BphK shows dechlorination activity against 4-chlorobenzoate, an end product of bph-promoted degradation of PCBs

Dechlorination of polychlorobiphenyl degradation metabolites by a recombinant glutathione S-transferase from Acidovorax sp. KKS102

A glutathione S-transferase (GST) with a potential dehalogenation function against various organochlorine substrates was identified from a polychlorobiphenyl (PCB)-degrading organism, Acidovorax sp. KKS102. A homolog of the gene BphK (biphenyl upper pathway K), named BphK-KKS, was cloned, purified and biochemically characterized. Bioinformatic analysis indicated several conserved amino acids that participated in the catalytic activity of the enzyme, and site-directed mutagenesis of these conserved amino acids revealed their importance in the enzyme's catalytic activity. The wild-type and mutant (C10F, K107T and A180P) recombinant proteins displayed wider substrate specificity. The wild-type recombinant GST reacted towards 1-chloro-2,4-dinitrobenzene (CDNB), ethacrynic acid, hydrogen peroxide and cumene hydroperoxide. The mutated recombinant proteins, however, showed significant variation in specific activities towards the substrates. A combination of a molecular docking study and a chloride ion detection assay showed potential interaction with and a dechlorination function against 2-, 3- and 4-chlorobenzoates (metabolites generated during PCB biodegradation) in addition to some organochlorine pesticides (dichlorodiphenyltrichloroethane, endosulfan and permethrin). It was demonstrated that the behavior of the dechlorinating activities varied among the wild-type and mutant recombinant proteins. Kinetic studies (using CDNB and glutathione) showed that the kinetic parameters K _m, V _max, K _cat and K _m/K _cat were all affected by the mutations. While C10F and A180P mutants displayed an increase in GST activity and the dechlorination function of the enzyme, the K107T mutant displayed variable results, suggesting a functional role of Lys107 in determining substrate specificity of the enzyme. These results demonstrated that the enzyme should be valuable in the bioremediation of metabolites generated during PCB biodegradation.

Intracellular toxicity exerted by PCBs and role of VBNC bacterial strains in biodegradation

Polychlorinated biphenyls (PCBs) are xenobiotic compounds that persists in the environment for long-term, though its productivity is banned. Abatement of the pollutants have become laborious due to it's recalcitrant nature in the environment leading to toxic effects in humans and other living beings. Biphenyl degrading bacteria co-metabolically degrade low chlorinated PCBs using the active metabolic pathway. bph operon possess different genetic arrangements in gram positive and gram negative bacteria. The binding ability of the genes and the active sites were determined by PCB docking studies. The active site of bphA gene with conserved amino acid residues determines the substrate specificity and biodegradability. Accumulation of toxic intermediates alters cellular behaviour, biomass production and downturn the metabolic activity. Several bacteria in the environment attain unculturable state which is viable and metabolically active but not cultivable (VBNC). Resuscitation-promoting factor (Rpf) and Rpf homologous protein retrieve the culturability of the so far uncultured bacteria. Recovery of this adaptive mechanism against various physical and chemical stressors make a headway in understanding the functionality of both environmental and medically important unculturable bacteria. Thus, this paper review about the general aspects of PCBs, cellular toxicity exerted by PCBs, role of unculturable bacterial strains in biodegradation, genes involved and degradation pathways. It is suggested to extrapolate the research findings on extracellular organic matters produced in culture supernatant of VBNC thus transforming VBNC to culturable state.

Effect of copper on in vivo fate of BDE-209 in pumpkin

A 60-day growth chamber experiments were performed to investigate the effect of Cu stress on the uptake, translocation and metabolism of decabromodiphenyl ether (BDE-209) by pumpkin. A total of nine debrominated metabolites (de-PBDEs), two hydroxylated PBDEs (OH-PBDEs) and one methoxylated PBDEs (MeO-PBDEs) were detected in the tested plants. Concentrations of the total debrominated, hydroxylated or methoxylated metabolites generally followed the order of roots>stems>leaves, and de-PBDEs>OH-PBDEs>MeO-PBDEs. These results indicate that metabolism occurred preferentially in roots than in stems and leaves. The addition of moderate dosage of Cu (50mg/kg) resulted in increment in OH-PBDE concentrations in plant tissues, whereas higher concentrations of Cu could inhibit uptake and metabolism of BDE-209. No in vivo mineralization of BDE-209 was detected in the plants. These results provide valuable information about the behavior of BDE-209 in plant tissues under heavy metal exposure.

In vitro biotransformation of PBDEs by root crude enzyme extracts: potential role of nitrate reductase (NaR) and glutathione S-transferase (GST) in their debromination

In order to investigate the enzyme transformation of PBDEs and to track the key enzymes involved in PBDE degradation in plants, in vivo exposure of plants of ryegrass, pumpkin and maize and in vitro exposure of their root crude enzyme extracts to PBDEs were conducted. Degradation of PBDEs in the root crude enzyme solutions fit well with the first order kinetics (R(2)=0.52-0.97, P<0.05), and higher PBDEs degraded faster than the lower ones. PBDEs could be transformed to lower brominated PBDEs and hydroxylated-PBDEs by the root crude enzyme extracts with debromination as the main pathway which contributed over 90% of PBDE depletion. In vitro and in vivo exposure to PBDEs produced similar responses in root enzyme activities of which the nitroreductase (NaR) and glutathione-transferase (GST) activities decreased significantly, while the peroxidase, catalase and cytochrome P-450 activities had no significant changes. Furthermore, higher enzyme concentrations of NaR and GST led to higher PBDE debromination rates, and the time-dependent activities of NaR and GST in the root crude enzyme extracts were similar to the trends of PBDE depletion. All these results suggest that NaR and GST were the key enzymes responsible for PBDE degradation. This conclusion was further confirmed by the in vitro debromination of PBDEs with the commercial pure NaR and GST.

Biodegradation of mono-hydroxylated PCBs by Burkholderia xenovorans

Three hydroxylated derivatives of PCBs, 2'-hydroxy-4-chlorobiphenyl (2'-OH-4-CB), 3'-hydroxy-4-chlorobiphenyl (3'-OH-4-CB), and 4'-hydroxy-4-chlorobiphenyl (4'-OH-4-CB), were transformed by the PCB degrader, Burkholderia xenovorans. When the bacterium was growing on biphenyl (biphenyl pathway-inducing conditions), all three hydroxylated isomers were transformed. However, only 2'-OH-4-CB was transformed by the bacterium growing on succinate (conditions non-inductive of the biphenyl pathway). Gene expression analyses showed a strong induction of key genes of the biphenyl pathway (bph) when cells were grown on biphenyl, which is consistent with the transformation of the three isomers by biphenyl-grown cells. When cells were grown on succinate, only exposure to 2'-OH-4-CB resulted in expression of biphenyl pathway genes, which suggests that this isomer was capable of inducing the biphenyl pathway. These results provide the first evidence that bacteria are able to metabolize PCB derivatives hydroxylated on the non-chlorinated ring.

Glutathione transferases in bacteria

Bacterial glutathione transferases (GSTs) are part of a superfamily of enzymes that play a key role in cellular detoxification. GSTs are widely distributed in prokaryotes and are grouped into several classes. Bacterial GSTs are implicated in a variety of distinct processes such as the biodegradation of xenobiotics, protection against chemical and oxidative stresses and antimicrobial drug resistance. In addition to their role in detoxification, bacterial GSTs are also involved in a variety of distinct metabolic processes such as the biotransformation of dichloromethane, the degradation of lignin and atrazine, and the reductive dechlorination of pentachlorophenol. This review article summarizes the current status of knowledge regarding the functional and structural properties of bacterial GSTs.

Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1

Mycobacterium vanbaalenii PYR-1 is well known for its ability to degrade a wide range of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs). The genome of this bacterium has recently been sequenced, allowing us to gain insights into the molecular basis for the degradation of PAHs. The 6.5 Mb genome of PYR-1 contains 194 chromosomally encoded genes likely associated with degradation of aromatic compounds. The most distinctive feature of the genome is the presence of a 150 kb major catabolic region at positions 494 approximately 643 kb (region A), with an additional 31 kb region at positions 4,711 approximately 4,741 kb (region B), which is predicted to encode most enzymes for the degradation of PAHs. Region A has an atypical mosaic structure made of several gene clusters in which the genes for PAH degradation are complexly arranged and scattered around the clusters. Significant differences in the gene structure and organization as compared to other well-known aromatic hydrocarbon degraders including Pseudomonas and Burkholderia were revealed. Many identified genes were enriched with multiple paralogs showing a remarkable range of diversity, which could contribute to the wide variety of PAHs degraded by M. vanbaalenii PYR-1. The PYR-1 genome also revealed the presence of 28 genes involved in the TCA cycle. Based on the results, we proposed a pathway in which HMW PAHs are degraded into the beta-ketoadipate pathway through protocatechuate and then mineralized to CO2 via TCA cycle. We also identified 67 and 23 genes involved in PAH degradation and TCA cycle pathways, respectively, to be expressed as proteins.

A glutathione S-transferase catalyzes the dehalogenation of inhibitory metabolites of polychlorinated biphenyls

BphK is a glutathione S-transferase of unclear physiological function that occurs in some bacterial biphenyl catabolic (bph) pathways. We demonstrated that BphK of Burkholderia xenovorans strain LB400 catalyzes the dehalogenation of 3-chloro 2-hydroxy-6-oxo-6-phenyl-2,4-dienoates (HOPDAs), compounds that are produced by the cometabolism of polychlorinated biphenyls (PCBs) by the bph pathway and that inhibit the pathway's hydrolase. A one-column protocol was developed to purify heterologously produced BphK. The purified enzyme had the greatest specificity for 3-Cl HOPDA (kcat/Km, approximately 10(4) M(-1) s(-1)), which it dechlorinated approximately 3 orders of magnitude more efficiently than 4-chlorobenzoate, a previously proposed substrate of BphK. The enzyme also catalyzed the dechlorination of 5-Cl HOPDA and 3,9,11-triCl HOPDA. By contrast, BphK did not detectably transform HOPDA, 4-Cl HOPDA, or chlorinated 2,3-dihydroxybiphenyls. The BphK-catalyzed dehalogenation proceeded via a ternary-complex mechanism and consumed 2 equivalents of glutathione (GSH) (Km for GSH in the presence of 3-Cl HOPDA, approximately 0.1 mM). A reaction mechanism consistent with the enzyme's specificity is proposed. The ability of BphK to dehalogenate inhibitory PCB metabolites supports the hypothesis that this enzyme was recruited to facilitate PCB degradation by the bph pathway.

Analysis of the C-terminal domain ofBurkholderiasp. strain LB400 BphK reveals a conserved motif that affects catalytic activity

The bphK gene encoding glutathione S-transferase (GST) is located in the bph operon (PCB co-metabolism) in Burkholderia sp. strain LB400 and the enzyme has recently been shown to have dechlorination activity in relation to 4-chlorobenzoate (4-CBA). Alignments using other glutathione S-transferase sequences found in PCB degradation operons identified a highly conserved region in the C-terminal domain of these enzymes that included a conserved motif implicated in protein folding in eukaryotic GSTs. Site-directed mutagenesis indicated that the region is indirectly involved in the catalytic activity and substrate specificity of BphK. Predicted hydrogen bond interactions involving Asp155 play an important role in the enzymatic properties of this glutathione S-transferase.