Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics

Wang, Yifan; Li, Jiasong; Liu, Aimin

doi:10.1007/s00775-017-1436-5

Cited by 77 publications

(75 citation statements)

References 108 publications

(120 reference statements)

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“…Typically, there are two types of dioxygenase involved in the ring-cleavage of aromatic compounds, intradiol and extradiol dioxygenases ( Wang et al, 2017 ). The diversity of dioxygenases significantly affects the metabolic versatility because the substituted groups on the benzene ring decide the position of ring-cleavage and potential toxicity of the substrate to the enzyme itself.…”

Section: Resultsmentioning

confidence: 99%

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1

et al. 2018

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The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.

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Section: Resultsmentioning

confidence: 99%

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1

et al. 2018

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“…The formation of a substrate-based epoxide intermediate has been found in other systems such as nonheme iron extradiol dioxygenase and Rieske dioxygenase. 39–40 The formation of an epoxyindole intermediate accompanied by a compound II-like species defines the key characteristic of heme dioxygenase mechanism. The high-valent Fe species is responsible for oxygen insertion and the pyrrole ring opening to complete the dioxygenation reaction.…”

Section: Discussionmentioning

confidence: 99%

Stepwise O-Atom Transfer in Heme-Based Tryptophan Dioxygenase: Role of Substrate Ammonium in Epoxide Ring Opening

et al. 2018

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Heme-based tryptophan dioxygenases are established immunosuppressive metalloproteins with significant biomedical interest. Here, we synthesized two mechanistic probes to specifically test if the α-amino group of the substrate directly participates in a critical step of the O atom transfer during catalysis in human tryptophan 2,3-dioxygenase (TDO). Substitution of the nitrogen atom of the substrate to a carbon (probe 1) or oxygen (probe 2) slowed the catalytic step following the first O atom transfer such that transferring the second O atom becomes less likely to occur, although the dioxygenated products were observed with both probes. A monooxygenated product was also produced from probe 2 in a significant quantity. Analysis of this new product by HPLC coupled UV–vis spectroscopy, high-resolution mass spectrometry, 1H NMR, 13C NMR, HSQC, HMBC, and infrared (IR) spectroscopies concluded that this monooxygenated product is a furoindoline compound derived from an unstable epoxyindole intermediate. These results prove that small molecules can manipulate the stepwise O atom transfer reaction of TDO and provide a showcase for a tunable mechanism by synthetic compounds. The product analysis results corroborate the presence of a substrate-based epoxyindole intermediate during catalysis and provide the first substantial experimental evidence for the involvement of the substrate α-amino group in the epoxide ring-opening step during catalysis. This combined synthetic, biochemical, and biophysical study establishes the catalytic role of the α-amino group of the substrate during the O atom transfer reactions and thus represents a substantial advance to the mechanistic comprehension of the heme-based tryptophan dioxygenases.

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“…). The intradiol and extradiol dioxygenases are non‐heme iron‐containing enzymes that have been extensively studied (Fielding et al ., ; Wang et al ., ). These enzymes catalyse the incorporation of two oxygen atoms resulting in concomitant C‐C bond fission, in which oxygen activation occurs through a substrate–oxygen–metal coordinated complex (Lipscomb, ; Fielding et al ., ; Pornsuwan et al ., ).…”

Section: Ring Breakage and Generation Of Common Metabolites By The Lomentioning

confidence: 97%

Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions

Pimviriyakul

Wongnate

Tinikul

et al. 2019

Microbial Biotechnology

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Summary Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low‐cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy‐producing metabolic pathways in cells. An in‐depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.

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Oxygen activation by mononuclear nonheme iron dioxygenases involved in the degradation of aromatics

Cited by 77 publications

References 108 publications

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1

Stepwise O-Atom Transfer in Heme-Based Tryptophan Dioxygenase: Role of Substrate Ammonium in Epoxide Ring Opening

Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions

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