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Zhang Y, Geng Y, Li S, Shi T, Ma X, Hua R, Fang L. Efficient Knocking Out of the Organophosphorus Insecticides Degradation Gene opdB in Cupriavidus nantongensis X1 T via CRISPR/ Cas9 with Red System. Int J Mol Sci 2023; 24:ijms24066003. [PMID: 36983076 PMCID: PMC10056268 DOI: 10.3390/ijms24066003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Cupriavidus nantongensis X1T is a type strain of the genus Cupriavidus, that can degrade eight kinds of organophosphorus insecticides (OPs). Conventional genetic manipulations in Cupriavidus species are time-consuming, difficult, and hard to control. The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) system has emerged as a powerful tool for genome editing applied in prokaryotes and eukaryotes due to its simplicity, efficiency, and accuracy. Here, we combined CRISPR/Cas9 with the Red system to perform seamless genetic manipulation in the X1T strain. Two plasmids, pACasN and pDCRH were constructed. The pACasN plasmid contained Cas9 nuclease and Red recombinase, and the pDCRH plasmid contained the dual single-guide RNA (sgRNA) of organophosphorus hydrolase (OpdB) in the X1T strain. For gene editing, two plasmids were transferred to the X1T strain and a mutant strain in which genetic recombination had taken place, resulting in the targeted deletion of opdB. The incidence of homologous recombination was over 30%. Biodegradation experiments suggested that the opdB gene was responsible for the catabolism of organophosphorus insecticides. This study was the first to use the CRISPR/Cas9 system for gene targeting in the genus Cupriavidus, and it furthered our understanding of the process of degradation of organophosphorus insecticides in the X1T strain.
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Affiliation(s)
- Yufei Zhang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Yuehan Geng
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Shengyang Li
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Taozhong Shi
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Xin Ma
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
| | - Rimao Hua
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
- Institute for Green Development, Anhui Agricultural University, Hefei 230036, China
| | - Liancheng Fang
- Anhui Provincial Key Laboratory for Quality and Safety of Agri-Products, School of Resource & Environment, Anhui Agricultural University, Hefei 230036, China
- Institute for Green Development, Anhui Agricultural University, Hefei 230036, China
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2
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Zhang J, Li X, Klümper U, Lei H, Berendonk TU, Guo F, Yu K, Yang C, Li B. Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches. MICROBIOME 2022; 10:180. [PMID: 36280854 PMCID: PMC9590159 DOI: 10.1186/s40168-022-01361-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
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. Video Abstract.
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Affiliation(s)
- Jiayu Zhang
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- School of Environment, Tsinghua University, Beijing, China
| | - Xiaoyan Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Huaxin Lei
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- School of Environment, Tsinghua University, Beijing, China
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Dresden, Germany
| | - Fangliang Guo
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- School of Environment, Tsinghua University, Beijing, China
| | - Ke Yu
- School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, China
| | - Chao Yang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Bing Li
- State Environmental Protection Key Laboratory of Microorganism Application and Risk Control, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
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Zhu C, Huang H, Chen Y. Recent advances in biological removal of nitroaromatics from wastewater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 307:119570. [PMID: 35667518 DOI: 10.1016/j.envpol.2022.119570] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/16/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Various nitroaromatic compounds (NACs) released into the environment cause potential threats to humans and animals. Biological treatment is valued for cost-effectiveness, environmental friendliness, and availability when treating wastewater containing NACs. Considering the significance and wide use of NACs, this review focuses on recent advances in biological treatment systems for NACs removal from wastewater. Meanwhile, factors affecting biodegradation and methods to enhance removal efficiency of NACs are discussed. The selection of biological treatment system needs to consider NACs loading and cost, and its performance is affected by configuration and operation strategy. Generally, sequential anaerobic-aerobic biological treatment systems perform better in mineralizing NACs and removing co-pollutants. Future research on mechanism exploration of NACs biotransformation and performance optimization will facilitate the large-scale application of biological treatment systems.
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Affiliation(s)
- Cuicui Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Haining Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yinguang Chen
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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Cheng M, Qian Y, Xing Z, Zylstra GJ, Huang X. The low-nanomolar 4-nitrobenzoate-responsive repressor PnbX negatively regulates the actinomycete-derived 4-nitrobenzoate-degrading pnb locus. Environ Microbiol 2021; 23:7028-7041. [PMID: 34554625 DOI: 10.1111/1462-2920.15787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
Abstract
Nitroaromatic compounds pose severe threats to public health and environmental safety. Nitro group removal via ammonia release is an important strategy for bacterial detoxification of nitroaromatic compounds, such as the conversion of 4-nitrobenzoate (4-NBA) to protocatechuate by the bacterial pnb operon. In contrast to the LysR-family transcriptional regulator PnbR in proteobacteria, the actinomycete-derived pnb locus (4-NBA degradation structural genes) formed an operon with the TetR-family transcriptional regulator gene pnbX, implying that it has a distinct regulatory mechanism. Here, pnbBA from the actinomycete Nocardioides sp. strain LMS-CY was biochemically confirmed to express 4-NBA degradation enzymes, and pnbX was essential for inducible degradation of 4-NBA. Purified PnbX-6His could bind the promoter probe of the pnb locus in vitro, and 4-NBA prevented this binding. 4-NBA could bind PnbX at a 1:1 molar ratio with KD = 26.7 ± 4.2 nM. Low-nanomolar levels of 4-NBA induced the transcription of the pnb operon in strain LMS-CY. PnbX bound a palindromic sequence motif (5'-TTACGTTACA-N8 -TGTAACGTAA-3') that encompasses the pnb promoter. This study identified a TetR-family repressor for the actinomycete-derived pnb operon that recognizes 10-8 M 4-NBA as its ligand, implying that nitro group removal of nitroaromatic compounds may be especially important for actinomycetes.
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Affiliation(s)
- Minggen Cheng
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yingying Qian
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ziyu Xing
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Gerben J Zylstra
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Xing Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Tomita H, Katsuyama Y, Ohnishi Y. Rapid evaluation of the substrate specificity of 3-nitrobenzoic acid dioxygenase MnbAB via colorimetric detection using Saltzman reagent. J Ind Microbiol Biotechnol 2021; 48:6359141. [PMID: 34453549 PMCID: PMC8788832 DOI: 10.1093/jimb/kuab064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 08/22/2021] [Indexed: 11/26/2022]
Abstract
Nitroaromatic compounds are essential materials for chemical industry, but they are also potentially toxic environmental pollutants. Therefore, their sensitive detection and degradation are important concerns. The microbial degradation pathways of nitroaromatic compounds have been studied in detail, but their usefulness needs to be evaluated to understand their potential applications in bioremediation. Here, we developed a rapid and relatively sensitive assay system to evaluate the activities and substrate specificities of nitroaromatic dioxygenases involved in the oxidative biodegradation of nitroaromatic compounds. In this system, nitrous acid, which was released from the nitroaromatic compounds by the dioxygenases, was detected and quantified using the Saltzman reagent. Escherichia coli producing the 3-nitrobenzoic acid dioxygenase complex MnbAB from Comamonas sp. JS46 clearly showed the apparent substrate specificity of MnbAB as follows. MnbAB accepted not only 3-nitrobenzoic acid but also several other p- and m-nitrobenzoic acid derivatives as substrates, although it much preferred 3-nitrobenzoic acid to others. Furthermore, the presence of a hydroxy or an amino group at the ortho position of the nitro group decreased the activity of MnbAB. In addition, MnbAB accepted 2-(4-nitrophenyl)acetic acid as a substrate, which has one additional methylene group between the aromatic ring and the carboxy group of 3-nitrobenzoic acid. This is the first report about the detailed substrate specificity of MnbAB. Our system can be used for other nitroaromatic dioxygenases and contribute to their characterization.
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Affiliation(s)
- Hiroya Tomita
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences
| | - Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Tiwari J, Gandhi D, Sivanesan S, Naoghare P, Bafana A. Remediation of different nitroaromatic pollutants by a promising agent of Cupriavidus sp. strain a3. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 205:111138. [PMID: 32836156 DOI: 10.1016/j.ecoenv.2020.111138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 08/01/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Nitrobenzene, nitrotoluenes and nitrobenzoic acid are toxic and mutagenic. Their removal from the environment is necessary to avoid health and environmental damage. In this study, Cupriavidus strain a3 was found to utilize 2-nitrotoluene (2NT), 3-nitrotoluene (3NT), 4-nitrotoluene (4NT), nitrobenzene (NB) and 2-nitrobenzoic acid (2NBA) as carbon and nitrogen source, resulting in their detoxification. The metabolism involved reductive transformation of nitroaromatics to the corresponding amines followed by cleavage of amino group to release ammonia. Cell free extract showed nitroreductase activity in the range of 310-389 units/mg. NB was reduced to form benzamine and 4-aminophenol, 2NT was reduced to 2-aminotoluene, whereas 2NBA was reduced to form 2-aminobenzoic acid. Similarly, 3NT was metabolized to 3-aminotoluene and 2-amino-4-methylphenol, while 4NT was reduced to 4-nitrosotoluene and 4-aminotoluene. Cytotoxicity and apoptosis assays using Jurkat cell line, and Ames test were used to evaluate the detoxification of nitroaromatics during biodegradation. Biodegradation with Cupriavidus resulted in 2.6-11 fold increase in cell viability, 1.3-2.3 fold reduction in apoptosis, 1.6-55 fold reduction in caspase-3 activation, and complete disappearance of mutagenic activity. In soil microcosm, bioaugmentation with Cupriavidus resulted in 16-59% degradation of various nitroaromatics, as against <14% degradation without bioaugmentation. Thus, the present study reflects promising capability of Cupriavidus strain a3 in degradation and detoxification of multiple nitroaromatics.
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Affiliation(s)
- Jyoti Tiwari
- AcSIR (Academy of Scientific and Innovative Research), Ghaziabad, 201002, India; Director's Research Cell, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, India
| | - Deepa Gandhi
- Biochemistry Division, CSIR-CDRI (Central Drug Research Institute), Lucknow, 226031, India
| | - Saravanadevi Sivanesan
- Health and Toxicity Cell, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, India
| | - Pravin Naoghare
- Environmental Impact and Sustainability Division, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, India
| | - Amit Bafana
- Director's Research Cell, CSIR-NEERI (National Environmental Engineering Research Institute), Nagpur, 440020, India.
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Xia J, Sun H, Ma X, Huang K, Ye L. Ozone pretreatment of wastewater containing aromatics reduces antibiotic resistance genes in bioreactors: The example of p-aminophenol. ENVIRONMENT INTERNATIONAL 2020; 142:105864. [PMID: 32563772 DOI: 10.1016/j.envint.2020.105864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/30/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
Aromatic matters are widely present in wastewater, especially industrial wastewater, and may lead to a high abundance of antibiotic resistance genes (ARGs) in wastewater treatment bioreactors and stimulate horizontal transfers of ARGs. Here, we investigated a practical approach that applying ozone pretreatment to mitigate ARGs in bioreactors treating wastewater containing a typical aromatic pollutant, p-aminophenol (PAP). The results showed that ozone pretreatment could effectively reduce the aromaticity of wastewater, and the relative abundance of ARGs in the bioreactor fed with ozone treated wastewater decreased by over 70% compared to the control reactor. Multidrug, quinolone, mupirocin, polymyxin, aminoglycoside, glycopeptide, beta-lactam, and trimethoprim resistance genes were all reduced in the bioreactors receiving wastewater pretreated by ozone. Metagenomic analysis suggested that the reduction of ARGs could be attributed to the co-occurrence of ARGs and aromatic degradation genes in bacteria. Furthermore, we expanded our analysis to investigate 71 metagenomes from different environments, and the results indicated that the impact of aromatics on ARG abundance widely occurs in various ecosystems and confirmed that high levels of aromatics could lead to high abundance of ARGs. Taken together, our work confirmed that the aromatics played critical roles in selecting ARGs and proposed a feasible approach to reduce ARGs in wastewater treatment bioreactors.
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Affiliation(s)
- Juntao Xia
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Haohao Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Xueyan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China; Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), School of Environmental Science and Engineering, Nanjing University of Information Science & Technology, Nanjing 210044, China
| | - Lin Ye
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, 163 Xianlin Avenue, Nanjing 210023, China.
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Ma X, Liang B, Qi M, Yun H, Shi K, Li Z, Guo Y, Yan P, Liu SJ, Wang A. Novel Pathway for Chloramphenicol Catabolism in the Activated Sludge Bacterial Isolate Sphingobium sp. CAP-1. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:7591-7600. [PMID: 32412239 DOI: 10.1021/acs.est.9b07324] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The chlorinated nitroaromatic antibiotic chloramphenicol (CAP) is a refractory contaminant that is widely present in various environments. However, few CAP-mineralizing bacteria have been documented, and a complete CAP catabolism pathway has yet to be identified. In this study, the bacterial strain Sphingobium sp. CAP-1 was isolated from an activated sludge sample and was shown to be capable of aerobically subsisting on CAP as the sole carbon, nitrogen, and energy source while simultaneously and efficiently degrading CAP. p-Nitrobenzoic acid (PNBA), p-nitrobenzaldehyde (PNBD), protocatechuate (PCA), and the novel side chain C3-hydroxy-oxygenated product of CAP (O-CAP) were identified during CAP degradation. Strain CAP-1 was able to convert O-CAP to intermediate product PNBA. The putative functional genes associated with PNBA catabolism into the tricarboxylic acid cycle via PCA and floc formation were also identified by genome sequencing and comparative proteome analysis. A complete pathway for CAP catabolism was proposed. The discovery of a novel CAP oxidation/detoxification process and a complete pathway for CAP catabolism enriches the fundamental understanding of the bacterial catabolism of antibiotics, providing new insights into the microbial-mediated fate, transformation, and resistance risk of CAP in the environment. The molecular basis of CAP catabolism and floc formation in strain CAP-1 also offers theoretical guidance for the enhanced bioremediation of CAP-containing environments.
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Affiliation(s)
- Xiaodan Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bin Liang
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Mengyuan Qi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Hui Yun
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Ke Shi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Zhiling Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Yuanqiang Guo
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300350, China
| | - Peisheng Yan
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Aijie Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
- School of Civil & Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Interactions between Biotite and the Mineral-Weathering Bacterium Pseudomonas azotoformans F77. Appl Environ Microbiol 2020; 86:AEM.02568-19. [PMID: 31953343 DOI: 10.1128/aem.02568-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/12/2020] [Indexed: 12/22/2022] Open
Abstract
In this study, the mineral-weathering bacterium Pseudomonas azotoformans F77, which was isolated from the soil of a debris flow area, was evaluated for its weathering activity under direct contact with biotite or without contact. Then, biotite-weathering behaviors of strain F77, mutants that had been created by deleting the gcd and adh genes (which are involved in gluconic acid metabolism and pilus formation, respectively), and the double mutant F77ΔgcdΔadh were compared. The relative gene expression levels of F77 and its mutants F77Δgcd and F77Δadh were also analyzed in the presence of biotite. Direct contact with biotite increased Fe and Al release from the mineral in the presence of F77. All strains had similar abilities to release Fe and Al from the mineral except for F77Δgcd and F77Δadh Mobilized Fe and Al concentrations were decreased by up to 72, 26, and 87% in the presence of F77Δgcd, F77Δadh, and F77ΔgcdΔadh, respectively, compared to levels observed in the presence of F77 during the mineral-weathering process. Gluconic acid production was decreased for F77Δgcd and F77ΔgcdΔadh, while decreased cell attachment on the mineral surface was observed for F77Δadh, compared to findings for F77. The F77 genes involved in pilus formation and gluconic acid metabolism showed increased expression levels in the presence of biotite. The results of this study showed important roles for the genes involved in gluconic acid metabolism and pilus formation in mineral weathering by F77 and demonstrated the distinctive effect of these genes on mineral weathering by F77.IMPORTANCE Bacteria play important roles in mineral weathering and soil formation, although the molecular mechanisms underlying the interactions between bacteria and silicate minerals are poorly understood. In this study, the interactions between biotite and the highly effective mineral-weathering bacterium P. azotoformans F77 were characterized. Our results showed that the genes involved in gluconic acid metabolism and pilus formation play important roles in mineral weathering by F77. The presence of biotite could promote the expression of these genes in F77, and a distinctive effect of these genes on mineral weathering by F77 was observed in this study. Our results provide new knowledge and promote better understanding regarding the interaction between silicate minerals and mineral-weathering bacteria, as well as the molecular mechanisms involved in these processes.
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Yang Y, Davis I, Matsui T, Rubalcava I, Liu A. Quaternary structure of α-amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) controls its activity. J Biol Chem 2019; 294:11609-11621. [PMID: 31189654 PMCID: PMC6663868 DOI: 10.1074/jbc.ra119.009035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
α-Amino-β-carboxymuconate-ϵ-semialdehyde decarboxylase (ACMSD) plays an important role in l-tryptophan degradation via the kynurenine pathway. ACMSD forms a homodimer and is functionally inactive as a monomer because its catalytic assembly requires an arginine residue from a neighboring subunit. However, how the oligomeric state and self-association of ACMSD are controlled in solution remains unexplored. Here, we demonstrate that ACMSD from Pseudomonas fluorescens can self-assemble into homodimer, tetramer, and higher-order structures. Using size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS) analysis, we investigated the ACMSD tetramer structure, and fitting the SAXS data with X-ray crystal structures of the monomeric component, we could generate a pseudo-atomic structure of the tetramer. This analysis revealed a tetramer model of ACMSD as a head-on dimer of dimers. We observed that the tetramer is catalytically more active than the dimer and is in equilibrium with the monomer and dimer. Substituting a critical residue of the dimer-dimer interface, His-110, altered the tetramer dissociation profile by increasing the higher-order oligomer portion in solution without changing the X-ray crystal structure. ACMSD self-association was affected by pH, ionic strength, and other electrostatic interactions. Alignment of ACMSD sequences revealed that His-110 is highly conserved in a few bacteria that utilize nitrobenzoic acid as a sole source of carbon and energy, suggesting a dedicated functional role of ACMSD's self-assembly into the tetrameric and higher-order structures. These results indicate that the dynamic oligomerization status potentially regulates ACMSD activity and that SEC-SAXS coupled with X-ray crystallography is a powerful tool for studying protein self-association.
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Affiliation(s)
- Yu Yang
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025
| | - Ivan Rubalcava
- Department of Chemistry, University of Texas, San Antonio, Texas 78249
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, To whom correspondence should be addressed. Tel.:
210-458-7062; E-mail:
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Diverse metabolic pathways in the degradation of phenylalkanoic acids and their monohydroxylated derivatives in Cupriavidus sp. strain ST-14. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.08.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Jiang L, Luo C, Zhang D, Song M, Sun Y, Zhang G. Biphenyl-Metabolizing Microbial Community and a Functional Operon Revealed in E-Waste-Contaminated Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8558-8567. [PMID: 29733586 DOI: 10.1021/acs.est.7b06647] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Primitive electronic waste (e-waste) recycling activities release massive amounts of persistent organic pollutants (POPs) and heavy metals into surrounding soils, posing a major threat to the ecosystem and human health. Microbes capable of metabolizing POPs play important roles in POPs remediation in soils, but their phylotypes and functions remain unclear. Polychlorinated biphenyls (PCBs), one of the main pollutants in e-waste contaminated soils, have drawn increasing attention due to their high persistence, toxicity, and bioaccumulation. In the present study, we employed the culture-independent method of DNA stable-isotope probing to identify active biphenyl and PCB degraders in e-waste-contaminated soil. A total of 19 rare operational taxonomic units and three dominant bacterial genera ( Ralstonia, Cupriavidus, and uncultured bacterium DA101) were enriched in the 13C heavy DNA fraction, confirming their functions in PCBs metabolism. Additionally, a 13.8 kb bph operon was amplified, containing a bphA gene labeled by 13C that was concentrated in the heavy DNA fraction. The tetranucleotide signature characteristics of the bph operon suggest that it originated from Ralstonia. The bph operon may be shared by horizontal gene transfer because it contains a transposon gene and is found in various bacterial species. This study gives us a deeper understanding of PCB-degrading mechanisms and provides a potential resource for the bioremediation of PCBs-contaminated soils.
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Affiliation(s)
- Longfei Jiang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640 , China
| | - Chunling Luo
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640 , China
- College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Dayi Zhang
- School of Environment , Tsinghua University , Beijing 100084 , China
| | - Mengke Song
- College of Natural Resources and Environment , South China Agricultural University , Guangzhou 510642 , China
| | - Yingtao Sun
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640 , China
| | - Gan Zhang
- Guangzhou Institute of Geochemistry, Chinese Academy of Sciences , Guangzhou 510640 , China
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Deb S, Basu S, Singha A, Dutta TK. Development of a 2-Nitrobenzoate-Sensing Bioreporter Based on an Inducible Gene Cluster. Front Microbiol 2018; 9:254. [PMID: 29491862 PMCID: PMC5817917 DOI: 10.3389/fmicb.2018.00254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/31/2018] [Indexed: 11/13/2022] Open
Abstract
Based on the sole information of structural genes of the 2-nitrobenzoate (2NBA) utilizing catabolic gene cluster (onbX1X2FCAR1EHJIGDBX3), 2NBA-sensing bioreporters were constructed by incorporating egfp into the onb gene cluster of Cupriavidus sp. strain ST-14. Incorporation of reporter gene in proximal to the hypothesized promoter region in conjunction with the disruption of the gene encoding inducer-metabolizing enzyme was turned out to be advantageous in reporter gene expression at low inducer concentration. The bioreporter strain was capable of expressing EGFP from the very 1st hour of induction and could detect 2NBA at (sub) nanomolar level exhibiting a strict specificity toward 2NBA, displaying no response to EGFP expression from its meta- and para-isomers as well as from a number of structurally related compounds. The present study is a successful demonstration of the development of a 2NBA-sensing bioreporter with respect to ease of construction, inducer specificity, and sensitivity, without prior knowledge of the associated inducer-responsive promoter-regulator elements. The present approach can be used as a model for the development of bioreporters for other environmental pollutants.
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Affiliation(s)
- Satamita Deb
- Department of Microbiology, Bose Institute, Kolkata, India
| | - Soumik Basu
- Department of Microbiology, Bose Institute, Kolkata, India
| | | | - Tapan K Dutta
- Department of Microbiology, Bose Institute, Kolkata, India
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