POLYCYCLIC AROMATIC COMPOUNDS
·
2016
·
IF 0.959
Hongyun Nie,Maiqian Nie,Yongzhe Yang,Jing Zhao,Xinyi Zhang,Yutao Guo,Yi Wan,Jing Zi
Characterization of phenol metabolization by P. stutzeri N2 was proposed based on the identification of relevant metabolites and enzyme activities of catechol 1,2-oxygenase and catechol 2,3-dioxygenase. P. stutzeri N2 started to grow on 400 mg l−1 phenol with no obvious lag phase, and then phenol decomposition was rapidly completed within 32 h. Results of enzyme activities, UV spectrums of cultures, and the mass spectrum identification of cis, cis-muconic and 2-HMS, which showed that catechol C12O and C23O were acting simultaneously on the fission of the phenol ring. The existence of P-hydroxybenzoic acid and straight-chain saturated dicarboxylic acids in the culture medium showed that carboxylation and hydrogenation were involved during the phenol degradation. Metabolites containing five or four carbons indicated that catechol and its immediate ring-cleavage intermediates could be furthermore metabolized by P. Stutzeri N2. Therefore, P. stutzeri N2 which could degrade phenol with high efficiency and diverse pathways could have potential applications in the treatment of wastewater containing phenol.
研究领域:
环境微生物学
·
生物化学
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产品关联
DOI
高影响因子
BIODEGRADATION
·
2015
·Vol. 26
·期 3
·197-210
·
IF 2.336
Wang Hong-Wei,Zhang Wei,Su Chun-Lun,Zhu Hong,Dai Chuan-Chao
Phytoestrogens are plant-derived hormonally-active compounds known to cause varied reproductive, immunosuppressive and behavioral effects in vertebrates. In this study, biodegradation of luteolin, a common phytoestrogen, was investigated during incubation with endophytic fungus Phomopsis liquidambari . The optimum concentration of luteolin as sole carbon source supplied in culture was 200 mg L −1 , which allowed 97 and 99 % degradation of luteolin by P. liquidambari in liquid culture and soil conditions, respectively. The investigation of the fungal metabolic pathway showed that luteolin was first decomposed to caffeic acid and phloroglucinol. These intermediate products were degraded to protocatechuic acid and hydroxyquinol, respectively, and then rings were opened by ring-cleavage dioxygenases. Two novel genes encoding the protocatechuate 3,4-dioxygenase and hydroxyquinol 1,2-dioxygenase were successfully cloned. Reverse-transcription quantitative polymerase chain reaction demonstrated that expression levels of mRNA of these two genes increased significantly after P. liquidambari was induced by the intermediate products caffeic acid and phloroglucinol, respectively. These results revealed that P. liquidambari can biodegrade luteolin efficiently and could potentially be used to bioremediate phytoestrogen contamination.
研究领域:
环境科学
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微生物学
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分子生物学
✓ 已验证
DOI
PubMed
高影响因子
JOURNAL OF HAZARDOUS MATERIALS
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2020
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IF 9.038
Yunli Liu,Haiyang Hu,Giulio Zanaroli,Ping Xu,Hongzhi Tang
Polycyclic aromatic hydrocarbons (PAHs) and heterocyclic derivatives are organic pollutants that pose a serious health risk to human beings. In this study, a newly isolated Pseudomonas brassicacearum strain MPDS could effectively degrade PAHs and heterocyclic derivatives, including naphthalene , fluorene, dibenzofuran (DBF) and dibenzothiophene (DBT). Notably, strain MPDS is able to degrade fluorene, DBF and DBT uniquely via a lateral dioxygenation pathway, while most reported strains degrade fluorene, DBF and DBT via an angular dioxygenation pathway or co-metabolize them via a lateral dioxygenation pathway. Strain MPDS completely degraded 50 mg naphthalene (in 50 mL medium) in 84 h, and OD 600 reached 1.0–1.1; while, it stabilized at OD 600 0.5–0.6 with 5 mg fluorene or DBF or DBT. Meanwhile, 65.7% DBF and 32.1% DBT were degraded in 96 h, and 40.3% fluorene was degraded in 72 h, respectively. Through genomic and transcriptomic analyses, and comparative genomic analysis with another DBF degradation strain, relevant gene clusters were predicted, and a naphthalene-degrading gene cluster was identified. This study provides understanding of degradation of PAHs and their heterocyclic derivatives, as well as new insights into the lateral dioxygenation pathway of relevant contaminants.
研究领域:
环境微生物学
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生物修复
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基因组学
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产品关联
DOI
PubMed
高影响因子
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
·
2023
·Vol. 30
·期 36
·85558-85568
·
IF 5.8
Jin
Jingnan,Shi Yahui,Zhang Baozhong,Wan Dongjin,Zhang Qingye
A bacterial strain Citrobacter sp. HJS-1 was discovered from the sludge in a drainage canal of a coal mine. Firstly, its biodegradation capacity for benzo[a]pyrene (BaP) was detected under different concentrations. The results proved that the strain possessed excellent biodegradation capacity for BaP with high-efficiency degradation rates ranging from 78.9 to 86.8%. The highest degradation rate was observed in the low-concentration sample, and the high-concentration BaP had a slight influence on the biodegradation capacity due to the potential toxicity of BaP and its oxygen-containing derivatives. Meanwhile, the degradation test for the other five aromatic hydrocarbons (2- to 4-ring) proved that the strain had a comprehensive degradation potential. To clarify the biodegradation mechanism of BaP, a dioxygenase structure was constructed by homology modeling. Then, the interactions between dioxygenase and BaP were researched by molecular simulation. Combined with the identification of the vital BaP-cis-7,8-dihydrodiol intermediate and the interaction analysis, the initial oxidation mode and the binding site of BaP were revealed in the dioxygenase. Taken together, this study has offered a way to understand the biodegradation process of BaP and its interaction mechanism based on experimental and theoretical analysis.
研究领域:
环境微生物学
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生物化学
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分子生物学
✓ 已验证
DOI
PubMed
高影响因子
BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY
·
2016
·Vol. 97
·期 5
·689-694
·
IF 1.191
Jin Jingnan,Yao Jun,Zhang Qingye
The strain Pseudomonas sp. JPN2 had a high potential to degrade phenanthrene degrading 98.52 % of the initial amount of 100 mg L −1 after 10 days incubation. The analysis of metabolites demonstrated that the cleavage of phenanthrene started at the C 9 and C 10 positions on the aromatic ring by the dioxygenation reaction, and then further degraded via a phthalate pathway. To understand the interaction between phenanthrene and the amino acid residues in the active site of the target enzyme, a molecular docking simulation was performed. The results showed that the distances of C 9 –O 1 and C 10 –O 2 atoms were 3.47 and 3.67 Å, respectively. The C 9 and C 10 positions of the phenanthrene ring are much closer to the dioxygen molecule in the active site relative to the other atoms. Therefore, the C 9 and C 10 positions are vulnerable to attack in the initial oxygenation process.
研究领域:
环境微生物学
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生物化学
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分子生物学
✓ 已验证
DOI
PubMed
高影响因子
JOURNAL OF BACTERIOLOGY
·
2017
·Vol. 200
·期 1
·
IF 3.143
Hao Yu,Shuxue Zhao,Lizhong Guo
The 1,125-bp mabB gene encoding 5-aminosalicylate (5ASA) 1,2-dioxygenase, a nonheme iron dioxygenase in the bicupin family that catalyzes the cleavage of the 5ASA aromatic ring to form cis-4-amino-6-carboxy-2-oxohexa-3,5-dienoate in the biodegradation of 3-aminobenzoate, was cloned from Comamonas sp. strain QT12 and characterized. The deduced amino acid sequence of the enzyme has low sequence identity with that of other reported ring-cleaving dioxygenases. MabB was heterologously expressed in Escherichia coli cells and purified as a His-tagged enzyme. The optimum pH and temperature for MabB are 8.0 and 10°C, respectively. FeII is required for the catalytic activity of the purified enzyme. The apparent Km and Vmax values of MabB for 5ASA are 52.0 ± 5.6 μM and 850 ± 33.2 U/mg, respectively. The two oxygen atoms incorporated into the product of the MabB-catalyzed reaction are both from the dioxygen molecule. Both 5ASA and gentisate could be converted by MabB; however, the catalytic efficiency of MabB for 5ASA was much higher (∼70-fold) than that for gentisate. The mabB-disrupted mutant lost the ability to grow on 3-aminobenzoate, and mabB expression was higher when strain QT12 was cultivated in the presence of 3-aminobenzoate. Thus, 5ASA is the physiological substrate of MabB.IMPORTANCE For several decades, 5-aminosalicylate (5ASA) has been advocated as the drug mesalazine to treat human inflammatory bowel disease and considered the key intermediate in the xenobiotic degradation of many aromatic organic pollutants. 5ASA biotransformation research will help us elucidate the microbial degradation of these pollutants. Most studies have reported that gentisate 1,2-dioxygenases (GDOs) can convert 5ASA with significantly high activity; however, the catalytic efficiency of these enzymes for gentisate is much higher than that for 5ASA. This study showed that MabB can convert 5ASA to cis-4-amino-6-carboxy-2-oxohexa-3,5-dienoate, incorporating two oxygen atoms from the dioxygen molecule into the product. Unlike GDOs, MabB uses 5ASA instead of gentisate as the primary substrate. mabB is the first reported 5-aminosalicylate 1,2-dioxygenase gene.
研究领域:
微生物学
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环境科学
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分子生物学
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产品关联
DOI
PubMed
高影响因子
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
·
2021
·
IF 6.291
Jing Liu,Ai-Ning Zhang,Yong-Jun Liu,Zhe Liu,Yu Liu,Xi-Jun Wu
A slow degradation rate and low transformation efficiency are the main problems in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). This study selected pyrene as the target PAH to investigate the effect of ferrous ion and ferric ion on pyrene degradation. The driving effect and mechanism, including the interaction between pyrene and iron ions and the bacterial physiological response during the biodegradation process by Rhodococcus ruber strain L9, were investigated. The results showed that iron ions did not enhance bacterial growth but improved bacteria’s pyrene removal capacity, contributing to the total efficiency of pyrene biodegradation. The process started with an initial formation of “cation-π” between Fe (III) and pyrene, which subsequently drove the pyrene removal process and accelerated the bacterial metabolic process. Moreover, a significant increase in the protein concentration, catechol dioxygenase (C12O and C23O) activities, and intracellular protein regulation in crude enzyme solution indicate a positive response of the bacteria during the iron ion-enhanced pyrene degradation process.
研究领域:
环境生物学
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微生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
APPLIED BIOCHEMISTRY AND MICROBIOLOGY
·
2022
·Vol. 58
·期 6
·796-805
·
IF 1.065
Li P.,Jiang Y.,Fei Y. Y.,Zeng X. C.
Abstract Benzo(a)pyrene (BaP) is one of the most common organic pollutants in the environment, and its microbial removal has great ecological and economic value. Here, using BaP (50 mg/L) as the sole carbon source, dynamic changes in camel rumen and gut bacterial communities were analyzed by high-throughput sequencing. Next, cultivable BaP-degrading isolates were obtained, and their degradation characteristics were explored. The relative abundance of most bacteria in the gut and rumen underwent apparent changes after BaP treatment. The rumen and gut bacteria have the ability to degrade BaP but fluctuated during iterative culturing from the first to the fifth generation of gut communities displaying the highest BaP degradation efficiency (BDE) (74.4 and 81.1%, respectively). Moreover, 37 isolates exhibiting BDE were identified. Among these isolates, CL9 ( Klebsiella sp.), CL16 ( Ochrobactrum sp.), CC6 ( Ochrobactrum sp.), and CC16 ( Bacillus sp.) showed BDEs of up to 70.8, 69.3, 68.4, and 76.2%, respectively. The enzyme catechol-2,3-dioxygenase was involved in BaP degradation in these four BaP-degrading isolates and represented the main BaP degradation pathway in isolates CL9 and CL16; however, the relative expression level of the gene phnAc was higher in isolates CC6 and CC16 than in isolates CL9 and CL16. Our results provided promising bacterial resources for the removal of BaP and laid the foundation for the application of animal gastrointestinal bacteria to degrade environmental pollutants.
研究领域:
环境微生物学
·
动物科学
·
生物修复
✓ 已验证
DOI
高影响因子
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
·
2024
·
IF 3.9
Jia Xu,Tao Li,Wei E. Huang,Ning-Yi Zhou
Rieske non-heme dioxygenase family enzymes play an important role in the aerobic biodegradation of nitroaromatic pollutants, but no active dioxygenases are available in nature for initial reactions in the degradation of many refractory pollutants like 2,4-dichloronitrobenzene (24DCNB). Here, we report the engineering of hotspots in 2,3-dichloronitrobenzene dioxygenase from Diaphorobacter sp. strain JS3051, achieved through molecular dynamic simulation analysis and site-directed mutagenesis, with the aim of enhancing its catalytic activity toward 24DCNB. The computationally predicted activity scores were largely consistent with the detected activities in wet experiments. Among them, the two most beneficial mutations (E204M and M248I) were obtained, and the combined mutant reached up to a 62-fold increase in activity toward 24DCNB, generating a single product, 3,5-dichlorocatechol, which is a naturally occurring compound. In silico analysis confirmed that residue 204 affected the substrate preference for meta-substituted nitroarenes, while residue 248 may influence substrate preference by interaction with residue 295. Overall, this study provides a framework for manipulating nitroarene dioxygenases using computational methods to address various nitroarene contamination problems.
研究领域:
环境生物学
·
酶工程
·
计算生物学
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产品关联
DOI
PubMed
高影响因子
Microorganisms
·
2019
·Vol. 7
·期 10
·379
·
IF 4.167
Huanhuan Shao,Meiju Chen,Xueting Fei,Ronglin Zhang,Yue Zhong,Weimin Ni,Xiang Tao,XinYi He,Erliang Zhang,Bin Yong,Xuemei Tan
A bacterial strain,Streptomyces albogriseolusLBX-2, was isolated from a soil sample in Chengdu, China.S. albogriseolusLBX-2 is an aerobic and Gram-positive microorganism that is capable of using the polyethylene as the sole carbon source. Results of scanning electron microscopy and tensile tests indicated thatS. albogriseolusLBX-2 could cause the damages to polyethylene (PE). Suspension culture of LBX-2 resulted in the weight loss in the PE powder over a 15-day period. The bacterial growth curve assay clearly demonstrated the utilization of n-hexadecane and n-octadecane for the strain LBX-2. Phylogenetic analysis showed that it was grouped in the same clade asS. albogriseolusbelonging toStreptomyces. The complete genome of strain LBX-2 consists of a chromosome of 7,210,477 bp and a linear plasmid of 336,677 bp. Compared with other strains ofStreptomyces, the genome size ofS. albogriseolusLBX-2 was smaller than the average but its guanine and cytosine content (72.47%) was higher than the others. The Non-Redundant Protein Database (NR), Kyoto Encyclopedia of Genes and Genomes (KEGG), SwissProt, Gene Ontology (GO) and Clusters of Orthologous Groups (COG) annotations provided information on the specific functions of encoded proteins. A total of 21 monooxygenase and 22 dioxygenase genes were found in its genome. Synteny comparison with the genome ofStreptomyces coelicolorA3(2) revealed a low overall genetic diversity between them. This study provides valuable information to reveal the underlying mechanisms on PE degradation byS. albogriseolusLBX-2.Keywords:Streptomyces albogriseolusLBX-2;polyethylene biodegradation;genome;synteny comparison
研究领域:
微生物学
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环境科学
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基因组学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
·
2022
·Vol. 195
·期 1
·298-313
·
IF 3.094
Liu Yani,Wei Fengdan,Xu Rui,Cheng Tao,Ma Yanling
Microbial remediation has become one of the promising ways to eliminate polycyclic aromatic hydrocarbons (PAHs) pollution due to its efficient enzyme metabolism system. Catechol 1,2-dioxygenase (C12O) is a crucial rate-limiting enzyme in the degradation pathway of PAHs in Achromobacter xylosoxidans DN002 that opens the benzene ring through the ortho-cleavage pathway. However, little attention has been given to explore the interaction mechanism of relevant enzyme–substrate. This study aims to investigate the binding interaction between C12O of strain DN002 and catechol by means of a molecular biological approach combined with homology modeling, molecular docking, and multiple spectroscopies. The removal rate of catechol in the mutant strain of cat A deletion was only 12.03%, compared to the wild-type strain (54.21%). A Ramachandran plot of active site regions of the primary amino acid sequences in the native enzyme showed that 93.5% sequences were in the most favored regions on account of the results of homology modeling, while an additional 6.2% amino acid sequences were found in conditionally allowed regions, and 0.4% in generously allowed regions. The binding pocket of C12O with catechol was analyzed to obtain that the catalytic trimeric group of Tyr164-His224-His226 was proven to be great vital for the ring-opening reaction of catechol by molecular docking. In the native enzyme, binding complexes were spontaneously formed by hydrophobic interactions. Binding constants and thermodynamic potentials from fluorescence spectra indicated that catechol effectively quenched the intrinsic fluorescence of C12O in the C12O/catechol complex via conventional static and dynamic quenching mechanisms of C12O. The results of ultraviolet and visible (UV) spectra, synchronous fluorescence, and circular dichroism (CD) spectra revealed conspicuous changes in the local conformation, and site-directed mutagenesis confirmed the role of predicted key residues during catalysis, wherein His 226 had a significant effect on catechol utilization by C12O. This is the first report to reveal interactions of C12O with substrate from the molecular docking results, providing the mechanistic understanding of representative dioxygenases involved in aromatic compound degradation, and a solid foundation for further site modifications as well as strategies for the directed evolution of this enzyme.
研究领域:
微生物学
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环境科学
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分子生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
EXPERIMENTAL NEUROLOGY
·
2025
·
IF 4.2
Chen-Meng Qiao,Xiao-Yu Ma,Lu-Lu Tan,Yi-Meng Xia,Ting Li,Jian Wu,Chun Cui,Wei-Jiang Zhao,Yan-Qin Shen
Abnormal tryptophan metabolism is closely linked with neurological disorders. Research has shown that indoleamine 2,3-dioxygenase 1 (IDO-1), the first rate-limiting enzyme in tryptophan degradation, is upregulated in Parkinson's disease (PD). However, the precise role of IDO-1 in PD pathogenesis remains elusive. In this study, we administered 1-methyl-tryptophan (1-MT), an IDO-1 inhibitor, intraperitoneally at 15 mg/kg daily for 21 days to PD mice induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) at 30 mg/kg daily for 5 days. Our results show that IDO-1 inhibition improves behavioral performance, reduces dopaminergic neuron loss, and decreases serum quinolinic acid (QA) content and the aryl hydrocarbon receptor (AHR) expression in the striatum and colon. It also alleviates glial-associated neuroinflammation and mitigates colonic inflammation (decreasing iNOS, COX2) by suppressing the Toll-like receptor 4/nuclear factor-κB (TLR4/NF-κB) pathway. Furthermore, IDO-1 inhibition promotes hippocampal neurogenesis (increasing doublecortin positive (DCX + ) cells and SOX2 + cells), which have recently been recognized as key pathological features and potential therapeutic targets in PD, likely through the activation of the BDNF/TrkB pathway. We further explored the gut-brain connection by depleting the gut microbiota in mice using antibiotics. Notably, the neuroprotective effects of IDO-1 inhibition were completely abolished in pseudo-germ-free mice (administrated an antibiotic mixture orally for 14 days prior to 1-MT treatment), highlighting the dependency of 1-MT's neuroprotective effects on the presence of gut microbiota. Finally, we found IDO-1 inhibition corrects the abnormal elevation of fecal short chain fatty acids (SCFAs). Collectively, these findings suggest that IDO-1 inhibition may represent a promising therapeutic approach for PD.
研究领域:
神经科学
·
药理学
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微生物学
✓ 已验证
产品关联
DOI
PubMed
高影响因子
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