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Leburu E, Qiao Y, Wang Y, Yang J, Liang S, Yu W, Yuan S, Duan H, Huang L, Hu J, Hou H. Flexible electronics for heavy metal ion detection in water: a comprehensive review. Biomed Microdevices 2024; 26:30. [PMID: 38913209 DOI: 10.1007/s10544-024-00710-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2024] [Indexed: 06/25/2024]
Abstract
Flexible electronics offer a versatile, rapid, cost-effective and portable solution to monitor water contamination, which poses serious threat to the environment and human health. This review paper presents a comprehensive exploration of the versatile platforms of flexible electronics in the context of heavy metal ion detection in water systems. The review overviews of the fundamental principles of heavy metal ion detection, surveys the state-of-the-art materials and fabrication techniques for flexible sensors, analyses key performance metrics and limitations, and discusses future opportunities and challenges. By highlighting recent advances in nanomaterials, polymers, wireless integration, and sustainability, this review aims to serve as an essential resource for researchers, engineers, and policy makers seeking to address the critical challenge of heavy metal contamination in water resources. The versatile promise of flexible electronics is thoroughly elucidated to inspire continued innovation in this emerging technology arena.
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Affiliation(s)
- Ely Leburu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Yuting Qiao
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Yanshen Wang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Jiakuan Yang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
- State Key Laboratory of Coal Combustion, Huazhong University of Science of and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
| | - Sha Liang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Wenbo Yu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Shushan Yuan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Huabo Duan
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Liang Huang
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China
| | - Jingping Hu
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China.
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China.
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China.
- State Key Laboratory of Coal Combustion, Huazhong University of Science of and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China.
| | - Huijie Hou
- School of Environmental Science and Engineering, Huazhong University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, P.R. China.
- Hubei Provincial Engineering Laboratory of Solid Waste Treatment, Disposal and Recycling, 1037 Luoyu Road, Wuhan, 430074, P.R. China.
- Hubei Key Laboratory of Multi-media Pollution Cooperative Control in Yangtze Basin, School of University of Science and Technology (HUST), 1037 Luoyu Road, Wuhan, 430074, China.
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Wei Y, Shi D, Chen T, Zhou S, Yang Z, Li H, Yang D, Li J, Jin M. CRISPR/Cas9-based engineered Escherichia coli biosensor for sensitive and specific detection of Cd(II) in drinking water. CHEMOSPHERE 2024; 362:142607. [PMID: 38876330 DOI: 10.1016/j.chemosphere.2024.142607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
Cadmium (Cd) is a ubiquitous pollutant that poses a potential threat to human health. Monitoring Cd(II) in drinking water has significant implications for preventing potential threats of Cd(II) to human. However, the weak signal output and response to nontarget interference limit the detection of Cd(II) using bacterial biosensors. In this study, to enable sensitive and specific detection of Cd(II) in water, a stable whole-cell biosensor, K12-PMP-luxCDABE-△cysI, was constructed in a dual-promoter mode by fusing the mercury promoter Pmer, regulatory gene merR(m), and luciferase gene luxCDABE into the E.coli chromosome based on CRISPR/Cas9 gene editing technology. By knocking out the cadmium-resistance-gene cysI, the sensitivity of the biosensor to Cd(II) was further enhanced. The constructed E. coli biosensor K12-PMP-luxCDABE-△cysI exhibited good nonlinear responses to 0.005-2 mg/L Cd(II). Notably, among the three constructed E. coli biosensor, it exhibited the strongest fluorescence intensity, with the limit of detection meeting the allowable limit for Cd(II) in drinking water. Simultaneously, it could specifically detect Cd(II). Nontarget metal ions, such as Zn(II), Hg(II), and Pb(II), did not affect its performance. Furthermore, it exhibited superior performance in detecting Cd(II) in real drinking water samples by avoiding background interference, and showed excellent stability with the relative standard deviation under 5%. Thus, K12-PMP-luxCDABE-△cysI holds promise as a potential tool for the detection of Cd(II) in drinking water.
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Affiliation(s)
- Yijun Wei
- Military Medical Sciences Academy, Academy of Military Sciences
| | - Danyang Shi
- Military Medical Sciences Academy, Academy of Military Sciences
| | - Tianjiao Chen
- Military Medical Sciences Academy, Academy of Military Sciences
| | - Shuqing Zhou
- Military Medical Sciences Academy, Academy of Military Sciences
| | - Zhongwei Yang
- Military Medical Sciences Academy, Academy of Military Sciences
| | - Haibei Li
- Military Medical Sciences Academy, Academy of Military Sciences
| | - Dong Yang
- Military Medical Sciences Academy, Academy of Military Sciences
| | - Junwen Li
- Military Medical Sciences Academy, Academy of Military Sciences
| | - Min Jin
- Military Medical Sciences Academy, Academy of Military Sciences.
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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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Kalvapalle PB, Sridhar S, Silberg JJ, Stadler LB. Long-duration environmental biosensing by recording analyte detection in DNA using recombinase memory. Appl Environ Microbiol 2024; 90:e0236323. [PMID: 38551351 PMCID: PMC11022584 DOI: 10.1128/aem.02363-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/20/2024] [Indexed: 04/18/2024] Open
Abstract
Microbial biosensors that convert environmental information into real-time visual outputs are limited in their sensing abilities in complex environments, such as soil and wastewater, due to optical inaccessibility. Biosensors that could record transient exposure to analytes within a large time window for later retrieval represent a promising approach to solve the accessibility problem. Here, we test the performance of recombinase-memory biosensors that sense a sugar (arabinose) and a microbial communication molecule (3-oxo-C12-L-homoserine lactone) over 8 days (~70 generations) following analyte exposure. These biosensors sense the analyte and trigger the expression of a recombinase enzyme which flips a segment of DNA, creating a genetic memory, and initiates fluorescent protein expression. The initial designs failed over time due to unintended DNA flipping in the absence of the analyte and loss of the flipped state after exposure to the analyte. Biosensor performance was improved by decreasing recombinase expression, removing the fluorescent protein output, and using quantitative PCR to read out stored information. Application of memory biosensors in wastewater isolates achieved memory of analyte exposure in an uncharacterized Pseudomonas isolate. By returning these engineered isolates to their native environments, recombinase-memory systems are expected to enable longer duration and in situ investigation of microbial signaling, cross-feeding, community shifts, and gene transfer beyond the reach of traditional environmental biosensors.IMPORTANCEMicrobes mediate ecological processes over timescales that can far exceed the half-lives of transient metabolites and signals that drive their collective behaviors. We investigated strategies for engineering microbes to stably record their transient exposure to a chemical over many generations through DNA rearrangements. We identify genetic architectures that improve memory biosensor performance and characterize these in wastewater isolates. Memory biosensors are expected to be useful for monitoring cell-cell signals in biofilms, detecting transient exposure to chemical pollutants, and observing microbial cross-feeding through short-lived metabolites within cryptic methane, nitrogen, and sulfur cycling processes. They will also enable in situ studies of microbial responses to ephemeral environmental changes, or other ecological processes that are currently challenging to monitor non-destructively using real-time biosensors and analytical instruments.
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Affiliation(s)
| | - Swetha Sridhar
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, Texas, USA
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, Texas, USA
- Department of Bioengineering, Rice University, Houston, Texas, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, USA
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas, USA
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Ma BC, Guo Y, Lin YR, Zhang J, Wang XQ, Zhang WQ, Luo JG, Chen YT, Zhang NX, Lu Q, Hui CY. High-throughput screening of human mercury exposure based on a low-cost naked eye-recognized biosensing platform. Biosens Bioelectron 2024; 248:115961. [PMID: 38150800 DOI: 10.1016/j.bios.2023.115961] [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: 10/07/2023] [Revised: 12/05/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
Whole-cell biosensors could be helpful for in situ disease diagnosis. However, their use in analyzing biological samples has been hindered by unstable responses, low signal enhancement, and growth inhibition in complex media. Here, we offered a solution by building a visual whole-cell biosensor for urinary mercury determination. With deoxyviolacein as the preferred signal for the mercury biosensor for the first time, it enabled the quantitative detection of urinary mercury with a favorable linear range from 1.57 to 100 nM. The biosensor can accurately diagnose urine mercury levels exceeding the biological exposure index with 95.8% accuracy. Thus, our study provided a biosensing platform with great potential to serve as a stable, user-friendly, and high-throughput alternative for the daily monitoring or estimating of urinary mercury.
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Affiliation(s)
- Bing-Chan Ma
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China; Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, 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
| | - Juan Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 828 Xinmin Street, Changchun, 130021, China
| | - Xiao-Qiang Wang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China
| | - Wen-Qi Zhang
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China
| | - Jin-Gan Luo
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China
| | - Yu-Ting Chen
- 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.
| | - Qing Lu
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China.
| | - Chang-Ye Hui
- Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Road, Shenzhen, 518020, China.
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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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Biggs BW, de Paz AM, Bhan NJ, Cybulski TR, Church GM, Tyo KEJ. Engineering Ca 2+-Dependent DNA Polymerase Activity. ACS Synth Biol 2023; 12:3301-3311. [PMID: 37856140 DOI: 10.1021/acssynbio.3c00302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Advancements in synthetic biology have provided new opportunities in biosensing, with applications ranging from genetic programming to diagnostics. Next generation biosensors aim to expand the number of accessible environments for measurements, increase the number of measurable phenomena, and improve the quality of the measurement. To this end, an emerging area in the field has been the integration of DNA as an information storage medium within biosensor outputs, leveraging nucleic acids to record the biosensor state over time. However, slow signal transduction steps, due to the time scales of transcription and translation, bottleneck many sensing-DNA recording approaches. DNA polymerases (DNAPs) have been proposed as a solution to the signal transduction problem by operating as both the sensor and responder, but there is presently a lack of DNAPs with functional sensitivity to many desirable target ligands. Here, we engineer components of the Pol δ replicative polymerase complex of Saccharomyces cerevisiae to sense and respond to Ca2+, a metal cofactor relevant to numerous biological phenomena. Through domain insertion and binding site grafting to Pol δ subunits, we demonstrate functional allosteric sensitivity to Ca2+. Together, this work provides an important foundation for future efforts in the development of DNAP-based biosensors.
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Affiliation(s)
- Bradley W Biggs
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexandra M de Paz
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Namita J Bhan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Thaddeus R Cybulski
- Interdepartmental Neuroscience Program, Northwestern University, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Keith E J Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
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Zhang C, Liu H, Li X, Xu F, Li Z. Modularized synthetic biology enabled intelligent biosensors. Trends Biotechnol 2023; 41:1055-1065. [PMID: 36967259 DOI: 10.1016/j.tibtech.2023.03.005] [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: 12/29/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023]
Abstract
Biosensors that sense the concentration of a specified target and produce a specific signal output have become important technology for biological analysis. Recently, intelligent biosensors have received great interest due to their adaptability to meet sophisticated demands. Advances in developing standard modules and carriers in synthetic biology have shed light on intelligent biosensors that can implement advanced analytical processing to better accommodate practical applications. This review focuses on intelligent synthetic biology-enabled biosensors (SBBs). First, we illustrate recent progress in intelligent SBBs with the capability of computation, memory storage, and self-calibration. Then, we discuss emerging applications of SBBs in point-of-care testing (POCT) and wearable monitoring. Finally, future perspectives on intelligent SBBs are proposed.
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Affiliation(s)
- Chao Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Hao Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China
| | - Xiujun Li
- Department of Chemistry and Biochemistry, University of Texas at El Paso, 500 West University Ave, El Paso, TX 79968, USA
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China.
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P.R. China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, P.R. China; TFX Group-Xi'an Jiaotong University Institute of Life Health, Xi'an 710049, P.R. China.
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Imran M, Ahmed S, Abdullah AZ, Hakami J, Chaudhary AA, Rudayni HA, Khan SUD, Khan A, Basher NS. Nanostructured material-based optical and electrochemical detection of amoxicillin antibiotic. LUMINESCENCE 2023; 38:1064-1086. [PMID: 36378274 DOI: 10.1002/bio.4408] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/19/2022] [Accepted: 11/13/2022] [Indexed: 07/22/2023]
Abstract
The penicillin derivative amoxicillin (AMX) plays an important role in treating various types of infections caused by bacteria. However, excessive use of AMX may have negative health effects. Therefore, it is of utmost importance to detect and quantify the AMX in pharmaceutical drugs, biological fluids, and environmental samples with high sensitivity. Therefore, this review article provides valuable and up-to-date information on nanostructured material-based optical and electrochemical sensors to detect AMX in various biological and chemical samples. The role of using different nanostructured materials on the performance of important optical sensors such as colorimetric sensors, fluorescence sensors, surface-enhanced Raman scattering sensors, chemiluminescence/electroluminescence sensors, optical immunosensors, optical fibre-based sensors, and several important electrochemical sensors based on different electrode types have been discussed. Moreover, nanocomposites, polymer, and MXenes-based electrochemical sensors have also been discussed, in which such materials are being used to further enhance the sensitivity of these sensors. Furthermore, nanocomposite-based photo-electrochemical sensors and the market availability of biosensors including AMX have also been discussed briefly. Finally, the conclusion, challenges, and future perspectives of the above-mentioned sensing techniques for AMX detection are presented.
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Affiliation(s)
- Mohd Imran
- Department of Chemical Engineering, College of Engineering, Jazan University, P.O. Box. 706, Jazan, Saudi Arabia
- School of Chemical Engineering, Universiti Sains Malaysia, Engineering Campus, Nibong Tebal, Penang, Malaysia
| | - Shahzad Ahmed
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Ahmad Zuhairi Abdullah
- School of Chemical Engineering, Universiti Sains Malaysia, Engineering Campus, Nibong Tebal, Penang, Malaysia
| | - Jabir Hakami
- Department of Physics, College of Science, Jazan University, P.O. Box. 114, Jazan, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Hassan Ahmad Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Afzal Khan
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou, China
| | - Nosiba Suliman Basher
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
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10
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Meyer L, Guyot S, Chalot M, Capelli N. The potential of microorganisms as biomonitoring and bioremediation tools for mercury-contaminated soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115185. [PMID: 37385017 DOI: 10.1016/j.ecoenv.2023.115185] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/20/2023] [Accepted: 06/24/2023] [Indexed: 07/01/2023]
Abstract
Mercury (Hg) pollution is a global issue due to the high toxicity and wide dispersion of Hg around the world. Whether due to anthropogenic activities or natural processes, Hg emissions are steadily increasing, with very high levels in some regions, directly threatening human and ecosystem health. However, bacteria and fungi have evolved and adapted in response to Hg-induced stress and have developed tolerance mechanisms, notably based on the mer operon system that is involved in Hg uptake and biovolatilization via Hg reduction reactions. Other processes, such as bioaccumulation or extracellular sequestration, are involved in Hg resistance, and the study of contaminated soils has allowed the isolation of a number of microorganisms capable of these mechanisms, with strong potential for the implementation of bioremediation approaches. In addition to playing an important role in determining the fate of Hg in the biogeochemical cycle, these microorganisms can indeed be applied to reduce Hg concentrations or at least stabilize Hg for the remediation of polluted soils. Moreover, thanks to the development of biotechnological tools, bioremediation based on Hg-tolerant microorganisms can be optimized. Finally, these microorganisms are relevant candidates for biomonitoring, for example, through the engineering of biosensors, because the detection of Hg is a major issue in preserving the health of living beings.
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Affiliation(s)
- Lorraine Meyer
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France
| | - Stéphane Guyot
- Université de Bourgogne, Institut Agro, PAM UMR A 02.102, F-21000 Dijon, France
| | - Michel Chalot
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France; Université de Lorraine, F-54000 Nancy, France
| | - Nicolas Capelli
- Chrono-environnement UMR 6249, Université de Franche-Comté CNRS, F-25000 Besançon, France.
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11
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Yang K, Lu ZJ, Zhu TY, Wang JX, Yang FQ, Abbas SZ, Zhou J, Yang Z, Mi JL, Ravi SK, Yong YC. Tailoring the whole-cell sensing spectrum with cyborgian redox machinery. Anal Chim Acta 2023; 1252:341046. [PMID: 36935150 DOI: 10.1016/j.aca.2023.341046] [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: 01/05/2023] [Revised: 02/18/2023] [Accepted: 03/03/2023] [Indexed: 03/06/2023]
Abstract
Whole-cell biosensors are an important class of analytical tools that offer the advantages of low cost, facile operation, and unique reproduction/regeneration ability. However, it has always been quite challenging to expand the sensing spectrum of the host. Here, a new approach to extend the cell sensing spectrum with biomineralized nanoparticles is developed. The nano-biohybrid design comprise biomineralized FeS nanoparticles firmly anchored onto the bacterium, Shewanella oneidensis MR-1, wherein the nanoparticles are wired to the cellular electron transfer machinery (MtrCAB/OmcA) of the bacterium, forming an artificial cyborgian redox machinery consisting of FeS-MtrCAB/OmcA-FccA. Strikingly, with this cyborgian redox machinery, the sensing spectrum of FeS hybridized S. oneidensis MR-1 cell is successfully expanded to enable whole-cell electrochemical detection of Vitamin B12, while an unhybridized native cell is incapable of sensing. This proof-of-concept nano-biohybrid design offers a new perspective on manipulating the microbial toolkit for an expanded sensing spectrum in whole-cell biosensors.
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Affiliation(s)
- Kai Yang
- Biofuels Institute, Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Emergency Management & School of Environment and Safety Engineering, Zhenjiang, 212013, Jiangsu Province, China
| | - Zi-Jie Lu
- Biofuels Institute, Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Emergency Management & School of Environment and Safety Engineering, Zhenjiang, 212013, Jiangsu Province, China
| | - Tian-Yu Zhu
- Biofuels Institute, Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Emergency Management & School of Environment and Safety Engineering, Zhenjiang, 212013, Jiangsu Province, China
| | - Jing-Xian Wang
- Biofuels Institute, Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Emergency Management & School of Environment and Safety Engineering, Zhenjiang, 212013, Jiangsu Province, China
| | - Fu-Qiao Yang
- Biofuels Institute, Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Emergency Management & School of Environment and Safety Engineering, Zhenjiang, 212013, Jiangsu Province, China
| | - Syed Zaghum Abbas
- Biofuels Institute, Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Emergency Management & School of Environment and Safety Engineering, Zhenjiang, 212013, Jiangsu Province, China
| | - Jun Zhou
- Bioenergy Research Institute, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu Province, China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Milton Keynes, MK43 0AL, United Kingdom
| | - Jian-Li Mi
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu Province, China
| | - Sai Kishore Ravi
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong Special Administrative Region of China
| | - Yang-Chun Yong
- Biofuels Institute, Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, School of Emergency Management & School of Environment and Safety Engineering, Zhenjiang, 212013, Jiangsu Province, China.
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12
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Ghataora JS, Gebhard S, Reeksting BJ. Chimeric MerR-Family Regulators and Logic Elements for the Design of Metal Sensitive Genetic Circuits in Bacillus subtilis. ACS Synth Biol 2023; 12:735-749. [PMID: 36629785 PMCID: PMC10028694 DOI: 10.1021/acssynbio.2c00545] [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: 01/12/2023]
Abstract
Whole-cell biosensors are emerging as promising tools for monitoring environmental pollutants such as heavy metals. These sensors constitute a genetic circuit comprising a sensing module and an output module, such that a detectable signal is produced in the presence of the desired analyte. The MerR family of metal-responsive regulators offers great potential for the construction of metal sensing circuits, due to their high sensitivity, tight transcription control, and large diversity in metal-specificity. However, the sensing diversity is broadest in Gram-negative systems, while chassis organisms are often selected from Gram-positive species, particularly sporulating bacilli. This can be problematic, because Gram-negative biological parts, such as promoters, are frequently observed to be nonfunctional in Gram-positive hosts. Herein, we combined construction of synthetic genetic circuits and chimeric MerR regulators, supported by structure-guided design, to generate metal-sensitive biosensor modules that are functional in the biotechnological work-horse species Bacillus subtilis. These chimeras consist of a constant Gram-positive derived DNA-binding domain fused to variable metal binding domains of Gram-negative origins. To improve the specificity of the whole-cell biosensor, we developed a modular "AND gate" logic system based on the B. subtilis two-subunit σ-factor, SigO-RsoA, designed to maximize future use for synthetic biology applications in B. subtilis. This work provides insights into the use of modular regulators, such as the MerR family, in the design of synthetic circuits for the detection of heavy metals, with potentially wider applicability of the approach to other systems and genetic backgrounds.
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Affiliation(s)
- Jasdeep S Ghataora
- Life Sciences Department, Milner Centre for Evolution, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Susanne Gebhard
- Life Sciences Department, Milner Centre for Evolution, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Bianca J Reeksting
- Life Sciences Department, Milner Centre for Evolution, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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13
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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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14
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Thai TD, Lim W, Na D. Synthetic bacteria for the detection and bioremediation of heavy metals. Front Bioeng Biotechnol 2023; 11:1178680. [PMID: 37122866 PMCID: PMC10133563 DOI: 10.3389/fbioe.2023.1178680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Toxic heavy metal accumulation is one of anthropogenic environmental pollutions, which poses risks to human health and ecological systems. Conventional heavy metal remediation approaches rely on expensive chemical and physical processes leading to the formation and release of other toxic waste products. Instead, microbial bioremediation has gained interest as a promising and cost-effective alternative to conventional methods, but the genetic complexity of microorganisms and the lack of appropriate genetic engineering technologies have impeded the development of bioremediating microorganisms. Recently, the emerging synthetic biology opened a new avenue for microbial bioremediation research and development by addressing the challenges and providing novel tools for constructing bacteria with enhanced capabilities: rapid detection and degradation of heavy metals while enhanced tolerance to toxic heavy metals. Moreover, synthetic biology also offers new technologies to meet biosafety regulations since genetically modified microorganisms may disrupt natural ecosystems. In this review, we introduce the use of microorganisms developed based on synthetic biology technologies for the detection and detoxification of heavy metals. Additionally, this review explores the technical strategies developed to overcome the biosafety requirements associated with the use of genetically modified microorganisms.
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15
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Usai F, Loi G, Scocozza F, Bellato M, Castagliuolo I, Conti M, Pasotti L. Design and biofabrication of bacterial living materials with robust and multiplexed biosensing capabilities. Mater Today Bio 2022; 18:100526. [PMID: 36632629 PMCID: PMC9826803 DOI: 10.1016/j.mtbio.2022.100526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
The intertwined adoption of synthetic biology and 3D bioprinting has the potential to improve different application fields by fabricating engineered living materials (ELMs) with unnatural genetically-encoded sense & response capabilities. However, efforts are still needed to streamline the fabrication of sensing ELMs compatible with field use and improving their functional complexity. To investigate these two unmet needs, we adopted a workflow to reproducibly construct bacterial ELMs with synthetic biosensing circuits that provide red pigmentation as visible readout in response to different proof-of-concept chemical inducers. We first fabricated single-input/single-output ELMs and we demonstrated their robust performance in terms of longevity (cell viability and evolutionary stability >15 days, and long-term storage >1 month), sensing in harsh, non-sterile or nutrient-free conditions compatible with field use (soil, water, and clinical samples, including real samples from Pseudomonas aeruginosa infected patients). Then, we fabricated ELMs including multiple spatially-separated biosensor strains to engineer: level-bar materials detecting molecule concentration ranges, multi-input/multi-output devices with multiplexed sensing and information processing capabilities, and materials with cell-cell communication enabling on-demand pattern formation. Overall, we showed successful field use and multiplexed functioning of reproducibly fabricated ELMs, paving the way to a future automation of the prototyping process and boosting applications of such devices as in-situ monitoring tools or easy-to-use sensing kits.
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Affiliation(s)
- Francesca Usai
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy
| | - Giada Loi
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy
| | - Franca Scocozza
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy
| | - Massimo Bellato
- Department of Information Engineering, University of Padua, Via Gradenigo 6b, 35131 Padua, Italy
| | - Ignazio Castagliuolo
- Department of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Michele Conti
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy,Corresponding author.
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Via Ferrata 5, 27100, Pavia, Italy,Corresponding author.
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16
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Chemla Y, Dorfan Y, Yannai A, Meng D, Cao P, Glaven S, Gordon DB, Elbaz J, Voigt CA. Parallel engineering of environmental bacteria and performance over years under jungle-simulated conditions. PLoS One 2022; 17:e0278471. [PMID: 36516154 PMCID: PMC9750038 DOI: 10.1371/journal.pone.0278471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Engineered bacteria could perform many functions in the environment, for example, to remediate pollutants, deliver nutrients to crops or act as in-field biosensors. Model organisms can be unreliable in the field, but selecting an isolate from the thousands that naturally live there and genetically manipulating them to carry the desired function is a slow and uninformed process. Here, we demonstrate the parallel engineering of isolates from environmental samples by using the broad-host-range XPORT conjugation system (Bacillus subtilis mini-ICEBs1) to transfer a genetic payload to many isolates in parallel. Bacillus and Lysinibacillus species were obtained from seven soil and water samples from different locations in Israel. XPORT successfully transferred a genetic function (reporter expression) into 25 of these isolates. They were then screened to identify the best-performing chassis based on the expression level, doubling time, functional stability in soil, and environmentally-relevant traits of its closest annotated reference species, such as the ability to sporulate and temperature tolerance. From this library, we selected Bacillus frigoritolerans A3E1, re-introduced it to soil, and measured function and genetic stability in a contained environment that replicates jungle conditions. After 21 months of storage, the engineered bacteria were viable, could perform their function, and did not accumulate disruptive mutations.
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Affiliation(s)
- Yonatan Chemla
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yuval Dorfan
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Adi Yannai
- School of Molecular Cell Biology & Biotechnology, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Dechuan Meng
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Paul Cao
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sarah Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, United States of America
| | - D. Benjamin Gordon
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Johann Elbaz
- School of Molecular Cell Biology & Biotechnology, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Christopher A. Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail:
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17
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Atkinson JT, Su L, Zhang X, Bennett GN, Silberg JJ, Ajo-Franklin CM. Real-time bioelectronic sensing of environmental contaminants. Nature 2022; 611:548-553. [DOI: 10.1038/s41586-022-05356-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 09/15/2022] [Indexed: 11/07/2022]
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18
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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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19
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Application study of RGB color extraction in water toxicity detection. Bioelectrochemistry 2022; 149:108270. [DOI: 10.1016/j.bioelechem.2022.108270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/21/2022]
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20
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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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21
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Delatour E, Pagnout C, Zaffino ML, Duval JFL. Comparative Analysis of Cell Metabolic Activity Sensing by Escherichia coli rrnB P1-lux and Cd Responsive-Lux Biosensors: Time-Resolved Experiments and Mechanistic Modelling. BIOSENSORS 2022; 12:763. [PMID: 36140148 PMCID: PMC9496673 DOI: 10.3390/bios12090763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Whole-cell bacterial sensors are used in medical/environmental applications to detect chemicals, and to assess medium toxicity or stress. Non-specific constitutive biosensors generally serve the latter purpose, whereas chemical detection is performed with biosensors involving a specific chemical-inducible promoter. Herein, we show that functioning principles of specific and non-specific whole-cell biosensors are not exclusive as both can probe modulations of cell metabolic activity under stressing conditions. The demonstration is based on (i) time-resolved measurements of bioluminescence produced by constitutive rrnB P1-luxCDABE Escherichia coli biosensor in media differing with respect to carbon source, (ii) theoretical reconstruction of the measured signals using a here-reported theory for bioluminescence generated by constitutive cells, (iii) comparison between time-dependent cell photoactivity (reflecting metabolic activity) retrieved by theory with that we reported recently for cadmium-inducible PzntA-luxCDABE E. coli in media of similar compositions. Whereas signals of constitutive and non-constitutive biosensors differ in terms of shape, amplitude and peak number depending on nutritional medium conditions, analysis highlights the features shared by their respective cell photoactivity patterns mediated by the interplay between stringent response and catabolite repressions. The work advocates for the benefits of a theoretical interpretation for the time-dependent response of biosensors to unravel metabolic and physicochemical contributions to the bioluminescence signal.
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Affiliation(s)
- Eva Delatour
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Christophe Pagnout
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Marie L. Zaffino
- Université de Lorraine, CNRS, LIEC (Laboratoire Interdisciplinaire des Environnements Continentaux), UMR7360, Campus Bridoux, F-57070 Metz, France
| | - Jérôme F. L. Duval
- Université de Lorraine, CNRS, LIEC, UMR7360, F-54501 Vandoeuvre-lès-Nancy, France
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22
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Hui Y, Huang Z, Alahi MEE, Nag A, Feng S, Mukhopadhyay SC. Recent Advancements in Electrochemical Biosensors for Monitoring the Water Quality. BIOSENSORS 2022; 12:bios12070551. [PMID: 35884353 PMCID: PMC9313366 DOI: 10.3390/bios12070551] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/10/2022] [Accepted: 07/13/2022] [Indexed: 05/06/2023]
Abstract
The release of chemicals and microorganisms from various sources, such as industry, agriculture, animal farming, wastewater treatment plants, and flooding, into water systems have caused water pollution in several parts of our world, endangering aquatic ecosystems and individual health. World Health Organization (WHO) has introduced strict standards for the maximum concentration limits for nutrients and chemicals in drinking water, surface water, and groundwater. It is crucial to have rapid, sensitive, and reliable analytical detection systems to monitor the pollution level regularly and meet the standard limit. Electrochemical biosensors are advantageous analytical devices or tools that convert a bio-signal by biorecognition elements into a significant electrical response. Thanks to the micro/nano fabrication techniques, electrochemical biosensors for sensitive, continuous, and real-time detection have attracted increasing attention among researchers and users worldwide. These devices take advantage of easy operation, portability, and rapid response. They can also be miniaturized, have a long-life span and a quick response time, and possess high sensitivity and selectivity and can be considered as portable biosensing assays. They are of special importance due to their great advantages such as affordability, simplicity, portability, and ability to detect at on-site. This review paper is concerned with the basic concepts of electrochemical biosensors and their applications in various water quality monitoring, such as inorganic chemicals, nutrients, microorganisms' pollution, and organic pollutants, especially for developing real-time/online detection systems. The basic concepts of electrochemical biosensors, different surface modification techniques, bio-recognition elements (BRE), detection methods, and specific real-time water quality monitoring applications are reviewed thoroughly in this article.
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Affiliation(s)
- Yun Hui
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Zhaoling Huang
- School of Mechanical and Electrical Engineering, Guilin University of Electronic Technology, Guilin 541004, China;
| | - Md Eshrat E. Alahi
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
- Correspondence: (M.E.E.A.); (S.F.)
| | - Anindya Nag
- Faculty of Electrical and Computer Engineering, Technische Universität Dresden, 01062 Dresden, Germany;
- Centre for Tactile Internet with Human-in-the-Loop (CeTI), Technische Universität Dresden, 01069 Dresden, Germany
| | - Shilun Feng
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
- Correspondence: (M.E.E.A.); (S.F.)
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23
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Cai Y, Zhu K, Shen L, Ma J, Bao L, Chen D, Wei L, Wei N, Liu B, Wu Y, Chen S. Evolved Biosensor with High Sensitivity and Specificity for Measuring Cadmium in Actual Environmental Samples. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:10062-10071. [PMID: 35762704 DOI: 10.1021/acs.est.2c00627] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial biosensors have great potential in contaminant detection for sensitivity, specificity, cost-effectiveness, and easy operation. However, the existing cadmium-responsive bacterial biosensors cannot meet the real-world detection requirements due to lack of sensitivity, specificity, and anti-interference capability. This study aimed to develop a bacterial biosensor for detecting the total and extractable cadmium in actual environmental samples. We constructed the cadmium-responsive biosensor with the regulatory element (cadmium resistance transcriptional regulatory, CadR) and the reporting element (GFP) and improved its performance by directed evolution. The mutant libraries of biosensors were generated by error-prone PCR and screened by continuous five-round fluorescence-activated cell sorting (FACS), and a bacteria variant epCadR5 with higher performance was finally isolated. Biosensor fluorescence intensity was measured by a microplate reader, and results showed that the evolved cadmium-responsive bacterial biosensor was of high sensitivity and specificity in detecting trace cadmium, with a detection limit of 0.45 μg/L, which is 6.8 times more specific to cadmium than that of the wild-type. Furthermore, microscopic qualitative analysis results showed that the bacteria could produce fluorescence response in a cadmium-contaminated soil matrix, and quantitative analysis results showed that the values of cadmium from epCadR5 bacteria were close to that from inductively coupled plasma-mass spectrometry. These results suggest that the biosensor may have a broad application prospect in the detection of cadmium-contaminated soil and water.
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Affiliation(s)
- Yeshen Cai
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Kaili Zhu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Liang Shen
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Jie Ma
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Lingzhi Bao
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Dongdong Chen
- Institute of Environmental Physics and Technology, Anhui University, Hefei 230039, China
| | - Liangchen Wei
- School of Public Health, Wannan Medical College, Wuhu 241002, China
| | - Nan Wei
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Binmei Liu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Yuejin Wu
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, 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
- School of Public Health, Wannan Medical College, Wuhu 241002, China
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24
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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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25
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Transcription Factor-Based Biosensors for Detecting Pathogens. BIOSENSORS 2022; 12:bios12070470. [PMID: 35884273 PMCID: PMC9312912 DOI: 10.3390/bios12070470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 12/23/2022]
Abstract
Microorganisms are omnipresent and inseparable from our life. Many of them are beneficial to humans, while some are not. Importantly, foods and beverages are susceptible to microbial contamination, with their toxins causing illnesses and even death in some cases. Therefore, monitoring and detecting harmful microorganisms are critical to ensuring human health and safety. For several decades, many methods have been developed to detect and monitor microorganisms and their toxicants. Conventionally, nucleic acid analysis and antibody-based analysis were used to detect pathogens. Additionally, diverse chromatographic methods were employed to detect toxins based on their chemical and structural properties. However, conventional techniques have several disadvantages concerning analysis time, sensitivity, and expense. With the advances in biotechnology, new approaches to detect pathogens and toxins have been reported to compensate for the disadvantages of conventional analysis from different research fields, including electrochemistry, nanotechnology, and molecular biology. Among them, we focused on the recent studies of transcription factor (TF)-based biosensors to detect microorganisms and discuss their perspectives and applications. Additionally, the other biosensors for detecting microorganisms reported in recent studies were also introduced in this review.
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26
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Re-engineering of CUP1 promoter and Cup2/Ace1 transactivator to convert Saccharomyces cerevisiae into a whole-cell eukaryotic biosensor capable of detecting 10 nM of bioavailable copper. Biosens Bioelectron 2022; 214:114502. [DOI: 10.1016/j.bios.2022.114502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022]
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27
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Hui CY, Guo Y, Li H, Chen YT, Yi J. Differential Detection of Bioavailable Mercury and Cadmium Based on a Robust Dual-Sensing Bacterial Biosensor. Front Microbiol 2022; 13:846524. [PMID: 35495723 PMCID: PMC9043898 DOI: 10.3389/fmicb.2022.846524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/17/2022] [Indexed: 11/22/2022] Open
Abstract
Genetically programmed biosensors have been widely used to monitor bioavailable heavy metal pollutions in terms of their toxicity to living organisms. Most bacterial biosensors were initially designed to detect specific heavy metals such as mercury and cadmium. However, most available biosensors failed to distinguish cadmium from various heavy metals, especially mercury. Integrating diverse sensing elements into a single genetic construct or a single host strain has been demonstrated to quantify several heavy metals simultaneously. In this study, a dual-sensing construct was assembled by employing mercury-responsive regulator (MerR) and cadmium-responsive regulator (CadR) as the separate sensory elements and enhanced fluorescent protein (eGFP) and mCherry red fluorescent protein (mCherry) as the separate reporters. Compared with two corresponding single-sensing bacterial sensors, the dual-sensing bacterial sensor emitted differential double-color fluorescence upon exposure to 0–40 μM toxic Hg(II) and red fluorescence upon exposure to toxic Cd(II) below 200 μM. Bioavailable Hg(II) could be quantitatively determined using double-color fluorescence within a narrow concentration range (0–5 μM). But bioavailable Cd(II) could be quantitatively measured using red fluorescence over a wide concentration range (0–200 μM). The dual-sensing biosensor was applied to detect bioavailable Hg(II) and Cd(II) simultaneously. Significant higher red fluorescence reflected the predominant pollution of Cd(II), and significant higher green fluorescence suggested the predominant pollution of Hg(II). Our findings show that the synergistic application of various sensory modules contributes to an efficient biological device that responds to concurrent heavy metal pollutants in the environment.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology and 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
| | - Han Li
- College of Lab Medicine, Hebei North University, Zhangjiakou, China
| | - Yu-Ting Chen
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Juan Yi
- Department of Pathology and Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
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28
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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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29
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Nasr M, Timmins LR, Martin VJJ, Kwan DH. A Versatile Transcription Factor Biosensor System Responsive to Multiple Aromatic and Indole Inducers. ACS Synth Biol 2022; 11:1692-1698. [PMID: 35316041 PMCID: PMC9017570 DOI: 10.1021/acssynbio.2c00063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Allosteric transcription factor (aTF) biosensors are valuable tools for engineering microbes toward a multitude of applications in metabolic engineering, biotechnology, and synthetic biology. One of the challenges toward constructing functional and diverse biosensors in engineered microbes is the limited toolbox of identified and characterized aTFs. To overcome this, extensive bioprospecting of aTFs from sequencing databases, as well as aTF ligand-specificity engineering are essential in order to realize their full potential as biosensors for novel applications. In this work, using the TetR-family repressor CmeR from Campylobacter jejuni, we construct aTF genetic circuits that function as salicylate biosensors in the model organisms Escherichia coli and Saccharomyces cerevisiae. In addition to salicylate, we demonstrate the responsiveness of CmeR-regulated promoters to multiple aromatic and indole inducers. This relaxed ligand specificity of CmeR makes it a useful tool for detecting molecules in many metabolic engineering applications, as well as a good target for directed evolution to engineer proteins that are able to detect new and diverse chemistries.
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Affiliation(s)
- Mohamed
A. Nasr
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
| | - Logan R. Timmins
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
| | - Vincent J. J. Martin
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
| | - David H. Kwan
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
- Department
of Chemistry and Biochemistry, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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30
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Vaiana CA, Kim H, Cottet J, Oai K, Ge Z, Conforti K, King AM, Meyer AJ, Chen H, Voigt CA, Buie CR. Characterizing chemical signaling between engineered "microbial sentinels" in porous microplates. Mol Syst Biol 2022; 18:e10785. [PMID: 35315586 PMCID: PMC8938921 DOI: 10.15252/msb.202110785] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Living materials combine a material scaffold, that is often porous, with engineered cells that perform sensing, computing, and biosynthetic tasks. Designing such systems is difficult because little is known regarding signaling transport parameters in the material. Here, the development of a porous microplate is presented. Hydrogel barriers between wells have a porosity of 60% and a tortuosity factor of 1.6, allowing molecular diffusion between wells. The permeability of dyes, antibiotics, inducers, and quorum signals between wells were characterized. A “sentinel” strain was constructed by introducing orthogonal sensors into the genome of Escherichia coli MG1655 for IPTG, anhydrotetracycline, L‐arabinose, and four quorum signals. The strain’s response to inducer diffusion through the wells was quantified up to 14 mm, and quorum and antibacterial signaling were measured over 16 h. Signaling distance is dictated by hydrogel adsorption, quantified using a linear finite element model that yields adsorption coefficients from 0 to 0.1 mol m−3. Parameters derived herein will aid the design of living materials for pathogen remediation, computation, and self‐organizing biofilms.
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Affiliation(s)
- Christopher A Vaiana
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hyungseok Kim
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jonathan Cottet
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Keiko Oai
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhifei Ge
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kameron Conforti
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew M King
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam J Meyer
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haorong Chen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cullen R Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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31
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Noori MT, Thatikayala D, Pant D, Min B. A critical review on microbe-electrode interactions towards heavy metal ion detection using microbial fuel cell technology. BIORESOURCE TECHNOLOGY 2022; 347:126589. [PMID: 34929327 DOI: 10.1016/j.biortech.2021.126589] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Implicit interaction of electroactive microbes with solid electrodes is an interesting phenomenon in nature, which supported development of bioelectrochemical systems (BESs), especially the microbial fuel cell (MFCs) for valorization of low-value waste streams into bioelectricity. Intriguingly, the metabolism of interacted microbes with electrode is affected by the microenvironment at electrodes, which influences the current response. For instance, when heavy metal ions (HMIs) are imposed in the medium, the current production decreases due to their intrinsic toxic effect. This event provides an immense opportunity to utilize MFC as a sensor to selectively detect HMIs in the environment, which has been explored vastly in recent decade. In this review, we have concisely discussed the microbial interaction with electrodes and mechanism of detection of HMIs using an MFC. Recent advancement in sensing elements and their application is elaborated with a future perspective section for follow-up research and development in this field.
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Affiliation(s)
- Md Tabish Noori
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Gyeonggi-do 446-701, Republic of Korea
| | - Dayakar Thatikayala
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Gyeonggi-do 446-701, Republic of Korea
| | - Deepak Pant
- Separation & Conversion Technology, Flemish Institute for Technological Research (VITO), Boeretang 200, Mol 2400, Belgium
| | - Booki Min
- Department of Environmental Science and Engineering, Kyung Hee University - Global Campus, Gyeonggi-do 446-701, Republic of Korea.
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32
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Tailoring Escherichia coli Chemotactic Sensing towards Cadmium by Computational Redesign of Ribose-Binding Protein. mSystems 2022; 7:e0108421. [PMID: 35014867 PMCID: PMC8751387 DOI: 10.1128/msystems.01084-21] [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] [Indexed: 11/20/2022] Open
Abstract
Periplasmic binding proteins such as ribose-binding proteins (RBPs) are involved in the bacterial chemotaxis two-component system. RBP selectively identifies and interacts with ribose to induce a conformational change that leads to chemotaxis. Here, we report the development of an engineered Escherichia coli (E. coli) strain expressing a redesigned RBP that can effectively sense cadmium ions and regulate chemotactic movement of cells toward a cadmium ion gradient. RBP was computationally redesigned to bind cadmium ions and produce the conformational change required for chemoreceptor binding. The successful design, CdRBP1, binds to cadmium ions with a dissociation constant of 268 nM. When CdRBP1 was expressed in the periplasmic space of E. coli, the bacteria became live cadmium ion hunters with high selectivity over other divalent metal ions. This work presents an example of making cadmium ions, which are toxic for most organisms, as an attractant to regulate cells movement. Our approach also demonstrates that RBP can be precisely designed to develop metal-detecting living systems for potential applications in synthetic biology and environmental studies. IMPORTANCE Cadmium pollution is one of the major environmental problems due to excessive release and accumulation. New technologies that can auto-detect cadmium ions with good biocompatibility are in urgent need. In this study, we engineered the bacterial chemotaxis system to positively sense cadmium ions by redesigning ribose-binding protein (RBP) to tightly bind cadmium ion and produce the right conformational change for receptor binding and signaling. Our engineered E. coli cells can auto-detect and chase cadmium ions with divalent metal ion selectivity. Many attempts have been carried out to redesign RBP at the ribose binding site with little success. Instead of the ribose binding site, we introduced the cadmium binding site in the opening of the ribose binding pocket by a specially developed computational algorithm. Our design strategy can be applied to engineer live bacteria with autonomous detection and remediation abilities for metal ions or other chemicals in the future.
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33
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Zhang G, Hu S, Jia X. Highly Sensitive Whole-Cell Biosensor for Cadmium Detection Based on a Negative Feedback Circuit. Front Bioeng Biotechnol 2021; 9:799781. [PMID: 34926437 PMCID: PMC8678453 DOI: 10.3389/fbioe.2021.799781] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 01/14/2023] Open
Abstract
Although many whole-cell biosensors (WCBs) for the detection of Cd2+ have been developed over the years, most lack sensitivity and specificity. In this paper, we developed a Cd2+ WCB with a negative feedback amplifier in P. putida KT2440. Based on the slope of the linear detection curve as a measure of sensitivity, WCB with negative feedback amplifier greatly increased the output signal of the reporter mCherry, resulting in 33% greater sensitivity than in an equivalent WCB without the negative feedback circuit. Moreover, WCB with negative feedback amplifier exhibited increased Cd2+ tolerance and a lower detection limit of 0.1 nM, a remarkable 400-fold improvement compared to the WCB without the negative feedback circuit, which is significantly below the World Health Organization standard of 27 nM (0.003 mg/L) for cadmium in drinking water. Due to the superior amplification of the output signal, WCB with negative feedback amplifier can provide a detectable signal in a much shorter time, and a fast response is highly preferable for real field applications. In addition, the WCB with negative feedback amplifier showed an unusually high specificity for Cd2+ compared to other metal ions, giving signals with other metals that were between 17.6 and 41.4 times weaker than with Cd2+. In summary, the negative feedback amplifier WCB designed in this work meets the requirements of Cd2+ detection with very high sensitivity and specificity, which also demonstrates that genetic negative feedback amplifiers are excellent tools for improving the performance of WCBs.
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Affiliation(s)
- Guangbao Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Shuting Hu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
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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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Detection of pks Island mRNAs Using Toehold Sensors in Escherichia coli. Life (Basel) 2021; 11:life11111280. [PMID: 34833155 PMCID: PMC8625898 DOI: 10.3390/life11111280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/14/2022] Open
Abstract
Synthetic biologists have applied biomolecular engineering approaches toward the goal of novel biological devices and have shown progress in diverse areas of medicine and biotechnology. Especially promising is the application of synthetic biological devices towards a novel class of molecular diagnostics. As an example, a de-novo-designed riboregulator called toehold switch, with its programmability and compatibility with field-deployable devices showed promising in vitro applications for viral RNA detection such as Zika and Corona viruses. However, the in vivo application of high-performance RNA sensors remains challenging due to the secondary structure of long mRNA species. Here, we introduced ‘Helper RNAs’ that can enhance the functionality of toehold switch sensors by mitigating the effect of secondary structures around a target site. By employing the helper RNAs, previously reported mCherry mRNA sensor showed improved fold-changes in vivo. To further generalize the Helper RNA approaches, we employed automatic design pipeline for toehold sensors that target the essential genes within the pks island, an important target of biomedical research in connection with colorectal cancer. The toehold switch sensors showed fold-changes upon the expression of full-length mRNAs that apparently depended sensitively on the identity of the gene as well as the predicted local structure within the target region of the mRNA. Still, the helper RNAs could improve the performance of toehold switch sensors in many instances, with up to 10-fold improvement over no helper cases. These results suggest that the helper RNA approaches can further assist the design of functional RNA devices in vivo with the aid of the streamlined automatic design software developed here. Further, our solutions for screening and stabilizing single-stranded region of mRNA may find use in other in vivo mRNA-sensing applications such as cas13 crRNA design, transcriptome engineering, and trans-cleaving ribozymes.
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Beabout K, Bernhards CB, Thakur M, Turner KB, Cole SD, Walper SA, Chávez JL, Lux MW. Optimization of Heavy Metal Sensors Based on Transcription Factors and Cell-Free Expression Systems. ACS Synth Biol 2021; 10:3040-3054. [PMID: 34723503 DOI: 10.1021/acssynbio.1c00331] [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] [Indexed: 02/03/2023]
Abstract
Many bacterial mechanisms for highly specific and sensitive detection of heavy metals and other hazards have been reengineered to serve as sensors. In some cases, these sensors have been implemented in cell-free expression systems, enabling easier design optimization and deployment in low-resource settings through lyophilization. Here, we apply the advantages of cell-free expression systems to optimize sensors based on three separate bacterial response mechanisms for arsenic, cadmium, and mercury. We achieved detection limits below the World Health Organization-recommended levels for arsenic and mercury and below the short-term US Military Exposure Guideline levels for all three. The optimization of each sensor was approached differently, leading to observations useful for the development of future sensors: (1) there can be a strong dependence of specificity on the particular cell-free expression system used, (2) tuning of relative concentrations of the sensing and reporter elements improves sensitivity, and (3) sensor performance can vary significantly with linear vs plasmid DNA. In addition, we show that simply combining DNA for the three sensors into a single reaction enables detection of each target heavy metal without any further optimization. This combined approach could lead to sensors that detect a range of hazards at once, such as a panel of water contaminants or all known variants of a target virus. For low-resource settings, such "all-hazard" sensors in a cheap, easy-to-use format could have high utility.
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Affiliation(s)
- Kathryn Beabout
- UES, Inc., Dayton, Ohio 45432, United States
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Casey B. Bernhards
- Excet, Inc., 6225 Brandon Avenue #360, Springfield, Virginia 22150, United States
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Meghna Thakur
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Kendrick B. Turner
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Stephanie D. Cole
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Scott A. Walper
- Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, D.C. 20375, United States
| | - Jorge L. Chávez
- Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, Ohio 45433, United States
| | - Matthew W. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, 8198 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
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Moraskie M, Roshid MHO, O'Connor G, Dikici E, Zingg JM, Deo S, Daunert S. Microbial whole-cell biosensors: Current applications, challenges, and future perspectives. Biosens Bioelectron 2021; 191:113359. [PMID: 34098470 PMCID: PMC8376793 DOI: 10.1016/j.bios.2021.113359] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/13/2021] [Accepted: 05/15/2021] [Indexed: 12/22/2022]
Abstract
Microbial Whole-Cell Biosensors (MWCBs) have seen rapid development with the arrival of 21st century biological and technological capabilities. They consist of microbial species which produce, or limit the production of, a reporter protein in the presence of a target analyte. The quantifiable signal from the reporter protein can be used to determine the bioavailable levels of the target analyte in a variety of sample types at a significantly lower cost than most widely used and well-established analytical instrumentation. Furthermore, the versatile and robust nature of MWCBs shows great potential for their use in otherwise unavailable settings and environments. While MWCBs have been developed for use in biomedical, environmental, and agricultural monitoring, they still face various challenges before they can transition from the laboratory into industrialized settings like their enzyme-based counterparts. In this comprehensive and critical review, we describe the underlying working principles of MWCBs, highlight developments for their use in a variety of fields, detail challenges and current efforts to address them, and discuss exciting implementations of MWCBs helping redefine what is thought to be possible with this expeditiously evolving technology.
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Affiliation(s)
- Michael Moraskie
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Md Harun Or Roshid
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA
| | - Gregory O'Connor
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sapna Deo
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA; The Dr. John T. Macdonald Foundation Biomedical Nanotechnology Institute - BioNIUM, University of Miami, Miami, FL, 33136, USA; Department of Chemistry, University of Miami, Miami, FL, 33146, USA; The Miami Clinical and Translational Science Institute, University of Miami, Miami, FL, 33146, USA; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, 33146, USA.
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Simple fabrication of a hexagonal prisms with hexagonal pyramid tips V2O5@MOF(V, Co) and its application as electrochemical sensor for Pb2+. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2021.108966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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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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Design and Evaluation of Synthetic RNA-Based Incoherent Feed-Forward Loop Circuits. Biomolecules 2021; 11:biom11081182. [PMID: 34439849 PMCID: PMC8391864 DOI: 10.3390/biom11081182] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/31/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
RNA-based regulators are promising tools for building synthetic biological systems that provide a powerful platform for achieving a complex regulation of transcription and translation. Recently, de novo-designed synthetic RNA regulators, such as the small transcriptional activating RNA (STAR), toehold switch (THS), and three-way junction (3WJ) repressor, have been utilized to construct RNA-based synthetic gene circuits in living cells. In this work, we utilized these regulators to construct type 1 incoherent feed-forward loop (IFFL) circuits in vivo and explored their dynamic behaviors. A combination of a STAR and 3WJ repressor was used to construct an RNA-only IFFL circuit. However, due to the fast kinetics of RNA–RNA interactions, there was no significant timescale difference between the direct activation and the indirect inhibition, that no pulse was observed in the experiments. These findings were confirmed with mechanistic modeling and simulation results for a wider range of conditions. To increase delay in the inhibition pathway, we introduced a protein synthesis process to the circuit and designed an RNA–protein hybrid IFFL circuit using THS and TetR protein. Simulation results indicated that pulse generation could be achieved with this RNA–protein hybrid model, and this was further verified with experimental realization in E. coli. Our findings demonstrate that while RNA-based regulators excel in speed as compared to protein-based regulators, the fast reaction kinetics of RNA-based regulators could also undermine the functionality of a circuit (e.g., lack of significant timescale difference). The agreement between experiments and simulations suggests that the mechanistic modeling can help debug issues and validate the hypothesis in designing a new circuit. Moreover, the applicability of the kinetic parameters extracted from the RNA-only circuit to the RNA–protein hybrid circuit also indicates the modularity of RNA-based regulators when used in a different context. We anticipate the findings of this work to guide the future design of gene circuits that rely heavily on the dynamics of RNA-based regulators, in terms of both modeling and experimental realization.
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41
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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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Jia X, Liu T, Ma Y, Wu K. Construction of cadmium whole-cell biosensors and circuit amplification. Appl Microbiol Biotechnol 2021; 105:5689-5699. [PMID: 34160647 DOI: 10.1007/s00253-021-11403-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/07/2023]
Abstract
Owing to the prevalence of cadmium contamination and its serious hazards, it is important to establish an efficient and low-cost monitoring technique for the detection of the heavy metal cadmium. In this study, we first designed 30 cadmium whole-cell biosensors (WCBs) using different combinations of detection elements, reporting elements, and the host. The best performing WCB KT-5-R with Pseudomonas putida KT2440 as the host and composed of CadR and mCherry was selected for further analysis and engineering. In order to enhance its sensitivity, a positive feedback amplifier was added or the gene dosage of the reporter gene was increased. The WCB with the T7RNAP amplification module, p2T7RNAPmut-68, had the best performance and improved tolerance to cadmium with a detection limit of 0.01 μM, which is the WHO standard. It also showed excellent specificity toward cadmium when assayed with mixed metal ions. This study demonstrated the power of circuit engineering in WCB design and provided valuable insights for the development of other WCBs. KEY POINTS: • KT-5-R was selected after prescreening and engineered for better performance. • Using multi-copy reporters and the T7RNAP amplifier greatly improved the performance. • p2T7RNAPmut-68 had a detection limit of 0.01 μM and improved tolerance to cadmium.
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Affiliation(s)
- Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin University), Tianjin, 300072, People's Republic of China.
| | - Teng Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Yubing Ma
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Kang Wu
- Department of Chemical Engineering, University of New Hampshire, Durham, NH, 03824, USA.
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Burgos-Morales O, Gueye M, Lacombe L, Nowak C, Schmachtenberg R, Hörner M, Jerez-Longres C, Mohsenin H, Wagner H, Weber W. Synthetic biology as driver for the biologization of materials sciences. Mater Today Bio 2021; 11:100115. [PMID: 34195591 PMCID: PMC8237365 DOI: 10.1016/j.mtbio.2021.100115] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 01/16/2023] Open
Abstract
Materials in nature have fascinating properties that serve as a continuous source of inspiration for materials scientists. Accordingly, bio-mimetic and bio-inspired approaches have yielded remarkable structural and functional materials for a plethora of applications. Despite these advances, many properties of natural materials remain challenging or yet impossible to incorporate into synthetic materials. Natural materials are produced by living cells, which sense and process environmental cues and conditions by means of signaling and genetic programs, thereby controlling the biosynthesis, remodeling, functionalization, or degradation of the natural material. In this context, synthetic biology offers unique opportunities in materials sciences by providing direct access to the rational engineering of how a cell senses and processes environmental information and translates them into the properties and functions of materials. Here, we identify and review two main directions by which synthetic biology can be harnessed to provide new impulses for the biologization of the materials sciences: first, the engineering of cells to produce precursors for the subsequent synthesis of materials. This includes materials that are otherwise produced from petrochemical resources, but also materials where the bio-produced substances contribute unique properties and functions not existing in traditional materials. Second, engineered living materials that are formed or assembled by cells or in which cells contribute specific functions while remaining an integral part of the living composite material. We finally provide a perspective of future scientific directions of this promising area of research and discuss science policy that would be required to support research and development in this field.
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Affiliation(s)
- O. Burgos-Morales
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - M. Gueye
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
| | - L. Lacombe
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
| | - C. Nowak
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - R. Schmachtenberg
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - M. Hörner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - C. Jerez-Longres
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine - SGBM, University of Freiburg, Freiburg, 79104, Germany
| | - H. Mohsenin
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - H.J. Wagner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Department of Biosystems Science and Engineering - D-BSSE, ETH Zurich, Basel, 4058, Switzerland
| | - W. Weber
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine - SGBM, University of Freiburg, Freiburg, 79104, Germany
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45
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Roy R, Ray S, Chowdhury A, Anand R. Tunable Multiplexed Whole-Cell Biosensors as Environmental Diagnostics for ppb-Level Detection of Aromatic Pollutants. ACS Sens 2021; 6:1933-1939. [PMID: 33973468 DOI: 10.1021/acssensors.1c00329] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Aromatics such as phenols, benzene, and toluene are carcinogenic xenobiotics which are known to pollute water resources. By employing synthetic biology approaches combined with a structure-guided design, we created a tunable array of whole-cell biosensors (WCBs). The MopR genetic system that has the natural ability to sense and degrade phenol was adapted to detect phenol down to ∼1 ppb, making this sensor capable of directly detecting phenol in permissible limits in drinking water. Importantly, by using a single WCB design, we engineered mutations into the MopR gene that enabled generation of a battery of sensors for a wide array of pollutants. The engineered WCBs were able to sense inert compounds like benzene and xylene which lack active functional groups, without any loss in sensitivity. Overall, this universal programmable biosensor platform can be used to create WCBs that can be deployed on field for rapid testing and screening of suitable drinking water sources.
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Affiliation(s)
- Rohita Roy
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
| | - Shamayeeta Ray
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
| | - Arindam Chowdhury
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay Powai, Mumbai 400076, India
- DBT-Welcome Trust India Alliance Senior Fellow, Mumbai 400076, India
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46
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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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47
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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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48
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He MY, Lin YJ, Kao YL, Kuo P, Grauffel C, Lim C, Cheng YS, Chou HHD. Sensitive and Specific Cadmium Biosensor Developed by Reconfiguring Metal Transport and Leveraging Natural Gene Repositories. ACS Sens 2021; 6:995-1002. [PMID: 33444502 DOI: 10.1021/acssensors.0c02204] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Whole-cell biosensors are useful for monitoring heavy metal toxicity in public health and ecosystems, but their development has been hindered by intrinsic trade-offs between sensitivity and specificity. Here, we demonstrated an effective engineering solution by building a sensitive, specific, and high-response biosensor for carcinogenic cadmium ions. We genetically programmed the metal transport system of Escherichia coli to enrich intracellular cadmium ions and deprive interfering metal species. We then selected 16 cadmium-sensing transcription factors from the GenBank database and tested their reactivity to 14 metal ions in the engineered E. coli using the expression of the green fluorescent protein as the readout. The resulting cadmium biosensor was highly specific and showed a detection limit of 3 nM, a linear increase in fluorescent intensities from 0 to 200 nM, and a maximal 777-fold signal change. Using this whole-cell biosensor, a smartphone, and low-tech equipment, we developed a simple assay capable of measuring cadmium ions at the same concentration range in irrigation water and human urine. This method is user-friendly and cost-effective, making it affordable to screen large amounts of samples for cadmium toxicity in agriculture and medicine. Moreover, our work highlights natural gene repositories as a treasure chest for bioengineering.
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Affiliation(s)
- Mei-Ying He
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Jen Lin
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Ling Kao
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Pu Kuo
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Sheng Cheng
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 106, Taiwan
| | - Hsin-Hung David Chou
- Department of Life Science, National Taiwan University, Taipei 106, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 106, Taiwan
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49
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Cao Y, Zhang B, Zhu Z, Xin X, Wu H, Chen B. Microfluidic Based Whole-Cell Biosensors for Simultaneously On-Site Monitoring of Multiple Environmental Contaminants. Front Bioeng Biotechnol 2021; 9:622108. [PMID: 33791284 PMCID: PMC8006271 DOI: 10.3389/fbioe.2021.622108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022] Open
Abstract
Monitoring of environmental contaminants serves a vital role in proactive environmental management and pollution control. Research efforts have been centered on the development of robust whole-cell biosensors in recent years. However, data acquisition, multiple contaminants detection and biosafety issues limit the on-site application of such biosensors. Microfluidic system exhibits great potential to face these challenges via coupling biosensors. Here, we prospect a novel microfluidic based whole-cell biosensor (MWCB) for multiplexing monitoring of diverse contaminants, and design strategies to further increase the specificity, sensitivity and accuracy, reduce signal delay and expand shelf life of the proposed MWCB for on-site environmental applications. The development of MWCB demands multidisciplinary cooperation, and the sensing platforms are highly promising for real-world contaminants monitoring.
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Affiliation(s)
- Yiqi Cao
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Zhiwen Zhu
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Xiayin Xin
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hongjing Wu
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Bing Chen
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL, Canada
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50
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Wu Y, Wang CW, Wang D, Wei N. A Whole-Cell Biosensor for Point-of-Care Detection of Waterborne Bacterial Pathogens. ACS Synth Biol 2021; 10:333-344. [PMID: 33496568 DOI: 10.1021/acssynbio.0c00491] [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] [Indexed: 11/28/2022]
Abstract
Water contamination by pathogenic bacteria is a major public health concern globally. Monitoring bacterial contamination in water is critically important to protect human health, but this remains a critical challenge. Engineered whole-cell biosensors created through synthetic biology hold great promise for rapid and cost-effective detection of waterborne pathogens. In this study, we created a novel whole-cell biosensor to detect water contamination by Pseudomonas aeruginosa and Burkholderia pseudomallei, which are two critical bacterial pathogens and are recognized as common causative agents for waterborne diseases. The biosensor detects the target bacterial pathogens by responding to the relevant quorum sensing signal molecules. Particularly, this study constructed and characterized the biosensor on the basis of the QscR quorum sensing signal system for the first time. We first designed and constructed a QscR on the basis of the sensing module in the E. coli host cell and integrated the QscR sensing module with a reporting module that expressed an enhanced green fluorescent protein (EGFP). The results demonstrated that the biosensor had high sensitivity in response to the quorum sensing signals of the target bacterial pathogens. We further engineered a biosensor that expressed a red pigment lycopene in the reporting module to produce a visible signal readout for the pathogen detection. Additionally, we investigated the feasibility of a paper-based assay by immobilizing the lycopene-based whole-cell biosensor on paper with the aim to build a prototype for developing portable detection devices. The biosensor would provide a simple and inexpensive alternative for timely and point-of-care detection of water contamination and protect human health.
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