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Benzoyl-CoA

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Georg Fuchs – One of the best experts on this subject based on the ideXlab platform.

  • Microbial degradation of aromatic compounds — from one strategy to four
    Nature Reviews Microbiology, 2011
    Co-Authors: Georg Fuchs, Matthias Boll, Johann Heider

    Abstract:

    Until recently, it was though that the microbial degradation of aromatic compounds was absolutely dependent on the use of molecular oxygen for ring cleavage. However, as described here by Fuchs and colleagues, microorganisms have other ways of breaking down these compounds when oxygen is scarce or absent. Aromatic compounds are common growth substrates for microorganisms and are also prominent environmental pollutants. The crucial step in their degradation is to overcome the huge resonance energy that stabilizes the aromatic ring. The microbial degradation of aromatic compounds includes a great variety of mechanisms and chemical reactions, some of which have only rare counterparts in organic chemistry. The classical strategy for aromatic-ring cleavage, which is restricted to aerobic organisms, comprises an attack by oxygenases that hydroxylate and finally cleave the ring with the help of activated molecular oxygen (O_2). However, three additional strategies exist that are based on completely different ring activation mechanisms and use CoA thioesters and ring cleavage by hydrolysis. The first strategy depends on the presence of O_2 and uses monooxygenases of the class I di-iron protein family. These enzymes are epoxidases that form non-aromatic ring-epoxides of Benzoyl-CoA and phenylacetyl-CoA, compounds that are further metabolized by ring hydrolysis. The other two strategies are O_2 independent, involve the reduction of the aromatic ring and, under anoxic conditions, convert most aromatic substrates into Benzoyl-CoA as a central intermediate. One of the O_2-independent strategies for aromatic-ring cleavage is used by facultative anaerobic bacteria when they are growing phototrophically or during anaerobic respiration. In these circumstances, these bacteria reduce Benzoyl-CoA by an ATP-driven Benzoyl-CoA reductase that hydrolyses two molecules of ATP. By contrast, during low-energy-yield anaerobic respiration or fermentation, strictly anaerobic bacteria use a different class of Benzoyl-CoA reductase that is ATP independent. The low redox potential that is required for Benzoyl-CoA reduction is probably achieved by a process called electron bifurcation. Electrons from two reduced ferredoxins are split via a flavin cofactor into low- and high-redox-potential electrons. Low-redox-potential electrons may reduce the aromatic ring, whereas high-redox-potential electrons may reduce NAD^+. Aromatic compounds are both common growth substrates for microorganisms and prominent environmental pollutants. The crucial step in their degradation is overcoming the resonance energy that stabilizes the ring structure. The classical strategy for degradation comprises an attack by oxygenases that hydroxylate and finally cleave the ring with the help of activated molecular oxygen. Here, we describe three alternative strategies used by microorganisms to degrade aromatic compounds. All three of these methods involve the use of CoA thioesters and ring cleavage by hydrolysis. However, these strategies are based on different ring activation mechanisms that consist of either formation of a non-aromatic ring-epoxide under oxic conditions, or reduction of the aromatic ring under anoxic conditions using one of two completely different systems.

  • Structure and Mechanism of the Diiron Benzoyl-Coenzyme A Epoxidase BoxB.
    Journal of Biological Chemistry, 2011
    Co-Authors: Liv J. Rather, Georg Fuchs, Wael Ismail, Tobias Weinert, Ulrike Demmer, Eckhard Bill, Ulrich Ermler

    Abstract:

    The coenzyme A (CoA)-dependent aerobic benzoate metabolic pathway uses an unprecedented chemical strategy to overcome the high aromatic resonance energy by forming the non-aromatic 2,3-epoxyBenzoyl-CoA. The crucial dearomatizing reaction is catalyzed by three enzymes, BoxABC, where BoxA is an NADPH-dependent reductase, BoxB is a Benzoyl-CoA 2,3-epoxidase, and BoxC is an epoxide ring hydrolase. We characterized the key enzyme BoxB from Azoarcus evansii by structural and Mossbauer spectroscopic methods as a new member of class I diiron enzymes. Several family members were structurally studied with respect to the diiron center architecture, but no structure of an intact diiron enzyme with its natural substrate has been reported. X-ray structures between 1.9 and 2.5 A resolution were determined for BoxB in the diferric state and with bound substrate Benzoyl-CoA in the reduced state. The substrate-bound reduced state is distinguished from the diferric state by increased iron-ligand distances and the absence of directly bridging groups between them. The position of Benzoyl-CoA inside a 20 A long channel and the position of the phenyl ring relative to the diiron center are accurately defined. The C2 and C3 atoms of the phenyl ring are closer to one of the irons. Therefore, one oxygen of activated O(2) must be ligated predominantly to this proximate iron to be in a geometrically suitable position to attack the phenyl ring. Consistent with the observed iron/phenyl geometry, BoxB stereoselectively should form the 2S,3R-epoxide. We postulate a reaction cycle that allows a charge delocalization because of the phenyl ring and the electron-withdrawing CoA thioester.

  • Coenzyme A-dependent Aerobic Metabolism of Benzoate via Epoxide Formation
    Journal of Biological Chemistry, 2010
    Co-Authors: Liv J. Rather, Bettina Knapp, Wolfgang Haehnel, Georg Fuchs

    Abstract:

    In the aerobic metabolism of aromatic substrates, oxygenases use molecular oxygen to hydroxylate and finally cleave the aromatic ring. In the case of the common intermediate benzoate, the ring cleavage substrates are either catechol (in bacteria) or 3,4-dihydroxybenzoate (protocatechuate, mainly in fungi). We have shown before that many bacteria, e.g. Azoarcus evansii, the organism studied here, use a completely different mechanism. This elaborate pathway requires formation of Benzoyl-CoA, followed by an oxygenase reaction and a nonoxygenolytic ring cleavage. Benzoyl-CoA transformation is catalyzed by the iron-containing Benzoyl-CoA oxygenase (BoxB) in conjunction with an FAD and iron-sulfur centers containing reductase (BoxA), which donates electrons from NADPH. Here we show that Benzoyl-CoA oxygenase actually does not form the 2,3-dihydrodiol of Benzoyl-CoA, as formerly postulated, but the 2,3-epoxide. An enoyl-CoA hydratase (BoxC) uses two molecules of water to first hydrolytically open the ring of 2,3-epoxyBenzoyl-CoA, which may proceed via its tautomeric seven-membered oxepin ring form. Then ring C2 is hydrolyzed off as formic acid, yielding 3,4-dehydroadipyl-CoA semialdehyde. The semialdehyde is oxidized by a NADP(+)-dependent aldehyde dehydrogenase (BoxD) to 3,4-dehydroadipyl-CoA. Final products of the pathway are formic acid, acetyl-CoA, and succinyl-CoA. This overlooked pathway occurs in 4-5% of all bacteria whose genomes have been sequenced and represents an elegant strategy to cope with the high resonance energy of aromatic substrates by forming a nonaromatic epoxide.

Matthias Boll – One of the best experts on this subject based on the ideXlab platform.

  • An Aerobic Hybrid Phthalate Degradation Pathway via Phthaloyl-Coenzyme A in Denitrifying Bacteria
    Applied and Environmental Microbiology, 2020
    Co-Authors: Christa Ebenau-jehle, Christina I. S. L. Soon, Jonathan Fuchs, Robin Geiger, Matthias Boll

    Abstract:

    ABSTRACT The degradation of the xenobiotic phthalic acid esters by microorganisms is initiated by the hydrolysis to the respective alcohols and ortho-phthalate (hereafter, phthalate). In aerobic bacteria and fungi, oxygenases are involved in the conversion of phthalate to protocatechuate, the substrate for ring-cleaving dioxygenases. In contrast, anaerobic bacteria activate phthalate to the extremely unstable phthaloyl-coenzyme A (CoA), which is decarboxylated by oxygen-sensitive UbiD-like phthaloyl-CoA decarboxylase (PCD) to the central Benzoyl-CoA intermediate. Here, we demonstrate that the facultatively anaerobic, denitrifying Thauera chlorobenzoica 3CB-1 and Aromatoleum evansii KB740 strains use phthalate as a growth substrate under aerobic and denitrifying conditions. In vitro assays with extracts from cells grown aerobically with phthalate demonstrated the succinyl-CoA-dependent activation of phthalate followed by decarboxylation to Benzoyl-CoA. In T. chlorobenzoica 3CB-1, we identified PCD as a highly abundant enzyme in both aerobically and anaerobically grown cells, whereas genes for phthalate dioxygenases are missing in the genome. PCD was highly enriched from aerobically grown T. chlorobenzoica cells and was identified as an identical enzyme produced under denitrifying conditions. These results indicate that the initial steps of aerobic phthalate degradation in denitrifying bacteria are accomplished by the anaerobic enzyme inventory, whereas the Benzoyl-CoA oxygenase-dependent pathway is used for further conversion to central intermediates. Such a hybrid pathway requires intracellular oxygen homeostasis at concentrations low enough to prevent PCD inactivation but sufficiently high to supply Benzoyl-CoA oxygenase with its cosubstrate. IMPORTANCE Phthalic acid esters (PAEs) are industrially produced on a million-ton scale per year and are predominantly used as plasticizers. They are classified as environmentally relevant xenobiotics with a number of adverse health effects, including endocrine-disrupting activity. Biodegradation by microorganisms is considered the most effective process to eliminate PAEs from the environment. It is usually initiated by the hydrolysis of PAEs to alcohols and o-phthalic acid. Degradation of o-phthalic acid fundamentally differs in aerobic and anaerobic microorganisms; aerobic phthalate degradation heavily depends on dioxygenase-dependent reactions, whereas anaerobic degradation employs the oxygen-sensitive key enzyme phthaloyl-CoA decarboxylase. We demonstrate that aerobic phthalate degradation in facultatively anaerobic bacteria proceeds via a previously unknown hybrid degradation pathway involving oxygen-sensitive and oxygen-dependent key enzymes. Such a strategy is essential for facultatively anaerobic bacteria that frequently switch between oxic and anoxic environments.

  • Breaking Benzene Aromaticity-Computational Insights into the Mechanism of the Tungsten-Containing Benzoyl-CoA Reductase.
    Journal of the American Chemical Society, 2017
    Co-Authors: Martin Culka, Matthias Boll, Simona G Huwiler, G. Matthias Ullmann

    Abstract:

    Aromatic compounds are environmental pollutants with toxic and carcinogenic properties. Despite the stability of aromatic rings, bacteria are able to degrade the aromatic compounds into simple metabolites and use them as growth substrates under oxic or even under anoxic conditions. In anaerobic microorganisms, most monocyclic aromatic growth substrates are converted to the central intermediate benzoyl-coenzyme A, which is enzymatically reduced to cyclohexa-1,5-dienoyl-CoA. The strictly anaerobic bacterium Geobacter metallireducens uses the class II Benzoyl-CoA reductase complex for this reaction. The catalytic BamB subunit of this complex harbors an active site tungsten-bis-pyranopterin cofactor with the metal being coordinated by five protein/cofactor-derived sulfur atoms and a sixth, so far unknown, ligand. Although BamB has been biochemically and structurally characterized, its mechanism still remains elusive. Here we use continuum electrostatic and QM/MM calculations to model Benzoyl-CoA reduction by …

  • Enzymes of the benzoyl-coenzyme A degradation pathway in the hyperthermophilic archaeon Ferroglobus placidus.
    Environmental Microbiology, 2015
    Co-Authors: Georg Schmid, Sandra Bosch René, Matthias Boll

    Abstract:

    The Fe(III)-respiring Ferroglobus placidus is the only known archaeon and hyperthermophile for which a complete degradation of aromatic substrates to CO2 has been reported. Recent genome and transcriptome analyses proposed a benzoyl-coenzyme A (CoA) degradation pathway similar to that found in the phototrophic Rhodopseudomonas palustris, which involves a cyclohex-1-ene-1-carboxyl-CoA (1-enoyl-CoA) forming, ATP-dependent key enzyme Benzoyl-CoA reductase (BCR). In this work, we demonstrate, by first in vitro studies, that Benzoyl-CoA is ATP-dependently reduced by two electrons to cyclohexa-1,5-dienoyl-CoA (1,5-dienoyl-CoA), which is further degraded by hydration to 6-hydroxycyclohex-1-ene-1-carboxyl-CoA (6-OH-1-enoyl-CoA); upon addition of NAD(+) , the latter was subsequently converted to β-oxidation intermediates. The four candidate genes of BCR were heterologously expressed, and the enriched, oxygen-sensitive enzyme catalysed the two-electron reduction of Benzoyl-CoA to 1,5-dienoyl-CoA. A gene previously assigned to a 2,3-didehydropimeloyl-CoA hydratase was heterologously expressed and shown to act as a typical 1,5-dienoyl-CoA hydratase that does not accept 1-enoyl-CoA. A gene previously assigned to a 1-enoyl-CoA hydratase was heterologously expressed and identified to code for a bifunctional crotonase/3-OH-butyryl-CoA dehydrogenase. In summary, the results consistently provide biochemical evidence that F. placidus and probably other archaea predominantly degrade aromatics via the Thauera/Azoarcus type and not or only to a minor extent via the predicted R. palustris-type Benzoyl-CoA degradation pathway.

Johannes W Kung – One of the best experts on this subject based on the ideXlab platform.

  • Structural basis of enzymatic benzene ring reduction
    Nature Chemical Biology, 2015
    Co-Authors: Tobias Weinert, Johannes W Kung, Simona G Huwiler, Sina Weidenweber, Petra Hellwig, Hans-joachim Stärk, Till Biskup, Stefan Weber, Julien J. H. Cotelesage, Graham N. George

    Abstract:

    Structural, spectroscopic and kinetic analyses suggest that class II Benzoyl-CoA reductases from anaerobic bacteria use an unusual tungsten cofactor and a conserved histidine to perform a reduction akin to the widely used Birch reduction in organic chemistry.

  • cyclohexanecarboxyl coenzyme a coa and cyclohex 1 ene 1 carboxyl coa dehydrogenases two enzymes involved in the fermentation of benzoate and crotonate in syntrophus aciditrophicus
    Journal of Bacteriology, 2013
    Co-Authors: Johannes W Kung, Jana Seifert, Martin Von Bergen, Matthias Boll

    Abstract:

    The strictly anaerobic Syntrophus aciditrophicus is a fermenting deltaproteobacterium that is able to degrade benzoate or crotonate in the presence and in the absence of a hydrogen-consuming partner. During growth in pure culture, both substrates are dismutated to acetate and cyclohexane carboxylate. In this work, the unknown enzymes involved in the late steps of cyclohexane carboxylate formation were studied. Using enzyme assays monitoring the oxidative direction, a cyclohex-1-ene-1-carboxyl-CoA (Ch1CoA)-forming cyclohexanecarboxyl-CoA (ChCoA) dehydrogenase was purified and characterized from S. aciditrophicus and after heterologous expression of its gene in Escherichia coli. In addition, a cyclohexa-1,5-diene-1-carboxyl-CoA (Ch1,5CoA)-forming Ch1CoA dehydrogenase was characterized after purification of the heterologously expressed gene. Both enzymes had a native molecular mass of 150 kDa and were composed of a single, 40- to 45-kDa subunit; both contained flavin adenine dinucleotide (FAD) as a cofactor. While the ChCoA dehydrogenase was competitively inhibited by Ch1CoA in the oxidative direction, Ch1CoA dehydrogenase further converted the product Ch1,5CoA to Benzoyl-CoA. The results obtained suggest that Ch1,5CoA is a common intermediate in benzoate and crotonate fermentation that serves as an electron-accepting substrate for the two consecutively operating acyl-CoA dehydrogenases characterized in this work. In the case of benzoate fermentation, Ch1,5CoA is formed by a class II Benzoyl-CoA reductase; in the case of crotonate fermentation, Ch1,5CoA is formed by reversing the reactions of the Benzoyl-CoA degradation pathway that are also employed during the oxidative (degradative) branch of benzoate fermentation.

  • cyclohexanecarboxyl coenzyme a coa and cyclohex 1 ene 1 carboxyl coa dehydrogenases two enzymes involved in the fermentation of benzoate and crotonate in syntrophus aciditrophicus
    Journal of Bacteriology, 2013
    Co-Authors: Johannes W Kung, Jana Seifert, Martin Von Bergen, Matthias Boll

    Abstract:

    The strictly anaerobic Syntrophus aciditrophicus is a fermenting deltaproteobacterium that is able to degrade benzoate or crotonate in the presence and in the absence of a hydrogen-consuming partner. During growth in pure culture, both substrates are dismutated to acetate and cyclohexane carboxylate. In this work, the unknown enzymes involved in the late steps of cyclohexane carboxylate formation were studied. Using enzyme assays monitoring the oxidative direction, a cyclohex-1-ene-1-carboxyl-CoA (Ch1CoA)-forming cyclohexanecarboxyl-CoA (ChCoA) dehydrogenase was purified and characterized from S. aciditrophicus and after heterologous expression of its gene in Escherichia coli. In addition, a cyclohexa-1,5-diene-1-carboxyl-CoA (Ch1,5CoA)-forming Ch1CoA dehydrogenase was characterized after purification of the heterologously expressed gene. Both enzymes had a native molecular mass of 150 kDa and were composed of a single, 40- to 45-kDa subunit; both contained flavin adenine dinucleotide (FAD) as a cofactor. While the ChCoA dehydrogenase was competitively inhibited by Ch1CoA in the oxidative direction, Ch1CoA dehydrogenase further converted the product Ch1,5CoA to Benzoyl-CoA. The results obtained suggest that Ch1,5CoA is a common intermediate in benzoate and crotonate fermentation that serves as an electron-accepting substrate for the two consecutively operating acyl-CoA dehydrogenases characterized in this work. In the case of benzoate fermentation, Ch1,5CoA is formed by a class II Benzoyl-CoA reductase; in the case of crotonate fermentation, Ch1,5CoA is formed by reversing the reactions of the Benzoyl-CoA degradation pathway that are also employed during the oxidative (degradative) branch of benzoate fermentation.