JOURNAL OF HAZARDOUS MATERIALS
·
2026
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IF 10.6
Kejian Tian,Jinming Gu,Lang Xie,Dandan Zhou,Fanxing Meng,Pengfei Hao,Yue Yu,Fan Li,Hongliang Huo,Shi Xie
17α-Ethynylestradiol (EE2) is a ubiquitous synthetic estrogen of global concern. Due to its recalcitrance to biodegradation, EE2 is often insufficiently removed during wastewater treatment and consequently released with effluents, posing significant ecological risks and potential threats to human health. In this study, Rhodococcus equi DSSKP-R-001 ( R. equi -001) was identified as one of the most potent EE2-degrading bacterium, achieving complete degradation of EE2 at low concentrations. Transcriptomic analysis revealed substantial upregulation and high functional similarity of genes encoding short-chain dehydrogenase/reductase (SDR) during EE2 degradation. Among these candidates, sdr R was functionally validated as the most catalytically efficient, achieving 97.88 % EE2 removal. Molecular docking analyses demonstrated that the sdr R -mediated conversion of EE2 to estrone (E1) is facilitated by multiple key amino acid residues through substrate binding, hydrogen bonding, and hydrophobic interactions. Furthermore, the sdr R -harboring genetically engineered bacterium (GEB) exhibited superior biodegradation potential, achieving up to 96.48 % EE2 removal individually and enabling complete elimination when applied for bioaugmentation. Concurrently, bioaugmentation with GEBs reshaped the sludge microbial community by optimizing interspecies interactions and increasing the abundance of denitrifying and phosphorus-accumulating microorganisms, thereby improving overall pollutant removal performance. Overall, this study expands the microbial and enzymatic repertoire for EE2 degradation and demonstrate the potential of genetic engineering strategies for improving the removal of recalcitrant micropollutants in biological wastewater treatment.
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高影响因子
ACS Omega
·
2020
·
IF 2.87
Li Wang,Shengxian Liu,Wenjing Du,Tongyi Dou,Changhai Liang
5-Cyanovaleramide (5-CVAM) is an important intermediate of a herbicide and chemical raw material. Herein, we found a novel nitrile hydratase from the strain Rhodococcus erythropolis CCM2595, exhibiting high regioselectivity with higher substrate specificity toward dinitriles than mononitriles. In the past, the strain was shown to degrade only phenol, hydroxybenzoate, p-chlorophenol, aniline, and other aromatic compounds. In our study, 20 mM adiponitrile was completely consumed within 10 min with 95% selectivity to 5-CVAM and 5% selectivity to adipamide. In addition to its high regioselectivity, our recombinant Escherichia coli showed a higher substrate tolerance of up to 200 mM adiponitrile even after 3 h when compared with two reported strains with their cyano-tolerance concentrations of up to 100 mM, which is considered to be the highest cyano-tolerance. Such a robust biocatalyst is a desirable attribute of a biocatalyst intended for use in commercial applications of 5-CVAM.
研究领域:
生物催化
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生物化学
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化学工程
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酶技术
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JOURNAL OF HAZARDOUS MATERIALS
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2022
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IF 14.224
Chunyan Li,Yueling Sun,Guanjun Sun,Hailian Zang,Shanshan Sun,Xinyue Zhao,Ning Hou,Dapeng Li
Triclocarban (TCC) is an emerging and intractable environmental contaminant due to its hydrophobicity and chemical stability. However, the antibacterial property of TCC limits its biodegradation, and only the functional enzyme TccA involved in TCC degradation has been characterized to date. In this study, we report a highly efficient TCC-degrading bacterium, Rhodococcus rhodochrous BX2, that could degrade and mineralize TCC (10 mg/L) by 76.8% and 56.5%, respectively, within 5 days. Subsequently, the TCC biodegradation pathway was predicted based on the detection of metabolites using modern mass spectrometry techniques. Furthermore, an amidase (TccS) and a novel phenol hydroxylase (PH IND ) encoded by the tccS and PH IND genes, respectively, were identified by genomic and transcriptomic analyses of strain BX2, and these enzymes were further unequivocally proven to be the key enzymes responsible for the metabolism of TCC and its intermediate 4-chloroaniline (4-CA) by using a combination of heterologous expression and gene knockout. Our results shed new light on the mechanism of TCC biodegradation and better utilization of microbes to remediate TCC contamination.
研究领域:
环境微生物学
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生物修复
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酶学
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PubMed
高影响因子
SCIENCE OF THE TOTAL ENVIRONMENT
·
2018
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IF 4.61
Hai-Ming Zhao,Rui-Wen Hu,Huan Du,Xiao-Ping Xin,Yan-Wen Li,Hui Li,Quan-Ying Cai,Ce-Hui Mo,Jie-Sheng Liu,Dong-Mei Zhou,Ming-Hung Wong,Zhen-Li He
Microbial degradation is considered the most promising method for removing phthalate acid esters (PAEs) from polluted environments; however, a comprehensive genomic understanding of the entire PAE catabolic process is still lacking. In this study, the repertoire of PAE catabolism genes in the metabolically versatile bacterium Rhodococcus sp. 2G was examined using genomic, metabolic, and bioinformatic analyses. A total of 4930 coding genes were identified from the 5.6 Mb genome of the 2G strain, including 337 esterase/hydrolase genes and 48 transferase and decarboxylase genes that were involved in hydrolysing PAEs into phthalate acid (PA) and decarboxylating PA into benzoic acid (BA). One gene cluster ( xyl ) responsible for transforming BA into catechol and two catechol-catabolism gene clusters controlling the ortho ( cat ) and meta ( xyl & mhp ) cleavage pathways were also identified. The proposed PAE catabolism pathway and some key degradation genes were validated by intermediate-utilising tests and real-time quantitative polymerase chain reaction. Our results provide novel insight into the mechanisms of PAE biodegradation at the molecular level and useful information on gene resources for future studies.
研究领域:
微生物学
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环境科学
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基因组学
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高影响因子
Journal of Environmental Chemical Engineering
·
2026
·Vol. 14
·期 3
·122943
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IF 7.5
Qiannan Li,Hanyu Pan,Yunna Jia,Zhenhua Ma,Ye Wang,Xiaojun Liang,Xiuzhen Yu,Yunhang Gao
The molecular mechanism by which microorganisms degrade the endocrine-disrupting contaminant 17β-estradiol (E2) at low temperatures remains largely unclear, with only limited studies available. Here, we investigated the adaptive strategy of the cryotolerant bacterium Rhodococcus sp . RCBS9 for sustaining E2 degradation at 10 °C, a temperature at which efficient estrogen degradation has rarely been reported. Using time-resolved multi-omics and phenotypic assays, we characterized a dynamic, staged adaptation process involving changes in oxidative stress defense, membrane composition, transcription factors, signaling factors, and stress proteins. We uncovered three major novelties. First, RCBS9 employs a distinct degradation pathway that first cleaves the saturated sterol rings, in contrast to the canonical 4,5-seco pathway that initiates with aromatic ring A cleavage. Second, we identified and functionally validated a cold-tolerant short-chain dehydrogenase/reductase (SDR) encoded by gene RQCS_RS03565 that converts E2 to estrone (E1), as confirmed by heterologous expression and site-directed mutagenesis. Third, subsequent sterol ring cleavage proceeds via a suite of oxidoreductases and hydrolases. The resulting aromatic intermediates are then mineralized through the β-ketoadipate pathway, as suggested by the coordinated upregulation of intradiol dioxygenase and carboxymuconolactone decarboxylase. Additionally, trace iron (50 μM) promoted E2 degradation and reduced E1 accumulation, partly attributable to enhanced metabolic activity and upregulation of iron-requiring enzyme genes. Overall, this work provides fundamental insights into a novel estrogen biodegradation logic under cold stress and proposes a practical iron-mediated strategy for low-temperature bioremediation.
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INTERNATIONAL BIODETERIORATION & BIODEGRADATION
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2022
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IF 4.907
Xiaoyong Song,Zihan Zhang,Yanran Dai,Deshou Cun,Baihui Cui,Yuewei Wang,Yaocheng Fan,Haibin Tang,Liang Qiu,Feihua Wang,Dongru Qiu,Wei Liang
Di-(2-ethylhexyl) phthalate (DEHP), the most extensively used phthalate acid esters (PAEs), poses a potential risk to human and environment. A novel bacterial strain , Rhodococcus sp. LW-XY12, with efficient PAE-degrading capability, was isolated from activated sludge. Strain LW-XY12 could degrade 96.91 ± 0.68% of DEHP (500 mg L −1 ) within 32 h. The degradation curves of DEHP (50–1500 mg L −1 ) and PAE mixture (500 mg L −1 each) fitted well with the modified Gomperz kinetics model. DEHP metabolic pathway was reconstructed by using genome annotation and metabolic intermediate analyses. The DEHP metabolic pathway might comprise de-esterification and β-oxidation. Homologous modeling and molecular docking analysis revealed that DEHP and MEHP (mono-(2-ethylhexyl) phthalate) could be bound to putative carboxylesterase (KXC42_04905) via hydrogen bonding and hydrophobic interaction. A conserved catalytic triad (Ser195-Glu319-His412) might act as an active protein pocket and catalyze the hydrolysis of DEHP. Carboxylesterase (KXC42_04905) could hydrolyze ester bond and a possible mechanism underlying ester bond hydrolysis catalyzed by the carboxylesterase was proposed. Protocatechuate 3,4-dioxygenase, 3-oxoadipate CoA-transferase, benzoate 1,2-dioxygenase, catechol 1,2-dioxygenase, and catechol 2,3-dioxygenase transcripts were detected and significantly up-regulated under DEHP induction. This study sheds light on the functional genes associated with DEHP degradation and metabolic mechanism in this versatile bacterium for degradation of PAEs.
研究领域:
环境微生物学
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基因组学
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生物降解
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生物化学
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高影响因子
ENVIRONMENTAL RESEARCH
·
2023
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IF 8.3
Wankui Jiang,Jingxiang Sun,Weiliang Dong,Jie Zhou,Yujia Jiang,Wenming Zhang,Fengxue Xin,Min Jiang
Bis (2-hydroxyethyl) terephthalate (BHET) is one of the main compounds produced by enzymatic hydrolysis or chemical depolymerization of polyethylene terephthalate (PET). However, the lack of understanding on BHET microbial metabolism is a main factor limiting the bio-upcycling of PET. In this study, BHET-degrading strains of Rhodococcus biphenylivorans GA1 and Burkholderia sp. EG1 were isolated and identified, which can grow with BHET as the sole carbon source. Furthermore, a novel esterase gene betH was cloned from strain GA1, which encodes a BHET hydrolyzing esterase with the highest activity at 30 °C and pH 7.0. In addition, the co-culture containing strain GA1 and strain EG1 could completely degrade high concentration of BHET, eliminating the inhibition on strain GA1 caused by the accumulation of intermediate metabolite ethylene glycol (EG). This work will provide potential strains and a feasible strategy for PET bio-upcycling.
研究领域:
环境微生物学
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生物化学
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高影响因子
Frontiers in Microbiology
·
2018
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IF 4.019
Zhang Hui,Yu Ting,Wang Yiran,Li Jie,Wang Guangli,Ma Yingqun,Liu Yu
4-Chlorophenol (4-CP) oxidation plays an essential role in the detoxification of 4-CP. However, oxidative regulation of 4-CP at the genetic and biochemical levels has not yet been studied. To explore the regulation mechanism of 4-CP oxidation, a novel gene cluster, cphRA2A1, involved in biodegradation of 4-CP was identified and cloned from Rhodococcus sp. strain YH-5B by genome walking. The sequence analysis showed that the cphRA2A1 gene cluster encoded an AraC-type transcriptional regulator and a two-component monooxygenase enzyme, while quantitative real-time PCR analysis further revealed that cphR was constitutively expressed and positively regulated the transcription of cphA2A1 genes in response to 4-CP or phenol, as evidenced by gene knockout and complementation experiments. Through the transcriptional fusion of the mutated cphA2A1 promoter with the lacZ gene, it was found that the CphR regulator binding sites had two 15-bp imperfect direct repeats (TGCA-N6-GGNTA) at −35 to −69 upstream of the cphA2A1 transcriptional start site. Notably, the sub-motifs at the −46 to −49 positions played a critical role in the appropriate interaction with the CphR dimer. In addition, it was confirmed that the monooxygenase subunits CphA1 and CphA2, which were purified by His-tag affinity chromatography, were able to catalyze the conversion of 4-CP to 4-chlorocatechol, suggesting that strain YH-5B could degrade 4-CP via the 4-chlorocatechol pathway. This study enhances our understanding of the genetic and biochemical diversity in the transcriptional regulation of 4-CP oxidation in Gram-positive bacteria.
研究领域:
微生物学
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环境生物技术
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遗传学
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生物化学
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PubMed
高影响因子
BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT
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2019
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IF 1.097
Yu Wang,Huanhuan Shao,Suiyi Zhu,Kejian Tian,Qing Qiu,Hongliang Huo
In this study, we investigated environmental oestrogen 17β-estradiol (E2) degradation by a mixed culture of Rhodococcus equi DSSKP-R-001(RS) and Comamonas testosteroni QYY20150409(CT). The results demonstrated that the two strains exhibited synergistic E2 degradation activity, showing that multispecies bacterial systems can improve microbial survival and activity. The E2 degradation rate for the mixed culture system was 94% under conditions in which E2 was the sole source of carbon and growth energy, while the degradation rates of the R. equi DSSKP-R-001 and C. testosteroni QYY20150409 single strains were 86% and 76%, respectively. Comparing and analyzing the degradation products of E2, intermediate cross-metabolism products were observed in the culture containing the two bacteria. The metabolic products of benzene were essentially removed during the process of E2 degradation in the mixed culture, which showed stronger degradation ability than cultures of the individual strains. The results from this investigation on the degradation of E2 by individual and mixed bacterial cultures provide a theoretical basis for the microbial remediation of environmental oestrogens.
研究领域:
环境科学
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微生物学
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高影响因子
MARINE POLLUTION BULLETIN
·
2025
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IF 4.9
Jia Shi,Dan Xu,Qiao Ma
p -Chloro- m -xylenol (PCMX), a widely used antimicrobial agent, poses potential ecological risks due to its ubiquitous distribution and documented toxicity to aquatic vertebrates. Although microbial degradation represents a key natural attenuation pathway, the molecular mechanisms governing PCMX biodegradation remain elusive. Here, we report the isolation of three novel Rhodococcus strains from marine sediments capable of mineralizing PCMX. Among these, strain R. ruber SJ-1 completely metabolized 30 mg/L PCMX within 72 h and maintained significant degradation capacity under high-salinity stress. Integrated genomic and transcriptomic analyses revealed that PCMX exposure triggered extensive transcriptional reprogramming in strain SJ-1, with 1063 genes upregulated and 533 downregulated. PCMX inhibited core cellular functions, including key genes related to cell stress resistance, energy production, central carbon metabolism, fatty acid metabolism, and protein biosynthesis. Concurrently, aromatic catabolism pathways were markedly induced. A highly upregulated gene cluster ( sj4821 - sj4838 ) was identified as pivotal for PCMX metabolism, encompassing a flavin-dependent monooxygenase (NphA1-sj, sj4831 ; 2145.26-fold) and catechol 2,3-dioxygenase (C23O, sj4838 , 2052.43-fold) genes. Quantitative PCR assays further validated the upregulation patterns. Based on bioinformatics and high-resolution mass spectrometry analyses, we proposed that strain SJ-1 converted PCMX to 4-chloro-3,5-dimethylcatechol via ortho -hydroxylation, followed by meta -cleavage of the aromatic ring. This study presents the first documented evidence of PCMX degradation by a marine Rhodococcus isolate. Our findings reveal the molecular mechanisms driving PCMX detoxification and cellular adaptation, establishing a foundation for bioremediation in saline ecosystems.
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CHEMOSPHERE
·
2015
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IF 3.34
Jing-Nan Jin,Jun Yao,Qing-Ye Zhang,Chan Yu,Peng Chen,Wen-Juan Liu,Dan-Ning Peng,Martin M.F. Choi
Naphthalene dioxygenase (NDO) is the initial enzyme catalyzing the biodegradation of aromatic compounds, and it plays a key role in microbial remediation of polluting sites. In this study, Rhodococcus sp. ustb-1 derived from crude oil was selected to investigate the biodegradation characters and dihydroxylation mechanism of pyrene by an integrated approach of bioassay and molecular docking. The biodegradation experiment proved that the strain ustb-1 shows high effective biodegradability to pyrene with a 70.8% degradation on the 28th day and the metabolite pyrene cis-4,5-dihydrodiol was found. The results of molecular docking indicated that the regions surrounding pyrene are defined by hydrophobic amino acids which are favorable for the binding of dioxygen molecule at C4 and C5 positions of pyrene in a side-on mode. The binding positions of dioxygen are in agreement with the mass spectral analysis of the metabolite pyrene cis-4,5-dihydrodiol. In summary, this study provides a promising explanation for the possible binding behavior between pyrene and active site of NDO.
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高影响因子
Foods
·
2025
·Vol. 14
·期 21
·3772
·
IF 5.1
Aiyuan Zhang,Xuewu Zhang,Jiguo Yang
Due to the high toxicity and widespread distribution of aflatoxin B1 (AFB1), there is significant interest in efficient, safe, and environmentally friendly microbial degradation methods.Rhodococcus opacusPD630 cell-free supernatant (RCFS) shows excellent activity in degrading AFB1, but its active components and mechanisms remain unclear. We assessed the feasibility of ethanol precipitation to enrich active components in RCFS and characterized the ethanol precipitate (RCFSC-EP). Metabolomics and proteomics were used to elucidate the active components, mechanisms, and products of AFB1 degradation by RCFS. The results indicate that ethanol precipitation enriches over 80% of the active components for AFB1 degradation in RCFS. RCFSC-EP exhibits excellent heat resistance, and inhibitors like EDTA-2Na and proteinase K significantly inhibit its activity. Multi-omics analysis suggests that active components in RCFS metabolize AFB1 into six products through four potential pathways, three of which withstand 135 °C for 20 min. The AFB1-degrading activity of RCFS is an intrinsic, constitutive trait ofR. opacusPD630 during normal growth. The active components are diverse proteins or enzymes, including glutathione S-transferases, aldo/keto reductase, peroxidases, and carbonyl reductases. This study enriches and reveals the active components, pathways, and products of AFB1 degradation by RCFS, providing a basis for developing RCFS as a biological agent for AFB1 degradation.
研究领域:
微生物学
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环境生物技术
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毒理学
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分子生物学
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蛋白质组学与代谢组学
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高影响因子
危险品化学品经营许可证（带存储）