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Gu Y, Li T, Zhou NY. Redundant and scattered genetic determinants for coumarin biodegradation in Pseudomonas sp. strain NyZ480. Appl Environ Microbiol 2023; 89:e0110923. [PMID: 37815346 PMCID: PMC10617510 DOI: 10.1128/aem.01109-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/18/2023] [Indexed: 10/11/2023] Open
Abstract
Coumarin (COU) is both a naturally derived phytotoxin and a synthetic pollutant which causes hepatotoxicity in susceptible humans. Microbes have potentials in COU biodegradation; however, its underlying genetic determinants remain unknown. Pseudomonas sp. strain NyZ480, a robust COU degrader, has been isolated and proven to grow on COU as its sole carbon source. In this study, five homologs of xenobiotic reductase A scattered throughout the chromosome of strain NyZ480 were identified, which catalyzed the conversion of COU to dihydrocoumarin (DHC) in vitro. Phylogenetic analysis indicated that these COU reductases belong to different subgroups of the old yellow enzyme family. Moreover, two hydrolases (CouB1 and CouB2) homologous to the 3,4-dihydrocoumarin hydrolase in the fluorene degradation were found to accelerate the generation of melilotic acid (MA) from DHC. CouC, a new member from the group A flavin monooxygenase, was heterologously expressed and purified, catalyzing the hydroxylation of MA to produce 3-(2,3-dihydroxyphenyl)propionate (DHPP). Gene deletion and complementation of couC indicated that couC played an essential role in the COU catabolism in strain NyZ480, considering that the genes involved in the downstream catabolism of DHPP have been characterized (Y. Xu and N. Y. Zhou, Appl Environ Microbiol 86:e02385-19, 2020) and homologous catabolic cluster exists in strain NyZ480. This study elucidated the genetic determinants for complete degradation of COU by Pseudomonas sp. strain NyZ480.IMPORTANCECoumarin (COU) is a phytochemical widely distributed in the plant kingdom and also artificially produced as an ingredient for personal care products. Hence, the environmental occurrence of COU has been reported in different places. Toxicologically, COU was proven hepatotoxic to individuals with mutations in the CYP2A6 gene and listed as a group 3 carcinogen by the International Agency for Research on Cancer and thus has raised increasing concerns. Until now, different physicochemical methods have been developed for the removal of COU, whereas their practical applications were hampered due to high cost and the risk of secondary contamination. In this study, genetic evidence and biochemical characterization of the COU degradation by Pseudomonas sp. strain NyZ480 are presented. With the gene and strain resources provided here, better managements of the hazards that humans face from COU could be achieved, and the possible microbiota-plant interaction mediated by the COU-utilizing rhizobacteria could also be investigated.
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Affiliation(s)
- Yichao Gu
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism & School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Shanghai, China
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Gu Y, Li T, Yin CF, Zhou NY. Elucidation of the coumarin degradation by Pseudomonas sp. strain NyZ480. JOURNAL OF HAZARDOUS MATERIALS 2023; 457:131802. [PMID: 37320896 DOI: 10.1016/j.jhazmat.2023.131802] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/12/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
As a phytotoxin and synthetic chemical, coumarin (COU) is known for its hepatotoxicity and carcinogenicity. However, no thorough characterization of its microbial degradation has been reported. Here, Pseudomonas sp. strain NyZ480 was isolated for its capability of utilizing COU as the sole carbon source. Studies on its growth and degradation efficiency of COU under various conditions suggested that strain NyZ480 performed the optimum degradation at 30 ℃, pH 7, and 0.5 mM COU was completely removed within 4 h with 1% inoculum. HPLC and LC-MS analyses indicated that dihydrocoumarin (DHC), melilotic acid (MA) and 3-(2,3-dihydroxyphenyl)propionate (DHPP) were the upstream biotransformation intermediates of COU. Enzyme assay established that the initial reaction transforming COU to DHC required an NAD(P)H-dependent reductase, followed by the hydrolysis of DHC to generate MA, and the third reaction catalyzing the monooxygenation of MA to DHPP utilized a strict NADH-dependent hydroxylase. Combining genomics and transcriptomics, we proposed that the COU downstream degradation (from DHPP) was catalyzed by enzymes encoded by a gene cluster homologous to the mhp cluster for 3(3-hydroxyphenyl)propionate degradation via DHPP in E. coli. This study thoroughly identified the intermediates from the COU catabolism, providing essential insights into the molecular evidences of its biodegradation pathway.
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Affiliation(s)
- Yichao Gu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chao-Fan Yin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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Huang S, Wang M, Mao D, Rasool A, Jia C, Yang P, Han L, Yan M. Isolation, Identification and Characterization of Growth Parameters of Pseudomonas putida HSM-C2 with Coumarin-Degrading Bacteria. Molecules 2022; 27:molecules27186007. [PMID: 36144743 PMCID: PMC9506499 DOI: 10.3390/molecules27186007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/02/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Natural coumarins contribute to the aroma of licorice, and they are often used as a flavoring and stabilizing agents. However, coumarins usage in food has been banned by various countries due to its toxic effect. In this study, a strain of HSM-C2 that can biodegrade coumarin with high efficiency was isolated from soil and identified as Pseudomonas putida through performing 16S rDNA sequence analysis. The HSM-C2 catalyzed the biodegradation up to 99.83% of 1 mg/mL coumarin within 24 h under optimal culture conditions, such as 30 °C and pH 7, which highlights the strong coumarin biodegrading potential of this strain. The product, such as dihydrocoumarin, generated after the biodegradation of coumarin was identified by performing GC-MS analysis. The present study provides a theoretical basis and microbial resource for further research on coumarin biodegradation.
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Affiliation(s)
- Shen Huang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Menghuan Wang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Duobin Mao
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
- Correspondence:
| | - Aamir Rasool
- Institute of Biochemistry, University of Balochistan, Quetta 87300, Pakistan
| | - Chunxiao Jia
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Pengfei Yang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Li Han
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China
| | - Meiling Yan
- Anhui Tobacco Industry Co., Ltd., Hefei Cigarette Factory, Hefei 230000, China
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Li SQ, Li GD, Peng KM, Yang LH, Huang XF, Lu LJ, Liu J. The combined effect of Diversispora versiformis and sodium bentonite contributes on the colonization of Phragmites in cadmium-contaminated soil. CHEMOSPHERE 2022; 293:133613. [PMID: 35032512 DOI: 10.1016/j.chemosphere.2022.133613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/19/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
To promote the colonization of Phragmites in Cd polluted, nutrient deprived and structural damaged soil, the combined remediation using chemical and microbial modifiers were carried out in potting experiments. The co-application of Diversispora versiformis and sodium bentonite significantly improved the soil structure and phosphorus utilization of the plant, while decreasing the content of cadmium bound by diethylenetriaminepentaacetic acid by 77.72%. As a result, the Phragmites height, tillers, and photosynthetic capacity were increased by 71.60%, 38.37%, and 17.54%, respectively. Further analysis suggested the co-application increased the abundance of phosphorus-releasing microbial communities like Pseudomonassp. and Gemmatimonadetes. Results of rhizosphere metabolites also proved that the signal molecule of lysophosphatidylcholine regulated the phosphorus fixation and utilization by the plant. This work finds composite modifiers are effective in the colonization of Phragmites in Cd contaminated soil by decreasing the bioavailable Cd, increasing the abundance of functional microbial communities and regulating the phosphorus fixation.
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Affiliation(s)
- Shuang-Qiang Li
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai, 200092, China
| | - Gen-Dong Li
- Inner Mongolia Hetao Irrigation District Water Conservancy Development Center, Bayan Nur, 015000, China
| | - Kai-Ming Peng
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai, 200092, China
| | - Li-Heng Yang
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai, 200092, China
| | - Xiang-Feng Huang
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai, 200092, China
| | - Li-Jun Lu
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai, 200092, China
| | - Jia Liu
- College of Environmental Science and Engineering, State Key Laboratory of Pollution Control and Resource Reuse, Ministry of Education Key Laboratory of Yangtze River Water Environment, Shanghai Institute of Pollution Control and Ecological Security, Tongji University, Shanghai, 200092, China; Frontiers Science Center for Intelligent Autonomous Systems, Shanghai, 201210, China.
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Zhao Z, Liu C, Xu Q, Ahmad S, Zhang H, Pang Y, Aikemu A, Liu Y, Yan H. Characterization and genomic analysis of an efficient dibutyl phthalate degrading bacterium Microbacterium sp. USTB-Y. World J Microbiol Biotechnol 2021; 37:212. [PMID: 34738191 DOI: 10.1007/s11274-021-03181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022]
Abstract
A promising bacterial strain for biodegrading dibutyl phthalate (DBP) was successfully isolated from activated sludge and characterized as a potential novel Microbacterium sp. USTB-Y based on 16S rRNA sequence analysis and whole genome average nucleotide identity (ANI). Initial DBP of 50 mg/L could be completely biodegraded by USTB-Y both in mineral salt medium and in DBP artificially contaminated soil within 12 h at the optimal culture conditions of pH 7.5 and 30 ℃, which indicates that USTB-Y has a strong ability in DBP biodegradation. Phthalic acid (PA) was identified as the end-product of DBP biodegraded by USTB-Y using GC/MS. The draft genome of USTB-Y was sequenced by Illumina NovaSeq and 29 and 188 genes encoding for putative esterase/carboxylesterase and hydrolase/alpha/beta hydrolase were annotated based on NR (non redundant protein sequence database) analysis, respectively. Gene3781 and gene3780 from strain USTB-Y showed 100% identity with dpeH and mpeH from Microbacterium sp. PAE-1. But no phthalate catabolic gene (pht) cluster was found in the genome of strain USTB-Y. The results in the present study are valuable for obtaining a more holistic understanding on diverse genetic mechanisms of PAEs biodegrading Microbacterium sp. strains.
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Affiliation(s)
- Zhenzhen Zhao
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Chao Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Qianqian Xu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Shahbaz Ahmad
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Haiyang Zhang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yu Pang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Abudumukeyiti Aikemu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hai Yan
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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