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Zhang Q, Wei Z, Jia X. Controllable detection threshold achieved through the toehold switch system in a mercury ion whole-cell biosensor. Biosens Bioelectron 2024; 256:116283. [PMID: 38608495 DOI: 10.1016/j.bios.2024.116283] [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: 01/15/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Due to the toxicity of mercury and its harmful effects on human health, it is essential to establish a low-cost, highly sensitive and highly specific monitoring method with a wide detection range, ideally with a simple visual readout. In this study, a whole-cell biosensor with adjustable detection limits was developed for the detection of mercury ions in water samples, allowing controllable threshold detection with an expanded detection range. Gene circuits were constructed by combining the toehold switch system with lactose operon, mercury-ion-specific operon, and inducible red fluorescent protein gene. Using MATLAB for design and selection, a total of eleven dual-input single-output sensing logic circuits were obtained based on the basic logic of gene circuit construction. Then, biosensor DTS-3 was selected based on its fluorescence response at different isopropyl β-D-Thiogalactoside (IPTG) concentrations, exhibiting the controllable detection threshold. At 5-20 μM IPTG, DTS-3 can achieve variable threshold detection in the range of 0.005-0.0075, 0.06-0.08, 1-2, and 4-6 μM mercury ion concentrations, respectively. Specificity experiments demonstrated that DTS-3 exhibits good specificity, not showing fluorescence response changes compared with other metal ions. Furthermore spiked sample experiments demonstrated its good resistance to interference, allowing it to distinguish mercury ion concentrations as low as 7.5 nM by the naked eye and 5 nM using a microplate reader. This study confirms the feasibility and performance of biosensor with controllable detection threshold, providing a new detection method and new ideas for expanding the detection range of biosensors while ensuring rapid and convenient measurements without compromising sensitivity.
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Affiliation(s)
- Qinglong Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.
| | - Zixiang Wei
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China.
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, PR China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, PR China.
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2
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Zhang J, Guo Y, Lin YR, Ma BC, Ge XR, Zhang WQ, Zhang NX, Yang SM, Hui CY. Detection of Cadmium in Human Biospecimens by a Cadmium-Selective Whole-Cell Biosensor Based on Deoxyviolacein. ACS Biomater Sci Eng 2024; 10:4046-4058. [PMID: 38722544 DOI: 10.1021/acsbiomaterials.3c01814] [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] [Indexed: 06/11/2024]
Abstract
Cadmium poses a severe health risk, impacting various bodily systems. Monitoring human exposure is vital. Urine and blood cadmium serve as critical biomarkers. However, current urine and blood cadmium detection methods are expensive and complex. Being cost-effective, user-friendly, and efficient, visual biosensing offers a promising complement to existing techniques. Therefore, we constructed a cadmium whole-cell biosensor using CadR10 and deoxyviolacein pigment in this study. We assessed the sensor for time-dose response, specific response to cadmium, sensitivity response to cadmium, and stability response to cadmium. The results showed that (1) the sensor had a preferred signal-to-noise ratio when the incubation time was 4 h; (2) the sensor showed excellent specificity for cadmium compared to the group 12 metals and lead; (3) the sensor was responsive to cadmium down to 1.53 nM under experimental conditions and had good linearity over a wide range from 1.53 nM to 100 μM with good linearity (R2 = 0.979); and (4) the sensor had good stability. Based on the excellent results of the performance tests, we developed a cost-effective, high-throughput method for detecting urinary and blood cadmium. Specifically, this was realized by adding the blood or urine samples into the culture system in a particular proportion. Then, the whole-cell biosensor was subjected to culture, n-butanol extraction, and microplate reading. The results showed that (1) at 20% urine addition ratio, the sensor had an excellent curvilinear relationship (R2 = 0.986) in the range of 3.05 nM to 100 μM, and the detection limit could reach 3.05 nM. (2) At a 10% blood addition ratio, the sensor had an excellent nonlinear relationship (R2 = 0.978) in the range of 0.097-50 μM, and the detection limit reached 0.195 μM. Overall, we developed a sensitive and wide-range method based on a whole-cell biosensor for the detection of cadmium in blood and urine, which has the advantages of being cost-effective, ease of operation, fast response, and low dependence on instrumentation and has the potential to be applied in the monitoring of cadmium exposure in humans as a complementary to the mainstream detection techniques.
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Affiliation(s)
- Juan Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, Jilin, China
| | - Yan Guo
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Yi-Ran Lin
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Bing-Chan Ma
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Xue-Ru Ge
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, Jilin, China
| | - Wen-Qi Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Nai-Xing Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
| | - Shu-Man Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun 130021, Jilin, China
| | - Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen 518020, China
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Martínez-Álvarez JA, Vicente-Gómez M, García-Contreras R, Wood TK, Ramírez Montiel FB, Vargas-Maya NI, España-Sánchez BL, Rangel-Serrano Á, Padilla-Vaca F, Franco B. High-Throughput Screening Method Using Escherichia coli Keio Mutants for Assessing Primary Damage Mechanism of Antimicrobials. Microorganisms 2024; 12:793. [PMID: 38674737 PMCID: PMC11051750 DOI: 10.3390/microorganisms12040793] [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: 03/22/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
The Escherichia coli Keio mutant collection has been a tool for assessing the role of specific genes and determining their role in E. coli physiology and uncovering novel functions. In this work, specific mutants in the DNA repair pathways and oxidative stress response were evaluated to identify the primary targets of silver nanoparticles (NPs) and their mechanism of action. The results presented in this work suggest that NPs mainly target DNA via double-strand breaks and base modifications since the recA, uvrC, mutL, and nfo mutants rendered the most susceptible phenotype, rather than involving the oxidative stress response. Concomitantly, during the establishment of the control conditions for each mutant, the katG and sodA mutants showed a hypersensitive phenotype to mitomycin C, an alkylating agent. Thus, we propose that KatG catalase plays a key role as a cellular chaperone, as reported previously for the filamentous fungus Neurospora crassa, a large subunit catalase. The Keio collection mutants may also be a key tool for assessing the resistance mechanism to metallic NPs by using their potential to identify novel pathways involved in the resistance to NPs.
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Affiliation(s)
- José A. Martínez-Álvarez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, Mexico
| | - Marcos Vicente-Gómez
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA
| | - Fátima Berenice Ramírez Montiel
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, Mexico
| | - Naurú Idalia Vargas-Maya
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, Mexico
| | - Beatriz Liliana España-Sánchez
- Centro de Investigación y Desarrollo Tecnológico en Electroquímica CIDETEQ S.C., Parque Tecnológico Querétaro s/n, Sanfandila, Pedro Escobedo, Querétaro 76703, Mexico
| | - Ángeles Rangel-Serrano
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, Mexico
| | - Felipe Padilla-Vaca
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, Mexico
| | - Bernardo Franco
- Departamento de Biología, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, Mexico
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Sun Y, Zhang F, Ouyang Q, Luo C. The dynamic-process characterization and prediction of synthetic gene circuits by dynamic delay model. iScience 2024; 27:109142. [PMID: 38384832 PMCID: PMC10879701 DOI: 10.1016/j.isci.2024.109142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024] Open
Abstract
Differential equation models are widely used to describe genetic regulations, predict multicomponent regulatory circuits, and provide quantitative insights. However, it is still challenging to quantitatively link the dynamic behaviors with measured parameters in synthetic circuits. Here, we propose a dynamic delay model (DDM) which includes two simple parts: the dynamic determining part and the doses-related steady-state-determining part. The dynamic determining part is usually supposed as the delay time but without a clear formula. For the first time, we give the detail formula of the dynamic determining function and provide a method for measuring all parameters of synthetic elements (include 8 activators and 5 repressors) by microfluidic system. Three synthetic circuits were built to show that the DDM can notably improve the prediction accuracy and can be used in various synthetic biology applications.
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Affiliation(s)
- Yanhong Sun
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fengyu Zhang
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
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5
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Shen L, Chen Y, Hu L, Zhang C, Liu L, Bao L, Ma J, Wang H, Xiao X, Wu L, Chen S. Development of a Highly Sensitive, Visual Platform for the Detection of Cadmium in Actual Wastewater Based on Evolved Whole-Cell Biosensors. ACS Sens 2024; 9:654-661. [PMID: 38329934 DOI: 10.1021/acssensors.3c01811] [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] [Indexed: 02/10/2024]
Abstract
A whole-cell biosensor (WCB) is a convenient and cost-effective method for detecting contaminants. However, the practical application of the cadmium WCBs has been hampered by performance deficiencies, such as low sensitivity, specificity, and responsive strength. In this study, to improve the performance of cadmium WCBs, the cadmium transcription factor (CadC) and its DNA binding site (CadO), the key sensing module of the biosensor, were successively and separately subjected to a two-step directed evolution: 6-round random mutagenesis for CadC and 2-round saturation mutagenesis for CadO. For practical application, the GFP reporter gene was replaced with the lacZ gene and a facile and rapid smartphone detection platform for actual water samples was established by optimizing the reaction systems with detergents. The results showed that the evolved cadmium fluorescent biosensor CadO66 exhibited a higher specificity and a detection limit of 0.034 μg/L, representing a 19-fold reduction compared to the wild-type cadmium biosensor. The detergent sodium dodecylbenzenesulfonate effectively enhanced the visualization of WCB B0033-lacZ. Using the fluorescent WCB CadO66 and the visual WCB B0033-lacZ to analyze the cadmium contents of the actual water samples, the results were also consistent with a graphite furnace atomic absorption spectrometer. Taken together, this study indicates that the two-step directed evolution of CadC and CadO can efficiently improve the performance of cadmium WCBs, further promoting the utilization of WCB in actual sample detection and presenting a promising and feasible method for rapid sample detection.
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Affiliation(s)
- Liang Shen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yiwen Chen
- Wannan Medical College, Wuhu 241002, China
| | - Liangwen Hu
- Wuhu Agricultural Products and Food Testing Center Co. Ltd., Wuhu 241000, China
| | | | | | | | - Jie Ma
- Wannan Medical College, Wuhu 241002, China
| | - Hongqiang Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Xiang Xiao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Lijun Wu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Shaopeng Chen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
- Wannan Medical College, Wuhu 241002, China
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6
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Lin PH, Tsai ST, Chang YC, Chou YJ, Yeh YC. Harnessing split fluorescent proteins in modular protein logic for advanced whole-cell detection. Anal Chim Acta 2023; 1275:341593. [PMID: 37524469 DOI: 10.1016/j.aca.2023.341593] [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: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023]
Abstract
Whole-cell biosensors have demonstrated promising capabilities in detecting target molecules. However, their limited selectivity and precision can be attributed to the broad substrate tolerance of natural proteins. In this study, we aim to enhance the performance of whole-cell biosensors by incorporating of logic AND gates. Specifically, we utilize the HrpR/S system, a widely employed hetero-regulation module from Pseudomonas syringae in synthetic biology, to construct an orthogonal AND gate in Escherichia coli. To accomplish this, we compare the HrpR/S system with self-associating split fluorescent proteins using the Spy Tag/Spy Catcher system. Our objective is to selectively activate a reporter gene in the presence of both IPTG and Hg(II) ions. Through systematic genetic engineering and evaluation of various biological parts under diverse working conditions, our research demonstrates the utility of self-associating split fluorescent proteins in developing high-performance whole-cell biosensors. This approach offers advantages such as engineering simplicity, reduced basal activity, and improved selectivity. Furthermore, the comparison with the HrpR/S system serves as a valuable control model, providing insights into the relative advantages and limitations of each approach. These findings present a systematic and adaptable strategy to overcome the substrate tolerance challenge faced by whole-cell biosensors.
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Affiliation(s)
- Ping-Heng Lin
- Department of Chemistry, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Ssu-Tzu Tsai
- Department of Chemistry, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Yu-Chia Chang
- Department of Chemistry, National Taiwan Normal University, Taipei, 116, Taiwan
| | - Yi-Ju Chou
- Institute of Applied Mechanics, National Taiwan University, Taipei, 106, Taiwan.
| | - Yi-Chun Yeh
- Department of Chemistry, National Taiwan Normal University, Taipei, 116, Taiwan.
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7
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Doshi A, Shaw M, Tonea R, Moon S, Minyety R, Doshi A, Laine A, Guo J, Danino T. Engineered bacterial swarm patterns as spatial records of environmental inputs. Nat Chem Biol 2023; 19:878-886. [PMID: 37142806 DOI: 10.1038/s41589-023-01325-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 04/06/2023] [Indexed: 05/06/2023]
Abstract
A diverse array of bacteria species naturally self-organize into durable macroscale patterns on solid surfaces via swarming motility-a highly coordinated and rapid movement of bacteria powered by flagella. Engineering swarming is an untapped opportunity to increase the scale and robustness of coordinated synthetic microbial systems. Here we engineer Proteus mirabilis, which natively forms centimeter-scale bullseye swarm patterns, to 'write' external inputs into visible spatial records. Specifically, we engineer tunable expression of swarming-related genes that modify pattern features, and we develop quantitative approaches to decoding. Next, we develop a dual-input system that modulates two swarming-related genes simultaneously, and we separately show that growing colonies can record dynamic environmental changes. We decode the resulting multicondition patterns with deep classification and segmentation models. Finally, we engineer a strain that records the presence of aqueous copper. This work creates an approach for building macroscale bacterial recorders, expanding the framework for engineering emergent microbial behaviors.
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Affiliation(s)
- Anjali Doshi
- Department of Biomedical Engineering, Columbia University, New York City, NY, USA
| | - Marian Shaw
- Department of Biomedical Engineering, Columbia University, New York City, NY, USA
| | - Ruxandra Tonea
- Department of Biomedical Engineering, Columbia University, New York City, NY, USA
| | - Soonhee Moon
- Department of Biomedical Engineering, Columbia University, New York City, NY, USA
| | - Rosalía Minyety
- Department of Biomedical Engineering, Columbia University, New York City, NY, USA
| | - Anish Doshi
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | - Andrew Laine
- Department of Biomedical Engineering, Columbia University, New York City, NY, USA
| | - Jia Guo
- Department of Psychiatry, Columbia University, New York City, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York City, NY, USA
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York City, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York City, NY, USA.
- Data Science Institute, Columbia University, New York City, NY, USA.
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He Z, Shen J, Li Q, Yang Y, Zhang D, Pan X. Bacterial metal(loid) resistance genes (MRGs) and their variation and application in environment: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162148. [PMID: 36758696 DOI: 10.1016/j.scitotenv.2023.162148] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Toxic metal(loid)s are widespread and permanent in the biosphere, and bacteria have evolved a wide variety of metal(loid) resistance genes (MRGs) to resist the stress of excess metal(loid)s. Via active efflux, permeability barriers, extracellular/intracellular sequestration, enzymatic detoxification and reduction in metal(loid)s sensitivity of cellular targets, the key components of bacterial cells are protected from toxic metal(loid)s to maintain their normal physiological functions. Exploiting bacterial metal(loid) resistance mechanisms, MRGs have been applied in many environmental fields. Based on the specific binding ability of MRGs-encoded regulators to metal(loid)s, MRGs-dependent biosensors for monitoring environmental metal(loid)s are developed. MRGs-related biotechnologies have been applied to environmental remediation of metal(loid)s by using the metal(loid) tolerance, biotransformation, and biopassivation abilities of MRGs-carrying microorganisms. In this work, we review the historical evolution, resistance mechanisms, environmental variation, and environmental applications of bacterial MRGs. The potential hazards, unresolved problems, and future research directions are also discussed.
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Affiliation(s)
- Zhanfei He
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Jiaquan Shen
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Qunqun Li
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Yingli Yang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xiangliang Pan
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China.
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Mathur S, Singh D, Ranjan R. Genetic circuits in microbial biosensors for heavy metal detection in soil and water. Biochem Biophys Res Commun 2023; 652:131-137. [PMID: 36842324 DOI: 10.1016/j.bbrc.2023.02.031] [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: 01/07/2023] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/19/2023]
Abstract
With the rapid population growth, the world is witnessing an ever-increasing demand for energy and natural resources. Consequently, soil, air, and water are polluted with diverse pollutants, including heavy metals (HM). The detection of heavy metals is necessary to remediate them, which is achieved with biosensors. Initially, these HM were detected using atomic absorption spectroscopy (AAS), emission spectroscopy, mass spectrometry, gas chromatography etc., but these were costly and time consuming which further paved a way for microbe-based biosensors. The development of genetic circuits for microbe-based biosensors has become more popular in recent years for heavy metal detection. In this review, we have especially discussed the various types of genetic circuits such as toggle switches, logic gates, and amplification modules used in these biosensors as they are used to enhance sensitivity and specificity. Genetic circuits also allow for rapid and multiple analyte detection at the same time. The use of microbial biosensors for the detection of HM in the soil as well as the water is also described below. Although with a higher success rate than classical biosensors, these microbial biosensors still have some drawbacks like bioavailability and size of the analyte which are needed to be addressed.
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Affiliation(s)
- Shivangi Mathur
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra, 282005, India
| | - Deeksha Singh
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra, 282005, India
| | - Rajiv Ranjan
- Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra, 282005, India.
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Hu S, Zhang G, Jia X. Improvement of a highly sensitive and specific whole-cell biosensor by adding a positive feedback amplifier. Synth Syst Biotechnol 2023; 8:292-299. [PMID: 37090062 PMCID: PMC10113786 DOI: 10.1016/j.synbio.2023.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
In this study, we designed a Cd2+ whole-cell biosensor with both positive and negative feedback cascade amplifiers in Pseudomonas putida KT2440 (LTCM) based on our previous design with only a negative feedback amplifier (TCM). The results showed that the newly developed biosensor LTCM was greatly improved compared to TCM. Firstly, the linear response range of LTCM was expanded while the maximum linear response range was raised from 0.05 to 0.1 μM. Meanwhile, adding a positive feedback amplifier further increased the fluorescence output signal of LTCM 1.11-2.64 times under the same culture conditions. Moreover, the response time of LTCM for detection of practical samples was reduced from 6 to 4 h. At the same time, LTCM still retained very high sensitivity and specificity, while its lowest detection limit was 0.1 nM Cd2+ and the specificity was 23.29 (compared to 0.1 nM and 17.55 in TCM, respectively). In summary, the positive and negative feedback cascade amplifiers effectively improved the performance of the biosensor LTCM, resulting in a greater linear response range, higher output signal intensity, and shorter response time than TCM while retaining comparable sensitivity and specificity, indicating better potential for practical applications.
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Sharma R, Lenaghan SC. Duckweed: a potential phytosensor for heavy metals. PLANT CELL REPORTS 2022; 41:2231-2243. [PMID: 35980444 DOI: 10.1007/s00299-022-02913-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Globally, heavy metal (HM) contamination is one of the primary causes of environmental pollution leading to decreased quality of life for those affected. In particular, HM contamination in groundwater poses a serious risk to human health and the potential for destabilization of aquatic ecosystems. At present, strategies to remove HM contamination from wastewater are inefficient, costly, laborious, and often the removal poses as much risk to the environment as the initial contamination. Phytoremediation, plant-based removal of contaminants from soil or water, has long been viewed as an economical and sustainable solution to remove toxic metals from the environment. However, to date, phytoremediation has demonstrated limited successes despite a large volume of literature supporting its potential. A key aspect for achieving robust and meaningful phytoremediation is the selection of a plant species that is well suited to the task. For the removal of pollutants from wastewater, hydrophytes, like duckweed, exhibit significant potential due to their rapid growth on nutrient-rich water, ease of collection, and ability to survive in various ecosystems. As a model for ecotoxicity studies, duckweed is an ideal candidate, as it is easy to cultivate under controlled and even sterile conditions, and the rapid growth enables multi-generational studies. Similarly, recent advances in the genetic engineering and genome-editing of duckweed will enable the transition from fundamental ecotoxicity studies to engineered solutions for phytoremediation of HMs. This review will provide insight into the suitability of duckweeds for phytoremediation of HMs and strategies for engineering next-generation duckweed to provide real-world environmental solutions.
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Affiliation(s)
- Reena Sharma
- Department of Food Science, University of Tennessee, 102 Food Safety and Processing Building 2600 River Dr., Knoxville, TN, 37996, USA
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, B012 McCord Hall, 2640 Morgan Circle Drive, Knoxville, TN, 37996, USA
| | - Scott C Lenaghan
- Department of Food Science, University of Tennessee, 102 Food Safety and Processing Building 2600 River Dr., Knoxville, TN, 37996, USA.
- Center for Agricultural Synthetic Biology, University of Tennessee Institute of Agriculture, B012 McCord Hall, 2640 Morgan Circle Drive, Knoxville, TN, 37996, USA.
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12
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Birnbaum DP, Vilardi KJ, Anderson CL, Pinto AJ, Joshi NS. Simple Affinity-Based Method for Concentrating Viruses from Wastewater Using Engineered Curli Fibers. ACS ES&T WATER 2022; 2:1836-1843. [PMID: 36778666 PMCID: PMC9916486 DOI: 10.1021/acsestwater.1c00208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Wastewater surveillance is a proven method for tracking community spread and prevalence of some infectious viral diseases. A primary concentration step is often used to enrich viral particles from wastewater prior to subsequent viral quantification and/or sequencing. Here, we present a simple procedure for concentrating viruses from wastewater using bacterial biofilm protein nanofibers known as curli fibers. Through simple genetic engineering, we produced curli fibers functionalized with single-domain antibodies (also known as nanobodies) specific for the coat protein of the model virus bacteriophage MS2. Using these modified fibers in a simple spin-down protocol, we demonstrated efficient concentration of MS2 in both phosphate-buffered saline (PBS) and in the wastewater matrix. Additionally, we produced nanobody-functionalized curli fibers capable of binding the spike protein of SARS-CoV-2, showing the versatility of the system. Our concentration protocol is simple to implement, can be performed quickly under ambient conditions, and requires only components produced through bacterial culture. We believe this technology represents an attractive alternative to existing concentration methods and warrants further research and optimization for field-relevant applications.
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Affiliation(s)
- Daniel P Birnbaum
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States; Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Katherine J Vilardi
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Christopher L Anderson
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ameet J Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Neel S Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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13
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VanArsdale E, Pitzer J, Wang S, Stephens K, Chen CY, Payne GF, Bentley WE. Enhanced electrochemical measurement of β-galactosidase activity in whole cells by coexpression of lactose permease, LacY. Biotechniques 2022; 73:233-237. [DOI: 10.2144/btn-2022-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Whole-cell biosensing links the sensing and computing capabilities of microbes to the generation of a detectable reporter. Whole cells enable dynamic biological computation (filtered noise, amplified signals, logic gating etc.). Enzymatic reporters enable in situ signal amplification. Electrochemical measurements are easily quantified and work in turbid environments. In this work we show how the coexpression of the lactose permease, LacY, dramatically improves electrochemical sensing of β-galactosidase (LacZ) expressed as a reporter in whole cells. The permease facilitates transport of the LacZ substrate, 4-aminophenyl β-d-galactopyranoside, which is converted to redox active p-aminophenol, which, in turn, is detected via cyclic voltammetry or chronocoulometry. We show a greater than fourfold improvement enabled by lacY coexpression in cells engineered to respond to bacterial signal molecules, pyocyanin and quorum-sensing autoinducer-2.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Chen-yu Chen
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - Gregory F Payne
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, MD 20742, USA
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14
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Hui CY, Guo Y, Zhu DL, Li LM, Yi J, Zhang NX. Metabolic engineering of the violacein biosynthetic pathway toward a low-cost, minimal-equipment lead biosensor. Biosens Bioelectron 2022; 214:114531. [PMID: 35810697 DOI: 10.1016/j.bios.2022.114531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 02/07/2023]
Abstract
Metabolic engineered bacteria have been successfully employed to produce various natural colorants, which are expected to be used as the visually recognizable signals to develop mini-equipment biological devices for monitoring toxic heavy metals. The violacein biosynthetic pathway has been reconstructed in Escherichia coli (E. coli). Here the successful production of four violacein derivatives was achieved by integrating metabolic engineering and synthetic biology. Lead binding to the metalloregulator enables whole-cell colorimetric biosensors capable of assessing bioavailable lead. Deoxyviolacein-derived signal showed the most satisfied biosensing properties among prodeoxyviolacein (green), proviolacein (blue), deoxyviolacein (purple), and violacein (navy). The limit of detection (LOD) of pigment-based biosensors was 2.93 nM Pb(II), which is lower than that of graphite furnace atomic absorption spectrometry. Importantly, a good linear dose-response model in a wide dose range (2.93-6000 nM) was obtained in a non-cytotoxic deoxyviolacein-based biosensor, which was significantly better than cytotoxic violacein-based biosensor (2.93-750 nM). Among ten metal ions, only Cd(II) and Hg(II) exerted a slight influence on the response of the deoxyviolacein-based biosensor toward Pb(II). The deoxyviolacein-based biosensor was validated in detecting bioaccessible Pb(II) in environmental samples. Factors such as low cost and minimal-equipment requirement make this biosensor a suitable biological device for monitoring toxic lead in the environment.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - De-Long Zhu
- School of Public Health , Guangdong Medical University, Dongguan, 523808, China
| | - Li-Mei Li
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China
| | - Nai-Xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, 518020, China.
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15
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Guo Y, Huang ZL, Zhu DL, Hu SY, Li H, Hui CY. Anthocyanin biosynthetic pathway switched by metalloregulator PbrR to enable a biosensor for the detection of lead toxicity. Front Microbiol 2022; 13:975421. [PMID: 36267188 PMCID: PMC9577363 DOI: 10.3389/fmicb.2022.975421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/21/2022] [Indexed: 11/26/2022] Open
Abstract
Environmental lead pollution mainly caused by previous anthropogenic activities continuously threatens human health. The determination of bioavailable lead is of great significance to predict its ecological risk. Bacterial biosensors using visual pigments as output signals have been demonstrated to have great potential in developing minimal-equipment biosensors for environmental pollutant detection. In this study, the biosynthesis pathway of anthocyanin was heterogeneously reconstructed under the control of the PbrR-based Pb(II) sensory element in Escherichia coli. The resultant metabolic engineered biosensor with colored anthocyanin derivatives as the visual signal selectively responded to concentrations as low as 0.012 μM Pb(II), which is lower than the detection limit of traditional fluorescent protein-based biosensors. A good linear dose–response pattern in a wide Pb(II) concentration range (0.012–3.125 μM) was observed. The color deepening of culture was recognized to the naked eye in Pb(II) concentrations ranging from 0 to 200 μM. Importantly, the response of metabolic engineered biosensors toward Pb(II) was not significantly interfered with by organic and inorganic ingredients in environmental water samples. Our findings show that the metabolic engineering of natural colorants has great potential in developing visual, sensitive, and low-cost bacterial biosensors for the detection and determination of pollutant heavy metals.
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Affiliation(s)
- Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Zhen-lie Huang
- Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, China
| | - De-long Zhu
- School of Public Health, Guangdong Medical University, Dongguan, China
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Shun-yu Hu
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
- Department of Toxicology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Han Li
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
- College of Lab Medicine, Hebei North University, Zhangjiakou, China
| | - Chang-ye Hui
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
- *Correspondence: Chang-ye Hui,
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16
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Mendoza JI, Lescano J, Soncini FC, Checa SK. The protein scaffold calibrates metal specificity and activation in MerR sensors. Microb Biotechnol 2022; 15:2992-3002. [PMID: 36134649 PMCID: PMC9733647 DOI: 10.1111/1751-7915.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
MerR metalloregulators are the central components of many biosensor platforms designed to report metal contamination. However, most MerR proteins are non-specific. This makes it difficult to apply these biosensors in the analysis of real environmental samples. On-demand implementation of molecular engineering to modify the MerR metal preferences is innovative, although it does not always yield the expected results. As the metal binding loop region (MBL) of these sensors has been proposed to be the major modulator of their specificity, we surgically switched this region for that of well-characterized specific and non-specific homologues. We found that identical modifications in different MerR proteins result in synthetic sensors displaying particular metal-detection patterns that cannot be predicted from the nature of the assembled modules. For instance, the MBL from a native Hg(II) sensor provided non-specificity or specificity toward Hg(II) or Cd(II) depending on the MerR scaffold into which it was integrated. These and other evidences reveal that residues outside the MBL are required to modulate ion recognition and transduce the input signal to the target promoter. Revealing their identity and their interactions with other residues is a critical step toward the design of more efficient biosensor devices for environmental metal monitoring.
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Affiliation(s)
- Julián I. Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina
| | - Julián Lescano
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina
| | - Fernando C. Soncini
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
| | - Susana K. Checa
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
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17
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Versatile tools of synthetic biology applied to drug discovery and production. Future Med Chem 2022; 14:1325-1340. [PMID: 35975897 DOI: 10.4155/fmc-2022-0063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although synthetic biology is an emerging research field, which has come to prominence within the last decade, it already has many practical applications. Its applications cover the areas of pharmaceutical biotechnology and drug discovery, bringing essential novel methods and strategies such as metabolic engineering, reprogramming the cell fate, drug production in genetically modified organisms, molecular glues, functional nucleic acids and genome editing. This review discusses the main avenues for synthetic biology application in pharmaceutical biotechnology. The authors believe that synthetic biology will reshape drug development and drug production to a similar extent as the advances in organic chemical synthesis in the 20th century. Therefore, synthetic biology already plays an essential role in pharmaceutical, biotechnology, which is the main focus of this review.
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18
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Liu C, Yu H, Zhang B, Liu S, Liu CG, Li F, Song H. Engineering whole-cell microbial biosensors: Design principles and applications in monitoring and treatment of heavy metals and organic pollutants. Biotechnol Adv 2022; 60:108019. [PMID: 35853551 DOI: 10.1016/j.biotechadv.2022.108019] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023]
Abstract
Biosensors have been widely used as cost-effective, rapid, in situ, and real-time analytical tools for monitoring environments. The development of synthetic biology has enabled emergence of genetically engineered whole-cell microbial biosensors. This review updates the design and optimization principles for a diverse array of whole-cell biosensors based on transcription factors (TF) including activators or repressors derived from heavy metal resistance systems, alkanes, and aromatics metabolic pathways of bacteria. By designing genetic circuits, the whole-cell biosensors could be engineered to intelligently sense heavy metals (Hg2+, Zn2+, Pb2+, Au3+, Cd2+, As3+, Ni2+, Cu2+, and UO22+) or organic compounds (alcohols, alkanes, phenols, and benzenes) through one-component or two-component system-based TFs, transduce signals through genetic amplifiers, and response as various outputs such as cell fluorescence and bioelectricity for monitoring heavy metals and organic pollutants in real conditions, synthetic curli and surface metal-binding peptides for in situ bio-sorption of heavy metals. We further review strategies that have been implemented to optimize the selectivity and correlation between ligand concentration and output signal of the TF-based biosensors, so as to meet requirements of practical applications. The optimization strategies include protein engineering to change specificities, promoter engineering to improve sensitivities, and genetic circuit-based amplification to enhance dynamic ranges via designing transcriptional amplifiers, logic gates, and feedback loops. At last, we outlook future trends in developing novel forms of biosensors.
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Affiliation(s)
- Changjiang Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huan Yu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Baocai Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shilin Liu
- Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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19
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Karthik V, Karuna B, Kumar PS, Saravanan A, Hemavathy RV. Development of lab-on-chip biosensor for the detection of toxic heavy metals: A review. CHEMOSPHERE 2022; 299:134427. [PMID: 35358561 DOI: 10.1016/j.chemosphere.2022.134427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Recently, a decrease in water availability and quality has been raised due to rapid industrialization, unsustainable agricultural activities and anthropogenic activities. Heavy metals are considered significant pollutants in the water environment, cause environmental hazards and health effects to humans. For monitoring water contaminants utilized different conventional techniques. Still, they have some drawbacks, such as cost expensive, ecological issues, and processing time, requiring technicians and researchers to operate them effectively. Biosensors have become reasonable devices for screening and identifying environmental contaminants because of their different benefits contrasted with other detecting techniques. This review summarizes the toxic effect of heavy metal and their source, occurrence. A detailed discussion is provided on the heavy metal recognition materials for detecting heavy metals in wastewater. Lab on chip (LOC) is an emerging micro-electrical mechanical system (MEMS) device that intakes liquid and makes it move through the micro-channels, to accomplish fast, cost-effective and profoundly sensitive analysis with significant yield. LOC also provided a discussion on numerous laboratory functions on a single platform. This article attempts to discuss the detection of heavy metals using lab on a chip by suitable recognition materials. Further, the design and fabrication mechanism and their recognition abilities of LOC were also reviewed. The review mainly focuses on the application of LOC biosensors, pros, and cons, and suggests a roadmap towards future development to enhance the practical use in pollutant monitoring.
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Affiliation(s)
- V Karthik
- Department of Industrial Biotechnology, Government College of Technology, Coimbatore, India
| | - B Karuna
- Department of Industrial Biotechnology, Government College of Technology, Coimbatore, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai, 603110, India.
| | - A Saravanan
- Department of Energy and Environmental Engineering, Saveetha School of Engineering, SIMATS, Chennai, 602105, India
| | - R V Hemavathy
- Department of Biotechnology, Rajalakshmi Engineering College, Chennai, 602105, India
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20
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Sankar K, Baer R, Grazon C, Sabatelle RC, Lecommandoux S, Klapperich CM, Galagan JE, Grinstaff MW. An Allosteric Transcription Factor DNA-Binding Electrochemical Biosensor for Progesterone. ACS Sens 2022; 7:1132-1137. [PMID: 35412319 PMCID: PMC9985479 DOI: 10.1021/acssensors.2c00133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We describe an electrochemical strategy to transduce allosteric transcription factor (aTF) binding affinity to sense steroid hormones. Our approach utilizes square wave voltammetry to monitor changes in current output as a progesterone (PRG)-specific aTF (SRTF1) unbinds from the cognate DNA sequence in the presence of PRG. The sensor detects PRG in artificial urine samples with sufficient sensitivity suitable for clinical applications. Our results highlight the capability of using aTFs as the biorecognition elements to develop electrochemical point-of-care biosensors for the detection of small-molecule biomarkers and analytes.
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Affiliation(s)
- Karthika Sankar
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA
| | - R Baer
- Department of Microbiology, Boston University, Boston, MA 02215, USA
| | - Chloé Grazon
- Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,University Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, F-33600, Pessac, France.,University Bordeaux, Institut des Sciences Moléculaires (CNRS UMR 5255), 33405 Talence, France
| | - Robert C. Sabatelle
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Catherine M. Klapperich
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - James E. Galagan
- Department of Microbiology, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Corresponding Author James E. Galagan; , Mark W. Grinstaff;
| | - Mark W. Grinstaff
- Division of Materials Science and Engineering, Boston University, Boston, MA 02215, USA.,Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.,Corresponding Author James E. Galagan; , Mark W. Grinstaff;
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21
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A Recombinase-Based Genetic Circuit for Heavy Metal Monitoring. BIOSENSORS 2022; 12:bios12020122. [PMID: 35200383 PMCID: PMC8870050 DOI: 10.3390/bios12020122] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022]
Abstract
Rapid progress in the genetic circuit design enabled whole-cell biosensors (WCBs) to become prominent in detecting an extensive range of analytes with promise in many fields, from medical diagnostics to environmental toxicity assessment. However, several drawbacks, such as high background signal or low precision, limit WCBs to transfer from proof-of-concept studies to real-world applications, particularly for heavy metal toxicity monitoring. For an alternative WCB module design, we utilized Bxb1 recombinase that provides tight control as a switch to increase dose-response behavior concerning leakiness. The modularity of Bxb1 recombinase recognition elements allowed us to combine an engineered semi-specific heat shock response (HSR) promoter, sensitive to stress conditions including toxic ions such as cadmium, with cadmium resistance regulatory elements; a cadmium-responsive transcription factor and its cognitive promoter. We optimized the conditions for the recombinase-based cadmium biosensor to obtain increased fold change and shorter response time. This system can be expanded for various heavy metals to make an all-in-one type of WCB, even using semi-specific parts of a sensing system.
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22
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OFF-switching property of quorum sensor LuxR via As(III)-induced insoluble form. J Biosci Bioeng 2022; 133:335-339. [PMID: 35120813 DOI: 10.1016/j.jbiosc.2021.12.013] [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: 08/31/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 11/21/2022]
Abstract
Whole-cell sensors for arsenite detection have been developed exclusively based on the natural arsenite (As(III)) sensory protein ArsR for arsenic metabolism. This study reports that the quorum-sensing LuxR/Plux system from Vibrio fischeri, which is completely unrelated to arsenic metabolism, responds to As(III) in a dose-dependent manner. Due to as many as 9 cysteine residues, which has a high binding affinity with As(III), LuxR underwent As(III)-induced insoluble form, thereby reducing its effective cellular concentration. Accordingly, the expression level of green fluorescent protein under the control of Plux gradually decreased with increasing As(III) concentration in the medium. This is a novel As(III)-detection system that has never been proposed before, with a unique ON-to-OFF transfer function.
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23
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Zúñiga A, Camacho M, Chang HJ, Fristot E, Mayonove P, Hani EH, Bonnet J. Engineered l-Lactate Responding Promoter System Operating in Glucose-Rich and Anoxic Environments. ACS Synth Biol 2021; 10:3527-3536. [PMID: 34851606 PMCID: PMC8689689 DOI: 10.1021/acssynbio.1c00456] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Indexed: 12/19/2022]
Abstract
Bacteria equipped with genetically encoded lactate biosensors are promising tools for biopharmaceutical production, diagnostics, and cellular therapies. However, many applications involve glucose-rich and anoxic environments, in which current whole-cell lactate biosensors show low performance. Here we engineer an optimized, synthetic lactate biosensor system by repurposing the natural LldPRD promoter regulated by the LldR transcriptional regulator. We removed glucose catabolite and anoxic repression by designing a hybrid promoter, containing LldR operators and tuned both regulator and reporter gene expressions to optimize biosensor signal-to-noise ratio. The resulting lactate biosensor, termed ALPaGA (A Lactate Promoter Operating in Glucose and Anoxia), can operate in glucose-rich, aerobic and anoxic conditions. We show that ALPaGA works reliably in the probiotic chassisEscherichia coliNissle 1917 and can detect endogenous l-lactate produced by 3D tumor spheroids with an improved dynamic range. In the future, the ALPaGA system could be used to monitor bioproduction processes and improve the specificity of engineered bacterial cancer therapies by restricting their activity to the lactate-rich microenvironment of solid tumors.
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Affiliation(s)
- Ana Zúñiga
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Miguel Camacho
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Hung-Ju Chang
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Elsa Fristot
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Pauline Mayonove
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - El-Habib Hani
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
| | - Jerome Bonnet
- Centre de Biologie Structurale (CBS),
INSERM U1054, CNRS UMR5048, University of
Montpellier, 29 Rue de Navacelles, Montpellier 34090, France
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Hui CY, Guo Y, Liu L, Yi J. Recent advances in bacterial biosensing and bioremediation of cadmium pollution: a mini-review. World J Microbiol Biotechnol 2021; 38:9. [PMID: 34850291 DOI: 10.1007/s11274-021-03198-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022]
Abstract
Cadmium (Cd) pollution has become a global environmental issue because Cd gets easily accumulated and translocated in the food chain, threatening human health. Considering the detrimental effects and non-biodegradability of environmental Cd, this is an urgent issue that needs to be addressed through the development of robust, cost-effective, and eco-friendly green routes for monitoring and remediating toxic levels of Cd. This article attempts to review various bacterial approaches toward biosensing and bioremediation of Cd in the environment. This review focuses on the recent development of bacterial cell-based biosensors for the detection of bioavailable Cd and the bioremediation of toxic Cd by natural or genetically-engineered bacteria. The present limitations and future perspectives of these available bacterial approaches are outlined. New trends for integrating synthetic biology and metabolic engineering into the design of bacterial biosensors and bioadsorbers are additionally highlighted.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Pennsylvania, USA
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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Hui CY, Guo Y, Wu J, Liu L, Yang XQ, Guo X, Xie Y, Yi J. Detection of Bioavailable Cadmium by Double-Color Fluorescence Based on a Dual-Sensing Bioreporter System. Front Microbiol 2021; 12:696195. [PMID: 34603225 PMCID: PMC8481780 DOI: 10.3389/fmicb.2021.696195] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023] Open
Abstract
Cadmium (Cd) is carcinogenic to humans and can accumulate in the liver, kidneys, and bones. There is widespread presence of cadmium in the environment as a consequence of anthropogenic activities. It is important to detect cadmium in the environment to prevent further exposure to humans. Previous whole-cell biosensor designs were focused on single-sensing constructs but have had difficulty in distinguishing cadmium from other metal ions such as lead (Pb) and mercury (Hg). We developed a dual-sensing bacterial bioreporter system to detect bioavailable cadmium by employing CadC and CadR as separate metal sensory elements and eGFP and mCherry as fluorescent reporters in one genetic construct. The capability of this dual-sensing biosensor was proved to simultaneously detect bioavailable cadmium and its toxic effects using two sets of sensing systems while still maintaining similar specificity and sensitivity of respective signal-sensing biosensors. The productions of double-color fluorescence were directly proportional to the exposure concentration of cadmium, thereby serving as an effective quantitative biosensor to detect bioavailable cadmium. This novel dual-sensing biosensor was then validated to respond to Cd(II) spiked in environmental water samples. This is the first report of the development of a novel dual-sensing, whole-cell biosensor for simultaneous detection of bioavailable cadmium. The application of two biosensing modules provides versatile biosensing signals and improved performance that can make a significant impact on monitoring high concentration of bioavailable Cd(II) in environmental water to reduce human exposure to the harmful effects of cadmium.
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Affiliation(s)
- Chang-ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Jian Wu
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Ambler, PA, United States
| | - Xue-qin Yang
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Xiang Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Ying Xie
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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Gupta D, Sharma G, Saraswat P, Ranjan R. Synthetic Biology in Plants, a Boon for Coming Decades. Mol Biotechnol 2021; 63:1138-1154. [PMID: 34420149 DOI: 10.1007/s12033-021-00386-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/16/2021] [Indexed: 02/01/2023]
Abstract
Recently an enormous expansion of knowledge is seen in various disciplines of science. This surge of information has given rise to concept of interdisciplinary fields, which has resulted in emergence of newer research domains, one of them is 'Synthetic Biology' (SynBio). It captures basics from core biology and integrates it with concepts from the other areas of study such as chemical, electrical, and computational sciences. The essence of synthetic biology is to rewire, re-program, and re-create natural biological pathways, which are carried through genetic circuits. A genetic circuit is a functional assembly of basic biological entities (DNA, RNA, proteins), created using typical design, built, and test cycles. These circuits allow scientists to engineer nearly all biological systems for various useful purposes. The development of sophisticated molecular tools, techniques, genomic programs, and ease of nucleic acid synthesis have further fueled several innovative application of synthetic biology in areas like molecular medicines, pharmaceuticals, biofuels, drug discovery, metabolomics, developing plant biosensors, utilization of prokaryotic systems for metabolite production, and CRISPR/Cas9 in the crop improvement. These applications have largely been dominated by utilization of prokaryotic systems. However, newer researches have indicated positive growth of SynBio for the eukaryotic systems as well. This paper explores advances of synthetic biology in the plant field by elaborating on its core components and potential applications. Here, we have given a comprehensive idea of designing, development, and utilization of synthetic biology in the improvement of the present research state of plant system.
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Affiliation(s)
- Dipinte Gupta
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Gauri Sharma
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Pooja Saraswat
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India
| | - Rajiv Ranjan
- Plant Biotechnology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute (Deemed to be University), Dayalbagh, Agra, 282005, India.
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Hui CY, Guo Y, Li LM, Liu L, Chen YT, Yi J, Zhang NX. Indigoidine biosynthesis triggered by the heavy metal-responsive transcription regulator: a visual whole-cell biosensor. Appl Microbiol Biotechnol 2021; 105:6087-6102. [PMID: 34291315 DOI: 10.1007/s00253-021-11441-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/22/2021] [Accepted: 07/03/2021] [Indexed: 10/20/2022]
Abstract
During the last few decades, whole-cell biosensors have attracted increasing attention for their enormous potential in monitoring bioavailable heavy metal contaminations in the ecosystem. Visual and measurable output signals by employing natural pigments have been demonstrated to offer another potential choice to indicate the existence of bioavailable heavy metals in recent years. The biosynthesis of the blue pigment indigoidine has been achieved in E. coli following heterologous expression of both BpsA (a single-module non-ribosomal peptide synthetase) and PcpS (a PPTase to activate apo-BpsA). Moreover, we demonstrated herein the development of the indigoidine-based whole-cell biosensors to detect bioavailable Hg(II) and Pb(II) in water samples by employing metal-responsive transcriptional regulator MerR and PbrR as the sensory elements, and the indigoidine biosynthesis gene cluster as a reporter element. The resulting indigoidine-based biosensors presented a good selectivity and high sensitivity to target metal ions. High concentration of target metal exposure could be clearly recognized by the naked eye due to the color change by the secretion of indigoidine, and quantified by measuring the absorbance of the culture supernatants at 600 nm. Dose-response relationships existed between the exposure concentrations of target heavy metals and the production of indigoidine. Although fairly good linear relationships were obtained in a relatively limited concentration range of the concentrations of heavy metal ions, these findings suggest that genetically controlled indigoidine biosynthesis triggered by the MerR family transcriptional regulator can enable a sensitive, visual, and qualitative whole-cell biosensor for bioindicating the presence of bioaccessible heavy metal in environmental water samples. KEY POINTS: • Biosynthesis pathway of indigoidine reconstructed in a high copy number plasmid in E. coli. • Visual and colorimetric detection of Hg(II) and Pb(II) by manipulation of indigoidine biosynthesis through MerR family metalloregulator. •Enhanced detection sensitivity toward Hg(II) and Pb(II) achieved using novel pigment-based whole-cell biosensors.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Li-Mei Li
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Yu-Ting Chen
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Nai-Xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
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Guo Y, Hui CY, Liu L, Chen MP, Huang HY. Development of a bioavailable Hg(II) sensing system based on MerR-regulated visual pigment biosynthesis. Sci Rep 2021; 11:13516. [PMID: 34188121 PMCID: PMC8242042 DOI: 10.1038/s41598-021-92878-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/14/2021] [Indexed: 12/02/2022] Open
Abstract
Engineered microorganisms have proven to be a highly effective and robust tool to specifically detect heavy metals in the environment. In this study, a highly specific pigment-based whole-cell biosensor has been investigated for the detection of bioavailable Hg(II) based on an artificial heavy metal resistance operon. The basic working principle of biosensors is based on the violacein biosynthesis under the control of mercury resistance (mer) promoter and mercury resistance regulator (MerR). Engineered biosensor cells have been demonstrated to selectively respond to Hg(II), and the specific response was not influenced by interfering metal ions. The response of violacein could be recognized by the naked eye, and the time required for the maximum response of violacein (5 h) was less than that of enhanced green fluorescence protein (eGFP) (8 h) in the single-signal output constructs. The response of violacein was almost unaffected by the eGFP in a double-promoter controlled dual-signals output construct. However, the response strength of eGFP was significantly decreased in this genetic construct. Exponentially growing violacein-based biosensor detected concentrations as low as 0.39 μM Hg(II) in a colorimetric method, and the linear relationship was observed in the concentration range of 0.78-12.5 μM. Non-growing biosensor cells responded to concentrations as low as 0.006 μM Hg(II) in a colorimetric method and in a Hg(II) containing plate sensitive assay, and the linear relationship was demonstrated in a very narrow concentration range. The developed biosensor was finally validated for the detection of spiked bioavailable Hg(II) in environmental water samples.
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Affiliation(s)
- Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Chang-Ye Hui
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Min-Peng Chen
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Hong-Ying Huang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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Ultrasensitive label-free electrochemical immunosensor based on core-shell Au@PtNPs functionalized rGO-TEPA/PB nanocomposite for HBsAg detection. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115216] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Giachino A, Focarelli F, Marles-Wright J, Waldron KJ. Synthetic biology approaches to copper remediation: bioleaching, accumulation and recycling. FEMS Microbiol Ecol 2021; 97:6021318. [PMID: 33501489 DOI: 10.1093/femsec/fiaa249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/02/2020] [Indexed: 12/20/2022] Open
Abstract
One of the current aims of synthetic biology is the development of novel microorganisms that can mine economically important elements from the environment or remediate toxic waste compounds. Copper, in particular, is a high-priority target for bioremediation owing to its extensive use in the food, metal and electronic industries and its resulting common presence as an environmental pollutant. Even though microbe-aided copper biomining is a mature technology, its application to waste treatment and remediation of contaminated sites still requires further research and development. Crucially, any engineered copper-remediating chassis must survive in copper-rich environments and adapt to copper toxicity; they also require bespoke adaptations to specifically extract copper and safely accumulate it as a human-recoverable deposit to enable biorecycling. Here, we review current strategies in copper bioremediation, biomining and biorecycling, as well as strategies that extant bacteria use to enhance copper tolerance, accumulation and mineralization in the native environment. By describing the existing toolbox of copper homeostasis proteins from naturally occurring bacteria, we show how these modular systems can be exploited through synthetic biology to enhance the properties of engineered microbes for biotechnological copper recovery applications.
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Affiliation(s)
- Andrea Giachino
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Francesca Focarelli
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Kevin J Waldron
- Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
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31
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Genetic circuits combined with machine learning provides fast responding living sensors. Biosens Bioelectron 2021; 178:113028. [DOI: 10.1016/j.bios.2021.113028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/05/2021] [Accepted: 01/19/2021] [Indexed: 12/24/2022]
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Rondon R, Wilson CJ. Engineering Alternate Ligand Recognition in the PurR Topology: A System of Novel Caffeine Biosensing Transcriptional Antirepressors. ACS Synth Biol 2021; 10:552-565. [PMID: 33689294 DOI: 10.1021/acssynbio.0c00582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent advances in synthetic biology and protein engineering have increased the number of allosteric transcription factors used to regulate independent promoters. These developments represent an important increase in our biological computing capacity, which will enable us to construct more sophisticated genetic programs for a broad range of biological technologies. However, the majority of these transcription factors are represented by the repressor phenotype (BUFFER), and require layered inversion to confer the antithetical logical function (NOT), requiring additional biological resources. Moreover, these engineered transcription factors typically utilize native ligand binding functions paired with alternate DNA binding functions. In this study, we have advanced the state-of-the-art by engineering and redesigning the PurR topology (a native antirepressor) to be responsive to caffeine, while mitigating responsiveness to the native ligand hypoxanthine-i.e., a deamination product of the input molecule adenine. Importantly, the resulting caffeine responsive transcription factors are not antagonized by the native ligand hypoxanthine. In addition, we conferred alternate DNA binding to the caffeine antirepressors, and to the PurR scaffold, creating 38 new transcription factors that are congruent with our current transcriptional programming structure. Finally, we leveraged this system of transcription factors to create integrated NOR logic and related feedback operations. This study represents the first example of a system of transcription factors (antirepressors) in which both the ligand binding site and the DNA binding functions were successfully engineered in tandem.
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Affiliation(s)
- Ronald Rondon
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, Georgia 30332-0100, United States
| | - Corey J. Wilson
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, 311 Ferst Drive, Atlanta, Georgia 30332-0100, United States
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Busnelli MP, Lazzarini Behrmann IC, Ferreira ML, Candal RJ, Ramirez SA, Vullo DL. Metal- Pseudomonas veronii 2E Interactions as Strategies for Innovative Process Developments in Environmental Biotechnology. Front Microbiol 2021; 12:622600. [PMID: 33746918 PMCID: PMC7965972 DOI: 10.3389/fmicb.2021.622600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
The increase of industrial discharges is the first cause of the contamination of water bodies. The bacterial survival strategies contribute to the equilibrium restoration of ecosystems being useful tools for the development of innovative environmental biotechnologies. The aim of this work was to study the Cu(II) and Cd(II) biosensing, removal and recovery, mediated by whole cells, exopolymeric substances (EPS) and biosurfactants of the indigenous and non-pathogenic Pseudomonas veronii 2E to be applied in the development of wastewater biotreatments. An electrochemical biosensor was developed using P. veronii 2E biosorption mechanism mediated by the cell surface associated to bound exopolymeric substances. A Carbon Paste Electrode modified with P. veronii 2E (CPEM) was built using mineral oil, pre-washed graphite power and 24 h-dried cells. For Cd(II) quantification the CPEM was immersed in Cd(II) (1-25 μM), detected by Square Wave Voltammetry. A similar procedure was used for 1-50 μM Cu(II). Regarding Cd(II), removal mediated by immobilized EPS was tested in a 50 ml bioreactor with 0.13 mM Cd(II), pH 7.5. A 54% metal retention by EPS was achieved after 7 h of continuous operation, while a 40% was removed by a control resin. In addition, surfactants produced by P. veronii 2E were studied for recovery of Cd(II) adsorbed on diatomite, obtaining a 36% desorption efficiency at pH 6.5. Cu(II) adsorption from a 1 mM solution was tested using P. veronii 2E purified soluble EPS in 50 mL- batch reactors (pH = 5.5, 32°C). An 80% of the initial Cu(II) was retained using 1.04 g immobilized EPS. Focusing on metal recovery, Cu nanoparticles (NPs) biosynthesis by P. veronii 2E was carried out in Cu(II)-PYG Broth at 25°C for 5 days. Extracellular CuNPs were characterized by UV-Vis spectral analysis while both extracellular and intracellular NPs were analyzed by SEM and TEM techniques. Responses of P. veronii 2E and its products as biosurfactants, bound and soluble EPS allowed Cu(II) and Cd(II) removal, recovery and biosensing resulting in a multiple and versatile tool for sustainable wastewater biotreatments.
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Affiliation(s)
- María Pia Busnelli
- Área Química, Instituto de Ciencias, Universidad Nacional de General Sarmiento, Los Polvorines, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Maria Laura Ferreira
- Área Química, Instituto de Ciencias, Universidad Nacional de General Sarmiento, Los Polvorines, Argentina
| | - Roberto J. Candal
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Investigación e Ingeniería Ambiental (IIIA), Universidad Nacional de General San Martin, San Martín, Argentina
| | - Silvana A. Ramirez
- Área Química, Instituto de Ciencias, Universidad Nacional de General Sarmiento, Los Polvorines, Argentina
| | - Diana L. Vullo
- Área Química, Instituto de Ciencias, Universidad Nacional de General Sarmiento, Los Polvorines, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Brooks SM, Alper HS. Applications, challenges, and needs for employing synthetic biology beyond the lab. Nat Commun 2021; 12:1390. [PMID: 33654085 PMCID: PMC7925609 DOI: 10.1038/s41467-021-21740-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Synthetic biology holds great promise for addressing global needs. However, most current developments are not immediately translatable to 'outside-the-lab' scenarios that differ from controlled laboratory settings. Challenges include enabling long-term storage stability as well as operating in resource-limited and off-the-grid scenarios using autonomous function. Here we analyze recent advances in developing synthetic biological platforms for outside-the-lab scenarios with a focus on three major application spaces: bioproduction, biosensing, and closed-loop therapeutic and probiotic delivery. Across the Perspective, we highlight recent advances, areas for further development, possibilities for future applications, and the needs for innovation at the interface of other disciplines.
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Affiliation(s)
- Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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Chaudhary T, Gera R, Shukla P. Emerging Molecular Tools for Engineering Phytomicrobiome. Indian J Microbiol 2021; 61:116-124. [PMID: 33927453 DOI: 10.1007/s12088-020-00915-1] [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: 02/18/2020] [Accepted: 12/05/2020] [Indexed: 10/22/2022] Open
Abstract
Microbial plant interaction plays a major role in the sustainability of plants. The understanding of phytomicrobiome interactions enables the gene-editing tools for the construction of the microbial consortia. In this interaction, microbes share several common secondary metabolites and terpenoid metabolic pathways with their host plants that ensure a direct connection between the microbiome and associated plant metabolome. In this way, the CRISPR-mediated gene-editing tool provides an attractive approach to accomplish the creation of microbial consortia. On the other hand, the genetic manipulation of the host plant with the help of CRISPR-Cas9 can facilitate the characterization and identification of the genetic determinants. It leads to the enhancement of microbial capacity for more trait improvement. Many plant characteristics like phytovolatilization, phytoextraction, phytodesalination and phytodegradation are targeted by these approaches. Alternatively, chemical communications by PGPB are accomplished by the exchange of different signal molecules. For example, quorum-sensing is the way of the cell to cell communication in bacteria that lead to the detection of metabolites produced by pathogens during adverse conditions and also helpful in devising some tactics towards understanding plant immunity. Along with quorum-sensing, different volatile organic compounds and N-acyl homoserine lactones play a significant role in cell to cell communication by microbe to plant and among the plants respectively. Therefore, it is necessary to get details of all the significant approaches that are useful in exploring cell to cell communications. In this review, we have described gene-editing tools and the cell to cell communication process by quorum-sensing based signaling. These signaling processes via CRISPR- Cas9 mediated gene editing can improve the microbe-plant community in adverse climatic conditions.
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Affiliation(s)
- Twinkle Chaudhary
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001 India
| | - Rajesh Gera
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004 India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001 India.,Present Address: School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
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Wang X, Zhu K, Chen D, Wang J, Wang X, Xu A, Wu L, Li L, Chen S. Monitoring arsenic using genetically encoded biosensors in vitro: The role of evolved regulatory genes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111273. [PMID: 32916524 DOI: 10.1016/j.ecoenv.2020.111273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Toxic pollutant (TP) detection in situ using analytical instruments or whole-cell biosensors is inconvenient. Designing and developing genetically coded biosensors in vitro for real-world TP detection is a promising alternative. However, because the bioactivity and stability of some key biomolecules are weakened in vitro, the response and regulation of reporter protein become difficult. Here, we established a genetically encoded biosensor in vitro with an arsenical resistance operon repressor (ArsR) and GFP reporter gene. Given that the wildtype ArsR did not respond to arsenic and activate GFP expression in vitro, we found, after screening, an evolved ArsR mutant ep3 could respond to arsenic and exhibited an approximately 3.4-fold fluorescence increase. Arsenic induced expression of both wildtype ArsR and ep3 mutant in vitro, however, only ep3 mutant regulated the expression of reporter gene. Furthermore, the effects of cell extracts, temperature, pH, incubation, and equilibrium time were investigated, and the equilibration of reaction mixtures for 30 min at 37 °C was found to be essential for in vitro arsenic detection prior to treatment with arsenic. Based on our data, we established a standard procedure for arsenic detection in vitro. Our results will facilitate the practical application of genetically encoded biosensors in TP monitoring.
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Affiliation(s)
- Xuanyu Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Kaili Zhu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Dongdong Chen
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Juan Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Xiaofei Wang
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui, 230601, China
| | - An Xu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Lijun Wu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China; Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Luzhi Li
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui, 230601, China
| | - Shaopeng Chen
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China.
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Guo M, Huang K, Xu W. Third Generation Whole-Cell Sensing Systems: Synthetic Biology Inside, Nanomaterial Outside. Trends Biotechnol 2020; 39:S0167-7799(20)30262-6. [PMID: 34756379 DOI: 10.1016/j.tibtech.2020.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 01/24/2023]
Abstract
Whole-cell sensing systems (WCSSs) are highly anticipated in the field of on-site detection. However, due to their low specificity, poor stability, and potential environmental problems, their commercial application is unrealistic. Recently, synthetic biology and nanomaterials have provided potential solutions to these problems, propelling WCSSs into a new generation. Synthetic biology provides a complete solution for the intelligent design and assembly of elements, modules, and genetic circuits. Nanomaterials covering the exterior of the cells provide stable protection, remote control capability, and catalytic ability for the WCSSs, and they can limit the horizontal transfer of genetic elements. These advancements enable personalized customization, intelligent control, and self-destruction in the next generation of cell sensors, promoting their industrialization.
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Affiliation(s)
- Mingzhang Guo
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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39
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Wang D, Zheng Y, Wei L, Wei N, Fan X, Huang S, Xiao Q. A signal-amplified whole-cell biosensor for sensitive detection of Hg 2+ based on Hg 2+-enhanced reporter module. J Environ Sci (China) 2020; 96:93-98. [PMID: 32819703 DOI: 10.1016/j.jes.2020.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
A signal-amplified mercury sensing biosensor with desired sensitivity was developed through firstly using the GFP mutant with fluorescence increasing response towards Hg2+ as the reporter module. The developed biosensor showed response for Hg2+ in a relatively wide range of 1-10,000 nmol/L, and the detection limit was improved one or two orders of magnitude in comparison with most metal-sensing biosensors in similar constructs. In addition, the biosensor could distinguish Hg2+ easily from multiple metal ions and displayed strong adaptability to extensive pH conditions (pH 4.0-10.0). More importantly, the developed biosensor was able to provide an initial assessment of Hg2+ spiked in the environmental water with the recoveries between 85.70% and 112.50%. The signal-amplified strategy performed by the modified reporter module will be widely applicable to many other whole-cell biosensors, meeting the practical requirements with sufficient sensing performance.
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Affiliation(s)
- Dan Wang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China.
| | - Yanan Zheng
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Liudan Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Na Wei
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Xiaosu Fan
- Experimental Center of College of Agriculture, Guangxi University, Nanning 530005, China
| | - Shan Huang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China
| | - Qi Xiao
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, China.
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40
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Recent advances in synthetic biology-enabled and natural whole-cell optical biosensing of heavy metals. Anal Bioanal Chem 2020; 413:73-82. [PMID: 32959111 DOI: 10.1007/s00216-020-02953-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
A large number of scientific works have been published on whole-cell heavy metal biosensing based on optical transduction. The advances in the application of biotechnological tools not only have continuously improved the sensitivity, selectivity, and detection range for biosensors but also have simultaneously unveiled new challenges and restrictions for further improvements. This review highlights selected aspects of whole-cell biosensing of heavy metals using optical transducers. We have focused on the progress in genetic modulation in regulatory and reporter modules of recombinant plasmids that has enabled improvement of biosensor performance. Simultaneously, an attempt has been made to present newer platforms such as microfluidics that have generated promising results and might give a new turn to the optical biosensing field.
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41
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Detection of biotin with zeptomole sensitivity using recombinant spores and a competition assay. Anal Bioanal Chem 2020; 412:7219-7226. [PMID: 32761258 DOI: 10.1007/s00216-020-02854-8] [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: 04/17/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
Detection of protein-binding analytes is important for many applications. Currently, various instrument-based techniques are used for detecting protein-binding analytes. However, such techniques have several limitations including high cost and time-consuming sample processing. In order to overcome these limitations, we developed a sensitive competition assay for the detection of protein-binding analytes using recombinant endospores as a sensing element. The method is based on the competition between the biotin, the model analyte, and a biotin-magnetic bead complex to bind the recombinant spores containing the biotin binding region of streptavidin. After magnetic attraction, the residual spores in the suspension are spread on plates to form colonies which are used to count the amount of the residual spores; the higher the residual ratio of spores, the more biotin in the samples. The linear range was from 150 zmol to 1.5 fmol and the limit of detection of the assay was 150 zmol. The assay proposed herein is sensitive and does not require any expensive equipment. It is suitable for qualitative or semi-quantitative analysis such as screening tests for the detection of toxic chemicals.
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42
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Mendoza JI, Soncini FC, Checa SK. Engineering of a Au-sensor to develop a Hg-specific, sensitive and robust whole-cell biosensor for on-site water monitoring. Chem Commun (Camb) 2020; 56:6590-6593. [PMID: 32406434 DOI: 10.1039/d0cc01323d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A highly sensitive and specific Hg-whole-cell biosensor was developed from a non-selective variant of the Au sensor GolS and its regulatory pathway. The performance of this analytical tool was validated under laboratory and field-like conditions. This biosensor can be easily applied in cost-effective and portable semiquantitative devices to report Hg contamination in water.
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Affiliation(s)
- Julián I Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario (UNR)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Argentina.
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43
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Elcin E, Öktem HA. Inorganic Cadmium Detection Using a Fluorescent Whole-Cell Bacterial Bioreporter. ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1755867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Evrim Elcin
- Department of Agricultural Biotechnology, Adnan Menderes University, Aydın, Turkey
| | - Huseyin Avni Öktem
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Nanobiz Technology Inc, Ankara, Turkey
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Graham G, Csicsery N, Stasiowski E, Thouvenin G, Mather WH, Ferry M, Cookson S, Hasty J. Genome-scale transcriptional dynamics and environmental biosensing. Proc Natl Acad Sci U S A 2020; 117:3301-3306. [PMID: 31974311 PMCID: PMC7022183 DOI: 10.1073/pnas.1913003117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome-scale technologies have enabled mapping of the complex molecular networks that govern cellular behavior. An emerging theme in the analyses of these networks is that cells use many layers of regulatory feedback to constantly assess and precisely react to their environment. The importance of complex feedback in controlling the real-time response to external stimuli has led to a need for the next generation of cell-based technologies that enable both the collection and analysis of high-throughput temporal data. Toward this end, we have developed a microfluidic platform capable of monitoring temporal gene expression from over 2,000 promoters. By coupling the "Dynomics" platform with deep neural network (DNN) and associated explainable artificial intelligence (XAI) algorithms, we show how machine learning can be harnessed to assess patterns in transcriptional data on a genome scale and identify which genes contribute to these patterns. Furthermore, we demonstrate the utility of the Dynomics platform as a field-deployable real-time biosensor through prediction of the presence of heavy metals in urban water and mine spill samples, based on the the dynamic transcription profiles of 1,807 unique Escherichia coli promoters.
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Affiliation(s)
- Garrett Graham
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Nicholas Csicsery
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth Stasiowski
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Gregoire Thouvenin
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | | | | | | | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093;
- Quantitative BioSciences, Inc., San Diego, CA 92121
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
- BioCircuits Institute, University of California San Diego, La Jolla, CA 92093
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Hui CY, Guo Y, Liu L, Zhang NX, Gao CX, Yang XQ, Yi J. Genetic control of violacein biosynthesis to enable a pigment-based whole-cell lead biosensor. RSC Adv 2020; 10:28106-28113. [PMID: 35519119 PMCID: PMC9055639 DOI: 10.1039/d0ra04815a] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
Environmental risks continue to grow due to heavy metal contamination caused by anthropogenic activities. Accumulation of harmful quantities of lead poses a threat to aquatic organisms, plants, and human beings. Whole-cell biosensors, which can proliferate independently, can detect the bioavailable fraction to assess the effect of target heavy metal on the environmental ecosystem. In this study, the biosynthesis pathway of violacein was heterogeneously constructed under the control of the T7 lac promoter in E. coli. A dose–response relationship existed between the inducer and the production of violacein. The biosynthesis pathway of violacein was finally engineered under the regulation of Pb(ii)-dependent metalloregulator PbrR to assemble Pb(ii)-inducible whole-cell biosensor. It permitted specific biosensing of Pb(ii) with extraordinary selectivity, and could resist the interferences from various metal ions. Color change by the intracellular accumulation of violacein could be recognized with the naked eye directly with high concentration of lead exposure, and quantified by determining the absorbance at 490 nm after butanol extraction. A good linear range for Pb(ii) concentrations of 0.1875–1.5 μM was obtained. The novel pigment-based whole-cell biosensor could detect concentrations as low as 0.1875 μM Pb(ii) based on in vitro quantification of violacein extracted by butanol, which is significantly lower than reported fluorescent protein-based PbrR-regulated biosensors based on direct measurement of whole cell fluorescence. These results indicate that genetically controlled violacein biosynthesis can enable a sensitive, visual, and qualitative biosensor for monitoring the presence of bioavailable Pb(ii) in lead-contaminated water. Genetically controlled violacein biosynthesis can enable a sensitive, visual, and qualitative biosensor for monitoring the presence of bioavailable lead.![]()
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Affiliation(s)
- Chang-ye Hui
- Department of Pathology & Toxicology
- Shenzhen Prevention and Treatment Center for Occupational Diseases
- Shenzhen
- China
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases
- Shenzhen Prevention and Treatment Center for Occupational Diseases
- Shenzhen
- China
| | - Lisa Liu
- Institute of Translational Medicine
- Shenzhen Second People's Hospital
- Shenzhen
- China
| | - Nai-xing Zhang
- National Key Clinical Specialty of Occupational Diseases
- Shenzhen Prevention and Treatment Center for Occupational Diseases
- Shenzhen
- China
| | - Chao-xian Gao
- Department of Pathology & Toxicology
- Shenzhen Prevention and Treatment Center for Occupational Diseases
- Shenzhen
- China
| | - Xue-qin Yang
- Department of Pathology & Toxicology
- Shenzhen Prevention and Treatment Center for Occupational Diseases
- Shenzhen
- China
| | - Juan Yi
- Department of Pathology & Toxicology
- Shenzhen Prevention and Treatment Center for Occupational Diseases
- Shenzhen
- China
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Differential protein profiling of soil diazotroph Rhodococcus qingshengii S10107 towards low-temperature and nitrogen deficiency. Sci Rep 2019; 9:20378. [PMID: 31889061 PMCID: PMC6937269 DOI: 10.1038/s41598-019-56592-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023] Open
Abstract
Protein-based biomarkers can be a promising approach for identification and real-time monitoring of the bio-inoculants employed under sustainable agricultural plans. In this perspective, differential proteomics of psychrophilic diazotroph Rhodococcus qingshengii S10107 (JX173283) was performed to unravel its adaptive responses towards low-temperature nitrogen deficiency and identification of a biomarker for respective physiological conditions. LC-MS/MS-based proteome analysis mapped more than 4830 proteins including 77 up-regulated and 47 down-regulated proteins (p ≤ 0.05). Differential expression of the structural genes of nif regulon viz. nifH, nifD, and nifK along with their response regulators i.e. nifA, nifL, and nifB indicated that the nitrogenase complex was activated successfully. Besides up-regulating the biosynthesis of certain amino acids viz. Leucine, Lysine, and Alanine; the expression of the peptidoglycan synthesis proteins were also increased; while, the enzymes involved in Lipid biosynthesis were found to decrease. Furthermore, two important enzymes of the pentose phosphate pathway viz. Transketolase and Transaldolase along with Ribose import ATP-binding protein RbsA were also found to induce significantly under low temperature a nitrogen deficient condition, which suggests the cellular need for ample ribose sugar instantly. Additionally, comparative protein profiling of S10107 strain with our previous studies revealed that CowN protein was significantly up-regulated in all the cases under low-temperature nitrogen deficient conditions and therefore, can be developed as a biomarker. Conclusively, present study for the first time provides an in-depth proteome profiling of R. qingshengii S10107 and proclaims CowN as a potential protein biomarker for monitoring BNF under cold niches.
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Ma C, Li J, Zhang B, Liu C, Zhang J, Liu Y. Hydrogel Microparticles Functionalized with Engineered Escherichia coli as Living Lactam Biosensors. SENSORS 2019; 19:s19245556. [PMID: 31888205 PMCID: PMC6960487 DOI: 10.3390/s19245556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/26/2022]
Abstract
Recently there has been an increasing need for synthesizing valued chemicals through biorefineries. Lactams are an essential family of commodity chemicals widely used in the nylon industry with annual production of millions of tons. The bio-production of lactams can substantially benefit from high-throughput lactam sensing strategies for lactam producer screening. We present here a robust and living lactam biosensor that is directly compatible with high-throughput analytical means. The biosensor is a hydrogel microparticle encapsulating living microcolonies of engineered lactam-responsive Escherichia coli. The microparticles feature facile and ultra-high throughput manufacturing of up to 10,000,000 per hour through droplet microfluidics. We show that the biosensors can specifically detect major lactam species in a dose-dependent manner, which can be quantified using flow cytometry. The biosensor could potentially be used for high-throughput metabolic engineering of lactam biosynthesis.
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Affiliation(s)
- Conghui Ma
- Materials and Physical Biology Division, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China; (C.M.); (J.L.); (B.Z.); (C.L.)
| | - Jie Li
- Materials and Physical Biology Division, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China; (C.M.); (J.L.); (B.Z.); (C.L.)
| | - Boyin Zhang
- Materials and Physical Biology Division, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China; (C.M.); (J.L.); (B.Z.); (C.L.)
| | - Chenxi Liu
- Materials and Physical Biology Division, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China; (C.M.); (J.L.); (B.Z.); (C.L.)
| | - Jingwei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- Correspondence: (J.Z.); (Y.L.)
| | - Yifan Liu
- Materials and Physical Biology Division, School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China; (C.M.); (J.L.); (B.Z.); (C.L.)
- Correspondence: (J.Z.); (Y.L.)
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Lopreside A, Wan X, Michelini E, Roda A, Wang B. Comprehensive Profiling of Diverse Genetic Reporters with Application to Whole-Cell and Cell-Free Biosensors. Anal Chem 2019; 91:15284-15292. [PMID: 31690077 PMCID: PMC6899433 DOI: 10.1021/acs.analchem.9b04444] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Whole-cell
and cell-free transcription-translation biosensors have
recently become favorable alternatives to conventional detection methods,
as they are cost-effective, environmental friendly, and easy to use.
Importantly, the biological responses from the biosensors need to
be converted into a physicochemical signal for easy detection, and
a variety of genetic reporters have been employed for this purpose.
Reporter gene selection is vital to a sensor performance and application
success. However, it was largely based on trial and error with very
few systematic side-by-side investigations reported. To address this
bottleneck, here we compared eight reporters from three reporter categories,
i.e., fluorescent (gfpmut3, deGFP, mCherry, mScarlet-I), colorimetric
(lacZ), and bioluminescent (luxCDABE from Aliivibrio fischeri and Photorhabdus
luminescens, NanoLuc) reporters, under the
control of two representative biosensors for mercury- and quorum-sensing
molecules. Both whole-cell and cell-free formats were investigated
to assess key sensing features including limit of detection (LOD),
input and output dynamic ranges, response time, and output visibility.
For both whole-cell biosensors, the lowest detectable concentration
of analytes and the fastest responses were achieved with NanoLuc.
Notably, we developed, to date, the most sensitive whole-cell mercury
biosensor using NanoLuc as reporter, with an LOD ≤ 50.0 fM
HgCl2 30 min postinduction. For cell-free biosensors, overall, NanoLuc and deGFP led to shorter response
time and lower LOD than the others. This comprehensive profile of
diverse reporters in a single setting provides a new important benchmark
for reporter selection, aiding the rapid development of whole-cell
and cell-free biosensors for various applications in the environment
and health.
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Affiliation(s)
- Antonia Lopreside
- Department of Chemistry "G. Ciamician", Alma Mater Studiorum , University of Bologna , 40126 Bologna , Italy
| | | | - Elisa Michelini
- Department of Chemistry "G. Ciamician", Alma Mater Studiorum , University of Bologna , 40126 Bologna , Italy
| | - Aldo Roda
- Department of Chemistry "G. Ciamician", Alma Mater Studiorum , University of Bologna , 40126 Bologna , Italy
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Engineered cells for selective detection and remediation of Hg2+ based on transcription factor MerR regulated cell surface displayed systems. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107289] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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50
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Wang D, Zheng Y, Fan X, Xu L, Pang T, Liu T, Liang L, Huang S, Xiao Q. Visual detection of Hg 2+ by manipulation of pyocyanin biosynthesis through the Hg 2+-dependent transcriptional activator MerR in microbial cells. J Biosci Bioeng 2019; 129:223-228. [PMID: 31492609 DOI: 10.1016/j.jbiosc.2019.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 01/16/2023]
Abstract
Mercury pollution has always been a huge threat to human health due to its significant toxicity. Thus, it's the continuing goal to obtain new mercury detection techniques that are cost-effective, operational stable, performance efficient, and applicable to the environmental and biological milieus. In this research, the soluble pigment pyocyanin with anti-bacterial and anti-fungal activities, the biosynthesis pathway of which was engineered under the regulation of Hg2+-dependent transcriptional activator MerR, was firstly used as the visual detection signal in the whole-cell biosensor. The engineered biosensor displayed optical sensing window and a good linearity for Hg2+ in the range of 25-1000 nM, and the detection limit could reach as low as 10 nM. It permitted on-site detection of bioavailable Hg2+ with extraordinary selectivity and could resist the interferences of extra metal ions. What's more, the developed biosensor performed function well in a wide pH range (pH 4-10) as well as the environmental water. By fully imitating and utilizing the biosystems from nature, the engineered colorimetric biosensor has great economic and performance advantages over most chemosensors as well as whole-cell biosensors in the practical application of detecting Hg2+ in the contaminated aquatic systems.
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Affiliation(s)
- Dan Wang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, PR China.
| | - Yanan Zheng
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, PR China
| | - Xiaosu Fan
- Experimental Center of College of Agriculture, Guangxi University, Nanning 530005, PR China
| | - Lina Xu
- Institute of Chemical Industry of Forestry Products, CAF, Nanjing 210042, PR China
| | - Ting Pang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, PR China
| | - Ting Liu
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, PR China
| | - Legui Liang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, PR China
| | - Shan Huang
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, PR China
| | - Qi Xiao
- College of Chemistry and Materials, Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, Nanning Normal University, Nanning 530001, PR China
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