Role of Dehalogenases in Aerobic Bacterial Degradation of Chlorinated Aromatic Compounds

Arora, Pankaj Kumar; Bae, Hanhong

doi:https://doi.org/10.1155/2014/157974

Journal of Chemistry

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Review Article | Open Access

Volume 2014 | Article ID 157974 | https://doi.org/10.1155/2014/157974

Role of Dehalogenases in Aerobic Bacterial Degradation of Chlorinated Aromatic Compounds

Pankaj Kumar Arora¹and Hanhong Bae¹

Academic Editor: Davide Vione

Received29 Jul 2014

Revised16 Oct 2014

Accepted22 Oct 2014

Published13 Nov 2014

Abstract

This review was conducted to provide an overview of dehalogenases involved in aerobic biodegradation of chlorinated aromatic compounds. Additionally, biochemical and molecular characterization of hydrolytic, reductive, and oxygenolytic dehalogenases was reviewed. This review will increase our understanding of the process of dehalogenation of chlorinated aromatic compounds.

1. Introduction

Chlorinated aromatic compounds including chlorobenzenes, chlorobenzoates, chlorophenols, chloroanilines, hexachlorobenzene, polychlorinated biphenyl, chloronitrophenols, chloroaminophenols, and atrazine comprise a major group of environmental pollutants that are used in the manufacture of dyes, drugs, pesticides, and other industrial products [1–7]. These compounds are stable due to the presence of carbon-chlorine bonds; therefore, the cleavage of carbon-chlorine bonds is a critical step in their degradation. Such cleavage may occur via two ways: (i) by spontaneous dechlorination of an unstable intermediate of unrelated enzymatic reactions [8] and (ii) by enzymatic dechlorination where the carbon-chlorine bond cleavage is catalyzed by specific enzymes [9–18].

Spontaneous dehalogenation occurs due to the chemical decomposition of an unstable intermediate after ring cleavage of chlorinated aromatic compounds [8]. This phenomenon has been observed in degradation of gamma-hexachlorocyclohexane where chlorohydroquinone-1,2-dioxygenase catalyzed the cleavage of the chlorohydroquinone to an acylchloride that spontaneously converted to maleylacetate with release of HCl [19]. Another example includes spontaneous dehalogenation during the degradation of chlorobenzoic acids [8]. Chlorobenzoic acids initially converted to chlorocatechols which were further degraded via modified ortho-cleavage pathway [8]. In this pathway, dehalogenation occurs spontaneously during further metabolism of ring-cleavage products [8].

Enzymatic dehalogenation involves the removal of chlorine atoms from aromatic rings by either hydrolytic, reductive, or oxygen dependent dehalogenation [9]. Hydrolytic dehalogenation includes replacement of the chlorine atom with the hydroxyl group in the aromatic ring. This hydroxyl group is derived from water [9]. Reductive dehalogenation involves replacement of the chlorine atom with a hydrogen atom [9]. Oxygenolytic dehalogenation involves replacement of the chlorine atom with a hydroxyl group containing an oxygen atom derived from O₂ [9]. Oxygenolytic dehalogenation is further divided into two classes, monooxygenase type dehalogenation and dioxygenase type dehalogenation [9]. Monooxygenase type dehalogenase adds one atom of oxygen to chlorinated compounds to remove the chlorine atom [9]. Dioxygenase type dehalogenase adds two atoms of oxygen into the substrate to remove the chlorine atom [9]. Dehalogenases involved in the aerobic dehalogenation of aromatic compounds are summarized in Table 1. In this review, we provide a detailed description of well-studied dehalogenases.

1.1. 4-Chlorobenzoyl-CoA Dehalogenase

4-Chlorobenzoyl-CoA dehalogenase is the best studied hydrolytic aromatic dehalogenase that catalyzes the conversion of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA with the release of a chloride ion (Figure 1(a)) [20]. This enzyme is involved in 4-chlorobenzoate degradation and found in several 4-chlorobenzoate degrading bacteria, including Burkholderia sp. CBS3 (previously known as Pseudomonas sp. CBS3), Arthrobacter sp. 4-CB1, and Arthrobacter sp. strain TM-1 [10, 20, 21].

(a)

(b)

(c)

The catalytic mechanism of 4-chlorobenzoyl dehalogenase proceeds by the formation of an aryl-enzyme covalent intermediate via nucleophilic aromatic substitution (Figure 1(b)) [22]. The first step in the hydrolytic dehalogenation involves binding of the enolate anion of the thioester link of 4-chlorobenzoyl-CoA with 4-chlorobenzoyl-CoA dehalogenase to form an enzyme substrate complex, which induces a partially positive charge on the chlorine bearing carbon atom to make it susceptible to nucleophilic attack by aspartate (Asp145) [23, 24]. In the second step, Asp145 attacks the C(4)-position of the benzoyl ring in the enzyme substrate complex to form Meisenheimer intermediate (or σ-complex), which then releases chloride to form an aryl-enzyme intermediate [25]. Finally, the aryl-enzyme intermediate is hydrolyzed by a histidine (His90)-bound water molecule to form a tetrahedral intermediate, which decomposes to 4-hydroxybenzoyl-CoA and free enzyme [25].

Crystallographic investigation revealed that the 4-chlorobenzoyl-CoA dehalogenase from strain CBS3 was a homotrimer and that each subunit folded into two motifs [23, 26]. The N-terminal domain is characterized by 10 strands of beta-pleated sheet that form two nearly perpendicular layers flanked by alpha helices [23]. The C-terminal domain involves trimerization of the protein and contains three amphiphilic alpha helices [23]. The N-terminal domain of the subunit is linked with the C-terminal domain of another subunit by a cation, most likely a calcium ion [26]. The authors concluded from the three-dimensional structure that the side-chain carboxylate group of Asp145 helps to form the Meisenheimer intermediate, while His90 serves as the general base for the hydrolysis step [26].

4-Chlorobenzoyl-CoA dehalogenase was also purified from Arthrobacter sp. strain 4-CB1 and strain TM-1 by homogeneity [10, 27]. In both strains, it is a homotetramer with subunits of 33 kD. In strain 4-CB1, it has a molecular weight of 116 kD with an optimal pH of 8.1 and an isoelectric point (pI) of 6.1, while it has a molecular weight of 131 kD with an optimum pH of 8.0 and a pI of 6.42 in strain TM-1 [10, 27]. The N-terminal sequence of the 4-chlorobenzoyl-CoA dehalogenase from strain 4-CB1 shows 30% identity with that from Burkholderia sp. CBS3 and differs from strain TM1 by the presence of additional alanine and valine [27].

1.2. Chlorothalonil Hydrolytic Dehalogenase (Chd)

This enzyme was first characterized from Pseudomonas sp. CTN-3 and it is involved in the hydrolytic dehalogenation of chlorothalonil at the para-position with respect to the cyano group (Figure 1(c)). Chd catalyzes the conversion of 2,4,5,6-tetrachloroisophthalonitrile (chlorothalonil) to 4-hydroxy-trichloroisophthalonitrile without the requirement of any cofactors [12]. There is no effect of the presence or absence of oxygen on the reaction [12]. The Chd enzyme belongs to the metallo-β-lactamase superfamily and exhibits 24 to 29% identity with metallohydrolases [12]. The enzyme has a monomer protein of 36 kD with a pI of 4.13, a dissociation constant () of 0.112 mM, and an average catalytic rate () of 207 s⁻¹ for chlorothalonil. Site-directed mutagenesis of the chd gene revealed that His128, His157, Ser126, Asp45, Asp130, Asp184, and Trp241 were important to maintain the dehalogenase activity [12]. Chd differs from 4-chlorobenzoyl-CoA dehalogenase due to its amino acid sequences and catalytic properties [12]. Furthermore, there were no conserved catalytic residues between 4-chlorobenzoyl-CoA dehalogenase and Chd [12]. Liang et al. [28] detected the chd gene in sixteen chlorothalonil-dechlorinating strains belonging to eight different genera, Ochrobactrum, Shinella, Caulobacter, Rhizobium, Bordetella, Pseudoxanthomonas, Pseudomonas, and Lysobacter. The chd genes detected in the sixteen strains were highly similar (99.4% to 100%) to each other and closely associated with a novel insertion sequence, ISOcsp1. The promoter of chd gene was located immediately downstream of the right inverted repeat of ISOcsp1, and the sequences between the ISOcsp1 and chd gene were also conserved. These observations strongly suggest that horizontal gene transfer was responsible for widespread distribution of the chd gene in these sixteen strains [28]. Further analysis using toxicity experiments revealed the ecological role of the horizontal transfer of the chd gene [29]. Horizontal gene transfer of chd facilitates bacterial adaptation to chlorothalonil-contaminated sites through biotransformation of chlorothalonil to less toxic 2,4,5-trichloro-6-hydroxybenzene-1,3-dicarbonitrile [29]. In another study, the chd gene was cloned from a chlorothalonil-degrading strain, Ochrobactrum lupine TP-D1, which showed 98.4% similarity with that of Pseudomonas sp. CTN-3 [30]. This gene was closely associated with the insertion element IS-Olup. This conserved sequence containing the chd gene and IS-Olup was also reported in seven degrading strains belonging to five genera, Pseudomonas sp., Achromobacter sp., Ochrobactrum sp., Ralstonia sp., and Lysobacter sp. [31]. The occurrence of the chd and IS-Olup in seven other degrading strains suggests horizontal gene transfer of the chd gene [31]. Further evidence of horizontal transfer of the chd gene by IS-Olup was found by inserting the IS-Olup containing chd gene into the chromosome of Escherichia coli DH10B [31].

1.3. Tetrachlorohydroquinone Reductive Dehalogenase (PcpC)

PcpC is a crucial enzyme of the degradation pathway of pentachlorophenol (PCP) that has been well-studied in the PCP-degrading aerobic bacterium, Sphingobium chlorophenolicum L-1 (previously known as strain ATCC 39723) [14]. This enzyme belongs to the glutathione-S-transferase (GST) superfamily and catalyzes sequential dehalogenation of tetrachlorohydroquinone (TeCHQ) to 2,6-dichlorohydroquinone (DCHQ) via 2,3,6-trichlorohydroquinone (TCHQ) (Figure 2(a)) [14]. Each dehalogenation step requires two molecules of glutathione [14].

(a)

(b)

PcpC has sequence identity (but not more than 25%) with members of the zeta classes of the GST superfamily [32]. The enzymes in the GST superfamily generally form glutathione conjugates via nucleophilic attack of glutathione upon an electrophilic substrate [32]. A few enzymes of the GST family, including PcpC, maleylacetoacetate isomerase, and maleylpyruvate isomerase, have complex and unusual mechanisms involving additional steps before and/or after the nucleophilic attack of glutathione on an electrophilic intermediate [32–36]. It has been suggested that PcpC originated from a maleylacetoacetate (MAA) isomerase or maleylpyruvate (MP) isomerase because it catalyzes isomerization of MAA and MP and its active site is highly conserved [32].

Cys13 at the active site of PcpC is required for dehalogenation of TCHQ to TriCHQ, as well as TriCHQ to DCHQ [33, 37]. In such a case, when cysteine 13 is oxidatively damaged, the damaged enzyme yields S-glutathionyl-TriCH (GS-TriCH) and GS-DiCH conjugates as products [38]. The oxidative damage of PcpC may be removed by treatment with dithiothreitol (DTT), indicating that this damage may involve a cysteine residue [38].

Habash et al. [39] carried out mutational studies in the N-terminal residues (serine and cysteine) of the PcpC in Sphingomonas sp. UG30 and observed functional and structural changes. UG30 PcpC showed 94% identity with PcpC from Sphingobium chlorophenolicum L-1, with differences being observed in their functional and kinetic properties. Additionally, the optimum temperature and pH of UG30 PcpC were higher than that of S. chlorophenolicum PcpC. S. chlorophenolicum PcpC was inhibited by TCHQ, whereas the UG30 PcpC was not inhibited by the substrate [39, 40].

1.4. 2,5-Dichlorohydroquinone Reductive Dehalogenase (LinD)

LinD is a glutathione-dependent reductive dehalogenase involved in the degradation of gamma-hexachlorocyclohexane by Sphingobium japonicum UT-26 [15]. This enzyme catalyzes the conversion of 2,5-dichlorohydroquinone to 2-chlorohydroquinone (CHQ) and slowly converts CHQ to hydroquinone (Figure 2(b)) [15]. LinD is a member of the GST family but is only 25% homologous with PcpC. The residues in the active sites of LinD and some maleylpyruvate isomerases are conserved, suggesting that LinD may have evolved from other members of the GST family [32]. This enzyme is encoded by the linD gene and consists of a peptide of 343 amino acids [15]. Comparison of the genome of UT-26 with those of Sphingomonas sp. SKA58, Sphingobium sp. SYK-6, Sphingomonas wittichii RW1, Sphingopyxis alaskensis RB2256, and Novosphingobium aromaticivorans DSM 12444 revealed that lin genes including linD are located on unique regions of strain UT-26 and are closely associated with insertion sequence IS6100, suggesting an important role of IS6100 in the distribution of specific lin genes [41–44].

1.5. Pentachlorophenol-4-Monooxygenase (PcpB)

PcpB, which is the first enzyme of the degradation pathway of pentachlorophenol (PCP) in Sphingobium chlorophenolicum L-1, converts PCP to TeCHQ with oxidative removal of the chloride ion (Figure 3(a)) [45]. This enzyme requires one molecule of oxygen and two molecules of NADPH for reaction [45]. PcpB catalyzes hydroxylation of the para position of a wide range of polyhalogenated phenols including 2,3,5,6-tetrachlorophenol, 2,4,6-triiodophenol, 2,4,6-tribromophenol, and 2,6-dichlorophenol [46]. PcpB is encoded by the pcpB gene in Sphingobium chlorophenolicum L-1, which has been identified in a variety of PCP-degrading and non-PCP degrading bacteria isolated from PCP-contaminated sites [9, 47]. The occurrence of the pcpB gene in a number of bacteria isolated from PCP-contaminated environments suggests the involvement of natural horizontal transfer of the gene [48]. The homologous enzymes from Novosphingobium lentum MT1 [49], several polychlorophenol-degrading Sphingomonads from Finland [48], Sphingomonas sp. UG30 [50], and those of several uncultured bacteria from environmental samples collected from PCP-contaminated soils [51] showed 72–98% identity with PcpB.

(a)

(b)

(c)

1.6. Chlorophenol-4-Monooxygenase

This enzyme converts 2,4,5-trichlorophenol to 2,5-dichloro-p-hydroquinone with the release of chloride ions in the degradation pathway of 2,4,5-trichlorophenoxyacetic acid by Burkholderia cepacia AC1100 (Figure 3(b)) [52]. The gene (tftD) encoding chlorophenol monooxygenase (TftD) has been characterized from B. cepacia AC1100 [52–55]. This enzyme has a molecular weight of 22 kD and requires O₂, FAD, and NADH to catalyze the reaction.

1.7. 2,4,6-Trichlorophenol Monooxygenase

This enzyme was characterized in Azotobacter sp. GP1 and Cupriavidus necator JMP134 (previously known as Ralstonia eutropha) JMP134 [56, 57]. The 2,4,6-trichlorophenol-4-monooxygenase from Azotobacter sp. GP1 converts 2,4,6-trichlorophenol (TCP) to 2,6-dichlorohydroquinone with the release of a chloride ion (Figure 3(c)) [57]. This enzymeis a homotetrameric protein with a molecular weight of 240 kD and a subunit weight of 60 kD that requires NADH, flavin adenine dinucleotide, and O₂ as cofactors [57]. Another 2,4,6-trichlorophenol-4-monooxygenase from Cupriavidus necator JMP134 converted 2,4,6-TCP to 2-chlorohydroxyquinone via sequential dehalogenation [56]. This monooxygenase is a monomeric protein of 60 kDa that converts 2,4,6-TCP to 2,6-dichloroquinone and finally to 2-chlorohydroxyquinone, which is reduced to 6-chlorohydroxyquinol and requires molecular oxygen, NADH, FAD, and riboflavin reductase [NAD(P)H]/FMN reductase for activity [56]. The gene (tcpA) encoding this enzyme (TcpA) has been identified and characterized in Cupriavidus necator JMP134 [58, 59].

1.8. 4-Chlorophenylacetate-3,4-Dioxygenase

This enzyme catalyzes the conversion of 4-chlorophenylacetate to 3,4-dihydroxyphenylacetate and requires NADH and Fe²⁺ as cofactors (Figure 4(a)) [60, 61]. This enzyme has been studied in Burkholderia sp. CBS3, which utilizes 2-chloroacetate, 4-chlorobenzoate, and 4-chlorophenyl acetate as the sole carbon and energy sources. 4-Chlorophenylacetate-3,4-dioxygenase is composed of two components, in which the large component (A) is an iron-sulfur protein that acts as a dioxygenase, and the small component (B) acts as a reductase [60, 61]. Component A is a trimetric protein with a molecular weight of 140 kD [60] that is composed of three subunits with a molecular range of 46 kD to 52 kD, whereas component B is a monomer protein with molecular weight of 35 kD that has a type iron-sulfur cluster [61].

(a)

(b)

(c)

1.9. 2-Halobenzoate-1,2-Dioxygenase

This enzyme, which was first studied in Burkholderia sp. 2CBS, converts 2-chlorobenzoate, 2-fluorobenzoate, 2-bromobenzoate, and 2-iodobenzoate to catechol with concomitant release of carbon dioxide and halides (Figure 4(b)) [62, 63] and requires NADH and Fe²⁺ as cofactors. The gene cluster encoding this enzyme, cbdABC, is located on the 70-kb plasmid pBAH1 in strain 2CBS [63]. The enzyme from strain 2CBS is a two-component protein consisting of a dioxygenase and an electron transfer component [63]. The dioxygenase is composed of 3 α- and 3 β-subunits encoded by the genes chdA and chdB, respectively [63]. Each α-subunit has a molecular weight of 52 kD, while each β-subunit has a molecular weight of 20 kD. The electron transfer component is a monomeric protein of 37 kD that is encoded by the gene cbdC and has NADH-acceptor reductase activity [63]. Suzuki et al. [64] cloned and sequenced the cbdABC genes from Burkholderia sp. TH2 and found predicted amino acid sequences highly similar to the cbd gene products of strain 2CBS. The halobenzoate-1,2-dioxygenase is similar to benzoate dioxygenases but differs from a three-component dioxygenase from Pseudomonas aeruginosa strain 14, which catalyzes ortho-dehalogenation of 2-chlorobenzoate and 2,4-dichlorobenzoate [65].

1.10. Chlorobenzene Dioxygenase (TecA)

The chlorobenzene dioxygenase (TecA) of Burkholderia sp. strain PS12 dechlorinates 1,2,4,5-tetrachlorobenzene to 3,4,6-trichlorocatechol (Figure 4(c)) [66, 67]. The gene (tecA) encoding this enzyme (TecA) was located in the plasmid [67]. This enzyme belongs to the Class IIB dioxygenases, which are composed of a terminal dioxygenase, a reductase (TecA3), and a ferredoxin (TecA4). The dioxygenase is composed of a large α-subunit (TecA1) and a small β-subunit (TecA2) with an (αβ)_n configuration [66]. The large α-subunit of TecA determines the substrate specificity of the enzyme and contains a Rieske (2Fe2S) centre and a mononuclear nonhaem iron [68].

2. Conclusions and Future Perspectives

(i)Bacterial aromatic dehalogenases play an important role in dehalogenation of chlorinated aromatic compounds, which is a crucial step in the degradation of these compounds. To date, many hydrolytic, reductive, and oxygenolytic aromatic dehalogenases have been identified; however, detailed mechanistic studies have only been conducted for a few.(ii)4-Chlorobenzoyl-CoA dehalogenase is a well-characterized hydrolytic dehalogenase and its catalytic mechanism has also been studied. Furthermore, the crystal structure of this dehalogenase provided detailed insight into the hydrolytic dehalogenation of chlorinated aromatic compounds.(iii)Chlorothalonil hydrolytic dehalogenase is a newly characterized hydrolytic dehalogenase. More efforts are needed to understand its catalytic mechanism. The crystal structure of this dehalogenase should be investigated to understand the dehalogenation of chlorothalonil.(iv)Tetrachlorohydroquinone reductive dehalogenase (PcpC) is the only aromatic reductive dehalogenase whose mechanism has been studied in detail. Similar studies should be carried out for other reductive aromatic dehalogenases such as LinD.(v)Pentachlorophenol-4-monooxygenase is the most important monooxygenase type dehalogenase. The genetics of this dehalogenase has been studied and the gene coding this enzyme (pcpB) has been identified in a variety of bacteria. The crystal structure of this dehalogenase may provide new insights into oxygenolytic dehalogenation of pentachlorophenol.(vi)The genetics and biochemical studies of dioxygenase type dehalogenases have been carried out. Further development can be done to improve the efficiency of these dehalogenases.(vii)The biocatalytic applications of the aromatic dehalogenases may be improved using the current approaches of genomics and proteomics. Metagenomic approach can be used to find out new dehalogenases from various environmental samples. Furthermore, the catalytic properties of dehalogenases can be enhanced by protein engineering. Directed evolution can be used to construct the engineered dehalogenases to improve their efficiency.(viii)Future studies on the biochemical and molecular characterization of aromatic dehalogenases will increase our understanding of this class of enzymes.

Conflict of Interests

The authors declare that they have no competing interests.

Authors’ Contribution

Pankaj Kumar Arora collected all the relevant publications, arranged the general structure of the review, drafted the text, and produced figures. Hanhong Bae revised the paper. All authors read and approved the final paper.

Acknowledgment

This work was carried out with the support of “Cooperative Research Program for Agriculture Science & Technology Development (PJ01049704)” Rural Development Administration, Republic of Korea.

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Copyright © 2014 Pankaj Kumar Arora and Hanhong Bae. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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