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Copeland C, Heitmeier CJ, Doan KD, Lee SC, Porche KB, Kwon YC. Expanding the Cell-Free Reporter Protein Toolbox by Employing a Split mNeonGreen System to Reduce Protein Synthesis Workload. ACS Synth Biol 2024; 13:1663-1668. [PMID: 38836603 PMCID: PMC11197088 DOI: 10.1021/acssynbio.3c00752] [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: 12/18/2023] [Revised: 05/28/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
The cell-free system offers potential advantages in biosensor applications, but its limited time for protein synthesis poses a challenge in creating enough fluorescent signals to detect low limits of the analyte while providing a robust sensing module at the beginning. In this study, we harnessed split versions of fluorescent proteins, particularly split superfolder green fluorescent protein and mNeonGreen, to increase the number of reporter units made before the reaction ceased and enhance the detection limit in the cell-free system. A comparative analysis of the expression of 1-10 and 11th segments of beta strands in both whole-cell and cell-free platforms revealed distinct fluorescence patterns. Moreover, the integration of SynZip peptide linkers substantially improved complementation. The split protein reporter system could enable higher reporter output when sensing low analyte levels in the cell-free system, broadening the toolbox of the cell-free biosensor repertoire.
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Affiliation(s)
- Caroline
E. Copeland
- Department
of Biological and Agricultural Engineering, Louisiana State University, Baton
Rouge, Louisiana 70803, United States
| | - Chloe J. Heitmeier
- Department
of Biological and Agricultural Engineering, Louisiana State University, Baton
Rouge, Louisiana 70803, United States
| | - Khoa D. Doan
- Department
of Biological and Agricultural Engineering, Louisiana State University, Baton
Rouge, Louisiana 70803, United States
| | - Shea C. Lee
- Department
of Biological and Agricultural Engineering, Louisiana State University, Baton
Rouge, Louisiana 70803, United States
| | - Kassidy B. Porche
- Department
of Biological and Agricultural Engineering, Louisiana State University, Baton
Rouge, Louisiana 70803, United States
| | - Yong-Chan Kwon
- Department
of Biological and Agricultural Engineering, Louisiana State University, Baton
Rouge, Louisiana 70803, United States
- Louisiana
State University Agricultural Center, Baton Rouge, Louisiana 70803, United States
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2
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Maharjan A, Park JH. Cell-free protein synthesis system: A new frontier for sustainable biotechnology-based products. Biotechnol Appl Biochem 2023; 70:2136-2149. [PMID: 37735977 DOI: 10.1002/bab.2514] [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: 05/31/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Cell-free protein synthesis (CFPS) system is an innovative technology with a wide range of potential applications that could challenge current thinking and provide solutions to environmental and health issues. CFPS system has been demonstrated to be a successful way of producing biomolecules in a variety of applications, including the biomedical industry. Although there are still obstacles to overcome, its ease of use, versatility, and capacity for integration with other technologies open the door for it to continue serving as a vital instrument in synthetic biology research and industry. In this review, we mainly focus on the cell-free based platform for various product productions. Moreover, the challenges in the bio-therapeutic aspect using cell-free systems and their future prospective for the improvement and sustainability of the cell free systems.
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Affiliation(s)
- Anoth Maharjan
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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3
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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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4
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Multiple Gene Expression in Cell-Free Protein Synthesis Systems for Reconstructing Bacteriophages and Metabolic Pathways. Microorganisms 2022; 10:microorganisms10122477. [PMID: 36557730 PMCID: PMC9786908 DOI: 10.3390/microorganisms10122477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
As a fast and reliable technology with applications in diverse biological studies, cell-free protein synthesis has become popular in recent decades. The cell-free protein synthesis system can be considered a complex chemical reaction system that is also open to exogenous manipulation, including that which could otherwise potentially harm the cell's viability. On the other hand, since the technology depends on the cell lysates by which genetic information is transformed into active proteins, the whole system resembles the cell to some extent. These features make cell-free protein synthesis a valuable addition to synthetic biology technologies, expediting the design-build-test-learn cycle of synthetic biology routines. While the system has traditionally been used to synthesize one protein product from one gene addition, recent studies have employed multiple gene products in order to, for example, develop novel bacteriophages, viral particles, or synthetic metabolisms. Thus, we would like to review recent advancements in applying cell-free protein synthesis technology to synthetic biology, with an emphasis on multiple gene expressions.
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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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6
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Yang C, Yang M, Zhao W, Ding Y, Wang Y, Li J. Establishing a Klebsiella pneumoniae-Based Cell-Free Protein Synthesis System. Molecules 2022; 27:molecules27154684. [PMID: 35897861 PMCID: PMC9330377 DOI: 10.3390/molecules27154684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/25/2022] [Accepted: 07/18/2022] [Indexed: 02/01/2023] Open
Abstract
Cell-free protein synthesis (CFPS) systems are emerging as powerful platforms for in vitro protein production, which leads to the development of new CFPS systems for different applications. To expand the current CFPS toolkit, here we develop a novel CFPS system derived from a chassis microorganism Klebsiella pneumoniae, an important industrial host for heterologous protein expression and the production of many useful chemicals. First, we engineered the K. pneumoniae strain by deleting a capsule formation-associated wzy gene. This capsule-deficient strain enabled easy collection of the cell biomass for preparing cell extracts. Then, we optimized the procedure of cell extract preparation and the reaction conditions for CFPS. Finally, the optimized CFPS system was able to synthesize a reporter protein (superfolder green fluorescent protein, sfGFP) with a maximum yield of 253 ± 15.79 μg/mL. Looking forward, our K. pneumoniae-based CFPS system will not only expand the toolkit for protein synthesis, but also provide a new platform for constructing in vitro metabolic pathways for the synthesis of high-value chemicals.
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Affiliation(s)
- Chen Yang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China;
| | - Miaomiao Yang
- Clinical Pathology Center, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China;
- Department of Biological Physics, University of Science and Technology of China, Hefei 230026, China
| | - Wanhua Zhao
- College of Life Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (W.Z.); (Y.D.)
| | - Yue Ding
- College of Life Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (W.Z.); (Y.D.)
| | - Yu Wang
- College of Life Sciences, Jiangxi Agricultural University, Nanchang 330045, China; (W.Z.); (Y.D.)
- Correspondence: (Y.W.); (J.L.)
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China;
- Correspondence: (Y.W.); (J.L.)
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Copeland CE, Kim J, Copeland PL, Heitmeier CJ, Kwon YC. Characterizing a New Fluorescent Protein for a Low Limit of Detection Sensing in the Cell-Free System. ACS Synth Biol 2022; 11:2800-2810. [PMID: 35850511 PMCID: PMC9396652 DOI: 10.1021/acssynbio.2c00180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cell-free protein synthesis-based biosensors have been developed as highly accurate, low-cost biosensors. However, since most biomarkers exist at low concentrations in various types of biopsies, the biosensor's dynamic range must be increased in the system to achieve low limits of detection necessary while deciphering from higher background signals. Many attempts to increase the dynamic range have relied on amplifying the input signal from the analyte, which can lead to complications of false positives. In this study, we aimed to increase the protein synthesis capability of the cell-free protein synthesis system and the output signal of the reporter protein to achieve a lower limit of detection. We utilized a new fluorescent protein, mNeonGreen, which produces a higher output than those commonly used in cell-free biosensors. Optimizations of DNA sequence and the subsequent cell-free protein synthesis reaction conditions allowed characterizing protein expression variability by given DNA template types, reaction environment, and storage additives that cause the greatest time constraint on designing the cell-free biosensor. Finally, we characterized the fluorescence kinetics of mNeonGreen compared to the commonly used reporter protein, superfolder green fluorescent protein. We expect that this finely tuned cell-free protein synthesis platform with the new reporter protein can be used with sophisticated synthetic gene circuitry networks to increase the dynamic range of a cell-free biosensor to reach lower detection limits and reduce the false-positive proportion.
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Affiliation(s)
- Caroline E Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Jeehye Kim
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Pearce L Copeland
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Chloe J Heitmeier
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Yong-Chan Kwon
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States.,Louisiana State University Agricultural Center, Baton Rouge, Louisiana 70803, United States
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8
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Tian X, Liu WQ, Xu H, Ji X, Liu Y, Li J. Cell-free expression of NO synthase and P450 enzyme for the biosynthesis of an unnatural amino acid L-4-nitrotryptophan. Synth Syst Biotechnol 2022; 7:775-783. [PMID: 35387232 PMCID: PMC8956912 DOI: 10.1016/j.synbio.2022.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/25/2022] [Accepted: 03/19/2022] [Indexed: 11/21/2022] Open
Abstract
Cell-free system has emerged as a powerful platform with a wide range of in vitro applications and recently has contributed to express metabolic pathways for biosynthesis. Here we report in vitro construction of a native biosynthetic pathway for L-4-nitrotryptophan (L-4-nitro-Trp) synthesis using an Escherichia coli-based cell-free protein synthesis (CFPS) system. Naturally, a nitric oxide (NO) synthase (TxtD) and a cytochrome P450 enzyme (TxtE) are responsible for synthesizing L-4-nitro-Trp, which serves as one substrate for the biosynthesis of a nonribosomal peptide herbicide thaxtomin A. Recombinant coexpression of TxtD and TxtE in a heterologous host like E. coli for L-4-nitro-Trp production has not been achieved so far due to the poor or insoluble expression of TxtD. Using CFPS, TxtD and TxtE were successfully expressed in vitro, enabling the formation of L-4-nitro-Trp. After optimization, the cell-free system was able to synthesize approximately 360 μM L-4-nitro-Trp within 16 h. Overall, this work expands the application scope of CFPS for study and synthesis of nitro-containing compounds, which are important building blocks widely used in pharmaceuticals, agrochemicals, and industrial chemicals.
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Ji X, Liu WQ, Li J. Recent advances in applying cell-free systems for high-value and complex natural product biosynthesis. Curr Opin Microbiol 2022; 67:102142. [DOI: 10.1016/j.mib.2022.102142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 11/03/2022]
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Chen S, Lin S, Han X, Han X. Handheld pH‐Meter‐Based Electrochemical Aptasensing of Carcinoembryonic Antigen on Multifuctional Magnetic Beads. ELECTROANAL 2022. [DOI: 10.1002/elan.202200050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shaobo Chen
- Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Basic Medical Sciences CHINA
| | | | | | - Xianlin Han
- Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Basic Medical Sciences CHINA
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11
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Li J, Kwon YC, Lu Y, Moore SJ. Editorial: Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2021; 9:799122. [PMID: 34912793 PMCID: PMC8666474 DOI: 10.3389/fbioe.2021.799122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/11/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yong-Chan Kwon
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, LA, United States
| | - Yuan Lu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Simon J Moore
- School of Biosciences, University of Kent, Canterbury, United Kingdom
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