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Ma Z, Meliana C, Munawaroh HSH, Karaman C, Karimi-Maleh H, Low SS, Show PL. Recent advances in the analytical strategies of microbial biosensor for detection of pollutants. CHEMOSPHERE 2022; 306:135515. [PMID: 35772520 DOI: 10.1016/j.chemosphere.2022.135515] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/10/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
Microbial biosensor which integrates different types of microorganisms, such as bacteria, microalgae, fungi, and virus have become suitable technologies to address limitations of conventional analytical methods. The main applications of biosensors include the detection of environmental pollutants, pathogenic bacteria and compounds related to illness, and food quality. Each type of microorganisms possesses advantages and disadvantages with different mechanisms to detect the analytes of interest. Furthermore, there is an increasing trend in genetic modifications for the development of microbial biosensors due to potential for high-throughput analysis and portability. Many review articles have discussed the applications of microbial biosensor, but many of them focusing only about bacterial-based biosensor although other microbes also possess many advantages. Additionally, reviews on the applications of all microbes as biosensor especially viral and microbial fuel cell biosensors are also still limited. Therefore, this review summarizes all the current applications of bacterial-, microalgal-, fungal-, viral-based biosensor in regard to environmental, food, and medical-related applications. The underlying mechanism of each microbes to detect the analytes are also discussed. Additionally, microbial fuel cell biosensors which have great potential in the future are also discussed. Although many advantageous microbial-based biosensors have been discovered, other areas such as forensic detection, early detection of bacteria or virus species that can lead to pandemics, and others still need further investigation. With that said, microbial-based biosensors have promising potential for vast applications where the biosensing performance of various microorganisms are presented in this review along with future perspectives to resolve problems related on microbial biosensors.
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Affiliation(s)
- Zengling Ma
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China.
| | - Catarina Meliana
- Department of Food Science and Nutrition, Faculty of Life Science, Indonesia International Institute of Life Sciences, Jakarta, 13210, Indonesia
| | - Heli Siti Halimatul Munawaroh
- Study Program of Chemistry, Department of Chemistry Education, Universitas Pendidikan Indonesia, Jalan Dr. Setiabudhi 229, Bandung, 40154, Indonesia
| | - Ceren Karaman
- Akdeniz University, Department of Electricity and Energy, Antalya, 07070, Turkey
| | - Hassan Karimi-Maleh
- School of Resources and Environment, University of Electronic Science and Technology of China, P.O. Box 611731, Xiyuan Ave, Chengdu, PR China; Department of Chemical Engineering and Energy, Quchan University of Technology, Quchan, 9477177870, Iran
| | - Sze Shin Low
- Research Centre of Life Science and Healthcare, China Beacons Institute, University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo, 315100, Zhejiang, China.
| | - Pau Loke Show
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035, China; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
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2
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Mendoza JI, Lescano J, Soncini FC, Checa SK. The protein scaffold calibrates metal specificity and activation in MerR sensors. Microb Biotechnol 2022; 15:2992-3002. [PMID: 36134649 PMCID: PMC9733647 DOI: 10.1111/1751-7915.14151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 12/14/2022] Open
Abstract
MerR metalloregulators are the central components of many biosensor platforms designed to report metal contamination. However, most MerR proteins are non-specific. This makes it difficult to apply these biosensors in the analysis of real environmental samples. On-demand implementation of molecular engineering to modify the MerR metal preferences is innovative, although it does not always yield the expected results. As the metal binding loop region (MBL) of these sensors has been proposed to be the major modulator of their specificity, we surgically switched this region for that of well-characterized specific and non-specific homologues. We found that identical modifications in different MerR proteins result in synthetic sensors displaying particular metal-detection patterns that cannot be predicted from the nature of the assembled modules. For instance, the MBL from a native Hg(II) sensor provided non-specificity or specificity toward Hg(II) or Cd(II) depending on the MerR scaffold into which it was integrated. These and other evidences reveal that residues outside the MBL are required to modulate ion recognition and transduce the input signal to the target promoter. Revealing their identity and their interactions with other residues is a critical step toward the design of more efficient biosensor devices for environmental metal monitoring.
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Affiliation(s)
- Julián I. Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina
| | - Julián Lescano
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina
| | - Fernando C. Soncini
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
| | - Susana K. Checa
- Instituto de Biología Molecular y Celular de Rosario (IBR)Universidad Nacional de Rosario (UNR)‐Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)RosarioArgentina,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
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3
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A Recombinase-Based Genetic Circuit for Heavy Metal Monitoring. BIOSENSORS 2022; 12:bios12020122. [PMID: 35200383 PMCID: PMC8870050 DOI: 10.3390/bios12020122] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/21/2022]
Abstract
Rapid progress in the genetic circuit design enabled whole-cell biosensors (WCBs) to become prominent in detecting an extensive range of analytes with promise in many fields, from medical diagnostics to environmental toxicity assessment. However, several drawbacks, such as high background signal or low precision, limit WCBs to transfer from proof-of-concept studies to real-world applications, particularly for heavy metal toxicity monitoring. For an alternative WCB module design, we utilized Bxb1 recombinase that provides tight control as a switch to increase dose-response behavior concerning leakiness. The modularity of Bxb1 recombinase recognition elements allowed us to combine an engineered semi-specific heat shock response (HSR) promoter, sensitive to stress conditions including toxic ions such as cadmium, with cadmium resistance regulatory elements; a cadmium-responsive transcription factor and its cognitive promoter. We optimized the conditions for the recombinase-based cadmium biosensor to obtain increased fold change and shorter response time. This system can be expanded for various heavy metals to make an all-in-one type of WCB, even using semi-specific parts of a sensing system.
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4
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Wu Y, Wang CW, Wang D, Wei N. A Whole-Cell Biosensor for Point-of-Care Detection of Waterborne Bacterial Pathogens. ACS Synth Biol 2021; 10:333-344. [PMID: 33496568 DOI: 10.1021/acssynbio.0c00491] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water contamination by pathogenic bacteria is a major public health concern globally. Monitoring bacterial contamination in water is critically important to protect human health, but this remains a critical challenge. Engineered whole-cell biosensors created through synthetic biology hold great promise for rapid and cost-effective detection of waterborne pathogens. In this study, we created a novel whole-cell biosensor to detect water contamination by Pseudomonas aeruginosa and Burkholderia pseudomallei, which are two critical bacterial pathogens and are recognized as common causative agents for waterborne diseases. The biosensor detects the target bacterial pathogens by responding to the relevant quorum sensing signal molecules. Particularly, this study constructed and characterized the biosensor on the basis of the QscR quorum sensing signal system for the first time. We first designed and constructed a QscR on the basis of the sensing module in the E. coli host cell and integrated the QscR sensing module with a reporting module that expressed an enhanced green fluorescent protein (EGFP). The results demonstrated that the biosensor had high sensitivity in response to the quorum sensing signals of the target bacterial pathogens. We further engineered a biosensor that expressed a red pigment lycopene in the reporting module to produce a visible signal readout for the pathogen detection. Additionally, we investigated the feasibility of a paper-based assay by immobilizing the lycopene-based whole-cell biosensor on paper with the aim to build a prototype for developing portable detection devices. The biosensor would provide a simple and inexpensive alternative for timely and point-of-care detection of water contamination and protect human health.
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5
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Baya G, Muhindi S, Ngendahimana V, Caguiat J. Potential Whole-Cell Biosensors for Detection of Metal Using MerR Family Proteins from Enterobacter sp. YSU and Stenotrophomonas maltophilia OR02. MICROMACHINES 2021; 12:mi12020142. [PMID: 33572806 PMCID: PMC7911910 DOI: 10.3390/mi12020142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 01/15/2023]
Abstract
Cell-based biosensors harness a cell's ability to respond to the environment by repurposing its sensing mechanisms. MerR family proteins are activator/repressor switches that regulate the expression of bacterial metal resistance genes and have been used in metal biosensors. Upon metal binding, a conformational change switches gene expression from off to on. The genomes of the multimetal resistant bacterial strains, Stenotrophomonas maltophilia Oak Ridge strain 02 (S. maltophilia 02) and Enterobacter sp. YSU, were recently sequenced. Sequence analysis and gene cloning identified three mercury resistance operons and three MerR switches in these strains. Transposon mutagenesis and sequence analysis identified Enterobacter sp. YSU zinc and copper resistance operons, which appear to be regulated by the protein switches, ZntR and CueR, respectively. Sequence analysis and reverse transcriptase polymerase chain reaction (RT-PCR) showed that a CueR switch appears to activate a S. maltophilia 02 copper transport gene in the presence of CuSO4 and HAuCl4·3H2O. In previous studies, genetic engineering replaced metal resistance genes with the reporter genes for β-galactosidase, luciferase or the green fluorescence protein (GFP). These produce a color change of a reagent, produce light, or fluoresce in the presence of ultraviolet (UV) light, respectively. Coupling these discovered operons with reporter genes has the potential to create whole-cell biosensors for HgCl2, ZnCl2, CuSO4 and HAuCl4·3H2O.
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Affiliation(s)
- Georgina Baya
- Department of Biological and Chemical Sciences, Youngstown State University, Youngstown, OH 44555, USA;
| | - Stephen Muhindi
- Department of Biological Sciences, University of Toledo, Toledo, OH 43606, USA;
| | - Valentine Ngendahimana
- Biology Department, Lone Star College-CyFair, 9191 Barker Cypress Rd, Cypress, TX 77433, USA;
| | - Jonathan Caguiat
- Department of Biological and Chemical Sciences, Youngstown State University, Youngstown, OH 44555, USA;
- Correspondence: ; Tel.: +1-330-941-2063
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6
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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7
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Mendoza JI, Soncini FC, Checa SK. Engineering of a Au-sensor to develop a Hg-specific, sensitive and robust whole-cell biosensor for on-site water monitoring. Chem Commun (Camb) 2020; 56:6590-6593. [PMID: 32406434 DOI: 10.1039/d0cc01323d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A highly sensitive and specific Hg-whole-cell biosensor was developed from a non-selective variant of the Au sensor GolS and its regulatory pathway. The performance of this analytical tool was validated under laboratory and field-like conditions. This biosensor can be easily applied in cost-effective and portable semiquantitative devices to report Hg contamination in water.
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Affiliation(s)
- Julián I Mendoza
- Instituto de Biología Molecular y Celular de Rosario (IBR), Universidad Nacional de Rosario (UNR)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Argentina.
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8
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Synthetic biology for microbial heavy metal biosensors. Anal Bioanal Chem 2017; 410:1191-1203. [DOI: 10.1007/s00216-017-0751-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/23/2017] [Accepted: 11/07/2017] [Indexed: 11/26/2022]
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9
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Dubé S, Orr D, Dempsey B, Wieden HJ. A synthetic biology approach to integrative high school STEM training. Nat Biotechnol 2017; 35:591-595. [PMID: 28591116 DOI: 10.1038/nbt.3896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sutherland Dubé
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Doug Orr
- Teaching Centre, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Brian Dempsey
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Hans-Joachim Wieden
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.,Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Alberta, Canada
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10
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Goers L, Ainsworth C, Goey CH, Kontoravdi C, Freemont PS, Polizzi KM. Whole-cell Escherichia coli lactate biosensor for monitoring mammalian cell cultures during biopharmaceutical production. Biotechnol Bioeng 2017; 114:1290-1300. [PMID: 28112405 PMCID: PMC5412874 DOI: 10.1002/bit.26254] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/11/2017] [Accepted: 01/19/2017] [Indexed: 02/06/2023]
Abstract
Many high-value added recombinant proteins, such as therapeutic glycoproteins, are produced using mammalian cell cultures. In order to optimize the productivity of these cultures it is important to monitor cellular metabolism, for example the utilization of nutrients and the accumulation of metabolic waste products. One metabolic waste product of interest is lactic acid (lactate), overaccumulation of which can decrease cellular growth and protein production. Current methods for the detection of lactate are limited in terms of cost, sensitivity, and robustness. Therefore, we developed a whole-cell Escherichia coli lactate biosensor based on the lldPRD operon and successfully used it to monitor lactate concentration in mammalian cell cultures. Using real samples and analytical validation we demonstrate that our biosensor can be used for absolute quantification of metabolites in complex samples with high accuracy, sensitivity, and robustness. Importantly, our whole-cell biosensor was able to detect lactate at concentrations more than two orders of magnitude lower than the industry standard method, making it useful for monitoring lactate concentrations in early phase culture. Given the importance of lactate in a variety of both industrial and clinical contexts we anticipate that our whole-cell biosensor can be used to address a range of interesting biological questions. It also serves as a blueprint for how to capitalize on the wealth of genetic operons for metabolite sensing available in nature for the development of other whole-cell biosensors. Biotechnol. Bioeng. 2017;114: 1290-1300. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Lisa Goers
- Department of Life SciencesImperial College LondonLondonSW7 2AZUK
- Centre for Synthetic Biology and InnovationImperial College LondonLondonUK
| | - Catherine Ainsworth
- Centre for Synthetic Biology and InnovationImperial College LondonLondonUK
- Department of BioengineeringImperial College LondonLondonUK
| | - Cher Hui Goey
- Department of Chemical EngineeringImperial College LondonLondonUK
| | - Cleo Kontoravdi
- Centre for Synthetic Biology and InnovationImperial College LondonLondonUK
- Department of Chemical EngineeringImperial College LondonLondonUK
| | - Paul S. Freemont
- Centre for Synthetic Biology and InnovationImperial College LondonLondonUK
- Department of MedicineImperial College LondonLondonUK
| | - Karen M. Polizzi
- Department of Life SciencesImperial College LondonLondonSW7 2AZUK
- Centre for Synthetic Biology and InnovationImperial College LondonLondonUK
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11
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Berset Y, Merulla D, Joublin A, Hatzimanikatis V, van der Meer JR. Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation. ACS Synth Biol 2017; 6:862-874. [PMID: 28215088 DOI: 10.1021/acssynbio.6b00364] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Bioreporters are living cells that generate an easily measurable signal in the presence of a chemical compound. They acquire their functionality from synthetic gene circuits, the configuration of which defines the response signal and signal-to-noise ratio. Bioreporters based on the Escherichia coli ArsR system have raised significant interest for quantifying arsenic pollution, but they need to be carefully optimized to accurately work in the required low concentration range (1-10 μg arsenite L-1). To better understand the general functioning of ArsR-based genetic circuits, we developed a comprehensive mechanistic model that was empirically tested and validated in E. coli carrying different circuit configurations. The model accounts for the different elements in the circuits (proteins, DNA, chemical species), and their detailed affinities and interactions, and predicts the (fluorescent) output from the bioreporter cell as a function of arsenite concentration. The model was parametrized using existing ArsR biochemical data, and then complemented by parameter estimations from the accompanying experimental data using a scatter search algorithm. Model predictions and experimental data were largely coherent for feedback and uncoupled circuit configurations, different ArsR alleles, promoter strengths, and presence or absence of arsenic efflux in the bioreporters. Interestingly, the model predicted a particular useful circuit variant having steeper response at low arsenite concentrations, which was experimentally confirmed and may be useful as arsenic bioreporter in the field. From the extensive validation we expect the mechanistic model to further be a useful framework for detailed modeling of other synthetic circuits.
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Affiliation(s)
- Yves Berset
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
- Laboratory
of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausane (EPFL), CH 1015 Lausanne, Switzerland
| | - Davide Merulla
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Aurélie Joublin
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory
of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausane (EPFL), CH 1015 Lausanne, Switzerland
| | - Jan R. van der Meer
- Department
of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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12
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van Rossum T, Muras A, Baur MJ, Creutzburg SC, van der Oost J, Kengen SW. A growth- and bioluminescence-based bioreporter for the in vivo detection of novel biocatalysts. Microb Biotechnol 2017; 10:625-641. [PMID: 28393499 PMCID: PMC5404197 DOI: 10.1111/1751-7915.12612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 11/28/2022] Open
Abstract
The use of bioreporters in high-throughput screening for small molecules is generally laborious and/or expensive. The technology can be simplified by coupling the generation of a desired compound to cell survival, causing only positive cells to stay in the pool of generated variants. Here, a dual selection/screening system was developed for the in vivo detection of novel biocatalysts. The sensor part of the system is based on the transcriptional regulator AraC, which controls expression of both a selection reporter (LeuB or KmR; enabling growth) for rapid reduction of the initially large library size and a screening reporter (LuxCDABE; causing bioluminescence) for further quantification of the positive variants. Of four developed systems, the best system was the medium copy system with KmR as selection reporter. As a proof of principle, the system was tested for the selection of cells expressing an l-arabinose isomerase derived from mesophilic Escherichia coli or thermophilic Geobacillus thermodenitrificans. A more than a millionfold enrichment of cells with l-arabinose isomerase activity was demonstrated by selection and exclusion of false positives by screening. This dual selection/screening system is an important step towards an improved detection method for small molecules, and thereby for finding novel biocatalysts.
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Affiliation(s)
- Teunke van Rossum
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Aleksandra Muras
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Marco J.J. Baur
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Sjoerd C.A. Creutzburg
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - John van der Oost
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
| | - Servé W.M. Kengen
- Laboratory of MicrobiologyWageningen University and ResearchStippeneng 46708WE WageningenThe Netherlands
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13
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Abstract
Bacteria live in an ever changing environment and, to adapt their physiology, they have to sense the changes. Our current understanding of the mechanisms and elements involved in the detection and processing of these environmental signals grant us access to an array of genetic components able to process such information. As engineers can use different electronic components to build a circuit, we can rewire the cellular components to create digital logic and analogue gene circuits that will program cell behaviour in a designed manner in response to a specific stimulus. Here we present the methods and protocols for designing and implementing synthetic cell-based biosensors that use engineered genetic logic and analogue amplifying circuits to significantly increase selectivity and sensitivity, for example, for heavy metal ions in an aqueous environment. The approach is modular and can be readily applied to improving the sensing limit and performance of a range of microbial cell-based sensors to meet their real world detection requirement.
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Affiliation(s)
- Elvis Bernard
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FF, 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 3FF, UK.
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14
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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.
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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
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15
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Abstract
As we become increasingly dependent on electronic information-processing systems at home and work, it’s easy to lose sight of the fact that our very survival depends on highly complex biological information-processing systems. Each of the trillions of cells that form the human body has the ability to detect and respond to a wide range of stimuli and inputs, using an extraordinary set of signaling proteins to process this information and make decisions accordingly. Indeed, cells in all organisms rely on these signaling proteins to survive and proliferate in unpredictable and sometimes rapidly changing environments. But how exactly do these proteins relay information within cells, and how do they keep a multitude of incoming signals straight? Here, I describe recent efforts to understand the fidelity of information flow inside cells. This work is providing fundamental insight into how cells function. Additionally, it may lead to the design of novel antibiotics that disrupt the signaling of pathogenic bacteria or it could help to guide the treatment of cancer, which often involves information-processing gone awry inside human cells. PLOS Biology's first ever Research Matters explains the importance of understanding the transmission and interpretation of complex biological signals by our own cells and by the bacterial cells that live in or on us.
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Affiliation(s)
- Michael T Laub
- Howard Hughes Medical Institute, Department of Biology, MIT, Cambridge, Massachusetts, United States of America
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16
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Transcriptional regulation with CRISPR-Cas9: principles, advances, and applications. Curr Opin Biotechnol 2016; 40:177-184. [PMID: 27344519 DOI: 10.1016/j.copbio.2016.06.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 11/21/2022]
Abstract
CRISPR-Cas9 has recently emerged as a promising system for multiplexed genome editing as well as epigenome and transcriptome perturbation. Due to its specificity, ease of use and highly modular programmable nature, it has been widely adopted for a variety of applications such as genome editing, transcriptional inhibition and activation, genetic screening, DNA localization imaging, and many more. In this review, we will discuss non-editing applications of CRISPR-Cas9 for transcriptome perturbation, metabolic engineering, and synthetic biology.
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17
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Durand MJ, Hua A, Jouanneau S, Cregut M, Thouand G. Detection of Metal and Organometallic Compounds with Bioluminescent Bacterial Bioassays. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015:77-99. [PMID: 26475470 DOI: 10.1007/10_2015_332] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Chemical detection of metal and organometallic compounds is very specific and sensitive, but these techniques are time consuming and expensive. Although these techniques provide information about the concentrations of compounds, they fail to inform us about the toxicity of a sample. Because the toxic effects of metals and organometallic compounds are influenced by a multitude of environmental factors, such as pH, the presence of chelating agents, speciation, and organic matter, bioassays have been developed for ecotoxicological studies. Among these bioassays, recombinant luminescent bacteria have been developed over the past 20 years, and many of them are specific for the detection of metals and metalloids. These bioassays are simple to use, are inexpensive, and provide information on the bioavailable fraction of metals and organometals. Thus, they are an essential complementary tool for providing information beyond chemical analysis. In this chapter, we propose to investigate the detection of metals and organometallic compounds with bioluminescent bacterial bioassays and the applications of these bioassays to environmental samples. Graphical Abstract.
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Affiliation(s)
- M J Durand
- University of Nantes, UMR CNRS GEPEA 6144, 18 Bd Gaston Defferre, 85000, La Roche sur Yon, France.
| | - A Hua
- University of Nantes, UMR CNRS GEPEA 6144, 18 Bd Gaston Defferre, 85000, La Roche sur Yon, France
| | - S Jouanneau
- University of Nantes, UMR CNRS GEPEA 6144, 18 Bd Gaston Defferre, 85000, La Roche sur Yon, France
| | - M Cregut
- Capacités SAS, 26 Bd Vincent Gâche, 44200, Nantes, France
| | - G Thouand
- University of Nantes, UMR CNRS GEPEA 6144, 18 Bd Gaston Defferre, 85000, La Roche sur Yon, France
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18
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Synthetic biology and biomimetic chemistry as converging technologies fostering a new generation of smart biosensors. Biosens Bioelectron 2015; 74:1076-86. [PMID: 26277908 DOI: 10.1016/j.bios.2015.07.078] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 01/05/2023]
Abstract
Biosensors are powerful tunable systems able to switch between an ON/OFF status in response to an external stimulus. This extraordinary property could be engineered by adopting synthetic biology or biomimetic chemistry to obtain tailor-made biosensors having the desired requirements of robustness, sensitivity and detection range. Recent advances in both disciplines, in fact, allow to re-design the configuration of the sensing elements - either by modifying toggle switches and gene networks, or by producing synthetic entities mimicking key properties of natural molecules. The present review considered the role of synthetic biology in sustaining biosensor technology, reporting examples from the literature and reflecting on the features that make it a useful tool for designing and constructing engineered biological systems for sensing application. Besides, a section dedicated to bioinspired synthetic molecules as powerful tools to enhance biosensor potential is reported, and treated as an extension of the concept of biomimetic chemistry, where organic synthesis is used to generate artificial molecules that mimic natural molecules. Thus, the design of synthetic molecules, such as aptamers, biomimetics, molecular imprinting polymers, peptide nucleic acids, and ribozymes were encompassed as "products" of biomimetic chemistry.
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19
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Shah N, Naseby D. Validation of constitutively expressed bioluminescent Pseudomonas aeruginosa as a rapid microbiological quantification tool. Biosens Bioelectron 2015; 68:447-453. [DOI: 10.1016/j.bios.2015.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/13/2014] [Accepted: 01/02/2015] [Indexed: 10/24/2022]
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Detection of 2,4-dinitrotoluene and 2,4,6-trinitrotoluene by an Escherichia coli bioreporter: performance enhancement by directed evolution. Appl Microbiol Biotechnol 2015; 99:7177-88. [DOI: 10.1007/s00253-015-6607-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/02/2015] [Accepted: 04/12/2015] [Indexed: 11/26/2022]
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Abstract
Synthetic cell therapy is a field that has broad potential for future applications in human disease treatment. Next generation therapies will consist of engineered bacterial strains capable of diagnosing disease, producing and delivering therapeutics, and controlling their numbers to meet containment and safety concerns. A thorough understanding of the microbial ecology of the human body and the interaction of the microbes with the immune system will benefit the choice of an appropriate chassis that engrafts stably and interacts productively with the resident community in specific body niches.
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Affiliation(s)
- Jan Claesen
- Department of Bioengineering
and Therapeutic Sciences and the California Institute for Quantitative
Biosciences, University of California, San
Francisco, San Francisco, California 94158, United States
| | - Michael A. Fischbach
- Department of Bioengineering
and Therapeutic Sciences and the California Institute for Quantitative
Biosciences, University of California, San
Francisco, San Francisco, California 94158, United States
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22
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Cerminati S, Soncini FC, Checa SK. A sensitive whole-cell biosensor for the simultaneous detection of a broad-spectrum of toxic heavy metal ions. Chem Commun (Camb) 2015; 51:5917-20. [PMID: 25730473 DOI: 10.1039/c5cc00981b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial biosensors are simple, cost-effective and efficient analytical tools for detecting bioavailable heavy metals in the environment. This work presents the design, construction and calibration of a novel whole-cell fluorescent biosensory device that, simultaneously and with high sensitivity, reports the presence of toxic mercury, lead, cadmium and/or gold ions in aqueous samples. This bio-reporter can be easily applied as an immediate alerting tool for detecting the presence of harmful pollutants in drinking water.
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Affiliation(s)
- S Cerminati
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas (UNR), Ocampo y Esmeralda, 2000-Rosario, Argentina.
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23
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Biosensors for inorganic and organic arsenicals. BIOSENSORS-BASEL 2014; 4:494-512. [PMID: 25587436 PMCID: PMC4287715 DOI: 10.3390/bios4040494] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 11/11/2014] [Accepted: 11/17/2014] [Indexed: 11/17/2022]
Abstract
Arsenic is a natural environmental contaminant to which humans are routinely exposed and is strongly associated with human health problems, including cancer, cardiovascular and neurological diseases. To date, a number of biosensors for the detection of arsenic involving the coupling of biological engineering and electrochemical techniques has been developed. The properties of whole-cell bacterial or cell-free biosensors are summarized in the present review with emphasis on their sensitivity and selectivity. Their limitations and future challenges are highlighted.
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Wang Z, Wu X, Peng J, Hu Y, Fang B, Huang S. Artificially constructed quorum-sensing circuits are used for subtle control of bacterial population density. PLoS One 2014; 9:e104578. [PMID: 25119347 PMCID: PMC4132116 DOI: 10.1371/journal.pone.0104578] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 07/15/2014] [Indexed: 01/31/2023] Open
Abstract
Vibrio fischeri is a typical quorum-sensing bacterium for which lux box, luxR, and luxI have been identified as the key elements involved in quorum sensing. To decode the quorum-sensing mechanism, an artificially constructed cell–cell communication system has been built. In brief, the system expresses several programmed cell-death BioBricks and quorum-sensing genes driven by the promoters lux pR and PlacO-1 in Escherichia coli cells. Their transformation and expression was confirmed by gel electrophoresis and sequencing. To evaluate its performance, viable cell numbers at various time periods were investigated. Our results showed that bacteria expressing killer proteins corresponding to ribosome binding site efficiency of 0.07, 0.3, 0.6, or 1.0 successfully sensed each other in a population-dependent manner and communicated with each other to subtly control their population density. This was also validated using a proposed simple mathematical model.
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Affiliation(s)
- Zhaoshou Wang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Xin Wu
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Jianghai Peng
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Yidan Hu
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
| | - Baishan Fang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Chemical Biology of Fujian Province, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
- * E-mail:
| | - Shiyang Huang
- Institute of Biochemical Engineering, Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- The Key Lab for Synthetic Biotechnology of Xiamen City, Xiamen University, Xiamen, China
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O'Leary ND, Mooney A, O'Mahony M, Dobson AD. Functional characterization of a StyS sensor kinase reveals distinct domains associated with intracellular and extracellular sensing of styrene in P. putida CA-3. Bioengineered 2014; 5:114-22. [PMID: 24637704 DOI: 10.4161/bioe.28354] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bacterial two-component systems (TCSs) are of vital importance in the translation of rapidly changing environmental conditions into appropriate cellular regulatory responses enabling adaptation, growth, and survival. The diverse range of environmental signals that TCSs can process, coupled with discrete modular domains within TCS proteins, offers considerable potential for the rational design of bio-sensor and/or bio-reporter strains. In this study we functionally characterize the multi-domain StyS sensor kinase associated with sensing of the aromatic pollutant styrene by Pseudomonas putida CA-3. Deletion analysis of discrete domains was performed and the ability of the truncated StyS sensor proteins to activate a cognate reporter system in an E. coli host assessed. The essential histidine kinase and PAS input domains were identified for StyS dependent activation of the reporter system. However, co-expression of an ABC-transporter protein StyE, previously linked to styrene transport in P. putida CA-3, enabled activation of the reporter system with a StyS construct containing a non-essential PAS input domain, suggesting a novel role for intracellular detection and/or activation. Site directed mutagenesis and amino acid deletions were employed to further characterize the PAS sensing domains of both input regions. The potential implications of these findings in the use of multi-domain sensor kinases in rational design strategies and the potential link between transport and intracellular sensing are discussed.
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Affiliation(s)
- Niall D O'Leary
- School of Microbiology and Environmental Research Institute; University College Cork; Cork, Ireland
| | - Aisling Mooney
- School of Microbiology and Environmental Research Institute; University College Cork; Cork, Ireland
| | - Mark O'Mahony
- School of Microbiology and Environmental Research Institute; University College Cork; Cork, Ireland
| | - Alan Dw Dobson
- School of Microbiology and Environmental Research Institute; University College Cork; Cork, Ireland
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26
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Kupferschmied P, Péchy-Tarr M, Imperiali N, Maurhofer M, Keel C. Domain shuffling in a sensor protein contributed to the evolution of insect pathogenicity in plant-beneficial Pseudomonas protegens. PLoS Pathog 2014; 10:e1003964. [PMID: 24586167 PMCID: PMC3930604 DOI: 10.1371/journal.ppat.1003964] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 01/16/2014] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas protegens is a biocontrol rhizobacterium with a plant-beneficial and an insect pathogenic lifestyle, but it is not understood how the organism switches between the two states. Here, we focus on understanding the function and possible evolution of a molecular sensor that enables P. protegens to detect the insect environment and produce a potent insecticidal toxin specifically during insect infection but not on roots. By using quantitative single cell microscopy and mutant analysis, we provide evidence that the sensor histidine kinase FitF is a key regulator of insecticidal toxin production. Our experimental data and bioinformatic analyses indicate that FitF shares a sensing domain with DctB, a histidine kinase regulating carbon uptake in Proteobacteria. This suggested that FitF has acquired its specificity through domain shuffling from a common ancestor. We constructed a chimeric DctB-FitF protein and showed that it is indeed functional in regulating toxin expression in P. protegens. The shuffling event and subsequent adaptive modifications of the recruited sensor domain were critical for the microorganism to express its potent insect toxin in the observed host-specific manner. Inhibition of the FitF sensor during root colonization could explain the mechanism by which P. protegens differentiates between the plant and insect host. Our study establishes FitF of P. protegens as a prime model for molecular evolution of sensor proteins and bacterial pathogenicity. Pseudomonas bacteria are well-known for their capability of adapting to different environments, which enables them to interact with various host organisms. Pseudomonas protegens is a plant-associated biocontrol bacterium with lifestyles that are of interest for agricultural applications, among them one as a competitive root colonizer protecting plants against pathogenic fungi and the other as an insect pathogen invading and killing insect species of importance as pests in agriculture. We recently discovered that P. protegens produces a potent insecticidal toxin only during infection of insects but not when growing on plant roots. Since sensor proteins enable bacteria to sense and respond to changing environments and are important for pathogen-host interactions, we investigated whether a specific sensory protein could explain our observation. We found that this particular protein tightly controls toxin production and during its evolution has recruited a common sensor domain from a regulatory protein involved in control of nutrient uptake. This so-called domain shuffling event was important for the ability of P. protegens to produce its insecticidal toxin only when it infects insects. Our study provides a prime example of how a sensory system can evolve and contribute to the evolution of bacterial pathogenicity.
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Affiliation(s)
- Peter Kupferschmied
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Maria Péchy-Tarr
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicola Imperiali
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Monika Maurhofer
- Plant Pathology, Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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27
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Abstract
Increasing interest in detecting metal ions in many chemical and biomedical fields has created demands for developing sensors and imaging agents for metal ions with high sensitivity and selectivity. This review covers recent progress in DNA-based sensors and imaging agents for metal ions. Through both combinatorial selection and rational design, a number of metal-ion-dependent DNAzymes and metal-ion-binding DNA structures that can selectively recognize specific metal ions have been obtained. By attachment of these DNA molecules with signal reporters such as fluorophores, chromophores, electrochemical tags, and Raman tags, a number of DNA-based sensors for both diamagnetic and paramagnetic metal ions have been developed for fluorescent, colorimetric, electrochemical, and surface Raman detection. These sensors are highly sensitive (with a detection limit down to 11 ppt) and selective (with selectivity up to millions-fold) toward specific metal ions. In addition, through further development to simplify the operation, such as the use of "dipstick tests", portable fluorometers, computer-readable disks, and widely available glucose meters, these sensors have been applied for on-site and real-time environmental monitoring and point-of-care medical diagnostics. The use of these sensors for in situ cellular imaging has also been reported. The generality of the combinatorial selection to obtain DNAzymes for almost any metal ion in any oxidation state and the ease of modification of the DNA with different signal reporters make DNA an emerging and promising class of molecules for metal-ion sensing and imaging in many fields of applications.
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Affiliation(s)
- Yu Xiang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Fax: 217-244-3186; Tel: 217-333-2619
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Fax: 217-244-3186; Tel: 217-333-2619
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28
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Tseng HW, Tsai YJ, Yen JH, Chen PH, Yeh YC. A fluorescence-based microbial sensor for the selective detection of gold. Chem Commun (Camb) 2014; 50:1735-7. [DOI: 10.1039/c3cc48028c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Roda A, Cevenini L, Borg S, Michelini E, Calabretta MM, Schüler D. Bioengineered bioluminescent magnetotactic bacteria as a powerful tool for chip-based whole-cell biosensors. LAB ON A CHIP 2013; 13:4881-4889. [PMID: 24193113 DOI: 10.1039/c3lc50868d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This paper describes the generation of genetically engineered bioluminescent magnetotactic bacteria (BL-MTB) and their integration into a microfluidic analytical device to create a portable toxicity detection system. Magnetospirillum gryphiswaldense strain MSR-1 was bioengineered to constitutively express a red-emitting click beetle luciferase whose bioluminescent signal is directly proportional to bacterial viability. The magnetic properties of these bacteria have been exploited as "natural actuators" to transfer the cells in the chip from the reaction to the detection area, optimizing the chip's analytical performance. A robust and cost-effective biosensor for the evaluation of sample toxicity, named MAGNETOX, based on lens-free contact imaging detection, has been developed. A microfluidic chip has been fabricated using multilayered black and transparent polydimethyl siloxane (PDMS) in which BL-MTB are incubated for 30 min with the sample, then moved by microfluidics, trapped, and concentrated in detection chambers by an array of neodymium-iron-boron magnets. The chip is placed in contact with a cooled CCD via a fiber optic taper to perform quantitative bioluminescence imaging after addition of luciferin substrate. A model toxic compound (dimethyl sulfoxide, DMSO) and a bile acid (taurochenodeoxycholic acid, TCDCA) were used to investigate the analytical performance of the MAGNETOX. Incubation with DMSO and TCDCA drastically reduces the bioluminescent signal in a dose-related manner. The generation of bacteria that are both magnetic and bioluminescent combines the advantages of easy 2D cell handling with ultra sensitive detection, offering undoubted potential to develop cell-based biosensors integrated into microfluidic chips.
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Affiliation(s)
- Aldo Roda
- Laboratory of Analytical and Bioanalytical Chemistry, Department of Chemistry "G. Ciamician", Alma Mater Studiorum-University of Bologna, Via Selmi 2, 40126 Bologna, Italy.
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30
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Macías-Díaz JE, Macías S, Medina-Ramírez IE. An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology. Comput Biol Chem 2013; 47:24-30. [PMID: 23850847 DOI: 10.1016/j.compbiolchem.2013.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 05/29/2013] [Accepted: 05/29/2013] [Indexed: 11/30/2022]
Abstract
In this manuscript, we present a computational model to approximate the solutions of a partial differential equation which describes the growth dynamics of microbial films. The numerical technique reported in this work is an explicit, nonlinear finite-difference methodology which is computationally implemented using Newton's method. Our scheme is compared numerically against an implicit, linear finite-difference discretization of the same partial differential equation, whose computer coding requires an implementation of the stabilized bi-conjugate gradient method. Our numerical results evince that the nonlinear approach results in a more efficient approximation to the solutions of the biofilm model considered, and demands less computer memory. Moreover, the positivity of initial profiles is preserved in the practice by the nonlinear scheme proposed.
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Affiliation(s)
- J E Macías-Díaz
- Departamento de Matemáticas y Física, Universidad Autónoma de Aguascalientes, Aguascalientes 20131, Mexico.
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31
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Michelini E, Cevenini L, Calabretta MM, Spinozzi S, Camborata C, Roda A. Field-deployable whole-cell bioluminescent biosensors: so near and yet so far. Anal Bioanal Chem 2013; 405:6155-63. [DOI: 10.1007/s00216-013-7043-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 04/26/2013] [Accepted: 05/02/2013] [Indexed: 12/24/2022]
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