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

Mini Review: Advances in 2-Haloacid Dehalogenases

The 2-haloacid dehalogenases (EC 3.8.1.X) are industrially important enzymes that catalyze the cleavage of carbon-halogen bonds in 2-haloalkanoic acids, releasing halogen ions and producing corresponding 2-hydroxyl acids. These enzymes are of particular interest in environmental remediation and environmentally friendly synthesis of optically pure chiral compounds due to their ability to degrade a wide range of halogenated compounds with astonishing efficiency for enantiomer resolution. The 2-haloacid dehalogenases have been extensively studied with regard to their biochemical characterization, protein crystal structures, and catalytic mechanisms. This paper comprehensively reviews the source of isolation, classification, protein structures, reaction mechanisms, biochemical properties, and application of 2-haloacid dehalogenases; current trends and avenues for further development have also been included.

Position 123 of halohydrin dehalogenase HheG plays an important role in stability, activity, and enantioselectivity

HheG from Ilumatobacter coccineus is a halohydrin dehalogenase with synthetically useful activity in the ring opening of cyclic epoxides with various small anionic nucleophiles. This enzyme provides access to chiral β-substituted alcohols that serve as building blocks in the pharmaceutical industry. Wild-type HheG suffers from low thermostability, which poses a significant drawback for potential applications. In an attempt to thermostabilize HheG by protein engineering, several single mutants at position 123 were identified which displayed up to 14 °C increased apparent melting temperatures and up to three-fold higher activity. Aromatic amino acids at position 123 resulted even in a slightly higher enantioselectivity. Crystal structures of variants T123W and T123G revealed a flexible loop opposite to amino acid 123. In variant T123G, this loop adopted two different positions resulting in an open or partially closed active site. Classical molecular dynamics simulations confirmed a high mobility of this loop. Moreover, in variant T123G this loop adopted a position much closer to residue 123 resulting in denser packing and increased buried surface area. Our results indicate an important role for position 123 in HheG and give first structural and mechanistic insight into the thermostabilizing effect of mutations T123W and T123G.

Transport of haloacids across biological membranes

Haloacids are considered to be environmental pollutants, but some of them have also been tested in clinical research. The way that haloacids are transported across biological membranes is important for both biodegradation and drug delivery purposes. In this review, we will first summarize putative haloacids transporters and the information about haloacids transport when studying carboxylates transporters. We will then introduce MCT1 and SLC5A8, which are respective transporter for antitumor agent 3-bromopyruvic acid and dichloroacetic acid, and monochloroacetic acid transporters Deh4p and Dehp2 from a haloacids-degrading bacterium. Phylogenetic analysis of these haloacids transporters and other monocarboxylate transporters reveals their evolutionary relationships. Haloacids transporters are not studied to the extent that they deserve compared with their great application potentials, thus future inter-discipline research are desired to better characterize their transport mechanisms for potential applications in both environmental and clinical fields.

Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes

The taxonomic position of a Gram-stain negative, non-violaceinpigmented bacterium isolated from an insecticide-contaminated site was characterized by a polyphasic approach. The bacterium was able to grow on three different halogenated compounds namely 1-hlorobutane, 1-hloropropane and 1,2-ichloroethane. As a critical step in the degradation of these haloalkanes, stoichiometric amounts of dechlorination were estimated. Based on selective enrichment method for three months, using a highly contaminated mixed chemical soil, a bacterium was obtained and designated as IITR-71T. Its versatility and novelty led us to further characterize it by polyphasic taxonomy. The 16S rRNA gene sequence (1446 bases) comparison showed highest similarity with those of members of the genus Chromobacterium with the most closely related species to strain IITR-71T being Chromobacterium aquaticum (99.3 %) followed by Chromobacterium haemolyticum (98.6 %) and Chromobacterium piscinae (97.1 %). The major ubiquinone was Q-8. Predominant polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The DNA G+C content of IITR-71T was estimated to be 61.2 mol%. The genotypic and phenotypic distinctiveness of IITR-71T and its phylogenetic relationships indicate that IITR-71T represents a novel species, for which the name Chromobacterium alkanivorans sp. nov. is proposed. The type strain is IITR-71T (=MTCC 11059T=JCM 30068T=KCTC 52433T).

Recent advances on halohydrin dehalogenases-from enzyme identification to novel biocatalytic applications

Halohydrin dehalogenases are industrially relevant enzymes that catalyze the reversible dehalogenation of vicinal haloalcohols with formation of the corresponding epoxides. In the reverse reaction, also other negatively charged nucleophiles such as azide, cyanide, or nitrite are accepted besides halides to open the epoxide ring. Thus, novel C-N, C-C, or C-O bonds can be formed by halohydrin dehalogenases, which makes them attractive biocatalysts for the production of various β-substituted alcohols. Despite the fact that only five individual halohydrin dehalogenase enzyme sequences have been known until recently enabling their heterologous production, a large number of different biocatalytic applications have been reported using these enzymes. The recent characterization of specific sequence motifs has facilitated the identification of novel halohydrin dehalogenase sequences available in public databases and has largely increased the number of recombinantly available enzymes. These will help to extend the biocatalytic repertoire of this enzyme family and to foster novel biotechnological applications and developments in the future. This review gives a general overview on the halohydrin dehalogenase enzyme family and their biochemical properties and further focuses on recent developments in halohydrin dehalogenase biocatalysis and protein engineering.

Interactions of non-natural halogenated substrates with D-specific dehalogenase (DehD) mutants using in silico studies

The D-2-haloacid dehalogenase of D-specific dehalogenase (DehD) from Rhizobium sp. RC1 catalyses the hydrolytic dehalogenation of D-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding L-hydroxyalkanoic acids. Our investigations were focused on DehD mutants: R134A and Y135A. We examined the possible interactions between these mutants with haloalkanoic acids and characterized the key catalytic residues in the wild-type dehalogenase, to design dehalogenase enzyme(s) with improved potential for dehalogenation of a wider range of substrates. Three natural substrates of wild-type DehD, specifically, monochloroacetate, monobromoacetate and D,L-2,3-dichloropropionate, and eight other non-natural haloalkanoic acids substrates of DehD, namely, L-2-chloropropionate; L-2-bromopropionate; 2,2-dichloropropionate; dichloroacetate; dibromoacetate; trichloroacetate; tribromoacetate; and 3-chloropropionate, were docked into the active site of the DehD mutants R134A and Y135A, which produced altered catalytic functions. The mutants interacted strongly with substrates that wild-type DehD does not interact with or degrade. The interaction was particularly enhanced with 3-chloropropionate, in addition to monobromoacetate, monochloroacetate and D,L-2,3-dichloropropionate. In summary, DehD variants R134A and Y135A demonstrated increased propensity for binding haloalkanoic acid and were non-stereospecific towards halogenated substrates. The improved characteristics in these mutants suggest that their functionality could be further exploited and harnessed in bioremediations and biotechnological applications.

Expanding the Halohydrin Dehalogenase Enzyme Family: Identification of Novel Enzymes by Database Mining

Halohydrin dehalogenases are very rare enzymes that are naturally involved in the mineralization of halogenated xenobiotics. Due to their catalytic potential and promiscuity, many biocatalytic reactions have been described that have led to several interesting and industrially important applications. Nevertheless, only a few of these enzymes have been made available through recombinant techniques; hence, it is of general interest to expand the repertoire of these enzymes so as to enable novel biocatalytic applications. After the identification of specific sequence motifs, 37 novel enzyme sequences were readily identified in public sequence databases. All enzymes that could be heterologously expressed also catalyzed typical halohydrin dehalogenase reactions. Phylogenetic inference for enzymes of the halohydrin dehalogenase enzyme family confirmed that all enzymes form a distinct monophyletic clade within the short-chain dehydrogenase/reductase superfamily. In addition, the majority of novel enzymes are substantially different from previously known phylogenetic subtypes. Consequently, four additional phylogenetic subtypes were defined, greatly expanding the halohydrin dehalogenase enzyme family. We show that the enormous wealth of environmental and genome sequences present in public databases can be tapped for in silico identification of very rare but biotechnologically important biocatalysts. Our findings help to readily identify halohydrin dehalogenases in ever-growing sequence databases and, as a consequence, make even more members of this interesting enzyme family available to the scientific and industrial community.

Purification, gene cloning, and characterization of a novel halohydrin dehalogenase from Agromyces mediolanus ZJB120203

A novel halohydrin dehalogenase (HHDH), catalyzing the transformation of 1,3-dichloro-2-propanol (1,3-DCP) to epichlorohydrin (ECH), was purified from Agromyces mediolanus ZJB120203. The molecular mass of the enzyme was estimated to be 28 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A 735-bp nucleotide fragment was obtained based on the N-terminal and internal amino acid sequences of the purified HHDH. The gene codes a protein sequence with 244 amino acid residues, and the protein sequence shows high similarity to Hhe AAD2 (HHDH from Arthrobacter sp. AD2), defined as Hhe AAm, which is the seventh reported HHDH. Expression of Hhe AAm was carried out in Escherichia coli and purification was performed by nickel-affinity chromatography. The recombinant HheAAm possessed an optimal pH of 8.5 and an optimal temperature of 50 °C and manifested a K m of 4.58 mM and a V max of 3.84 μmol/min(/)mg. The activity of Hhe AAm was not significantly affected by metal ions such as Zn(2+), Ca(2+), Cu(2+), and EDTA, but was strongly inhibited by Hg(2+) and Ag(+). In particular, the Hhe AAm exhibits an enantioselectivity for the conversion of prochiral 1,3-DCP to (S)-ECH. The applications of the Hhe AAm as a catalyst for asymmetric synthesis are promising.

Expression, characterization, and improvement of a newly cloned halohydrin dehalogenase from Agrobacterium tumefaciens and its application in production of epichlorohydrin

A gene encoding halohydrin dehalogenase (HHDH) from Agrobacterium tumefaciens CCTCC M 87071 was cloned and expressed in Escherichia coli. To increase activity and stability of HHDH, 14 amino acid residues around the active site and substrate-binding pocket based on the structural analysis and molecular docking were selected as targets for site-directed mutagenesis. The studies showed that the mutant HHDH (Mut-HHDH) enzyme had a more accessible substrate-binding pocket than the wild-type HHDH (Wt-HHDH). Molecular docking revealed that the distance between the substrate and active site was closer in mutant which improved the catalytic activity. The expressed Wt-HHDH and Mut-HHDH were purified and characterized using 1,3-dichloro-2-propanol (1,3-DCP) as substrates. The specific activity of the mutant was enhanced 26-fold and the value of k cat was 18.4-fold as compared to the Wt-HHDH, respectively. The Mut-HHDH showed threefold extension of half-life at 45 °C than that of Wt-HHDH. Therefore it is possible to add 1,3-DCP concentration up to 100 mM and epichlorohydrin (ECH) was produced at a relatively high conversion and yield (59.6 %) using Mut-HHDH as catalyst. This Mut-HHDH could be a potential candidate for the upscale production of ECH.

Novel dehalogenase mechanism for 2,3-dichloro-1-propanol utilization in Pseudomonas putida strain MC4

A Pseudomonas putida strain (MC4) that can utilize 2,3-dichloro-1-propanol (DCP) and several aliphatic haloacids and haloalcohols as sole carbon and energy source for growth was isolated from contaminated soil. Degradation of DCP was found to start with oxidation and concomitant dehalogenation catalyzed by a 72-kDa monomeric protein (DppA) that was isolated from cell lysate. The dppA gene was cloned from a cosmid library and appeared to encode a protein equipped with a signal peptide and that possessed high similarity to quinohemoprotein alcohol dehydrogenases (ADHs), particularly ADH IIB and ADH IIG from Pseudomonas putida HK. This novel dehalogenating dehydrogenase has a broad substrate range, encompassing a number of nonhalogenated alcohols and haloalcohols. With DCP, DppA exhibited a k(cat) of 17 s(-1). (1)H nuclear magnetic resonance experiments indicated that DCP oxidation by DppA in the presence of 2,6-dichlorophenolindophenol (DCPIP) and potassium ferricyanide [K(3)Fe(CN)(6)] yielded 2-chloroacrolein, which was oxidized to 2-chloroacrylic acid.

Transformation and biodegradation of 1,2,3-trichloropropane (TCP)

PURPOSE

1,2,3-Trichloropropane (TCP) is a persistent groundwater pollutant and a suspected human carcinogen. It is also is an industrial chemical waste that has been formed in large amounts during epichlorohydrin manufacture. In view of the spread of TCP via groundwater and its toxicity, there is a need for cheap and efficient technologies for the cleanup of TCP-contaminated sites. In situ or on-site bioremediation of TCP is an option if biodegradation can be achieved and stimulated. This paper presents an overview of methods for the remediation of TCP-contaminated water with an emphasis on the possibilities of biodegradation.

CONCLUSIONS

Although TCP is a xenobiotic chlorinated compound of high chemical stability, a number of abiotic and biotic conversions have been demonstrated, including abiotic oxidative conversion in the presence of a strong oxidant and reductive conversion by zero-valent zinc. Biotransformations that have been observed include reductive dechlorination, monooxygenase-mediated cometabolism, and enzymatic hydrolysis. No natural organisms are known that can use TCP as a carbon source for growth under aerobic conditions, but anaerobically TCP may serve as electron acceptor. The application of biodegradation is hindered by low degradation rates and incomplete mineralization. Protein engineering and genetic modification can be used to obtain microorganisms with enhanced TCP degradation potential.

Biodegradation and metabolic pathway of β-chlorinated aliphatic acid in Bacillus sp. CGMCC no. 4196

In this study, a bacterial Bacillus sp. CGMCC no. 4196 was isolated from mud. This strain exhibited the ability to degrade high concentration of 3-chloropropionate (3-CPA, 120 mM) or 3-chlorobutyrate (30 mM), but not chloroacetate or 2-chloropropionate (2-CPA). The growing cells, resting cells, and cell-free extracts from this bacterium had the capability of 3-CPA degradation. The results indicated that the optimum biocatalyst for 3-CPA biodegradation was the resting cells. The 3-CPA biodegradation pathway was further studied through the metabolites and critical enzymes analysis by HPLC, LC-MS, and colorimetric method. The results demonstrated that the metabolites of 3-CPA were 3-hydroxypropionic acid (3-HP) and malonic acid semialdehyde, and the critical enzymes were 3-CPA dehalogenase and 3-HP dehydroxygenase. Thus, the mechanism of the dehalogenase-catalyzed reaction was inferred as hydrolytic dehalogenation which was coenzyme A-independent and oxygen-independent. Finally, the pathway of β-chlorinated aliphatic acid biodegradation could be concluded as follows: the β-chlorinated acid is first hydrolytically dehalogenated to the β-hydroxyl aliphatic acid, and the hydroxyl aliphatic acid is oxidized to β-carbonyl aliphatic acid by β-hydroxy aliphatic acid dehydroxygenase. It is the first report that 3-HP was produced from 3-CPA by β-chlorinated aliphatic acid dehalogenase.

A study of the conformational stability and the vibrational spectra of 2,3-dichloro-1-propanol

The conformational stability and the three rotor internal rotations in 2,3-dichloro-1-propanol were investigated at DFT-B3LYP/6-311+G**, MP2/6-311+G** and MP4(SDQ) levels of theory. From the calculated potential energy surface, ten distinct minima were located all of which were predicted to have real frequencies at the B3LYP level of theory. The calculated lowest energy minima in the potential curves of the molecule were predicted to correspond to the Ggg and Gtg1 structures. The observed broad and very intense infrared band centered at about 3370 cm(-1) supports the existence of the strong intermolecular H-bonding in 2,3-dichloro-1-propanol. The equilibrium constants for the conformational interconversion in the molecule were estimated from the calculated Gibb's energies at the B3LYP/6-311+G** level of calculation and found to correspond to an equilibrium mixture of about 49% Ggg, 27% Gtg1, 5% Ggt and 5% Tgg conformations at 298.15K.

Analysis of vibrational spectra of 3-halo-1-propanols CH(2)XCH(2)CH(2)OH (X is Cl and Br)

The conformational stability and the three rotor internal rotations in 3-chloro- and 3-bromo-1-propanols were investigated by DFT-B3LYP/6-311+G and ab initio MP2/6-311+G, MP3/6-311+G and MP4(SDTQ)//MP3/6-311+G levels of theory. On the calculated potential energy surface twelve distinct minima were located all of which were not predicted to have imaginary frequencies at the B3LYP level of theory. The calculated lowest energy minimum in the potential curves of both molecules was predicted to correspond to the Gauche-gauche-trans (Ggt) conformer in excellent agreement with earlier microwave and electron diffraction results. The equilibrium constants for the conformational interconversion of the two 3-halo-1-propanols were calculated at the B3LYP/6-311+G level of calculation and found to correspond to an equilibrium mixture of about 32% Ggt, 18% Ggg1, 13% Tgt, 8% Tgg and 8% Gtt conformations for 3-chloro-1-propanol and 34% Ggt, 15% Tgt, 13% Ggg1, 9% Tgg and 7% Gtt conformations for 3-bromo-1-propanol at 298.15K. The nature of the high energy conformations was verified by carrying out solvent experiments using formamide ( epsilon=109.5) and MP3 and MP4//MP3 calculations. The vibrational frequencies of each molecule in its three most stable forms were computed at the B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecules.

Solvent dependence of conformational stability and analysis of vibrational spectra of 2,2,3,3,3-pentafluoro-1-propanol

The conformational stability of 2,2,3,3,3-pentafluoro-1-propanol was investigated by the DFT-B3LYP/6-311+G** and the ab initio MP2/6-311+G** calculations. The calculated potential energy curves of 2,2,3,3,3-pentafluoro-1-propanol at both levels of theory were consistent with three distinct minima that correspond to Trans-gauche-gauche (Tgg), trans-trans-gauche (Ttg) and trans-gauche-gauche(-) (Tgg1) conformers in the order of decreasing relative stability. The equilibrium constants for the conformational interconversion of 2,2,3,3,3-pentafluoro-1-propanol were calculated and found to correspond to an equilibrium mixture of about 46% Tgg, 43% Ttg and 11% Tgg1 conformations at 298.15K. The calculated (%Ttg/%Tgg) ratio of 0.93 is consistent with the 0.85 ratio of the observed intensities of the 772 and 794 cm(-1) lines in the Raman spectrum of the liquid. The nature of the high energy Ttg conformation was verified by solvent experiments using formamide (epsilon = 109.5) and acetonitrile (epsilon = 37). The vibrational frequencies of the molecule in its stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.

Three rotor potential energy scans, conformational equilibrium constants and vibrational analysis of 3-fluoro-1-propanol CH(2)FCH(2)CH(2)OH

The conformational stability and the three rotor internal rotations in 3-fluoro-1-propanol were investigated by the DFT-B3LYP/6-311+G** and the ab initio MP2/6-311+G** levels of theory. The calculated potential energy curves of the molecule at both levels of theory were consistent with complex conformational equilibria of about 12 minima, all of which were predicted to have real frequencies at both the B3LYP and the MP2 levels. The lowest energy minimum in the potential curves of 3-fluoro-1-propanol was predicted to correspond to the Gauche-gauche-trans (Ggt) conformer in excellent agreement with microwave and electron diffraction results. The equilibrium constants for the conformational interconversion of the molecule were calculated and found to correspond to an equilibrium mixture of about 33% Ggt, 14% Ggg1 and 13% Gg1g and about 43% Ggt, 12% Ggg1 and 10% Gg1g distribution by the B3LYP/6-311+G** and the MP2/6-311+G** calculations, respectively, at 298.15K. The vibrational frequencies of each molecule in its three stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.

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.

Conformational analysis and vibrational assignments of 2,2,3,3-tetrafluoro-1-propanol CHF2CF2CH2OH as three-rotors system

The conformational stability of 2,2,3,3-tetrafluoro-1-propanol was investigated by DFT-B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. The calculated potential energy curves of the molecule at DFT-B3LYP level were consistent with five distinct minima that correspond to gauche(-)-gauche-gauche (G1gg), trans-trans-gauche (Ttg), trans-gauche-gauche (Tgg), trans-gauche-gauche(-) (Tgg1) and gauche(-)-gauche-trans (G1gt) conformers in the order of decreasing relative stability. The equilibrium constants for the conformational interconversion of 2,2,3,3-tetrafluoro-1-propanol were calculated and found to correspond to an equilibrium mixture of about 38% G1gg, 28% Ttg, 13% Tgg, 11% Tggt and 10% G1gt conformations at 298.15K. The vibrational frequencies of 2,2,3,3,-tetrafluoro-1-propanol in its five stable forms were computed at B3LYP level and complete vibrational assignments were made based on normal coordinate calculations and comparison with experimental data of the molecule.

Isolation of novel bacteria able to degrade alpha-halocarboxylic acids by enrichment from environmental samples

In order to isolate novel bacteria able to degrade alpha-halocarboxylic acids a variety of culturing strategies were implemented. Eight pure cultures were obtained and were found to be associated with the Gram negative Proteobacteria and the Gram positive Bacillus and Enterococcus genera. Furthermore, several strains were obtained which were able to degrade the DL-halocarboxylic acids anaerobically. Molecular analysis of the pure cultures led us to conclude that they may possess novel enzymes involved in the biodegradation of the alpha-halocarboxylic acids. These results are the first for nearly 40 years to describe the isolation of Gram positive isolates on an alpha-halocarboxylic acid as the sole source of carbon and energy, which also show the ability to de-toxify the test substrate by releasing chloride.