Conversion of 2-fluoromuconate to cis-dienelactone by purified enzymes of Rhodococcus opacus 1cp

Core taxa, co-occurrence pattern, diversity, and metabolic pathways contributing to robust anaerobic biodegradation of chlorophenol

It is hard to achieve robustness in anaerobic biodegradation of trichlorophenol (TCP). We hypothesized that specific combinations of environmental factors determine phylogenetic diversity and play important roles in the decomposition and stability of TCP-biodegrading bacteria. The anaerobic bioreactor was operated at 35 °C (H condition) or 30 °C (L condition) and mainly fed with TCP (from 28 μM to 180 μM) and organic material. Metagenome sequencing was combined with 16S rRNA gene amplicon sequencing for the microbial community analysis. The results exhibited that the property of robustness occurred in specific conditions. The corresponding co-occurrence and diversity patterns suggest high collectivization, degree and evenness for robust communities. Two types of core functional taxa were recognized: dechlorinators (unclassified Anaerolineae, Thermanaerothrix and Desulfovibrio) and ring-opening members (unclassified Proteobacteria, Methanosarcina, Methanoperedens, and Rubrobacter). The deterministic process of the expansion of niche of syntrophic bacteria at higher temperatures was confirmed. The reductive and hydrolytic dechlorination mechanisms jointly lead to C-Cl bond cleavage. H ultimately adapted to the stress of high TCP loading, with more abundant ring-opening enzyme (EC 3.1.1.45, ∼55%) and hydrolytic dechlorinase (EC 3.8.1.5, 26.5%) genes than L (∼47%, 10.5%). The functional structure (based on KEGG) in H was highly stable despite the high loading of TCP (up to 60 μM), but not in L. Furthermore, an unknown taxon with multiple functions (dechlorinating and ring-opening) was found based on genetic sequencing; its functional contribution of EC 3.8.1.5 in H (26.5%) was higher than that in L (10.5%), and it possessed a new metabolic pathway for biodegradation of halogenated aromatic compounds. This new finding is supplementary to the robust mechanisms underlying organic chlorine biodegradation, which can be used to support the engineering, regulation, and design of synthetic microbiomes.

Metabolic engineering of Escherichia coli for efficient degradation of 4-fluorophenol

As a kind of refractory organic pollutant, 4-fluorophenol (4-FP) can be degraded by only a few microorganisms with low efficiency because of the great electron-withdrawing ability of fluorine atoms. So it is necessary to artificially construct engineered strain to improve the degradation efficiency and meet the requirements of pollutant degradation. In this study, four genes (fpdA2, fpdB, fpdC, and fpdD) for 4-FP degradation from Arthrobacter sp. strain IF1 were optimized and synthesized and then reconstructed into Escherichia coli by a multi-monocistronic vector to obtain recombinant BL-fpd that could degrade 4-FP efficiently. Under optimized induction conditions (inducing the strain by 2 g/L L-arabinose and 1 mM IPTG at 37 ℃), BL-fpd could completely degrade 2 mM 4-FP, 4-chlorophenol, 4-bromophenol, and 4-nitrophenol into β-ketoadipate, which could be further metabolized by the bacteria. FpdA2 showed the highest activity towards 4-bromophenol. The strain could completely degrade 1 mM 4-FP in industrial wastewater within 3 h. This study provided a promising strain for the degradation of 4-FP and some other 4-substituted phenols. The construction technologies of multi-monocistronic expression vector may also be used to construct other organic pollutants degrading bacteria.

Carbon-fluorine bond cleavage mediated by metalloenzymes

Fluorochemicals are a widely distributed class of compounds and have been utilized across a wide range of industries for decades. Given the environmental toxicity and adverse health threats of some fluorochemicals, the development of new methods for their decomposition is significant to public health. However, the carbon-fluorine (C-F) bond is among the most chemically robust bonds; consequently, the degradation of fluorinated hydrocarbons is exceptionally difficult. Here, metalloenzymes that catalyze the cleavage of this chemically challenging bond are reviewed. These enzymes include histidine-ligated heme-dependent dehaloperoxidase and tyrosine hydroxylase, thiolate-ligated heme-dependent cytochrome P450, and four nonheme oxygenases, namely, tetrahydrobiopterin-dependent aromatic amino acid hydroxylase, 2-oxoglutarate-dependent hydroxylase, Rieske dioxygenase, and thiol dioxygenase. While much of the literature regarding the aforementioned enzymes highlights their ability to catalyze C-H bond activation and functionalization, in many cases, the C-F bond cleavage has been shown to occur on fluorinated substrates. A copper-dependent laccase-mediated system representing an unnatural radical defluorination approach is also described. Detailed discussions on the structure-function relationships and catalytic mechanisms provide insights into biocatalytic defluorination, which may inspire drug design considerations and environmental remediation of halogenated contaminants.

A bifunctional enzyme from Rhodococcus erythropolis exhibiting secondary alcohol dehydrogenase-catalase activities

Alcohol dehydrogenases have long been recognized as potential biocatalyst for production of chiral fine and bulk chemicals. They are relevant for industry in enantiospecific production of chiral compounds. In this study, we identified and purified a nicotinamide adenine dinucleotide (NAD)-dependent secondary alcohol dehydrogenase (SdcA) from Rhodococcus erythropolis oxidizing γ-lactols into γ-lactones. SdcA showed broad substrate specificity on γ-lactols; secondary aliphatic alcohols with 8 and 10 carbon atoms were also substrates and oxidized with (2S)-stereospecificity. The enzyme exhibited moderate stability with a half-life of 5 h at 40 °C and 20 days at 4 °C. Mass spectrometric identification revealed high sequence coverage of SdcA amino acid sequence to a highly conserved catalase from R. erythropolis. The corresponding encoding gene was isolated from genomic DNA and subsequently overexpressed in Escherichia coli BL21 DE3 cells. In addition, the recombinant SdcA was purified and characterized in order to confirm that the secondary alcohol dehydrogenase and catalase activity correspond to the same enzyme.

Proteomics and metabolomics: the molecular make-up of toxic aromatic pollutant bioremediation

Microbial-mediated attenuation of toxic aromatic pollutants offers great potential for the restoration of contaminated environments in an ecologically acceptable manner. However, incomplete biological information regarding the regulation of growth and metabolism in many microbial communities restricts progress in the site-specific mineralization process. In the postgenomic era, recent advances in MS have allowed enormous progress in proteomics and elucidated many complex biological interactions. These research forefronts are now expanding toward the analysis of low-molecular-weight primary and secondary metabolites analysis, i.e., metabolomics. The advent of 2-DE in conjunction with MS offers a promising approach to address the molecular mechanisms of bioremediation. The two fields of proteomics and metabolomics have thus far worked separately to identify proteins and primary and secondary metabolites during bioremediation. A simultaneous study combining functional proteomics and metabolomics, i.e., proteometabolomics would create a system-wide approach to studying site-specific microorganisms during active mineralization processes. This article deals with advances in environmental proteomics and metabolomics and advocates the simultaneous study of both technologies to implement cell-free bioremediation.

Bacterial degradation of chlorophenols: pathways, biochemica, and genetic aspects

Chlorophenols belong to the group of toxic and persistent to microbial attack xenobiotics. Nevertheless, due to the adaptation microorganisms acquire the ability to use chlorophenols as the sole source of carbon and energy. The present review describes the diversity of aerobic pathways for the utilization of halogenated phenols by bacteria with the emphasis on the main reactions and intermediates formed, enzymes responsible for these reactions and their genetic basis. Taking into account (i) the fact that enzymes degrading chlorophenols are similar to the ones involved in the conversion of other (chloro)aromatic compounds and (ii) that present numerous publications describing the properties of separated enzymes or encoding their genes are published, this review was planned as the attempt to present both, the most general and specific aspects in chlorophenols degradation with the emphasis on the literature of the last ten years.