Unusual reactions involved in anaerobic metabolism of phenolic compounds

Aerobic bacteria use molecular oxygen as a common co-substrate for key enzymes of aromatic metabolism. In contrast, in anaerobes all oxygen-dependent reactions are replaced by a set of alternative enzymatic processes. The anaerobic degradation of phenol to a non-aromatic product involves enzymatic processes that are uniquely found in the aromatic metabolism of anaerobic bacteria: (i) ATP-dependent phenol carboxylation to 4-hydroxybenzoate via a phenylphosphate intermediate (biological Kolbe-Schmitt carboxylation); (ii) reductive dehydroxylation of 4-hydroxybenzoyl-CoA to benzoyl-CoA; and (iii) ATP-dependent reductive dearomatization of the key intermediate benzoyl-CoA in a 'Birch-like' reduction mechanism. This review summarizes the results of recent mechanistic studies of the enzymes involved in these three key reactions.     

Key enzymes in the anaerobic aromatic metabolism catalysing Birch-like reductions

Several novel enzyme reactions have recently been discovered in the aromatic metabolism of anaerobic bacteria. Many of these reactions appear to be catalyzed by oxygen-sensitive enzymes by means of highly reactive radical intermediates. This contribution deals with two key reactions in this metabolism: the ATP-driven reductive dearomatisation of the benzene ring and the reductive removal of a phenolic hydroxyl group. The two reactions catalyzed by benzoyl-CoA reductase (BCR) and 4-hydroxybenzoyl-CoA reductase (4-HBCR) are both mechanistically difficult to achieve; both are considered to proceed in 'Birch-like' reductions involving single electron and proton transfer steps to the aromatic ring. The problem of both reactions is the extremely high redox barrier for the first electron transfer to the substrate (e.g., -1.9 V in case of a benzoyl-CoA (BCoA) analogue), which is solved in the two enzymes in different manners. Studying these enzymatic reactions provides insights into general principles of how oxygen-dependent reactions are replaced by alternative processes under anoxic conditions.     

Key enzymes in the anaerobic aromatic metabolism catalysing Birch-like reductions

Several novel enzyme reactions have recently been discovered in the aromatic metabolism of anaerobic bacteria. Many of these reactions appear to be catalyzed by oxygen-sensitive enzymes by means of highly reactive radical intermediates. This contribution deals with two key reactions in this metabolism: the ATP-driven reductive dearomatisation of the benzene ring and the reductive removal of a phenolic hydroxyl group. The two reactions catalyzed by benzoyl-CoA reductase (BCR) and 4-hydroxybenzoyl-CoA reductase (4-HBCR) are both mechanistically difficult to achieve; both are considered to proceed in ‘Birch-like’ reductions involving single electron and proton transfer steps to the aromatic ring. The problem of both reactions is the extremely high redox barrier for the first electron transfer to the substrate (e.g., −1.9 V in case of a benzoyl-CoA (BCoA) analogue), which is solved in the two enzymes in different manners. Studying these enzymatic reactions provides insights into general principles of how oxygen-dependent reactions are replaced by alternative processes under anoxic conditions.     

Basic and applied aspects in the microbial degradation of azo dyes

Azo dyes are the most important group of synthetic colorants. They are generally considered as xenobiotic compounds that are very recalcitrant against biodegradative processes. Nevertheless, during the last few years it has been demonstrated that several microorganisms are able, under certain environmental conditions, to transform azo dyes to non-colored products or even to completely mineralize them. Thus, various lignolytic fungi were shown to decolorize azo dyes using ligninases, manganese peroxidases or laccases. For some model dyes, the degradative pathways have been investigated and a true mineralization to carbon dioxide has been shown. The bacterial metabolism of azo dyes is initiated in most cases by a reductive cleavage of the azo bond, which results in the formation of (usually colorless) amines. These reductive processes have been described for some aerobic bacteria, which can grow with (rather simple) azo compounds. These specifically adapted microorganisms synthesize true azoreductases, which reductively cleave the azo group in the presence of molecular oxygen. Much more common is the reductive cleavage of azo dyes under anaerobic conditions. These reactions usually occur with rather low specific activities but are extremely unspecific with regard to the organisms involved and the dyes converted. In these unspecific anaerobic processes, low-molecular weight redox mediators (e.g. flavins or quinones) which are enzymatically reduced by the cells (or chemically by bulk reductants in the environment) are very often involved. These reduced mediator compounds reduce the azo group in a purely chemical reaction. The (sulfonated) amines that are formed in the course of these reactions may be degraded aerobically. Therefore, several (laboratory-scale) continuous anaerobic/aerobic processes for the treatment of wastewaters containing azo dyes have recently been described.     

NAD(P)H依赖型氧化还原酶不对称还原胺化制备手性胺的研究进展

不对称还原胺化反应是制备医药中间体手性胺结构单元的重要反应。目前已有许多不同种类的酶被应用于合成手性胺,其中NAD(P)H依赖型氧化还原酶催化的还原胺化反应最为引人注目,因为其能够一步将潜手性酮化合物完全转化为光学纯的手性胺化合物。文中以亚胺还原酶、氨基酸脱氢酶、冠瘿碱脱氢酶和还原性酮胺化酶为例,从NAD(P)H依赖型氧化还原酶的结构特征、作用机理、分子改造及催化应用等方面,综述了其在不对称还原胺化合成手性胺领域的研究进展。     

Physiological meaning and potential for application of reductive dechlorination by anaerobic bacteria

Abstract: The physiological meaning of reductive dechlorination reactions catalyzed by anaerobic bacteria can be explained as a co-metabolic activity or as a novel type of respiration. Co-metabolic activities have been found mainly with alkyl halides. They are non-specific reactions catalyzed by various enzyme systems of facultative as well as obligate anaerobic bacteria. In contrast, the reductive dechlorinations involved in metabolic respiration processes are very specific reactions. Only a limited number of alkyl and aryl chlorinated compounds is presently known to function as a terminal electron acceptor in a few, recently isolated bacteria. Metabolic dechlorination rates are in general several orders of magnitude higher than co-metabolic ones. Both reaction types are suitable for the anaerobic treatment of waste streams.     

Ancient genes in contemporary persistent microbial pathogens

Autotrophs, the earliest prokaryotes, use CO(2) as the sole or the key source in the reductive citric acid cycle for carbon fixation. This pathway, also known as the reductive tricarboxylic acid (rTCA) cycle, has as its center the Krebs cycle running in the reductive direction, using reduced cofactors for energy. During the infection process, persistent pathogenic bacteria like Mycobacterium tuberculosis, Helicobacter pylori, and Salmonella typhi experience diverse and hostile environments both intracellularly (in macrophages) and extracellularly. M. tuberculosis, for example, must adapt to nutrient-deprived, hypoxic conditions in the granuloma. Genomic annotations reveal the presence of the key enzymes of the rTCA cycle--citrate lyase (Enzyme Commission number EC 4.1.3.6) and 2-oxoglutarate synthase (EC 1.2.7.3)--along with the rest of the TCA cycle enzymes. It is possible that there is a metabolic switch to anaerobic respiration in which a complete or a partial TCA cycle may operate in the reductive mode. This switch would both facilitate carbon fixation and restore the balance of oxidative and reductive reactions during environmental transitions, thus enabling the pathogen to survive, grow, and persist. Verification of enzyme function by biochemical investigations and validation of gene essentiality by knockout studies may reveal these enzymes to be rational drug targets for treatment of persistent microbial infections in mechanism-based drug discovery processes.     

A theoretical approach to the link between oxidoreductions and pyrite formation in the early stage of evolution

There are two fundamental axioms of surface metabolism theory: (i) pyrite formation from H2S and FeS is proposed as a source of energy for life, and (ii) archaic reductive citric acid cycle is put into the center of a metabolic network. However, the concept fails to indicate how sulfide oxidation ought to be coupled to processes driven by free energy change occurring during pyrite production, and secondly, how reductive citric acid cycle ought to be supplied with row material(s). Recently, the non-enzymatic methylglyoxalase pathway has been recommended as the anaplerotic route for the reductive citric acid cycle. In this paper a mechanism is proposed by which the oxidation of lactate, the essential step of the anaplerotic path, becomes possible and a coupling system between sulfide oxidation and endergonic reaction(s) is also presented. Oxidoreduction for other redox pairs is discussed too. It is concluded that the S(o)/H2S system may have been the clue to energy production at the early stage of evolution, as hydrogen sulfide produced by the metabolic network may have functioned as a coupling molecule between endergonic and exergonic reactions.     

Cloning of a gene encoding choline transport in Saccharomyces cerevisiae.

Sulfur isotope effects during the oxidation of thiosulfate by Thiobacillus versutus were found to be negligible. This result is considered in relation to other oxidative and reductive processes to assess which reactions are most likely to control the isotopic compositions of sulfur compounds in microbial sulfureta.     

Electronically excited state generation during the reaction of p-benzoquinone with H2O2. Relation to product formation: 2-OH- and 2,3-epoxy-p-benzoquinone. The effect of glutathione

The reaction between H2O2 and p-benzoquinone proceeds with consumption of both reactants with second order rate constants of 1.66- and 0.77 M-1S-1, respectively. The process is mainly supported by oxygen addition reactions to the quinone resulting in the formation of both 2,3-epoxy-p-benzoquinone and 2-OH-p-benzoquinone. The former product accumulates in the assay mixture without participating in further reactions. The formation of the latter product implies free radical intermediates such as 2-OH-p-benzosemiquinone anion, which supports the generation of electronically excited states upon its oxidation by H2O2, presumably as part of an organic Fenton reaction. The relaxation of the excited state is accompanied by photoemission at 485-530 nm. Glutathione was found to counteract the oxidative aspects of the reaction between p-benzoquinone and H2O2 by a series of processes involving (a) a rapid reductive addition to the quinone with formation of a substituted p-benzohydroquinone; (b) an effective quenching of photoemission, which might be attributed to the deactivation of the excited state by the p-benzohydroquinone-glutathione adduct, and (c) the decomposition of the formed 2,3-epoxy-p-benzoquinone, also by reductive cleavage of the epoxide ring.     

Biocatalytic ketone reduction—a powerful tool for the production of chiral alcohols—part II: whole-cell reductions

The tricarboxylic acid (TCA) cycle is an energy-producing pathway for aerobic organisms. However, it is widely accepted that the phylogenetic origin of the TCA cycle is the reductive TCA cycle, which is a non-Calvin-type carbon-dioxide-fixing pathway. Most of the enzymes responsible for the oxidative and reductive TCA cycles are common to the two pathways, the difference being the direction in which the reactions operate. Because the reductive TCA cycle operates in an energetically unfavorable direction, some specific mechanisms are required for the reductive TCA-cycle-utilizing organisms. Recently, the molecular mechanism for the “citrate cleavage reaction” and the “reductive carboxylating reaction from 2-oxoglutarate to isocitrate” in Hydrogenobacter thermophilus have been demonstrated. Both of these reactions comprise two distinct consecutive reactions, each catalyzed by two novel enzymes. Sequence analyses of the newly discovered enzymes revealed phylogenetic and functional relationships between other TCA-cycle-related enzymes. The occurrence of novel enzymes involved in the citrate-cleaving reaction seems to be limited to the family Aquificaceae. In contrast, the key enzyme in the reductive carboxylation of 2-oxoglutarate appears to be more widely distributed in extant organisms. The four newly discovered enzymes have a number of potential biotechnological applications.     

A theoretical approach to the link between oxidoreductions and pyrite formation in the early stage of evolution

There are two fundamental axioms of surface metabolism theory: (i) pyrite formation from H₂S and FeS is proposed as a source of energy for life, and (ii) archaic reductive citric acid cycle is put into the center of a metabolic network. However, the concept fails to indicate how sulfide oxidation ought to be coupled to processes driven by free energy change occurring during pyrite production, and secondly, how reductive citric acid cycle ought to be supplied with row material(s). Recently, the non-enzymatic methylglyoxalase pathway has been recommended as the anaplerotic route for the reductive citric acid cycle. In this paper a mechanism is proposed by which the oxidation of lactate, the essential step of the anaplerotic path, becomes possible and a coupling system between sulfide oxidation and endergonic reaction(s) is also presented. Oxidoreduction for other redox pairs is discussed too. It is concluded that the S^o/H₂S system may have been the clue to energy production at the early stage of evolution, as hydrogen sulfide produced by the metabolic network may have functioned as a coupling molecule between endergonic and exergonic reactions.     

Protein-based models offer mechanistic insight into complex nickel metalloenzymes

There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox–neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.     

Bio-reductive dechlorination of 1,1,1-trichloroethane and chloroform using a hydrogen-based membrane biofilm reactor

A H(2)-based, denitrifying and sulfate-reducing membrane biofilm reactor (MBfR) was effective for removing 1,1,1-trichloroethane (TCA) and chloroform (CF) by reductive dechlorination. When either TCA or CF was first added to the MBfR, reductive dechlorination took place immediately and then increased over 3 weeks, suggesting enrichment for TCA- or CF-dechlorinating bacteria. Increasing the H(2) pressure increased the dechlorination rates of TCA or CF, and it also increased the rate of sulfate reduction. Increased sulfate loading allowed more sulfate reduction, and this competed with reductive dechlorination, particularly the second steps. The acceptor flux normalized by effluent concentration can be an efficient indicator to gauge the intrinsic kinetics of the MBfR biofilms for the different reduction reactions. The analysis of normalized rates showed that the kinetics for reductive-dechlorination reactions were slowed by reduced H(2) bio-availability caused by a low H(2) pressure or competition from sulfate reduction.     

H2 consumption during the microbial reductive dehalogenation of chlorinated phenols and tetrachloroethene

Competition for molecular hydrogen exists amonghydrogen-utilizing microorganismsin anoxic environments, and evidence suggeststhat lower hydrogen concentrations areobserved with more energetically favorableelectron-accepting processes. The transferof electrons to organochlorines via reductivedehalogenation reactions plays an importantrole in hydrogen dynamics in impacted systems. Westudied the flux of aqueous hydrogenconcentrations in methanogenic sediment microcosmsprior to and during reductivedehalogenation of a variety of substituted chlorophenols(CP) and tetrachloroethene(perchloroethylene, PCE). Mean hydrogen concentrationsduring reductive dehalogenationof 2,4-CP, 2,3,4-CP, and PCP were 3.6 nM, 4.1 nM,and 0.34 nM, respectively. Sedimentmicrocosms that were not dosed with chlorophenolsyet were actively methanogenicmaintained a significantly higher mean hydrogenconcentration of 9.8 nM. Duringactive PCE dehalogenation, sediment microcosmsmaintained a mean hydrogenconcentration of 0.82 nM. These data indicate thatduring limiting hydrogen production,the threshold ecosystem hydrogen concentration iscontrolled by microbial populationsthat couple hydrogen oxidation to thermodynamicallyfavorable electron acceptingreactions, including reductive dehalogenationof chloroaromatic compounds. Wealso present revised estimates for the Gibbsfree energy available from the reductivedehalogenation of a variety of substitutedchlorophenols based on recently publishedvalues of vapor pressure, solubility, and pKafor these compounds.     

Melanin biosynthesis and the metabolism of flaviolin and 2-hydroxyjuglone inWangiella dermatitidis

Melanin biosynthesis in the human pathogenWangiella dermatitidis was inhibited by tricyclazole, causing pentaketide melanin metabolites to accumulate in the cultures. One of these metabolites, scytalone, was racemic and thus different than the (+)-enantiomer fromVerticillium dahliae. An albino mutant ofW. dermatitidis metabolized scytalone to a pigment ultrastructurally identical to wild-type melanin. Cell-free homogenates of the wild type carried out typical reductive and dehydrative reactions with known melanin intermediates and the reductive reactions were inhibited by tricyclazole. Other reductive and dehydrative reactions that utilize flaviolin and 2-hydroxyjuglone were studied anaerobically with homogenates from both the wild type and the albino mutant. The homogenates converted flaviolin to 5-hydroxyscytalone and products identical to those obtained from 2-hydroxyjuglone. The albino, in culture, carried out the same reactions with 2-hydroxyjuglone but metabolized flaviolin to a number of unknown colored products apparently through oxidative reactions. Similarities between the melanin pathway and the flaviolin and 2-hydroxyjuglone branch pathways are discussed and tricyclazole is shown to inhibit reductive reactions with naphthols in the three pathways.Abbreviations DHN dihydroxynaphtalene - HJ hydroxyjuglone - THT trihydroxytetralone - THN trihydroxynaphthalene or tetrahydroxynaphthalene - DTT dithiothreitol - HS hydroxyscytalone - PHN pentahydroxynaphthalene     

<Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> NADP-malic enzyme isoforms: high degree of identity but clearly distinct properties

The Arabidopsis thaliana genome contains four NADP-malic enzymes genes (NADP-ME1-4). NADP-ME4 is localized to plastids whereas the other isoforms are cytosolic. NADP-ME2 and 4 are constitutively expressed, while NADP-ME1 is restricted to secondary roots and NADP-ME3 to trichomes and pollen. Although the four isoforms share remarkably high degree of identity (75-90%), recombinant NADP-ME1 through 4 show distinct kinetic properties, both in the forward (malate oxidative decarboxylation) and reverse (pyruvate reductive carboxylation) reactions. The four isoforms behave differently in terms of reversibility, with NADP-ME2 presenting the highest reverse catalytic efficiency. When analyzing the activity of each isoform in the presence of metabolic effectors, NADP-ME2 was the most highly regulated isoform, especially in its activation by certain effectors. Several metabolites modulate both the forward and reverse reactions, exhibiting dual effects in some cases. Therefore, pyruvate reductive carboxylation may be relevant in vivo, especially in some cellular compartments and conditions. In order to identify residues or segments of the NADP-ME primary structure that could be involved in the differences among the isoforms, NADP-ME2 mutants and deletions were analysed. The results obtained show that Arg115 is involved in fumarate activation, while the amino-terminal part is critical for aspartate and CoA activation, as well as for the reverse reaction. As a whole, these studies show that minimal changes in the primary structure are responsible for the different kinetic behaviour of each AtNADP-ME isoform. In this way, the co-expression of some isoforms in the same cellular compartment would not imply redundancy but represents specificity of function.     

Properties of D(+)-lysopine dehydrogenase from crown gall tumour tissue.

D(+)-Lysopine dehydrogenase of an octopine-type Crown Gall tumour has been partially purified and a number of kinetic parameters have been determined. D(+)-Lysopine dehydrogenase catalyzes the reductive condensation of pyruvate and one of at least six different L-amino acids, as well as the reverse reactions, with preferential use of NADP(H) as a cofactor. The optimal pH for both reductive and oxidative reactions has been determined. At pH 6.8, L-lysine has of all the amino acids the lowest Km value, while at the same pH the highest V was found with L-arginine and L-histidine. The isoelectric point of D(+)-lysopine dehydrogenase is about 4.5.     

Direct detection of radical generation in rat liver nuclei on treatment with tumour-promoting hydroperoxides and related compounds

EPR spin trapping has been employed to directly detect radical production in isolated rat nuclei on exposure to a variety of hydroperoxides and related compounds which are known, or suspect, tumour promoters. The hydroperoxides, in the absence of reducing equivalents, undergo oxidative cleavage, generating peroxyl radicals. In the presence of NADPH (and to a lesser extent NADH) reductive cleavage of the OO bond generates alkoxyl radicals. These radicals undergo subsequent rearrangements and reactions (dependent on the structure of the alkoxyl radical), generating carbon-centred radicals. Acyl peroxides and peracids appear to undergo only reductive cleavage of the OO bond. With peracids this cleavage can generate aryl carboxyl (RCO₂·) or hydroxyl radicals (HO·); with acyl peroxides, aryl carboxyl radicals are formed and, in the case of t-butyl peroxybenzoate, alkoxyl radicals (RO·). The radicals detected with each peroxide are similar in type to those detected in the rat liver microsomal fraction, although the extent of radical production is lower. The subsequent reactions of the initially generated radicals are similar to those determined in homogenous chemical systems, suggesting that they are in free solution. Experiments with NADPH/NADH, heat denaturation of the nuclei and various inhibitors suggest that radical generation is an enzymatic process catalysed by haemproteins, in particular cytochrome P-450, and that NADPH/cytochrome P-450 reductase is involved in the reductive cleavage of the OO bond. The generation of these radicals by the rat liver nuclear fraction is potentially highly damaging for the cell due to the proximity of the generating source to DNA. Several previous studies have shown that some of the radicals detected in this study, such as aryl carboxyl and aryl radicals, can damage DNA, via various reactions which results in the generation of strand breaks and adducts to DNA bases: these processes are suggested to play an important role in the tumour promoting activity of these hydroperoxides and related compounds.