ type, a proportion very similar to that reported in Japanese. However, among 43 Indian specimens there was not a single case of atypical ADH₂. In Indians, the gene frequency of ADH₃ ¹ is 0.64 and of ADH₃ ² 0.36, similar to the frequencies in Caucasians, whereas in Chinese, the gene frequency for ADH₃ ¹ and ADH₃ ² is 0.91 and 0.09, respectively. We also report some unusual enzymatic characteristics in the course of our study.     

Isolation of a new paramutagenic allele of thesulfurea locus in the tomato cultivar Moneymaker following in vitro culture

A new allele, SC148, of thesulfurea locus inLycopersicon esculentum was detected in a line derived after repeated selfing of plants that had been regenerated from tissue culture. Like the originalsulf mutant, SC148 displayed two mutant phenotypes: green-yellow speckled plants in which thesulf ^vag allele is present and pure yellow plants homozygous for thesulf ^tpura allele. Although the mutant alleles are recessive to wild-type, an unpredictable number of variegated and pura plants appeared in F₁ progenies that had been derived from crosses between SC148 and wild-type tomato plants. The presence of the wild-typesulf ⁺ allele in these variegated heterozygotes was demonstrated using a cytological marker that is linked tosulf. It is concluded that the mutantsulf allele of SC148, imposes its variegated expression state on the wild-typesulf ⁺ allele present insulf ⁺/sulf^vag heterozygotes. This behaviour, known as paramutation, has also been described for the originalsulf allele. The SC148 allele, however, seems to induce changes at an earlier stage in development. The analogy of this paramutagenic system to dominant position effect variegation inDrosophila is discussed.     

Typing forHLA-DPB1 * 03 andHLA-DPB1 * 06 using allele-specific DNA in vitro amplification and allele-specific oligonucleotide probes. Detection of “new” DPB1*06 variants

DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes has recently been reported. The resulting DNA amplification was specific for theHLA-DPB locus. Typing for the individualDPB alleles was exclusively dependent on the hybridizations of the probes but hampered by close sequence homology between differentDP alleles yielding complex patterns of reactivity with a panel of probes. We report the combined use of allele-specific DNA in vitro amplification and allele-specific oligonucleotides in typing forDPB1 ^* 03 andDPB1 ^* 06. Complete concordance with PLT typing was observed for theDPB1 ^* 03 alleles, while in the DPB1^*06 group, at least three variantDPB1 ^* 06 alleles were identified which have not been described previously.     

Structural and evolutionary comparisons of four alleles of the mouse Igk-J locus which encodes immunoglobulin kappa light chain joining (J K ) segments

The Igk-J locus of the mouse encodes the immunoglobulin light chain joining (J) segments. Four Igk-J alleles have been described on the basis of restriction enzyme length polymorphisms. The nucleotide sequences of the Igk-J ^a allele (type strain, C.C58), Igk-J ^c allele (type strain, SJL/J), and Igk-J ^d allele (type strain, SK/CamRk) have been determined and are compared with the previously reported Igk-J ^b allele sequence (type strain, BALB/c). The mouse sequences are also compared with published sequences for rat and human J _k sequences. Far more differences were found between the Igk-J ^a allele and the other mouse alleles than between any two of the latter. These result in two amino acid substitutions which distinguish the J2 and J3 ¹ segments of the Igk-J ^a allele from the other three alleles. Use of the Phylogenetic Analysis Using Parsimony program to generate a phylogenetic tree strongly indicates that after divergence from the rat ancestor, there appears to have been an early split between the Igk-J ^a allele and the evolutionary precursor of the other mouse alleles. There also appears to have been far less divergence from the ancestral condition in the Igk-J ^a allele than in the other alleles. Also, the presence of only one convergent mutation among the four mouse alleles provides strong evidence against any crossing over within the Igk-J locus during the history of these alleles. Finally, the differences in rates of evolution of the Igk-J alleles are in marked contrast to the relatively uniform rates of divergence of four alleles of a mouse V _k gene, Igk-VSer.     

Gc subtypes identified by isoelectric focusing in Baboons (Papio hamadryas)

Summary Phenotyping for Gc variants by conventional electrophoresis in 835 Papio hamadryas baboons demonstrated a monomorphic population. Gc subtyping by polyacrylamide IEF gels, pH 4–6, on 394 of these baboons revealed the existence of two common alleles which we named Gc _Papio ¹ and Gc _Papio ² . Pedigree data confirmed the inheritance of a single locus, two allele system and the observed gene frequencies were 0.593 for Gc _Papio ¹ and 0.407 for Gc _Papio ² .     

Genetic analysis of human lymphocyte proteins by two-dimensional gel electrophoresis

Summary We describe a genetic polymorphism of cytosol polypeptide with mol. wt. of 38,000 detected in phytohemagglutinin (PHA)-stimulated peripheral blood lymphocytes by two-dimensional gel electrophoresis. Three different electrophoretic phenotypes (type 1-1, 2-1, 2-2) of the polypeptide have been identified in a Japanese population. Family and population studies indicate that three phenotypes are determined by two common alleles at a single autosomal locus. Since the polypeptide is mainly present in cytosol of cells, we propose that the polypeptide be temporarily designated as cytosol polypeptide with mol. wt. of 38,000 (CP 38) and that the gene for CP 38 be designated as CP 38. The gene frequencies of two common alleles (CP 38 ¹ and CP 38 ²) are 0.899 and 0.101, respectively, in a Japanese population. The data on gel filtration of cytosol proteins on a Sephadex G-100 column suggest that CP 38 exists as a dimer in the cytosol. CP 38 was observed in the wide range of different cells, including B-lymphoblastoid cells, adult skin fibroblasts, HeLa cells, and erythrocytes. In 11 out of 72 individuals, the phenotypes of CP 38 were different from those of adenosine deaminase which is similar to CP 38 in subunit size, cell distribution, and allele frequencies. These data indicate that CP 38 is a new polymorphic polypeptide encoded by an autosomal locus.     

Direct detection of usual and atypical alleles on the human aldehyde dehydrogenase-2 (ALDH2) locus.

A method for determining human mitochondrial aldehyde dehydrogenase (ALDH2) genotypes was developed. Two 21-base synthetic oligonucleotides, one complementary to the usual ALDH2(1) gene and the other complementary to the atypical ALDH2(2) gene, were used as specific probes for in-gel hybridization analysis of human genomic DNA from either peripheral blood cells or livers. Under appropriate hybridization conditions, these two probes can hybridize to their specific complementary alleles and thus allow the genotyping of the ALDH2 locus.     

Sequence analysis and HLA-DR genotyping of a novel HLA-DRw14 allele

Analysis of a Japanese population by oligonucleotide genotyping revealed that one Japanese HLA-DRw14 allele had a DRB1 genotype different from that of the known HLA-DRw14-related alleles, DRB1 ^* 1401 (DRw14-Dw9) and DRB1 ^* 1402 (DRw14-Dw16). The second exon of the DRB1 gene of the novel DRw14 allele (designated DRB1-14c) was amplified enzymatically and sequenced after cloning intto a plasmid vector. The amino acid sequence of the first domain in the DR1 chain encoded in the DRB1-14c allele was more similar to that of the DRB1 ^* 1401 allele (three amino acid substitutions).than to that of the DRB1 ^* 1402 allele (six amino acid substitutions). No polymorphic amino acid residue that could explain the common serologic HLA-DRw14 specificity was identified among the sequences of the three DRw14-related alleles. Sequence-specific oligonucleotides (SSOs) were synthesized on the basis of the DRB1-14c nucleotide sequence and used for genotyping of the Japanese population. These SSOs served as useful probes for identifying the DRB1-14c allele in a wide range of donors.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M33693.