Microbial dehalogenation of halogenated alkanoic acids, alcohols and alkanes

Postdiagenetic Changes in Kerogen Properties and Type by Bacterial Oxidation and Dehydrogenation

A significant part of organic carbon found on the earth is deposited as fossil organic matter in the lithosphere. The most important reservoir of carbon is shale rocks enriched with organic matter in the form of kerogen created during diagenesis. The purpose of this study was to analyze whether the bacterial communities currently inhabiting the shale rocks have had any impact on the properties and type of kerogen. We used the shale rock located on the Fore-Sudetic Monocline, which is characterized by oil-prone kerogen type II. We were able to show that shale rock inhabited by bacterial communities are characterized by oxidized and dehydrated kerogen type III (gas-prone) and type IV (nonproductive, residual, and hydrogen-free). Bacterial communities inhabiting shale rock were dominated by heterotrophs of the Proteobacteria, Firmicutes, and Actinobacteria phyla. Additionally, we detected a number of protein sequences in the metaproteomes of bacterial communities matched with enzymes involved in the oxidative metabolism of aliphatic and aromatic hydrocarbons, which may potentially contribute to the postdiagenetic oxidation and dehydrogenation of kerogen. The kerogen transformation contributes to the mobilization of fossil carbon in the form of extractable bitumen dominated by oxidized organic compounds.

Isolation and Characterization of a Novel Bacterium from the Marine Environment for Trichloroacetic Acid Bioremediation

Halogenated compounds are an important class of environmental pollutants that are widely used in industrial chemicals such as solvents, herbicides, and pesticides. Many studies have been carried out to explore the biodegradation of these chemicals. Trichloroacetic acid (TCA) is one of the main halogenated compounds that are carcinogenic to humans and animals. The bacterium was isolated from the northern coastline of Johor Strait. In this study, the ability of strain MH2 to biodegrade TCA was evaluated by a growth experiment and dehalogenase enzyme assay. The growth profile of the isolated strain was examined. The doubling time for L. boronitolerans MH2 was found to be 32 h. The release of chloride ion in the degradation process was measured at 0.33 × 10−3 ± 0.03 mol∙L−1 after 96 h when the growth curve had reached its maximum within the late bacterial exponential phase. The results showed that the strain had a promising ability to degrade TCA by producing dehalogenase enzyme when cell-free extracts were prepared from growth on TCA as the sole carbon source with enzyme-specific activity, 1.1 ± 0.05 µmolCl−min−1∙mg−1 protein. Furthermore, the morphological, and biochemical aspects of the isolated bacterium were studied to identify and characterize the strain. The morphological observation of the isolated bacterium was seen to be a rod-shaped, Gram-positive, motile, heterotrophic, and spore-forming bacterium. The amplification of the 16S rRNA and gene analysis results indicated that the isolated bacterium had 98% similarity to Lysinibacillus boronitolerans. The morphological and biochemical tests supported the 16S rRNA gene amplification. To the best of the authors’ knowledge, this is the first reported case of this genus of bacteria to degrade this type of halogenated compound.

Effect of Zn2+ on halohydrin dehalogenase expression and accumulation through multi-parameter correlation research with Escherichia coli P84A/MC1061

Using 5 Zn²⁺ supplementation strategies in a 50 L batch bioreactor named FUS-50L(A), possible correlations among Zn²⁺ content and addition timing, physiologic activity (PA), halohydrin dehalogenase (HheC) accumulation of Escherichia coli P84A/MC1061 were systematically investigated. First, Zn²⁺ was confirmed as the significant factor, and its optimal concentration for HheC expression was 3.87 mg/L through fermentation experiments in shaking flasks. Second, based on experimental results from the different strategies, it was found that PA, nutrient consumption rate (NCR) and specific growth rate (μ) for E. coli P84A/MC1061 were promoted in the log phase (4-8 h) under appropriate Zn²⁺ concentrations in the lag phase and late log phase. Furthermore cell biomass was also increased to a higher level and the maximum HheC activity (i.e. HheC_max) was increased by 9.80%, and the time to reach HheC_max was reduced from 16 to 12 hours. Furthermore, appropriate supplementation of Zn²⁺ caused higher μ for E. coli P84A/MC1061, which resulted in more rapid accumulation of increased acetic acid concentrations, leading to higher acetic acid consumption avoiding any negative effects on producing HheC because of carbon source being exhausted prematurely and acetic acid being consumed rapidly.

l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1

l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1 is a stereospecific enzyme that acts exclusively on l-isomers of 2-chloropropionate and dichloroacetate. The amino acid sequence of this enzyme is substantially different from those of other l-specific dehalogenases produced by other organisms. DehL has not been crystallised, and hence its three-dimensional structure is unavailable. Herein, we review what is known concerning DehL and tentatively identify the amino acid residues important for catalysis based on a comparative structural and sequence analysis with well-characterised l-specific dehalogenases.

L-2-Haloacid dehalogenase from Ancylobacter aquaticus UV5: Sequence determination and structure prediction

A novel 25 kDa L-2-haloacid dehalogenase (L-2-DhlB) from a recently isolated Ancylobacter aquaticus strain UV5 indigenous to contaminated site in South Africa is reported here with its gene sequence. The enzyme was purified to 22.1-fold increase in specific activity of 72.9 U/mg protein when the organism was grown in medium supplemented with 5 mM 1,2-dichloroethane (1,2-DCA). L-2-DhlB was optimally active at pH 9.0 and 37°C with poor stability at 50°C, retaining 50% of its activity after 30 min, but inactivated rapidly at 60°C. L-2-DhlB catalyzed monochloroacetate (MCA) with Km and Vmax values of 0.47 mM and 2.4 μM/min, respectively. L-2-DhlB exhibited the kcat value of 4.8/min. Expression of about 100% relative activity of L-2-DhlB on the substrate L-2-monochloropropionate (L-2-MCPA) as compared to 5% on D-2-monochloropropionate (D-2-MCPA) suggested that L-2-DhlB belongs to the family of L-2-haloacid dehalogenases. ES-mass spectroscopy and bioinformatics tools resulted in 693 bp ORF sequence corresponding to 230 amino acid protein. NCBI-BLAST of L-2-DhlB resulted in the detection of a putative conserved domain of hypothetical haloacid dehalogenase (HAD)-like superfamily and subfamily IA.

Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward d- and l-2-chloropropionate

Halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. Notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the d-specific dehalogenase from Rhizobium sp. RCI (DehD), which acts on d-2-chloropropionate but not on its l-enantiomer. The catalytic residues of this dehalogenase responsible for its affinity toward d-2-chloropropionate have not been experimentally determined, although its three-dimensional crystal structure has been solved. For this study, we performed in silico docking and molecular dynamic simulations of complexes formed by this dehalogenase and d- or l-2-chloropropionate. Arg134 of the enzyme plays the key role in the stereospecific binding and Arg16 is in a position that would allow it to activate a water molecule for hydrolytic attack on the d-2-chloropropionate chiral carbon for release of the halide ion to yield l-2-hydroxypropionate. We propose that within the DehD active site, the NH group of Arg134 can form a hydrogen bond with the carboxylate of d-2-chloropropionate with a strength of ∼4 kcal/mol that may act as an acid–base catalyst, whereas, when l-2-chloropropionate is present, this bond cannot be formed. The significance of the present work is vital for rational design of this dehalogenase in order to confirm the involvement of Arg16 and Arg134 residues implicated in hydrolysis and binding of d-2-chloropropionate in the active site of d-specific dehalogenase from Rhizobium sp. RC1.

Structure prediction, molecular dynamics simulation and docking studies of D-specific dehalogenase from Rhizobium sp. RC1

Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD) in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD) simulation and docking of D-2-chloropropionate (D-2CP), D-2-bromopropionate (D-2BP), monochloroacetate (MCA), monobromoacetate (MBA), 2,2-dichloropropionate (2,2-DCP), d,l-2,3-dichloropropionate (d,l-2,3-DCP), and 3-chloropropionate (3-CP) into the DehD active site. The sequences of DehD and D-2-haloacid dehalogenase (HadD) from Pseudomonas putida AJ1 have 15% sequence similarity. The model had 80% of the amino acid residues in the most favored region when compared to the crystal structure of DehI from Pseudomonas putida PP3. Docking analysis revealed that Arg107, Arg134 and Tyr135 interacted with D-2CP, and Glu20 activated the water molecule for hydrolytic dehalogenation. Single residue substitutions at 25-30 °C showed that polar residues of DehD were stable when substituted with nonpolar residues and showed a decrease in activity within the same temperature range. The molecular dynamics simulation of DehD and its variants showed that in R134A variant, Arg107 interacted with D-2CP, while in Y135A, Gln221 and Arg231 interacted with D-2CP. It is our emphatic belief that the new model will be useful for the rational design of DehDs with enhanced potentials.

Isolation and survey of novel fluoroacetate-degrading bacteria belonging to the phylum Synergistetes

Microbial dehalogenation of chlorinated compounds in anaerobic environments is well known, but the degradation of fluorinated compounds under similar conditions has rarely been described. Here, we report on the isolation of a bovine rumen bacterium that metabolizes fluoroacetate under anaerobic conditions, the mode of degradation and its presence in gut ecosystems. The bacterium was identified using 16S rRNA gene sequence analysis as belonging to the phylum Synergistetes and was designated strain MFA1. Growth was stimulated by amino acids with greater quantities of amino acids metabolized in the presence of fluoroacetate, but sugars were not fermented. Acetate, formate, propionate, isobutryate, isovalerate, ornithine and H(2) were end products of amino acid metabolism. Acetate was the primary end product of fluoroacetate dehalogenation, and the amount produced correlated with the stoichiometric release of fluoride which was confirmed using fluorine nuclear magnetic resonance ((19) F NMR) spectroscopy. Hydrogen and formate produced in situ were consumed during dehalogenation. The growth characteristics of strain MFA1 indicated that the bacterium may gain energy via reductive dehalogenation. This is the first study to identify a bacterium that can anaerobically dehalogenate fluoroacetate. Nested 16S rRNA gene-specific PCR assays detected the bacterium at low numbers in the gut of several herbivore species.

Biochemical and structural studies of a L-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii

Haloacid dehalogenases have potential applications in the pharmaceutical and fine chemical industry as well as in the remediation of contaminated land. The L: -2-haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii has been cloned and over-expressed in Escherichia coli and successfully purified to homogeneity. Here we report the structure of the recombinant dehalogenase solved by molecular replacement in two different crystal forms. The enzyme is a homodimer with each monomer being composed of a core-domain of a beta-sheet bundle surrounded by alpha-helices and an alpha-helical sub-domain. This fold is similar to previously solved mesophilic L: -haloacid dehalogenase structures. The monoclinic crystal form contains a putative inhibitor L: -lactate in the active site. The enzyme displays haloacid dehalogenase activity towards carboxylic acids with the halide attached at the C2 position with the highest activity towards chloropropionic acid. The enzyme is thermostable with maximum activity at 60 degrees C and a half-life of over 1 h at 70 degrees C. The enzyme is relatively stable to solvents with 25% activity lost when incubated for 1 h in 20% v/v DMSO.

Isolation and characterization of a novel haloacid permease from Burkholderia cepacia MBA4

Burkholderia cepacia MBA4 is a bacterium that can utilize 2-haloacids as carbon and energy sources for growth. It has been proposed that dehalogenase-associated permease mediates the uptake of haloacid. In this paper, we report the first cloning and characterization of such a haloacid permease. The structural gene, designated deh4p, was found 353 bases downstream of the dehalogenase gene deh4a. Quantitative analysis of the expression of deh4p showed that it was induced by monochloroacetate (MCA), to a level similar to the MCA-induced level of deh4a. The nucleotide sequence of deh4p was determined, and an open reading frame of 1,656 bp encoding a putative peptide of 552 amino acids was identified. Deh4p has a putative molecular weight of 59,414 and an isoelectric point of 9.88. Deh4p has the signatures of sugar transport proteins and integral membrane proteins of the major facilitator superfamily. Uptake of [(14)C]MCA into the cell was Deh4p dependent. Deh4p has apparent K(m)s of 5.5 and 8.9 muM and V(max)s of 9.1 and 23.1 nmol mg(-1) min(-1) for acetate and MCA, respectively. A mutant with a transposon-inactivated haloacid operon failed to grow on MCA even when deh4a was provided in trans.

Biochemical and molecular characterisation of the 2,3-dichloro-1-propanol dehalogenase and stereospecific haloalkanoic dehalogenases from a versatile Agrobacterium sp

We previously reported the presence of both haloalcohol and haloalkanoate dehalogenase activity in the Agrobacterium sp. strain NHG3. The versatile nature of the organism led us to further characterise the genetic basis of these dehalogenation activities. Cloning and sequencing of the haloalcohol dehalogenase and subsequent analysis suggested that it was part of a highly conserved catabolic gene cluster. Characterisation of the haloalkanoate dehalogenase enzyme revealed the presence of two stereospecific enzymes with a narrow substrate range which acted on D-2-chloropropionic and L-2-chloropropionoic acid, respectively. Cloning and sequencing indicated that the two genes were separated by 87 bp of non-coding DNA and were preceded by a putative transporter gene 66 bp upstream of the D-specific enzyme.

Purification, crystallization and preliminary crystallographic analysis of DehIVa, a dehalogenase from Burkholderia cepacia MBA4

DehIVa is one of two dehalogenases produced by the soil- and water-borne bacterium Burkholderia cepacia MBA4. It acts to break down short-chain halogenated aliphatic acids through a nucleophilic attack and subsequent hydrolysis of an enzyme-substrate intermediate to remove the halide ions from L-enantiomers substituted at the C2 position (e.g L-2-monochloropropionic acid). Dehalogenases are an important group of enzymes that are responsible for breaking down a diverse range of halogenated environmental pollutants. The dhlIVa gene coding for DehIVa was expressed in Escherichia coli and the protein was purified and crystallized using the hanging-drop method. Crystals grown in PEG 4000 and ammonium sulfate diffracted to 3.1 A. The crystals had a primitive hexagonal unit cell, with unit-cell parameters a = b = 104.2, c = 135.8 A, alpha = beta = 90, gamma = 120 degrees. Determining this structure will provide valuable insights into the characterization of the catalytic mechanisms of this group of enzymes.

Biodegradation of chlorinated alkanes and their commercial mixtures by Pseudomonas sp. strain 273

The biodegradation of chlorinated alkanes was studied under oxic conditions with the objective of identifying favorable and unfavorable intramolecular chlorination sequences with respect to the enzymes studied. Several dehalogenating bacterial strains were screened for their ability to degrade middle-chain polychlorinated alkanes as well as a commercial mixture. Of the organisms tested, the most promising was Pseudomonas sp. strain 273, which possesses an oxygenolytic dehalogenase. The effects of carbon chain length (C(6)-C(16)), halogen position, and overall chlorine content (14-61% w/w) were examined using both commercially available compounds and molecules synthesized in our laboratory. The effects of co-substrates, solvents, and inducing agents were also studied. The results with pure chlorinated alkanes showed that the relative positions of the chlorine atoms strongly influenced the total amount of dehalogenation achieved. The greatest dehalogenation yields were associated with terminally chlorinated alkanes. The alpha- and alpha,omega-chlorinated compounds yielded similar results. Vicinal chlorination had the most dramatic impact on degradation. When present on both ends or at the center of the molecule, no dehalogenation was detected. Although partial dehalogenation of 1,2-dichlorodecane was observed, it was likely due to a combination of beta-oxidation and an abiotic mechanism. Cereclor S52 was appreciably dehalogenated in shake flasks only when 1,10-dichlorodecane was present as a co-substrate and after increasing the oil surface area through mechanical emulsification, demonstrating the importance of abiotic factors in degrading commercial polychlorinated alkane mixtures.

Halometabolites and cellular dehalogenase systems: an evolutionary perspective

We review the role of iodothyronine deiodinases (IDs) in the evolution of vertebrate thyroidal systems within the larger context of biological metabolism of halogens. Since the beginning of life, the ubiquity of organohalogens in the biosphere has provided a major selective pressure for the evolution and conservation of cellular mechanisms specialized in halogen metabolism. Among naturally available halogens, iodine emerged as a critical component of unique developmental and metabolic messengers. Metabolism of iodinated compounds occurs in the three major domains of life, and invertebrate deuterostomes possess several biochemical traits and molecular homologs of vertebrate thyroidal systems, including ancestral homologs of IDs identified in urochordates. The finely tuned cellular regulation of iodometabolite uptake and disposal is a remarkable event in evolution and might have been decisive for the explosive diversification of ontogenetic strategies in vertebrates.

Diversity of alpha-halocarboxylic acid dehalogenases in bacteria isolated from a pristine soil after enrichment and selection on the herbicide 2,2-dichloropropionic acid (Dalapon)

Five pure cultures of bacteria (strains DA1-5) able to degrade 2,2-dichloropropionic acid (22DCPA) were isolated for the first time from pristine bulk soil samples. From 16S rDNA analysis, it was concluded that strains DA2, DA3 and DA4 were members of the Bradyrhizobium subgroup (alpha-Proteobacteria), strain DA5 clustered in the Brucella assemblage (alpha-Proteobacteria) and strain DA1 clustered in the beta-Proteobacteria. Biochemical and molecular analysis of the dehalogenases from the isolates showed that these enzymes were quite diverse. Several dehalogenases were closely related to group I and II alpha-halocarboxylic acid dehalogenases, and partial polymerase chain reaction (PCR) products were obtained from isolates DA1, 2, 3 and 4 using degenerate dehalogenase primers. However, no PCR products were obtained from isolate DA5 using either of the group I or II alpha-halocarboxylic acid dehalogenase primers. Isolates DA2 and DA4 contained putative silent dehalogenases. The investigation highlighted the endemic nature of these genes in pristine environments and how diverse these were even from spatially close samples.

Sec-dependent and Sec-independent translocation of haloacid dehalogenase Chd1 of Burkholderia cepacia MBA4 in Escherichia coli

2-Haloacid dehalogenases are hydrolytic enzymes that cleave the halogen-carbon bond(s) in haloalkanoic acids. We have previously isolated a cryptic haloacid dehalogenase gene from Burkholderia cepacia MBA4 and expressed it in Escherichia coli. This recombinant protein is unusual in having a long leader sequence, a property of periplasmic enzymes. In this paper, we report the functional role of this leader sequence. Western blot analyses showed that Chd1 is translocated to the periplasm. The results on the expression of Chd1 in the presence of sodium azide suggested the cleavage of the leader to be Sec-dependent. Chimeras of Chd1 and green fluorescent protein demonstrated that the leader sequence is fully functional in translocating the fusion protein to the periplasm. The expression of the chimeras in Sec mutants supported the Sec-dependent translocation. Surprisingly, recombinant Chd1 and a chimera with no leader sequence were also found in the periplasm.

Mutagenic analysis of the conserved residues in dehalogenase IVa of Burkholderia cepacia MBA4

Amino and carboxyl terminal deletion derivatives of dehalogenase IVa (DehIVa) of Burkholderia cepacia MBA4 were constructed and analyzed for enzyme activity and for protein integrity. The results suggested that the majority of the protein is indispensable. Point mutations on 29 conserved charged and/or polar residues were generated and characterized. Derivatives D11E, D11N, D11S and D181N were totally inactive while mutant N178D was defective in catalysis. Mutations of other conserved residues displayed varying effects. Mutation that enhances DehIVa activity has been shown to be inhibitory in other dehalogenase and essential conserved residues in DehIVa have been shown to be dispensable in others. This suggests there is no general rule for the importance of these conserved residues.

QSAR modeling of oxidative stress in vitro following hepatocyte exposures to halogenated methanes

Volatile halogenated aliphatic compounds are among those chemicals that can cause oxidative stress in vitro and in vivo. Relationships can be identified between the potential of these chemicals to elicit certain biological responses and their specific chemical descriptors, such as molecular orbital energies (LUMO) or partition coefficients (logP). A quantitative structure-activity relationship (QSAR) model has not been reported previously for the potential of a series of brominated and chlorinated methanes to induce oxidative stress in primary rat hepatocytes. By utilizing a novel in vitro methodology to expose cultures of rat primary hepatocytes to volatile chemicals, biological responses were assessed from exposures of hepatocytes to individual halogenated methanes. Indicators of lipid peroxidation, reactive oxygen species and cytotoxicity were measured. For the 10 brominated and chlorinated methanes tested, semi-empirical molecular orbital methods were used to calculate the physical/chemical descriptors used in the QSAR models. These models were used to explain the relative potential for a given halogenated methane to induce markers of oxidative stress or related damage in vitro. The results showed that certain descriptors, such as the molecular orbital energies, bond lengths, and lipophilicity are quantitatively correlated with induction of indicators for oxidative stress and cytotoxicity by halogenated methanes in primary rat hepatocytes.

The fate and persistence of trifluoroacetic and chloroacetic acids in pond waters

The environmental fate of trichloro-, dichloro-, and monochloroacetic acids, and trifluoroacetic acid was investigated using field aquatic microcosms and laboratory sediment-water systems. Trifluoroacetic acid was extremely persistent and showed no degradation during a one-year field study, though it appeared to undergo transient partitioning within an unknown pond phase as the temperature of the surroundings was reduced. Of the three chloroacetic acids, trichloro had the longest residence time (induction and decay) (approximately 40 d), dichloro the shortest (approximately 4 d), and monochloro an intermediate residence time (approximately 14 d). Laboratory studies suggest that the biodegradation of trichloro-, dichloro-, and monochloroacetic acids leads primarily to the formation of chloride and oxalic, glyoxalic, and glycolic acids, respectively.

Identification of the dimerization domain of dehalogenase IVa of Burkholderia cepacia MBA4

Haloacid dehalogenases are enzymes that catalyze the hydrolytic removal of halogens from haloalkanoic acids. Dehalogenase IVa (DehIVa) from Burkholderia cepacia MBA4 and dehalogenase CI (DehCI) from Pseudomonas sp. strain CBS3 exhibit 68% identity. Despite their similarity DehIVa is a dimeric enzyme while DehCI is a monomer. In this work, we describe the identification of the domain that confers the dimerization function of DehIVa. Recombinant DNA molecules were constructed by fusion of the respective dehalogenase genes hdlIVa and dehCI. When amino acids 73 to 89 of DehCI were replaced by amino acids 74 to 90 of DehIVa, the recombinant molecule migrated like that of DehIVa in a nondenaturing activity-stained gel. Similarly, when residues 73 to 89 of DehIVa were replaced by the corresponding residues of DehCI, the chimera migrated as a monomer. These 17 amino acid changes were able to determine the aggregation states of the molecules. The retention of the catalytic function in these chimeras indicated that the overall folding of these proteins was not affected. Site-directed mutagenesis on hdlIVa however indicated that amino acids Phe58, Thr65, Leu78, and Phe92 of DehIVa are also important for the aggregation state of the protein. This indicates that the 17 residues are not sufficient for the dimerization of the protein.

Isolation and characterization of 2,3-dichloro-1-propanol-degrading rhizobia

2,3-Dichloro-1-propanol is more chemically stable than its isomer, 1, 3-dichloro-2-propanol, and is therefore more difficult to degrade. The isolation of bacteria capable of complete mineralization of 2, 3-dichloro-1-propanol was successful only from enrichments at high pH. The bacteria thus isolated were found to be members of the alpha division of the Proteobacteria in the Rhizobium subdivision, most likely Agrobacterium sp. They could utilize both dihaloalcohol substrates and 2-chloropropionic acid. The growth of these strains in the presence of 2,3-dichloro-1-propanol was strongly affected by the pH and buffer strength of the medium. Under certain conditions, a ladder of four active dehalogenase bands could be visualized from this strain in activity gels. The enzyme involved in the complete mineralization of 2,3-dichloro-1-propanol was shown to have a native molecular weight of 114,000 and consisted of four subunits of similar molecular weights.

Cloning and characterization of a cryptic haloacid dehalogenase from Burkholderia cepacia MBA4

Burkholderia cepacia MBA4 has been shown to produce a single dehalogenase batch culture. Moreover, other cryptic dehalogenases were also detected when the cells were grown in continuous culture. In this paper, we report the cloning and characterization of one of the cryptic dehalogenases in MBA4. This cryptic haloacid dehalogenase, designated Chd1, was expressed constitutively in Escherichia coli. This recombinant Chd1 had a relative molecular weight of 58,000 and existed predominantly as a dimer. The subunits had a relative molecular weight of 27,000. Chd1 exhibited isomer specificity, being active towards the L-isomer of 2-monochloropropionic acid only. The structural gene, chd1, was isolated on a 1.7-kb PstI fragment. This fragment contains a functional promoter, because expression of chd1 in E. coli is orientation independent. The nucleotide sequence of this fragment was determined and characterized. An open reading frame of 840 bp encoding a putative peptide of 280 amino acids was identified. This corresponds closely with the size of the subunit. The nucleotide sequence of chd1 did not show any homology with those of other dehalogenase genes. Comparison of the predicted amino acid sequence, however, shows significant homology, ranging from 42 to 50%, with the amino acid sequences of many other dehalogenases. Chd1 is unusual in having a long leader sequence, a property of periplasmic enzymes.

Dehalogenases applied to industrial-scale biocatalysis

In the recent past, the development of dehalogenating enzymes for industrial biocatalysis has been limited, but significant advances have been made. Three classes of enzymes have received attention and development: halalkanoic acid dehalogenases (EC 3.8.1.2), hydrogen-halide lyases (EC 4.5.1), and haloalkane dehalogenases (EC 3.8.1). Applications range from the manufacture of chiral intermediates, to recycling of chlorinated byproducts from chemical manufacturing, and selective treatment of process waste streams.

Investigation of two evolutionarily unrelated halocarboxylic acid dehalogenase gene families

Dehalogenases are key enzymes in the metabolism of halo-organic compounds. This paper describes a systematic approach to the isolation and molecular analysis of two families of bacterial alpha-halocarboxylic acid (alphaHA) dehalogenase genes, called group I and group II deh genes. The two families are evolutionarily unrelated and together represent almost all of the alphaHA deh genes described to date. We report the design and evaluation of degenerate PCR primer pairs for the separate amplification and isolation of group I and II deh genes. Amino acid sequences derived from 10 of 11 group I deh partial gene products of new and previously reported bacterial isolates showed conservation of five residues previously identified as essential for activity. The exception, DehD from a Rhizobium sp., had only two of these five residues. Group II deh gene sequences were amplified from 54 newly isolated strains, and seven of these sequences were cloned and fully characterized. Group II dehalogenases were stereoselective, dechlorinating L- but not D-2-chloropropionic acid, and derived amino acid sequences for all of the genes except dehII degrees P11 showed conservation of previously identified essential residues. Molecular analysis of the two deh families highlighted four subdivisions in each, which were supported by high bootstrap values in phylogenetic trees and by enzyme structure-function considerations. Group I deh genes included two putative cryptic or silent genes, dehI degrees PP3 and dehI degrees 17a, produced by different organisms. Group II deh genes included two cryptic genes and an active gene, dehIIPP3, that can be switched off and on. All alphaHA-degrading bacteria so far described were Proteobacteria, a result that may be explained by limitations either in the host range for deh genes or in isolation methods.