51
|
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.
Collapse
|
52
|
Wang X, Wei W, Zhao J. Using a Riboswitch Sensor to Detect Co 2+/Ni 2+ Transport in E. coli. Front Chem 2021; 9:631909. [PMID: 33659237 PMCID: PMC7917058 DOI: 10.3389/fchem.2021.631909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Intracellular concentrations of essential mental ions must be tightly maintained to avoid metal deprivation and toxicity. However, their levels in cells are still difficult to monitor. In this report, the combination of a Co2+Ni2+-specific riboswitch and an engineered downstream mCherry fluorescent protein allowed a highly sensitive and selective whole-cell Co2+/Ni2+ detection process. The sensors were applied to examine the resistance system of Co2+/Ni2+ in E. coli, and the sensors were able to monitor the effects of genetic deletions. These results indicate that riboswitch-based sensors can be employed in the study of related cellular processes.
Collapse
Affiliation(s)
- Xiaoying Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wei Wei
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| |
Collapse
|
53
|
Gaffney EM, Simoska O, Minteer SD. The Use of Electroactive Halophilic Bacteria for Improvements and Advancements in Environmental High Saline Biosensing. BIOSENSORS-BASEL 2021; 11:bios11020048. [PMID: 33673343 PMCID: PMC7917972 DOI: 10.3390/bios11020048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 01/20/2023]
Abstract
Halophilic bacteria are remarkable organisms that have evolved strategies to survive in high saline concentrations. These bacteria offer many advances for microbial-based biotechnologies and are commonly used for industrial processes such as compatible solute synthesis, biofuel production, and other microbial processes that occur in high saline environments. Using halophilic bacteria in electrochemical systems offers enhanced stability and applications in extreme environments where common electroactive microorganisms would not survive. Incorporating halophilic bacteria into microbial fuel cells has become of particular interest for renewable energy generation and self-powered biosensing since many wastewaters can contain fluctuating and high saline concentrations. In this perspective, we highlight the evolutionary mechanisms of halophilic microorganisms, review their application in microbial electrochemical sensing, and offer future perspectives and directions in using halophilic electroactive microorganisms for high saline biosensing.
Collapse
|
54
|
Del Valle I, Fulk EM, Kalvapalle P, Silberg JJ, Masiello CA, Stadler LB. Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences. Front Microbiol 2021; 11:618373. [PMID: 33633695 PMCID: PMC7901896 DOI: 10.3389/fmicb.2020.618373] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.
Collapse
Affiliation(s)
- Ilenne Del Valle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Emily M. Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Caroline A. Masiello
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, United States
| |
Collapse
|
55
|
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.
Collapse
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.
| |
Collapse
|
56
|
Zielinski DC, Patel A, Palsson BO. The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale. Microorganisms 2020; 8:E2050. [PMID: 33371386 PMCID: PMC7767376 DOI: 10.3390/microorganisms8122050] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
Microbial strains are being engineered for an increasingly diverse array of applications, from chemical production to human health. While traditional engineering disciplines are driven by predictive design tools, these tools have been difficult to build for biological design due to the complexity of biological systems and many unknowns of their quantitative behavior. However, due to many recent advances, the gap between design in biology and other engineering fields is closing. In this work, we discuss promising areas of development of computational tools for engineering microbial strains. We define five frontiers of active research: (1) Constraint-based modeling and metabolic network reconstruction, (2) Kinetics and thermodynamic modeling, (3) Protein structure analysis, (4) Genome sequence analysis, and (5) Regulatory network analysis. Experimental and machine learning drivers have enabled these methods to improve by leaps and bounds in both scope and accuracy. Modern strain design projects will require these tools to be comprehensively applied to the entire cell and efficiently integrated within a single workflow. We expect that these frontiers, enabled by the ongoing revolution of big data science, will drive forward more advanced and powerful strain engineering strategies.
Collapse
Affiliation(s)
- Daniel Craig Zielinski
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
| | - Bernhard O. Palsson
- Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; (D.C.Z.); (A.P.)
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| |
Collapse
|
57
|
Recent advances in synthetic biology-enabled and natural whole-cell optical biosensing of heavy metals. Anal Bioanal Chem 2020; 413:73-82. [PMID: 32959111 DOI: 10.1007/s00216-020-02953-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
A large number of scientific works have been published on whole-cell heavy metal biosensing based on optical transduction. The advances in the application of biotechnological tools not only have continuously improved the sensitivity, selectivity, and detection range for biosensors but also have simultaneously unveiled new challenges and restrictions for further improvements. This review highlights selected aspects of whole-cell biosensing of heavy metals using optical transducers. We have focused on the progress in genetic modulation in regulatory and reporter modules of recombinant plasmids that has enabled improvement of biosensor performance. Simultaneously, an attempt has been made to present newer platforms such as microfluidics that have generated promising results and might give a new turn to the optical biosensing field.
Collapse
|
58
|
Abstract
The ability to detect disease early and deliver precision therapy would be transformative for the treatment of human illnesses. To achieve these goals, biosensors that can pinpoint when and where diseases emerge are needed. Rapid advances in synthetic biology are enabling us to exploit the information-processing abilities of living cells to diagnose disease and then treat it in a controlled fashion. For example, living sensors could be designed to precisely sense disease biomarkers, such as by-products of inflammation, and to respond by delivering targeted therapeutics in situ. Here, we provide an overview of ongoing efforts in microbial biosensor design, highlight translational opportunities, and discuss challenges for enabling sense-and-respond precision medicines.
Collapse
Affiliation(s)
- Maria Eugenia Inda
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Timothy K. Lu
- MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
59
|
Capeness MJ, Horsfall LE. Synthetic biology approaches towards the recycling of metals from the environment. Biochem Soc Trans 2020; 48:1367-1378. [PMID: 32627824 PMCID: PMC7458392 DOI: 10.1042/bst20190837] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/29/2020] [Accepted: 06/08/2020] [Indexed: 01/05/2023]
Abstract
Metals are a finite resource and their demand for use within existing and new technologies means metal scarcity is increasingly a global challenge. Conversely, there are areas containing such high levels of metal pollution that they are hazardous to life, and there is loss of material at every stage of the lifecycle of metals and their products. While traditional resource extraction methods are becoming less cost effective, due to a lowering quality of ore, industrial practices have begun turning to newer technologies to tap into metal resources currently locked up in contaminated land or lost in the extraction and manufacturing processes. One such technology uses biology for the remediation of metals, simultaneously extracting resources, decontaminating land, and reducing waste. Using biology for the identification and recovery of metals is considered a much 'greener' alternative to that of chemical methods, and this approach is about to undergo a renaissance thanks to synthetic biology. Synthetic biology couples molecular genetics with traditional engineering principles, incorporating a modular and standardised practice into the assembly of genetic parts. This has allowed the use of non-model organisms in place of the normal laboratory strains, as well as the adaption of environmentally sourced genetic material to standardised parts and practices. While synthetic biology is revolutionising the genetic capability of standard model organisms, there has been limited incursion into current practices for the biological recovery of metals from environmental sources. This mini-review will focus on some of the areas that have potential roles to play in these processes.
Collapse
Affiliation(s)
- Michael J. Capeness
- Centre for Systems and Synthetic Biology, and the Centre for Science at Extreme Conditions, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
| | - Louise E. Horsfall
- Centre for Systems and Synthetic Biology, and the Centre for Science at Extreme Conditions, School of Biological Sciences, University of Edinburgh, Roger Land Building, Alexander Crum Brown Road, Edinburgh EH9 3FF, U.K
| |
Collapse
|
60
|
Detection of biotin with zeptomole sensitivity using recombinant spores and a competition assay. Anal Bioanal Chem 2020; 412:7219-7226. [PMID: 32761258 DOI: 10.1007/s00216-020-02854-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
Detection of protein-binding analytes is important for many applications. Currently, various instrument-based techniques are used for detecting protein-binding analytes. However, such techniques have several limitations including high cost and time-consuming sample processing. In order to overcome these limitations, we developed a sensitive competition assay for the detection of protein-binding analytes using recombinant endospores as a sensing element. The method is based on the competition between the biotin, the model analyte, and a biotin-magnetic bead complex to bind the recombinant spores containing the biotin binding region of streptavidin. After magnetic attraction, the residual spores in the suspension are spread on plates to form colonies which are used to count the amount of the residual spores; the higher the residual ratio of spores, the more biotin in the samples. The linear range was from 150 zmol to 1.5 fmol and the limit of detection of the assay was 150 zmol. The assay proposed herein is sensitive and does not require any expensive equipment. It is suitable for qualitative or semi-quantitative analysis such as screening tests for the detection of toxic chemicals.
Collapse
|
61
|
Kim H, Jang G, Kim BG, Yoon Y. Modulation of the Metal(loid) Specificity of Whole-Cell Bioreporters by Genetic Engineering of ZntR Metal-Binding Loops. J Microbiol Biotechnol 2020; 30:681-688. [PMID: 32482933 PMCID: PMC9728388 DOI: 10.4014/jmb.1911.11053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/09/2020] [Indexed: 12/15/2022]
Abstract
Bacterial cell-based biosensors, or whole-cell bioreporters (WCBs), are an alternative tool for the quantification of hazardous materials. Most WCBs share similar working mechanisms. In brief, the recognition of a target by sensing domains induces a biological event, such as changes in protein conformation or gene expression, providing a basis for quantification. WCBs targeting heavy metal(loid)s employ metalloregulators as sensing domains and control the expression of genes in the presence of target metal(loid) ions, but the diversity of targets, specificity, and sensitivity of these WCBs are limited. In this study, we genetically engineered the metal-binding loop (MBL) of ZntR, which controls the znt-operon in Escherichia coli. In the MBL of ZntR, three Cys sites interact with metal ions. Based on the crystal structure of ZntR, MBL sequences were modified by sitedirected mutagenesis. As a result, the metal-sensing properties of WCBs differed depending on amino acid sequences and the new selectivity to Cr or Pb was observed. Although there is room for improvement, our results support the use of currently available WCBs as a platform to generate new WCBs to target other environmental pollutants including metal(loid)s.
Collapse
Affiliation(s)
- Hyojin Kim
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Republic of Korea
| | - Geupil Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Bong-Gyu Kim
- Department of Forest Resources, Gyeongnam National University of Science and Technology, Jinju 52725, Republic of Korea
| | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Republic of Korea
| |
Collapse
|
62
|
Mendoza JI, Soncini FC, Checa SK. Engineering of a Au-sensor to develop a Hg-specific, sensitive and robust whole-cell biosensor for on-site water monitoring. Chem Commun (Camb) 2020; 56:6590-6593. [PMID: 32406434 DOI: 10.1039/d0cc01323d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A highly sensitive and specific Hg-whole-cell biosensor was developed from a non-selective variant of the Au sensor GolS and its regulatory pathway. The performance of this analytical tool was validated under laboratory and field-like conditions. This biosensor can be easily applied in cost-effective and portable semiquantitative devices to report Hg contamination in water.
Collapse
Affiliation(s)
- Julián I Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario (UNR)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Argentina.
| | | | | |
Collapse
|
63
|
Tan SI, You SC, Shih IT, Ng IS. Quantification, regulation and production of 5-aminolevulinic acid by green fluorescent protein in recombinant Escherichia coli. J Biosci Bioeng 2020; 129:387-394. [PMID: 31678067 DOI: 10.1016/j.jbiosc.2019.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 11/22/2022]
Abstract
5-Aminolevulinic acid (5-ALA) is an unnatural amino acid and has been approved as a biodegradable, non-toxic pesticide and herbicide with applications in sustainable agriculture. 5-ALA can also be applied for cancer targeting via tumor localization and photodynamic therapy. Herein, we developed a feasible quantification, regulation and production method of 5-ALA in Escherichia coli is based on the chimera of 5-ALA synthetase from Rhodobacter sphaeroides (RshemA) and super-fold green fluorescent protein (sfGFP) under the control of dual promoters/double plasmids. 5-ALA production based on quantification with the reporter sfGFP was unsuccessfully for the RshemA-sfGFP fusion protein owing to a steric hindrance effect, but was effective using dual constitutive promoters (i.e., J23100 and PLacI) for RshemA and sfGFP independently. Moreover, a simple quantification method based on the linear relationship between 5-ALA concentration and the change in sfGFP intensity was calculated with the Hill equation according to the results of dual plasmids which composed of RshemA-threonine/homoserine exporter (RhtA) and the sensing plasmid pSU-T7-sfGFP. Compared with the conventional detection method for 5-ALA using Ehrlich's reagent, our proposed method is advantages in effectiveness, real-time detection, and outstanding sensitivity. Finally, the highest yield of 5-ALA was obtained in E. coli D2TT strain, reaching 2.46 g/L of 5-ALA produced in a 2.5-L baffle flask fermentation. Hence, this approach shows strong potential for improving 5-ALA production with appropriate regulation and detection based on the fluorescent signal.
Collapse
Affiliation(s)
- Shih-I Tan
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Shao-Chun You
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - I-Tai Shih
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
| |
Collapse
|
64
|
High-Sensitivity Terahertz Refractive Index Sensor in a Multilayered Structure with Graphene. NANOMATERIALS 2020; 10:nano10030500. [PMID: 32164280 PMCID: PMC7153478 DOI: 10.3390/nano10030500] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 12/14/2022]
Abstract
In this paper, we propose a high-sensitivity optical sensor at terahertz frequencies based on a composite structure containing a one-dimensional photonic crystal (1D PC) coated with a layer of monolayer graphene. Between the 1D PC and the graphene there is a sensing medium. This high-sensitivity phenomenon originates from the excitation of optical resonance between the graphene and the 1D PC. The proposed sensor is highly sensitive to the Fermi energy of graphene, the thickness and refractive index of the sensing medium, and the number of graphene layers. By selecting appropriate parameters, the maximum sensitivity (407.36∘/RIU) is obtained. We believe the proposed configuration is promising for fabricating graphene-based biosensor- or gas-sensor devices and other related applications in the terahertz band.
Collapse
|
65
|
|
66
|
Baksh KA, Zamble DB. Allosteric control of metal-responsive transcriptional regulators in bacteria. J Biol Chem 2020; 295:1673-1684. [PMID: 31857375 PMCID: PMC7008368 DOI: 10.1074/jbc.rev119.011444] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many transition metals are essential trace nutrients for living organisms, but they are also cytotoxic in high concentrations. Bacteria maintain the delicate balance between metal starvation and toxicity through a complex network of metal homeostasis pathways. These systems are coordinated by the activities of metal-responsive transcription factors-also known as metal-sensor proteins or metalloregulators-that are tuned to sense the bioavailability of specific metals in the cell in order to regulate the expression of genes encoding proteins that contribute to metal homeostasis. Metal binding to a metalloregulator allosterically influences its ability to bind specific DNA sequences through a variety of intricate mechanisms that lie on a continuum between large conformational changes and subtle changes in internal dynamics. This review summarizes recent advances in our understanding of how metal sensor proteins respond to intracellular metal concentrations. In particular, we highlight the allosteric mechanisms used for metal-responsive regulation of several prokaryotic single-component metalloregulators, and we briefly discuss current open questions of how metalloregulators function in bacterial cells. Understanding the regulation and function of metal-responsive transcription factors is a fundamental aspect of metallobiochemistry and is important for gaining insights into bacterial growth and virulence.
Collapse
Affiliation(s)
- Karina A Baksh
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Deborah B Zamble
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.
| |
Collapse
|
67
|
Lee W, Kim H, Jang G, Kim BG, Yoon Y. Antimony sensing whole-cell bioreporters derived from ArsR genetic engineering. Appl Microbiol Biotechnol 2020; 104:2691-2699. [PMID: 32002600 DOI: 10.1007/s00253-020-10413-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/15/2020] [Accepted: 01/24/2020] [Indexed: 12/01/2022]
Abstract
Despite the known hazardous effects of antimony (Sb) on human health, Sb monitoring biosensors have not been as actively investigated as arsenic (As) biosensors. Whole-cell bioreporters (WCBs) employing an arsenic-responsive operon and a regulatory protein (ArsR) are reportedly capable of monitoring arsenite, arsenate, and antimonite. However, the potential of WCBs as Sb biosensors has been largely ignored. Here, the metal-binding site of ArsR (sequenced as ELCVCDLCTA from amino acid number 30 to 39) was modified via genetic engineering to enhance Sb specificity. By relocating cysteine residues and introducing point mutations, nine ArsR mutants were generated and tested for metal(loid) ion specificity. The Sb specificity of WCBs was enhanced by the C37S/A39C and L36C/C37S mutations on the As binding site of ArsR. Additionally, WCBs with other ArsR mutants exhibited new target sensing capabilities toward Cd and Pb. Although further research is required to enhance the specificity and sensitivity of WCBs and to broaden their practical applications, our proposed strategy based on genetic engineering of regulatory proteins provides a valuable basis to generate WCBs to monitor novel targets.
Collapse
Affiliation(s)
- Woonwoo Lee
- Department of Environmental Health Science, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyojin Kim
- Department of Environmental Health Science, Konkuk University, Seoul, 05029, Republic of Korea
| | - Geupil Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Bong-Gyu Kim
- Department of Forest Resources, Gyeongnam National University of Science and Technology, Jinju, 52725, Republic of Korea
| | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul, 05029, Republic of Korea.
| |
Collapse
|
68
|
Hicks M, Bachmann TT, Wang B. Synthetic Biology Enables Programmable Cell-Based Biosensors. Chemphyschem 2020; 21:132-144. [PMID: 31585026 PMCID: PMC7004036 DOI: 10.1002/cphc.201900739] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/03/2019] [Indexed: 01/10/2023]
Abstract
Cell-based biosensors offer cheap, portable and simple methods of detecting molecules of interest but have yet to be truly adopted commercially. Issues with their performance and specificity initially slowed the development of cell-based biosensors. With the development of rational approaches to tune response curves, the performance of biosensors has rapidly improved and there are now many biosensors capable of sensing with the required performance. This has stimulated an increased interest in biosensors and their commercial potential. However the reliability, long term stability and biosecurity of these sensors are still barriers to commercial application and public acceptance. Research into overcoming these issues remains active. Here we present the state-of-the-art tools offered by synthetic biology to allow construction of cell-based biosensors with customisable performance to meet the real world requirements in terms of sensitivity and dynamic range and discuss the research progress to overcome the challenges in terms of the sensor stability and biosecurity fears.
Collapse
Affiliation(s)
- Maggie Hicks
- School of Biological SciencesUniversity of EdinburghEdinburghUK
- Centre for Synthetic and Systems BiologyUniversity of EdinburghEdinburghUK
| | - Till T. Bachmann
- Infection MedicineEdinburgh Medical School: Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Baojun Wang
- School of Biological SciencesUniversity of EdinburghEdinburghUK
- Centre for Synthetic and Systems BiologyUniversity of EdinburghEdinburghUK
| |
Collapse
|
69
|
Shahdeo D, Roberts A, Abbineni N, Gandhi S. Graphene based sensors. ANALYTICAL APPLICATIONS OF GRAPHENE FOR COMPREHENSIVE ANALYTICAL CHEMISTRY 2020. [PMCID: PMC7518956 DOI: 10.1016/bs.coac.2020.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The two dimensional, honeycomb structured, single carbon layered graphene has extensively been used in the field of sensor detection due to its unique physicochemical properties. These properties such as excellent electrical conductivity, high electron mobility, tunable optical properties, room temperature quantum Hall effect, large surface to volume ratio, high mechanical strength, and ease of functionalization, make it an ideal nanomaterial for sensor development. This has enabled the fabrication of a large variety of highly sensitive sensors which include colorimetric, electrochemical, potentiometric, fluorescence, etc. based sensors. These sensors in conjugation with graphene or its derivatives such as graphene quantum dots, graphene oxide, reduced graphene oxide, etc. show highly desirable properties such as high sensitivity (detecting minute amounts of target analyte), specificity (no cross reactivity while detecting the target analyte), rapid results, low cost, extended storage shelf life and robustness (stability), and easy-to-use capabilities (user-friendly). This book chapter gives a detailed overview of all the advances made in the development and fabrication of novel graphene based sensors and their application in point of care (PoC) detection of various diseases as well as health monitoring devices. The different sensors, their methods of fabrication, their sensitivity and the analytes and biomolecules used have been discussed in detail and compared.
Collapse
|
70
|
A novel biosensor for zinc detection based on microbial fuel cell system. Biosens Bioelectron 2019; 147:111763. [PMID: 31654820 DOI: 10.1016/j.bios.2019.111763] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/26/2019] [Accepted: 10/03/2019] [Indexed: 01/08/2023]
Abstract
Microbial fuel cell (MFC) biosensors are self-sustainable device for monitoring of various substrates; however, for heavy metals detection are still scarce. In this study, E. coli BL21 was engineered to express the zntR, ribB, and oprF genes with PzntA promoter, which could sense zinc (Zn2+) for riboflavin and porin production. The engineered strain produced high levels of riboflavin (2.4-3.6 μM) and improved cell membrane permeability, with a positive correlation of Zn2+ (0-400 μM). The strain was then employed in MFC biosensor under the following operational parameters: external resistance 1000 Ω, pH 9, and temperature 37 °C for Zn2+ sensing. The maximum voltages (160, 183, 260, 292, and 342 mV) of the constructed MFC biosensor have a linear relationship with Zn2+ concentrations (0, 100, 200, 300, and 400 μM, respectively) (R2 = 0.9777). An Android App was developed for the biosensor system that could sense Zn2+ in real-time and in situ. The biosensor was applied to wastewater with different Zn2+ concentrations and the results showed that the detection range for Zn2+ was 20-100 μM, which covers common Zn2+ safety standards. The results obtained with developed MFC biosensor were comparable to conventional methods such as colorimetric, flame atomic absorption spectroscopy (FAAS), and inductively coupled plasma optical emission spectroscopy (ICP-OES). In summary, MFC biosensor with biosynthetic strain is an efficient and affordable system for real-time monitoring and sensing of heavy metals.
Collapse
|
71
|
Using the promoters of MerR family proteins as "rheostats" to engineer whole-cell heavy metal biosensors with adjustable sensitivity. J Biol Eng 2019; 13:70. [PMID: 31452678 PMCID: PMC6702742 DOI: 10.1186/s13036-019-0202-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022] Open
Abstract
Background Whole cell biosensors provide a simple method for the detection of heavy metals. However, previous designs of them rely primarily on simulation of heavy metal resistance systems of bacteria. Results This study proposes a strategy for the rational design of metal detection circuits based on sensor proteins of the MerR family. Our results indicate the expression level of sensor protein can be used as a "rheostat" for tuning detection sensitivity with parabola curves to represent the relationships between the detection slopes and the sensor protein levels. This circuits design strategy (named as "Parabola Principle"), is used as a guide for the discovery of optimum metal detection circuits, and the design of biosensors with specific metal detection characteristics. For example, visible qualitative Hg (II) biosensors with a threshold of 0.05 mg/L are successfully constructed. Conclusions These results indicate the feasibility of developing a sensor that is much more tunable than what is presented. Graphical abstract
Collapse
|
72
|
Sensitive and Specific Whole-Cell Biosensor for Arsenic Detection. Appl Environ Microbiol 2019; 85:AEM.00694-19. [PMID: 30952659 DOI: 10.1128/aem.00694-19] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 03/27/2019] [Indexed: 01/30/2023] Open
Abstract
Whole-cell biosensors (WCBs) have been designed to detect As(III), but most suffer from poor sensitivity and specificity. In this paper, we developed an arsenic WCB with a positive feedback amplifier in Escherichia coli DH5α. The output signal from the reporter mCherry was significantly enhanced by the positive feedback amplifier. The sensitivity of the WCB with positive feedback is about 1 order of magnitude higher than that without positive feedback when evaluated using a half-saturation As(III) concentration. The minimum detection limit for As(III) was reduced by 1 order of magnitude to 0.1 µM, lower than the World Health Organization standard for the arsenic level in drinking water, 0.01 mg/liter or 0.13 µM. Due to the amplification of the output signal, the WCB was able to give detectable signals within a shorter period, and a fast response is essential for in situ operations. Moreover, the WCB with the positive feedback amplifier showed exceptionally high specificity toward As(III) when compared with other metal ions. Collectively, the designed positive feedback amplifier WCB meets the requirements for As(III) detection with high sensitivity and specificity. This work also demonstrates the importance of genetic circuit engineering in designing WCBs, and the use of genetic positive feedback amplifiers is a good strategy to improve the performance of WCBs.IMPORTANCE Arsenic poisoning is a severe public health issue. Rapid and simple methods for the sensitive and specific monitoring of arsenic concentration in drinking water are needed. In this study, we designed an arsenic WCB with a positive feedback amplifier. It is highly sensitive and able to detect arsenic below the WHO limit level. In addition, it also significantly improves the specificity of the biosensor toward arsenic, giving a signal that is about 10 to 20 times stronger in response to As(III) than to other metals. This work not only provides simple but effective arsenic biosensors but also demonstrates the importance of genetic engineering, particularly the use of positive feedback amplifiers, in designing WCBs.
Collapse
|
73
|
Extracellular electron transfer features of Gram-positive bacteria. Anal Chim Acta 2019; 1076:32-47. [PMID: 31203962 DOI: 10.1016/j.aca.2019.05.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/23/2019] [Accepted: 05/05/2019] [Indexed: 12/20/2022]
Abstract
Electroactive microorganisms possess the unique ability to transfer electrons to or from solid phase electron conductors, e.g., electrodes or minerals, through various physiological mechanisms. The processes are commonly known as extracellular electron transfer and broadly harnessed in microbial electrochemical systems, such as microbial biosensors, microbial electrosynthesis, or microbial fuel cells. Apart from a few model microorganisms, the nature of the microbe-electrode conductive interaction is poorly understood for most of the electroactive species. The interaction determines the efficiency and a potential scaling up of bioelectrochemical systems. Gram-positive bacteria generally have a thick electron non-conductive cell wall and are believed to exhibit weak extracellular electron shuttling activity. This review highlights reported research accomplishments on electroactive Gram-positive bacteria. The use of electron-conducting polymers as mediators is considered as one promising strategy to enhance the electron transfer efficiency up to application scale. In view of the recent progress in understanding the molecular aspects of the extracellular electron transfer mechanisms of Enterococcus faecalis, the electron transfer properties of this bacterium are especially focused on. Fundamental knowledge on the nature of microbial extracellular electron transfer and its possibilities can provide insight in interspecies electron transfer and biogeochemical cycling of elements in nature. Additionally, a comprehensive understanding of cell-electrode interactions may help in overcoming insufficient electron transfer and restricted operational performance of various bioelectrochemical systems and facilitate their practical applications.
Collapse
|
74
|
Park DM, Taffet MJ. Combinatorial Sensor Design in Caulobacter crescentus for Selective Environmental Uranium Detection. ACS Synth Biol 2019; 8:807-817. [PMID: 30897331 DOI: 10.1021/acssynbio.8b00484] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to detect uranium (U) through environmental monitoring is of critical importance for informing water resource protection and nonproliferation efforts. While technologies exist for environmental U detection, wide-area environmental monitoring, i.e. sampling coverage over large areas not known to possess U contamination, remains a challenging prospect that necessitates the development of novel detection approaches. Herein, we describe the development of a whole-cell U sensor by integrating two functionally independent, native U-responsive two-component signaling systems (TCS), UzcRS and UrpRS, within an AND gate circuit in the bacterium Caulobacter crescentus. Through leverage of the distinct but imperfect selectivity profiles of both TCS, this combinatorial approach enabled greater selectivity relative to a prior biosensor developed with UzcRS alone; no cross-reactivity was observed with most common environmental metals (e.g, Fe, As, Cu, Ca, Mg, Cd, Cr, Al) or the U decay-chain product Th, and the selectivity against Zn and Pb was significantly improved. In addition, integration of the UzcRS signal amplifier protein UzcY within the AND gate circuit further enhanced overall sensitivity and selectivity for U. The functionality of the sensor in an environmental context was confirmed by detection of U concentrations as low as 1 μM in groundwater samples. The results highlight the value of a combinatorial approach for constructing whole-cell sensors for the selective detection of analytes for which there are no known evolved regulators.
Collapse
Affiliation(s)
- Dan M. Park
- Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Michael J. Taffet
- Environmental Restoration Department (ERD), Operations and Business Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| |
Collapse
|
75
|
Bilal M, Iqbal HM. Microbial-derived biosensors for monitoring environmental contaminants: Recent advances and future outlook. PROCESS SAFETY AND ENVIRONMENTAL PROTECTION 2019. [DOI: 10.1016/j.psep.2019.01.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
76
|
Krishnan SK, Singh E, Singh P, Meyyappan M, Nalwa HS. A review on graphene-based nanocomposites for electrochemical and fluorescent biosensors. RSC Adv 2019; 9:8778-8881. [PMID: 35517682 PMCID: PMC9062009 DOI: 10.1039/c8ra09577a] [Citation(s) in RCA: 265] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/15/2019] [Indexed: 12/16/2022] Open
Abstract
Biosensors with high sensitivity, selectivity and a low limit of detection, reaching nano/picomolar concentrations of biomolecules, are important to the medical sciences and healthcare industry for evaluating physiological and metabolic parameters.
Collapse
Affiliation(s)
- Siva Kumar Krishnan
- CONACYT-Instituto de Física
- Benemérita Universidad Autónoma de Puebla
- Puebla 72570
- Mexico
| | - Eric Singh
- Department of Computer Science
- Stanford University
- Stanford
- USA
| | - Pragya Singh
- Department of Electrical Engineering and Computer Science
- National Chiao Tung University
- Hsinchu 30010
- Taiwan
| | - Meyya Meyyappan
- Center for Nanotechnology
- NASA Ames Research Center
- Moffett Field
- Mountain View
- USA
| | | |
Collapse
|
77
|
Berberich J, Li T, Sahle-Demessie E. Biosensors for Monitoring Water Pollutants: A Case Study With Arsenic in Groundwater. SEP SCI TECHNOL 2019. [DOI: 10.1016/b978-0-12-815730-5.00011-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
78
|
Guo KH, Lu KH, Yeh YC. Cell-Based Biosensor with Dual Signal Outputs for Simultaneous Quantification of Phenylacetic Acid and Phenylethylamine. ACS Synth Biol 2018; 7:2790-2795. [PMID: 30418753 DOI: 10.1021/acssynbio.8b00416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Despite the importance of 2-phenylacetic acid, a plant hormone in the endogenous auxin family, its biosynthesis pathway has yet to be elucidated. In this study, we developed a novel whole-cell biosensor for the simultaneous quantification of 2-phenylacetic acid (PA) and 2-phenylethylamine (PEA) through the regulation of bacterial catabolism of aromatic compounds. We used the PA regulon to enable the recognition of PA and PEA. Differentiation of PEA from PA involves the incorporation of the FeaR regulon within the same whole-cell biosensor to report the presence of aromatic amines. The proposed system is highly sensitive to PA as well as PEA.
Collapse
Affiliation(s)
- Kai-Hong Guo
- Department of Chemistry, National Taiwan Normal University, 88, Section 4, Tingzhou Road, Taipei 11677, Taiwan
| | - Kun-Hua Lu
- Department of Chemistry, National Taiwan Normal University, 88, Section 4, Tingzhou Road, Taipei 11677, Taiwan
| | - Yi-Chun Yeh
- Department of Chemistry, National Taiwan Normal University, 88, Section 4, Tingzhou Road, Taipei 11677, Taiwan
| |
Collapse
|
79
|
Han J, Liang C, Cui Y, Xiong L, Guo X, Yuan X, Yang D. Encapsulating Microorganisms inside Electrospun Microfibers as a Living Material Enables Room-Temperature Storage of Microorganisms. ACS APPLIED MATERIALS & INTERFACES 2018; 10:38799-38806. [PMID: 30339345 DOI: 10.1021/acsami.8b14978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Room-temperature storage and transportation of microorganisms maximize the power of microorganisms in healthcare, energy, and environment. Recently, paper-based biotechnologies have been developed to enable room-temperature storage of a variety of nonliving biosystems such as diagnostic devices and cell-free systems. Herein, room-temperature storage of living microorganisms is realized by an electrospun nonwoven paper containing convex region, which is composed of coiled microfibers with dense distribution of microorganisms. Microorganisms are encapsulated into the microfibers and remain intact after electrospinning. Poly(ethylene oxide) is used as polymer matrix, and glycerol and dextran are used as additives. When the contents of glycerol and dextran are optimized as 5 and 0.4%, the room-temperature time is prolonged to 2 days, more than 8 folds as compared with the control group. Upon demand, the microorganisms can be activated by adding water and used for culturing microorganisms directly. Furthermore, mechanisms which account for microbial activity and storage are studied. Our microfiber-based strategy is universal for the room-temperature storage of prokaryotic and eukaryotic microorganisms in the solid formulation. Besides, our microorganism/polymer complex structures represent novel living materials via a bottom-up strategy, which are of great potential for new biomedical applications.
Collapse
|
80
|
Prabhakaran R, Rajkumar SN, Ramprasath T, Selvam GS. Identification of promoter P cadR, in silico characterization of cadmium resistant gene cadR and molecular cloning of promoter P cadR from Pseudomonas aeruginosa BC15. Toxicol Ind Health 2018; 34:819-833. [PMID: 30407121 DOI: 10.1177/0748233718795934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cadmium (Cd) remediation in Pseudomonas aeruginosa is achieved through the function of two vital genes, cadA and cadR, that code for P-type ATPase (CadA) and transcription regulatory protein (CadR), respectively. Although numerous studies are available on these metal-sensing and regulatory proteins, the promoter of these genes, metal sensing and binding ability, are poorly understood. The present work is aimed at the characterization of the CadR protein, identification of the PcadR promoter and protein-promoter-metal binding affinity using bioinformatics and to validate the results by cloning the PcadR promoter in Escherichia coli DH5α. The promoter regions and its curvature were identified and analysed using PePPER software (University of Groningen, The Netherland) and the Bendit program (Version: v.1.0), respectively. Using Phyre, the three-dimensional structure of CadR was modelled, and the structure was validated by Ramachandran plots. The DNA-binding domain was present in the N-terminal region of CadR. A dimeric interface was observed in helix-turn-helix and metal ion-binding sites at the C-terminal. Docking studies showed higher affinity of Cd to both CadR (Atomic contact energy = -15.04 kcal/Mol) and PcadR (Atomic contact energy = -40.18 kcal/Mol) when compared to other metal ions. CadR with PcadR showed the highest binding affinity (Atomic contact energy= -250.40 kcal/Mol) when compared with PcadA. In vitro studies using green fluorescent protein tagged with PcadR (gfp-PcadR) cloned in E. coli-expressed gfp protein in a concentration-dependent manner upon Cd exposure. Based on our in silico studies and in vitro molecular cloning analysis, we conclude that PcadR and CadR are active only in the presence of Cd. The CadR protein has the highest binding affinity with PcadR. As it became apparent that the cadR gene regulates the PcadR activity in the presence of Cd with high specificity, and the cadR and PcadR can be used as a biological tool for development of a microbial biosensor.
Collapse
Affiliation(s)
- Rajkumar Prabhakaran
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | | | - Tharmarajan Ramprasath
- Center for Molecular and Translational Medicine, Petit Science Center, Georgia State University, Atlanta, GA, USA
| | - Govindan Sadasivam Selvam
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| |
Collapse
|
81
|
Caglar MU, Hockenberry AJ, Wilke CO. Predicting bacterial growth conditions from mRNA and protein abundances. PLoS One 2018; 13:e0206634. [PMID: 30388153 PMCID: PMC6214550 DOI: 10.1371/journal.pone.0206634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 10/16/2018] [Indexed: 01/30/2023] Open
Abstract
Cells respond to changing nutrient availability and external stresses by altering the expression of individual genes. Condition-specific gene expression patterns may thus provide a promising and low-cost route to quantifying the presence of various small molecules, toxins, or species-interactions in natural environments. However, whether gene expression signatures alone can predict individual environmental growth conditions remains an open question. Here, we used machine learning to predict 16 closely-related growth conditions using 155 datasets of E. coli transcript and protein abundances. We show that models are able to discriminate between different environmental features with a relatively high degree of accuracy. We observed a small but significant increase in model accuracy by combining transcriptome and proteome-level data, and we show that measurements from stationary phase cells typically provide less useful information for discriminating between conditions as compared to exponentially growing populations. Nevertheless, with sufficient training data, gene expression measurements from a single species are capable of distinguishing between environmental conditions that are separated by a single environmental variable.
Collapse
Affiliation(s)
- M. Umut Caglar
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Adam J. Hockenberry
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Claus O. Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
| |
Collapse
|
82
|
Xiang Y, Dalchau N, Wang B. Scaling up genetic circuit design for cellular computing: advances and prospects. NATURAL COMPUTING 2018; 17:833-853. [PMID: 30524216 PMCID: PMC6244767 DOI: 10.1007/s11047-018-9715-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or FALSE digital logic and graded analog computation. Key principles for gene circuit engineering include modularity, orthogonality, predictability and reliability. Initial circuits in the field were small and hampered by a lack of modular and orthogonal components, however in recent years the library of available parts has increased vastly. New tools for high throughput DNA assembly and characterization have been developed enabling rapid prototyping, systematic in situ characterization, as well as automated design and assembly of circuits. Recently implemented computing paradigms in circuit memory and distributed computing using cell consortia will also be discussed. Finally, we will examine existing challenges in building predictable large-scale circuits including modularity, context dependency and metabolic burden as well as tools and methods used to resolve them. These new trends and techniques have the potential to accelerate design of larger gene circuits and result in an increase in our basic understanding of circuit and host behaviour.
Collapse
Affiliation(s)
- Yiyu Xiang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| | | | - Baojun Wang
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF UK
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, EH9 3JR UK
| |
Collapse
|
83
|
Khatun MA, Hoque MA, Zhang Y, Lu T, Cui L, Zhou NY, Feng Y. Bacterial Consortium-Based Sensing System for Detecting Organophosphorus Pesticides. Anal Chem 2018; 90:10577-10584. [DOI: 10.1021/acs.analchem.8b02709] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
84
|
Tang Q, Lu T, Liu SJ. Developing a Synthetic Biology Toolkit for Comamonas testosteroni, an Emerging Cellular Chassis for Bioremediation. ACS Synth Biol 2018; 7:1753-1762. [PMID: 29860823 DOI: 10.1021/acssynbio.7b00430] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Synthetic biology is rapidly evolving into a new phase that emphasizes real-world applications such as environmental remediation. Recently, Comamonas testosteroni has become a promising chassis for bioremediation due to its natural pollutant-degrading capacity; however, its application is hindered by the lack of fundamental gene expression tools. Here, we present a synthetic biology toolkit that enables rapid creation of functional gene circuits in C. testosteroni. We first built a shuttle system that allows efficient circuit construction in E. coli and necessary phenotypic testing in C. testosteroni. Then, we tested a set of wildtype inducible promoters, and further used a hybrid strategy to create engineered promoters to expand expression strength and dynamics. Additionally, we tested the T7 RNA Polymerase-PT7 promoter system and reduced its leaky expression through promoter mutation for gene expression. By coupling random library construction with FACS screening, we further developed a synthetic T7 promoter library to confer a wider range of expression strength and dynamic characteristics. This study provides a set of valuable tools to engineer gene circuits in C. testosteroni, facilitating the establishment of the organism as a useful microbial chassis for bioremediation purposes.
Collapse
Affiliation(s)
- Qiang Tang
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Environmental Microbiology Research Center, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
85
|
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.
Collapse
|
86
|
Jia X, Zhao T, Liu Y, Bu R, Wu K. Gene circuit engineering to improve the performance of a whole-cell lead biosensor. FEMS Microbiol Lett 2018; 365:5046421. [DOI: 10.1093/femsle/fny157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/26/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Xiaoqiang Jia
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Tianjin University), Ministry of Education, Tianjin 300072, China
- Synthetic Biology Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Tingting Zhao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yilin Liu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Rongrong Bu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Kang Wu
- Department of Chemical Engineering, University of New Hampshire, Durham NH 03824, USA
| |
Collapse
|
87
|
Cheng HY, Masiello CA, Del Valle I, Gao X, Bennett GN, Silberg JJ. Ratiometric Gas Reporting: A Nondisruptive Approach To Monitor Gene Expression in Soils. ACS Synth Biol 2018; 7:903-911. [PMID: 29366321 DOI: 10.1021/acssynbio.7b00405] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fluorescent proteins are ubiquitous tools that are used to monitor the dynamic functions of natural and synthetic genetic circuits. However, these visual reporters can only be used in transparent settings, a limitation that complicates nondisruptive measurements of gene expression within many matrices, such as soils and sediments. We describe a new ratiometric gas reporting method for nondisruptively monitoring gene expression within hard-to-image environmental matrices. With this approach, C2H4 is continuously synthesized by ethylene forming enzyme to provide information on viable cell number, and CH3Br is conditionally synthesized by placing a methyl halide transferase gene under the control of a conditional promoter. We show that ratiometric gas reporting enables the creation of Escherichia coli biosensors that report on acylhomoserine lactone (AHL) autoinducers used for quorum sensing by Gram-negative bacteria. Using these biosensors, we find that an agricultural soil decreases the bioavailable concentration of a long-chain AHL up to 100-fold. We also demonstrate that these biosensors can be used in soil to nondisruptively monitor AHLs synthesized by Rhizobium leguminosarum and degraded by Bacillus thuringiensis. Finally, we show that this new reporting approach can be used in Shewanella oneidensis, a bacterium that lives in sediments.
Collapse
|
88
|
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
| |
Collapse
|
89
|
Ueki T, DiDonato LN, Lovley DR. Toward establishing minimum requirements for extracellular electron transfer in Geobacter sulfurreducens. FEMS Microbiol Lett 2017; 364:3796320. [PMID: 28472266 DOI: 10.1093/femsle/fnx093] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/03/2017] [Indexed: 11/12/2022] Open
Abstract
The highly redundant pathways for extracellular electron transfer in Geobacter sulfurreducens must be simplified for this microorganism to serve as an effective chassis for applications such as the development of sensors and biocomputing. Five homologs of the periplasmic c-type cytochromes, PpcA-E, offer the possibility of multiple routes of electron transfer across the periplasm. The presence of a large number of outer membrane c-type cytochromes allows G. sulfurreducens to adapt to disruption of an electron transfer pathway in the outer membrane. A strain in which genes for all five periplasmic cytochromes, PpcA-E, were deleted did not reduce Fe(III). Introducing ppcA under the control of an IPTG-inducible system in the quintuple deletion strain yielded a strain that reduced Fe(III) only in the presence of IPTG. A strain lacking known major outer membrane cytochromes, OmcB, OmcE, OmcS and OmcT, and putative functional homologs of OmcB, did not reduce Fe(III). Introduction of omcB in this septuple deletion strain restored the ability to reduce Fe(III). These results demonstrate that it is possible to trim redundancy from the extracellular electron transfer pathways in G. sulfurreducens in order to construct strains with defined extracellular electron transfer routes.
Collapse
|
90
|
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]
|
91
|
Abstract
Synthetically engineered cells are powerful and potentially useful biosensors, but it remains problematic to deploy such systems due to practical difficulties and biosafety concerns. To overcome these hurdles, we developed a microfluidic device that serves as an interface between an engineered cellular system, environment, and user. We created a biodisplay consisting of 768 individually programmable biopixels and demonstrated that it can perform multiplexed, continuous sampling. The biodisplay detected 10 μg/L sodium-arsenite in tap water using a research grade fluorescent microscope, and reported arsenic contamination down to 20 μg/L with an easy to interpret "skull and crossbones" symbol detectable with a low-cost USB microscope or by eye. The biodisplay was designed to prevent release of chemical or biological material to avoid environmental contamination. The microfluidic biodisplay thus provides a practical solution for the deployment and application of engineered cellular systems.
Collapse
Affiliation(s)
- Francesca Volpetti
- Institute of Bioengineering,
School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Ekaterina Petrova
- Institute of Bioengineering,
School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | - Sebastian J. Maerkl
- Institute of Bioengineering,
School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| |
Collapse
|
92
|
Dvořák P, Nikel PI, Damborský J, de Lorenzo V. Bioremediation 3 . 0 : Engineering pollutant-removing bacteria in the times of systemic biology. Biotechnol Adv 2017; 35:845-866. [DOI: 10.1016/j.biotechadv.2017.08.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 01/07/2023]
|
93
|
Bereza-Malcolm L, Aracic S, Kannan R, Mann G, Franks AE. Functional characterization of Gram-negative bacteria from different genera as multiplex cadmium biosensors. Biosens Bioelectron 2017; 94:380-387. [PMID: 28319906 DOI: 10.1016/j.bios.2017.03.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 12/22/2022]
Abstract
Widespread presence of cadmium in soil and water systems is a consequence of industrial and agricultural processes. Subsequent accumulation of cadmium in food and drinking water can result in accidental consumption of dangerous concentrations. As such, cadmium environmental contamination poses a significant threat to human health. Development of microbial biosensors, as a novel alternative method for in situ cadmium detection, may reduce human exposure by complementing traditional analytical methods. In this study, a multiplex cadmium biosensing construct was assembled by cloning a single-output cadmium biosensor element, cadRgfp, and a constitutively expressed mrfp1 onto a broad-host range vector. Incorporation of the duplex fluorescent output [green and red fluorescence proteins] allowed measurement of biosensor functionality and viability. The biosensor construct was tested in several Gram-negative bacteria including Pseudomonas, Shewanella and Enterobacter. The multiplex cadmium biosensors were responsive to cadmium concentrations ranging from 0.01 to 10µgml-1, as well as several other heavy metals, including arsenic, mercury and lead at similar concentrations. The biosensors were also responsive within 20-40min following exposure to 3µgml-1 cadmium. This study highlights the importance of testing biosensor constructs, developed using synthetic biology principles, in different bacterial genera.
Collapse
Affiliation(s)
- Lara Bereza-Malcolm
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Plenty Road, Melbourne, Victoria 3086, Australia.
| | - Sanja Aracic
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Plenty Road, Melbourne, Victoria 3086, Australia.
| | - Ruban Kannan
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Plenty Road, Melbourne, Victoria 3086, Australia.
| | - Gülay Mann
- Land Division, Defence Science and Technology Group, Melbourne, Victoria 3207, Australia.
| | - Ashley E Franks
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Plenty Road, Melbourne, Victoria 3086, Australia.
| |
Collapse
|
94
|
Rampley CPN, Davison PA, Qian P, Preston GM, Hunter CN, Thompson IP, Wu LJ, Huang WE. Development of SimCells as a novel chassis for functional biosensors. Sci Rep 2017; 7:7261. [PMID: 28775370 PMCID: PMC5543166 DOI: 10.1038/s41598-017-07391-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/28/2017] [Indexed: 01/31/2023] Open
Abstract
This work serves as a proof-of-concept for bacterially derived SimCells (Simple Cells), which contain the cell machinery from bacteria and designed DNA (or potentially a simplified genome) to instruct the cell to carry out novel, specific tasks. SimCells represent a reprogrammable chassis without a native chromosome, which can host designed DNA to perform defined functions. In this paper, the use of Escherichia coli MC1000 ∆minD minicells as a non-reproducing chassis for SimCells was explored, as demonstrated by their ability to act as sensitive biosensors for small molecules. Highly purified minicells derived from E. coli strains containing gene circuits for biosensing were able to transduce the input signals from several small molecules (glucarate, acrylate and arabinose) into the production of green fluorescent protein (GFP). A mathematical model was developed to fit the experimental data for induction of gene expression in SimCells. The intracellular ATP level was shown to be important for SimCell function. A purification and storage protocol was developed to prepare SimCells which could retain their functions for an extended period of time. This study demonstrates that SimCells are able to perform as ‘smart bioparticles’ controlled by designed gene circuits.
Collapse
Affiliation(s)
- Cordelia P N Rampley
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Paul A Davison
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Pu Qian
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Gail M Preston
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, Oxford, United Kingdom
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom
| | - Ling Juan Wu
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, United Kingdom
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, United Kingdom.
| |
Collapse
|
95
|
Gui Q, Lawson T, Shan S, Yan L, Liu Y. The Application of Whole Cell-Based Biosensors for Use in Environmental Analysis and in Medical Diagnostics. SENSORS 2017; 17:s17071623. [PMID: 28703749 PMCID: PMC5539819 DOI: 10.3390/s17071623] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/07/2017] [Accepted: 07/08/2017] [Indexed: 01/11/2023]
Abstract
Various whole cell-based biosensors have been reported in the literature for the last 20 years and these reports have shown great potential for their use in the areas of pollution detection in environmental and in biomedical diagnostics. Unlike other reviews of this growing field, this mini-review argues that: (1) the selection of reporter genes and their regulatory proteins are directly linked to the performance of celllular biosensors; (2) broad enhancements in microelectronics and information technologies have also led to improvements in the performance of these sensors; (3) their future potential is most apparent in their use in the areas of medical diagnostics and in environmental monitoring; and (4) currently the most promising work is focused on the better integration of cellular sensors with nano and micro scaled integrated chips. With better integration it may become practical to see these cells used as (5) real-time portable devices for diagnostics at the bedside and for remote environmental toxin detection and this in situ application will make the technology commonplace and thus as unremarkable as other ubiquitous technologies.
Collapse
Affiliation(s)
- Qingyuan Gui
- Laboratory of Nanoscale Biosensing and Bioimaging, Instiute of Advanced Materials for Nano-Bio Applications, School of Ophthalmology and Optometry, Wenzhou Medical University, 270 Xueyuanxi Road, Wenzhou 325027, China.
| | - Tom Lawson
- ARC Center of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia.
| | - Suyan Shan
- Laboratory of Nanoscale Biosensing and Bioimaging, Instiute of Advanced Materials for Nano-Bio Applications, School of Ophthalmology and Optometry, Wenzhou Medical University, 270 Xueyuanxi Road, Wenzhou 325027, China.
| | - Lu Yan
- Laboratory of Nanoscale Biosensing and Bioimaging, Instiute of Advanced Materials for Nano-Bio Applications, School of Ophthalmology and Optometry, Wenzhou Medical University, 270 Xueyuanxi Road, Wenzhou 325027, China.
| | - Yong Liu
- Laboratory of Nanoscale Biosensing and Bioimaging, Instiute of Advanced Materials for Nano-Bio Applications, School of Ophthalmology and Optometry, Wenzhou Medical University, 270 Xueyuanxi Road, Wenzhou 325027, China.
| |
Collapse
|
96
|
Wang H, Ling MH, Chua TK, Poh CL. Two cellular resource‐based models linking growth and parts characteristics aids the study and optimisation of synthetic gene circuits. ENGINEERING BIOLOGY 2017. [DOI: 10.1049/enb.2017.0005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Huijuan Wang
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Maurice H.T. Ling
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Tze Kwang Chua
- School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering National University of Singapore Singapore 117583 Singapore
| |
Collapse
|
97
|
Cayron J, Prudent E, Escoffier C, Gueguen E, Mandrand-Berthelot MA, Pignol D, Garcia D, Rodrigue A. Pushing the limits of nickel detection to nanomolar range using a set of engineered bioluminescent Escherichia coli. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:4-14. [PMID: 26498802 DOI: 10.1007/s11356-015-5580-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
The detection of nickel in water is of great importance due to its harmfulness for living organism. A way to detect Ni is the use of whole-cell biosensors. The aim of the present work was to build a light-emitting bacterial biosensor for the detection of Ni with high specificity and low detection limit properties. For that purpose, the regulatory circuit implemented relied on the RcnR Ni/Co metallo-regulator and its rcnA natural target promoter fused to the lux reporter genes. To convert RcnR to specifically detect Ni, several mutations were tested and the C35A retained. Deleting the Ni efflux pump rcnA and introducing genes encoding several Ni-uptake systems lowered the detection thresholds. When these constructs were assayed in several Escherichia coli strains, it appeared that the detection thresholds were highly variable. The TD2158 wild-type E. coli gave rise to a biosensor ten times more active and sensitive than its W3110 E. coli K12 equivalent. This biosensor was able to confidently detect Ni concentrations as little as 80 nM (4.7 μg l-1), which makes its use compatible with the norms governing the drinking water quality.
Collapse
Affiliation(s)
- Julien Cayron
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Elsa Prudent
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Camille Escoffier
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Erwan Gueguen
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - Marie-Andrée Mandrand-Berthelot
- Université de Lyon, Lyon, 69003, France
- INSA de Lyon, Villeurbanne, 69621, France
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France
| | - David Pignol
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Daniel Garcia
- CEA, DSV, IBEB, Lab Bioenerget Cellulaire, Saint-Paul-lez-Durance, France
- CNRS, UMR Biol Veget & Microbiol Environ, Aix-Marseille Université, Saint-Paul-lez-Durance, 13108, France
| | - Agnès Rodrigue
- Université de Lyon, Lyon, 69003, France.
- INSA de Lyon, Villeurbanne, 69621, France.
- CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Lyon 1, 10 rue Dubois, 69622, Villeurbanne Cedex, France.
| |
Collapse
|
98
|
Li S, Zhou L, Yao Y, Fan K, Li Z, Zhang L, Wang W, Yang K. A platform for the development of novel biosensors by configuring allosteric transcription factor recognition with amplified luminescent proximity homogeneous assays. Chem Commun (Camb) 2017; 53:99-102. [DOI: 10.1039/c6cc07244e] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using isolated allosteric transcription factors as recognition elements, a versatile platform was established in vitro to develop sensitive biosensors for the detection of various chemicals.
Collapse
Affiliation(s)
- Shanshan Li
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Li Zhou
- Institute of Health Sciences
- Anhui University
- Hefei
- China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Zilong Li
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Lixin Zhang
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| | - Keqian Yang
- State Key Laboratory of Microbial Resources
- Institute of Microbiology
- Chinese Academy of Sciences
- 100101 Beijing
- China
| |
Collapse
|
99
|
Kou S, Yang Z, Luo J, Sun F. Entirely recombinant protein-based hydrogels for selective heavy metal sequestration. Polym Chem 2017. [DOI: 10.1039/c7py01206c] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Green mining and heavy metal remediation enabled by metalloprotein hydrogels.
Collapse
Affiliation(s)
- Songzi Kou
- Department of Chemical and Biological Engineering
- The Hong Kong University of Science and Technology
- Kowloon
- Hong Kong
| | - Zhongguang Yang
- Department of Chemical and Biological Engineering
- The Hong Kong University of Science and Technology
- Kowloon
- Hong Kong
| | - Jiren Luo
- Department of Chemical and Biological Engineering
- The Hong Kong University of Science and Technology
- Kowloon
- Hong Kong
| | - Fei Sun
- Department of Chemical and Biological Engineering
- The Hong Kong University of Science and Technology
- Kowloon
- Hong Kong
| |
Collapse
|
100
|
Bereza-Malcolm L, Aracic S, Franks AE. Development and Application of a Synthetically-Derived Lead Biosensor Construct for Use in Gram-Negative Bacteria. SENSORS (BASEL, SWITZERLAND) 2016; 16:E2174. [PMID: 27999352 PMCID: PMC5191153 DOI: 10.3390/s16122174] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 02/05/2023]
Abstract
The use of lead in manufacturing has decreased significantly over the last few decades. However, previous widespread use of lead-containing products and their incorrect disposal has resulted in environmental contamination. Accumulation of harmful quantities of lead pose a threat to all living organisms, through inhalation, ingestion, or direct contact, resulting in lead poisoning. This study utilized synthetic biology principles to develop plasmid-based whole-cell bacterial biosensors for detection of lead. The genetic element of the lead biosensor construct consists of pbrR, which encodes the regulatory protein, together with its divergent promoter region and a promoterless gfp. GFP expression is controlled by PbrR in response to the presence of lead. The lead biosensor genetic element was cloned onto a low-copy number broad host range plasmid, which can stably exist in a range of laboratory and environmental isolates, including Pseudomonas, Shewanella, and Enterobacter. The biosensors constructed were found to be sensitive, rapid, and specific and could, as such, serve as monitoring tools for lead-contaminated water.
Collapse
Affiliation(s)
- Lara Bereza-Malcolm
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Sanja Aracic
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Ashley E Franks
- Applied and Environmental Microbiology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria 3086, Australia.
| |
Collapse
|