1
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Huang Y, Zhang J, Sui B, Chai G, Yu A, Chen S, Zhang M, Zhang S, Zhang Y, Zhao W. Development of an angle-adjustable photonic crystal fluorescence platform for sensitive detection of oxytetracycline. Chem Commun (Camb) 2024; 60:8115-8118. [PMID: 38994726 DOI: 10.1039/d4cc02363c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
We pioneered an angle-adjustable photonic crystal fluorescence platform (APC-Fluor) that integrates PCs, an angular resolution spectrometer and a strategically aligned laser source. This configuration, featuring a coaxial rotating swing arm, allows for precise control over the angles of incidence and emission. The presence of photonic crystal microcavities facilitates the dispersion of fluorescent materials and promotes the transition of electrons from the excited state to the lowest vibrational energy level. The optical resonance effect triggered by modulating the alignment of the reflection peaks of the photonic crystals with the emission peaks of the fluorescent materials can significantly enhance the fluorescence intensity. Compared with the single BSA-AuNCs, the optimized fluorescence intensity can be significantly increased by 11.9-fold. The APC-Fluor system showcases rapid and highly sensitive detection capabilities for oxytetracycline (OTC), exhibiting a response across a concentration range from 2 to 1 × 104 nM and achieving a notably low detection limit of 1.03 nM.
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Affiliation(s)
- Yunhuan Huang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jiaheng Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
- Food Laboratory of Zhongyuan - Zhengzhou University, Luohe 462300, P. R. China
| | - Bo Sui
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Guobi Chai
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Ajuan Yu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Sheng Chen
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Miaomiao Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Shusheng Zhang
- Food Laboratory of Zhongyuan - Zhengzhou University, Luohe 462300, P. R. China
| | - Yanhao Zhang
- College of Ecology and Environment, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Wuduo Zhao
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
- College of Ecology and Environment, Zhengzhou University, Zhengzhou 450001, P. R. China.
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2
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Li S, Li Z, Tan GY, Xin Z, Wang W. In vitro allosteric transcription factor-based biosensing. Trends Biotechnol 2023; 41:1080-1095. [PMID: 36967257 DOI: 10.1016/j.tibtech.2023.03.001] [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: 01/03/2023] [Revised: 02/15/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
A biosensor is an analytical device that converts a biological response into a measurable output signal. Bacterial allosteric transcription factors (aTFs) have been utilized as a novel class of recognition elements for in vitro biosensing, which circumvents the limitations of aTF-based whole-cell biosensors (WCBs) and helps to meet the increasing requirement of small-molecule biosensors for diverse applications. In this review, we summarize the recent advances related to the configuration of aTF-based biosensors in vitro. Particularly, we evaluate the advantages of aTFs for in vitro biosensing and highlight their great potential for the establishment of robust and easy-to-implement biosensing strategies. We argue that key technical innovations and generalizable workflows will enhance the pipeline for facile construction of diverse aTF-based small-molecule biosensors.
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Affiliation(s)
- Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, CAS, Beijing 100101, PR China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai 200237, PR China
| | - Zhenguo Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, CAS, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, CAS, Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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3
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Bi H, Zhao C, Zhang Y, Zhang X, Xue B, Li C, Wang S, Yang X, Li C, Qiu Z, Wang J, Shen Z. IVT cell-free biosensors for tetracycline and macrolide detection based on allosteric transcription factors (aTFs). ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4545-4554. [PMID: 36314439 DOI: 10.1039/d2ay01316a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In recent years, the issue of food safety has received a lot of attention. The Food and Drug Administration (FDA) prescribes the antibiotic's maximum residue limit (MRL) in food production. The standard detection methods of antibiotics are liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) and high-performance liquid chromatography (HPLC), with complex operations and precision instruments. In this study, allosteric transcription factor (aTF)-based in vitro transcription (IVT) cell-free biosensors were developed for tetracyclines and macrolides with nucleic acid sequence-based amplification (NASBA). Characterization of binding and dissociation processes between aTF and DNA was carried out by BIAcore assay and electrophoretic mobility shift assay (EMSA). BIAcore was innovatively used to directly observe the real-time process of binding and dissociation of aTF with DNA. The biosensors produce more fluorescence RNA when target antibiotics are added to the three-way junction dimeric Broccoli (3WJdB). Four tetracyclines and two macrolides were quantified in the 0.5-15 μM range, while erythromycin and clarithromycin were detected over a range of 0.1-15 μM. NASBA, commonly used for viral detection, was used to amplify 3WJdB RNA generated by IVT, which greatly increased the LOD for tetracyclines and macrolides to 0.01 μM. The use of biosensors in milk samples demonstrated their on-site detection performance. Overall, our proposed biosensors are simple, rapid, selective, and sensitive, with the potential for field application.
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Affiliation(s)
- Huaixiu Bi
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Yongkang Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Xiaobo Yang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Chao Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Zhigang Qiu
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Zhiqiang Shen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
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4
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A cell-free biosensor based on strand displacement amplification and hybridization chain reaction for fluorescence detection of tetracycline. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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5
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A novel biosensor based on antibody controlled isothermal strand displacement amplification (ACISDA) system. Biosens Bioelectron 2022; 209:114185. [DOI: 10.1016/j.bios.2022.114185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/25/2022] [Accepted: 03/10/2022] [Indexed: 11/24/2022]
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6
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Xiao D, Hu C, Xu X, Lü C, Wang Q, Zhang W, Gao C, Xu P, Wang X, Ma C. A d,l-lactate biosensor based on allosteric transcription factor LldR and amplified luminescent proximity homogeneous assay. Biosens Bioelectron 2022; 211:114378. [PMID: 35617798 DOI: 10.1016/j.bios.2022.114378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/02/2022]
Abstract
Lactate, a hydroxycarboxylic acid commercially produced by microbial fermentation, is widely applied in diverse industrial fields. Lactate exists in two stereoisomeric forms (d-lactate and l-lactate). d-Lactate and l-lactate are often simultaneously present in many biological samples. Therefore, a biosensor able to detect both d- and l-lactate is required but previously unavailable. Herein, an allosteric transcription factor LldR from Pseudomonas aeruginosa PAO1, which responds to both d-lactate and l-lactate, was combined with amplified luminescent proximity homogeneous assay technology to develop a d,l-lactate biosensor. The proposed biosensor was optimized by mutation of DNA sequence in binding site of LldR. The optimized biosensor BLac-6 can accurately detect the concentration of lactate independent on ratio of the two isomers in pending test samples. The biosensor was also tentatively used in quantitative analysis of d-lactate, l-lactate, or d,l-lactate in fermentation samples produced by three recombinant strains of Klebsiella oxytoca. With its desirable properties, the biosensor BLac-6 may be a potential choice for monitoring the concentration of lactate during industrial fermentation.
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Affiliation(s)
- Dan Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Chunxia Hu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Xianzhi Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Wen Zhang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, PR China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Xia Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
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7
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Mao Z, Chen R, Wang X, Zhou Z, Peng Y, Li S, Han D, Li S, Wang Y, Han T, Liang J, Ren S, Gao Z. CRISPR/Cas12a-based technology: A powerful tool for biosensing in food safety. Trends Food Sci Technol 2022; 122:211-222. [PMID: 35250172 PMCID: PMC8885088 DOI: 10.1016/j.tifs.2022.02.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND In the context of the current pandemic caused by the novel coronavirus, molecular detection is not limited to the clinical laboratory, but also faces the challenge of the complex and variable real-time detection fields. A series of novel coronavirus events were detected in the process of food cold chain packaging and transportation, making the application of molecular diagnosis in food processing, packaging, transportation, and other links urgent. There is an urgent need for a rapid detection technology that can adapt to the diversity and complexity of food safety. SCOPE AND APPROACH This review introduces a new molecular diagnostic technology-biosensor analysis technology based on CRISPR-Cas12a. Systematic clarification of its development process and detection principles. It summarizes and systematically organizes its applications in viruses, food-borne pathogenic bacteria, small molecule detection, etc. In the past four years, which provides a brand-new and comprehensive solution for food detection. Finally, this article puts forward the challenges and the prospects for food safety. KEY FINDINGS AND CONCLUSIONS The novel coronavirus hazards infiltrated every step of the food industry, from processing to packaging to transportation. The biosensor analytical technology based on CRISPR-Cas12a has great potential in the qualitative and quantitative analysis of infectious pathogens. CRISPR-Cas12a can effectively identify the presence of the specific nucleic acid targets and the small changes in sequences, which is particularly important for nucleic acid identification and pathogen detection. In addition, the CRISPR-Cas12a method can be adjusted and reconfigured within days to detect other viruses, providing equipment for nucleic acid diagnostics in the field of food safety. The future work will focus on the development of portable microfluidic devices for multiple detection. Shao et al. employed physical separation methods to separate Cas proteins in different microfluidic channels to achieve multiple detection, and each channel simultaneously detected different targets by adding crRNA with different spacer sequences. Although CRISPR-Cas12a technology has outstanding advantages in detection, there are several technical barriers in the transformation from emerging technologies to practical applications. The newly developed CRISPR-Cas12a-based applications and methods promote the development of numerous diagnostic and detection solutions, and have great potential in medical diagnosis, environmental monitoring, and especially food detection.
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Affiliation(s)
- Zefeng Mao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Ruipeng Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiaojuan Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Zixuan Zhou
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yuan Peng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Shuang Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Dianpeng Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Sen Li
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Tie Han
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China
| | - Jun Liang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, 300457, China,Corresponding author
| | - Shuyue Ren
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,Corresponding author
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, China,Corresponding author
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8
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Dong H, Huang F, Guo X, Xu X, Liu Q, Li X, Feng Y. Characterization of Argonaute nucleases from mesophilic bacteria Paenibacillus borealis and Brevibacillus laterosporus. BIORESOUR BIOPROCESS 2021; 8:133. [PMID: 38650276 PMCID: PMC10992608 DOI: 10.1186/s40643-021-00478-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
Thermophilic Argonaute proteins (Agos) have been shown to utilize small DNA guides for cleaving complementary DNA in vitro, which shows great potential for nucleic acid detection. In this study, we explored mesophilic Agos for the detection of small molecule by cooperating with allosteric transcription factors (aTFs). Two Agos from mesophilic bacteria, Paenibacillus borealis (PbAgo) and Brevibacillus laterosporus (BlAgo), showed nuclease activity for single-stranded DNA at moderate temperatures (37 °C) by using 5'-phosphorylated and 5'-hydroxylated DNA guides. Both Agos perform programmable cleavage of double-stranded DNA, especially in AT-rich regions of plasmid. Furthermore, we developed a simple and low-cost p-hydroxybenzoic acid detection method based on DNA-guided DNA cleavage of Agos and the allosteric effect of HosA, which expands the potential application of small molecule detection by Agos.
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Affiliation(s)
- Huarong Dong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Fei Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiang Guo
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiaoyi Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiao Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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9
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A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR. Nat Commun 2021; 12:7108. [PMID: 34876568 PMCID: PMC8651671 DOI: 10.1038/s41467-021-27357-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/16/2021] [Indexed: 12/02/2022] Open
Abstract
D-2-Hydroxyglutarate (D-2-HG) is a metabolite involved in many physiological metabolic processes. When D-2-HG is aberrantly accumulated due to mutations in isocitrate dehydrogenase or D-2-HG dehydrogenase, it functions in a pro-oncogenic manner and is thus considered a therapeutic target and biomarker in many cancers. In this study, DhdR from Achromobacter denitrificans NBRC 15125 is identified as an allosteric transcriptional factor that negatively regulates D-2-HG dehydrogenase expression and responds to the presence of D-2-HG. Based on the allosteric effect of DhdR, a D-2-HG biosensor is developed by combining DhdR with amplified luminescent proximity homogeneous assay (AlphaScreen) technology. The biosensor is able to detect D-2-HG in serum, urine, and cell culture medium with high specificity and sensitivity. Additionally, this biosensor is used to identify the role of D-2-HG metabolism in lipopolysaccharide biosynthesis of Pseudomonas aeruginosa, demonstrating its broad usages.
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10
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Chen M, Grazon C, Sensharma P, Nguyen TT, Feng Y, Chern M, Baer RC, Varongchayakul N, Cook K, Lecommandoux S, Klapperich CM, Galagan JE, Dennis AM, Grinstaff MW. Hydrogel-Embedded Quantum Dot-Transcription Factor Sensors for Quantitative Progesterone Detection. ACS APPLIED MATERIALS & INTERFACES 2020; 12:43513-43521. [PMID: 32893612 DOI: 10.1021/acsami.0c13489] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Immobilization of biosensors in or on a functional material is critical for subsequent device development and translation to wearable technology. Here, we present the development and assessment of an immobilized quantum dot-transcription factor-nucleic acid complex for progesterone detection as a first step toward such device integration. The sensor, composed of a polyhistidine-tagged transcription factor linked to a quantum dot and a fluorophore-modified cognate DNA, is embedded within a hydrogel as an immobilization matrix. The hydrogel is optically transparent, soft, and flexible as well as traps the quantum dot-transcription factor DNA assembly but allows free passage of the analyte, progesterone. Upon progesterone exposure, DNA dissociates from the quantum dot-transcription factor DNA assembly resulting in an attenuated ratiometric fluorescence output via Förster resonance energy transfer. The sensor performs in a dose-dependent manner with a limit of detection of 55 nM. Repeated analyte measurements are similarly successful. Our approach combines a systematically characterized hydrogel as an immobilization matrix and a transcription factor-DNA assembly as a recognition/transduction element, offering a promising framework for future biosensor devices.
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Affiliation(s)
- Mingfu Chen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Chloé Grazon
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- CNRS, Bordeaux INP, LCPO, UMR 5629, Univ. Bordeaux, F-33600 Pessac, France
| | - Prerana Sensharma
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Thuy T Nguyen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Yunpeng Feng
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Margaret Chern
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - R C Baer
- Department of Microbiology, Boston University, Boston, Massachusetts 02118, United States
| | - Nitinun Varongchayakul
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Katherine Cook
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | | | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Microbiology, Boston University, Boston, Massachusetts 02118, United States
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Mark W Grinstaff
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts 02215, United States
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11
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Chern M, Garden PM, Baer RC, Galagan JE, Dennis AM. Transcription Factor Based Small‐Molecule Sensing with a Rapid Cell Phone Enabled Fluorescent Bead Assay. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Margaret Chern
- Division of Materials Science and Engineering Boston University Boston MA USA
| | - Padric M. Garden
- Department of Biomedical Engineering Boston University Boston MA USA
| | - R C. Baer
- Department of Microbiology Boston University Boston MA USA
| | - James E. Galagan
- Department of Biomedical Engineering Boston University Boston MA USA
- Department of Microbiology Boston University Boston MA USA
- National Emerging Infectious Diseases Laboratories Boston University Boston MA USA
| | - Allison M. Dennis
- Division of Materials Science and Engineering Boston University Boston MA USA
- Department of Biomedical Engineering Boston University Boston MA USA
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12
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Chern M, Garden PM, Baer RC, Galagan JE, Dennis AM. Transcription Factor Based Small-Molecule Sensing with a Rapid Cell Phone Enabled Fluorescent Bead Assay. Angew Chem Int Ed Engl 2020; 59:21597-21602. [PMID: 32945589 DOI: 10.1002/anie.202007575] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Indexed: 12/26/2022]
Abstract
Recently, allosteric transcription factors (TFs) were identified as a novel class of biorecognition elements for in vitro sensing, whereby an indicator of the differential binding affinity between a TF and its cognate DNA exhibits dose-dependent responsivity to an analyte. Described is a modular bead-based biosensor design that can be applied to such TF-DNA-analyte systems. DNA-functionalized beads enable efficient mixing and spatial separation, while TF-labeled semiconductor quantum dots serve as bright fluorescent indicators of the TF-DNA bound (on bead) and unbound states. The prototype sensor for derivatives of the antibiotic tetracycline exhibits nanomolar sensitivity with visual detection of bead fluorescence. Facile changes to the sensor enable sensor response tuning without necessitating changes to the biomolecular affinities. Assay components self-assemble, and readout by eye or digital camera is possible within 5 minutes of analyte addition, making sensor use facile, rapid, and instrument-free.
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Affiliation(s)
- Margaret Chern
- Division of Materials Science and Engineering, Boston University, Boston, MA, USA
| | - Padric M Garden
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - R C Baer
- Department of Microbiology, Boston University, Boston, MA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Department of Microbiology, Boston University, Boston, MA, USA.,National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Allison M Dennis
- Division of Materials Science and Engineering, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
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13
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Chen M, Nguyen TT, Varongchayakul N, Grazon C, Chern M, Baer RC, Lecommandoux S, Klapperich CM, Galagan JE, Dennis AM, Grinstaff MW. Surface Immobilized Nucleic Acid-Transcription Factor Quantum Dots for Biosensing. Adv Healthc Mater 2020; 9:e2000403. [PMID: 32691962 DOI: 10.1002/adhm.202000403] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/17/2020] [Indexed: 12/23/2022]
Abstract
Immobilization of biosensors on surfaces is a key step toward development of devices for real-world applications. Here the preparation, characterization, and evaluation of a surface-bound transcription factor-nucleic acid complex for analyte detection as an alternative to conventional systems employing aptamers or antibodies are described. The sensor consists of a gold surface modified with thiolated Cy5 fluorophore-labeled DNA and an allosteric transcription factor (TetR) linked to a quantum dot (QD). Upon addition of anhydrotetracycline (aTc)-the analyte-the TetR-QDs release from the surface-bound DNA, resulting in loss of the Förster resonance energy transfer signal. The sensor responds in a dose-dependent manner over the relevant range of 0-200 µm aTc with a limit of detection of 80 nm. The fabrication of the sensor and the subsequent real-time quantitative measurements establish a framework for the design of future surface-bound, affinity-based biosensors using allosteric transcription factors for molecular recognition.
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Affiliation(s)
- Mingfu Chen
- Department of Biomedical Engineering Boston University Boston MA 02215 USA
| | - Thuy T. Nguyen
- Department of Biomedical Engineering Boston University Boston MA 02215 USA
| | | | - Chloé Grazon
- Department of Chemistry Boston University Boston MA 02215 USA
- CNRS Bordeaux INP LCPO UMR 5629 Univ. Bordeaux Pessac F‐33600 France
| | - Margaret Chern
- Division of Materials Science and Engineering Boston University Boston MA 02215 USA
| | - R. C. Baer
- Department of Microbiology Boston University Boston MA 02118 USA
| | | | - Catherine M. Klapperich
- Department of Biomedical Engineering Boston University Boston MA 02215 USA
- Division of Materials Science and Engineering Boston University Boston MA 02215 USA
| | - James E. Galagan
- Department of Biomedical Engineering Boston University Boston MA 02215 USA
- Department of Microbiology Boston University Boston MA 02118 USA
| | - Allison M. Dennis
- Department of Biomedical Engineering Boston University Boston MA 02215 USA
- Division of Materials Science and Engineering Boston University Boston MA 02215 USA
| | - Mark W. Grinstaff
- Department of Biomedical Engineering Boston University Boston MA 02215 USA
- Department of Chemistry Boston University Boston MA 02215 USA
- Division of Materials Science and Engineering Boston University Boston MA 02215 USA
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14
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Nguyen TT, Chern M, Baer RC, Galagan J, Dennis AM. A Förster Resonance Energy Transfer-Based Ratiometric Sensor with the Allosteric Transcription Factor TetR. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1907522. [PMID: 32249506 PMCID: PMC7359203 DOI: 10.1002/smll.201907522] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/03/2020] [Indexed: 05/02/2023]
Abstract
A recent description of an antibody-free assay is significantly extended for small molecule analytes using allosteric transcription factors (aTFs) and Förster resonance energy transfer (FRET). The FRET signal indicates the differential binding of an aTF-DNA pair with a dose-dependent response to its effector molecule, i.e., the analyte. The new sensors described here, based on the well-characterized aTF TetR, demonstrate several new features of the assay approach: 1) the generalizability of the sensors to additional aTF-DNA-analyte systems, 2) sensitivity modulation through the choice of donor fluorophore (quantum dots or fluorescent proteins, FPs), and 3) sensor tuning using aTF variants with differing aTF-DNA binding affinities. While all of these modular sensors self-assemble, the design reported here based on a recombinant aTF-FP chimera with commercially available dye-labeled DNA uses readily accessible sensor components to facilitate easy adoption of the sensing approach by the broader community.
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Affiliation(s)
- Thuy T Nguyen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - R C Baer
- Department of Microbiology, Boston University, Boston, MA, 02218, USA
| | - James Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Department of Microbiology, Boston University, Boston, MA, 02218, USA
- National Emerging Infections Diseases Laboratories, Boston University, Boston, MA, 02218, USA
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
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15
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Grazon C, Baer RC, Kuzmanović U, Nguyen T, Chen M, Zamani M, Chern M, Aquino P, Zhang X, Lecommandoux S, Fan A, Cabodi M, Klapperich C, Grinstaff MW, Dennis AM, Galagan JE. A progesterone biosensor derived from microbial screening. Nat Commun 2020; 11:1276. [PMID: 32152281 PMCID: PMC7062782 DOI: 10.1038/s41467-020-14942-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/03/2020] [Indexed: 01/08/2023] Open
Abstract
Bacteria are an enormous and largely untapped reservoir of biosensing proteins. We describe an approach to identify and isolate bacterial allosteric transcription factors (aTFs) that recognize a target analyte and to develop these TFs into biosensor devices. Our approach utilizes a combination of genomic screens and functional assays to identify and isolate biosensing TFs, and a quantum-dot Förster Resonance Energy Transfer (FRET) strategy for transducing analyte recognition into real-time quantitative measurements. We use this approach to identify a progesterone-sensing bacterial aTF and to develop this TF into an optical sensor for progesterone. The sensor detects progesterone in artificial urine with sufficient sensitivity and specificity for clinical use, while being compatible with an inexpensive and portable electronic reader for point-of-care applications. Our results provide proof-of-concept for a paradigm of microbially-derived biosensors adaptable to inexpensive, real-time sensor devices.
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Affiliation(s)
- Chloé Grazon
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
- University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France
| | - R C Baer
- Department of Microbiology, Boston University, Boston, MA, 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA
| | - Uroš Kuzmanović
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Thuy Nguyen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Mingfu Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Marjon Zamani
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Margaret Chern
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Patricia Aquino
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Xiaoman Zhang
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | | | - Andy Fan
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Catherine Klapperich
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Mark W Grinstaff
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - Allison M Dennis
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Division of Materials Science and Engineering, Boston University, Boston, MA, 02215, USA
| | - James E Galagan
- Department of Microbiology, Boston University, Boston, MA, 02118, USA.
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02118, USA.
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
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16
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A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules. Nat Commun 2019; 10:3672. [PMID: 31413315 PMCID: PMC6694116 DOI: 10.1038/s41467-019-11648-1] [Citation(s) in RCA: 251] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 07/04/2019] [Indexed: 12/26/2022] Open
Abstract
Besides genome editing, CRISPR-Cas12a has recently been used for DNA detection applications with attomolar sensitivity but, to our knowledge, it has not been used for the detection of small molecules. Bacterial allosteric transcription factors (aTFs) have evolved to sense and respond sensitively to a variety of small molecules to benefit bacterial survival. By combining the single-stranded DNA cleavage ability of CRISPR-Cas12a and the competitive binding activities of aTFs for small molecules and double-stranded DNA, here we develop a simple, supersensitive, fast and high-throughput platform for the detection of small molecules, designated CaT-SMelor (CRISPR-Cas12a- and aTF-mediated small molecule detector). CaT-SMelor is successfully evaluated by detecting nanomolar levels of various small molecules, including uric acid and p-hydroxybenzoic acid among their structurally similar analogues. We also demonstrate that our CaT-SMelor directly measured the uric acid concentration in clinical human blood samples, indicating a great potential of CaT-SMelor in the detection of small molecules. Bacterial allosteric transcription factors can sense and respond to a variety of small molecules. Here the authors present CaT-SMelor which uses Cas12a and allosteric transcription factors to detect small molecules in the nanomolar range.
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17
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Engineering the effector specificity of regulatory proteins for the in vitro detection of biomarkers and pesticide residues. Appl Microbiol Biotechnol 2019; 103:3205-3213. [PMID: 30770965 DOI: 10.1007/s00253-019-09679-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/30/2019] [Accepted: 02/02/2019] [Indexed: 02/07/2023]
Abstract
Transcriptional regulatory proteins (TRPs)-based whole-cell biosensors are promising owing to their specificity and sensitivity, but their applications are currently limited. Herein, TRPs were adapted for the extracellular detection of a disease biomarker, uric acid, and a typical pesticide residue, carbaryl. A mutant regulatory protein that specifically recognizes carbaryl as its non-natural effector and activates transcription upon carbaryl binding was developed by engineering the regulatory protein TtgR from Pseudomonas putida. The TtgR mutant responsive to carbaryl and a regulatory protein responsive to uric acid were used for in vitro detection, based on their allosteric binding of operator DNA and inducer molecules. Based on the quantitative polymerase chain reactions (qPCRs) output, the minimum detectable concentration was between 1 nM-1 μM and 1-10 nM for uric acid and carbaryl, respectively. Our results demonstrated that engineering the effector specificity of regulatory proteins is a potential technique for generating molecular recognition elements for not only in vivo but also in vitro applications.
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18
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Design and optimization of genetically encoded biosensors for high-throughput screening of chemicals. Curr Opin Biotechnol 2018; 54:18-25. [DOI: 10.1016/j.copbio.2018.01.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/08/2018] [Accepted: 01/11/2018] [Indexed: 02/07/2023]
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19
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Cao J, Yao Y, Fan K, Tan G, Xiang W, Xia X, Li S, Wang W, Zhang L. Harnessing a previously unidentified capability of bacterial allosteric transcription factors for sensing diverse small molecules in vitro. SCIENCE ADVANCES 2018; 4:eaau4602. [PMID: 30498782 PMCID: PMC6261655 DOI: 10.1126/sciadv.aau4602] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/30/2018] [Indexed: 05/15/2023]
Abstract
A plethora of bacterial allosteric transcription factors (aTFs) have been identified to sense a variety of small molecules. Introduction of a novel aTF-based approach to sense diverse small molecules in vitro will signify a broad series of detection applications. Here, we found that aTFs could interact with their nicked DNA binding sites. Building from this new finding, we designed and implemented a novel aTF-based nicked DNA template-assisted signal transduction system (aTF-NAST) by using the competition between aTFs and T4 DNA ligase to bind to the nicked DNA. This aTF-NAST could reliably and modularly transduce the signal of small molecules recognized by aTFs to the ligated DNA signal, thus enabling the small molecules to be measured via various mature and robust DNA detection methods. Coupling this aTF-NAST with three DNA detection methods, we demonstrated nine novel biosensors for the detection of an antiseptic 4-hydroxybenzoic acid, a disease marker uric acid and an antibiotic tetracycline. These biosensors show impressive sensitivity and robustness in real-life analysis, highlighting the great potential of our aTF-NAST for biosensing applications.
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Affiliation(s)
- Jiaqian Cao
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
| | - Gaoyi Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Xuekui Xia
- Key Laboratory for Biosensor of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250013, P.R. China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
- Corresponding author. (L.Z.); (W.W.); (S.L.)
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
- Corresponding author. (L.Z.); (W.W.); (S.L.)
| | - Lixin Zhang
- State Key Laboratory of Microbial Resources and Chinese Academy of Sciences (CAS) Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS, Beijing 100101, P.R. China
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266061, P.R. China
- Corresponding author. (L.Z.); (W.W.); (S.L.)
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20
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A novel signal transduction system for development of uric acid biosensors. Appl Microbiol Biotechnol 2018; 102:7489-7497. [DOI: 10.1007/s00253-018-9056-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 10/28/2022]
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21
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Yao Y, Li S, Cao J, Liu W, Fan K, Xiang W, Yang K, Kong D, Wang W. Development of small molecule biosensors by coupling the recognition of the bacterial allosteric transcription factor with isothermal strand displacement amplification. Chem Commun (Camb) 2018; 54:4774-4777. [PMID: 29546904 DOI: 10.1039/c8cc01764f] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here, we demonstrate an easy-to-implement and general biosensing strategy by coupling the small-molecule recognition of the bacterial allosteric transcription factor (aTF) with isothermal strand displacement amplification (SDA) in vitro. Based on this strategy, we developed two biosensors for the detection of an antiseptic, p-hydroxybenzoic acid, and a disease marker, uric acid, using bacterial aTF HosA and HucR, respectively, highlighting the great potential of this strategy for the development of small-molecule biosensors.
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Affiliation(s)
- Yongpeng Yao
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Shanshan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Jiaqian Cao
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Weiwei Liu
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
| | - Wensheng Xiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Keqian Yang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
| | - Deming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, 300071, P. R. China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources and CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
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22
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Learn from microbial intelligence for avermectins overproduction. Curr Opin Biotechnol 2017; 48:251-257. [DOI: 10.1016/j.copbio.2017.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 08/30/2017] [Indexed: 11/21/2022]
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23
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Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. Biotechnol Adv 2017; 35:950-970. [PMID: 28723577 DOI: 10.1016/j.biotechadv.2017.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022]
Abstract
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.
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24
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Deochand DK, Grove A. MarR family transcription factors: dynamic variations on a common scaffold. Crit Rev Biochem Mol Biol 2017; 52:595-613. [PMID: 28670937 DOI: 10.1080/10409238.2017.1344612] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Members of the multiple antibiotic resistance regulator (MarR) family of transcription factors are critical for bacterial cells to respond to chemical signals and to convert such signals into changes in gene activity. Obligate dimers belonging to the winged helix-turn-helix protein family, they are critical for regulation of a variety of functions, including degradation of organic compounds and control of virulence gene expression. The conventional regulatory paradigm is based on a genomic locus in which the gene encoding the MarR protein is divergently oriented from a gene under its control; MarR binding to the intergenic region controls expression of both genes by changing the interaction of RNA polymerase with gene promoters. MarR protein oxidation or binding of a small molecule ligand adversely affects DNA binding, resulting in altered expression of the divergent genes. The generality of this simple paradigm, including the regulation of Escherichia coli MarR by direct binding of antibiotics, has been challenged by reports published in recent years. In addition, structural and biochemical analyses of ligand binding to numerous MarR homologs are converging to identify a shared ligand-binding "hot-spot". This review highlights recent research advances that point to shared features, yet at the same time highlights the remarkable flexibility with which members of this protein family implement responses to inducing signals. A more comprehensive understanding of protein function will pave the way towards the development of both antibacterial agents and biosensors that are based on MarR family proteins.
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Affiliation(s)
- Dinesh K Deochand
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
| | - Anne Grove
- a Department of Biological Sciences , Louisiana State University , Baton Rouge , LA , USA
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25
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Grove A. Regulation of Metabolic Pathways by MarR Family Transcription Factors. Comput Struct Biotechnol J 2017; 15:366-371. [PMID: 28694934 PMCID: PMC5487221 DOI: 10.1016/j.csbj.2017.06.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/05/2017] [Accepted: 06/08/2017] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved sophisticated mechanisms for regulation of metabolic pathways. Such regulatory circuits ensure that anabolic pathways remain repressed unless final products are in short supply and that catabolic enzymes are not produced in absence of their substrates. The precisely tuned gene activity underlying such circuits is in the purview of transcription factors that may bind pathway intermediates, which in turn modulate transcription factor function and therefore gene expression. This review focuses on the role of ligand-responsive MarR family transcription factors in controlling expression of genes encoding metabolic enzymes and the mechanisms by which such control is exerted. Prospects for exploiting these transcription factors for optimization of gene expression for metabolic engineering and for the development of biosensors are considered.
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Affiliation(s)
- Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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