1
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Mendoza ASG, Acosta MFM, Sánchez JAM, Vázquez LEC. Principles and challenges of whole cell microbial biosensors in the food industry. J Food Sci 2024; 89:5255-5269. [PMID: 39175184 DOI: 10.1111/1750-3841.17294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Whole cell microbial biosensors (WCMB) are mostly genetically modified microorganisms used to detect target molecules as indicators of biological and chemical contaminants as well as in the identification of compounds of interest in the food industry. The specificity and sensitivity of these biosensors are achieved through the design of genetic circuits that make use of genetic sequences such as promoters, terminators, genes encoding regulatory proteins or reporter proteins, among others. Despite the advances of WCMBs for their application, significant challenges are faced, such as cell stability, regulatory restrictions, and the need to optimize response times so that they can be a competitive detection tool in the market. This review explores the technological progress, potential and limitations of WCMBs in the food industry, starting by reviewing the operating principles of biosensors. The importance of selecting appropriate chassis cells and the integration of recognition elements and transducers to maximize their effectiveness in the detection of contaminants and compounds of interest in the food industry is highlighted.
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Affiliation(s)
- América Selene Gaona Mendoza
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
| | - María Fernanda Mendoza Acosta
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
| | - Julio Armando Massange Sánchez
- Plant Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco A.C. (CIATEJ), Guadalajara, Mexico
| | - Luz Edith Casados Vázquez
- Graduate Program in Biosciences, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- Food Department, Life Science Division, University of Guanajuato Campus Irapuato-Salamanca, Irapuato, Guanajuato, México
- CONAHCyT-University of Guanajuato, Guanajuato, México
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2
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McSweeney MA, Patterson AT, Loeffler K, de Larrea RCL, McNerney MP, Kane RS, Styczynski MP. A modular cell-free protein biosensor platform using split T7 RNA polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604303. [PMID: 39071415 PMCID: PMC11275916 DOI: 10.1101/2024.07.19.604303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Conventional laboratory protein detection techniques are not suitable for point-of-care (POC) use because they require expensive equipment and laborious protocols, and existing POC assays suffer from long development timescales. Here, we describe a modular cell-free biosensing platform for generalizable protein detection that we call TLISA (T7 RNA polymerase-Linked ImmunoSensing Assay), designed for extreme flexibility and equipment-free use. TLISA uses a split T7 RNA polymerase fused to affinity domains against a protein. The target antigen drives polymerase reassembly, inducing reporter expression. We characterize the platform, then demonstrate its modularity by using 16 affinity domains against four different antigens with minimal protocol optimization. We show TLISA is suitable for POC use by sensing human biomarkers in serum and saliva with a colorimetric readout within one hour and by demonstrating functionality after lyophilization. Altogether, this technology could have potentially revolutionary impacts, enabling truly rapid, reconfigurable, equipment-free detection of virtually any protein.
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Affiliation(s)
- Megan A. McSweeney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Alexandra T. Patterson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Kathryn Loeffler
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | | | - Monica P. McNerney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Ravi S. Kane
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Mark P. Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
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3
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Li Y, Lucci T, Dujovne MV, Jung JK, Capdevila DA, Lucks JB. Engineering a cell-free biosensor signal amplification circuit with polymerase strand recycling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591074. [PMID: 38712145 PMCID: PMC11071457 DOI: 10.1101/2024.04.25.591074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cell-free systems are powerful synthetic biology technologies because of their ability to recapitulate sensing and gene expression without the complications of living cells. Cell-free systems can perform even more advanced functions when genetic circuits are incorporated as information processing components. Here we expand cell-free biosensing by engineering a highly specific isothermal signal amplification circuit called polymerase strand recycling (PSR) that leverages T7 RNA polymerase off-target transcription to recycle nucleic acid inputs within DNA strand displacement circuits. We develop design rules for PSR circuit components and use these rules to construct modular biosensors that can directly sense different RNA targets with limits of detection in the nM range and high specificity. We then use PSR for signal amplification within allosteric transcription factor-based biosensors for small molecule detection. We use a double equilibrium model of transcription factor:DNA and transcription factor:ligand binding interactions to predict biosensor sensitivity enhancement by PSR, and then demonstrate this approach experimentally by achieving 3.6-4.6-fold decreases in biosensor EC50 to sub micromolar ranges. We believe this work expands the current capabilities of cell-free circuits by incorporating PSR, which we anticipate will have a wide range of uses within biotechnology.
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Affiliation(s)
- Yueyi Li
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | - Tyler Lucci
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | | | - Jaeyoung Kirsten Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
| | | | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, USA
- Interdiscipinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, USA
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, USA
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, Illinois 60208, USA
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4
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Wu Y, Zhu L, Zhang Y, Xu W. Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2304852. [PMID: 37658499 DOI: 10.1002/smll.202304852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/15/2023] [Indexed: 09/03/2023]
Abstract
Riboswitches have received significant attention over the last two decades for their multiple functionalities and great potential for applications in various fields. This article highlights and reviews the recent advances in biosensing and biotherapy. These fields involve a wide range of applications, such as food safety detection, environmental monitoring, metabolic engineering, live cell imaging, wearable biosensors, antibacterial drug targets, and gene therapy. The discovery, origin, and optimization of riboswitches are summarized to help readers better understand their multidimensional applications. Finally, this review discusses the multidimensional challenges and development of riboswitches in order to further expand their potential for novel applications.
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Affiliation(s)
- Yifan Wu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Yangzi Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Beijing Laboratory for Food Quality and Safety, Department of Nutrition and Health, China Agricultural University, Beijing, 100191, China
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5
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Piorino F, Patterson AT, Han Y, Styczynski MP. Plasmid Crosstalk in Cell-Free Expression Systems. ACS Synth Biol 2023; 12:2843-2856. [PMID: 37756020 PMCID: PMC10594874 DOI: 10.1021/acssynbio.3c00412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 09/28/2023]
Abstract
Although cell-free protein expression has been widely used for the synthesis of single proteins, cell-free synthetic biology has rapidly expanded to new, more complex applications. One such application is the prototyping or implementation of complex genetic networks involving the expression of multiple proteins at precise ratios, often from different plasmids. However, expression of multiple proteins from multiple plasmids may inadvertently result in unexpected, off-target changes to the levels of the proteins being expressed, a phenomenon termed plasmid crosstalk. Here, we show that the effects of plasmid crosstalk─even at the qualitative level of increases vs decreases in protein expression─depend on the concentration of plasmids in the reaction and the type of transcriptional machinery involved in the expression. This crosstalk can have a significant impact on genetic circuitry function and even interpretation of simple experimental results and thus should be taken into consideration during the development of cell-free applications.
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Affiliation(s)
- Fernanda Piorino
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Alexandra T. Patterson
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Yue Han
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Mark P. Styczynski
- School
of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
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6
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Quispe Haro JJ, Wegner SV. An Adenosylcobalamin Specific Whole-Cell Biosensor. Adv Healthc Mater 2023; 12:e2300835. [PMID: 37070155 DOI: 10.1002/adhm.202300835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/12/2023] [Indexed: 04/19/2023]
Abstract
Vitamin B12 (cobalamin) is essential for human health and its deficiency results in anemia and neurological damage. Vitamin B12 exists in different forms with various bioactivity but most sensors are unable to discriminate between them. Here, a whole-cell agglutination assay that is specific for adenosylcobalamin (AboB12), which is one of two bioactive forms, is reported. This biosensor consists of Escherichia coli that express the AdoB12 specific binding domain of CarH at their surface. In the presence of AdoB12, CarH forms tetramers, which leads to specific bacterial cell-cell adhesions and agglutination. These CarH tetramers disassemble upon green light illumination such that reversion of the bacterial aggregation can serve as internal quality control. The agglutination assay has a detection limit of 500 nм AdoB12, works in protein-poor biofluids such as urine, and has high specificity to AdoB12 over other forms of vitamin B12 as also demonstrated with commercially available supplements. This work is a proof of concept for a cheap and easy-to-readout AdoB12 sensor that can be implemented at the point-of-care to monitor high-dose vitamin B12 supplementation.
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Affiliation(s)
- Juan José Quispe Haro
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstrasse 15, 48149, Münster, Germany
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstrasse 15, 48149, Münster, Germany
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7
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Piorino F, Johnson S, Styczynski MP. A Cell-Free Biosensor for Assessment of Hyperhomocysteinemia. ACS Synth Biol 2023; 12:2487-2492. [PMID: 37459448 PMCID: PMC10443029 DOI: 10.1021/acssynbio.3c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Indexed: 08/19/2023]
Abstract
Hyperhomocysteinemia─a condition characterized by elevated levels of homocysteine in the blood─is associated with multiple health conditions including folate deficiency and birth defects, but there are no convenient, low-cost methods to measure homocysteine in plasma. A cell-free biosensor that harnesses the native homocysteine sensing machinery of Escherichia coli bacteria could satisfy the need for a detection platform with these characteristics. Here, we describe our efforts to engineer a cell-free biosensor for point-of-care, low-cost assessment of homocysteine status. This biosensor can detect physiologically relevant concentrations of homocysteine in plasma with a colorimetric output visible to the naked eye in under 1.5 h, making it a fast, convenient tool for point-of-use diagnosis and monitoring of hyperhomocysteinemia and related health conditions.
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Affiliation(s)
- Fernanda Piorino
- School of Chemical &
Biomolecular Engineering, Georgia Institute
of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | | | - Mark P. Styczynski
- School of Chemical &
Biomolecular Engineering, Georgia Institute
of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
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8
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McSweeney MA, Zhang Y, Styczynski MP. Short Activators and Repressors of RNA Toehold Switches. ACS Synth Biol 2023; 12:681-688. [PMID: 36802167 PMCID: PMC10028691 DOI: 10.1021/acssynbio.2c00641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
RNA toehold switches are a widely used class of molecule to detect specific RNA "trigger" sequences, but their design, intended function, and characterization to date leave it unclear whether they can function properly with triggers shorter than 36 nucleotides. Here, we explore the feasibility of using standard toehold switches with 23-nucleotide truncated triggers. We assess the crosstalk of different triggers with significant homology and identify a highly sensitive trigger region where just one mutation from the consensus trigger sequence can reduce switch activation by 98.6%. However, we also find that triggers with as many as seven mutations outside of this region can still lead to 5-fold induction of the switch. We also present a new approach using 18- to 22-nucleotide triggers as translational repressors for toehold switches and assess the off-target regulation for this strategy as well. The development and characterization of these strategies could help enable applications like microRNA sensors, where well-characterized crosstalk between sensors and detection of short target sequences are critical.
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Affiliation(s)
- Megan A McSweeney
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yan Zhang
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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9
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Piorino F, Styczynski MP. Harnessing Escherichia coli's Native Machinery for Detection of Vitamin C (Ascorbate) Deficiency. ACS Synth Biol 2022; 11:3592-3600. [PMID: 36300901 PMCID: PMC9807260 DOI: 10.1021/acssynbio.2c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Vitamin C (l-ascorbate) deficiency is a global public health issue most prevalent in resource-limited regions, creating a need for an inexpensive detection platform. Here, we describe efforts to engineer whole-cell and cell-free ascorbate biosensors. Both sensors used the protein UlaR, which binds to a metabolite of ascorbate and regulates transcription. The whole-cell sensor could detect lower, physiologically relevant concentrations of ascorbate, which we attributed to intact functionality of a phosphotransferase system (PTS) that transports ascorbate across the cell membrane and phosphorylates it to form UlaR's ligand. We used multiple strategies to enhance cell-free PTS functionality (which has received little previous attention), improving the cell-free sensor's performance, but the whole-cell sensor remained more sensitive. These efforts demonstrated an advantage of whole-cell sensors for detection of molecules─like ascorbate─transformed by a PTS, but also proof of principle for cell-free sensors requiring membrane-bound components like the PTS. In addition, the cell-free sensor was functional in plasma, setting the stage for future implementation of ascorbate sensors for clinically relevant biofluids in field-deployable formats.
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Affiliation(s)
- Fernanda Piorino
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Mark P. Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
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10
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Wu Y, Zhu L, Li S, Chu H, Wang X, Xu W. High content design of riboswitch biosensors: All-around rational module-by-module design. Biosens Bioelectron 2022; 220:114887. [DOI: 10.1016/j.bios.2022.114887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/27/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022]
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11
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Piorino F, Patterson AT, Styczynski MP. Low-cost, point-of-care biomarker quantification. Curr Opin Biotechnol 2022; 76:102738. [PMID: 35679813 PMCID: PMC9807261 DOI: 10.1016/j.copbio.2022.102738] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 04/24/2022] [Accepted: 04/27/2022] [Indexed: 01/04/2023]
Abstract
Low-cost, point-of-care (POC) devices that allow fast, on-site disease diagnosis could have a major global health impact, particularly if they can provide quantitative measurement of molecules indicative of a diseased state (biomarkers). Accurate quantification of biomarkers in patient samples is already challenging when research-grade, sophisticated equipment is available; it is even more difficult when constrained to simple, cost-effective POC platforms. Here, we summarize the main challenges to accurate, low-cost POC biomarker quantification. We also review recent efforts to develop and implement POC tools beyond qualitative readouts, and we conclude by identifying important future research directions.
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Affiliation(s)
- Fernanda Piorino
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332-0100, United States
| | - Alexandra T Patterson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332-0100, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA 30332-0100, United States.
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12
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Harbaugh SV, Silverman AD, Chushak YG, Zimlich K, Wolfe M, Thavarajah W, Jewett MC, Lucks JB, Chávez JL. Engineering a Synthetic Dopamine-Responsive Riboswitch for In Vitro Biosensing. ACS Synth Biol 2022; 11:2275-2283. [PMID: 35775197 DOI: 10.1021/acssynbio.1c00560] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The detection of chemicals using natural allosteric transcription factors is a powerful strategy for point-of-use molecular sensing, particularly using fieldable cell-free gene expression (CFE) systems. However, the reliance of detection schemes on characterized protein-based sensors limits the number of measurable analytes. One alternative solution to this issue is to develop new sensors by generating RNA aptamers against the target analyte and then incorporating them directly into a riboswitch scaffold for ligand-inducible genetic control of a reporter protein. However, this strategy has not generated more than a handful of successful portable cell-free molecular sensors. To address this gap, here we convert dopamine-binding aptamers into functional dopamine-sensing riboswitches that regulate gene expression in a freeze-dried CFE reaction. We then develop an assay for direct detection and semi-quantification of dopamine in human urine. We anticipate that this work will be broadly applicable for converting many in vitro-generated RNA aptamers into fieldable molecular diagnostics.
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Affiliation(s)
- Svetlana V Harbaugh
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Adam D Silverman
- Sherlock Biosciences, Boston, Massachusetts 02135, United States
| | - Yaroslav G Chushak
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States.,Henry M. Jackson Foundation, Dayton, Ohio 45433, United States
| | - Kathryn Zimlich
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States.,Henry M. Jackson Foundation, Dayton, Ohio 45433, United States
| | - Monica Wolfe
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States.,UES, Inc., Dayton, Ohio 45432, United States
| | - Walter Thavarajah
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States.,International Institute of Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States.,International Institute of Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
| | - Jorge L Chávez
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
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13
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Lee YJ, Lee S, Kim DM. Translational Detection of Indole by Complementary Cell-free Protein Synthesis Assay. Front Bioeng Biotechnol 2022; 10:900162. [PMID: 35646868 PMCID: PMC9136167 DOI: 10.3389/fbioe.2022.900162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
The information encoded in a single copy of DNA is processed into a plethora of protein molecules via the cascade of transcription and translation. Thus, the molecular process of gene expression can be considered an efficient biological amplifier from the viewpoint of synthetic biology. Cell-free protein synthesis (CFPS) enables the implementation of this amplification module for in vitro analysis of important biomolecules and avoids many of the problems associated with whole cell-based approaches. Here, we developed a method to analyze indole by using a combination of enzymatic conversion of indole and amino acid-dependent CFPS. In this method, indole molecules in the assay sample are used to generate tryptophan, which is incorporated into signal-generating proteins in the subsequent cell-free synthesis reaction. The activity of cell-free synthesized proteins was successfully used to estimate the indole concentration in the assay sample. In principle, the developed method could be extended to analyses of other important bioactive compounds.
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Affiliation(s)
- You Jin Lee
- Department of Chemical Engineering and Applied Chemistry, Daejeon, Korea
| | - Soojin Lee
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Daejeon, Korea
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14
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Padmanabhan S, Pérez-Castaño R, Osete-Alcaraz L, Polanco MC, Elías-Arnanz M. Vitamin B 12 photoreceptors. VITAMINS AND HORMONES 2022; 119:149-184. [PMID: 35337618 DOI: 10.1016/bs.vh.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Photoreceptor proteins enable living organisms to sense light and transduce this signal into biochemical outputs to elicit appropriate cellular responses. Their light sensing is typically mediated by covalently or noncovalently bound molecules called chromophores, which absorb light of specific wavelengths and modulate protein structure and biological activity. Known photoreceptors have been classified into about ten families based on the chromophore and its associated photosensory domain in the protein. One widespread photoreceptor family uses coenzyme B12 or 5'-deoxyadenosylcobalamin, a biological form of vitamin B12, to sense ultraviolet, blue, or green light, and its discovery revealed both a new type of photoreceptor and a novel functional facet of this vitamin, best known as an enzyme cofactor. Large strides have been made in our understanding of how these B12-based photoreceptors function, high-resolution structural descriptions of their functional states are available, as are details of their unusual photochemistry. Additionally, they have inspired notable applications in optogenetics/optobiochemistry and synthetic biology. Here, we provide an overview of what is currently known about these B12-based photoreceptors, their discovery, distribution, molecular mechanism of action, and the structural and photochemical basis of how they orchestrate signal transduction and gene regulation, and how they have been used to engineer optogenetic control of protein activities in living cells.
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Affiliation(s)
- S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Lucía Osete-Alcaraz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - María Carmen Polanco
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain.
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15
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Lee YJ, Lim HJ, Kim DM. Quantitative Analysis of γ-Aminobutyric Acid by Combined Cell-Free Protein Synthesis and Transamination Reactions. ACS Synth Biol 2022; 11:1208-1212. [PMID: 35191303 DOI: 10.1021/acssynbio.1c00501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthetic power of cells can be harnessed for assaying important analytes, as well as for producing biomolecules. In particular, cell-free protein synthesis (CFPS) can be implemented as a signal amplification module for bioassays, while avoiding many problems associated with whole cell-based microbial biosensors. Here, we developed a method for analyzing γ-aminobutyric acid (GABA) by combining the enzymatic conversion of GABA and amino-acid-dependent CFPS. In this method, GABA molecules in the assay sample are used to generate alanine, which is incorporated into signal-generating proteins in the subsequent cell-free synthesis reaction. The activity of cell-free synthesized proteins was successfully used to estimate the GABA concentration in the assay sample. In principle, the developed method could be extended for the analyses of other important bioactive compounds.
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Affiliation(s)
- You Jin Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Hye Jin Lim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
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16
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Sridharan H, Piorino F, Styczynski MP. Systems biology-based analysis of cell-free systems. Curr Opin Biotechnol 2022; 75:102703. [PMID: 35247659 DOI: 10.1016/j.copbio.2022.102703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/07/2021] [Accepted: 02/03/2022] [Indexed: 11/28/2022]
Abstract
Cell-free expression systems are becoming increasingly widely used due to their diverse applications in biotechnology. Despite this rapid expansion in adoption, many aspects of cell-free systems remain surprisingly poorly understood. Systems biology approaches make it possible to characterize cell-free systems deeply and broadly to better understand their underlying complexity. Here, we review recent systems biology studies that have provided insight into cell-free systems. We focus on characterization of the cell-free proteome, including its dependence on preparation protocol and host strain, as well as the cell-free metabolome and the relationship of endogenous metabolism to system performance. We conclude by highlighting promising future research directions.
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Affiliation(s)
- Harini Sridharan
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0100, United States
| | - Fernanda Piorino
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0100, United States
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0100, United States.
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17
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McNerney MP, Doiron KE, Ng TL, Chang TZ, Silver PA. Theranostic cells: emerging clinical applications of synthetic biology. Nat Rev Genet 2021; 22:730-746. [PMID: 34234299 PMCID: PMC8261392 DOI: 10.1038/s41576-021-00383-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Synthetic biology seeks to redesign biological systems to perform novel functions in a predictable manner. Recent advances in bacterial and mammalian cell engineering include the development of cells that function in biological samples or within the body as minimally invasive diagnostics or theranostics for the real-time regulation of complex diseased states. Ex vivo and in vivo cell-based biosensors and therapeutics have been developed to target a wide range of diseases including cancer, microbiome dysbiosis and autoimmune and metabolic diseases. While probiotic therapies have advanced to clinical trials, chimeric antigen receptor (CAR) T cell therapies have received regulatory approval, exemplifying the clinical potential of cellular therapies. This Review discusses preclinical and clinical applications of bacterial and mammalian sensing and drug delivery platforms as well as the underlying biological designs that could enable new classes of cell diagnostics and therapeutics. Additionally, we describe challenges that must be overcome for more rapid and safer clinical use of engineered systems.
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Affiliation(s)
- Monica P McNerney
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Kailyn E Doiron
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Tai L Ng
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Timothy Z Chang
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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18
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19
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Protocell arrays for simultaneous detection of diverse analytes. Nat Commun 2021; 12:5724. [PMID: 34588445 PMCID: PMC8481512 DOI: 10.1038/s41467-021-25989-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 09/03/2021] [Indexed: 01/05/2023] Open
Abstract
Simultaneous detection of multiple analytes from a single sample (multiplexing), particularly when done at the point of need, can guide complex decision-making without increasing the required sample volume or cost per test. Despite recent advances, multiplexed analyte sensing still typically faces the critical limitation of measuring only one type of molecule (e.g., small molecules or nucleic acids) per assay platform. Here, we address this bottleneck with a customizable platform that integrates cell-free expression (CFE) with a polymer-based aqueous two-phase system (ATPS), producing membrane-less protocells containing transcription and translation machinery used for detection. We show that multiple protocells, each performing a distinct sensing reaction, can be arrayed in the same microwell to detect chemically diverse targets from the same sample. Furthermore, these protocell arrays are compatible with human biofluids, maintain function after lyophilization and rehydration, and can produce visually interpretable readouts, illustrating this platform's potential as a minimal-equipment, field-deployable, multi-analyte detection tool.
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20
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Miguez AM, Zhang Y, Piorino F, Styczynski MP. Metabolic Dynamics in Escherichia coli-Based Cell-Free Systems. ACS Synth Biol 2021; 10:2252-2265. [PMID: 34478281 PMCID: PMC9807262 DOI: 10.1021/acssynbio.1c00167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The field of metabolic engineering has yielded remarkable accomplishments in using cells to produce valuable molecules, and cell-free expression (CFE) systems have the potential to push the field even further. However, CFE systems still face some outstanding challenges, including endogenous metabolic activity that is poorly understood yet has a significant impact on CFE productivity. Here, we use metabolomics to characterize the temporal metabolic changes in CFE systems and their constituent components, including significant metabolic activity in central carbon and amino acid metabolism. We find that while changing the reaction starting state via lysate preincubation impacts protein production, it has a comparatively small impact on metabolic state. We also demonstrate that changes to lysate preparation have a larger effect on protein yield and temporal metabolic profiles, though general metabolic trends are conserved. Finally, while we improve protein production through targeted supplementation of metabolic enzymes, we show that the endogenous metabolic activity is fairly resilient to these enzymatic perturbations. Overall, this work highlights the robust nature of CFE reaction metabolism as well as the importance of understanding the complex interdependence of metabolites and proteins in CFE systems to guide optimization efforts.
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21
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Jung JK, Alam KK, Verosloff MS, Capdevila DA, Desmau M, Clauer PR, Lee JW, Nguyen PQ, Pastén PA, Matiasek SJ, Gaillard JF, Giedroc DP, Collins JJ, Lucks JB. Cell-free biosensors for rapid detection of water contaminants. Nat Biotechnol 2020; 38:1451-1459. [PMID: 32632301 PMCID: PMC7718425 DOI: 10.1038/s41587-020-0571-7] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/19/2020] [Indexed: 12/23/2022]
Abstract
Lack of access to safe drinking water is a global problem, and methods to reliably and easily detect contaminants could be transformative. We report the development of a cell-free in vitro transcription system that uses RNA Output Sensors Activated by Ligand Induction (ROSALIND) to detect contaminants in water. A combination of highly processive RNA polymerases, allosteric protein transcription factors and synthetic DNA transcription templates regulates the synthesis of a fluorescence-activating RNA aptamer. The presence of a target contaminant induces the transcription of the aptamer, and a fluorescent signal is produced. We apply ROSALIND to detect a range of water contaminants, including antibiotics, small molecules and metals. We also show that adding RNA circuitry can invert responses, reduce crosstalk and improve sensitivity without protein engineering. The ROSALIND system can be freeze-dried for easy storage and distribution, and we apply it in the field to test municipal water supplies, demonstrating its potential use for monitoring water quality.
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Affiliation(s)
- Jaeyoung K Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Khalid K Alam
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Matthew S Verosloff
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.,Center for Water Research, Northwestern University, Evanston, IL, USA.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | | | - Morgane Desmau
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Phillip R Clauer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Pablo A Pastén
- Departmento de Ingeniería Hidráulica y Ambiental, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro de Desarrollo Urbano Sustentable, Santiago, Chile
| | - Sandrine J Matiasek
- Department of Geological and Environmental Sciences, California State University, Chico, Chico, CA, USA.,Center for Water and the Environment, California State University, Chico, Chico, CA, USA
| | - Jean-François Gaillard
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - David P Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA
| | - James J Collins
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA. .,Center for Synthetic Biology, Northwestern University, Evanston, IL, USA. .,Center for Water Research, Northwestern University, Evanston, IL, USA. .,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA.
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