1
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Zhang C, Dang W, Zhang J, Wang C, Zhong P, Wang Z, Yang Y, Wang Y, Yan X. Development of a paper-based transcription aptasensor for convenient urinary uric acid self-testing. Int J Biol Macromol 2024; 271:132241. [PMID: 38768916 DOI: 10.1016/j.ijbiomac.2024.132241] [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: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
The abnormal uric acid (UA) level in urine can serve as warning signals of many diseases, such as gout and metabolic cardiovascular diseases. The current methods for detecting UA face limitations of instrument dependence and the requirement for non-invasiveness, making it challenging to fulfill the need for home-based application. In this study, we designed an aptasensor that combined UA-specific transcriptional regulation and a fluorescent RNA aptamer for convenient urinary UA testing. The concentration of UA can be translated into the intensity of fluorescent signals. The aptasensor showed higher sensitivity and more robust anti-interference performance. UA levels in the urine of different volunteers could be accurately tested using this method. In addition, a paper-based aptasensor for UA self-testing was manufactured, in which the urinary UA levels could be determined using a smartphone-based colorimetric approach. This work not only demonstrates a new approach for the design of disease-associated aptasensor, but also offers promising ideas for home-based detection of UA.
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Affiliation(s)
- Chengyu Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Weifan Dang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jingjing Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Cong Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Peng Zhong
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zhaoxin Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yufan Yang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yuefei Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Xiaohui Yan
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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2
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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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3
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Li M, Lv S, Yang R, Chu X, Wang X, Wang Z, Peng L, Yang J. Development of lycopene-based whole-cell biosensors for the visual detection of trace explosives and heavy metals. Anal Chim Acta 2023; 1283:341934. [PMID: 37977799 DOI: 10.1016/j.aca.2023.341934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/28/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
Residual explosives in conflicting zones have caused irreversible damage to human safety and the environment. Whole-cell biosensors can to detect remnants of buried explosives, such as 2,4-dinitrotoluene (DNT), a stable and highly volatile compound in explosives. However, all the reported whole-cell biosensors utilize fluorescence or luminescence as the biological markers, making their detection difficult in real minefields. Here, we presented a lycopene-based whole-cell biosensor in Escherichia coli to output visible signals in response to DNT, which can help in the visual detection of buried explosives. To construct the whole-cell biosensor, the DNT-responsive promoter yqjF was used as the sensing element, and the lycopene synthetic gene cassette crtEBI was served as the reporting element. Then, the metabolic flux for lycopene production was enhanced to improve the output signal of the whole-cell biosensor, and a terminator was utilized to reduce the background interference. The optimized biosensor LSZ05 could perceive at least 1 mg/L DNT. The DNT-specificity and robust performance of the biosensor under different environmental factors were confirmed. Our results showed that converting the biosensor into a lyophilized powder was an effective storage method. The biosensor LSZ05 could effectively detect DNT in two kinds of soil samples. The lycopene-based whole-cell biosensor could also be used to visually detect heavy metals. Our findings laid the foundation for visually detecting buried explosives in minefields, which was a valuable supplement to the reported biosensors. The methods used for optimizing the lycopene-based whole-cell biosensor, including the improvement of the output signal and reduction of background interference, were quite effective.
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Affiliation(s)
- Meijie Li
- Energy-rich Compound Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No. 700 Changchen Road, Qingdao, 266109, PR China.
| | - Shuzhe Lv
- Energy-rich Compound Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No. 700 Changchen Road, Qingdao, 266109, PR China.
| | - Rumeng Yang
- Energy-rich Compound Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No. 700 Changchen Road, Qingdao, 266109, PR China.
| | - Xiaohan Chu
- Energy-rich Compound Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No. 700 Changchen Road, Qingdao, 266109, PR China.
| | - Xu Wang
- Energy-rich Compound Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No. 700 Changchen Road, Qingdao, 266109, PR China.
| | - Ziyu Wang
- Energy-rich Compound Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No. 700 Changchen Road, Qingdao, 266109, PR China.
| | - Limin Peng
- Shandong TV University, Jinan, 250014, PR China.
| | - Jianming Yang
- Energy-rich Compound Production By Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, No. 700 Changchen Road, Qingdao, 266109, PR China.
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4
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Ge ZB, Chen MM, Xie WY, Huang K, Zhao FJ, Wang P. Natural Microbial Reactor-Based Sensing Platform for Highly Sensitive Detection of Inorganic Arsenic in Rice Grains. Anal Chem 2023; 95:11467-11474. [PMID: 37462477 DOI: 10.1021/acs.analchem.3c01857] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Rice is a major dietary source of inorganic arsenic (iAs), a highly toxic arsenical that accumulates in rice and poses health risks to rice-based populations. However, the availability of detection methods for iAs in rice grains is limited. In this study, we developed a novel approach utilizing a natural bacterial biosensor, Escherichia coli AW3110 (pBB-ArarsR-mCherry), in conjunction with amylase hydrolysis for efficient extraction, enabling high-throughput and quantitative detection of iAs in rice grains. The biosensor exhibits high specificity for arsenic and distinguishes between arsenite [As(III)] and arsenate [As(V)] by modulating the concentration of PO43- in the detection system. We determined the iAs concentrations in 19 rice grain samples with varying total As concentrations and compared our method with the standard technique of microwave digestion coupled with HPLC-ICP-MS. Both methods exhibited comparable results, without no significant bias in the concentrations of As(III) and As(V). The whole-cell biosensor demonstrated excellent reproducibility and a high signal-to-noise ratio, achieving a limit of detection of 16 μg kg-1 [As(III)] and 29 μg kg-1 [As(V)]. These values are considerably lower than the maximum allowable level (100 μg kg-1) for infant rice supplements established by the European Union. Our straightforward sensing strategy presents a promising tool for detecting iAs in other food samples.
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Affiliation(s)
- Zhan-Biao Ge
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming-Ming Chen
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Wan-Ying Xie
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ke Huang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Wang
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Centre for Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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5
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Hao N, Donnelly AJ, Dodd IB, Shearwin KE. When push comes to shove - RNA polymerase and DNA-bound protein roadblocks. Biophys Rev 2023; 15:355-366. [PMID: 37396453 PMCID: PMC10310618 DOI: 10.1007/s12551-023-01064-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/21/2023] [Indexed: 07/04/2023] Open
Abstract
In recent years, transcriptional roadblocking has emerged as a crucial regulatory mechanism in gene expression, whereby other DNA-bound obstacles can block the progression of transcribing RNA polymerase (RNAP), leading to RNAP pausing and ultimately dissociation from the DNA template. In this review, we discuss the mechanisms by which transcriptional roadblocks can impede RNAP progression, as well as how RNAP can overcome these obstacles to continue transcription. We examine different DNA-binding proteins involved in transcriptional roadblocking and their biophysical properties that determine their effectiveness in blocking RNAP progression. The catalytically dead CRISPR-Cas (dCas) protein is used as an example of an engineered programmable roadblock, and the current literature in understanding the polarity of dCas roadblocking is also discussed. Finally, we delve into a stochastic model of transcriptional roadblocking and highlight the importance of transcription factor binding kinetics and its resistance to dislodgement by an elongating RNAP in determining the strength of a roadblock.
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Affiliation(s)
- Nan Hao
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Alana J. Donnelly
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Ian B. Dodd
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Keith E. Shearwin
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
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6
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Zhu Y, Gao H, Zhang J, Zhao J, Qi Q, Wang Q. De novo design of the global transcriptional factor Cra-regulated promoters enables highly sensitive glycolysis flux biosensor for dynamic metabolic control. Microb Biotechnol 2023; 16:605-617. [PMID: 36541030 PMCID: PMC9948231 DOI: 10.1111/1751-7915.14166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Glycolytic flux is a fundamental index in microbial cell factories. A glycolytic flux biosensor that can monitor glucose metabolism efficiency is a promising strategy in rewiring metabolic flux to balance growth and biosynthesis. A key design feature of the glycolytic flux biosensors is the interaction between the global transcriptional factor Cra and its regulated promoters. However, overexpression and mutation of Cra has unpredictable effects on global metabolism in Escherichia coli. Therefore, new orthogonal biosensor design strategies should be developed to circumvent metabolic issues. In this report, the promoters in glycolytic flux biosensor were replaced with synthetic promoters of varying strengths or phage-derived promoters, and the Cra DNA-binding sites were deployed into promoters at different positions and distances to yield biosensors. The de nova biosensors that depended on Cra could sense Fructose-1,6-diphosphate (FBP) with broad dynamic ranges and low basal leakage. Then the negative-response biosensors were applied to fine-tune the target ATP synthesis gene, leading to the desired increase in pyruvate production (the highest 9.66 g/L) and cell growth. Moreover, the membrane synthesis gene plsC was also dynamically activated by the positive-response biosensor, leading to effective accumulation of lycopene in the cell membrane and a 50-fold increase in lycopene titre (100.3 mg/L) when compared with the control strain, demonstrating the effective and broader usages of our biosensors.
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Affiliation(s)
- Yuan Zhu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaxiao Gao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Zhang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jingyu Zhao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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7
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Somayaji A, Sarkar S, Balasubramaniam S, Raval R. Synthetic biology techniques to tackle heavy metal pollution and poisoning. Synth Syst Biotechnol 2022; 7:841-846. [PMID: 35572766 PMCID: PMC9078997 DOI: 10.1016/j.synbio.2022.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/26/2022] [Accepted: 04/14/2022] [Indexed: 11/28/2022] Open
Abstract
The requirement for natural resources and energy increases continually with the increase in population. An inevitable result of this is soil, water, and air pollution with diverse pollutants, including heavy metals. Synthetic Biology involves using modular, interchangeable biological parts, devices in standard chassis or whole organisms to achieve a programmed result that can be quantified and optimized till it meets the required efficiency. This makes synthetic biology techniques very popular to tackle pressing global issues such as heavy metal poisoning. This review aimed to highlight various advancements as well as benefits, risks, and problems in synthetic biology techniques for detection, bioaccumulation, and biosorption of various heavy metals using engineered organisms. We found that while such an approach is cost-effective, accessible, and efficient, there are several inherent technological and ethical issues including but not limited to metabolic burden and consequences of use of genetically modified organisms respectively. Overcoming these hurdles will probably take time and innumerable conversations, and should be done through education and a culture of responsible research, rather than enforcing restrictions on the development of synthetic biology.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
- Manipal BioMachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Soumodeep Sarkar
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
- Manipal BioMachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Shravan Balasubramaniam
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
- Manipal BioMachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Ritu Raval
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
- Manipal BioMachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
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8
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Chen SY, Zhang Y, Li R, Wang B, Ye BC. De Novo Design of the ArsR Regulated P ars Promoter Enables a Highly Sensitive Whole-Cell Biosensor for Arsenic Contamination. Anal Chem 2022; 94:7210-7218. [PMID: 35537205 PMCID: PMC9134189 DOI: 10.1021/acs.analchem.2c00055] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Whole-cell biosensors for arsenic contamination are typically designed based on natural bacterial sensing systems, which are often limited by their poor performance for precisely tuning the genetic response to environmental stimuli. Promoter design remains one of the most important approaches to address such issues. Here, we use the arsenic-responsive ArsR-Pars regulation system from Escherichia coli MG1655 as the sensing element and coupled gfp or lacZ as the reporter gene to construct the genetic circuit for characterizing the refactored promoters. We first analyzed the ArsR binding site and a library of RNA polymerase binding sites to mine potential promoter sequences. A set of tightly regulated Pars promoters by ArsR was designed by placing the ArsR binding sites into the promoter's core region, and a novel promoter with maximal repression efficiency and optimal fold change was obtained. The fluorescence sensor PlacV-ParsOC2 constructed with the optimized ParsOC2 promoter showed a fold change of up to 63.80-fold (with green fluorescence visible to the naked eye) at 9.38 ppb arsenic, and the limit of detection was as low as 0.24 ppb. Further, the optimized colorimetric sensor PlacV-ParsOC2-lacZ with a linear response between 0 and 5 ppb was used to perform colorimetric reactions in 24-well plates combined with a smartphone application for the quantification of the arsenic level in groundwater. This study offers a new approach to improve the performance of bacterial sensing promoters and will facilitate the on-site application of arsenic whole-cell biosensors.
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Affiliation(s)
- Sheng-Yan Chen
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Yan Zhang
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Renjie Li
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China
| | - Baojun Wang
- College
of Chemical and Biological Engineering & ZJU-Hangzhou Global Scientific
and Technological Innovation Center, Zhejiang
University, Hangzhou 311200, China,Research
Center of Biological Computation, Zhejiang
Laboratory, Hangzhou 311100, China,Centre
for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom,
| | - Bang-Ce Ye
- School
of Chemistry and Chemical Engineering, Shihezi
University, Shihezi 832003, China,Institute
of Engineering Biology and Health, Collaborative Innovation Center
of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical
Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China,Lab of Biosystem
and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China,. Tel/Fax: 0086-21-64252094
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9
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Zhang Y, Zou ZP, Chen SY, Wei WP, Zhou Y, Ye BC. Design and optimization of E. coli artificial genetic circuits for detection of explosive composition 2,4-dinitrotoluene. Biosens Bioelectron 2022; 207:114205. [PMID: 35339074 DOI: 10.1016/j.bios.2022.114205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/07/2022] [Accepted: 03/18/2022] [Indexed: 11/26/2022]
Abstract
The detection of mine-based explosives poses a serious threat to the lives of deminers, and carcinogenic residues may cause severe environmental pollution. Whole-cell biosensors that can detect on-site in dangerous or inaccessible environments have great potential to replace conventional methods. Synthetic biology based on engineering modularity serves as a new tool that could be used to engineer microbes to acquire desired functions through artificial design and precise regulation. In this study, we designed artificial genetic circuits in Escherichia coli MG1655 by reconstructing the transcription factor YhaJ-based system to detect explosive composition 2,4-dinitrotoluene (2,4-DNT). These genetic circuits were optimized at the transcriptional, translational, and post-translational levels. The binding affinity of the transcription factor YhaJ with inducer 2,4-DNT metabolites was enhanced via directed evolution, and several activator binding sites were inserted in sensing yqjF promoter (PyqjF) to further improve the output level. The optimized biosensor PyqjF×2-TEV-(mYhaJ + GFP)-Ssr had a maximum induction ratio of 189 with green fluorescent signal output, and it could perceive at least 1 μg/mL 2,4-DNT. Its effective and robust performance was verified in different water samples. Our results demonstrate the use of synthetic biology tools to systematically optimize the performance of sensors for 2,4-DNT detection, that lay the foundation for practical applications.
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Affiliation(s)
- Yan Zhang
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; School of Chemistry and Chemical Engineering/Key Laboratory of Environmental Monitoring and Pollutant Control of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, China
| | - Zhen-Ping Zou
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Sheng-Yan Chen
- School of Chemistry and Chemical Engineering/Key Laboratory of Environmental Monitoring and Pollutant Control of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, China
| | - Wen-Ping Wei
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Ying Zhou
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, Institute of Engineering Biology and Health, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China; School of Chemistry and Chemical Engineering/Key Laboratory of Environmental Monitoring and Pollutant Control of Xinjiang Bingtuan, Shihezi University, Shihezi, 832003, China; Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China.
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10
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Mahas A, Wang Q, Marsic T, Mahfouz MM. Development of Cas12a-Based Cell-Free Small-Molecule Biosensors via Allosteric Regulation of CRISPR Array Expression. Anal Chem 2022; 94:4617-4626. [PMID: 35266687 PMCID: PMC8943526 DOI: 10.1021/acs.analchem.1c04332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Cell-free biosensors
can detect various molecules, thus promising
to transform the landscape of diagnostics. Here, we developed a simple,
rapid, sensitive, and field-deployable small-molecule detection platform
based on allosteric transcription factor (aTF)-regulated expression
of a clustered regularly interspaced short palindromic repeats (CRISPR)
array coupled to Cas12a activity. To this end, we engineered an expression
cassette harboring a T7 promoter, an aTF binding sequence, a Cas12a
CRISPR array, and protospacer adjacent motif-flanked Cas12a target
sequences. In the presence of the ligand, dissociation of the aTF
allows transcription of the CRISPR array; this leads to activation
of Cas12a collateral activity, which cleaves a single-stranded DNA
linker to free a quenched fluorophore, resulting in a rapid, significant
increase of fluorescence. As a proof of concept, we used TetR as the
aTF to detect different tetracycline antibiotics with high sensitivity
and specificity and a simple, hand-held visualizer to develop a fluorescence-based
visual readout. We also adapted a mobile phone application to further
simplify the interpretation of the results. Finally, we showed that
the reagents could be lyophilized to facilitate storage and distribution.
This detection platform represents a valuable addition to the toolbox
of cell-free, CRISPR-based biosensors, with great potential for in-field
deployment to detect non-nucleic acid small molecules.
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Affiliation(s)
- Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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11
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Glutathione is involved in the reduction of methylarsenate to generate antibiotic methylarsenite in Enterobacter sp. CZ-1. Appl Environ Microbiol 2022; 88:e0246721. [PMID: 35080903 DOI: 10.1128/aem.02467-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methylarsenate (MAs(V)) is a product of microbial arsenic (As) biomethylation and has also been widely used as an herbicide. Some microbes are able to reduce nontoxic MAs(V) to highly toxic methylarsenite (MAs(III)) possibly as an antibiotic. The mechanism of MAs(V) reduction in microbes has not been elucidated. Here, we found that the bacterium Enterobacter sp. CZ-1 isolated from an As-contaminated paddy soil has a strong ability to reduce MAs(V) to MAs(III). Using a MAs(III)-responsive biosensor to detect MAs(V) reduction in E. coli Trans5α transformants of a genomic library of Enterobacter sp. CZ-1, we identified gshA, encoding a glutamate-cysteine ligase, as a key gene involved in MAs(V) reduction. Heterologous expression of gshA increased the biosynthesis of glutathione (GSH) and MAs(V) reduction in E. coli Trans5α. Deletion of gshA in Enterobacter sp. CZ-1 abolished its ability to synthesize GSH and decreased its MAs(V) reduction ability markedly, which could be restored by supplementation of exogenous GSH. In the presence of MAs(V), Enterobacter sp. CZ-1 was able to inhibit the growth of Bacillus subtilis 168; this ability was lost in the gshA-deleted mutant. In addition, deletion of gshA greatly decreased the reduction of arsenate to arsenite. These results indicate that GSH plays an important role in MAs(V) reduction to generate MAs(III) as an antibiotic. IMPORTANCE Arsenic is a ubiquitous environmental toxin. Some microbes detoxify inorganic arsenic through biomethylation, generating relatively nontoxic pentavalent methylated arsenicals, such as methylarsenate. Methylarsenate has also been widely used as an herbicide. Surprisingly, some microbes reduce methylarsenate to highly toxic methylarsenite possibly to use the latter as an antibiotic. How microbes reduce methylarsenate to methylarsenite is unknown. Here, we show that gshA encoding a glutamate-cysteine ligase in the glutathione biosynthesis pathway is involved in methylarsenate reduction in Enterobacter sp. CZ-1. Our study provides new insights into the crucial role of glutathione in the transformation of a common arsenic compound to a natural antibiotic.
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12
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Lee JY, Cha S, Lee JH, Lim HG, Noh MH, Kang CW, Jung GY. Plug-in repressor library for precise regulation of metabolic flux in Escherichia coli. Metab Eng 2021; 67:365-372. [PMID: 34333137 DOI: 10.1016/j.ymben.2021.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
In metabolic engineering, enhanced production of value-added chemicals requires precise flux control between growth-essential competing and production pathways. Although advances in synthetic biology have facilitated the exploitation of a number of genetic elements for precise flux control, their use requires expensive inducers, or more importantly, needs complex and time-consuming processes to design and optimize appropriate regulator components, case-by-case. To overcome this issue, we devised the plug-in repressor libraries for target-specific flux control, in which expression levels of the repressors were diversified using degenerate 5' untranslated region (5' UTR) sequences employing the UTR Library Designer. After we validated a wide expression range of the repressor libraries, they were applied to improve the production of lycopene from glucose and 3-hydroxypropionic acid (3-HP) from acetate in Escherichia coli via precise flux rebalancing to enlarge precursor pools. Consequently, we successfully achieved optimal carbon fluxes around the precursor nodes for efficient production. The most optimized strains were observed to produce 2.59 g/L of 3-HP and 11.66 mg/L of lycopene, which were improved 16.5-fold and 2.82-fold, respectively, compared to those produced by the parental strains. These results indicate that carbon flux rebalancing using the plug-in library is a powerful strategy for efficient production of value-added chemicals in E. coli.
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Affiliation(s)
- Ji Yeon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Sanghak Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Ji Hoon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea.
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13
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Ali SA, Mittal D, Kaur G. In-situ monitoring of xenobiotics using genetically engineered whole-cell-based microbial biosensors: recent advances and outlook. World J Microbiol Biotechnol 2021; 37:81. [PMID: 33843020 DOI: 10.1007/s11274-021-03024-3] [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: 08/01/2020] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
Industrialisation, directly or indirectly, exposes humans to various xenobiotics. The increased magnitude of chemical pesticides and toxic heavy metals in the environment, as well as their intrusion into the food chain, seriously threatens human health. Therefore, the surveillance of xenobiotics is crucial for social safety and security. Online investigation by traditional methods is not sufficient for the detection and identification of such compounds because of the high costs and their complexity. Advancement in the field of genetic engineering provides a potential opportunity to use genetically modified microorganisms. In this regard, whole-cell-based microbial biosensors (WCBMB) represent an essential tool that couples genetically engineered organisms with an operator/promoter derived from a heavy metal-resistant operon combined with a regulatory protein in the gene circuit. The plasmid controls the expression of the reporter gene, such as gfp, luc, lux and lacZ, to an inducible gene promoter and has been widely applied to assay toxicity and bioavailability. This review summarises the recent trends in the development and application of microbial biosensors and the use of mobile genes for biomedical and environmental safety concerns.
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Affiliation(s)
- Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal, Haryana, India. .,Proteomics and Cell Biology Lab, Animal Biotechnology Center, ICAR-National Dairy Research Institute, 132001, Karnal, Haryana, India.
| | - Deepti Mittal
- Animal Biochemistry Division, National Dairy Research Institute, Karnal, Haryana, India
| | - Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052, Sydney, NSW, Australia
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14
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Wang X, Zhu K, Chen D, Wang J, Wang X, Xu A, Wu L, Li L, Chen S. Monitoring arsenic using genetically encoded biosensors in vitro: The role of evolved regulatory genes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111273. [PMID: 32916524 DOI: 10.1016/j.ecoenv.2020.111273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Toxic pollutant (TP) detection in situ using analytical instruments or whole-cell biosensors is inconvenient. Designing and developing genetically coded biosensors in vitro for real-world TP detection is a promising alternative. However, because the bioactivity and stability of some key biomolecules are weakened in vitro, the response and regulation of reporter protein become difficult. Here, we established a genetically encoded biosensor in vitro with an arsenical resistance operon repressor (ArsR) and GFP reporter gene. Given that the wildtype ArsR did not respond to arsenic and activate GFP expression in vitro, we found, after screening, an evolved ArsR mutant ep3 could respond to arsenic and exhibited an approximately 3.4-fold fluorescence increase. Arsenic induced expression of both wildtype ArsR and ep3 mutant in vitro, however, only ep3 mutant regulated the expression of reporter gene. Furthermore, the effects of cell extracts, temperature, pH, incubation, and equilibrium time were investigated, and the equilibration of reaction mixtures for 30 min at 37 °C was found to be essential for in vitro arsenic detection prior to treatment with arsenic. Based on our data, we established a standard procedure for arsenic detection in vitro. Our results will facilitate the practical application of genetically encoded biosensors in TP monitoring.
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Affiliation(s)
- Xuanyu Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Kaili Zhu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Dongdong Chen
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Juan Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Xiaofei Wang
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui, 230601, China
| | - An Xu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Lijun Wu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China; Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Luzhi Li
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui, 230601, China
| | - Shaopeng Chen
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China.
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15
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Wan X, Pinto F, Yu L, Wang B. Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity. Nat Commun 2020; 11:5961. [PMID: 33235249 PMCID: PMC7686491 DOI: 10.1038/s41467-020-19552-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/20/2020] [Indexed: 12/17/2022] Open
Abstract
Versatile tools for gene expression regulation are vital for engineering gene networks of increasing scales and complexity with bespoke responses. Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in Escherichia coli. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by >20-fold, increasing system output amplitude by >130-fold and dynamic range by >70-fold, and mitigating host growth inhibition by >20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications. Decoy binding sites are natural regulators of gene expression. Here the authors design synthetic DNA sponges that fine tune the performance of synthetic gene circuits in a simple yet systematic manner, expanding the synthetic biology toolkit for gene regulation.
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Affiliation(s)
- Xinyi Wan
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Filipe Pinto
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK
| | - Luyang Yu
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.,Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, 314400, China
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, UK. .,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK. .,College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. .,Joint Research Centre for Engineering Biology, Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, 314400, China.
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16
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Chen SY, Wei W, Yin BC, Tong Y, Lu J, Ye BC. Development of a Highly Sensitive Whole-Cell Biosensor for Arsenite Detection through Engineered Promoter Modifications. ACS Synth Biol 2019; 8:2295-2302. [PMID: 31525958 DOI: 10.1021/acssynbio.9b00093] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Whole-cell biosensors have attracted considerable interests because they are robust, eco-friendly, and cost-effective. However, most of the biosensors harness the naturally occurring wild-type promoter, which often suffers from high background noise and low sensitivity. In this study, we demonstrate how to design the core elements (i.e., RNA polymerase binding site and transcription factor binding site) of the promoters to obtain a significant gain in the signal-to-noise output ratio of the whole-cell biosensor circuits. As a proof of concept, we modified the arsenite-regulated promoter from Escherichia coli K-12 genome, such that it has a lower background and higher expression. This was achieved by balancing the relationship between the number of ArsR binding sites (ABS) and the activity of the promoter and adjusting the location of the auxiliary ABS. A promoter variant ParsD-ABS-8 was obtained with an induction ratio of 179 (11-fold increase over the wild-type promoter) when induced with 1 μM arsenite. Importantly, the developed biosensor exhibited good dose-response in the range of 0.1 to 4 μM (R2 = 0.9928) of arsenite with a detection limit of ca. 10 nM. These results indicated that the engineered promoter modification approach could be used to improve the performance of whole-cell biosensors, thereby facilitating their practical application.
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Affiliation(s)
- Sheng-Yan Chen
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Wenping Wei
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanbin Tong
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Jianjiang Lu
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Bang-Ce Ye
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang China
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17
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Wan X, Volpetti F, Petrova E, French C, Maerkl SJ, Wang B. Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals. Nat Chem Biol 2019; 15:540-548. [PMID: 30911179 DOI: 10.1038/s41589-019-0244-3] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/11/2019] [Indexed: 11/09/2022]
Abstract
Cell-based biosensors have great potential to detect various toxic and pathogenic contaminants in aqueous environments. However, frequently they cannot meet practical requirements due to insufficient sensing performance. To address this issue, we investigated a modular, cascaded signal amplifying methodology. We first tuned intracellular sensory receptor densities to increase sensitivity, and then engineered multi-layered transcriptional amplifiers to sequentially boost output expression level. We demonstrated these strategies by engineering ultrasensitive bacterial sensors for arsenic and mercury, and improved detection limit and output up to 5,000-fold and 750-fold, respectively. Coupled by leakage regulation approaches, we developed an encapsulated microbial sensor cell array for low-cost, portable and precise field monitoring, where the analyte can be readily quantified via displaying an easy-to-interpret volume bar-like pattern. The ultrasensitive signal amplifying methodology along with the background regulation and the sensing platform will be widely applicable to many other cell-based sensors, paving the way for their real-world applications.
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Affiliation(s)
- Xinyi Wan
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Francesca Volpetti
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Ekaterina Petrova
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Chris French
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK. .,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK.
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18
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In vivo biosensors: mechanisms, development, and applications. ACTA ACUST UNITED AC 2018; 45:491-516. [DOI: 10.1007/s10295-018-2004-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 12/30/2017] [Indexed: 01/09/2023]
Abstract
Abstract
In vivo biosensors can recognize and respond to specific cellular stimuli. In recent years, biosensors have been increasingly used in metabolic engineering and synthetic biology, because they can be implemented in synthetic circuits to control the expression of reporter genes in response to specific cellular stimuli, such as a certain metabolite or a change in pH. There are many types of natural sensing devices, which can be generally divided into two main categories: protein-based and nucleic acid-based. Both can be obtained either by directly mining from natural genetic components or by engineering the existing genetic components for novel specificity or improved characteristics. A wide range of new technologies have enabled rapid engineering and discovery of new biosensors, which are paving the way for a new era of biotechnological progress. Here, we review recent advances in the design, optimization, and applications of in vivo biosensors in the field of metabolic engineering and synthetic biology.
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19
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Fang Y, Zhu C, Chen X, Wang Y, Xu M, Sun G, Guo J, Yoo J, Tie C, Jiang X, Li X. Copy number of ArsR reporter plasmid determines its arsenite response and metal specificity. Appl Microbiol Biotechnol 2018; 102:5753-5761. [PMID: 29766244 DOI: 10.1007/s00253-018-9042-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Accepted: 04/19/2018] [Indexed: 10/16/2022]
Abstract
The key component in bacteria-based biosensors is a transcriptional reporter employed to monitor induction or repression of a reporter gene corresponding to environmental change. In this study, we made a series of reporters in order to achieve highly sensitive detection of arsenite. From these reporters, two biosensors were developed by transformation of Escherichia coli DH5α with pLHPars9 and pLLPars9, consisting of either a high or low copy number plasmid, along with common elements of ArsR-luciferase fusion and addition of two binding sequences, one each from E. coli and Acidithiobacillus ferrooxidans chromosome, in front of the R773 ArsR operon. Both of them were highly sensitive to arsenite, with a low detection limit of 0.04 μM arsenite (~ 5 μg/L). They showed a wide dynamic range of detection up to 50 μM using high copy number pLHPars9 and 100 μM using low copy number pLLPars9. Significantly, they differ in metal specificity, pLLPars9 more specific to arsenite, while pLHPars9 to both arsenite and antimonite. The only difference between pLHPars9 and pLLPars9 is their copy numbers of plasmid and corresponding ratios of ArsR to its binding promoter/operator sequence. Therefore, we propose a working model in which DNA bound-ArsR is different from its free form in metal specificity.
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Affiliation(s)
- Yun Fang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou, 510070, Guangdong, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Chunjie Zhu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou, 510070, Guangdong, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Xingjuan Chen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou, 510070, Guangdong, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Yan Wang
- Science and Technology Library of Guangdong Province, Guangdong Institute of Science and Technology Information and Development Strategy, Guangzhou, China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou, 510070, Guangdong, China. .,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China.
| | - Guoping Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou, 510070, Guangdong, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Jun Guo
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou, 510070, Guangdong, China.,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China
| | - Jinnon Yoo
- Signosis Inc., 1700 Wyatt Drive, suite10-12, Santa Clara, CA, USA
| | - Cuijuan Tie
- Signosis Inc., 1700 Wyatt Drive, suite10-12, Santa Clara, CA, USA
| | - Xin Jiang
- Signosis Inc., 1700 Wyatt Drive, suite10-12, Santa Clara, CA, USA
| | - Xianqiang Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, 100 Central Xianlie Road, Guangzhou, 510070, Guangdong, China. .,State Key Laboratory of Applied Microbiology Southern China, Guangzhou, China. .,Signosis Inc., 1700 Wyatt Drive, suite10-12, Santa Clara, CA, USA.
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20
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Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli. Proc Natl Acad Sci U S A 2018; 115:2964-2969. [PMID: 29507236 DOI: 10.1073/pnas.1716920115] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbial production of value-added chemicals from biomass is a sustainable alternative to chemical synthesis. To improve product titer, yield, and selectivity, the pathways engineered into microbes must be optimized. One strategy for optimization is dynamic pathway regulation, which modulates expression of pathway-relevant enzymes over the course of fermentation. Metabolic engineers have used dynamic regulation to redirect endogenous flux toward product formation, balance the production and consumption rates of key intermediates, and suppress production of toxic intermediates until later in the fermentation. Most cases, however, have utilized a single strategy for dynamically regulating pathway fluxes. Here we layer two orthogonal, autonomous, and tunable dynamic regulation strategies to independently modulate expression of two different enzymes to improve production of D-glucaric acid from a heterologous pathway. The first strategy uses a previously described pathway-independent quorum sensing system to dynamically knock down glycolytic flux and redirect carbon into production of glucaric acid, thereby switching cells from "growth" to "production" mode. The second strategy, developed in this work, uses a biosensor for myo-inositol (MI), an intermediate in the glucaric acid production pathway, to induce expression of a downstream enzyme upon sufficient buildup of MI. The latter, pathway-dependent strategy leads to a 2.5-fold increase in titer when used in isolation and a fourfold increase when added to a strain employing the former, pathway-independent regulatory system. The dual-regulation strain produces nearly 2 g/L glucaric acid, representing the highest glucaric acid titer reported to date in Escherichia coli K-12 strains.
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21
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Chen X, Xia X, Lee SY, Qian Z. Engineering tunable biosensors for monitoring putrescine inEscherichia coli. Biotechnol Bioeng 2018; 115:1014-1027. [DOI: 10.1002/bit.26521] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/29/2017] [Accepted: 12/13/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Xue‐Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Xiao‐Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical & Biomolecular Engineering (BK21 Program)BioProcess Engineering Research Center, Bioinformatics Research Center, and Institute for the BioCentury, KAISTYuseong‐guDaejeonRepublic of Korea
| | - Zhi‐Gang Qian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople's Republic of China
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22
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Synthetic biology for microbial heavy metal biosensors. Anal Bioanal Chem 2017; 410:1191-1203. [DOI: 10.1007/s00216-017-0751-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/23/2017] [Accepted: 11/07/2017] [Indexed: 11/26/2022]
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23
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Sense and sensitivity in bioprocessing — detecting cellular metabolites with biosensors. Curr Opin Chem Biol 2017; 40:31-36. [DOI: 10.1016/j.cbpa.2017.05.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/23/2017] [Accepted: 05/26/2017] [Indexed: 11/23/2022]
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Berset Y, Merulla D, Joublin A, Hatzimanikatis V, van der Meer JR. Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation. ACS Synth Biol 2017; 6:862-874. [PMID: 28215088 DOI: 10.1021/acssynbio.6b00364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Bioreporters are living cells that generate an easily measurable signal in the presence of a chemical compound. They acquire their functionality from synthetic gene circuits, the configuration of which defines the response signal and signal-to-noise ratio. Bioreporters based on the Escherichia coli ArsR system have raised significant interest for quantifying arsenic pollution, but they need to be carefully optimized to accurately work in the required low concentration range (1-10 μg arsenite L-1). To better understand the general functioning of ArsR-based genetic circuits, we developed a comprehensive mechanistic model that was empirically tested and validated in E. coli carrying different circuit configurations. The model accounts for the different elements in the circuits (proteins, DNA, chemical species), and their detailed affinities and interactions, and predicts the (fluorescent) output from the bioreporter cell as a function of arsenite concentration. The model was parametrized using existing ArsR biochemical data, and then complemented by parameter estimations from the accompanying experimental data using a scatter search algorithm. Model predictions and experimental data were largely coherent for feedback and uncoupled circuit configurations, different ArsR alleles, promoter strengths, and presence or absence of arsenic efflux in the bioreporters. Interestingly, the model predicted a particular useful circuit variant having steeper response at low arsenite concentrations, which was experimentally confirmed and may be useful as arsenic bioreporter in the field. From the extensive validation we expect the mechanistic model to further be a useful framework for detailed modeling of other synthetic circuits.
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Affiliation(s)
- Yves Berset
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
- Laboratory
of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausane (EPFL), CH 1015 Lausanne, Switzerland
| | - Davide Merulla
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Aurélie Joublin
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory
of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausane (EPFL), CH 1015 Lausanne, Switzerland
| | - Jan R. van der Meer
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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Roggo C, van der Meer JR. Miniaturized and integrated whole cell living bacterial sensors in field applicable autonomous devices. Curr Opin Biotechnol 2017; 45:24-33. [PMID: 28088093 DOI: 10.1016/j.copbio.2016.11.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 11/19/2022]
Abstract
Live-cell based bioreporters are increasingly being deployed in microstructures, which facilitates their handling and permits the development of instruments that could perform autonomous environmental monitoring. Here we review recent developments of on-chip integration of live-cell bioreporters, the coupling of their reporter signal to the devices, their longer term preservation and multi-analyte capacity. We show examples of instruments that have attempted to fully integrate bioreporters as their sensing elements.
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Affiliation(s)
- Clémence Roggo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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Arruda LM, Monteiro LMO, Silva-Rocha R. The Chromobacterium violaceum ArsR Arsenite Repressor Exerts Tighter Control on Its Cognate Promoter Than the Escherichia coli System. Front Microbiol 2016; 7:1851. [PMID: 27917165 PMCID: PMC5116461 DOI: 10.3389/fmicb.2016.01851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/03/2016] [Indexed: 11/13/2022] Open
Abstract
Environmental bacteria are endowed with several regulatory systems that have potential applications in biotechnology. In this report, we characterize the arsenic biosensing features of the ars response system from Chromobacterium violaceum in the heterologous host Escherichia coli. We show that the native Pars/arsR system of C. violaceum outperforms the chromosomal ars copy of E. coli when exposed to micromolar concentrations of arsenite. To understand the molecular basis of this phenomenon, we analyzed the interaction between ArsR regulators and their promoter target sites as well as induction of the system at saturating concentrations of the regulators. In vivo titration experiments indicate that ArsR from C. violaceum has stronger binding affinity for its target promoter than the regulator from E. coli does. Additionally, arsenite induction experiments at saturating regulator concentration demonstrates that although the Pars/arsR system from E. coli displays a gradual response to increasing concentration of the inducer, the system from C. violaceum has a steeper response with a stronger promoter induction after a given arsenite threshold. Taken together, these data demonstrate the characterization of a novel arsenic response element from an environmental bacterium with potentially enhanced performance that could be further explored for the construction of an arsenic biosensor.
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Affiliation(s)
- Letícia M Arruda
- Systems and Synthetic Biology Lab, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Lummy M O Monteiro
- Systems and Synthetic Biology Lab, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Lab, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
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Bradley RW, Buck M, Wang B. Recognizing and engineering digital-like logic gates and switches in gene regulatory networks. Curr Opin Microbiol 2016; 33:74-82. [DOI: 10.1016/j.mib.2016.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 06/14/2016] [Accepted: 07/06/2016] [Indexed: 02/08/2023]
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