A two-component monooxygenase for continuous denitration and dechlorination of chlorinated 4-nitrophenol in Ensifer sp. strain 22-1

Polluticaenibacter yanchengensis gen. nov., sp. nov., A Novel Taxon Within the Family Chitinophagaceae Isolated from Activated Sludge

A Gram-stain-negative bacterium, designated strain LY-5 T, was isolated from an activated sludge sample collected from a river in Yancheng city, Jiangsu province, China. Cells of strain LY-5 T, were strictly aerobic, non-motile and rod-shaped. Growth occurred at 15-37 °C (optimum, 30 °C), at pH 5.0-9.0 (optimum 7.0) and at 0-3% (w/v) NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that strain LY-5 T formed a distinct phyletic branch within the family Chitinophagaceae, with closest relatives being members of the genera Phnomibacter, Aurantisolimonas, and Chitinophaga, sharing 88.5-90.3% sequence similarity. Moreover, the average amino acid identity (AAI) between strain LY-5 T and its closed phylogenetic neighbors was below 70%, indicating it belongs to a novel genus. The predominant cellular fatty acids of LY-5 T were iso-C15:0, iso-C15:1 G and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), and the only isoprenoid quinone was menaquinone-7 (MK-7). The major polar lipids identified in strain LY-5 T comprised phosphatidylethanolamine, two unidentified aminolipids and five unidentified lipids. The genome size of strain LY-5 T was 4.8 Mbp with a G + C content of 38.9%. Based on the evidence presented in this study, strain LY-5 T represents a novel species of a new genus in the family Chitinophagaceae, for which the name Polluticaenibacter yanchengensis gen. nov., sp. nov. (Type strain LY-5 T = CCTCC AB 2023260 T = KCTC 102218 T) is proposed.

Facile synthesis of Ag/ZIF-8@ZIF-67 as an electrochemical sensing platform for sensitive detection of halonitrophenols in drinking water

Halonitrophenols (HNPs) are an emerging type of aromatic disinfection byproduct, with detected concentrations of ∼nmol L-1 in source water and drinking water. Currently, there are no standard methods for identifying HNPs, and most of the reported methods are time-consuming and equipment-dependent. A core-shell metal-organic framework (MOF) based electrochemical sensor (Ag/ZIF-8@ZIF-67) capable of detecting 2,6-dichloro-4-nitrophenol (2,6-DCNP) is reported in this study. The electrochemical sensor obtains the concentration of 2,6-DCNP by detecting the peak current passing through the sensor. In this sensor, Ag nanoparticles (AgNPs) play a key role in electrochemical sensing by reducing nitro groups via electron transfer, and porous structure with a large surface area is offered by ZIF-8@ZIF-67. The cyclic voltammetry (CV) response of Ag/ZIF-8@ZIF-67 was found to be approximately 1.75 times and 2.23 times greater than that of Ag/ZIF-8 and Ag/ZIF-67, respectively, suggesting an ideal synergistic effect of the core-shell structures. The Ag/ZIF-8@ZIF-67 sensor exhibited exceptional sensitivity to 2,6-DCNP, exhibiting a broad linear response range (R2 = 0.992) from 240 nmol L-1 to 288 μmol L-1 and a low detection limit of 20 nmol L-1. Furthermore, the sensor exhibited good anti-interference for isomers and common distractors in water, excellent stability and reproducibility, and high recovery in actual water samples. Our reported sensor gives a novel strategy for sensitive, selective, and in situ detection of 2,6-DCNP in practical analysis.

Formation and stabilization of C4a-hydroperoxy-FAD by the Arg/Asn pair in HadA monooxygenase

HadA monooxygenase catalyses the detoxification of halogenated phenols and nitrophenols via dehalogenation and denitration respectively. C4a-hydroperoxy-FAD is a key reactive intermediate wherein its formation, protonation and stabilization reflect enzyme efficiency. Herein, transient kinetics, site-directed mutagenesis and pH-dependent behaviours of HadA reaction were employed to identify key features stabilizing C4a-adducts in HadA. The formation of C4a-hydroperoxy-FAD is pH independent, whereas its decay and protonation of distal oxygen are associated with pK_a values of 8.5 and 8.4 respectively. These values are correlated with product formation within a pH range of 7.6-9.1, indicating the importance of adduct stabilization to enzymatic efficiency. We identified Arg101 as a key residue for reduced FAD (FADH^- ) binding and C4a-hydroperoxy-FAD formation due to the loss of these abilities as well as enzyme activity in HadA_R101A and HadA_R101Q . Mutations of the neighbouring Asn447 do not affect the rate of C4a-hydroperoxy-FAD formation; however, they impair FADH^- binding. The disruption of Arg101/Asn447 hydrogen bond networking in HadA_N447A increases the pK_a value of C4a-hydroperoxy-FAD decay to 9.5; however, this pK_a was not altered in HadA_N447D (pK_a of 8.5). Thus, Arg101/Asn447 pair should provide important interactions for FADH^- binding and maintain the pK_a associated with H₂ O₂ elimination from C4a-hydroperoxy-FAD in HadA. In the presence of substrate, the formation of C4a-hydroxy-FAD at the hydroxylation step is pH insensitive, and it dehydrates to form the oxidized FAD with pK_a of 7.9. This structural feature might help elucidate how the reactive intermediate was stabilized in other flavin-dependent monooxygenases.

Genetic bioaugmentation with triclocarban-catabolic plasmid effectively removes triclocarban from wastewater

Triclocarban, one of the emerging pollutants, has been accumulating, and it is frequently detected in wastewater. Due to its toxicity and persistence, the efficient removal of triclocarban from wastewater systems is challenging. Genetic bioaugmentation with transferable catabolic plasmids has been considered to be a long-lasting method to clean up pollutants in continuous flow wastewater treatment systems. In this study, bioaugmentation with Pseudomonas putida KT2440, harboring the transferrable triclocarban-catabolic plasmid pDCA-1-gfp-tccA2, rapidly converted 50 μM triclocarban in wastewater into 3,4-dichloroaniline and 4-chloroaniline, which are further mineralized more easily. RT-qPCR results showed that the ratio of the copy number of pDCA-1-gfp-tccA2 to the cell number of strain KT2440 gradually increased during genetic bioaugmentation, suggesting horizontal transfer and proliferation of the plasmid. By using DNA stable isotope probing (SIP) and amplicon sequencing, OTU86 (Escherichia-Shigella), OTU155 (Citrobacter), OTU5 (Brucella), and OTU15 (Enterobacteriaceae) were found to be the potential recipients of the plasmid pDCA-1-gfp-tccA2 in the wastewater bacterial community. Furthermore, three transconjugants in the genera of Escherichia, Citrobacter, and Brucella showing triclocarban-degrading abilities were isolated from the wastewater. This study develops a new method for removing triclocarban from wastewater and provides insights into the environmental behavior of transferrable catabolic plasmids in bacterial community in wastewater systems.

Precise Regulation of Differential Transcriptions of Various Catabolic Genes by OdcR via a Single Nucleotide Mutation in the Promoter Ensures the Safety of Metabolic Flux

Synergistic regulation of the expression of various genes in a catabolic pathway is crucial for the degradation, survival, and adaptation of microorganisms in polluted environments. However, how a single regulator accurately regulates and controls differential transcriptions of various catabolic genes to ensure metabolic safety remains largely unknown. Here, a LysR-type transcriptional regulator (LTTR), OdcR, encoded by the regulator gene odcR, was confirmed to be essential for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism and simultaneously activated the transcriptions of a gene with unknown function, orf419, and three genes, odcA, odcB, and odcC, involved in the DBHB catabolism in Pigmentiphaga sp. strain H8. OdcB further metabolized the highly toxic intermediate 2,6-dibromohydroquinone, which was produced from DBHB by OdcA. The upregulated transcriptional level of odcB was 7- to 9-fold higher than that of orf419, odcA, or odcC in response to DBHB. Through an electrophoretic mobility shift assay and DNase I footprinting assay, DBHB was found to be the effector and essential for OdcR binding to all four promoters of orf419, odcA, odcB, and odcC. A single nucleotide mutation in the regulatory binding site (RBS) of the promoter of odcB (TAT-N₁₁-ATG), compared to those of odcA/orf419 (CAT-N₁₁-ATG) and odcC (CAT-N₁₁-ATT), was identified and shown to enable the significantly higher transcription of odcB. The precise regulation of these genes by OdcR via a single nucleotide mutation in the promoter avoided the accumulation of 2,6-dibromohydroquinone, ensuring the metabolic safety of DBHB. IMPORTANCE Prokaryotes use various mechanisms, including improvement of the activity of detoxification enzymes, to cope with toxic intermediates produced during catabolism. However, studies on how bacteria accurately regulate differential transcriptions of various catabolic genes via a single regulator to ensure metabolic safety are scarce. This study revealed a LysR-type transcriptional activator, OdcR, which strongly activated odcB transcription for the detoxification of the toxic intermediate 2,6-dibromohydroquinone and slightly activated the transcriptions of other genes (orf419, odcA, and odcC) for 3,5-dibromo-4-hydroxybenozate (DBHB) catabolism in Pigmentiphaga sp. strain H8. Interestingly, the differential transcription/expression of the four genes, which ensured the metabolic safety of DBHB in cells, was determined by a single nucleotide mutation in the regulatory binding sites of the four promoters. This study describes a new and ingenious regulatory mode of ensuring metabolic safety in bacteria, expanding our understanding of synergistic transcriptional regulation in prokaryotes.

Genetic redundancy of 4-hydroxybenzoate 3-hydroxylase genes ensures the catabolic safety of Pigmentiphaga sp. H8 in 3-bromo-4-hydroxybenzoate-contaminated habitats

Genetic redundancy is prevalent in organisms and plays important roles in the evolution of biodiversity and adaptation to environmental perturbation. However, selective advantages of genetic redundancy in overcoming metabolic disturbance due to structural analogues have received little attention. Here, functional divergence of the three 4-hydroxybenzoate 3-hydroxylase (PHBH) genes (phbh1~3) was found in Pigmentiphaga sp. strain H8. The genes phbh1/phbh2 were responsible for 3-bromo-4-hydroxybenzoate (3-Br-4-HB, an anthropogenic pollutant) catabolism, whereas phbh3 was primarily responsible for 4-hydroxybenzoate (4-HB, a natural intermediate of lignin) catabolism. 3-Br-4-HB inhibited 4-HB catabolism by competitively binding PHBH3, and was toxic to strain H8 cells especially at high concentrations. The existence of phbh1/phbh2 not only enabled strain H8 to utilize 3-Br-4-HB, but also ensured the catabolic safety of 4-HB. Molecular docking and site-directed mutagenesis analyses revealed that Val199 and Phe384 of PHBH1/PHBH2 were required for the hydroxylation activity towards 3-Br-4-HB. Phylogenetic analysis indicated that phbh1 and phbh2 originated from a common ancestor and evolved specifically in strain H8 to adapt to 3-Br-4-HB-contaminated habitats, whereas phbh3 evolved independently. This study deepens our understanding of selective advantages of genetic redundancy in prokaryote's metabolic robustness and reveals the factors driving the divergent evolution of redundant genes in adaptation to environmental perturbation. This article is protected by copyright. All rights reserved.

Degradation of dimethachlon by a newly isolated bacterium Paenarthrobacter sp. strain JH-1 relieves its toxicity against Chlorella ellipsoidea

Dimethachlon, a broad-spectrum dicarboximide fungicide, poses a hazard to the safety of human and ecosystem due to its residue in the environment. A high-efficient dimethachlon degrading bacteria JH-1 belonging to Paenarthrobacter sp. was isolated and characterized. Strain JH-1 can utilize high concentration of dimethachlon as sole carbon source for growth and degrade 98.53% of 300 mg·L^-1 dimethachlon within 72 h. Crude enzyme of strain JH-1 could degrade 99.76% of 100 mg·L^-1 dimethachlon within 2 h. The optimum degradation condition of dimethachlon by strain JH-1 was at 35 °C and pH 7.0. Dimethachlon was degraded in Paenarthrobacter sp. JH-1 as following: it was firstly converted to 4-(3,5-dichloroanilino)-4-oxobutanoic acid and then subjected to the hydrolysis to 3,5-dichloroaniline and succinic acid, the latter was further degraded. Dimethachlon inhibited the growth of Chlorella ellipsoidea, while Paenarthrobacter sp. JH-1 could degrade dimethachlon to relieve its toxicity. This work facilitates our knowledge of the degradation mechanism of dimethachlon and offers potential resource of microbial strains for the bioremediation of dimethachlon-contaminated environments in the future.