Molecular cloning and characterization of a novel Dehydrogenase/reductase (SDR family) member 1 genea from human fetal brain

Short-chain dehydrogenases/reductases (SDR) constitute a large protein family of NAD(P)(H)-dependent oxidoreductase. They are defined by distinct, common sequence motifs and show a wide range of substrate specialisms. By large-scale sequencing analysis of a human fetal brain cDNA library, we isolated a novel human SDR-type dehydrogenase/reductase gene named Dehydrogenase/reductase (SDR family) member 1 (DHRS1). The DHRS1 cDNA is 1411 base pair in length, encoding a 314-amino-acid polypeptide which has a SDR motif. Northern blot reveals two bands, of about 0.9 and 1.4 kb in size. These two forms are expressed in many tissues. The DHRS1 gene is localized on chromosome 14q21.3. It has 9 exons and spans 9.2 kb of the genomic DNA.     

Characterization of a novel airway epithelial cell-specific short chain alcohol dehydrogenase/reductase gene whose expression is up-regulated by retinoids and is involved in the metabolism of retinol

Multiple retinoic acid responsive cDNAs were isolated from a high density cDNA microarray membrane, which was developed from a cDNA library of human tracheobronchial epithelial cells. Five selected cDNA clones encoded the sequence of the same novel gene. The predicted open reading frame of the novel gene encoded a protein of 319 amino acids. The deduced amino acid sequence contains four motifs that are conserved in the short-chain alcohol dehydrogenase/reductase (SDR) family of proteins. The novel gene shows the greatest homology to a group of dehydrogenases that can oxidize retinol (retinol dehydrogenases). The mRNA of the novel gene was found in trachea, colon, tongue, and esophagus. In situ hybridization of airway tissue sections demonstrated epithelial cell-specific gene expression, especially in the ciliated cell type. Both all-trans-retinoic acid and 9-cis-retinoic acid were able to elevate the expression of the novel gene in primary human tracheobronchial epithelial cells in vitro. This elevation coincided with an enhanced retinol metabolism in these cultures. COS cells transfected with an expression construct of the novel gene were also elevated in the metabolism of retinol. The results suggested that the novel gene represents a new member of the SDR family that may play a critical role in retinol metabolism in airway epithelia as well as in other epithelia of colon, tongue, and esophagus.     

SDR-O: an orphan short-chain dehydrogenase/reductase localized at mouse chromosome 10/human chromosome 12

We report cloning a cDNA that encodes a novel short-chain dehydrogenase/reductase, SDR-O, conserved in mouse, human and rat. Human and mouse liver express SDR-O (short-chain dehydrogenase/reductase-orphan) mRNA intensely. The mouse embryo expresses SDR-O mRNA as early as day seven. Human SDR-O localizes on chromosome 12; mouse SDR-O localizes on chromosome 10 with CRAD1, CRAD2 and RDH4. SDR-O shares highest amino acid similarity with rat RoDH1 and mouse RDH1 (69-70%), but does not have the retinol and 3alpha-hydroxysteroid dehydrogenase activity of either, nor is it active as a 17beta- or 11beta-hydroxysteroid dehydrogenase. Short-chain dehydrogenase/reductases catalyse the metabolism of ligands that bind with nuclear receptors: the occurrence of 'orphan' nuclear receptors may imply existence of 'orphan' SDR, suggesting that SDR-O may catalyse the metabolism of another class of nuclear receptor ligand. Alternatively, SDR-O may not have a catalytic function, but may regulate metabolism by binding substrates/products and/or by serving as a regulatory factor.     

Cloning and bacterial expression of monomeric short-chain dehydrogenase/reductase (carbonyl reductase) from CHO-K1 cells.

Mammalian carbonyl reductase (EC 1.1.1.184) is an enzyme that can catalyze the reduction of many carbonyl compounds, using NAD(P)H. We isolated a cDNA of carbonyl reductase (CHO-CR) from CHO-K1 cells which was 1208 bp long, including a poly(A) tail, and contained an 831-bp ORF. The deduced amino-acid sequence of 277 residues contained a typical motif for NADP+-binding (TGxxxGxG) and an SDR active site motif (S-Y-K). CHO-CR closely resembles mammalian carbonyl reductases with 71-73% identity. CHO-CR cDNA had the highest similarity to human CBR3 with 86% identity. Using the pET-28a expression vector, recombinant CHO-CR (rCHO-CR) was expressed in Escherichia coli BL21 (DE3) cells and purified with a Ni2+-affinity resin to homogeneity with a 35% yield. rCHO-CR had broad substrate specificity towards xenobiotic carbonyl compounds. RT-PCR of Chinese hamster tissues suggest that CHO-CR is highly expressed in kidney, testis, brain, heart, liver, uterus and ovary. Southern blotting analysis indicated the complexity of the Chinese hamster carbonyl reductase gene.     

Identification of a mouse short-chain dehydrogenase/reductase gene,retinol dehydrogenase-similar. Function of non-catalytic amino acid residues in enzyme activity

We report a mouse short-chain dehydrogenase/reductase (SDR), retinol dehydrogenase-similar (RDH-S), with intense mRNA expression in liver and kidney. The RDH-S gene localizes to chromosome 10D3 with the SDR subfamily that catalyzes metabolism of retinoids and 3 alpha-hydroxysteroids. RDH-S has no activity with prototypical retinoid/steroid substrates, despite 92% amino acid similarity to mouse RDH1. This afforded the opportunity to analyze for functions of non-catalytic SDR residues. We produced RDH-S Delta 3 by mutating RDH-S to remove an "additional" Asn residue relative to RDH1 in its center, to convert three residues into RDH1 residues (L121P, S122N, and Q123E), and to substitute RDH1 sequence G208FKTCVTSSD for RDH-S sequence F208-FLTGMASSA. RDH-S Delta 3 catalyzed all-trans-retinol and 5 alpha-androstane-3 alpha,17 alpha-diol (3 alpha-adiol) metabolism 60-70% as efficiently (Vm/Km) as RDH1. Conversely, substituting RDH-S sequence F208FLTGMASSA into RDH1 produced a chimera (viz. C3) that was inactive with all-trans-retinol, but was 4-fold more efficient with 3 alpha-adiol. A single RDH1 mutation in the C3 region (K210L) reduced efficiency for all-trans-retinol by >1250-fold. In contrast, the C3 area mutation C212G enhanced efficiency with all-trans-retinol by approximately 2.4-fold. This represents a >6000-fold difference in catalytic efficiency for two enzymes that differ by a single non-catalytic amino acid residue. Another chimera (viz. C5) retained efficiency with all-trans-retinol, but was not saturated and was weakly active with 3 alpha-adiol, stemming from three residue differences (K224Q, K229Q, and A230T). The residues studied contribute to the substrate-binding pocket: molecular modeling indicated that they would affect orientation of substrates with the catalytic residues. These data report a new member of the SDR gene family, provide insight into the function of non-catalytic SDR residues, and illustrate that limited changes in the multifunctional SDR yield major alterations in substrate specificity and/or catalytic efficiency.     

Structural role of conserved Asn179 in the short-chain dehydrogenase/reductase scaffold.

Short-chain dehydrogenases/reductases (SDR) constitute a large family of enzymes found in all forms of life. Despite a low level of sequence identity, the three-dimensional structures determined display a nearly superimposable alpha/beta folding pattern. We identified a conserved asparagine residue located within strand betaF and analyzed its role in the short-chain dehydrogenase/reductase architecture. Mutagenetic replacement of Asn179 by Ala in bacterial 3beta/17beta-hydroxysteroid dehydrogenase yields a folded, but enzymatically inactive enzyme, which is significantly more resistant to denaturation by guanidinium hydrochloride. Crystallographic analysis of the wild-type enzyme at 1.2-A resolution reveals a hydrogen bonding network, including a buried and well-ordered water molecule connecting strands betaE to betaF, a common feature found in 16 of 21 known three-dimensional structures of the family. Based on these results, we hypothesize that in mammalian 11beta-hydroxysteroid dehydrogenase the essential Asn-linked glycosylation site, which corresponds to the conserved segment, displays similar structural features and has a central role to maintain the SDR scaffold.     

Identification of the hRDH-E2 gene,a novel member of the SDR family,and its increased expression in psoriatic lesion

To identify novel psoriasis-associated genes, we focused on several ESTs (expressed sequence tags) whose expression was predominantly increased in the affected skin in patients with psoriasis vulgaris, as assessed by microarray assay. In this paper, a full-length cDNA corresponding to one of those ESTs (AI440266) was isolated by screening of cultured human keratinocyte cDNA libraries. This cDNA has an open reading frame of a 309-amino-acid protein, sharing significant homology to one of the short-chain alcohol dehydrogenase/reductase (SDR) families that can catalyze the first and rate-limiting step that generates retinaldehyde from retinol. So, this gene was designated as hRDH-E2 (human epidermal retinal dehydrogenase 2). The hRDH-E2 gene has a single functional copy on chromosome 8q12.1, spanning approximately 20kb with seven exons. The deduced amino acid sequence contains three motifs that are conserved in the SDR family. Qualitative RT-PCR demonstrated that the mRNA levels of hRDH-E2 were significantly elevated in the affected skin in psoriasis patients as compared to the unaffected skin in patients and the normal skin in healthy individual. These results suggest that hRDH-E2 may be involved in the pathogenesis of psoriasis through its critical role in retinol metabolism in keratinocyte proliferation.     

Evidence that the human gene for prostate short-chain dehydrogenase/reductase (PSDR1) encodes a novel retinal reductase (RalR1)

All-trans-retinoic acid is a metabolite of vitamin A (all-trans-retinol) that functions as an activating ligand for a family of nuclear retinoic acid receptors. The intracellular levels of retinoic acid in tissues are tightly regulated, although the mechanisms underlying the control of retinoid metabolism at the level of specific enzymes are not completely understood. In this report we present the first characterization of the retinoid substrate specificity of a novel short-chain dehydrogenase/reductase (SDR) encoded by RalR1/PSDR1, a cDNA recently isolated from the human prostate (Lin, B., White, J. T., Ferguson, C., Wang, S., Vessella, R., Bumgarner, R., True, L. D., Hood, L., and Nelson, P. S. (2001) Cancer Res. 61, 1611-1618). We demonstrate that RalR1 exhibits an oxidoreductive catalytic activity toward retinoids, but not steroids, with at least an 800-fold lower apparent K(m) values for NADP+ and NADPH versus NAD+ and NADH as cofactors. The enzyme is approximately 50-fold more efficient for the reduction of all-trans-retinal than for the oxidation of all-trans-retinol. Importantly, RalR1 reduces all-trans-retinal in the presence of a 10-fold molar excess of cellular retinol-binding protein type I, which is believed to sequester all-trans-retinal from nonspecific enzymes. As shown by immunostaining of human prostate and LNCaP cells with monoclonal anti-RalR1 antibodies, the enzyme is highly expressed in the epithelial cell layer of human prostate and localizes to the endoplasmic reticulum. The enzymatic properties and expression pattern of RalR1 in prostate epithelium suggest that it might play a role in the regulation of retinoid homeostasis in human prostate.     

Predicting protein function from structure--the roles of short-chain dehydrogenase/reductase enzymes in Bordetella O-antigen biosynthesis

The pathogenic bacteria Bordetella parapertussis and Bordetella bronchiseptica express a lipopolysaccharide O antigen containing a polymer of 2,3-diacetamido-2,3-dideoxy-l-galacturonic acid. The O-antigen cluster contains three neighbouring genes that encode proteins belonging to the short-chain dehydrogenase/reductase (SDR) family, wbmF, wbmG and wbmH, and we aimed to elucidate their individual functions. Mutation and complementation implicate each gene in O-antigen expression but, as their putative sugar nucleotide substrates are not currently available, biochemical characterisation of WbmF, WbmG and WbmH is impractical at the present time. SDR family members catalyse a wide range of chemical reactions including oxidation, reduction and epimerisation. Because they typically share low sequence conservation, however, catalytic function cannot be predicted from sequence analysis alone. In this context, structural characterisation of the native proteins, co-crystals and small-molecule soaks enables differentiation of the functions of WbmF, WbmG and WbmH. These proteins exhibit typical SDR architecture and coordinate NAD. In the substrate-binding domain, all three enzymes bind uridyl nucleotides. WbmG contains a typical SDR catalytic TYK triad, which is required for oxidoreductase function, but the active site is devoid of additional acid-base functionality. Similarly, WbmH possesses a TYK triad, but an otherwise feature-poor active site. Consequently, 3,5-epimerase function can probably be ruled out for these enzymes. The WbmF active site contains conserved 3,5-epimerase features, namely, a positionally conserved cysteine (Cys133) and basic side chain (His90 or Asn213), but lacks the serine/threonine component of the SDR triad and therefore may not act as an oxidoreductase. The data suggest a pathway for synthesis of the O-antigen precursor UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid and illustrate the usefulness of structural data in predicting protein function.     

Chinese hamster monomeric carbonyl reductases of the short-chain dehydrogenase/reductase superfamily

Chinese hamster monomeric carbonyl reductases (CHCRs) belong to the short-chain dehydrogenase/reductase (SDR) superfamily, which is a family of enzymes that metabolize many endogenous and xenobiotic compounds. We previously cloned three carbonyl reductase cDNAs-Chcr1, Chcr2, and Chcr3. By performing spectrophotometric analyses, we indicated that the enzymes CHCR1, CHCR2, and CHCR3 had similar specificities toward steroids; only CHCR3 did not show any reactivity with prostaglandins (PGs). In the present study, we investigated the characteristics of CHCRs in detail, that is, the differences in their expression patterns, physicochemical properties, and enzymatic activities. CHCR1 exhibited sex-dependent expression patterns. CHCRs showed multiple surface potentials in the zeta potential analysis and CHCR3 exhibited an isatin reductase activity with a high K(m) value. By the present HPLC-analysis, all the three enzymes exhibited PGF(2alpha) dehydrogenase activity and could oxidize PGF(2alpha) to PGE(2) and 15-keto-PGF(2alpha), i.e., the three enzymes exhibited 9- and 15-hydroxy PG dehydrogenase activities. Moreover, 15-keto-PGE(2) was detected in a comparatively higher amount in the dehydrogenase reaction products of CHCR2 than in those of CHCR1 and CHCR3, suggesting that CHCR2 can oxidize PGE(2) and/or 15-keto-PGF(2alpha) to 15-keto-PGE(2); however, these two PGs did not seem to be efficient substrates of CHCR1. Despite the differences in the dehydrogenase activities between CHCR1 and CHCR2, PGE(2) reductase activities of the two enzymes were similar, and PGF(2alpha) was predominantly produced from PGE(2) as a result of the PG 9-keto reductase activity. On the other hand, CHCR3 exhibited a reduced PGE(2) reductase activity. In conclusion, although the CHCRs share a high degree of sequence identity (>70%), they clearly differed in their enzymatic characteristics.     

一种新的短链脱氢/还原酶家族新成员:NADP(H)-依赖的视黄醇脱氢酶基因的克隆和分析

从牛的肝脏中快速抽提总RNA,根据GenBank已发表NADP(H)-依赖的视黄醇脱氢酶基因(NRDR)的cDNA序列,设计并合成特异引物,利用cDNA末端快速扩增(RACE)方法和反转录-聚合酶链式反应(RT-PCR),得到牛肝内的NRDR cDNA的全长序列。经测序证实,牛肝NRDR的全长cDNA序列为1266bp,其开放读码框架在24～806bp,编码260个氨基酸(GenBank登录号：AF487454)。根据NRDR基因推导出的氨基酸序列与人、鼠、兔有高度同源性,并含有SDR超家族成员的两个高度保守的模序,在其C-端含有过氧化物酶体的靶向序列为SHL。结果表明,牛的NRDR应属于过氧化物酶体内SDR超家族成员并在维甲酸合成的限速步骤起作用的酶,也为维甲酸合成的传统通路提供一个补充。     

Cloning of a rat cDNA encoding retinol dehydrogenase isozyme type III

The primary and rate-limiting step in retinoic acid (RA) biosynthesis requires the conversion of retinol into retinal. Previously, two genes encoding retinol dehydrogenases (RoDH), which recognize holo-cellular retinol-binding protein as substrate, had been cloned, expressed and identified as members of the short-chain dehydrogenase/reductase (SDR) gene family. This work reports the cloning of a cDNA encoding a third RoDH isozyme, RoDH(III). The deduced amino-acid sequence of RoDH(III) indicates 97.8% identity with RoDH(I) and 82.3% identity with RoDH(II). RNase protection assays revealed RoDH(III) mRNA expression only in rat liver, in contrast to RoDH(I) and RoDH(II), which had their mRNA expressed in rat liver, kidney, lung, testis and brain. These data extend the insight that a subfamily of SDR isozymes, tissue-distinctively expressed, catalyzes the first step in RA biogenesis     

Molecular cloning and expression analysis of a new gene for short-chain dehydrogenase/reductase 9

We report here the cloning and characterization of a novel human short-chain dehydrogenases/reductase gene SCDR9, isolated from a human liver cDNA library, and mapped to 4q22.1 by browsing the UCSC genomic database. SCDR9 containing an ORF with a length of 900 bp, encoding a protein with a signal peptide sequence and an adh_short domain. GFP localization shows SCDR9 protein concentrated in some site of the cytoplasm, but not in the ER. Expression pattern in eighteen tissues revealed that SCDR9 is expressed highly in liver. Soluble recombinant protein was successfully purified from Escherichia coli using pET28A(+) expression vector. Our data provides important information for further study of the function of the SCDR9 gene and its products.     

Mutational analysis of the Sinorhizobium meliloti short-chain dehydrogenase/reductase family reveals substantial contribution to symbiosis and catabolic diversity

The short-chain dehydrogenase/reductase (SDR) family is one of the largest and most ubiquitous protein families in bacterial genomes. Despite there being a few well-characterized examples, the substrate specificities or functions of most members of the family are unknown. In this study, we carried out a large-scale mutagenesis of the SDR gene family in the alfalfa root nodule symbiont Sinorhizobium meliloti. Subsequent phenotypic analysis revealed phenotypes for mutants of 21 of the SDR-encoding genes. This brings the total number of S. meliloti SDR-encoding genes with known function or associated phenotype to 25. Several of the mutants were deficient in the utilization of specific carbon sources, while others exhibited symbiotic deficiencies on alfalfa (Medicago sativa), ranging from partial ineffectiveness to complete inability to form root nodules. Five of the mutants had both symbiotic and carbon utilization phenotypes. These results clearly demonstrate the importance of the SDR family in both symbiosis and saprotrophy, and reinforce the complex nature of the interaction of S. meliloti with its plant hosts. Further analysis of the genes identified in this study will contribute to the overall understanding of the biology and metabolism of S. meliloti in relation to its interaction with alfalfa.     

Molecular modeling and site-directed mutagenesis reveal the benzylisoquinoline binding site of the short-chain dehydrogenase/reductase salutaridine reductase

Recently, the NADPH-dependent short-chain dehydrogenase/reductase (SDR) salutaridine reductase (E.C. 1.1.1.248) implicated in morphine biosynthesis was cloned from Papaver somniferum. In this report, a homology model of the Papaver bracteatum homolog was created based on the x-ray structure of human carbonyl reductase 1. The model shows the typical alpha/beta-folding pattern of SDRs, including the four additional helices alphaF'-1 to alphaF'-4 assumed to prevent the dimerization of the monomeric short-chain dehydrogenases/reductases. Site-directed mutagenesis of asparagine-152, serine-180, tyrosine-236, and lysine-240 resulted in enzyme variants with strongly reduced performance or inactive enzymes, showing the involvement of these residues in the proton transfer system for the reduction of salutaridine. The strong preference for NADPH over NADH could be abolished by replacement of arginine residues 44 and 48 by glutamic acid, confirming the interaction between the arginines and the 2'-phosphate group. Docking of salutaridine into the active site revealed nine amino acids presumably responsible for the high substrate specificity of salutaridine reductase. Some of these residues are arranged in the right position by an additional alphaE' helix, which is not present in SDRs analyzed so far. Enzyme kinetic data from mutagenic replacement emphasize the critical role of these residues in salutaridine binding and provide the first data on the molecular interaction of benzylisoquinoline alkaloids with enzymes.