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Fang S, Cao W, Wu Q, Cheng S, Jin H, Pang H, Zhou A, Feng L, Cao J, Luo J. Dynamic microbiome disassembly and evolution induced by antimicrobial methylisothiazolinone in sludge anaerobic fermentation for volatile fatty acids generation. WATER RESEARCH 2024; 251:121139. [PMID: 38237458 DOI: 10.1016/j.watres.2024.121139] [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: 11/24/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 02/12/2024]
Abstract
In the post-COVID-19 pandemic era, various antimicrobials have emerged and concentrated in waste-activated sludge (WAS), affecting the biological treatment of WAS. However, there is still a knowledge gap in the dynamic response and adaptive mechanism of anaerobic microbiome under exogenous antimicrobial stress. This study found that methylisothiazolinone (MIT, as a typic antimicrobial) caused an interesting lag effect on the volatile fatty acids (VFAs) promotion in the WAS anaerobic fermentation process. MIT was effective to disintegrate the extracellular polymeric substances (EPS), and those functional anaerobic microorganisms were easily exposed and negatively impacted by the MIT interference after the loss of protective barriers. Correspondingly, the ecological interactions and microbial metabolic functions related to VFA biosynthesis (e.g., pyruvate metabolism) were downregulated at the initial stage. The syntrophic consortia gradually adapted to the interference and attenuated the MIT stress by activating chemotaxis and resistance genes (e.g., excreting, binding, and inactivating). Due to the increased bioavailable substrates in the fermentation systems, the dominant microorganisms (i.e., Clostridium and Caloramator) with both VFAs production and MIT-tolerance functions have been domesticated. Moreover, MIT disrupted the syntrophic interaction between acetogens and methanogens and totally suppressed methanogens' metabolic activities. The VFA production derived from WAS anaerobic fermentation was therefore enhanced due to the interference of antimicrobial MIT stress. This work deciphered dynamic changes and adaptive evolution of anaerobic syntrophic consortia in response to antimicrobial stress and provided guidance on the evaluation and control of the ecological risks of exogenous pollutants in WAS treatment.
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Affiliation(s)
- Shiyu Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Wangbei Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Qian Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Song Cheng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Hongqi Jin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Heliang Pang
- School of Environmental and Municipal Engineering, Xi 'an University of Architecture and Technology, Xi 'an 710055, China
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Leiyu Feng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
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Bhattacharya S, Junghare V, Hazra M, Pandey NK, Mukherjee A, Dhankhar K, Das N, Roy P, Dubey RC, Hazra S. Characterization of a Class A β-Lactamase from Francisella tularensis (Ftu-1) Belonging to a Unique Subclass toward Understanding AMR. ACS BIO & MED CHEM AU 2023; 3:174-188. [PMID: 37101813 PMCID: PMC10125328 DOI: 10.1021/acsbiomedchemau.2c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 04/28/2023]
Abstract
β-lactamase production with vast catalytic divergence in the pathogenic strain limits the antibiotic spectrum in the clinical environment. Class A carbapenemase shares significant sequence similarities, structural features, and common catalytic mechanisms although their resistance spectrum differs from class A β-lactamase in carbapenem and monobactam hydrolysis. In other words, it limited the antibiotic treatment option against infection, causing carbapenemase-producing superbugs. Ftu-1 is a class A β-lactamase expressed by the Francisella tularensis strain, a potent causative organism of tularemia. The chromosomally encoded class A β-lactamase shares two conserved cysteine residues, a common characteristic of a carbapenemase, and a distinctive class in the phylogenetic tree. Complete biochemical and biophysical characterization of the enzyme was performed to understand the overall stability and environmental requirements to perform optimally. To comprehend the enzyme-drug interaction and its profile toward various chemistries of β-lactam and β-lactamase inhibitors, comprehensive kinetic and thermodynamic analyses were conducted using various β-lactam drugs. The dynamic property of Ftu-1 β-lactamase was also predicted using molecular dynamics (MD) simulation to compare its loop flexibility and ligand binding with other related class A β-lactamases. Overall, this study fosters a comprehensive understanding of Ftu-1, proposed to be an intermediate class by characterizing its kinetic profiling, stability by biochemical and biophysical methodologies, and susceptibility profiling. This understanding would be beneficial for the design of new-generation therapeutics.
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Affiliation(s)
- Sourya Bhattacharya
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Vivek Junghare
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Mousumi Hazra
- Department
of Botany and Microbiology, Gurukula Kangri
(Deemed to be University), Haridwar 249404, Uttarakhand, India
| | - Niteesh Kumar Pandey
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Abirlal Mukherjee
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Kunal Dhankhar
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Neeladrisingha Das
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Partha Roy
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Ramesh Chandra Dubey
- Department
of Botany and Microbiology, Gurukula Kangri
(Deemed to be University), Haridwar 249404, Uttarakhand, India
| | - Saugata Hazra
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
- Centre
of Nanotechnology, Indian Institute of Technology
Roorkee, Roorkee 247667, India
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Monitoring protein conformational changes using fluorescent nanoantennas. Nat Methods 2022; 19:71-80. [PMID: 34969985 DOI: 10.1038/s41592-021-01355-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 11/10/2021] [Indexed: 01/03/2023]
Abstract
Understanding the relationship between protein structural dynamics and function is crucial for both basic research and biotechnology. However, methods for studying the fast dynamics of structural changes are limited. Here, we introduce fluorescent nanoantennas as a spectroscopic technique to sense and report protein conformational changes through noncovalent dye-protein interactions. Using experiments and molecular simulations, we detect and characterize five distinct conformational states of intestinal alkaline phosphatase, including the transient enzyme-substrate complex. We also explored the universality of the nanoantenna strategy with another model protein, Protein G and its interaction with antibodies, and demonstrated a rapid screening strategy to identify efficient nanoantennas. These versatile nanoantennas can be used with diverse dyes to monitor small and large conformational changes, suggesting that they could be used to characterize diverse protein movements or in high-throughput screening applications.
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Bi X, Li L, Liu X, Luo L, Cheng Z, Sun J, Cai Z, Liu J, You T. Inner filter effect-modulated ratiometric fluorescence aptasensor based on competition strategy for zearalenone detection in cereal crops: Using mitoxantrone as quencher of CdTe QDs@SiO 2. Food Chem 2021; 349:129171. [PMID: 33582542 DOI: 10.1016/j.foodchem.2021.129171] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 12/16/2022]
Abstract
Herein, an innovative ratiometric fluorescence (FL) aptasensor was successfully fabricated for the accurate analysis of zearalenone (ZEN) in corn and barley flour. The ZEN aptamer-modified nitrogen doped graphene quantum dots (NGQDs-apt) and silica sphere-encapsulated cadmium telluride quantum dots (CdTe QDs@SiO2) were directly mixed and applied as ratiometric probes. In the absence of ZEN, mitoxantrone (MTX), which was innovatively introduced as quencher, was captured by NGQDs-apt and its inner filter effect (IFE) on CdTe QDs@SiO2 was inhibited. When ZEN existed, MTX separated from NGQDs-apt and re-dispersed around CdTe QDs@SiO2 owing to the competitive binding of ZEN with its aptamer. As the IFE of free MTX on CdTe QDs@SiO2 recovering, the FL intensity of CdTe QDs@SiO2 was quenched, while the FL intensity of NGQDs-apt was nearly invariant. On this basis, a ratiometric FL aptasensor for ZEN was fabricated, which exhibited outstanding detection performances with a desirable detection limit of 0.32 pg mL-1.
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Affiliation(s)
- Xiaoya Bi
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Libo Li
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Xiaohong Liu
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lijun Luo
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China; Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zhiliang Cheng
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jinying Sun
- Longgang District Center for Disease Control and Prevention, Shenzhen 518172, China
| | - Zhibin Cai
- Longgang District Center for Disease Control and Prevention, Shenzhen 518172, China
| | - Jinming Liu
- Longgang District Center for Disease Control and Prevention, Shenzhen 518172, China
| | - Tianyan You
- Key Laboratory of Modern Agricultural Equipment and Technology, Ministry of Education, School of Agricultural Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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Au HW, Tsang MW, Chen YW, So PK, Wong KY, Leung YC. BADAN-conjugated β-lactamases as biosensors for β-lactam antibiotic detection. PLoS One 2020; 15:e0241594. [PMID: 33125437 PMCID: PMC7598492 DOI: 10.1371/journal.pone.0241594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/16/2020] [Indexed: 11/19/2022] Open
Abstract
β-Lactam antibiotic detection has significant implications in food safety control, environmental monitoring and pharmacokinetics study. Here, we report the development of two BADAN-conjugated β-lactamases, E166Cb and E166Cb/N170Q, as sensitive biosensors for β-lactam antibiotic detection. These biosensors were constructed by coupling an environment-sensitive BADAN probe onto location 166 at the active site of the PenP β-lactamase E166C and E166C/N170Q mutants. They gave fluorescence turn-on signals in response to β-lactam antibiotics. Molecular dynamics simulation of E166Cb suggested that the turn-on signal might be attributed to a polarity change of the microenvironment of BADAN and the removal of the fluorescence quenching effect on BADAN exerted by a nearby Tyr-105 upon the antibiotic binding. In the detection of four β-lactams (penicillin G, penicillin V, cefotaxime and moxalactam), both E166Cb and E166Cb/N170Q delivered signal outputs in an antibiotic-concentration dependent manner with a dynamic range spanning from 10 nM to 1 μM. Compared to E166Cb, E166Cb/N170Q generally exhibited more stable signals owing to its higher deficiency in hydrolyzing the antibiotic analyte. The overall biosensor performance of E166Cb and E166Cb/N170Q was comparable to that of their respective fluorescein-modified counterparts, E166Cf and E166Cf/N170Q. But comparatively, the BADAN-conjugated enzymes showed a higher sensitivity, displayed a faster response in detecting moxalactam and a more stable fluorescence signals towards penicillin G. This study illustrates the potential of BADAN-conjugated β-lactamases as biosensing devices for β-lactam antibiotics.
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Affiliation(s)
- Ho-Wah Au
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Man-Wah Tsang
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Yu Wai Chen
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Pui-Kin So
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- * E-mail: (KYW); (YCL)
| | - Yun-Chung Leung
- Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Lo Ka Chung Research Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- * E-mail: (KYW); (YCL)
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