1
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Kim D, Kim J, Han J, Shin J, Park KS. Split T7 switch-mediated cell-free protein synthesis system for detecting target nucleic acids. Biosens Bioelectron 2024; 261:116517. [PMID: 38924814 DOI: 10.1016/j.bios.2024.116517] [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: 04/17/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Cell-free protein synthesis (CFPS) reactions can be used to detect nucleic acids. However, most CFPS systems rely on a toehold switch and exhibit the following critical limitations: (i) off-target signals due to leaky translation in the absence of target nucleic acids, (ii) a suboptimal detection limit of approximately 30 nM without pre-amplification, and (iii) labor-intensive screening processes due to sequence constraints for the target nucleic acids. To overcome these shortcomings, we developed a new split T7 switch-mediated CFPS system in which the split T7 promoter was applied to a three-way junction structure to selectively initiate transcription-translation only in the presence of target nucleic acids. Both fluorescence and colorimetric detection systems were constructed by employing different reporter proteins. Notably, we introduced the self-complementation of split fluorescent proteins to streamline preparation of the proposed system, enabling versatile applications. Operation of this one-pot approach under isothermal conditions enabled the detection of target nucleic acids at concentrations as low as 10 pM, representing more than a thousand times improvement over previous toehold switch-based approaches. Furthermore, the proposed system demonstrated high specificity in detecting target nucleic acids and compatibility with various reporter proteins encoded in the expression region. By eliminating issues associated with the previous toehold switch system, our split T7 switch-mediated CFPS system could become a core platform for detecting various target nucleic acids.
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Affiliation(s)
- Doyeon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junhyeong Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jinjoo Han
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jiye Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
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2
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Wang C, Gu Y, Chen C, Li Y, Li L, Chai Y, Jiang Z, Chen X, Yuan Y. One-Step Synthesis and Oriented Immobilization of Strep-Tag II Fused PDGFRβ for Screening Intracellular Domain-Targeted Ligands. Anal Chem 2024; 96:11479-11487. [PMID: 38943570 DOI: 10.1021/acs.analchem.4c02067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2024]
Abstract
Accurate orientations and stable conformations of membrane receptor immobilization are particularly imperative for accurate drug screening and ligand-protein affinity analysis. However, there remain challenges associated with (1) traditional recombination, purification, and immobilization of membrane receptors, which are time-consuming and labor-intensive; (2) the orientations on the stationary phase are not easily controlled. Herein, a novel one-step synthesis and oriented-immobilization membrane-receptor affinity chromatography (oSOMAC) method was developed to realize high-throughput and accurate drug screening targeting specific domains of membrane receptors. We employed Strep-tag II as a noncovalent immobilization tag fused into platelet-derived growth factor receptor β (PDGFRβ) through CFPS, and meanwhile, the Strep-Tactin-modified monolithic columns are prepared in batches. The advantages of oSOMAC are as follows: (1) targeted membrane receptors can be expressed independent of living cell within 1-2 h; (2) orientation of membrane receptors can be flexibly controlled and active sites can expose accurately; and (3) targeted membrane receptors can be synthesized, purified, and orientation-immobilized on monolithic columns in one step. Accordingly, three potential PDGFRβ intracellular domain targeted ligands: tanshinone IIA (Tan IIA), hydroxytanshinone IIA, and dehydrotanshinone IIA were successfully screened out from Salvia miltiorrhiza extract through oSOMAC. Pharmacological experiments and molecular docking further demonstrated that Tan IIA could attenuate hepatic stellate cells activation by targeting the protein kinase domain of PDGFRβ with a KD value of 9.7 μM. Ultimately, the novel oSOMAC method provides an original insight for accurate drug screening and interaction analysis which can be applied in other membrane receptors.
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Affiliation(s)
- Chengliang Wang
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Yanqiu Gu
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Chun Chen
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Yanting Li
- Department of Pharmaceutical Analysis, School of Pharmacy, Ningxia Medical University, 1160 Shenli Street, Yinchuan 750004, China
| | - Ling Li
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Yifeng Chai
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Zhengjin Jiang
- Institute of Pharmaceutical Analysis, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiaofei Chen
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Yongfang Yuan
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
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3
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Free TJ, Talley JP, Hyer CD, Miller CJ, Griffitts JS, Bundy BC. Engineering the Signal Resolution of a Paper-Based Cell-Free Glutamine Biosensor with Genetic Engineering, Metabolic Engineering, and Process Optimization. SENSORS (BASEL, SWITZERLAND) 2024; 24:3073. [PMID: 38793927 PMCID: PMC11124800 DOI: 10.3390/s24103073] [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: 04/03/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Specialized cancer treatments have the potential to exploit glutamine dependence to increase patient survival rates. Glutamine diagnostics capable of tracking a patient's response to treatment would enable a personalized treatment dosage to optimize the tradeoff between treatment success and dangerous side effects. Current clinical glutamine testing requires sophisticated and expensive lab-based tests, which are not broadly available on a frequent, individualized basis. To address the need for a low-cost, portable glutamine diagnostic, this work engineers a cell-free glutamine biosensor to overcome assay background and signal-to-noise limitations evident in previously reported studies. The findings from this work culminate in the development of a shelf-stable, paper-based, colorimetric glutamine test with a high signal strength and a high signal-to-background ratio for dramatically improved signal resolution. While the engineered glutamine test is important progress towards improving the management of cancer and other health conditions, this work also expands the assay development field of the promising cell-free biosensing platform, which can facilitate the low-cost detection of a broad variety of target molecules with high clinical value.
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Affiliation(s)
- Tyler J. Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Joseph P. Talley
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Chad D. Hyer
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Catherine J. Miller
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT 84602, USA
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4
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Lee MS, Lee JA, Biondo JR, Lux JE, Raig RM, Berger PN, Bernhards CB, Kuhn DL, Gupta MK, Lux MW. Cell-Free Protein Expression in Polymer Materials. ACS Synth Biol 2024; 13:1152-1164. [PMID: 38467017 PMCID: PMC11036507 DOI: 10.1021/acssynbio.3c00628] [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: 10/12/2023] [Revised: 01/26/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024]
Abstract
While synthetic biology has advanced complex capabilities such as sensing and molecular synthesis in aqueous solutions, important applications may also be pursued for biological systems in solid materials. Harsh processing conditions used to produce many synthetic materials such as plastics make the incorporation of biological functionality challenging. One technology that shows promise in circumventing these issues is cell-free protein synthesis (CFPS), where core cellular functionality is reconstituted outside the cell. CFPS enables genetic functions to be implemented without the complications of membrane transport or concerns over the cellular viability or release of genetically modified organisms. Here, we demonstrate that dried CFPS reactions have remarkable tolerance to heat and organic solvent exposure during the casting processes for polymer materials. We demonstrate the utility of this observation by creating plastics that have spatially patterned genetic functionality, produce antimicrobials in situ, and perform sensing reactions. The resulting materials unlock the potential to deliver DNA-programmable biofunctionality in a ubiquitous class of synthetic materials.
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Affiliation(s)
- Marilyn S. Lee
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Jennifer A. Lee
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
- Defense
Threat Reduction Agency, 2800 Bush River Road, Gunpowder, Maryland 21010, United States
| | - John R. Biondo
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
- Excet
Inc., 6225 Brandon Avenue,
Suite 360, Springfield, Virginia 22150, United States
| | - Jeffrey E. Lux
- US
Air Force Research Laboratory, 2179 12th Street, B652/R122, Wright-Patterson Air Force Base, Ohio 45433, United States
- UES
Inc., 4401 Dayton-Xenia
Road, Dayton, Ohio 45432, United States
| | - Rebecca M. Raig
- US
Air Force Research Laboratory, 2179 12th Street, B652/R122, Wright-Patterson Air Force Base, Ohio 45433, United States
- UES
Inc., 4401 Dayton-Xenia
Road, Dayton, Ohio 45432, United States
| | - Pierce N. Berger
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Casey B. Bernhards
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Danielle L. Kuhn
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Maneesh K. Gupta
- US
Air Force Research Laboratory, 2179 12th Street, B652/R122, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Matthew W. Lux
- U.S.
Army Combat Capabilities Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, Maryland 21010, United States
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5
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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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6
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Smith SA, Lindgren CM, Ebbert LE, Free TJ, Nelson JAD, Simonson KM, Hunt JP, Bundy BC. "Just add small molecules" cell-free protein synthesis: Combining DNA template and cell extract preparation into a single fermentation. Biotechnol Prog 2023:e3332. [PMID: 36799109 DOI: 10.1002/btpr.3332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/19/2023] [Accepted: 02/08/2023] [Indexed: 02/18/2023]
Abstract
Cell-free protein synthesis (CFPS) is a versatile biotechnology platform enabling a broad range of applications including clinical diagnostics, large-scale production of officinal therapeutics, small-scale on-demand production of personal magistral therapeutics, and exploratory research. The shelf stability and scalability of CFPS systems also have the potential to overcome cost and infrastructure challenges for distributing and using essential medical tests at home in both high- and low-income countries. However, CFPS systems are often more time-consuming and expensive to prepare than traditional in vivo systems, limiting their broader use. Much work has been done to lower CFPS costs by optimizing cell extract preparation, small molecule reagent recipes, and DNA template preparation. In order to further reduce reagent cost and preparation time, this work presents a CFPS system that does not require separately purified DNA template. Instead, a DNA plasmid encoding the recombinant protein is transformed into the cells used to make the extract, and the extract preparation process is modified to allow enough DNA to withstand homogenization-induced shearing. The finished extract contains sufficient levels of intact DNA plasmid for the CFPS system to operate. For a 10 mL scale CFPS system expressing recombinant sfGFP protein for a biosensor, this new system reduces reagent cost by more than half. This system is applied to a proof-of-concept glutamine sensor compatible with smartphone quantification to demonstrate its viability for further cost reduction and use in low-resource settings.
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Affiliation(s)
- Sydney A Smith
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Caleb M Lindgren
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Landon E Ebbert
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Tyler J Free
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - J Andrew D Nelson
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Katelyn M Simonson
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
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7
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Van Raad D, Huber T. eCell Technology for Cell-Free Protein Synthesis, Biosensing, and Remediation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:129-146. [PMID: 37306701 DOI: 10.1007/10_2023_225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The eCell technology is a recently introduced, specialized protein production platform with uses in a multitude of biotechnological applications. This chapter summarizes the use of eCell technology in four selected application areas. Firstly, for detecting heavy metal ions, specifically mercury, in an in vitro protein expression system. Results show improved sensitivity and lower limit of detection compared to comparable in vivo systems. Secondly, eCells are semipermeable, stable, and can be stored for extended periods of time, making them a portable and accessible technology for bioremediation of toxicants in extreme environments. Thirdly and fourthly, applications of eCell technology are shown to facilitate expression of correctly folded disulfide-rich proteins and incorporate chemically interesting derivatives of amino acids into proteins which are toxic to in vivo protein expression. Overall, eCell technology presents a cost-effective and efficient method for biosensing, bioremediation, and protein production.
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Affiliation(s)
- Damian Van Raad
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia.
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8
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Mathur D, Thakur M, Díaz SA, Susumu K, Stewart MH, Oh E, Walper SA, Medintz IL. Hybrid Nucleic Acid-Quantum Dot Assemblies as Multiplexed Reporter Platforms for Cell-Free Transcription Translation-Based Biosensors. ACS Synth Biol 2022; 11:4089-4102. [PMID: 36441919 PMCID: PMC9829448 DOI: 10.1021/acssynbio.2c00394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell-free synthetic biology has emerged as a valuable tool for the development of rapid, portable biosensors that can be readily transported in the freeze-dried form to the point of need eliminating cold chain requirements. One of the challenges associated with cell-free sensors is the ability to simultaneously detect multiple analytes within a single reaction due to the availability of a limited set of fluorescent and colorimetric reporters. To potentially provide multiplexing capabilities to cell-free biosensors, we designed a modular semiconductor quantum dot (QD)-based reporter platform that is plugged in downstream of the transcription-translation functionality in the cell-free reaction and which converts enzymatic activity in the reaction into distinct optical signals. We demonstrate proof of concept by converting restriction enzyme activity, utilized as our prototypical sensing output, into optical changes across several distinct spectral output channels that all use a common excitation wavelength. These hybrid Förster resonance energy transfer (FRET)-based QD peptide PNA-DNA-Dye reporters (QD-PDDs) are completely self-assembled and consist of differentially emissive QD donors paired to a dye-acceptor displayed on a unique DNA encoding a given enzyme's cleavage site. Three QD-based PDDs, independently activated by the enzymes BamHI, EcoRI, and NcoI, were prototyped in mixed enzyme assays where all three demonstrated the ability to convert enzymatic activity into fluorescent output. Simultaneous monitoring of each of the three paired QD-donor dye-acceptor spectral channels in cell-free biosensing reactions supplemented with added linear genes encoding each enzyme confirmed robust multiplexing capabilities for at least two enzymes when co-expressed. The modular QD-PDDs are easily adapted to respond to other restriction enzymes or even proteases if desired.
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Affiliation(s)
| | | | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Kimihiro Susumu
- Jacobs Corporation, Hanover, Maryland 21076, United States; Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Michael H. Stewart
- Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Eunkeu Oh
- Optical Sciences Division Code 5600, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington 20375, United States
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9
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Soltani M, Hunt JP, Smith AK, Zhao EL, Knotts TA, Bundy BC. Assessing the predictive capabilities of design heuristics and coarse-grain simulation toward understanding and optimizing site-specific covalent immobilization of β-lactamase. Biotechnol J 2022; 17:e2100535. [PMID: 35189031 DOI: 10.1002/biot.202100535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 11/12/2022]
Abstract
For industrial applications, covalent immobilization of enzymes provides minimum leakage, recoverability, reusability, and high stability. Yet, the suitability of a given site on the enzyme for immobilization remains a trial-and-error procedure. Here, we investigate the reliability of design heuristics and a coarse-grain molecular simulation in predicting the optimum sites for covalent immobilization of TEM-1 β-lactamase. We utilized E. coli-lysate-based cell-free protein synthesis (CFPS) to produce variants containing a site-specific incorporated unnatural amino acid with a unique moiety to facilitate site directed covalent immobilization. To constrain the number of potential immobilization sites, we investigated the predictive capability of several design heuristics. The suitability of immobilization sites was determined by analyzing expression yields, specific activity, immobilization efficiency, and stability of variants. These experimental findings are compared with coarse-grain simulation of TEM-1 domain stability and thermal stability and analyzed for a priori predictive capabilities. This work demonstrates that the design heuristics successfully identify a subset of locations for experimental validation. Specifically, the nucleotide following amber stop codon and domain stability correlate well with the expression yield and specific activity of the variants, respectively. Our approach highlights the advantages of combining coarse-grain simulation and high-throughput experimentation using CFPS to identify optimal enzyme immobilization sites. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mehran Soltani
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Addison K Smith
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Emily Long Zhao
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
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10
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Hunt JP, Zhao EL, Free TJ, Soltani M, Warr CA, Benedict AB, Takahashi MK, Griffitts JS, Pitt WG, Bundy BC. Towards detection of SARS-CoV-2 RNA in human saliva: A paper-based cell-free toehold switch biosensor with a visual bioluminescent output. N Biotechnol 2022; 66:53-60. [PMID: 34555549 PMCID: PMC8452453 DOI: 10.1016/j.nbt.2021.09.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic has illustrated the global demand for rapid, low-cost, widely distributable and point-of-care nucleic acid diagnostic technologies. Such technologies could help disrupt transmission, sustain economies and preserve health and lives during widespread infection. In contrast, conventional nucleic acid diagnostic procedures require trained personnel, complex laboratories, expensive equipment, and protracted processing times. In this work, lyophilized cell-free protein synthesis (CFPS) and toehold switch riboregulators are employed to develop a promising paper-based nucleic acid diagnostic platform activated simply by the addition of saliva. First, to facilitate distribution and deployment, an economical paper support matrix is identified and a mass-producible test cassette designed with integral saliva sample receptacles. Next, CFPS is optimized in the presence of saliva using murine RNase inhibitor. Finally, original toehold switch riboregulators are engineered to express the bioluminescent reporter NanoLuc in response to SARS-CoV-2 RNA sequences present in saliva samples. The biosensor generates a visible signal in as few as seven minutes following administration of 15 μL saliva enriched with high concentrations of SARS-CoV-2 RNA sequences. The estimated cost of this test is less than 0.50 USD, which could make this platform readily accessible to both the developed and developing world. While additional research is needed to decrease the limit of detection, this work represents important progress toward developing a diagnostic technology that is rapid, low-cost, distributable and deployable at the point-of-care by a layperson.
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Affiliation(s)
- J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Emily Long Zhao
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Tyler J Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Mehran Soltani
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Chandler A Warr
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Alex B Benedict
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Melissa K Takahashi
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Joel S Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - William G Pitt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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11
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Streamlining cell-free protein synthesis biosensors for use in human fluids: In situ RNase inhibitor production during extract preparation. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Hunt JP, Galiardi J, Free TJ, Yang SO, Poole D, Zhao EL, Andersen JL, Wood DW, Bundy BC. Mechanistic discoveries and simulation-guided assay optimization of portable hormone biosensors with cell-free protein synthesis. Biotechnol J 2021; 17:e2100152. [PMID: 34761537 DOI: 10.1002/biot.202100152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023]
Abstract
Nuclear receptors (NRs) influence nearly every system of the body and our lives depend on correct NR signaling. Thus, a key environmental and pharmaceutical quest is to identify and detect chemicals which interact with nuclear hormone receptors, including endocrine disrupting chemicals (EDCs), therapeutic receptor modulators, and natural hormones. Previously reported biosensors of nuclear hormone receptor ligands facilitated rapid detection of NR ligands using cell-free protein synthesis (CFPS). In this work, the advantages of CFPS are further leveraged and combined with kinetic analysis, autoradiography, and western blot to elucidate the molecular mechanism of this biosensor. Additionally, mathematical simulations of enzyme kinetics are used to optimize the biosensor assay, ultimately lengthening its readable window by five-fold and improving sensor signal strength by two-fold. This approach enabled the creation of an on-demand thyroid hormone biosensor with an observable color-change readout. This mathematical and experimental approach provides insight for engineering rapid and field-deployable CFPS biosensors and promises to improve methods for detecting natural hormones, therapeutic receptor modulators, and EDCs.
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Affiliation(s)
- John Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Jackelyn Galiardi
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Tyler J Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Seung Ook Yang
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Daniel Poole
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Emily Long Zhao
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Joshua L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - David W Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
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13
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Burrington LR, Watts KR, Oza JP. Characterizing and Improving Reaction Times for E. coli-Based Cell-Free Protein Synthesis. ACS Synth Biol 2021; 10:1821-1829. [PMID: 34269580 DOI: 10.1021/acssynbio.1c00195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cell-free protein synthesis (CFPS) is a platform biotechnology that has enabled the on-demand synthesis of proteins for a variety of applications. Numerous advances have improved the productivity of the CFPS platform to result in high-yielding reactions; however, many applications remain limited due to long reaction times. To overcome this limitation, we first established the benchmarks reaction times for CFPS across in-house E. coli extracts and commercial kits. We then set out to fine-tune our in-house extract systems to improve reaction times. Through the optimization of reaction composition and titration of low-cost additives, we have identified formulations that reduce reaction times by 30-50% to obtain high protein titers for biomanufacturing applications, and reduce times by more than 50% to reach the sfGFP detection limit for applications in education and diagnostics. Under optimum conditions, we report the visible observation of sfGFP signal in less than 10 min. Altogether, these advances enhance the utility of CFPS as a rapid, user-defined platform.
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Affiliation(s)
- Logan R. Burrington
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Katharine R. Watts
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Javin P. Oza
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
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14
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Soltani M, Hunt JP, Bundy BC. Rapid RNase inhibitor production to enable low-cost, on-demand cell-free protein synthesis biosensor use in human body fluids. Biotechnol Bioeng 2021; 118:3973-3983. [PMID: 34185319 DOI: 10.1002/bit.27874] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/22/2022]
Abstract
Human body fluids contain biomarkers which are used extensively for prognostication, diagnosis, monitoring, and evaluation of different treatments for a variety of diseases and disorders. The application of biosensors based on cell-free protein synthesis (CFPS) offers numerous advantages including on-demand and at-home use for fast, accurate detection of a variety of biomarkers in human fluids at an affordable price. However, current CFPS-based biosensors use commercial RNase inhibitors to inhibit different RNases present in human fluids and this reagent is approximately 90% of the expense of these biosensors. Here the flexible nature of Escherichia coli-lysate-based CFPS was used for the first time to produce murine RNase Inhibitor (m-RI) and to optimize its soluble and active production by tuning reaction temperature, reaction time, reduced potential, and addition of GroEL/ES folding chaperons. Furthermore, RNase inhibition activity of m-RI with the highest activity and stability was determined against increasing amounts of three human fluids of serum, saliva, and urine (0%-100% v/v) in lyophilized CFPS reactions. To further demonstrate the utility of the CFPS-produced m-RI, a lyophilized saliva-based glutamine biosensor was demonstrated to effectively work with saliva samples. Overall, the use of CFPS-produced m-RI reduces the total reagent costs of CFPS-based biosensors used in human body fluids approximately 90%.
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Affiliation(s)
- Mehran Soltani
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
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15
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Del Valle I, Fulk EM, Kalvapalle P, Silberg JJ, Masiello CA, Stadler LB. Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences. Front Microbiol 2021; 11:618373. [PMID: 33633695 PMCID: PMC7901896 DOI: 10.3389/fmicb.2020.618373] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/26/2022] Open
Abstract
The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.
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Affiliation(s)
- Ilenne Del Valle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Emily M. Fulk
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Prashant Kalvapalle
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, United States
| | - Jonathan J. Silberg
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Caroline A. Masiello
- Department of BioSciences, Rice University, Houston, TX, United States
- Department of Earth, Environmental and Planetary Sciences, Rice University, Houston, TX, United States
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Lauren B. Stadler
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, United States
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16
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Wang X, Zhu K, Chen D, Wang J, Wang X, Xu A, Wu L, Li L, Chen S. Monitoring arsenic using genetically encoded biosensors in vitro: The role of evolved regulatory genes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 207:111273. [PMID: 32916524 DOI: 10.1016/j.ecoenv.2020.111273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Toxic pollutant (TP) detection in situ using analytical instruments or whole-cell biosensors is inconvenient. Designing and developing genetically coded biosensors in vitro for real-world TP detection is a promising alternative. However, because the bioactivity and stability of some key biomolecules are weakened in vitro, the response and regulation of reporter protein become difficult. Here, we established a genetically encoded biosensor in vitro with an arsenical resistance operon repressor (ArsR) and GFP reporter gene. Given that the wildtype ArsR did not respond to arsenic and activate GFP expression in vitro, we found, after screening, an evolved ArsR mutant ep3 could respond to arsenic and exhibited an approximately 3.4-fold fluorescence increase. Arsenic induced expression of both wildtype ArsR and ep3 mutant in vitro, however, only ep3 mutant regulated the expression of reporter gene. Furthermore, the effects of cell extracts, temperature, pH, incubation, and equilibrium time were investigated, and the equilibration of reaction mixtures for 30 min at 37 °C was found to be essential for in vitro arsenic detection prior to treatment with arsenic. Based on our data, we established a standard procedure for arsenic detection in vitro. Our results will facilitate the practical application of genetically encoded biosensors in TP monitoring.
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Affiliation(s)
- Xuanyu Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Kaili Zhu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Dongdong Chen
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Juan Wang
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Xiaofei Wang
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui, 230601, China
| | - An Xu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China
| | - Lijun Wu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China; Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Luzhi Li
- School of Biology, Food and Environment, Hefei University, Hefei, Anhui, 230601, China
| | - Shaopeng Chen
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, China Academy of Sciences, Hefei, Anhui, 230031, China; Key Laboratory of Environmental Toxicology and Pollution Control Technology of Anhui Province, Hefei, Anhui, 230031, China.
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17
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Adhikari A, Vilkhovoy M, Vadhin S, Lim HE, Varner JD. Effective Biophysical Modeling of Cell Free Transcription and Translation Processes. Front Bioeng Biotechnol 2020; 8:539081. [PMID: 33324619 PMCID: PMC7726328 DOI: 10.3389/fbioe.2020.539081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 11/02/2020] [Indexed: 12/18/2022] Open
Abstract
Transcription and translation are at the heart of metabolism and signal transduction. In this study, we developed an effective biophysical modeling approach to simulate transcription and translation processes. The model, composed of coupled ordinary differential equations, was tested by comparing simulations of two cell free synthetic circuits with experimental measurements generated in this study. First, we considered a simple circuit in which sigma factor 70 induced the expression of green fluorescent protein. This relatively simple case was then followed by a more complex negative feedback circuit in which two control genes were coupled to the expression of a third reporter gene, green fluorescent protein. Many of the model parameters were estimated from previous biophysical studies in the literature, while the remaining unknown model parameters for each circuit were estimated by minimizing the difference between model simulations and messenger RNA (mRNA) and protein measurements generated in this study. In particular, either parameter estimates from published studies were used directly, or characteristic values found in the literature were used to establish feasible ranges for the parameter estimation problem. In order to perform a detailed analysis of the influence of individual model parameters on the expression dynamics of each circuit, global sensitivity analysis was used. Taken together, the effective biophysical modeling approach captured the expression dynamics, including the transcription dynamics, for the two synthetic cell free circuits. While, we considered only two circuits here, this approach could potentially be extended to simulate other genetic circuits in both cell free and whole cell biomolecular applications as the equations governing the regulatory control functions are modular and easily modifiable. The model code, parameters, and analysis scripts are available for download under an MIT software license from the Varnerlab GitHub repository.
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Affiliation(s)
- Abhinav Adhikari
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, College of Engineering, Cornell University, Ithaca, NY, United States
| | - Michael Vilkhovoy
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, College of Engineering, Cornell University, Ithaca, NY, United States
| | - Sandra Vadhin
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, College of Engineering, Cornell University, Ithaca, NY, United States
| | - Ha Eun Lim
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, College of Engineering, Cornell University, Ithaca, NY, United States
| | - Jeffrey D Varner
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, College of Engineering, Cornell University, Ithaca, NY, United States
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18
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Dopp JL, Reuel NF. Simple, functional, inexpensive cell extract for in vitro prototyping of proteins with disulfide bonds. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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19
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Nelson JAD, Barnett RJ, Hunt JP, Foutz I, Welton M, Bundy BC. Hydrofoam and oxygen headspace bioreactors improve cell-free therapeutic protein production yields through enhanced oxygen transport. Biotechnol Prog 2020; 37:e3079. [PMID: 32920987 DOI: 10.1002/btpr.3079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 12/19/2022]
Abstract
Protein therapeutics are powerful tools in the fight against diabetes, cancers, growth disorders, and many other debilitating diseases. However, availability is limited due to cost and complications of production from living organisms. To make life-saving protein therapeutics more available to the world, the possibility of magistral or point-of-care protein therapeutic production has gained focus. The recent invention and optimization of lyophilized "cell-free" protein synthesis reagents and its demonstrated ability to produce highly active versions of FDA-approved cancer therapeutics have increased its potential for low-cost, single-batch, magistral medicine. Here we present for the first time the concept of increased oxygen mass transfer in small-batch, cell-free protein synthesis (CFPS) reactions through air-water foams. These "hydrofoam" reactions increased CFPS yields by up to 100%. Contrary to traditional protein synthesis using living organisms, where foam bubbles cause cell-lysis and production losses, hydrofoam CFPS reactions are "cell-free" and better tolerate foaming. Simulation and experimental results suggest that oxygen transfer is limiting in even small volume batch CFPS reactors and that the hydrofoam format improved oxygen transfer. This is further supported by CFPS reactions achieving higher yields when oxygen gas replaces air in the headspace of batch reactions. Improving CFPS yields with hydrofoam reduces the overall cost of biotherapeutic production, increasing availability to the developing world. Beyond protein therapeutic production, hydrofoam CFPS could also be used to enhance other CFPS applications including biosensing, biomanufacturing, and biocatalysis.
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Affiliation(s)
- J Andrew D Nelson
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - R Jordan Barnett
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Isaac Foutz
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Meagan Welton
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, Utah, USA
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20
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Hunt JP, Barnett RJ, Robinson H, Soltani M, Nelson JAD, Bundy BC. Rapid sensing of clinically relevant glutamine concentrations in human serum with metabolically engineered E. coli-based cell-free protein synthesis. J Biotechnol 2020; 325:389-394. [PMID: 32961202 DOI: 10.1016/j.jbiotec.2020.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/06/2020] [Accepted: 09/14/2020] [Indexed: 12/27/2022]
Abstract
Bioavailable glutamine (Gln) is critical for metabolism, intestinal health, immune function, and cell signaling. Routine measurement of serum Gln concentrations could facilitate improved diagnosis and treatment of severe infections, anorexia nervosa, chronic kidney disease, diabetes, and cancer. Current methods for quantifying tissue Gln concentrations rely mainly on HPLC, which requires extensive sample preparation and expensive equipment. Consequently, patient Gln levels may be clinically underutilized. Cell-free protein synthesis (CFPS) is an emerging sensing platform with promising clinical applications, including detection of hormones, amino acids, nucleic acids, and other biomarkers. In this work, in vitro E. coli amino acid metabolism is engineered with methionine sulfoximine to inhibit glutamine synthetase and create a CFPS Gln sensor. The sensor features a strong signal-to-noise ratio and a detection range ideally suited to physiological Gln concentrations. Furthermore, it quantifies Gln concentration in the presence of human serum. This work demonstrates that CFPS reactions which harness the metabolic power of E. coli lysate may be engineered to detect clinically relevant analytes in human samples. This approach could lead to transformative point-of-care diagnostics and improved treatment regimens for a variety of diseases including cancer, diabetes, anorexia nervosa, chronic kidney disease, and severe infections.
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Affiliation(s)
- J Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, United States
| | - R Jordan Barnett
- Department of Chemical Engineering, Brigham Young University, Provo, UT, United States
| | - Hannah Robinson
- Department of Chemical Engineering, Brigham Young University, Provo, UT, United States
| | - Mehran Soltani
- Department of Chemical Engineering, Brigham Young University, Provo, UT, United States
| | - J Andrew D Nelson
- Department of Chemical Engineering, Brigham Young University, Provo, UT, United States
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, United States.
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21
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Zhang L, Guo W, Lu Y. Advances in Cell‐Free Biosensors: Principle, Mechanism, and Applications. Biotechnol J 2020; 15:e2000187. [DOI: 10.1002/biot.202000187] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/22/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Liyuan Zhang
- Key Laboratory of Industrial Biocatalysis Ministry of Education Department of Chemical Engineering Tsinghua University Beijing 100084 China
- Department of Ecology Shenyang Agricultural University Shenyang Liaoning Province 110866 China
| | - Wei Guo
- Department of Ecology Shenyang Agricultural University Shenyang Liaoning Province 110866 China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis Ministry of Education Department of Chemical Engineering Tsinghua University Beijing 100084 China
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22
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Hoang Trung Chau T, Hoang Anh Mai D, Ngoc Pham D, Thi Quynh Le H, Yeol Lee E. Developments of Riboswitches and Toehold Switches for Molecular Detection-Biosensing and Molecular Diagnostics. Int J Mol Sci 2020; 21:E3192. [PMID: 32366036 PMCID: PMC7247568 DOI: 10.3390/ijms21093192] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Riboswitches and toehold switches are considered to have potential for implementation in various fields, i.e., biosensing, metabolic engineering, and molecular diagnostics. The specific binding, programmability, and manipulability of these RNA-based molecules enable their intensive deployments in molecular detection as biosensors for regulating gene expressions, tracking metabolites, or detecting RNA sequences of pathogenic microorganisms. In this review, we will focus on the development of riboswitches and toehold switches in biosensing and molecular diagnostics. This review introduces the operating principles and the notable design features of riboswitches as well as toehold switches. Moreover, we will describe the advances and future directions of riboswitches and toehold switches in biosensing and molecular diagnostics.
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Affiliation(s)
| | | | | | | | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Korea; (T.H.T.C.); (D.H.A.M.); (D.N.P.); (H.T.Q.L.)
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23
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Gregorio NE, Kao WY, Williams LC, Hight CM, Patel P, Watts KR, Oza JP. Unlocking Applications of Cell-Free Biotechnology through Enhanced Shelf Life and Productivity of E. coli Extracts. ACS Synth Biol 2020; 9:766-778. [PMID: 32083847 DOI: 10.1021/acssynbio.9b00433] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell-free protein synthesis (CFPS) is a platform biotechnology that enables a breadth of applications. However, field applications remain limited due to the poor shelf-stability of aqueous cell extracts required for CFPS. Lyophilization of E. coli extracts improves shelf life but remains insufficient for extended storage at room temperature. To address this limitation, we mapped the chemical space of ten low-cost additives with four distinct mechanisms of action in a combinatorial manner to identify formulations capable of stabilizing lyophilized cell extract. We report three key findings: (1) unique additive formulations that maintain full productivity of cell extracts stored at 4 °C and 23 °C; (2) additive formulations that enhance extract productivity by nearly 2-fold; (3) a machine learning algorithm that provides predictive capacity for the stabilizing effects of additive formulations that were not tested experimentally. These findings provide a simple and low-cost advance toward making CFPS field-ready and cost-competitive for biomanufacturing.
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Affiliation(s)
- Nicole E. Gregorio
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Wesley Y. Kao
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Layne C. Williams
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Christopher M. Hight
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Pratish Patel
- Department of Finance, Orfalea College of Business, California Polytechnic State University, San Luis Obispo, California 93407, United States
| | - Katharine R. Watts
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
| | - Javin P. Oza
- Chemistry and Biochemistry Department, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
- Center for Applications in Biotechnology, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California 93407, United States
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24
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Ayoubi-Joshaghani MH, Dianat-Moghadam H, Seidi K, Jahanban-Esfahalan A, Zare P, Jahanban-Esfahlan R. Cell-free protein synthesis: The transition from batch reactions to minimal cells and microfluidic devices. Biotechnol Bioeng 2020; 117:1204-1229. [PMID: 31840797 DOI: 10.1002/bit.27248] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/23/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Thanks to the synthetic biology, the laborious and restrictive procedure for producing a target protein in living microorganisms by biotechnological approaches can now experience a robust, pliant yet efficient alternative. The new system combined with lab-on-chip microfluidic devices and nanotechnology offers a tremendous potential envisioning novel cell-free formats such as DNA brushes, hydrogels, vesicular particles, droplets, as well as solid surfaces. Acting as robust microreactors/microcompartments/minimal cells, the new platforms can be tuned to perform various tasks in a parallel and integrated manner encompassing gene expression, protein synthesis, purification, detection, and finally enabling cell-cell signaling to bring a collective cell behavior, such as directing differentiation process, characteristics of higher order entities, and beyond. In this review, we issue an update on recent cell-free protein synthesis (CFPS) formats. Furthermore, the latest advances and applications of CFPS for synthetic biology and biotechnology are highlighted. In the end, contemporary challenges and future opportunities of CFPS systems are discussed.
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Affiliation(s)
| | | | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
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25
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Hunt JP, Wilding KM, Barnett RJ, Robinson H, Soltani M, Cho JE, Bundy BC. Engineering Cell‐Free Protein Synthesis for High‐Yield Production and Human Serum Activity Assessment of Asparaginase: Toward On‐Demand Treatment of Acute Lymphoblastic Leukemia. Biotechnol J 2020; 15:e1900294. [DOI: 10.1002/biot.201900294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/13/2019] [Indexed: 12/22/2022]
Affiliation(s)
- J. Porter Hunt
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Kristen M. Wilding
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - R. Jordan Barnett
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Hannah Robinson
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Mehran Soltani
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Jae Eun Cho
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
| | - Bradley C. Bundy
- Department of Chemical Engineering Brigham Young University Provo UT 84602 USA
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26
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Hunt JP, Zhao EL, Soltani M, Frei M, Nelson JAD, Bundy BC. Streamlining the preparation of "endotoxin-free" ClearColi cell extract with autoinduction media for cell-free protein synthesis of the therapeutic protein crisantaspase. Synth Syst Biotechnol 2019; 4:220-224. [PMID: 31890926 PMCID: PMC6926305 DOI: 10.1016/j.synbio.2019.11.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/29/2022] Open
Abstract
An "endotoxin-free" E. coli-based cell-free protein synthesis system has been reported to produce therapeutic proteins rapidly and on-demand. However, preparation of the most complex CFPS reagent - the cell extract - remains time-consuming and labor-intensive because of the relatively slow growth kinetics of the endotoxin-free ClearColiTMBL21(DE3) strain. Here we report a streamlined procedure for preparing E. coli cell extract from ClearColi™ using auto-induction media. In this work, the term auto-induction describes cell culture media which eliminates the need for manual induction of protein expression. Culturing Clearcoli™ cells in autoinduction media significantly reduces the hands-on time required during extract preparation, and the resulting "endotoxin-free" cell extract maintained the same cell-free protein synthesis capability as extract produced with traditional induction as demonstrated by the high-yield expression of crisantaspase, an FDA approved leukemia therapeutic. It is anticipated that this work will lower the barrier for researchers to enter the field and use this technology as the method to produce endotoxin-free E. coli-based extract for CFPS.
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Affiliation(s)
| | | | | | | | | | - Bradley C. Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
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27
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Chen SY, Wei W, Yin BC, Tong Y, Lu J, Ye BC. Development of a Highly Sensitive Whole-Cell Biosensor for Arsenite Detection through Engineered Promoter Modifications. ACS Synth Biol 2019; 8:2295-2302. [PMID: 31525958 DOI: 10.1021/acssynbio.9b00093] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Whole-cell biosensors have attracted considerable interests because they are robust, eco-friendly, and cost-effective. However, most of the biosensors harness the naturally occurring wild-type promoter, which often suffers from high background noise and low sensitivity. In this study, we demonstrate how to design the core elements (i.e., RNA polymerase binding site and transcription factor binding site) of the promoters to obtain a significant gain in the signal-to-noise output ratio of the whole-cell biosensor circuits. As a proof of concept, we modified the arsenite-regulated promoter from Escherichia coli K-12 genome, such that it has a lower background and higher expression. This was achieved by balancing the relationship between the number of ArsR binding sites (ABS) and the activity of the promoter and adjusting the location of the auxiliary ABS. A promoter variant ParsD-ABS-8 was obtained with an induction ratio of 179 (11-fold increase over the wild-type promoter) when induced with 1 μM arsenite. Importantly, the developed biosensor exhibited good dose-response in the range of 0.1 to 4 μM (R2 = 0.9928) of arsenite with a detection limit of ca. 10 nM. These results indicated that the engineered promoter modification approach could be used to improve the performance of whole-cell biosensors, thereby facilitating their practical application.
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Affiliation(s)
- Sheng-Yan Chen
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Wenping Wei
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanbin Tong
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Jianjiang Lu
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
| | - Bang-Ce Ye
- School of Chemistry and Chemical Engineering, Shihezi University, Shihezi 832003, China
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, Zhejiang China
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28
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Lee KH, Kim DM. In Vitro Use of Cellular Synthetic Machinery for Biosensing Applications. Front Pharmacol 2019; 10:1166. [PMID: 31680954 PMCID: PMC6803485 DOI: 10.3389/fphar.2019.01166] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/10/2019] [Indexed: 12/25/2022] Open
Abstract
The application of biosensors is expanding in diverse fields due to their high selectivity and sensitivity. Biosensors employ biological components for the recognition of target analytes. In addition, the amplifying nature of biosynthetic processes can potentially be harnessed to for biological transduction of detection signals. Recent advances in the development of highly productive and cost-effective cell-free synthesis systems make it possible to use these systems as the biological transducers to generate biosensing signals. This review surveys recent developments in cell-free biosensors, focusing on the newly devised mechanisms for the biological recognition of analytes to initiate the amplification processes of transcription and translation.
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Affiliation(s)
- Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, South Korea
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29
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Custom-made transcriptional biosensors for metabolic engineering. Curr Opin Biotechnol 2019; 59:78-84. [DOI: 10.1016/j.copbio.2019.02.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/31/2019] [Accepted: 02/19/2019] [Indexed: 01/20/2023]
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30
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Pandi A, Grigoras I, Borkowski O, Faulon JL. Optimizing Cell-Free Biosensors to Monitor Enzymatic Production. ACS Synth Biol 2019; 8:1952-1957. [PMID: 31335131 DOI: 10.1021/acssynbio.9b00160] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell-free systems are promising platforms for rapid and high-throughput prototyping of biological parts in metabolic engineering and synthetic biology. One main limitation of cell-free system applications is the low fold repression of transcriptional repressors. Hence, prokaryotic biosensor development, which mostly relies on repressors, is limited. In this study, we demonstrate how to improve these biosensors in cell-free systems by applying a transcription factor (TF)-doped extract, a preincubation strategy with the TF plasmid, or reinitiation of the cell-free reaction (two-step cell-free reaction). We use the optimized biosensor to sense the enzymatic production of a rare sugar, D-psicose. This work provides a methodology to optimize repressor-based systems in cell-free to further increase the potential of cell-free systems for bioproduction.
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Affiliation(s)
- Amir Pandi
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas 78352, France
| | - Ioana Grigoras
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
| | - Olivier Borkowski
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
| | - Jean-Loup Faulon
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas 78352, France
- iSSB Laboratory, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057 Evry, France
- SYNBIOCHEM Center, School of Chemistry, University of Manchester, Manchester M13 9PL, U.K
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31
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Liu WQ, Zhang L, Chen M, Li J. Cell-free protein synthesis: Recent advances in bacterial extract sources and expanded applications. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2018.10.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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32
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Bundy BC, Hunt JP, Jewett MC, Swartz JR, Wood DW, Frey DD, Rao G. Cell-free biomanufacturing. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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