The soybean aldehyde dehydrogenase (ALDH) protein superfamily

Aldehyde dehydrogenases (ALDHs) are members of NAD(P)(+)-dependent protein superfamily that catalyze the oxidation of a wide range of endogenous and exogenous highly reactive aliphatic and aromatic aldehyde molecules to their corresponding non toxic carboxylic acids. Research evidence has shown that ALDHs represent a promising class of genes to improve growth development, seed storage and environmental stress adaptation in higher plants. The recently completed genome sequences of several plant species have resulted in the identification of a large number of ALDH genes, most of which still need to be functionally characterized. In this paper, we identify members of the ALDH gene superfamily in soybean genome, and provide a unified nomenclature for the entire soybean ALDH gene families. The soybean genome contains 18 unique ALDH sequences encoding members of five ALDH families involved in a wide range of metabolic and molecular detoxification pathways. In addition, we describe the biochemical requirements and cellular metabolic pathways of selected members of ALDHs in soybean responses to environmental stress conditions.     

Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

In recent years, there has been a significant increase in the number of completely sequenced plant genomes. The comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. The aldehyde dehydrogenase (ALDH) gene superfamily comprises a group of enzymes involved in the NAD⁺- or NADP⁺-dependent conversion of various aldehydes to their corresponding carboxylic acids. ALDH enzymes are involved in processing many aldehydes that serve as biogenic intermediates in a wide range of metabolic pathways. In addition, many of these enzymes function as ‘aldehyde scavengers’ by removing reactive aldehydes generated during the oxidative degradation of lipid membranes, also known as lipid peroxidation. Plants and animals share many ALDH families, and many genes are highly conserved between these two evolutionarily distinct groups. Conversely, both plants and animals also contain unique ALDH genes and families. Herein we carried out genome-wide identification of ALDH genes in a number of plant species—including Arabidopsis thaliana (thale crest), Chlamydomonas reinhardtii (unicellular algae), Oryza sativa (rice), Physcomitrella patens (moss), Vitis vinifera (grapevine) and Zea mays (maize). These data were then combined with previous analysis of Populus trichocarpa (poplar tree), Selaginella moellindorffii (gemmiferous spikemoss), Sorghum bicolor (sorghum) and Volvox carteri (colonial algae) for a comprehensive evolutionary comparison of the plant ALDH superfamily. As a result, newly identified genes can be more easily analyzed and gene names can be assigned according to current nomenclature guidelines; our goal is to clarify previously confusing and conflicting names and classifications that might confound results and prevent accurate comparisons between studies.     

葡萄生长素响应基因家族生物信息学鉴定和表达分析

生长素响应基因家族能调节植物体内生长素平衡和生长素信号途径。文章采用生物信息学方法检索获得葡萄(Vitisvinifera L.)基因组数据库中的生长素响应基因,通过分析其染色体定位、基因共线性和系统进化,发现葡萄基因组含有25个AUX_IAA基因、19个ARF基因、9个GH3基因、42个LBD基因。这些生长素响应基因不均匀分布在葡萄的19条染色体上,部分家族基因在染色体上形成基因簇。葡萄芯片数据结果表明,生长素响应基因在葡萄不同时期的果实和叶芽中均有表达,尤其在果实转色期、叶芽萌发或休眠期表达量急剧变化。研究结果为葡萄生长素响应基因在叶片和果实发育过程中的功能研究提供参考。     

葡萄CHS和STS基因家族生物信息学鉴定和表达分析

查尔酮合成酶(CHS,chalcone synthase)是植物体类黄酮类化合物合成的第1个关键酶和限速酶,它能够催化丙二酰-Co A和对香豆酸-Co A合成柚皮素查尔酮。二苯乙烯合成酶(STS,stilbene synthase)是芪类化合物合成路径的关键酶,与查尔酮合成酶有共同的作用底物,二者具有很高的相似度。为更好地了解葡萄中CHS和STS基因的种类和数量,本研究采用生物信息学方法检索获得葡萄(Vitis vinifera L.)基因组数据库中的CHS和STS基因,通过分析其染色体定位、系统进化和保守基序,发现葡萄基因组可能含有33个STS基因,9个CHS基因,这些基因集中分布在6条葡萄染色体上,部分家族基因在染色体上形成基因簇。葡萄CHS和STS基因家族蛋白长度、基因结构和蛋白基序非常保守,具有很近的进化关系。葡萄芯片数据结果表明,葡萄CHS和STS基因在葡萄果实不同发育时期的果皮和果肉中均有表达,尤其葡萄CHS GroupsⅢ亚家族基因在葡萄果皮中大量表达。葡萄STS基因家族在果实中的表达量较低,部分探针在葡萄果实成熟期的果皮中表达量急剧增加。本研究结果可为葡萄CHS和STS基因在果实发育过程中的功能研究提供参考。     

cDNA cloning and expression of a human aldehyde dehydrogenase (ALDH) active with 9-cis-retinal and identification of a rat ortholog, ALDH12

This report describes the isolation of a heretofore uncharacterized aldehyde dehydrogenase (ALDH) with retinal dehydrogenase activity from rat kidney and the cloning and expression of a cDNA that encodes its human ortholog, the previously unknown ALDH12. The human ALDH12 cDNA predicts a 487-residue protein with the 23 invariant amino acids, four conserved regions, cofactor binding motif (G(209)XGX(3)G), and active site cysteine residue (Cys(287)) that typify members of the ALDH superfamily. ALDH12 seems at least as efficient (V(m)/K(m)) in converting 9-cis-retinal into the retinoid X receptor ligand 9-cis-retinoic acid as two previously identified ALDHs with 9-cis-retinal dehydrogenase activity, rat retinal dehydrogenase (RALDH) 1 and RALDH2. ALDH12, however, has approximately 40-fold higher activity with 9-cis- retinal than with all-trans-retinal, whereas RALDH1 and RALDH2 have equivalent and approximately 4-fold less efficiencies for 9-cis-retinal versus all-trans-retinal, respectively. Therefore, ALDH12 is the first known ALDH to show a preference for 9-cis-retinal relative to all-trans-retinal. Evidence consistent with the possibility that ALDH12 could function in a pathway of 9-cis-retinoic acid biosynthesis in vivo includes biosynthesis of 9-cis-retinoic acid from 9-cis-retinol in cells co-transfected with cDNAs encoding ALDH12 and the 9-cis-retinol/androgen dehydrogenase, cis-retinoid/androgen dehydrogenase type 1. Intense ALDH12 mRNA expression in adult and fetal liver and kidney, two organs that reportedly have relatively high concentrations of 9-cis-retinol, reinforces this notion.     

The ALDH gene superfamily of Arabidopsis

Aldehyde dehydrogenases (ALDHs) represent a protein superfamily of NAD(P)(+)-dependent enzymes that oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes. The Arabidopsis genome contains 14 unique ALDH sequences encoding members of nine ALDH families, including eight known families and one novel family (ALDH22) that is currently known only in plants. Here, we identify members of the ALDH gene superfamily in Arabidopsis; provide a revised, unified nomenclature for these ALDH genes; analyze the molecular relationship among Arabidopsis ALDH genes and compare them to ALDH genes from other species, including prokaryotes and mammals; and describe the role of ALDHs in cytoplasmic male sterility, plant defense and abiotic stress tolerance.     

赤散囊菌MAPKs超家族的鉴定及分析

本研究以赤散囊菌Eurotium rubrum全基因组序列为对象,利用HMMER软件构建隐马尔可夫模型（hidden markov models,HMM）结合BLAST的方法鉴定了促分裂原活化蛋白激酶（mitogen-activated protein kinase,MAPK）超家族。通过构建系统发育树对鉴定蛋白进行分析,并利用MEME软件进行了保守性基序的预测及活性位点注释。分析结果表明,赤散囊菌基因组包含了4个MAPK蛋白,分别属于Hog1-type、MpkC-type、Slt2-type和Fus3/Kss1-type类型;3个MAPK kinase（MAPKK）蛋白,分别属于MKK1-type、Pbs2-type和Ste7-type类型;3个MAPK kinase kinase（MAPKKK）蛋白,分别属于BCK1-type、Ste11-type和Ssk22-type类型。保守性基序分析及注释结果表明,MAPKs超家族蛋白都包含了蛋白激酶活性位点“-D[L/I/V]K-”以及保守性的ATP-binding标签序列。MAPK与MAPKK蛋白分别包含了“-TxY-”和“-SD[I/V]WS-”磷酸化位点,且MAPK蛋白还包含一个保守性的common docking基序（CD motif）,而MAPKKK蛋白则包含了一个功能不明的保守性基序,其一致性序列为“-GTPYWMAPEV-”。研究结果为揭示MAPKs信号途径在赤散囊菌中参与调控的生物学过程奠定了基础。     

Single nucleotide polymorphism detection in aldehyde dehydrogenase 2 (ALDH2) gene using bacterial magnetic particles based on dissociation curve analysis

Single nucleotide polymorphism (SNP) detection for aldehyde dehydrogenase 2 (ALDH2) gene based on DNA thermal dissociation curve analysis was successfully demonstrated using an automated system with bacterial magnetic particles (BMPs) by developing a new method for avoiding light scattering caused by nanometer-size particles when using commercially available fluorescent dyes such as FITC, Cy3, and Cy5 as labeling chromophores. Biotin-labeled PCR products in ALDH2, two allele-specific probes (Cy3-labeled detection probe for ALDH2*1 and Cy5-labeled detection probe for ALDH2*2), streptavidin-immobilized BMPs (SA-BMPs) were simultaneously mixed. The mixture was denatured at 70 degrees C for 3 min, cooled slowly to 25 degrees C, and incubated for 10 min, allowing the DNA duplex to form between Cy3- or Cy5-labeled detection probes and biotin-labeled PCR products on SA-BMPs. Then duplex DNA-BMP complex was heated to 58 degrees C, a temperature determined by dissociation curve analysis and a dissociated single-base mismatched detection probe was removed at the same temperature under precise control. Furthermore, fluorescence signal from the detection probe was liberated into the supernatant from completely matched duplex DNA-BMP complex by heating to 80 degrees C and measured. In the homozygote target DNA (ALDH2*1/*1 and ALDH2*2/*2), the fluorescence signals from single-base mismatched were decreased to background level, indicating that mismatched hybridization was efficiently removed by the washing process. In the heterozygote target DNA (ALDH2*1/*2), each fluorescence signals was at a similar level. Therefore, three genotypes of SNP in ALDH2 gene were detected using the automated detection system with BMPs.     

Gene frequencies of alcohol dehydrogenase2 (ADH2) and aldehyde dehydrogenase2 (ALDH2) in five Chinese minorities

The gene frequencies of ADH ₂ ² and ALDH ₂ ² were lower in Tibetan and Mongolian populations than in Vietnamese, Han Chinese, and three Chinese minority populations.     

Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily of Gossypium raimondii

Background

Aldehyde dehydrogenases (ALDHs) are members of the NAD(P)⁺-dependent protein superfamily which catalyzes aliphatic and aromatic aldehyde oxidation to non-toxic carboxylic acids. ALDH genes may offer promise for improving plant adaptation to environmental stress. Recently, elucidated genome sequences of Gossypium raimondii provide a foundation for systematic identification and analysis of ALDH genes. To date, this has been accomplished for many plant species except G. raimondii.

Results

In this study, thirty unique ALDH sequences that code for 10 ALDH families were identified in the G. raimondii genome. Phylogenetic analysis revealed that ALDHs were split into six clades in G. raimondii, and ALDH proteins from the same families were clustered together. Phylogenetic relationships of ALDHs from 11 plant species suggest that ALDHs in G. raimondii shared the highest protein homology with ALDHs from poplar. Members within ALDH families possessed homologous exon–intron structures. Chromosomal distribution of ALDH did not occur evenly in the G. raimondii genome and many ALDH genes were involved in the syntenic region as documented by identification of physical locations among single chromosomes. In addition, syntenic analysis revealed that homologues of many G. raimondii ALDHs appeared in corresponding Arabidopsis and poplar syntenic blocks, indicating that these genes arose prior to G. raimondii, Arabidopsis and poplar speciation. Finally, based on gene expression analysis of microarray and RNA-seq, we can speculate that some G. raimondii ALDH genes might respond to drought or waterlogging stresses.

Conclusion

Genome-wide identification and analysis of the evolution and expression of ALDH genes in G. raimondii laid a foundation for studying this gene superfamily and offers new insights into the evolution history and speculated roles in Gossypium. These data can be used to inform functional genomic studies and molecular breeding in cotton.     

Acetaldehyde detoxification mechanisms in Drosophila melanogaster adults involving aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) enzymes

The mechanism of acetaldehyde detoxification in Drosophila melanogaster adults has been studied by comparing physiological in vitro and in vivo data. ADH⁺ and ADH⁻ flies, both lacking aldehyde dehydrogenase activity from ADH (ALDH^ADH, ALDH (ALDH) or both enzymes were exposed to acetaldehyde or ethanol, and the toxicity and internal accumulation of both compounds were determined. Acetaldehyde was extremely lethal for flies whose ALDH activity had been inhibited by cyanamide, though acetaldehyde was effectively detoxified by flies whose ALDH^ADH activity had been inhibited by acetone. After exposure to acetaldehyde, both acetaldehyde and ethanol rapidly accumulated in flies lacking ALDH activity, but not in flies lacking ALDH^ADH activity. However, ethanol but not acetaldehyde quickly accumulated in flies lacking ALDH activity after exposure to ethanol. Our results provide in vivo evidence that, as opposed to larvae, in D. melanogaster adults acetaldehyde is mainly oxidized into acetate by means of ALDH enzymes. However, the reducing activity of the ADH enzyme, which transforms acetaldehyde into ethanol, also plays an essential role in the detoxification of acetaldehyde. Differences in ALDH activity might be important to explain the differences in ethanol tolerance found in natural populations.     

Scallop lens Omega-crystallin (ALDH1A9): a novel tetrameric aldehyde dehydrogenase

Scallop eye lens Omega-crystallin is an inactive aldehyde dehydrogenase (ALDH1A9) related to cytoplasmic ALDH1A1 and mitochondrial ALDH2 that migrates by gel filtration chromatography as a homodimer. Because mammalian ALDH1A1 and ALDH2 are homotetramers, we investigated the native molecular mass of scallop Omega-crystallin by multi-angle laser light scattering. The results indicate that the scallop Omega-crystallin is a tetrameric, not a dimeric protein. Moreover, phylogenetic tree analysis shows that scallop Omega-crystallin clusters with the mitochondrial ALDH2 and ALDH1B1 rather than the cytoplasmic ALDH1A, yet it lacks the mitochondrial N-terminal leader sequence characteristic of the mitochondrial ALDHs. The mitochondrial grouping, enzymatic inactivity, and anomalous gel filtration behavior make scallop cytoplasmic Omega-crystallin an interesting protein for structural studies of evolutionary adaptations to become an enzyme-crystallin.     

Determination of genotypes of human aldehyde dehydrogenase ALDH2 locus

Virtually all Caucasians have two major aldehyde dehydrogenase isozymes, ALDH1 and ALDH2, in their livers, while approximately 50% of Japanese and other Orientals are "atypical" in that they have only ALDH1 and are missing ALDH2. We previously demonstrated the existence of an enzymatically inactive but immunologically cross-reactive material (CRM) in atypical Japanese livers. Among 10 Japanese livers examined, five had ALDH1 but not ALDH2 isozyme. These are considered to be homozygous atypical at the ALDH2 locus. Four had both ALDH1 and ALDH2 components detected by starch gel electrophoresis, that is, they are apparently usual. However, biochemical and immunological studies revealed that three of these four livers contained CRM. These three livers should be heterozygous atypical in the ALDH2 locus, that is, genotype ALDH2(1)/ALDH2(2). A Japanese liver, as well as control Caucasian livers, had no CRM, and they must be homozygous usual ALDH2(1)/ALDH2(1). Although the number of liver specimens examined is limited, the frequencies of three genotypes determined in this study are compatible with the values calculated based on the genetic model that two common alleles ALDH2(1) and ALDH2(2) for the same locus are codominantly expressed in Orientals. The remaining liver had only ALDH2 isozyme and was missing ALDH1. This type was not previously found in Caucasians and Orientals. The two-dimensional crossed immunoelectrophoresis revealed the existence of a CRM corresponding to ALDH1 in this liver. The abnormality can be considered to be due to structural mutation at the ALDH1 locus producing a defective ALDH1 molecule, although other possibilities such as post-translational modifications are not ruled out.     

Genome-wide analysis of the Tetrahymena thermophila glutathione S-transferase gene superfamily

The ciliate Tetrahymena thermophila has a rapid response to detoxify xenobiotics, which presents opportunity to study the diversification of Glutathione S-Transferase superfamily. In-silico identification of putative GST genes were resulted with 70 GST genes; 49 TtGSTmu, 7 TtGSTomega, 5 TtGSTtheta, 2 TtGSTzeta, 4 TtMAPEG and 3 TtEF1G. TtGST superfamily has short intron carrying or intronless genes. The most expressed mRNAs of TtGST are limited to 4 members at all life stages. TtGST genes are widely distributed to all five micronuclear chromosomes with the highest diversified members from different classes in chromosome 4. The clustering and the orientation of some TtGSTs in the T. thermophila genome give clues about the recent gene duplication. Analysis of GSH affinity-purified GST proteins with Western blot and activity assay showed GST activity carrying purified TtGST populations. In conclusion, the enhanced genome capacity of TtGST superfamily may have evolved through improved GST enzymatic activity.     

Genome-wide identification and analysis of membrane-bound O-acyltransferase (MBOAT) gene family in plants

Membrane bound O-acyl transferase (MBOAT) family is composed of gene members encoding a variety of acyltransferase enzymes, which play important roles in plant acyl lipid metabolism. Here, we present the first genome-enabled identification and analysis of MBOAT gene models in plants. In total, we identified 136 plant MBOAT sequences from 14 plant species with complete genomes. Phylogenetic relationship analyses suggested the plant MBOAT gene models fell into four major groups, two of which likely encode enzymes of diacylglycerol acyltransferase 1 (DGAT1) and lysophospholipid acyltransferase (LPLAT), respectively, with one–three copies of paralogs present in each of the most plant species. A group of gene sequences, which are homologous to Saccharomyces cerevisiae glycerol uptake proteins (GUP), was identified in plants; copy numbers were conserved, with only one copy represented in each of the most plant species; analyses showed that residues essential for acyltransferases were more prone to be conserved than vertebrate orthologs. Among four groups, one was inferred to emerge in land plants and experience a rapid expansion in genomes of angiosperms, which suggested their important roles in adaptation of plants in lands. Sequence and phylogeny analyses indicated that genes in all four groups encode enzymes with acyltransferases. Comprehensive sequence identification of MBOAT family members and investigation into classification provide a complete picture of the MBOAT gene family in plants, and could shed light into enzymatic functions of different MBOAT genes in plants.     

Molecular cloning and baculovirus expression of the rabbit corneal aldehyde dehydrogenase (ALDH1A1) cDNA

Most mammalian species express high concentrations of ALDH3A1 in corneal epithelium with the exception of the rabbit, which expresses high amounts of ALDH1A1 rather than ALDH3A1. Several hypotheses that involve catalytic and/or structural functions have been postulated regarding the role of these corneal ALDHs. The aim of the present study was to characterize the biochemical properties of the rabbit ALDH1A1. We have cloned and sequenced the rabbit ALDH1A1 cDNA, which is 2,073 bp in length (excluding the poly(A+) tail), and has 5' and 3' nontranslated regions of 46 and 536 bp, respectively. This ALDH1A1 cDNA encodes a protein of 496 amino acids (Mr = 54,340) that is: 86-91% identical to mammalian ALDH1A1 proteins, 83-85% identical to phenobarbital-inducible mouse and rat ALDH1A7 proteins, 84% identical to elephant shrew ALDH1A8 proteins (eta-crystallins), 69-73% identical to vertebrate ALDH1A2 and ALDH1A3 proteins, 65% identical to scallop ALDH1A9 protein (omega-crystallin), and 55-57% to cephalopod ALDH1C1 and ALDH1C2 (omega-crystallins). Recombinant rabbit ALDH1A1 protein was expressed using the baculovirus system and purified to homogeneity with affinity chromatography. We found that rabbit ALDH1A1 is catalytically active and efficiently oxidizes hexanal (Km = 3.5 microM), 4-hydroxynonenal (Km = 2.1 microM) and malondialdehyde (Km = 14.0 microM), which are among the major products of lipid peroxidation. Similar kinetic constants were observed with the human recombinant ALDH1A1 protein, which was expressed and purified using similar experimental conditions. These data suggest that ALDH1A1 may contribute to corneal cellular defense against oxidative damage by metabolizing toxic aldehydes produced during UV-induced lipid peroxidation.     

Differences in nucleotide specificity and catalytic mechanism between Vibrio harveyi aldehyde dehydrogenase and other members of the aldehyde dehydrogenase superfamily

The fatty aldehyde dehydrogenase (Vh-ALDH) isolated from the luminescent bacterium, Vibrio harveyi, differs from other aldehyde dehydrogenases in its high affinity for NADP(+). The binding of NADP(+) appears to arise from the interaction of the 2'-phosphate of the adenosine moiety of NADP(+) with a threonine (T175) in the nucleotide recognition site just after the beta(B) strand as well as with an arginine (R210) that pi stacks over the adenosine moiety. The active site of Vh-ALDH contains the usual suspects of a cysteine (C289), two glutamates (E253 and E377) and an asparagine (N147) involved in the aldehyde dehydrogenase mechanism. However, Vh-ALDH has one polar residue in the active site that distinguishes it from other ALDHs; a histidine (H450) is in close contact with the cysteine nucleophile. As a glutamate has been implicated in promoting the nucleophilicity of the active site cysteine residue in ALDHs, the close contact of a histidine with the cysteine nucleophile in Vh-ALDH raises the possibility of alternate routes to increase the reactivity of the cysteine nucleophile. The effects of mutation of these residues on the different functions catalyzed by Vh-ALDH including acylation, (thio)esterase, reductase and dehydrogenase activities should help define the specific roles of the residues in the active site of ALDHs.