Bacterial attack on phenolic ethers: An enzyme system demethylating vanillic acid

1. A cell-free system from Pseudomonas fluorescens catalysed the oxidative demethylation and subsequent ring-cleavage of vanillate, with uptake of 2·5 moles of oxygen/mole of substrate. 2. Demethylation involved absorption of 0·5 mole of oxygen/mole, and required reduced glutathione (GSH) and nucleotide (probably NADPH) as cofactors, with further possible requirements, the natures of which are discussed. 3. Incomplete evidence suggested that the aromatic ring was opened via protocatechuate and the appropriate oxygenase, with absorption of 1 mole of oxygen/mole of substrate, eventually yielding β-oxoadipate. 4. The methyl group was removed sequentially as formaldehyde, formate and carbon dioxide, the steps catalysed respectively by formaldehyde dehydrogenase, which required GSH and NAD⁺, and formate dehydrogenase. Each enzyme was cytochrome-linked and accounted for absorption of 0·5mole of oxygen/mole of substrate. 5. All enzymes except formate dehydrogenase, which was a cell-wall enzyme, resided in the soluble fraction of the extract. The demethylase could not be resolved because of unknown cofactor requirements.     

A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6

Vanillate and syringate are converted into protocatechuate (PCA) and 3-O-methylgallate (3MGA), respectively, by O-demethylases in Sphingomonas paucimobilis SYK-6. PCA is further degraded via the PCA 4,5-cleavage pathway, while 3MGA is degraded through multiple pathways in which PCA 4,5-dioxygenase (LigAB), 3MGA 3,4-dioxygenase (DesZ), and an unidentified 3MGA O-demethylase and gallate dioxygenase are participants. For this study, we isolated a 4.7-kb SmaI fragment that conferred on Escherichia coli the activity required for the conversion of vanillate to PCA. The nucleotide sequence of this fragment revealed an open reading frame of 1,413 bp (ligM), the deduced amino acid sequence of which showed 49% identity with that of the tetrahydrofolate (H4folate)-dependent syringate O-demethylase gene (desA). The metF and ligH genes, which are thought to be involved in H4folate-mediated C1 metabolism, were located just downstream of ligM. The crude LigM enzyme expressed in E. coli converted vanillate and 3MGA to PCA and gallate, respectively, with similar specific activities, and only in the presence of H4folate; however, syringate was not a substrate for LigM. The disruption of ligM led to significant growth retardation on both vanillate and syringate, indicating that ligM is involved in the catabolism of these substrates. The ability of the ligM mutant to transform vanillate was markedly decreased, and this mutant completely lost the 3MGA O-demethylase activity. A ligM desA double mutant completely lost the ability to transform vanillate, thus indicating that desA also contributes to vanillate degradation. All of these results indicate that ligM encodes vanillate/3MGA O-demethylase and plays an important role in the O demethylation of vanillate and 3MGA, respectively.     

Degradation of methoxylated aromatic acids by Pseudomonas putida

J.E. TURNER AND N. ALLISON. 1995. A newly-isolated strain of Pseudomonas putida (HVA-1) utilized homovanillic acid as sole carbon and energy source. Homovanillate-grown bacteria oxidized homovanillate and homoprotocatechuate but monohydroxylated and other methoxylated phenylacetic acids were oxidized poorly; methoxy-substituted benzoates were not oxidized. Extracts of homovanillate-grown cells contained homoprotocatechuate 2,3-dioxygenase but the primary homovanillate-degrading enzyme could not be detected. No other methoxylated phenylacetic acid supported growth of the organism but vanillate was utilized as a carbon and energy source. When homovanillate-grown cells were used to inoculate media containing vanillate a 26 h lag period occurred before growth commenced. Vanillate-grown bacteria oxidized vanillate and protocatechuate but no significant oxygen uptake was obtained with homovanillate and other phenylacetic acid derivatives. Analysis of pathway intermediates revealed that homovanillate-grown bacteria produced homoprotocatechuate, formaldehyde and the ring-cleavage product 5-carboxymethyl 2-hydroxymuconic semialdehyde (CHMS) when incubated with homovanillate but monohydroxylated or monomethoxylated phenylacetic acids were not detected. These results suggest that homovanillate is degraded directly to the ring-cleavage substrate homoprotocatechuate by an unstable but highly specific demethylase and then undergoes extradiol cleavage to CHMS. It would also appear that the uptake/degradatory pathways for homovanillate and vanillate in this organism are entirely separate and independently controlled. If stabilization of the homovanillate demethylase can be achieved, there is potential for exploiting the substrate specificity of this enzyme in both medical diagnosis and in the paper industry.     

Vanillin catabolism in Rhodococcus jostii RHA1

Genes encoding vanillin dehydrogenase (vdh) and vanillate O-demethylase (vanAB) were identified in Rhodococcus jostii RHA1 using gene disruption and enzyme activities. During growth on vanillin or vanillate, vanA was highly upregulated while vdh was not. This study contributes to our understanding of lignin degradation by RHA1 and other actinomycetes.     

Characterization of the 5-carboxyvanillate decarboxylase gene and its role in lignin-related biphenyl catabolism in Sphingomonas paucimobilis SYK-6

Sphingomonas paucimobilis SYK-6 degrades a lignin-related biphenyl compound, 5,5'-dehydrodivanillate (DDVA), to 5-carboxyvanillate (5CVA) by the enzyme reactions catalyzed by the DDVA O-demethylase (LigX), the ring cleavage oxygenase (LigZ), and the meta-cleavage compound hydrolase (LigY). In this study we examined the degradation step of 5CVA. 5CVA was transformed to vanillate, O-demethylated, and further degraded via the protocatechuate 4,5-cleavage pathway by this strain. A cosmid clone which conferred the 5CVA degradation activity to a host strain was isolated. In the 7.0-kb EcoRI fragment of the cosmid we found a 1,002-bp open reading frame responsible for the conversion of 5CVA to vanillate, and we designated it ligW. The gene product of ligW (LigW) catalyzed the decarboxylation of 5CVA to produce vanillate along with the specific incorporation of deuterium from deuterium oxide, indicating that LigW is a nonoxidative decarboxylase of 5CVA. LigW did not require any metal ions or cofactors for its activity. The decarboxylase activity was specific to 5CVA. Inhibition experiments with 5CVA analogs suggested that two carboxyl groups oriented meta to each other in 5CVA are important to the substrate recognition by LigW. Gene walking analysis indicated that the ligW gene was located on the 18-kb DNA region with other DDVA catabolic genes, including ligZ, ligY, and ligX.     

Bacterial degradation of p-methoxybenzoic acid

Summary A cell-free system from a Pseudomonas sp., strain PM3, catalysed the oxidative demethylation, hydroxylation and subsequent ring cleavage of p-methoxybenzoate. Demethylation, to yield p-hydroxybenzoate, involved absorption of 1.0 mole of oxygen/mole of p-methoxybenzoate, and required reduced pyridine nucleotide (either NADH or NADPH) as cofactor. p-Hydroxybenzoate was hydroxylated to yield protocatechuate with the absorption of 1 mole of oxygen/mole of substrate, and required NADPH as cofactor. Protocatechuate was oxidized, with absorption of 1 mole of oxygen/mole of substrate, to 3-oxoadipate. The methyl group of p-methoxybenzoate was removed as formaldehyde, and oxidized to formate and carbon dioxide by formaldehyde dehydrogenase, which required GSH and NAD⁺, and formate dehydrogenase, which required NAD⁺.     

Regulation of the utilization of 4-hydroxybenzoate and vanillate in batch and continuous cultures of Pseudomonas acidovorans

In Pseudomonas acidovorans, the pathways of 4-hydroxybenzoate and vanillate metabolism converge on the early intermediate, protocatechuate, which undergoes meta-cleavage. The methoxyl group of vanillate is almost completely oxidized, as shown by an experiment with (¹⁴C-methoxyl) vanillate. In batch cultures, 4-hydroxybenzoate and vanillate are simultaneously oxidized. Simultaneous oxidation was explained above all by the fact that both substrates mutually repress the ability of the cells to utilize the partner substrate.If P. acidovorans is growing in a turbidostat on one of the two substrates and is suddenly exposed to an equimolar mixture of both substrates, the respiration rates for the two substrates reciprocate, the for the substrate utilized first passing through a transient minimum, that for the added substrate passing through a transient maximum. Finally, a balance appears to be established, the for 4-hydroxybenzoate being slightly above that for vanillate. Transient phenomena also occur if a chemostat culture with both substrates is suddenly operated as a turbidostat culture or if cells not adapted to either substrate are suddenly exposed to a mixture of both substrates in the turbidostat.If a chemostat culture of P. acidovorans, growing at the expense of an equimolar mixture of 4-hydroxybenzoate and vanillate, is operated under conditions of increasing oxygen deficiency, the utilization ratio of the two substrates increases in favour of 4-hydroxybenzoate. However, if the culture is operated under conditions of increasing nitrogen deficiency, the utilization ratio increases in favour of vanillate.Abbreviations 4HB 4-hydroxybenzoate - VA vanillate - OD optical density     

High-performance liquid chromatography determination of N- and O-demethylase activities of chemicals in human liver microsomes: application of postcolumn fluorescence derivatization using Nash reagent

Formaldehyde is liberated in the process of cytochrome P450 (CYP) mediated demethylation of a wide variety of compounds containing the CH(3)N or CH(3)O functionality. A highly sensitive method using a high-performance liquid chromatography (HPLC) system with postcolumn derivatization was developed to measure the liberated formaldehyde as N- and O-demethylase activity of drugs in human liver microsomes. Following the chromatographic separation of formaldehyde on a C18 column, the formaldehyde was reacted with the Nash reagent in the postcolumn reactor at 100 degrees C and detected by the fluorescence method. The results showed that the present method has excellent precision and accuracy. The intra- and interassay variances of this method were less than 10%. The newly developed HPLC method was found to be about 80-fold more sensitive than the colorimetric method in detection of formaldehyde. The N-demethylase activity of sertraline in rat liver microsomes determined by the present method did not differ from those detected by previous methods quantifying produced desmethyl metabolite. The present method has been successfully applied to determine the N-demethylase activities of several drugs, including aminopyrine, erythromycin, fluoxetine, S-mephenytoin, and sertraline, in human liver microsomes. This assay should be useful for generic analysis of N- and O-demethylase activities of xenobiotic and endobiotic chemicals by CYP enzymes.     

Isolation and characterization of a veratrol:corrinoid protein methyl transferase from Acetobacterium dehalogenans

From 3-methoxyphenol-grown cells of Acetobacterium dehalogenans, an inducible enzyme was purified that mediated the transfer of the methyl groups of veratrol (1,2-dimethoxybenzene) to a corrinoid protein enriched from the same cells. In this reaction, veratrol was converted via 2-methoxyphenol to 1,2-dihydroxybenzene. The veratrol:corrinoid protein methyl transferase, designated MTIver, had an apparent molecular mass of about 32 kDa. With respect to the N-terminal amino acid sequence and other characteristics, MTIver is different from the vanillate:corrinoid protein methyl transferase (MTIvan) isolated earlier from the same bacterium. For the methyl transfer from veratrol to tetrahydrofolate, two additional protein fractions were required, one of which contained a corrinoid protein. This protein was not identical with the corrinoid protein of the vanillate O-demethylase system. However, the latter corrinoid protein could also serve as methyl acceptor for the veratrol:corrinoid protein methyl transferase. MTIver catalyzed the demethylation of veratrol, 3,4-dimethoxybenzoate, 2-methoxyphenol, and 3-methoxyphenol. Vanillate (3-methoxy-4-hydroxybenzoate), 2-methoxybenzoate, or 4-methoxybenzoate could not serve as substrates.     

Crystal structure of the outer membrane protein OpdK from Pseudomonas aeruginosa

In Gram-negative bacteria that do not have porins, most water-soluble and small molecules are taken up by substrate-specific channels belonging to the OprD family. We report here the X-ray crystal structure of OpdK, an OprD family member implicated in the uptake of vanillate and related small aromatic acids. The OpdK structure reveals a monomeric, 18-stranded beta barrel with a kidney-shaped central pore. The OpdK pore constriction is relatively wide for a substrate-specific channel (approximately 8 A diameter), and it is lined by a positively charged patch of arginine residues on one side and an electronegative pocket on the opposite side-features likely to be important for substrate selection. Single-channel electrical recordings of OpdK show binding of vanillate to the channel, and they suggest that OpdK forms labile trimers in the outer membrane. Comparison of the OpdK structure with that of Pseudomonas aeruginosa OprD provides the first qualitative insights into the different substrate specificities of these closely related channels.     

Aerobic and Anaerobic Catabolism of Vanillic Acid and Some Other Methoxy-Aromatic Compounds by Pseudomonas sp. Strain PN-1

Vanillic acid (4-hydroxy-3-methoxybenzoic acid) supported the anaerobic (nitrate respiration) but not the aerobic growth of Pseudomonas sp. strain PN-1. Cells grown anaerobically on vanillate oxidized vanillate, p-hydroxybenzoate, and protocatechuic acid (3,4-dihydroxybenzoic acid) with O₂ or nitrate. Veratric acid (3,4-dimethoxybenzoic acid) but not isovanillic acid (3-hydroxy-4-methoxybenzoic acid) induced cells for the oxic and anoxic utilization of vanillate, and protocatechuate was detected as an intermediate of vanillate breakdown under either condition. Aerobic catabolism of protocatechuate proceeded via 4,5-meta cleavage, whereas anaerobically it was probably dehydroxylated to benzoic acid. Formaldehyde was identified as a product of aerobic demethylation, indicating a monooxygenase mechanism, but was not detected during anaerobic demethylation. The aerobic and anaerobic systems had similar but not identical substrate specificities. Both utilized m-anisic acid (3-methoxybenzoic acid) and veratrate but not o- or p-anisate and isovanillate. Syringic acid (4-hydroxy-3,5-dimethoxybenzoic acid), 3-O-methylgallic acid (3-methoxy-4,5-dihydroxybenzoic acid), and 3,5-dimethoxybenzoic acid were attacked under either condition, and formaldehyde was liberated from these substrates in the presence of O₂. The anaerobic demethylating system but not the aerobic enzyme was also active upon guaiacol (2-methoxyphenol), ferulic acid (3-[4-hydroxy-3-methoxyphenyl]-2-propenoic acid), 3,4,5-trimethoxycinnamic acid (3-[3,4,5-trimethoxyphenyl]-2-propenoic acid), and 3,4,5-trimethoxybenzoic acid. The broad specificity of the anaerobic demethylation system suggests that it probably is significant in the degradation of lignoaromatic molecules in anaerobic environments.     

Anaerobic c(1) metabolism of the o-methyl-C-labeled substituent of vanillate

The O-methyl substituents of aromatic compounds constitute a C(1) growth substrate for a number of taxonomically diverse anaerobic acetogens. In this study, strain TH-001, an O-demethylating obligate anaerobe, was chosen to represent this physiological group, and the carbon flow when cells were grown on O-methyl substituents as a C(1) substrate was determined by C radiotracer techniques. O-[methyl-C]vanillate (4-hydroxy-3-methoxy-benzoate) was used as the labeled C(1) substrate. The data showed that for every O-methyl carbon converted to [C]acetate, two were oxidized to CO(2). Quantitation of the carbon recovered in the two products, acetate and CO(2), indicated that acetate was formed in part by the fixation of unlabeled CO(2). The specific activity of C in acetate was 70% of that in the O-methyl substrate, suggesting that only one carbon of acetate was derived from the O-methyl group. Thus, it is postulated that the carboxyl carbon of the product acetate is derived from CO(2) and the methyl carbon is derived from the O-methyl substituent of vanillate. The metabolism of O-[methyl-C]vanillate by strain TH-001 can be described as follows: 3CH(3)OC(7)H(5)O(3) + CO(2) + 4H(2)O --> CH(3)COOH + 2CO(2) + 10H + 10e + 3HOC(7)H(5)O(3).     

Vanillate Metabolism in Corynebacterium glutamicum

Corynebacterium glutamicum, a Gram-positive soil bacterium belonging to the mycolic acids-containing actinomycetes, is able to use the lignin degradation products ferulate, vanillate, and protocatechuate as sole carbon sources. The gene cluster responsible for vanillate catabolism was identified and characterized. The vanAB genes encoding vanillate demethylase are organized in an operon together with the vanK gene, coding for a transport system most likely responsible for protocatechuate uptake. While gene disruption mutagenesis revealed that vanillate demethylase is indispensable for ferulate and vanillate utilization, a vanK mutation does not lead to a complete growth arrest but to a decreased growth rate on protocatechuate, indicating that one or more additional protocatechuate transporter(s) are present in C. glutamicum.     

Microbial degradation of piperonylic acid

Several organisms were isolated for their ability to utilize piperonylate as a sole carbon source for growth and aPseudomonas species (Ps. PP-2) was selected for a study of the degradation of this substrate. Only vanillate, isovanillate,p-hydroxybenzoate and protocatechuate, of several possible catabolities, served as growth and oxidation substrates for the organism. Detailed analysis of the culture fluid from piperonylate-grown cells revealed the presence of vanillate and protocatechuate but isovanillate,p-hydroxybenzoate andm-hydroxybenzoate were not detected. The evidence presented suggests that piperonylate is metabolized first to vanillate by methylenedioxy ring cleavage and next to protocatechuate by direct demethylation of vanillate.     

Role of the novel OprD family of porins in nutrient uptake in Pseudomonas aeruginosa

To circumvent the permeability barrier of its outer membrane, Pseudomonas aeruginosa has evolved a series of specific porins. These channels have binding sites for related classes of molecules that facilitate uptake under nutrient-limited conditions. Here, we report on the identification of a 19-member family of porins similar to the basic-amino-acid-specific porin OprD. The members of this family fell into one of two phylogenetically distinct clusters, one bearing high similarity to OprD and the other bearing most similarity to the putative phenylacetic acid uptake porin PhaK of Pseudomonas putida. Analysis of the genome context, operon arrangement, and regulation of the PhaK-like porin OpdK indicated that it might be involved in vanillate uptake. This result was confirmed by demonstrating that an opdK mutant had a deficiency in the ability to grow on vanillate as a carbon source. To extrapolate these data to other paralogues within this family, the substrate specificities of 6 of the 17 remaining OprD homologues were inferred using an approach similar to that used with opdK. The specificities determined were as follows: OpdP, glycine-glutamate; OpdC, histidine; OpdB, proline; OpdT, tyrosine; OpdH, cis-aconitate; and OpdO, pyroglutamate. Thus, members of the OprD subfamily took up amino acids and related molecules, and those characterized members most similar to PhaK were responsible for the uptake of a diverse array of organic acids. These results imply that there is a functional basis for the phylogenetic clustering of these proteins and provide a framework for studying OprD homologues in other organisms.     

Molecular dynamics simulation study of the vanillate transport channel of Opdk

Most water-soluble and small molecules are taken up by substrate-specific channels belonging to the Gram-negative bacteria. The protein named OpdK, a member of OprD family, plays an important role in transporting the vanillate as the only carbon source of Pseudomonas aeruginosa. P. aeruginosa infections can be serious due to the high intrinsic antibiotic resistance owing to the present of the OprD family. We applied standard molecular dynamics, steered molecular dynamics and umbrella sampling, to investigate the thermodynamics of vanillate passing through the pore of OpdK protein at physiological temperature. The results indicate that hydrogen bonds of vanillate-L3 (L3: Gly92-Gln111) and hydrophobic interactions of vanillate-L7 (Gly252-Asn278) are crucial to the transport of vanillate. Compared to L7, L3 can hardly change the shape of the pore, but its amino acids can effectively affect the transport process. The important role of charged residues in the barrel of the protein for the substrate transport has been proved in the experiment researches and our simulations also determinate that these residues may prevent the vanillate from entering the cell. These results provide detailed information that will facilitate the development of effective drugs.     

Metabolism of a proline analogue, l-thiazolidine-4-carboxylic acid, by Escherichia coli

Unger, Leon (University of Illinois, Urbana), and R. D. DeMoss. Metabolism of a proline analogue, l-thiazolidine-4-carboxylic acid, by Escherichia coli. J. Bacteriol. 91:1564-1569. 1966.-Resting cells of Escherichia coli K-12, pregrown in a proline- and thioproline-free medium, oxidize the proline analogue, l-thiazolidine-4-carboxylic acid (l-thioproline), without a lag with the consumption of 1 atom of oxygen per mole of thioproline. The organism also oxidizes cysteine and formaldehyde, the chemical precursors of thioproline. The total oxygen consumed is the same whether the substrate is thioproline, cysteine, formaldehyde, or an equimolar mixture of cysteine and formaldehyde. The results suggest that neither cysteine nor formaldehyde are free intermediates in the oxidative pathway. Thioproline is available as a metabolic carbon source for the synthesis of the ribonucleic acid bases, guanine and uracil.     

Energetics of mixotrophic and autotrophic C1-metabolism by Thiobacillus acidophilus

Although the facultatively autotrophic acidophile Thiobacillus acidophilus is unable to grow on formate and formaldehyde in batch cultures, cells from glucose-limited chemostat cultures exhibited substrate-dependent oxygen uptake with these C₁-compounds. Oxidation of formate and formaldehyde was uncoupler-sensitive, suggesting that active transport was involved in the metabolism of these compounds. Formate- and formaldehyde-dependent oxygen uptake was strongly inhibited at substrate concentrations above 150 and 400 M, respectively. However, autotrophic formate-limited chemostat cultures were obtained by carefully increasing the formate to glucose ratio in the reservoir medium of mixotrophic chemostat cultures. The molar growth yield on formate (Y=2.5 g ·mol^-1 at a dilution rate of 0.05 h^-1) and RuBPCase activities in cell-free extracts suggested that T. acidophilus employs the Calvin cycle for carbon assimilation during growth on formate. T. acidophilus was unable to utilize the C₁-compounds methanol and methylamine. Formate-dependent oxygen uptake was expressed constitutively under a variety of growth conditions. Cell-free extracts contained both dye-linked and NAD-dependent formate dehydrogenase activities. NAD-dependent oxidation of formaldehyde required reduced glutathione. In addition, cell-free extracts contained a dye-linked formaldehyde dehydrogenase activity. Mixotrophic growth yields were higher than the sum of the heterotrophic and autotrophic yields. A quantitative analysis of the mixotrophic growth studies revealed that formaldehyde was a more effective energy source than formate.