Properties and biotechnological applications of natural and engineered haloalkane dehalogenases

Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism

BACKGROUND

Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules.

RESULTS

To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites.

CONCLUSION

The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.

Probing the functional hotspots inside protein hydrophobic pockets by in situ photochemical trifluoromethylation and mass spectrometry

Due to the complex high-order structures and interactions of proteins within an aqueous solution, a majority of chemical functionalizations happen on the hydrophilic sites of protein external surfaces which are naturally exposed to the solution. However, the hydrophobic pockets inside proteins are crucial for ligand binding and function as catalytic centers and transporting tunnels. Herein, we describe a reagent pre-organization and in situ photochemical trifluoromethylation strategy to profile the functional sites inside the hydrophobic pockets of native proteins. Unbiased mass spectrometry profiling was applied for the characterization of trifluoromethylated sites with high sensitivity. Native proteins including myoglobin, trypsin, haloalkane dehalogenase, and human serum albumin have been engaged in this mild photochemical process and substantial hydrophobic site-specific and structure-selective trifluoromethylation substitutes are obtained without significant interference to their bioactivity and structures. Sodium triflinate is the only reagent required to functionalize the unprotected proteins with wide pH-range tolerance and high biocompatibility. This "in-pocket" activation model provides a general strategy to modify the potential binding pockets and gain essential structural insights into the functional hotspots inside protein hydrophobic pockets.

Multimeric structure of a subfamily III haloalkane dehalogenase-like enzyme solved by combination of cryo-EM and x-ray crystallography

Haloalkane dehalogenase (HLD) enzymes employ an SN 2 nucleophilic substitution mechanism to erase halogen substituents in diverse organohalogen compounds. Subfamily I and II HLDs are well-characterized enzymes, but the mode and purpose of multimerization of subfamily III HLDs are unknown. Here we probe the structural organization of DhmeA, a subfamily III HLD-like enzyme from the archaeon Haloferax mediterranei, by combining cryo-electron microscopy (cryo-EM) and x-ray crystallography. We show that full-length wild-type DhmeA forms diverse quaternary structures, ranging from small oligomers to large supramolecular ring-like assemblies of various sizes and symmetries. We optimized sample preparation steps, enabling three-dimensional reconstructions of an oligomeric species by single-particle cryo-EM. Moreover, we engineered a crystallizable mutant (DhmeAΔGG ) that provided diffraction-quality crystals. The 3.3 Å crystal structure reveals that DhmeAΔGG forms a ring-like 20-mer structure with outer and inner diameter of ~200 and ~80 Å, respectively. An enzyme homodimer represents a basic repeating building unit of the crystallographic ring. Three assembly interfaces (dimerization, tetramerization, and multimerization) were identified to form the supramolecular ring that displays a negatively charged exterior, while its interior part harboring catalytic sites is positively charged. Localization and exposure of catalytic machineries suggest a possible processing of large negatively charged macromolecular substrates.

An integrated metagenomic model to uncover the cooperation between microbes and magnetic biochar during microplastics degradation in paddy soil

The free radicals released from the advanced oxidation processes can enhance microplastics degradation, however, the existence of microbes acting synergistically in this process is still uncertain. In this study, magnetic biochar was used to initiate the advanced oxidation process in flooded soil. paddy soil was contaminated with polyethylene and polyvinyl chloride microplastics in a long-term incubation experiment, and subsequently subjected to bioremediation with biochar or magnetic biochar. After incubation, the total organic matter present in the samples containing polyvinyl chloride or polyethylene, and treated with magnetic biochar, significantly increased compared to the control. In the same samples there was an accumulation of "UVA humic" and "protein/phenol-like" substances. The integrated metagenomic investigation revealed that the relative abundance of some key genes involved in fatty acids degradation and in dehalogenation changed in different treatments. Results from genome-centric investigation suggest that a Nocardioides species can cooperate with magnetic biochar in the degradation of microplastics. In addition, a species assigned to the Rhizobium taxon was identified as a candidate in the dehalogenation and in the benzoate metabolism. Overall, our results suggest that cooperation between magnetic biochar and some microbial species involved in microplastic degradation is relevant in determining the fate of microplastics in soil.

Identification and synergetic mechanism of TCE, H2 and O2 metabolic microorganisms in the joint H2/O2 system

The sole H₂ and O₂ usually promote chlorinated hydrocarbons (CHCs) biotransformation by several mechanisms, including reductive dechlorination and aerobic oxidation. However, the mechanism of the CHCs transformation in joint H₂ and O₂ system (H₂/O₂ system) is still unclear. In this study, the degradation kinetics of trichloroethene (TCE) were investigated and DNA stable isotope probing (DNA-SIP) were used to explore the synergistic mechanism of functional microorganisms on TCE degradation under the condition of H₂/O₂ coexistence. In the H₂/O₂ microcosm, TCE was significantly removed by 13.00 μM within 40 days, much higher than N₂, H₂ and O₂ microcosms, and 1,1-DCE was detected as an intermediate. DNA-SIP technology identified three anaerobic TCE metabolizers, five aerobic TCE metabolizers, nine hydrogen-oxidizing bacteria (HOB), some TCE metabolizers utilizing limited O₂, and some anaerobic dechlorinating bacteria reductively using H₂ to dechlorinate TCE. It is also confirmed for the first time that 3 OUTs belonging to Methyloversatilis and SH-PL14 can simultaneously utilize H₂ and O₂ as energy sources to grow and metabolize TCE or 1,1-DCE. HOB may provide carbon sources or electron acceptors or donors for TCE biotransformation. These findings confirm the coexistence of anaerobic and aerobic TCE metabolizers and degraders, which synergistically promoted the conversion of TCE in the joint H₂/O₂ system. Our results provide more information about the functional microbe resources and synergetic mechanisms for TCE degradation.

Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria

A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation.

Feasibility and potential of laccase-based enzyme in wastewater treatment through sustainable approach: A review

The worldwide increase in metropolitan cities and rise in industrialization have resulted in the assimilation of hazardous pollutants into the ecosystems. Different physical, chemical and biological techniques have been employed to remove these toxins from water bodies. Several bioprocess applications using microbes and their enzymes are utilized to achieve the goal. Biocatalysts, such as laccases, are employed explicitly to deplete a variety of organic pollutants. However, the degradation of contaminants using biocatalysts has many disadvantages concerning the stability and activity of the enzyme. Hence, they are immobilized on different supports to improve the enzyme kinetics and recyclability. Furthermore, standard wastewater treatment methods are not effective in eliminating all the contaminants. As a result, membrane separation technologies have emerged to overcome the limitations of traditional wastewater treatment methods. Moreover, enzymes immobilized onto these membranes have generated new avenues in wastewater purification technology. This review provides the latest information on laccases from diverse sources, their molecular framework and their mode of action. This report also gives information about various immobilization techniques and the application of membrane bioreactors to eliminate and biotransform hazardous contaminants. In a nutshell, laccases appear to be the most promising biocatalysts for green and cost-efficient wastewater treatment technologies.

Improvement in the Environmental Stability of Haloalkane Dehalogenase with Self-Assembly Directed Nano-Hybrid with Iron Phosphate

Haloalkane dehalogenase (DhaA) catalyzes the hydrolysis of halogenated compounds through the cleavage of carbon halogen bonds. However, the low activity, poor environmental stability, and difficult recycling of free DhaA greatly increases the economic cost of practical application. Inspired by the organic–inorganic hybrid system, an iron-based hybrid nanocomposite biocatalyst FeHN@DhaA is successfully constructed to enhance its environmental tolerability. A series of characterization methods demonstrate that the synthesized enzyme–metal iron complexes exhibit granular nanostructures with good crystallinity. Under optimized conditions, the activity recovery and the effective encapsulation yield of FeHN@DhaA are 138.54% and 87.21%, respectively. Moreover, it not only exhibits excellent immobilized enzymatic properties but also reveals better tolerance to extreme acid, and is alkali compared with the free DhaA. In addition, the immobilized enzyme FeHN@DhaA can be easily recovered and has a satisfactory reusability, retaining 57.8% of relative activity after five reaction cycles. The results of this study might present an alternative immobilized DhaA-based clean biotechnology for the decontamination of organochlorine pollutants.

Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling

HaloTag labeling technology has introduced unrivaled potential in protein chemistry and molecular and cellular biology. A wide variety of ligands have been developed to meet the specific needs of diverse applications, but only a single protein tag, DhaAHT, is routinely used for their incorporation. Following a systematic kinetic and computational analysis of different reporters, a tetramethylrhodamine- and three 4-stilbazolium-based fluorescent ligands, we showed that the mechanism of incorporating different ligands depends both on the binding step and the efficiency of the chemical reaction. By studying the different haloalkane dehalogenases DhaA, LinB, and DmmA, we found that the architecture of the access tunnels is critical for the kinetics of both steps and the ligand specificity. We showed that highly efficient labeling with specific ligands is achievable with natural dehalogenases. We propose a simple protocol for selecting the optimal protein tag for a specific ligand from the wide pool of available enzymes with diverse access tunnel architectures. The application of this protocol eliminates the need for expensive and laborious protein engineering.

Genome evolution related to γ-hexachlorocyclohexane metabolic function in the soil microbial population

γ-Hexachlorocyclohexane (γ-HCH)-degrading strain, Sphingobium sp. TA15, was newly isolated from an experimental field soil from which the archetypal γ-HCH-degrading strain, S. japonicum UT26, was isolated previously. Comparison of the complete genome sequences of these 2 strains revealed that TA15 shares the same basic genome backbone with UT26, but also has the variable regions that are presumed to have changed either from UT26 or from a putative common ancestor. Organization and localization of lin genes of TA15 were different from those of UT26. It was inferred that transposition of IS6100 had played a crucial role in these genome rearrangements. The accumulation of toxic dead-end products in TA15 was lower than in UT26, suggesting that TA15 utilizes γ-HCH more effectively than UT26. These results suggested that genome evolution related to the γ-HCH metabolic function in the soil microbial population is ongoing.

Bioaugmentation as a green technology for hydrocarbon pollution remediation. Problems and prospects

Environmental pollution mitigation measure involving bioremediation technology is a sustainable intervention for a greener ecosystem biorecovery, especially the obnoxious hydrocarbons, xenobiotics, and other environmental pollutants induced by anthropogenic stressors. Several successful case studies have provided evidence to this paradigm including the putative adoption that the technology is eco-friendly, cost-effective, and shows a high tendency for total contaminants mineralization into innocuous bye-products. The present review reports advances in bioremediation, types, and strategies conventionally adopted in contaminant clean-up. It identified that natural attenuation and biostimulation are faced with notable limitations including the poor remedial outcome under the natural attenuation system and the residual contamination occasion following a biostimulation operation. It remarks that the use of genetically engineered microorganisms shows a potentially promising insight as a prudent remedial approach but is currently challenged by few ethical restrictions and the rural unavailability of the technology. It underscores that bioaugmentation, particularly the use of high cell density assemblages referred to as microbial consortia possess promising remedial prospects thus offers a more sustainable environmental security. The authors, therefore, recommend bioaugmentation for large scale contaminated sites in regions where environmental degradation is commonplace.

Conjugation of haloalkane dehalogenase DhaA with arabinogalactan to increase its stability

Haloalkane dehalogenase DhaA can catalyze the hydrolytic cleavage of carbonhalogen bonds, along with production of the corresponding alcohol, a proton and a halide. However, DhaA suffers from poor environmental tolerance, such as sensitivity to high temperature, low pH and hypersaline. Arabinogalactan (AG) is a hydrophilic polysaccharide with highly branched long chains. DhaA was conjugated with AG to improve the environmental stability of DhaA in the present study. Each DhaA was averagely conjugated with 4∼5 AG molecules. Conjugation of AG essentially maintained the enzymatic activity of DhaA (91.4 %) without apparent structural alteration. The hydration layer formed by AG could reduce the solvent accessible area of DhaA and slow the protonation process, thereby improving the pH and high salt stability of DhaA. In particular, the remaining activities of the conjugate (AG-DhaA) were 35.3 % after treatment at pH4.0 for 1 h, and 80.8 % in 1 M NaCl after treatment for 16 h. As compared with DhaA, AG-DhaA showed slightly different kinetic parameters (K M of 1.90 μmol/L and k cat of 2.60 s -1).

New insights into the degradation of synthetic pollutants in contaminated environments

The environment is contaminated by synthetic contaminants owing to their extensive applications globally. Hence, the removal of synthetic pollutants (SPs) from the environment has received widespread attention. Different remediation technologies have been investigated for their abilities to eliminate SPs from the ecosystem; these include photocatalysis, sonochemical techniques, nanoremediation, and bioremediation. SPs, which can be organic or inorganic, can be degraded by microbial metabolism at contaminated sites. Owing to their diverse metabolisms, microbes can adapt to a wide variety of environments. Several microbial strains have been reported for their bioremediation potential concerning synthetic chemical compounds. The selection of potential strains for large-scale removal of organic pollutants is an important research priority. Additionally, novel microbial consortia have been found to be capable of efficient degradation owing to their combined and co-metabolic activities. Microbial engineering is one of the most prominent and promising techniques for providing new opportunities to develop proficient microorganisms for various biological processes; here, we have targeted the SP-degrading mechanisms of microorganisms. This review provides an in-depth discussion of microbial engineering techniques that are used to enhance the removal of both organic and inorganic pollutants from different contaminated environments and under different conditions. The degradation of these pollutants is investigated using abiotic and biotic approaches; interestingly, biotic approaches based on microbial methods are preferable owing to their high potential for pollutant removal and cost-effectiveness.

The ever-expanding limits of enzyme catalysis and biodegradation: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds

Biodegradation is simply the metabolism of anthropogenic, or otherwise unwanted, chemicals in our environment, typically by microorganisms. The metabolism of compounds commonly found in living things is limited to several thousand metabolites whereas ∼100 million chemical substances have been devised by chemical synthesis, and ∼100 000 are used commercially. Since most of those compounds are not natively found in living things, and some are toxic or carcinogenic, the question arises as to whether there is some organism somewhere with the enzymes that can biodegrade them. Repeatedly, anthropogenic chemicals have been denoted 'non-biodegradable,' only to find they are reactive with one or more enzyme(s). Enzyme reactivity has been organized into categories of functional group transformations. The discovery of new functional group transformations has continually expanded our knowledge of enzymes and biodegradation. This expansion of new-chemical biodegradation is driven by the evolution and spread of newly evolved enzymes. This review describes the biodegradation of widespread commercial chemicals with a focus on four classes: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds. Polyaromatic hydrocarbons include some of the most carcinogenic compounds known. Polychlorinated compounds include polychlorinated biphenyls (PCBs) and many pesticides of the twentieth century. Polyfluorinated compounds are a major focus of bioremediation efforts today. Polymers are clogging landfills, killing aquatic species in the oceans and increasingly found in our bodies. All of these classes of compounds, each thought at one time to be non-biodegradable, have been shown to react with natural enzymes. The known limits of enzyme catalysis, and hence biodegradation, are continuing to expand.

Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17

Haloalkane dehalogenases are enzymes with a broad application potential in biocatalysis, bioremediation, biosensing and cell imaging. The new haloalkane dehalogenase DmxA originating from the psychrophilic bacterium Marinobacter sp. ELB17 surprisingly possesses the highest thermal stability (apparent melting temperature Tm,app = 65.9 °C) of all biochemically characterized wild type haloalkane dehalogenases belonging to subfamily II. The enzyme was successfully expressed and its crystal structure was solved at 1.45 Å resolution. DmxA structure contains several features distinct from known members of haloalkane dehalogenase family: (i) a unique composition of catalytic residues; (ii) a dimeric state mediated by a disulfide bridge; and (iii) narrow tunnels connecting the enzyme active site with the surrounding solvent. The importance of narrow tunnels in such paradoxically high stability of DmxA enzyme was confirmed by computational protein design and mutagenesis experiments.

Lessons from the genomes of lindane-degrading sphingomonads

Bacterial strains capable of degrading man-made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ-hexachlorocyclohexane, γ-HCH, or γ-BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane-degrading sphingomonad strains clearly demonstrated that (i) lindane-degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane-degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic 'gene pool' available to bacteria.

Bacillus subtilis Spore Surface Display of Haloalkane Dehalogenase DhaA

The haloalkane dehalogenase DhaA can degrade sulfur mustard (2,2'-dichlorethyl sulfide; also known by its military designation HD) in a rapid and environmentally safe manner. However, DhaA is sensitive to temperature and pH, which limits its applications in natural or harsh environments. Spore surface display technology using resistant spores as a carrier to ensure enzymatic activity can reduce production costs and extend the range of applications of DhaA. To this end, we cloned recombinant Bacillus subtilis spores pHY300PLK-cotg-dhaa-6his/DB104(FH01) for the delivery of DhaA from Rhodococcus rhodochrous NCIMB 13064. A dot blotting showed that the fusion protein CotG-linker-DhaA accounted for 0.41% ± 0.03% (P < 0.01) of total spore coat proteins. Immunofluorescence analyses confirmed that DhaA was displayed on the spore surface. The hydrolyzing activity of DhaA displayed on spores towards the HD analog 2-chloroethyl ethylsulfide was 1.74 ± 0.06 U/mL (P < 0.01), with a specific activity was 0.34 ± 0.04 U/mg (P < 0.01). This is the first demonstration that DhaA displayed on the surface of B. subtilis spores retains enzymatic activity, which suggests that it can be used effectively in real-world applications including bioremediation of contaminated environments.

Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5

Haloalkane dehalogenases (HLDs) convert halogenated aliphatic pollutants to less toxic compounds by a hydrolytic mechanism. Owing to their broad substrate specificity and high enantioselectivity, haloalkane dehalogenases can function as biosensors to detect toxic compounds in the environment or can be used for the production of optically pure compounds. Here, the structural analysis of the haloalkane dehalogenase DpcA isolated from the psychrophilic bacterium Psychrobacter cryohalolentis K5 is presented at the atomic resolution of 1.05 Å. This enzyme exhibits a low temperature optimum, making it attractive for environmental applications such as biosensing at the subsurface environment, where the temperature typically does not exceed 25°C. The structure revealed that DpcA possesses the shortest access tunnel and one of the most widely open main tunnels among structural homologs of the HLD-I subfamily. Comparative analysis revealed major differences in the region of the α4 helix of the cap domain, which is one of the key determinants of the anatomy of the tunnels. The crystal structure of DpcA will contribute to better understanding of the structure-function relationships of cold-adapted enzymes.

Kinetics and stereochemistry of LinB-catalyzed δ-HBCD transformation: Comparison of in vitro and in silico results

LinB is a haloalkane dehalogenase found in Sphingobium indicum B90A, an aerobic bacterium isolated from contaminated soils of hexachlorocyclohexane (HCH) dumpsites. We showed that this enzyme also converts hexabromocyclododecanes (HBCDs). Here we give new insights in the kinetics and stereochemistry of the enzymatic transformation of δ-HBCD, which resulted in the formation of two pentabromocyclododecanols (PBCDols) as first- (P_1δ, P_2δ) and two tetrabromocyclododecadiols (TBCDdiols) as second-generation products (T_1δ, T_2δ). Enzymatic transformations of δ-HBCD, α₁-PBCDol, one of the transformation products, and α₂-PBCDol, its enantiomer, were studied and modeled with Michaelis-Menten (MM) kinetics. Respective MM-parameters K_M, v_max, k_cat/K_M indicated that δ-HBCD is the best LinB substrate followed by α₂- and α₁-PBCDol. The stereochemistry of these transformations was modeled in silico, investigating respective enzyme-substrate (ES) and enzyme-product (EP) complexes. One of the four predicted ES-complexes led to the PBCDol product P_1δ, identical to α₂-PBCDol with the 1R,2R,5S,6R,9R,10S-configuration. An S_N2-like substitution of bromine at C6 of δ-HBCD by Asp-108 of LinB and subsequent hydrolysis of the alkyl-enzyme led to α₂-PBCDol. Modeling results further indicate that backside attacks at C1, C9 and C10 are reasonable too, selectively binding leaving bromide ions in a halide pocket found in LinB. Docking with α₂-PBCDol, also allowed productive enzyme binding. A TBCD-1,5-diol with the 1S,2S,5R,6R,9S,10R-configuration is the predicted second-generation product T_1δ. In conclusion, in vitro- and in silico findings now allow a detailed description of step-wise enzymatic dehalohydroxylation reactions of δ-HBCD to specific PBCDols and TBCDdiols at Å-resolution and predictions of their stereochemistry.

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site

Haloalkane dehalogenases catalyze the hydrolysis of halogen-carbon bonds in organic halogenated compounds and as such are of great utility as biocatalysts. The crystal structures of the haloalkane dehalogenase DhlA from the bacterium from Xanthobacter autotrophicus GJ10, specifically adapted for the conversion of the small 1,2-dichloroethane (DCE) molecule, display the smallest catalytic site (110 Å3) within this enzyme family. However, during a substrate-specificity screening, we noted that DhlA can catalyze the conversion of far bulkier substrates, such as the 4-(bromomethyl)-6,7-dimethoxy-coumarin (220 Å3). This large substrate cannot bind to DhlA without conformational alterations. These conformational changes have been previously inferred from kinetic analysis, but their structural basis has not been understood. Using molecular dynamic simulations, we demonstrate here the intrinsic flexibility of part of the cap domain that allows DhlA to accommodate bulky substrates. The simulations displayed two routes for transport of substrates to the active site, one of which requires the conformational change and is likely the route for bulky substrates. These results provide insights into the structure-dynamics function relationships in enzymes with deeply buried active sites. Moreover, understanding the structural basis for the molecular adaptation of DhlA to 1,2-dichloroethane introduced into the biosphere during the industrial revolution provides a valuable lesson in enzyme design by nature.

Ligand Access Channels in Cytochrome P450 Enzymes: A Review

Quantitative structure-activity relationships may bring invaluable information on structural elements of both enzymes and substrates that, together, govern substrate specificity. Buried active sites in cytochrome P450 enzymes are connected to the solvent by a network of channels exiting at the distal surface of the protein. This review presents different in silico tools that were developed to uncover such channels in P450 crystal structures. It also lists some of the experimental evidence that actually suggest that these predicted channels might indeed play a critical role in modulating P450 functions. Amino acid residues at the entrance of the channels may participate to a first global ligand recognition of ligands by P450 enzymes before they reach the buried active site. Moreover, different P450 enzymes show different networks of predicted channels. The plasticity of P450 structures is also important to take into account when looking at how channels might play their role.

Contemporary enzyme based technologies for bioremediation: A review

The persistent disposal of xenobiotic compounds like insecticides, pesticides, fertilizers, plastics and other hydrocarbon containing substances is the major source of environmental pollution which needs to be eliminated. Many contemporary remediation methods such as physical, chemical and biological are currently being used, but they are not sufficient to clean the environment. The enzyme based bioremediation is an easy, quick, eco-friendly and socially acceptable approach used for the bioremediation of these recalcitrant xenobiotic compounds from the natural environment. Several microbial enzymes with bioremediation capability have been isolated and characterized from different natural sources, but less production of such enzymes is a limiting their further exploitation. The genetic engineering approach has the potential to get large amount of recombinant enzymes. Along with this, enzyme immobilization techniques can boost the half-life, stability and activity of enzymes at a significant level. Recently, nanozymes may offer the potential bioremediation ability towards a broad range of pollutants. In the present review, we have described a brief overview of the microbial enzymes, different enzymes techniques (genetic engineering and immobilization of enzymes) and nanozymes involved in bioremediation of toxic, carcinogenic and hazardous environmental pollutants.

OleB from Bacterial Hydrocarbon Biosynthesis Is a β-Lactone Decarboxylase That Shares Key Features with Haloalkane Dehalogenases

OleB is an α/β-hydrolase found in bacteria that biosynthesize long-chain olefinic hydrocarbons, but its function has remained obscure. We report that OleB from the Gram-negative bacterium Xanthomonas campestris performs an unprecedented β-lactone decarboxylation reaction, to complete cis-olefin biosynthesis. OleB reactions monitored by ¹H nuclear magnetic resonance spectroscopy revealed a selectivity for decarboxylating cis-β-lactones and no discernible activity with trans-β-lactones, consistent with the known configuration of pathway intermediates. Protein sequence analyses showed OleB proteins were most related to haloalkane dehalogenases (HLDs) and retained the canonical Asp-His-Asp catalytic triad of HLDs. Unexpectedly, it was determined that an understudied subfamily, denoted as HLD-III, is comprised mostly of OleB proteins encoded within oleABCD gene clusters, suggesting a misannotation. OleB from X. campestris showed very low dehalogenase activity only against haloalkane substrates with long alkyl chains. A haloalkane substrate mimic alkylated wild-type X. campestris OleB but not OleB_D114A, implicating this residue as the active site nucleophile as in HLDs. A sequence-divergent OleB, found as part of a natural OleBC fusion and classified as an HLD-III, from the Gram-positive bacterium Micrococcus luteus was demonstrated to have the same activity, stereochemical preference, and dependence on the proposed Asp nucleophile. H₂¹⁸O studies with M. luteus OleBC suggested that the canonical alkyl-enzyme intermediate of HLDs is hydrolyzed differently by OleB enzymes, as ¹⁸O is not incorporated into the nucleophilic aspartic acid. This work defines a previously unrecognized reaction in nature, functionally identifies some HLD-III enzymes as β-lactone decarboxylases, and posits an enzymatic mechanism of β-lactone decarboxylation.

Biotransformation of hexabromocyclododecanes with hexachlorocyclohexane-transforming Sphingobium chinhatense strain IP26

Bacterial evolution has resulted in the appearance of several Sphingomonadacea strains that gained the ability to metabolize hexachlorocyclohexanes (HCHs). HCHs have been widely used as pesticides but were banned under the Stockholm Convention on persistent organic pollutants (POPs) in 2009. Here we present evidence for bacterial transformation reactions of hexabromocyclododecanes (HBCDs), which are structurally related to HCHs. HBCDs were used as flame retardants. They are now also considered as POPs and their production and use is restricted since 2013. Racemic α-, β-, and γ-HBCDs and their mixture were exposed to Sphingobium chinhatense IP26 in resting cell assays in parallel to β-HCH. All HBCD stereoisomers were converted with (-)β-HBCD being the best and both α-HBCD enantiomers the poorest substrates. HBCD conversion rates were 27-430 times slower than that of β-HCH. Three generations of hydroxylated transformation products were observed, 7 pentabromocyclododecanol isomers (PeBCD-ols), 11 tetrabromocyclododecadiols (TeBCD-diols) and 3 tribromocyclododecatriols (TrBCD-triols). The conversion of (+)α-, (-)β- and (-)γ-HBCD was faster than those of their enantiomers. Therefore the respective enantiomeric excess increased to 3 ± 1%, 36 ± 1% and 6 ± 2% during 48 h of bacterial exposure. PeBCD-ols appeared first, followed by TeBCD-diols and TrBCD-triols indicating stepwise hydrolytic dehalogenation reactions. In conclusion, severe HCH pollution at geographically distinct dumpsites triggered bacterial evolution to express enzymes transforming such compounds. We used S. chinhatense IP26 bacteria to transform structurally related HBCDs, also regulated under the Stockholm Convention. Such bacteria might be useful for bioremediation but the toxicity of the numerous transformation products observed must be assessed in advance.

Complete sampling of an enzyme reaction pathway: a lesson from gas phase simulations

With proper sampling strategy, convergence of free energy profiles of biomolecular reactions in the gas phase can be achieved in microseconds of simulation.

Comparison of the complete genome sequences of four γ-hexachlorocyclohexane-degrading bacterial strains: insights into the evolution of bacteria able to degrade a recalcitrant man-made pesticide

γ-Hexachlorocyclohexane (γ-HCH) is a recalcitrant man-made chlorinated pesticide. Here, the complete genome sequences of four γ-HCH-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-HCH degrader, were compared. Together with several experimental data, we showed that (i) all the four strains carry almost identical linA to linE genes for the conversion of γ-HCH to maleylacetate (designated “specific” lin genes), (ii) considerably different genes are used for the metabolism of maleylacetate in one of the four strains, and (iii) the linKLMN genes for the putative ABC transporter necessary for γ-HCH utilization exhibit structural divergence, which reflects the phylogenetic relationship of their hosts. Replicon organization and location of the lin genes in the four genomes are significantly different with one another, and that most of the specific lin genes are located on multiple sphingomonad-unique plasmids. Copies of IS6100, the most abundant insertion sequence in the four strains, are often located in close proximity to the specific lin genes. Analysis of the footprints of target duplication upon IS6100 transposition and the experimental detection of IS6100 transposition strongly suggested that the IS6100 transposition has caused dynamic genome rearrangements and the diversification of lin-flanking regions in the four strains.