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

Comprehensive review on Haloalkane dehalogenase (LinB): a β-hexachlorocyclohexane (HCH) degrading enzyme

Haloalkane dehalogenase, LinB, is a member of the α/β hydrolase family of enzymes. It has a wide range of halogenated substrates, but, has been mostly studied in context of degradation of hexachlorocyclohexane (HCH) isomers, especially β-HCH (5-12% of total HCH isomers), which is the most recalcitrant and persistent among all the HCH isomers. LinB was identified to directly act on β-HCH in a one or two step transformation which decreases its toxicity manifold. Thereafter, many studies focused on LinB including its structure determination using X-ray crystallographic studies, structure comparison with other haloalkane dehalogenases, substrate specificity and kinetic studies, protein engineering and site-directed mutagenesis studies in search of better catalytic activity of the enzyme. LinB was mainly identified and characterized in bacteria belonging to sphingomonads. Detailed sequence comparison of LinB from different sphingomonads further revealed the residues critical for its activity and ability to catalyze either one or two step transformation of β-HCH. Association of LinB with IS6100 elements is also being discussed in detail in sphingomonads. In this review, we summarized vigorous efforts done by different research groups on LinB for developing better bioremediation strategies against HCH contamination. Also, kinetic studies, protein engineering and site directed mutagenesis studies discussed here forms the basis of further exploration of LinB's role as an efficient enzyme in bioremediation projects.

The effects of long-term hexabromocyclododecanes contamination on microbial communities in the microcosms

The adaptation of microbial community to the long-term contamination of hexabromocyclododecanes (HBCDs) has not been well studied. Our previous study found that the HBCDs contamination in the microcosms constructed of sediments from two different mangrove forests in 8 months resulted in serious acidification (pH2-3). This study reanalyzed previous sequencing data and compared them with data after 20 months to investigate the adaptive properties of microbial communities in the stress of HBCDs and acidification. It hypothesized that the reassembly was based on the fitness of taxa. The results indicated that eukaryotes and fungi might have better adaptive capacity to these deteriorated habitats. Eukaryotic taxa Eufallia and Syncystis, and fungal taxa Wickerhamomyces were only detected after 20 months of contamination. Moreover, eukaryotic taxa Caloneis and Nitzschia, and fungal taxa Talaromyces were dominant in most of microbial communities (14.467-95.941%). The functional compositions were sediment-dependent and more divergent than community reassemblies. Network and co-occurrence analysis suggested that acidophiles such as Acidisoma and Acidiphilium were gaining more positive relations in the long-term stress. The acidophilic taxa and genes involved in resistance to the acidification and toxicity of HBCDs were enriched, for example, bacteria Acidisoma and Acidiphilium, archaea Thermogymnomonas, and eukaryotes Nitzschia, and genes kdpC, odc1, polA, gst, and sod-2. These genes involved in oxidative stress response, energy metabolism, DNA damage repair, potassium transportation, and decarboxylation. It suggested that the microbial communities might cope with the stress from HBCDs and acidification via multiple pathways. The present research shed light on the evolution of microbial communities under the long-term stress of HBCDs contamination and acidification.

Efficient degradation of hexabromocyclododecane using montmorillonite supported nano-zero-valent iron and Citrobacter sp. Y3

The coupling of modified nanoscale zero-valent iron (nZVI) with organohalide-degrading bacteria provides a promising solution for the remediation of hexabromocyclododecane (HBCD)-contaminated environments. However, the interactions between modified nZVI and dehalogenase bacteria are intricate, and the mechanisms of synergistic action and electron transfer are not clear, and requires further specific investigation. In this study, HBCD was used as a model pollutant, and stable isotope analysis revealed that organic montmorillonite (OMt)-supported nZVI coupled with the degrading bacterial strain Citrobacter sp. Y3 (nZVI/OMt-Y3) can use [¹³C]HBCD as the sole carbon source and degrade or even mineralise it into ¹³CO₂ with a maximum conversion rate of 100% within approximately 5 days. Analysis of the intermediates showed that the degradation of HBCD mainly involves three different pathways: dehydrobromination, hydroxylation, and debromination. The proteomics results showed that nZVI introduction promoted the transport of electrons and debromination. Combining the results from XPS, FTIR, and Raman spectroscopy with the analysis results of proteinomics and biodegradation products, we verified the process of electron transport and proposed a metabolic mechanism of HBCD degradation by the nZVI/OMt-Y3. Moreover, this study provides insightful avenues and models for the further remediation of HBCD and other similar pollutants in the environment.

Citrobacter sp. Y3 harbouring novel gene HBCD-hd-1 mineralizes hexabromocyclododecane via new metabolic pathways according to multi-omics characterization

Hexabromocyclododecane (HBCD) is a typical persistent organic pollutant that is widely detected in the environment. Despite the significant efforts put into its mineralisation, there is still a lack of microorganism resources that can completely mineralise HBCD. Stable isotope analysis revealed that the Citrobacter sp. Y3 can use [¹³C]HBCD as its sole carbon source and degrade or even mineralise it into ¹³CO₂, with a maximum conversion rate of 100% in approximately 14 days. Strain Y3 could completely mineralise HBCD, which it used as its only carbon source, and six debromination enzymes related to HBCD degradation were found in Y3, including haloalkane dehalogenase (DhaA), haloacid dehalogenase (HAD), etc. A functional gene named HBCD-hd-1, encoding a HAD, was found to be upregulated during HBCD degradation and heterologously expressed in Escherichia coli. Recombinant E. coli with the HBCD-hd-1 gene transformed the typical intermediate 4-bromobutyric acid to 4-hydroxybutanoic acid and showed excellent degradation performance on HBCD, accompanied by nearly 100% bromine (Br) ion generation. The expression of HBCD-hd-1 in Y3 rapidly accelerated the biodegradation of HBCD. With HBCD as its sole carbon source, strain Y3 could potentially degrade HBCD, especially in a low-nutrient environment.

Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms

The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.

Enzymatic synthesis and formation kinetics of mono- and di-hydroxylated chlorinated paraffins with the bacterial dehalogenase LinB from Sphingobium indicum

Transformation studies of chlorinated paraffins (CPs) and the effects of CP transformation products on humans, biota and environment are rare. The focus here is on hydroxylation reactions. As for polyhalogenated persistent organic pollutants (POPs) in general, hydroxylation reactions convert lipophilic material to more polar compounds with increased mobility. We investigated the in-vitro transformation of single-chain CP-mixtures to hydroxylated products with the dehalogenase LinB from Sphingobium indicum. C₁₁-, C₁₂- and C₁₃-single-chain CP-homologues were exposed to LinB and mono-hydroxylated (CP-ols) and di-hydroxylated (CP-diols) transformation products were formed. Liquid-chromatography coupled to mass-spectrometry (LC-MS) was used to detect hydroxylated products and to separate them from the starting material. The presented data can be used to identify these CP-ol and CP-diol homologues in other samples. Hydroxylated products had lower chlorination degrees (n_Cl) than respective CP-starting-materials. Reactive and persistent CP-material was found in each homologue group. Reactive material is converted within hours by LinB, while more persistent CPs are transformed within days. Homologue-specific kinetic models were established to simulate the stepwise hydroxylation of persistent CPs to mono- and di-hydroxylated products. First-order rate constants for the formation of CP-ols (k₁) and CP-diols (k₂) were deduced for different homologues. Lower-chlorinated CP-ols did not accumulate to large extent and were transformed quickly to CP-diols, while higher-chlorinated CP-ols and -diols both accumulated. By enzymatic transformation of single-chain CPs with LinB, we synthesized unique sets of mono- and di-hydroxylated materials, which can be used as analytical standards and as starting materials for metabolic, toxicity and environmental fate studies.

Hexabromocyclododecanes Are Dehalogenated by CYP168A1 from Pseudomonas aeruginosa Strain HS9

Hexabromocyclododecanes (HBCDs) are widely used brominated flame retardants that cause antidiuretic hormone syndrome and even induce cancer. However, little information is available about the degradation mechanisms of HBCDs. In this study, genomic and proteomic analyses, reverse transcription-quantitative PCR, and gene knockout assays reveal that a cytochrome P450-encoding gene is responsible for HBCD catabolism in Pseudomonas aeruginosa HS9. The CO difference spectrum of the enzyme CYP168A1 was matched to P450 characteristics via UV visibility. We demonstrate that the reactions of debromination and hydrogenation are carried out one after another based on detection of the metabolites pentabromocyclododecanols (PBCDOHs), tetrabromocyclododecadiols (TBCDDOHs), and bromide ion. In the ¹⁸O isotope experiments, PBCD¹⁸OHs were only detected in the H₂¹⁸O group, proving that the added oxygen is derived from H₂O, not from O₂. This study elucidates the degradation mechanism of HBCDs by Pseudomonas. IMPORTANCE Hexabromocyclododecanes (HBCDs) are environmental pollutants that are widely used in industry. In this study, we identified and characterized a novel key dehalogenase, CYP168A1, that is responsible for HBCD degradation from Pseudomonas aeruginosa strain HS9. This study provides new insights into understanding biodegradation of HBCDs.

Kinetics, pathways and toxicity of hexabromocyclododecane biodegradation: Isolation of the novel bacterium Citrobacter sp. Y3

This research investigated the biodegradation kinetics, pathways and ecological risk of hexabromocyclododecane (HBCD) by a novel bacterium Citrobacter sp. Y3. Results showed the biodegradation followed a first-order model. The specific degradation rate constant of HBCD were obviously higher in batch experiments with combined carbon sources (k: 0.156-0.290 d^-1) than those using HBCD as the sole carbon source (k: 0.055 d^-1). Correspondingly, the degradation half-life became much shorter (T_1/2: 2.39-4.44 d vs T_1/2: 13.7 d). HBCD could be degraded through dehydrobromination and dehalohydroxylation, of which six possible degradation products were detected. To evaluate the ecological risk of HBCD biodegradation products, acute toxicity tests were assessed for the first time. The acute toxicity decreased slowly during treatment for 3-5 d and then decreased sharply. In general, treatment by Strain Y3 is not only a biodegradation process but also a detoxification process, thus it shows potential for bioremediation of HBCD contaminated sites.

Microbial debromination of hexabromocyclododecanes

Hexabromocyclododecanes (HBCDs), a new sort of brominated flame retardants (BFRs), are globally prevalent and recalcitrant toxic environmental pollutants. HBCDs have been found in many environmental media and even in the human body, leading to serious health concerns. HBCDs are biodegradable in the environment. By now, dozens of bacteria have been discovered with the ability to transform HBCDs. Microbial debromination of HBCDs is via HBr-elimination, HBr-dihaloelimination, and hydrolytic debromination. Biotic transformation of HBCDs yields many hydroxylated and lower brominated compounds which lack assessment of ecological toxicity. Bioremediation of HBCD pollution has only been applied in the laboratory. Here, we review the current knowledge about microbial debromination of HBCDs, aiming to promote the bioremediation applied in HBCD contaminated sites. KEY POINTS: • Microbial debromination of HBCDs is via hydrolytic debromination, HBr-elimination, and HBr-dihaloelimination. • Newly occurred halogenated contaminants such as HBCDs hitch the degradation pathway tamed by previously discharged anthropogenic organohalides. • Strategy that combines bioaugmentation with phytoremediation for bioremediation of HBCD pollution is promising.

Transformation of ε-HBCD with the Sphingobium Indicum enzymes LinA1, LinA2 and LinATM, a triple mutant of LinA2

Hexabromocyclododecanes (HBCDs) were used as flame-retardants until their ban in 2013. Among the 16 stereoisomers known, ε-HBCD has the highest symmetry. This makes ε-HBCD an interesting substrate to study the selectivity of biotransformations. We expressed three LinA dehydrohalogenase enzymes in E. coli bacteria, two wild-type, originating from Sphingobium indicum B90A bacteria and LinATM, a triple mutant of LinA2, with mutations of L96C, F113Y and T133 M. These enzymes are involved in the hexachlorocyclohexane (HCH) metabolism, specifically of the insecticide γ-HCH (Lindane). We studied the reactivity of those eight HBCD stereoisomers found in technical HBCD. Furthermore, we compared kinetics and selectivity of these LinA variants with respect to ε-HBCD. LC-MS data indicate that all enzymes converted ε-HBCD to pentabromocyclododecenes (PBCDens). Transformations followed Michaelis-Menten kinetics. Rate constants k_cat and enzyme specificities k_cat/K_M indicate that ε-HBCD conversion was fastest and most specific with LinA2. Only one PBCDen stereoisomer was formed by LinA2, while LinA1 and LinATM produced mixtures of two PBCDE enantiomers at three times lower rates than LinA2. In analogy to the biotransformation of (-)β-HBCD, with selective conversion of dibromides in R-S-configuration, we assume that 1E,5S,6R,9S,10R-PBCDen is the ε-HBCD transformation product from LinA2. Implementing three amino acids of the LinA1 substrate-binding site into LinA2 resulted in a triple mutant with similar kinetics and product specificity like LinA1. Thus, point-directed mutagenesis is an interesting tool to modify the substrate- and product-specificity of LinA enzymes and enlarge their scope to metabolize other halogenated persistent organic pollutants regulated under the Stockholm Convention.

The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step

Transport of ligands between bulk solvent and the buried active sites is a critical event in the catalytic cycle of many enzymes. The rational design of transport pathways is far from trivial due to the lack of knowledge about the effect of mutations on ligand transport. The main and an auxiliary tunnel of haloalkane dehalogenase LinB have been previously engineered for improved dehalogenation of 1,2-dibromoethane (DBE). The first chemical step of DBE conversion was enhanced by L177W mutation in the main tunnel, but the rate-limiting product release was slowed down because the mutation blocked the main access tunnel and hindered protein dynamics. Three additional mutations W140A + F143L + I211L opened-up the auxiliary tunnel and enhanced the product release, making this four-point variant the most efficient catalyst with DBE. Here we study the impact of these mutations on the catalysis of bulky aromatic substrates, 4-(bromomethyl)-6,7-dimethoxycoumarin (COU) and 8-chloromethyl-4,4'-difluoro-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (BDP). The rate-limiting step of DBE conversion is the product release, whereas the catalysis of COU and BDP is limited by the chemical step. The catalysis of COU is mainly impaired by the mutation L177W, whereas the conversion of BDP is affected primarily by the mutations W140A + F143L + I211L. The combined computational and kinetic analyses explain the differences in activities between the enzyme-substrate pairs. The effect of tunnel mutations on catalysis depends on the rate-limiting step, the complementarity of the tunnels with the substrates and is clearly specific for each enzyme-substrate pair.

The effects of prosperity indices and land use indicators of an urban conurbation on the occurrence of hexabromocyclododecanes and tetrabromobisphenol A in surface soil in South China

Hexabromocyclododecane (HBCD) and tetrabromobisphenol A (TBBPA) are legacy brominated flame retardants which are still produced and used in China. In this study, 187 surface soils from the Pearl River Delta (PRD) urban conurbation in China were collected, and the effects of urban conurbation development on the concentrations, distributions and human exposure risk of HBCDs and TBBPA were investigated. The concentration ranges of Σ₃HBCD (sum of α-, β-, and γ-HBCD) and TBBPA in soil were below the limit of quantification (<LOQ) to 300 ng g^-1 dry weight (dw) and < LOQ to 53.1 ng g^-1 dw, respectively. Concentration levels of HBCDs and TBBPA in the PRD were affected both by distributions of land-use type and by the location of the city. Soils from residential areas contained the highest concentrations of Σ₃HBCD (median: 1.75 ng g^-1 dw) and TBBPA (1.92 ng g^-1 dw) among all land-use types. In addition, soils from the central PRD had higher Σ₃HBCD and TBBPA levels (0.46 and 0.90 ng g^-1 dw) than those from the surrounding areas (0.17 and 0.07 ng g^-1 dw). The concentrations of Σ₃HBCD and TBBPA were highly correlated with urbanization level, population density, regional GDP and per capita income in all cities studied (p < 0.01), which indicates that the prosperity of the urban conurbation may play an important role in soil contamination of HBCDs and TBBPA in the PRD. Children living in residential areas had the highest estimated daily intakes of Σ₃HBCD (7.09 pg kg^-1 d^-1) and TBBPA (7.76 pg kg^-1 d^-1), suggesting that people living in residential areas have a relatively higher exposure risk of HBCDs and TBBPA. This is a comprehensive study to report the effects of prosperity indices and land use indicators of an urban conurbation on the occurrence of HBCDs and TBBPA in soil in China.

Biodegradation of decabromodiphenyl ether (BDE-209) using a novel microbial consortium GY1: Cells viability, pathway, toxicity assessment, and microbial function prediction

GY1, a novel microbial consortium with efficient ability to degrade decabromodiphenyl ether (BDE-209) has been isolated and the sequencing analysis has been conducted. The results revealed that Hyphomicrobium, Pseudomonas, Aminobacter, Sphingopyxis, Chryseobacterium, Bacillus, Pseudaminobacter, Stenotrophomonas, Sphingobacterium and Microbacterium were the dominant genera, and the function genes involved in BDE-209 conversion were predicted by PICRUSt. When BDE-209 concentration increased from 0.5 to 10mg/L, its degradation efficiency declined from 57.2% to 22.3%. Various kinds of debrominated metabolites were detected during the biodegradation process, including BDE-208, BDE-207, BDE-206, BDE-205, BDE-190, BDE-181, BDE-155, BDE-154, BDE-99, BDE-47, BDE-17 and BDE-7. Also, the proportion of necrotic cells was observed during GY1 mediated degradation of BDE-209 to reveal the changes of cells viability under BDE-209 stress. Subsequent analysis showed that the reaction of BDE-209 with GY1 was a detoxification process and bioaugmentation with GY1 effectively enhanced BDE-209 degradation in actual water and water-sediment system.