Structure and substrate specificity determinants of NfnB, a dinitroaniline herbicide–catabolizing nitroreductase from Sphingopyxis sp. strain HMH

Kim, Sang-Hoon; Park, Sangyun; Park, Eun‐Young; Kim, Jeong‐Han; Ghatge, Sunil; Hur, Hor‐Gil; Rhee, Sangkee

doi:10.1016/j.jbc.2021.101143

Cited by 6 publications

(5 citation statements)

References 30 publications

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“…4 and 6 a–c). The nitro group of PNB was reduced to an amino group and then to a hydroxylamine group producing 4-nitrosobenzoate (4-NOBA) and 4-hydroxylaminobenzoate (4-HABA) via catalysis through a nitroreductase (nfnB or pnbA) [ 43 , 44 ]. Then, the product 4-HABA was transformed to protocatechuate (PCA) catalyzed by 4-hydroxylaminobenzoate lyase (pnbB) [ 45 ].…”

Section: Resultsmentioning

confidence: 99%

Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches

Zhang

Klümper

et al. 2022

Microbiome

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Background As a widely used broad-spectrum antibiotic, chloramphenicol is prone to be released into environments, thus resulting in the disturbance of ecosystem stability as well as the emergence of antibiotic resistance genes. Microbes play a vital role in the decomposition of chloramphenicol in the environment, and the biotransformation processes are especially dependent on synergistic interactions and metabolite exchanges among microbes. Herein, the comprehensive chloramphenicol biotransformation pathway, key metabolic enzymes, and interspecies interactions in an activated sludge-enriched consortium were elucidated using integrated multi-omics and cultivation-based approaches. Results The initial biotransformation steps were the oxidization at the C1-OH and C3-OH groups, the isomerization at C2, and the acetylation at C3-OH of chloramphenicol. Among them, the isomerization is an entirely new biotransformation pathway of chloramphenicol discovered for the first time. Furthermore, we identified a novel glucose-methanol-choline oxidoreductase responsible for the oxidization of the C3-OH group in Sphingomonas sp. and Caballeronia sp. Moreover, the subsequent biotransformation steps, corresponding catalyzing enzymes, and the microbial players responsible for each step were deciphered. Synergistic interactions between Sphingomonas sp. and Caballeronia sp. or Cupriavidus sp. significantly promoted chloramphenicol mineralization, and the substrate exchange interaction network occurred actively among key microbes. Conclusion This study provides desirable strain and enzyme resources for enhanced bioremediation of chloramphenicol-contaminated hotspot sites such as pharmaceutical wastewater and livestock and poultry wastewater. The in-depth understanding of the chloramphenicol biotransformation mechanisms and microbial interactions will not only guide the bioremediation of organic pollutants but also provide valuable knowledge for environmental microbiology and biotechnological exploitation.

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Section: Resultsmentioning

confidence: 99%

Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches

Zhang

Klümper

et al. 2022

Microbiome

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“…shows sequence similarity with nitroreductase (21)(22)(23), which is a redox enzyme, it is plausible to assume that it catalyzes a redox reaction in CPS biosynthesis to generate a structural moiety of CPS for its interaction with P49. A comparison between CPS from ∆hm3342 and the parent strain will help to uncover this structural moiety of CPS.…”

Section: Discussionmentioning

confidence: 99%

Capsular polysaccharide-mediated protein loading onto extracellular membrane vesicles of a fish intestinal bacterium,Shewanella vesiculosaHM13

Kamasaka

Kawamoto

Tsudzuki

et al. 2023

Preprint

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Bacterial extracellular membrane vesicles (EMVs) play various physiologically important roles mediated by cargo proteins. However, our understanding of the molecular mechanism underlying cargo loading onto EMVs is limited. In this study, we analyzed the mechanism of cargo protein loading onto EMVs from a fish intestinal Gram-negative bacterium,Shewanella vesiculosaHM13. This strain secretes EMVs carrying a major cargo protein, P49. Near the P49 gene, we found genes having homology to genes involved in protein secretion and surface polysaccharide-chain synthesis. Among them, the deletion of genes encoding homologs of a flippase involved in bacterial extracellular polysaccharide synthesis (HM3343), phosphoethanolamine transferase (HM3344), and glycerophosphodiester phosphodiesterase (HM3345) resulted in the loss of capsular polysaccharide (CPS) of EMVs. We conducted anin vitroP49 loading assay onto P49-free EMVs to examine whether P49 was loaded onto the EMVs via its interaction with the CPS of the EMVs. We found that purified P49 was loaded onto EMVs harboring CPSin vitro, whereas it was not loaded onto EMVs from the mutants lacking CPS production due to the loss of HM3343, HM3344, and HM3345. Transmission electron microscopy of EMVs loaded with P49in vitroandin vivoshowed spherical nanoparticles around the EMVs, whereas such particles were not observed for EMVs without loaded P49, implying that P49 constitutes those particles on the surface of EMVs. These results indicate that P49 is loaded onto EMVs via its interaction with the CPS of EMVs.

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“…NRs selectively mediate the reduction of aryl nitro groups. There are two classes of NR, namely, type I, which are oxygen-insensitive and type II, which are oxygen-sensitive. , Comprehensive works have elucidated much of the mechanism of action for NRs and shown they do not convert from the hydroxylamine to the aniline, indeed stopping at the hydroxylamine via short-lived nitroso intermediates. , They can be coupled with other catalysts to effect overall reduction to the more synthetically useful anilines, however (Figure ). This presents a chemoenzymatic alternative to synthetic hydrogenation, running under atmospheric pressure, in aqueous media, and with perfect chemoselectivity.…”

Section: Introductionmentioning

confidence: 99%

“…There are two classes of NR, namely, type I, which are oxygen-insensitive and type II, which are oxygen-sensitive. 14 , 15 Comprehensive works have elucidated much of the mechanism of action for NRs and shown they do not convert from the hydroxylamine to the aniline, indeed stopping at the hydroxylamine via short-lived nitroso intermediates. 16 , 17 They can be coupled with other catalysts to effect overall reduction to the more synthetically useful anilines, however ( Figure 1 ).…”

Section: Introductionmentioning

confidence: 99%

Realizing the Continuous Chemoenzymatic Synthesis of Anilines Using an Immobilized Nitroreductase

Cosgrove

Miller

Bornadel

et al. 2023

ACS Sustainable Chem. Eng.

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The use of biocatalysis for classically synthetic transformations has seen an increase in recent years, driven by the sustainability credentials bio-based approaches can offer the chemical industry. Despite this, the biocatalytic reduction of aromatic nitro compounds using nitroreductase biocatalysts has not received significant attention in the context of synthetic chemistry. Herein, a nitroreductase (NR-55) is demonstrated to complete aromatic nitro reduction in a continuous packed-bed reactor for the first time. Immobilization on an amino-functionalized resin with a glucose dehydrogenase (GDH-101) permits extended reuse of the immobilized system, all operating at room temperature and pressure in aqueous buffer. By transferring into flow, a continuous extraction module is incorporated, allowing the reaction and workup to be continuously undertaken in a single operation. This is extended to showcase a closed-loop aqueous phase, permitting reuse of the contained cofactors, with a productivity of >10 gproduct gNR‑55 –1 and milligram isolated yields >50% for the product anilines. This facile method removes the need for high-pressure hydrogen gas and precious-metal catalysts and proceeds with high chemoselectivity in the presence of hydrogenation-labile halides. Application of this continuous biocatalytic methodology to panels of aryl nitro compounds could offer a sustainable approach to its energy and resource-intensive precious-metal-catalyzed counterpart.

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Structure and substrate specificity determinants of NfnB, a dinitroaniline herbicide–catabolizing nitroreductase from Sphingopyxis sp. strain HMH

Cited by 6 publications

References 30 publications

Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches

Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches

Capsular polysaccharide-mediated protein loading onto extracellular membrane vesicles of a fish intestinal bacterium,Shewanella vesiculosaHM13

Realizing the Continuous Chemoenzymatic Synthesis of Anilines Using an Immobilized Nitroreductase

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