Nocardia sp. carboxylic acid reductase: cloning, expression, and characterization of a new aldehyde oxidoreductase family

We have cloned, sequenced, and expressed the gene for a unique ATP- and NADPH-dependent carboxylic acid reductase (CAR) from a Nocardia species that reduces carboxylic acids to their corresponding aldehydes. Recombinant CAR containing an N-terminal histidine affinity tag had K(m) values for benzoate, ATP, and NADPH that were similar to those for natural CAR, and recombinant CAR reduced benzoic, vanillic, and ferulic acids to their corresponding aldehydes. car is the first example of a new gene family encoding oxidoreductases with remote acyl adenylation and reductase sites.     

Oxidation of N-Nitrosoalkylamines by Human Cytochrome P450 2A6: SEQUENTIAL OXIDATION TO ALDEHYDES AND CARBOXYLIC ACIDS AND ANALYSIS OF REACTION STEPS*

Cytochrome P450 (P450) 2A6 activates nitrosamines, including N,N-dimethylnitrosamine (DMN) and N,N-diethylnitrosamine (DEN), to alkyl diazohydroxides (which are DNA-alkylating agents) and also aldehydes (HCHO from DMN and CH₃CHO from DEN). The N-dealkylation of DMN had a high intrinsic kinetic deuterium isotope effect (^Dk_app ∼ 10), which was highly expressed in a variety of competitive and non-competitive experiments. The ^Dk_app for DEN was ∼3 and not expressed in non-competitive experiments. DMN and DEN were also oxidized to HCO₂H and CH₃CO₂H, respectively. In neither case was a lag observed, which was unexpected considering the k_cat and K_m parameters measured for oxidation of DMN and DEN to the aldehydes and for oxidation of the aldehydes to the carboxylic acids. Spectral analysis did not indicate strong affinity of the aldehydes for P450 2A6, but pulse-chase experiments showed only limited exchange with added (unlabeled) aldehydes in the oxidations of DMN and DEN to carboxylic acids. Substoichiometric kinetic bursts were observed in the pre-steady-state oxidations of DMN and DEN to aldehydes. A minimal kinetic model was developed that was consistent with all of the observed phenomena and involves a conformational change of P450 2A6 following substrate binding, equilibrium of the P450-substrate complex with a non-productive form, and oxidation of the aldehydes to carboxylic acids in a process that avoids relaxation of the conformation following the first oxidation (i.e. of DMN or DEN to an aldehyde).     

Aldehyde oxidoreductase as a biocatalyst: Reductions of vanillic acid

Aldehyde oxidoreductase (carboxylic acid reductase) catalyzes the Mg(2+), ATP and NADPH dependent reduction of carboxylic acids to their corresponding aldehydes. The identification of the gene from Nocardia sp. NRRL 5646 and its expression in E. coli BL21-CodonPlus(?)(DE3)-RP/pHAT305 provided an avenue to develop a biocatalyst for reduction of carboxylic acids. In addition to aromatic acids, the recombinant carboxylic acid reductase also accepts several aliphatic mono, di and tri carboxylic acids as substrates. A recently identified Nocardia sp., phosphopantetheinyl transferase gene (npt) enhanced the activity of carboxylic acid reductase. Coexpression of car and npt in E. coli BL21-CodonPlus(?)(DE3)-RP/pPV2.83 resulted in a purified recombinant carboxylic acid reductase with improved specific activity of 2.2U/mg protein. The utility of the recombinant carboxylic acid reductase as a biocatalyst has been demonstrated using vanillic acid as substrate. E. coli BL21-CodonPlus(?)(DE3)-RP/pHAT305 expressing Car reduced 50% of vanillic acid to vanillin in 10h. E. coli BL21-CodonPlus(?)(DE3)-RP/pPV2.83 resting cells expressing Car and Npt reduced 90% of vanillic acid to vanillin in 6h. Enhanced, in vivo cofactor NADPH regeneration by glucose dehydrogenase (gdh) was accomplished using E. coli BL21-CodonPlus(?)(DE3)-RP/pPV2.85, that carried car, npt, and gdh. Resting cell reactions using E. coli BL21-CodonPlus(?)(DE3)-RP/pPV2.85 with in situ product removal by XAD-2 resin efficiently reduced 5g/L of vanillic and benzoic acids within 2h.     

Aldehyde metabolism and the aroma quality of stored golden delicious apples

Aldehyde production by intact apples was monitored by reversed phase HPLC of headspace concentrates, after reaction with 2,4-dinitrophenylhydrazine. Depending on the degree of maturity and their storage history, Golden Delicious apples showed a variable headspace composition, differences being mostly of a quantitative nature. Whereas the headspace of pre-climacteric fruits was particularly rich in C₁C₆ aldehydes, that of climacteric, ripening apples was greatly reduced, and some aldehydes were only present in trace amounts. Treatment of pre-climacteric or cold stored fruits with carboxylic acid vapours had a negligible effect on the aldehyde composition. Controlled atmospheric storage, however, led to a notable increase in the aldehydes derived from the added carboxylic acids or from those shortened by β-oxidation. This confirms the presence of a reductive path of carboxylic acids into aldehydes. Further results suggest that high carbon dioxide (CA-storage) interferes with carboxylic acid metabolism and alcohol dehydrogenase activity, leading to a deterioration of the aroma quality.     

Substrate specificity,plasma membrane localization,and lipid modification of the aldehyde dehydrogenase ALDH3B1

The accumulation of reactive aldehydes is implicated in the development of several disorders. Aldehyde dehydrogenases (ALDHs) detoxify aldehydes by oxidizing them to the corresponding carboxylic acids. Among the 19 human ALDHs, ALDH3A2 is the only known ALDH that catalyzes the oxidation of long-chain fatty aldehydes including C16 aldehydes (hexadecanal and trans-2-hexadecenal) generated through sphingolipid metabolism. In the present study, we have identified that ALDH3B1 is also active in vitro toward C16 aldehydes and demonstrated that overexpression of ALDH3B1 restores the sphingolipid metabolism in the ALDH3A2-deficient cells. In addition, we have determined that ALDH3B1 is localized in the plasma membrane through its C-terminal dual lipidation (palmitoylation and prenylation) and shown that the prenylation is required particularly for the activity toward hexadecanal. Since knockdown of ALDH3B1 does not cause further impairment of the sphingolipid metabolism in the ALDH3A2-deficient cells, the likely physiological function of ALDH3B1 is to oxidize lipid-derived aldehydes generated in the plasma membrane and not to be involved in the sphingolipid metabolism in the endoplasmic reticulum.     

Chemical Composition of Lipids from Peat-Forming Leafy Mosses of Eutrophic Swamps of Western Siberia and Altai

The molecular composition of lipids in three samples of leafy mosses (Aulacomnium palustre, Warnstorfia fluitans, and Calliergon giganteum) has been determined. The revealed acyclic compounds included normal and isoprenoid alkanes, isoprenoid alkenes, normal and isoprenoid ketones, carboxylic acids and their esters, alcohols, and aldehydes. Among cyclic compounds, bi-, tri- and tetracyclic polycycloaromatic hydrocarbons (PAHs), bicyclic and pentacyclic terpenoids, steroids and tocopherols have been observed. The identified organic compounds consisted mainly of carbocyclic acids and n-alkanes with the prevalence of C₂₇ homologues. A. palustre is characterized by a reduced content of isoprenoid compounds, alcohols, and ketones, while the content of unsaturated acids, pentacyclic terpenoids, and aldehydes is rather heightened. A. palustre differs from W. fluitans and C. giganteum in the steroid composition and contains eremophylene, a sesquiterpenoid, which is absent in the mosses of the family Amblystegiaceae. Compared to C. giganteum, W. fluitans has a higher content of lycopadiene, carboxylic acids, n-alkanes, phyt-2-ene, aldehydes, esters, squalene, diploptene, α-tocopherol, and triphenyl phosphates.     

An Efficient Conversion of Carboxylic Acids to One-Carbon Degraded Aldehydes via 2-Hydroperoxy Acids

After the formation of dianions of a carboxylic acid with lithium diisopropylamide, oxygen was bubbled into the solution to produce 2-hydroperoxy acid. Then the reaction mixture was acidified with a 2 N HCl solution and subsequently elevated to 50 °C to afford the aldehyde with the loss of one carbon atom. Even saturated (C₁₀–C₂₀) and unsaturated (C_18:1) carboxylic acids were converted into the odd aldehydes (C₉–C₁₉, C_17:1) in high yields. This conversion was found to be an efficient method for the preparation of carboxylic acids (Cn) to one-carbon degraded aldehydes (Cn-1) via 2-hydroperoxy acids.     

Properties and tissue distribution of a novel aldo-keto reductase encoding in a rat gene (Akr1b10)

A recent rat genomic sequencing predicts a gene Akr1b10 that encodes a protein with 83% sequence similarity to human aldo-keto reductase (AKR) 1B10. In this study, we isolated the cDNA for the rat AKR1B10 (R1B10) from rat brain, and examined the enzymatic properties of the recombinant protein. R1B10 utilized NADPH as the preferable coenzyme, and reduced various aldehydes (including cytotoxic 4-hydroxy-2-hexenal and 4-hydroxy- and 4-oxo-2-nonenals) and α-dicarbonyl compounds (such as methylglyoxal and 3-deoxyglucosone), showing low K_m values of 0.8-6.1 μM and 3.7-67 μM, respectively. The enzyme also reduced glyceraldehyde and tetroses (K_m = 96-390 μM), although hexoses and pentoses were inactive and poor substrates, respectively. Among the substrates, 4-oxo-2-nonenal was most efficiently reduced into 4-oxo-2-nonenol, and its cytotoxicity against bovine endothelial cells was decreased by the overexpression of R1B10. R1B10 showed low sensitivity to aldose reductase inhibitors, and was activated to approximately two folds by valproic acid, and alicyclic and aromatic carboxylic acids. The mRNA for R1B10 was expressed highly in rat brain and heart, and at low levels in other rat tissues and skin fibroblasts. The results suggest that R1B10 functions as a defense system against oxidative stress and glycation in rat tissues.     

Tetrahydro-1H,5H-pyrazolo[1,2-a]pyrazole-1-carboxylates as inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase

The reactions between 5-substituted pyrazolidine-3-ones, aldehydes, and methyl methacrylate provided tetrahydropyrazolo[1,2-a]pyrazole-1-carboxylates as mixtures of syn- and anti-diastereomers. Testing for inhibition of dihydroorotate dehydrogenase of Plasmodium falciparum (PfDHODH) revealed high activity of some anti-isomers of the methyl esters, while the corresponding carboxylic acids and carboxamides were not active. The most active representative, methyl (1S*,3S*,5R*)-1,5-dimethyl-7-oxo-3-phenyltetrahydro-1H,5H-pyrazolo[1,2-a]pyrazole-1-carboxylate (IC₅₀ = 2.9 ± 0.3 μM), also exhibited very high selectivity of the parasite enzyme vs. the human enzyme, PfDHODH/HsDHODH > 350. According to the molecular docking score, this high activity is explainable by synergic interactions of the methyl, phenyl and the CO₂Me substituent with the hydrophobic pockets in the active site of the enzyme. The carboxylic acid and carboxamides derived from this compound did not inhibit PfDHODH.     

Liquid hydrocarbon fuels obtained by the pyrolysis of soybean oils

The pyrolysis reactions of soybean oils have been studied. The pyrolytic products were analyzed by GC–MS and FTIR and show the formation of olefins, paraffins, carboxylic acids and aldehydes. Several kinds of catalysts were compared. It was found that the amounts of carboxylic acids and aldehydes were significantly decreased by using base catalysts such as Na₂CO₃ and K₂CO₃. The low acid value pyrolytic products showed good cold flow properties and good solubility in diesel oil at low temperature. The results presented in this work have shown that the pyrolysis of soybean oils generates fuels that have chemical composition similar to petroleum based fuels.     

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.     

The carboxylic acid reduction pathway in Nocardia. Purification and characterization of the aldehyde reductase

Whole cultures of Nocardia sp. NRRL 5646 reduce carboxylic acids, first to aldehydes, then to alcohols and subsequently to the corresponding acetyl esters. This work describes an NADPH-dependent reductase responsible for catalyzing the reduction of aldehyde intermediates, which was purified 3240-fold by a combination of Mono-Q, hydroxyapatite, and ADP-agarose chromatographies. By sodium dodecyl sulfate–polyacrylamide gel electrophoresis, the purified enzyme ran as a single band of 47 kDa. A native molecular mass estimated at 101 kDa indicated that the enzyme was a homodimer in the native, active state. Edman degradation indicated a unique N-terminal sequence as NH₂-X-X-Ala-Ala-Ala-Tyr-Ala-Val-Pro-Ala-Pro-Asp-Gly-Cys-Phe-Glu-Lys-Val-Thr-Ile-Glu-Arg-Arg-Glu-Leu-Gly. The enzyme catalyzed reductions of many aryl- and alkyl-aldehyde substrates. Reactions were most favorable in the direction of aldehyde reduction to alcohols. Journal of Industrial Microbiology & Biotechnology (2000) 25, 328–332. Received 08 May 2000/ Accepted in revised form 20 October 2000     

Structural insights into UbiD reversible decarboxylation

The ubiquitous UbiX-UbiD system is associated with a wide range of microbial (de)carboxylation reactions. Recent X-ray crystallographic studies have contributed to elucidating the enigmatic mechanism underpinning the conversion of α,β-unsaturated acids by this system. The UbiD component utilises a unique cofactor, prenylated flavin (prFMN), generated by the bespoke action of the associated UbiX flavin prenyltransferase. Structure determination of a range of UbiX/UbiD representatives has revealed a generic mode of action for both the flavin-to-prFMN metamorphosis and the (de)carboxylation. In contrast to the conserved UbiX, the UbiD superfamily is associated with a versatile substrate range. The latter is reflected in the considerable variety of UbiD quaternary structure, dynamic behaviour and active site architecture. Directed evolution of UbiD enzymes has taken advantage of this apparent malleability to generate new variants supporting in vivo hydrocarbon production. Other applications include coupling UbiD to carboxylic acid reductase to convert alkenes into α,β-unsaturated aldehydes via enzymatic CO₂ fixation.     

Accumulation of l-Glutamic Acid from Dibasic Carboxylic Acids by a Hydrocarbon Utilizing Bacterium

In order to know the substrate specificity in a hydrocarbon utilizing bacterium, the following materials were examined: n-alkanes, n-alkenes, monohydric alcohols, aldehydes, monobasic carboxylic acids, dihydric alcohols and dibasic carboxylic acids.

It was found that dibasic carboxylic acids were well utilized, and a great deal of l-glutamic acid was accumulated from them. Then suberic acid, which is C₈ dibasic carboxylic acid, was compared with n-dodecane in the effects of thiamine, penicillin, C/N ratio and substrate concentration on l-glutamic acid accumulation and cell growth.     

Microbial Oxidation of Hydrocarbons and Related Compounds by Whole-Cell Suspensions of the Methane-Oxidizing Bacterium H-2

Previously, a thermophilic obligate methane-oxidizing bacterium, H-2 (type I), was isolated in our laboratory. H-2 is a new type of methylotroph because of the G+C content of DNA; it uses both the ribulose monophosphate pathway and the serine pathway for carbon assimilation and possesses a new quinone. In addition, we found that resting cell suspensions of H-2 had the ability to oxidize a variety of compounds different from the other methane-oxidizing bacteria as follows. (i) C₁ to C₈n-alkanes are hydroxylated and further oxidized, yielding mixtures of the corresponding alcohols, aldehydes, acids, and ketones. Liquid alkanes are transformed through a different oxidative pathway from that of gaseous ones. (ii) Both gaseous (C₂ to C₄) and liquid (C₅, C₆) n-alkenes are oxidized to their corresponding 1,2-epoxides. (iii) Liquid monochloro and dichloro n-alkanes (C₅, C₆) are oxidized, yielding their corresponding acids or haloacids. (iv) Diethyl ether is oxidized to acetic acid; no ethanol and acetaldehyde are detected. (v) Cyclic and aromatic compounds are also oxidized. (vi) Secondary alcohols (C₃ to C₁₀) are oxidized to their corresponding methyl ketones.     

Identification of the coding region for the putidaredoxin reductase gene from the plasmid of Pseudomonas putida

The first 12 NH₂-terminal amino acids of the Pseudomonas putida putidaredoxin reductase were shown to be Met-Asn-Ala-Asn-Asp-Asn-Val-Val-Ile-Val-Gly-Thr. Comparison of these data with the DNA sequence of the BamHI-HindIII 197-base fragment derived from the PstI 2.2-kb fragment obtained from the P. putida plasmid showed that the putidaredoxin reductase gene was downstream from the cytochrome P-450 gene and the intergenic region had the 24-nucleotide sequence TAAACACATGGGAGTGCGTGCTAA. The Shine-Dalgarno sequence GGAG was detected in this region. The initiating triplet for the reductase gene was GTG, which normally codes for valine, but in the initiating codon position codes for methionine. From the amino acid sequence and X-ray data comparisons with other flavoproteins, what appears to be the AMP binding region of the FAD can be recognized in the NH₂-terminal portion of the reductase involving residues 5–35.