Enzymes of anaerobic metabolism of phenolic compounds. 4-Hydroxybenzoate-CoA ligase from a denitrifying Pseudomonas species

Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications

This review is a survey of bacterial dehalogenases that catalyze the cleavage of halogen substituents from haloaromatics, haloalkanes, haloalcohols, and haloalkanoic acids. Concerning the enzymatic cleavage of the carbon-halogen bond, seven mechanisms of dehalogenation are known, namely, reductive, oxygenolytic, hydrolytic, and thiolytic dehalogenation; intramolecular nucleophilic displacement; dehydrohalogenation; and hydration. Spontaneous dehalogenation reactions may occur as a result of chemical decomposition of unstable primary products of an unassociated enzyme reaction, and fortuitous dehalogenation can result from the action of broad-specificity enzymes converting halogenated analogs of their natural substrate. Reductive dehalogenation either is catalyzed by a specific dehalogenase or may be mediated by free or enzyme-bound transition metal cofactors (porphyrins, corrins). Desulfomonile tiedjei DCB-1 couples energy conservation to a reductive dechlorination reaction. The biochemistry and genetics of oxygenolytic and hydrolytic haloaromatic dehalogenases are discussed. Concerning the haloalkanes, oxygenases, glutathione S-transferases, halidohydrolases, and dehydrohalogenases are involved in the dehalogenation of different haloalkane compounds. The epoxide-forming halohydrin hydrogen halide lyases form a distinct class of dehalogenases. The dehalogenation of alpha-halosubstituted alkanoic acids is catalyzed by halidohydrolases, which, according to their substrate and inhibitor specificity and mode of product formation, are placed into distinct mechanistic groups. beta-Halosubstituted alkanoic acids are dehalogenated by halidohydrolases acting on the coenzyme A ester of the beta-haloalkanoic acid. Microbial systems offer a versatile potential for biotechnological applications. Because of their enantiomer selectivity, some dehalogenases are used as industrial biocatalysts for the synthesis of chiral compounds. The application of dehalogenases or bacterial strains in environmental protection technologies is discussed in detail.

The bacterial degradation of benzoic acid and benzenoid compounds under anaerobic conditions: unifying trends and new perspectives

Simple homocyclic aromatic compounds are extremely abundant in the environment and are derived largely from lignin. Such compounds may enter anaerobic environments and several groups of bacteria, exhibiting diverse energy-yielding mechanisms, have evolved the capacity to overcome the thermodynamic stability of the benzene nucleus and degrade aromatic compounds under these conditions. Over the last few years considerable advances have been made in our understanding of the biochemical strategies underlying the bacterial degradation of aromatic compounds in anoxic environments. The study of the biochemistry, and more recently the molecular genetics of the photosynthetic bacterium Rhodopseudomonas palustris and several strains of denitrifying pseudomonads, has provided the greatest insight into the mechanism and regulation of aromatic degradation under anaerobic conditions. Research has centred around the anaerobic degradation of benzoic acid. This involves the initial activation to form benzoyl-Coenzyme A, reduction of the aromatic nucleus--a reaction that has only recently been demonstrated in vitro--and the subsequent degradation of the alicyclic intermediates. Recently, much information regarding the exact nature of these intermediates has been obtained. Also through recent studies, it has become increasingly clear that benzoyl-CoA is a central metabolic intermediate during the anaerobic degradation of structurally diverse aromatic compounds. The initial metabolism of these compounds involves the formation of a carboxyl group on the aromatic nucleus (if necessary) and the synthesis of the respective Coenzyme A thioester; this results in the direct formation of benzoyl-Coenzyme A rather than benzoate. In many cases of anaerobic aromatic degradation studied in batch culture, aromatic intermediates are transiently excreted into the medium. It is argued that the study of this phenomenon may facilitate the understanding of the regulation and kinetics of the aromatic degradative pathways.

4-Hydroxybenzoate-coenzyme A ligase from Rhodopseudomonas palustris: purification, gene sequence, and role in anaerobic degradation

Anaerobic metabolism of most aromatic acids is initiated by coenzyme A thioester formation. Rhodopseudomonas palustris grows well under anaerobic, phototrophic conditions with many aromatic acids, including benzoate and 4-hydroxybenzoate, as a carbon source. A coenzyme A ligase that reacts with 4-hydroxybenzoate was purified from 4-hydroxybenzoate-grown cells of R. palustris. This enzyme required MgATP, reduced coenzyme A, and 4-hydroxybenzoate, benzoate, or cyclohex-1,4-dienecarboxylate for optimal activity but also used phosphopantetheine, cyclohex-2,5-dienecarboxylate, and 4-fluorobenzoate at lower rates. The 4-hydroxybenzoate-coenzyme A ligase differed in molecular characteristics from a previously described benzoate-coenzyme A ligase from R. palustris, and the two ligases did not cross-react immunologically. The gene encoding the 4-hydroxybenzoate enzyme was cloned and sequenced. The deduced gene product showed about 20% amino acid identity with bacterial coenzyme A ligases involved in aerobic degradation of aromatic acids. An R. palustris mutant carrying a disrupted 4-hydroxybenzoate-coenzyme A ligase gene was unable to grow with 4-hydroxybenzoate under anaerobic conditions, indicating that the enzyme is essential for anaerobic degradation of this compound.

Evidence that phenol phosphorylation to phenylphosphate is the first step in anaerobic phenol metabolism in a denitrifying Pseudomonas sp

Anaerobic phenol degradation has been shown to proceed via carboxylation of phenol to 4-hydroxybenzoate. However, in vitro the carboxylating enzyme was inactive with phenol; only phenylphosphate (phosphoric acid monophenyl ester) was readily carboxylated. We demonstrate in a denitrifying Pseudomonas strain that phenylphosphate is the first detectable product formed from phenol in whole cells and that subsequent phenylphosphate consumption parallels 4-hydroxybenzoate formation. These kinetics are consistent with phosphorylation being the first step in anaerobic phenol degradation. Various cosubstrates failed so far to act as phosphoryl donor for net phosphorylation of phenol in cell extracts. Yet, cells anaerobically grown with phenol contained an enzyme that catalyzed an isotope exchange between [U-14C]phenol and phenylphosphate. This transphosphorylation activity was anaerobically induced by phenol but was stable under aerobic conditions and required Mn2+ and polyethylene glycol. Activity was optimal at pH 5.5 and half-maximal with 0.6 mM Mn2+, 0.2 mM phenylphosphate, and 1 mM phenol. It is proposed that the phenol exchange/transphosphorylation reaction is catalyzed as partial reaction by an inducible phenol phosphorylating enzyme. The isotope exchange demands that a phosphorylated enzyme was formed in the course of the reaction, which might be similar to the phosphotransferase system of sugar transport.

New aerobic benzoate oxidation pathway via benzoyl-coenzyme A and 3-hydroxybenzoyl-coenzyme A in a denitrifying Pseudomonas sp

A denitrifying Pseudomonas sp. is able to oxidize aromatic compounds compounds completely to CO2, both aerobically and anaerobically. It is shown that benzoate is aerobically oxidized by a new degradation pathway via benzoyl-coenzyme A (CoA) and 3-hydroxybenzoyl-CoA. The organism grew aerobically with benzoate, 3-hydroxybenzoate, and gentisate; catechol, 2-hydroxybenzoate, and protocatechuate were not used, and 4-hydroxybenzoate was a poor substrate. Mutants were obtained which were not able to utilize benzoate as the sole carbon source aerobically but still used 3-hydroxybenzoate or gentisate. Simultaneous adaptation experiments with whole cells seemingly suggested a sequential induction of enzymes of a benzoate oxidation pathway via 3-hydroxybenzoate and gentisate. Cells grown aerobically with benzoate contained a benzoate-CoA ligase (AMP forming) (0.1 mumol min-1 mg-1) which converted benzoate but not 3-hydroxybenzoate into its CoA thioester. The enzyme of 130 kDa composed of two identical subunits of 56 kDa was purified and characterized. Cells grown aerobically with 3-hydroxybenzoate contained a similarly active CoA ligase for 3-hydroxybenzoate, 3-hydroxybenzoate-CoA ligase (AMP forming). Extracts from cells grown aerobically with benzoate catalyzed a benzoyl-CoA- and flavin adenine dinucleotide-dependent oxidation of NADPH with a specific activity of at least 25 nmol NADPH oxidized min-1 mg of protein-1; NADH and benzoate were not used. This new enzyme, benzoyl-CoA 3-monooxygenase, was specifically induced during aerobic growth with benzoate and converted [U-14C]benzoyl-CoA stoichiometrically to [14C]3-hydroxybenzoyl-CoA.

Purification and characterization of phenylacetate-coenzyme A ligase from a denitrifying Pseudomonas sp., an enzyme involved in the anaerobic degradation of phenylacetate

The enzyme catalysing the first step in the anaerobic degradation pathway of phenylacetate was purified from a denitrifying Pseudomonas strain KB 740. It catalyses the reaction phenylacetate + CoA + ATP-->phenylacetyl-CoA + AMP + PPi and requires Mg2+. Phenylacetate-CoA ligase (AMP forming) was found in cells grown anaerobically with phenylacetate and nitrate. Maximal specific enzyme activity was 0.048 mumol min-1 x mg-1 protein in the mid-exponential growth phase. After 640-fold purification with 18% yield, a specific activity of 24.4 mumol min-1 mg-1 protein was achieved. The enzyme is a single polypeptide with Mr of 52 +/- 2 kDa. The purified enzyme shows high specificity towards the aromatic inducer substrate phenylacetate and uses ATP preferentially; Mn2+ can substitute for Mg2+. The apparent Km values for phenylacetate, CoA, and ATP are 60, 150, and 290 microM, respectively. The soluble enzyme has an optimum pH of 8.5, is insensitive to oxygen, but is rather labile and requires the presence of glycerol and/or phenylacetate for stabilization. The N-terminal amino acid sequence showed no homology to other reported CoA-ligases. The expression of the enzyme was studied by immunodetection. It is present in cells grown anaerobically with phenylacetate, but not with mandelate, phenylglyoxylate, benzoate; small amounts were detected in cells grown aerobically with phenylacetate.

Enzymes of anaerobic metabolism of phenolic compounds. 4-Hydroxybenzoyl-CoA reductase (dehydroxylating) from a denitrifying Pseudomonas species

The reductive removal of aromatic hydroxyl functions plays an important role in the anaerobic metabolism of many phenolic compounds. We describe a new enzyme from a denitrifying Pseudomonas sp., 4-hydroxybenzoyl-CoA reductase (dehydroxylating), which reductively dehydroxylates 4-hydroxybenzoyl-CoA to benzoyl-CoA. The enzyme plays a role in the anaerobic degradation of phenol, 4-hydroxybenzoate, p-cresol, 4-hydroxyphenylacetate, and other aromatic compounds of which 4-hydroxybenzoyl-CoA is an intermediate. The enzyme is therefore induced only under anoxic conditions with these aromatic substrates, but not with benzoate or under aerobic conditions. A similar enzyme which reductively dehydroxylates 3-hydroxybenzoyl-CoA is induced during anaerobic growth with 3-hydroxybenzoate. The soluble enzyme 4-hydroxybenzoyl-CoA reductase was purified. It has a molecular mass of 260 kDa and consists of three subunits of 75, 35, and 17 kDa. The subunit composition is likely to be a2b2c2. The enzyme contains 12 mol iron/mol and 12 mol acid-labile sulfur/mol and exhibits a typical ultraviolet/visible spectrum of an iron-sulfur protein. The reaction requires a reduced electron donor such as reduced viologen dyes; no other co-catalysts are required, the product is benzoyl-CoA and oxidized dye. The reductase is rapidly inactivated by oxygen. The inactivation by low concentrations of cyanide or azide in a pseudo-first-order time course suggests that it may contain a transition metal in an oxidation state which reacts with these ligands. 4-Hydroxybenzoyl-CoA reductase represents a type of enzyme which is common in anaerobic aromatic metabolism of phenolic compounds. A similar enzyme is demonstrated in Rhodopseudomonas palustris anaerobically grown with 4-hydroxybenzoate. The biological significance of reductive dehydroxylation of aromatics and a possible reaction mechanism similar to the Birch reduction are discussed.