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

Dual C-Cl isotope fractionation offers potential to assess biodegradation of 1,2-dichloropropane and 1,2,3-trichloropropane by Dehalogenimonas cultures

1,2-dichloropropane (1,2-DCP) and 1,2,3-trichloropropane (1,2,3-TCP) are hazardous chemicals frequently detected in groundwater near agricultural zones due to their historical use in chlorinated fumigant formulations. In this study, we show that the organohalide-respiring bacterium Dehalogenimonas alkenigignens strain BRE15 M can grow during the dihaloelimination of 1,2-DCP and 1,2,3-TCP to propene and allyl chloride, respectively. Our work also provides the first application of dual isotope approach to investigate the anaerobic reductive dechlorination of 1,2-DCP and 1,2,3-TCP. Stable carbon and chlorine isotope fractionation values for 1,2-DCP (ƐC = -13.6 ± 1.4 ‰ and ƐCl = -27.4 ± 5.2 ‰) and 1,2,3-TCP (ƐC = -3.8 ± 0.6 ‰ and ƐCl = -0.8 ± 0.5 ‰) were obtained resulting in distinct dual isotope slopes (Λ12DCP = 0.5 ± 0.1, Λ123TCP = 4 ± 2). However direct comparison of ΛC-Cl among different substrates is not possible and investigation of the C and Cl apparent kinetic isotope effects lead to the hypothesis that concerted dichloroelimination mechanism is more likely for both compounds. In fact, whole cell activity assays using cells suspensions of the Dehalogenimonas-containing culture grown with 1,2-DCP and methyl viologen as electron donor suggest that the same set of reductive dehalogenases was involved in the transformation of 1,2-DCP and 1,2,3-TCP. This study opens the door to the application of isotope techniques for evaluating biodegradation of 1,2-DCP and 1,2,3-TCP, which often co-occur in groundwaters near agricultural fields.

Abiotic natural attenuation of 1,2,3-trichloropropane by natural magnetite under O2 perturbation

1,2,3-Trichloropropane (TCP) is an emerging groundwater pollutant, but there is a lack of reported studies on the abiotic natural attenuation of TCP by iron minerals. Furthermore, perturbation by O2 is common in the shallow subsurface by both natural and artificial processes. In this study, natural magnetite was selected as the reactive iron mineral to investigate its role in the degradation of TCP under O2 perturbation. The results indicated that the mineral structural Fe(II) on magnetite reacted with dissolved oxygen to generate O2-· and HO·. Both O2-· and HO· contributed to TCP degradation, with O2-· playing a more important role. After 56 days of reaction, 66.7% of TCP was completely dechlorinated. This study revealed that higher magnetite concentrations, smaller magnetite particle sizes, and lower initial TCP concentrations favored TCP degradation. The presence of <10 mg/L natural organic matter (NOM) did not affect TCP degradation. These findings significantly advance our understanding of the abiotic natural attenuation mechanisms facilitated by iron minerals under O2 perturbation, providing crucial insights for the study of natural attenuation.

A new method to treat fumigant pesticides-spent granular activated carbon utilizing alkaline hydrolysis

Groundwater treatment of recalcitrant fumigant pesticides (1,2-dibromo-3-chloropropane (DBCP), 1,2-dibromoethane (EDB), 1,2-dichloropropane (DCP), and 1,2,3-trichloropropane (TCP)) often involves a pump and treat system with granular activated carbon (GAC). A novel and promising method of treating the pesticide-spent GAC is based on alkaline hydrolysis, a well-understood abiotic transformation mechanism, that offers a potentially greener approach to conventional thermal regeneration. Here, alkaline hydrolysis of these pesticide chemicals was evaluated under homogeneous (aqueous), and heterogeneous (pesticide spent-GAC) conditions involving bituminous- and coconut-based GAC. Aqueous treatment occurred at elevated pH (pH 12.0-12.4) and the pesticide rate of hydrolysis transformation was first-order (DBCP ≫ TCP ≫ EDB ≫ DCP). Significant pesticide loss (94.95-99.98%) was achieved in both types of GAC (pH 12.0-12.4; 30 d). GAC suspensions held (5 d) at pH 11.0, 12.0, and 12.6, resulted in the DBCP loss of 74%, 89%, and 99%, respectively. The pH dependency of DBCP hydrolysis underscores the correlation between alkaline conditions, aggressive hydrolysis treatment, and reaction time for engineered systems. The estimated time (4-8 min) for full OH^- intraparticle diffusion into the GAC from bulk solution was much less than the pesticide hydrolysis half-lives indicating that alkaline hydrolysis treatment of pesticides in GAC was reaction rate limited. Rapid small scale column tests demonstrated that the post-treatment (i.e., base hydrolysis) impact on adsorptive characteristics of the GAC was limited.

Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications

Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH₄ ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH₄ , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH₄ monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.

Degradation of 1,2,3-trichloropropane by unactivated persulfate and the implications for groundwater remediation

Persulfate (PS) is widely used as an in situ chemical oxidation (ISCO) technology for groundwater and soil remediation. While conventional theory generally assumes that PS needs to be "activated" to produce reactive radicals for pollutant degradation, herein, PS without explicit activation system was discovered for the degradation of 1,2,3-TCP with the generation of reactive oxidation species (ROS). Comparison of five common ISCO oxidants (PS, peroxymonosulfate, hydrogen peroxide, potassium permanganate, and sodium percarbonate) indicated that only unactivated PS was able to degrade 1,2,3-TCP in both pure water and 12 natural water samples. 50 μM 1,2,3-TCP degradation can be continued as long as there is enough PS (50 mM). The degradation rate of 1,2,3-TCP increased 450 % when the PS concentration increased from 10 mM to 50 mM and 500 % when the temperature increased from 25 °C to 45 °C. Electron paramagnetic resonance (EPR) analyzes, hydroxyl radicals (·OH) probe reaction and radical quenching experiments confirmed the involvement of both sulfate radicals (SO₄·-) and ·OH that were responsible for 1,2,3-TCP degradation and ·OH played a more important role. HCO₃^-, Cl^- and NOM are three groundwater matrix species that are most likely to inhibit PS oxidation of 1,2,3-TCP. Compared to activated PS, unactivated PS is more promising and more practical for groundwater remediation, since it has several advantages: (1) longer lifetime and better long-term availability; (2) ability of enduring contaminant degradation; (3) applicable for low-permeability zones remediation and potential to alleviate contaminant rebound or tailing problems; (4) environmental friendly; and (5) lower cost. Overall, results of this study show that unactivated PS is a promising in situ remediation technology that may be a good candidate for the most challenging low permeable zone remediation.

Using Compound Specific Isotope Analysis to decipher the 1,2,3-trichloropropane-to-Allyl chloride transformation by groundwater microbial communities

1,2,3-trichloropropane (TCP), a refractory contaminant, can be reductive dehalogenated to allyl chloride (AC) by microorganisms, which has been shown a potential in situ bioremediation (ISB) strategy for TCP remediation in groundwater. In practice, however, it is hard to monitor the bioreduction extent because the TCP concentrations may also be decreased by non-biodegradation processes. Compound specific isotope analysis (CSIA) can be promising in determining the extent of degradation by quantifying the isotope enrichment factors (ε) of relevant degradation mechanisms. To date, no CSIA study has been reported on TCP degradation. In this study, a novel TCP-to-AC transformation enrichment culture (dominated by Azotobacter, Parabacteroides, Fusibacter, Hydrogenophaga, Trichococcus Desulfovibrio, etc) in the absence of the already identified TCP anaerobic reductive dechlorinating microorganisms (e.g., Dehalogenimonas) was derived from a chlorinated hydrocarbon-contaminated aquifer. A TCP degradation experiment was carried out by adding yeast extract to produce hydrogen as an electron donor. The TCP-to-AC transformation was found to conform to zero-order conversion kinetics with the rate constant 11 ± 0.34 μmol L^-1 d^-1 during the main biodegradation stage. The bulk carbon isotope enrichment factor (ε_bulk) of the TCP-to-AC transformation was firstly evaluated as -5.2 ± 0.1‰. This study for the first time characterized the carbon isotope fractionations during TCP biodegradation using a novel enrichment culture, which would provide a promising tool for the incorporation of ISB for TCP removal in the future.

Biocatalytic degradation of organophosphate pesticide from the wastewater and hydrolytic enzyme properties of consortium isolated from the pesticide contaminated water

The indiscriminate application of various pesticides leads to toxicity to the humans, animals, fishes and threatens the environment and ecosystem. The present study was aimed to investigate pesticide degrading bacteria from the pesticide contaminated sample and to localize organophophate hydrolase activity from the bacteria. Sediment sample was selected as the source of microorganism for the degradation of chlorpyrifos. Enterobacter aerogenes CP2 and Streptococcus pyogenes CP11 isolated from the contaminated sample removed 77 ± 1.8%, 74.2 ± 3.1 chlorpyrifos. These strains have the potential to utilize pesticide as the source of carbon and energy. The pesticides inoculated with both CP 2 and CP 11 enhanced biodegradation of chlorpyrifos at optimized condition. E. aerogenes CP2 and S. pyogenes CP11 produced organophosphate hydrolase activity and localized enzyme biosynthesis. Organophosphate hydrolase activity was high in intracellular, followed by outer membrane and extracellular sample for both bacteria. The treated wastewater has no impact on the seed germination indicated normal cell division, cell elongation and indole-3 acetic acid synthesis. The strain CP2 has the rapid rate of organophosphate degradation among Enterobacter species.

Biocatalytic approaches for the synthesis of optically pure vic-halohydrins

Enantiopure vicinal halohydrins (vic-halohydrins) are highly valuable building blocks for the synthesis of many different natural products and pharmaceuticals, and biocatalytic methods for their synthesis have received considerable interest. This review emphasizes the application of biocatalytic approaches as an efficient alternative or complement to conventional chemical reactions, with a special focus on the asymmetric reductions catalyzed by ketoreductases, kinetic resolution catalyzed using lipases or esterases, stereoselective biotransformation catalyzed by halohydrin dehalogenases, asymmetric hydroxylation catalyzed by cytochrome P450 monooxygenases, asymmetric dehalogenation catalyzed by haloalkane dehalogenases, and aldehyde condensation catalyzed by aldolases. Although many chiral vic-halohydrins have been successfully synthesized using wild-type biocatalysts, their enantioselectivity is often too low for enantiopure synthesis. To overcome these limitations, catalytic properties of wild-type enzymes have been improved by rational and semi-rational protein design or directed evolution. This review briefly introduces the research status in this field, highlighting aspects of basic academic research in the biocatalytic synthesis of optically active vic-halohydrins by employing such unconventional approaches. KEY POINTS: • Outlines the enzymatic strategies for the production of enantiopure vic-halohydrins • Highlights recent advances in biocatalytic production of enantiopure vic-halohydrins • Provide guidance for efficient preparation of enantiopure vic-halohydrins.

Perspectives of genetically engineered microbes for groundwater bioremediation

Biodegradation is the main process for the removal of organic compounds from the environment, but proceeds slowly for many synthetic chemicals of environmental concern. Research on microbial biodegradation pathways revealed that recalcitrance is - among other factors - caused by biochemical blockages resulting in dysfunctional catabolic routes. This has raised interest in the possibility to construct microorganisms with improved catabolic activities by genetic engineering. Although this goal has been pursued for decades, no full-scale applications have emerged. This perspective explores the lagging implementation of genetically engineered microorganisms in practical bioremediation. The major technical and scientific issues are illustrated by comparing two examples, that of 1,2-dichloroethane where successful full-scale application of pump-and-treat biotreatment processes has been achieved, and 1,2,3-trichloropropane, for which protein and genetic engineering yielded effective bacterial cultures that still await application.

Reduction of 1,2,3-trichloropropane (TCP): pathways and mechanisms from computational chemistry calculations

The characteristic pathway for degradation of halogenated aliphatic compounds in groundwater or other environments with relatively anoxic and/or reducing conditions is reductive dechlorination. For 1,2-dihalocarbons, reductive dechlorination can include hydrogenolysis and dehydrohalogenation, the relative significance of which depends on various structural and energetic factors. To better understand how these factors influence the degradation rates and products of the lesser halogenated hydrocarbons (in contrast to the widely studied per-halogenated hydrocarbons, like trichloroethylene and carbon tetrachloride), density functional theory calculations were performed to compare all of the possible pathways for reduction and elimination of 1,2,3-trichloropropane (TCP). The results showed that free energies of each species and reaction step are similar for all levels of theory, although B3LYP differed from the others. In all cases, the reaction coordinate diagrams suggest that β-elimination of TCP to allyl chloride followed by hydrogenolysis to propene is the thermodynamically favored pathway. This result is consistent with experimental results obtained using TCP, 1,2-dichloropropane, and 1,3-dichloropropane in batch experiments with zerovalent zinc (Zn⁰, ZVI) as a reductant.

Biodegradation of 1,2,3-Trichloropropane to Valuable (S)-2,3-DCP Using a One-Pot Reaction System

1,2,3-trichloropropane (TCP) being one of the important environmental pollutants, has drawn significant concern due to its highly toxic and carcinogenic effects. In this study, we built a one-pot reaction system in which immobilized haloalkane dehalogenase (DhaA31) and halohydrin dehalognase (HheC) were used to catalyze the recalcitrant TCP to produce 2,3-dichloro-1-propanol (2,3-DCP) by removing epichlorohydrin (ECH). Since HheC displays a high R enantiopreference toward 2,3-DCP, the production of enantiopure (S)-2,3-DCP was expected. However, the enantioselective resolution of (R,S)-2,3-DCP by HheC was greatly inhibited by the circular reaction occurring between the product ECH and 1,3-dichloro-2-propanol (1.3-DCP). To resolve this problem, HZD-9 resin-based in situ product removal was implemented. Under the optimized conditions, TCP was completely consumed, resulting in optically pure (S)-2,3-DCP with enantiomer excess (e.e) > 99% and 40% yield (out of the 44% theoretical maximum). The scale-up resin-integrated reaction system was successfully carried out in 0.5 L batch reactor. Moreover, the system could be reused for 6 rounds with 64% of original activity retained, showing that it could be applied in the treatment of large volumes of liquid waste and producing enantiopure (S)-2,3-DCP.

In Situ Persulfate Oxidation of 1,2,3-Trichloropropane in Groundwater of North China Plain

In situ injection of Fe(II)-activated persulfate was carried out to oxidize chlorinated hydrocarbons and benzene, toluene, ethylbenzene, and xylene (BTEX) in groundwater in a contaminated site in North China Plain. To confirm the degradation of contaminants, an oxidant mixture of persulfate, ferrous sulfate, and citric acid was mixed with the main contaminants including 1,2,3-trichloropropane (TCP) and benzene before field demonstration. Then the mixed oxidant solution of 6 m³ was injected into an aquifer with two different depths of 8 and 15 m to oxidize a high concentration of TCP, other kinds of chlorinated hydrocarbons, and BTEX. In laboratory tests, the removal efficiency of TCP reached 61.4% in 24 h without other contaminants but the removal rate was decreased by the presence of benzene. Organic matter also reduced the TCP degradation rate and the removal efficiency was only 8.3% in 24 h. In the field test, as the solution was injected, the oxidation reaction occurred immediately, accompanied by a sharp increase of oxidation–reduction potential (ORP) and a decrease in pH. Though the concentration of pollutants increased due to the dissolution of non-aqueous phase liquid (NAPL) at the initial stage, BTEX could still be effectively degraded in subsequent time by persulfate in both aquifers, and their removal efficiency approached 100%. However, chlorinated hydrocarbon was relatively difficult to degrade, especially TCP, which had a relatively higher initial concentration, only had a removal efficiency of 30%–45% at different aquifers and monitoring wells. These finding are important for the development of injection technology for chlorinated hydrocarbon and BTEX contaminated site remediation.

Factors affecting 1,2,3-trichloropropane contamination in groundwater in California

1,2,3-Trichloropropane (1,2,3-TCP) is a volatile organic chemical of eminent concern due to its carcinogenic, mutagenic, and reproductive effects, and its frequent occurrence at concentrations of concern worldwide. In California, 1,2,3-TCP was detected in 6.5% of 1237 wells sampled by the U. S. Geological Survey (USGS). About 8% of domestic wells had a detection of 1,2,3-TCP, compared to 5% of public-supply wells. 1,2,3-TCP was detected in 5.5% of most recent samples from 7787 public-supply well sources of the California State Water Resources Control Board Division of Drinking Water (DDW). Concentrations ranged from <0.005 to 2.7 μg/L. The California maximum contaminant level (MCL) is 0.005 μg/L. Most of the detections occurred in the San Joaquin Valley, where 1,2,3-TCP was detected above the MCL in 16% of USGS sampled wells and 18% of DDW wells. 1,2,3-TCP occurrence and concentrations are related to legacy fumigant use and hydrogeologic factors. Understanding factors affecting 1,2,3-TCP will aid in determining vulnerability and long term persistence in the San Joaquin Valley, which can help focus efforts to manage drinking water resources on the most vulnerable areas and also inform efforts in other areas of the state and worldwide. Widespread occurrence of 1,2,3-TCP is related to nonpoint source agricultural contaminant inputs. High concentrations of 1,2,3-TCP are in young, shallow, oxic groundwater beneath primarily orchard/vineyard crops. These areas are in coarse-grained sediments that promote rapid recharge, related to proximal alluvial fan sediments deposited by large streams that drain glaciated watersheds of the Sierra Nevada. 1,2,3-TCP co-occurs with 1,2-dibromo-3-chloropropane (DBCP) and 1,2-dichloropropane (1,2-DCP) throughout modern age groundwater, indicating its long term persistence with little degradation. The highest concentrations of 1,2,3-TCP were observed at point source cleanup sites in urban areas; depending on the age and source of groundwater to nearby public-supply wells, these areas may see increasing concentrations of 1,2,3-TCP.

Computational Study of Protein-Ligand Unbinding for Enzyme Engineering

The computational prediction of unbinding rate constants is presently an emerging topic in drug design. However, the importance of predicting kinetic rates is not restricted to pharmaceutical applications. Many biotechnologically relevant enzymes have their efficiency limited by the binding of the substrates or the release of products. While aiming at improving the ability of our model enzyme haloalkane dehalogenase DhaA to degrade the persistent anthropogenic pollutant 1,2,3-trichloropropane (TCP), the DhaA31 mutant was discovered. This variant had a 32-fold improvement of the catalytic rate toward TCP, but the catalysis became rate-limited by the release of the 2,3-dichloropropan-1-ol (DCP) product from its buried active site. Here we present a computational study to estimate the unbinding rates of the products from DhaA and DhaA31. The metadynamics and adaptive sampling methods were used to predict the relative order of kinetic rates in the different systems, while the absolute values depended significantly on the conditions used (method, force field, and water model). Free energy calculations provided the energetic landscape of the unbinding process. A detailed analysis of the structural and energetic bottlenecks allowed the identification of the residues playing a key role during the release of DCP from DhaA31 via the main access tunnel. Some of these hot-spots could also be identified by the fast CaverDock tool for predicting the transport of ligands through tunnels. Targeting those hot-spots by mutagenesis should improve the unbinding rates of the DCP product and the overall catalytic efficiency with TCP.

Removal enactment of organo-phosphorous pesticide using bacteria isolated from domestic sewage

Three bacteria (MS I, II and III) i.e., Pseudomonas aeruginosa (KY781886), Enterobactor ludwigii (KX881423) and Enterobacter cloacae (KX881513) isolated from domestic sewage were identified on the basis of 16S rDNA sequencing and are capable to growth in the presence of organo-phosphorous pesticide (chlorpyrifos). The mega plasmid size >23 kb was found in MS I and III. Biosurfactants of the significant amount were produced by three isolates. The ability of the isolates to degrade pesticide over 3 days in the presence of pesticides containing chlorpyrifos as the active component was estimated. Results of UV-visible, FTIR spectroscopy and GC-MS studies confirmed the removal of chlorpyrifos rather than degradation. Pesticide uptake results showed chlorpyrifos in intracellular components and bound to the cell surface in its native state. Removal of pesticide from soil was also recorded by these bacteria. Microbial treated pesticide did not have any effect on Vigna radita seedlings and goat erythrocytes.

Adsorption of 1,2,3-Trichloropropane (TCP) to meet a MCL of 5 ppt

1,2,3-Trichloropropane (TCP) is a groundwater contaminant in the drinking water aquifers in Hawaii and some other states. Granular activated carbon (GAC) has been used for 30 years to treat approximately 60 million gallons per day of TCP-contaminated groundwater in Hawaii. The State of Hawaii's current maximum contaminant level (MCL) for TCP is 600 ng/L (ppt), and consideration is being given to lower the MCL to 5 ppt. There is no EPA MCL for TCP. A study was conducted to determine if any GAC could meet a 5 ppt MCL for TCP, and if so, how many bedvolumes (BVs) could be treated prior to breakthrough. Constant Diffusivity-Rapid Small-Scale Column Tests (CD-RSSCTs) were performed to evaluate GAC adsorption of TCP. Three different groundwaters and six different GACs were utilized. The RSSCTs with the currently-utilized GAC were predictive of the performance of the GAC contactors (50,000 BVs to breakthrough). Any of the six GACs could meet a MCL of 5 ppt and some could do so for 150,000 or more BVs. No single GAC was optimal for all three well sites, indicating effects of subtle undefined differences in the water matrix and/or GAC physiochemical properties. The coal-based direct-activated carbon currently being used is the least optimal for all three well sites with respect to meeting a potential new TCP MCL of 5 ppt. The most effective GACs for Kunia were the Calgon coal-based GAC and the Siemens enhanced coconut shell GAC, while the most effective for Waipahu were the Siemens regular and enhanced coconut shell GACs, and the most effective for Mililani was the Calgon coal-based GAC. Choosing just one GAC for use at all three well sites (rather than the optimal for each site) would result in a reduction of treatment run time of 1 year at one well site (63% reduction).

Cometabolic biodegradation of 1,2,3-trichloropropane by propane-oxidizing bacteria

1,2,3-Trichloropropane (TCP) is an emerging groundwater pollutant and suspected human carcinogen. TCP, a recalcitrant contaminant, has been detected in the subsurface near TCP manufacture facilities and many superfund sites. Considering the toxicity and the occurence of TCP, there is a need to seek for cost-effective treatment technologies for TCP-contaminated sites. This paper investigated TCP biodegradation by propane-oxidizing bacteria (PrOB) which are known to express propane monooxygenase (PrMO). PrMO can cometabolically degrade many different contaminants. Four PrOB, Rhodococus jostii RHA1, Mycobacterium vaccae JOB5, Rhodococcus rubber ENV425 and one isolate Sphingopyxis sp. AX-A were examined for their ability to degrade TCP. All the four PrOB resting cells were able to degrade TCP. Strain JOB5 exhibited the best TCP degradation ability (v_initial = 9.7 ± 0.7 μg TCP (mg protein)^-1h^-1). No TCP was degraded in the presence of acetylene (an inhibitor for PrMO), suggesting that PrMO might be responsible for TCP degradation. Furthermore, competitive inhibition was observed between propane and TCP, and between trichloroethylene (TCE) and TCP.

A Pseudomonas putida strain genetically engineered for 1,2,3-trichloropropane bioremediation

1,2,3-Trichloropropane (TCP) is a toxic compound that is recalcitrant to biodegradation in the environment. Attempts to isolate TCP-degrading organisms using enrichment cultivation have failed. A potential biodegradation pathway starts with hydrolytic dehalogenation to 2,3-dichloro-1-propanol (DCP), followed by oxidative metabolism. To obtain a practically applicable TCP-degrading organism, we introduced an engineered haloalkane dehalogenase with improved TCP degradation activity into the DCP-degrading bacterium Pseudomonas putida MC4. For this purpose, the dehalogenase gene (dhaA31) was cloned behind the constitutive dhlA promoter and was introduced into the genome of strain MC4 using a transposon delivery system. The transposon-located antibiotic resistance marker was subsequently removed using a resolvase step. Growth of the resulting engineered bacterium, P. putida MC4-5222, on TCP was indeed observed, and all organic chlorine was released as chloride. A packed-bed reactor with immobilized cells of strain MC4-5222 degraded >95% of influent TCP (0.33 mM) under continuous-flow conditions, with stoichiometric release of inorganic chloride. The results demonstrate the successful use of a laboratory-evolved dehalogenase and genetic engineering to produce an effective, plasmid-free, and stable whole-cell biocatalyst for the aerobic bioremediation of a recalcitrant chlorinated hydrocarbon.

Maximizing the efficiency of multienzyme process by stoichiometry optimization

Multienzyme processes represent an important area of biocatalysis. Their efficiency can be enhanced by optimization of the stoichiometry of the biocatalysts. Here we present a workflow for maximizing the efficiency of a three-enzyme system catalyzing a five-step chemical conversion. Kinetic models of pathways with wild-type or engineered enzymes were built, and the enzyme stoichiometry of each pathway was optimized. Mathematical modeling and one-pot multienzyme experiments provided detailed insights into pathway dynamics, enabled the selection of a suitable engineered enzyme, and afforded high efficiency while minimizing biocatalyst loadings. Optimizing the stoichiometry in a pathway with an engineered enzyme reduced the total biocatalyst load by an impressive 56 %. Our new workflow represents a broadly applicable strategy for optimizing multienzyme processes.

Immobilized synthetic pathway for biodegradation of toxic recalcitrant pollutant 1,2,3-trichloropropane

The anthropogenic compound 1,2,3-trichloropropane (TCP) has recently drawn attention as an emerging groundwater contaminant. No living organism, natural or engineered, is capable of the efficient aerobic utilization of this toxic industrial waste product. We describe a novel biotechnology for transforming TCP based on an immobilized synthetic pathway. The pathway is composed of three enzymes from two different microorganisms: engineered haloalkane dehalogenase from Rhodococcus rhodochrous NCIMB 13064, and haloalcohol dehalogenase and epoxide hydrolase from Agrobacterium radiobacter AD1. Together, they catalyze consecutive reactions converting toxic TCP to harmless glycerol. The pathway was immobilized in the form of purified enzymes or cell-free extracts, and its performance was tested in batch and continuous systems. Using a packed bed reactor filled with the immobilized biocatalysts, 52.6 mmol of TCP was continuously converted into glycerol within 2.5 months of operation. The efficiency of the TCP conversion to the intermediates was 97%, and the efficiency of conversion to the final product glycerol was 78% during the operational period. Immobilized biocatalysts are suitable for removing TCP from contaminated water up to a 10 mM solubility limit, which is an order of magnitude higher than the concentration tolerated by living microorganisms.

Computer-assisted engineering of the synthetic pathway for biodegradation of a toxic persistent pollutant

Anthropogenic halogenated compounds were unknown to nature until the industrial revolution, and microorganisms have not had sufficient time to evolve enzymes for their degradation. The lack of efficient enzymes and natural pathways can be addressed through a combination of protein and metabolic engineering. We have assembled a synthetic route for conversion of the highly toxic and recalcitrant 1,2,3-trichloropropane to glycerol in Escherichia coli, and used it for a systematic study of pathway bottlenecks. Optimal ratios of enzymes for the maximal production of glycerol, and minimal toxicity of metabolites were predicted using a mathematical model. The strains containing the expected optimal ratios of enzymes were constructed and characterized for their viability and degradation efficiency. Excellent agreement between predicted and experimental data was observed. The validated model was used to quantitatively describe the kinetic limitations of currently available enzyme variants and predict improvements required for further pathway optimization. This highlights the potential of forward engineering of microorganisms for the degradation of toxic anthropogenic compounds.