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Gao R, Wang W, Wang Z, Fan Y, Zhang L, Sun J, Hong M, Pan M, Wu J, Mei Q, Wang Y, Qiao L, Liu J, Tong F. Hibernating/Awakening Nanomotors Promote Highly Efficient Cryopreservation by Limiting Ice Crystals. Adv Healthc Mater 2024:e2401833. [PMID: 39101314 DOI: 10.1002/adhm.202401833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/20/2024] [Indexed: 08/06/2024]
Abstract
The disruptions caused by ice crystal formation during the cryopreservation of cells and tissues can cause cell and tissue damage. Thus, preventing such damage during cryopreservation is an important but challenging goal. Here, a hibernating/awakening nanomotor with magnesium/palladium covering one side of a silica platform (Mg@Pd@SiO2) is proposed. This nanomotor is used in the cultivation of live NCM460 cells to demonstrate a new method to actively limit ice crystal formation and enable highly efficient cryopreservation. Cooling Mg@Pd@SiO2 in solution releases Mg2+/H2 and promotes the adsorption of H2 at multiple Pd binding sites on the cell surface to inhibit ice crystal formation and cell/tissue damage; additionally, the Pd adsorbs and stores H2 to form a hibernating nanomotor. During laser-mediated heating, the hibernating nanomotor is activated (awakened) and releases H2, which further suppresses recrystallization and decreases cell/tissue damage. These hibernating/awakening nanomotors have great potential for promoting highly efficient cryopreservation by inhibiting ice crystal formation.
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Affiliation(s)
- Rui Gao
- Department of Pharmacology, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P. R. China
| | - Weixin Wang
- Department of Pharmacology, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P. R. China
| | - Zhongchao Wang
- Institute of Cardiovascular Disease, Shanxi Medical University, Taiyuan, 030001, P. R. China
| | - Yapeng Fan
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, P. R. China
| | - Lin Zhang
- Department of Pharmacology, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P. R. China
| | - Jiahui Sun
- Department of Pharmacology, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P. R. China
| | - Miaofang Hong
- Department of Pharmacology, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P. R. China
| | - Min Pan
- Department of Pharmacology, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P. R. China
| | - Jianming Wu
- Education Ministry Key Laboratory of Medical Electrophysiology, Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, School of Pharmacy, Southwest Medical University, Luzhou, 646000, P. R. China
| | - Qibing Mei
- Education Ministry Key Laboratory of Medical Electrophysiology, Sichuan Key Medical Laboratory of New Drug Discovery and Druggability Evaluation, Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, School of Pharmacy, Southwest Medical University, Luzhou, 646000, P. R. China
| | - Yini Wang
- Clinical Medical College, Binzhou Medical University, Yantai, 264003, P. R. China
| | - Lingyan Qiao
- Clinical Medical College, Binzhou Medical University, Yantai, 264003, P. R. China
| | - Jin Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, P. R. China
| | - Fei Tong
- Department of Pharmacology, School of Pharmacy, Binzhou Medical University, Yantai, 264003, P. R. China
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2
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Abdul Aziz SFN, Salleh AB, Normi YM, Mohammad Latif MA, Alang Ahmad SA. Bioinspired mp20 mimicking uricase in ZIF-8: Metal ion dependent for controllable activity. Enzyme Microb Technol 2024; 178:110439. [PMID: 38579423 DOI: 10.1016/j.enzmictec.2024.110439] [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: 02/01/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/07/2024]
Abstract
Mini protein mimicking uricase (mp20) has shown significant potential as a replacement for natural enzymes in the development of uric acid biosensors. However, the design of mp20 has resulted to an inactive form of peptide, causing of loss their catalytic activity. Herein, this paper delineates the impact of various metal cofactors on the catalytic activity of mp20. The metal ion-binding site prediction and docking (MIB) web server was employed to identify the metal ion binding sites and their affinities towards mp20 residues. Among the tested metal ions, Cu2+ displayed the highest docking score, indicating its preference for interaction with Thr16 and Asp17 residues of mp20. To assess the catalytic activity of mp20 in the presence of metal ions, uric acid assays was monitored using a colorimetric method. The presence of Cu2+ in the assays promotes the activation of mp20, resulting in a color change based on quinoid production. Furthermore, the encapsulation of the mp20 within zeolitic imidazolate framework-8 (ZIF-8) notably improved the stability of the biomolecule. In comparison to the naked mp20, the encapsulated ZIFs biocomposite (mp20@ZIF-8) demonstrates superior stability, selectivity and sensitivity. ZIF's porous shells provides excellent protection, broad detection (3-100 μM) with a low limit (4.4 μM), and optimal function across pH (3.4-11.4) and temperature (20-100°C) ranges. Cost-effective and stable mp20@ZIF-8 surpasses native uricase, marking a significant biosensor technology breakthrough. This integration of metal cofactor optimization and robust encapsulation sets new standards for biosensing applications.
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Affiliation(s)
- Siti Fatimah Nur Abdul Aziz
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; School of Chemical Sciences, Universiti Sains Malaysia (USM), Gelugor, Pulau Pinang 11800, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor 43400, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Technology Research Centre (EMTech), Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor 43400, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Institute of Nanoscience and Nanotechnology (ION2), Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Muhammad Alif Mohammad Latif
- Integrated Chemical BioPhysics Research, Faculty of Science, Universiti Putra Malaysia, UPM, Serdang, Selangor 43400, Malaysia; Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia
| | - Shahrul Ainliah Alang Ahmad
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; Institute of Nanoscience and Nanotechnology (ION2), Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia.
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3
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Morini L, Sakai A, Vibhute MA, Koch Z, Voss M, Schoenmakers LLJ, Huck WTS. Leveraging Active Learning to Establish Efficient In Vitro Transcription and Translation from Bacterial Chromosomal DNA. ACS OMEGA 2024; 9:19227-19235. [PMID: 38708277 PMCID: PMC11064174 DOI: 10.1021/acsomega.4c00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024]
Abstract
Gene expression is a fundamental aspect in the construction of a minimal synthetic cell, and the use of chromosomes will be crucial for the integration and regulation of complex modules. Expression from chromosomes in vitro transcription and translation (IVTT) systems presents limitations, as their large size and low concentration make them far less suitable for standard IVTT reactions. Here, we addressed these challenges by optimizing lysate-based IVTT systems at low template concentrations. We then applied an active learning tool to adapt IVTT to chromosomes as template DNA. Further insights into the dynamic data set led us to adjust the previous protocol for chromosome isolation and revealed unforeseen trends pointing at limiting transcription kinetics in our system. The resulting IVTT conditions allowed a high template DNA efficiency for the chromosomes. In conclusion, our system shows a protein-to-chromosome ratio that moves closer to in vivo biology and represents an advancement toward chromosome-based synthetic cells.
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Affiliation(s)
- Leonardo Morini
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Andrei Sakai
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Mahesh A. Vibhute
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Zef Koch
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 AJ, The Netherlands
- HAN
University of Applied Sciences, Nijmegen 6503GL, The Netherlands
| | - Margo Voss
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Ludo L. J. Schoenmakers
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Konrad
Lorenz Institute for Evolution and Cognition Research, Klosterneuburg 3400, Austria
| | - Wilhelm T. S. Huck
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525 AJ, The Netherlands
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4
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Dinglasan JLN, Sword TT, Barker JW, Doktycz MJ, Bailey CB. Investigating and Optimizing the Lysate-Based Expression of Nonribosomal Peptide Synthetases Using a Reporter System. ACS Synth Biol 2023; 12:1447-1460. [PMID: 37039644 PMCID: PMC11236431 DOI: 10.1021/acssynbio.2c00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Lysate-based cell-free expression (CFE) systems are accessible platforms for expressing proteins that are difficult to synthesize in vivo, such as nonribosomal peptide synthetases (NRPSs). NRPSs are large (>100 kDa), modular enzyme complexes that synthesize bioactive peptide natural products. This synthetic process is analogous to transcription/translation (TX/TL) in lysates, resulting in potential resource competition between NRPS expression and NRPS activity in cell-free environments. Moreover, CFE conditions depend on the size and structure of the protein. Here, a reporter system for rapidly investigating and optimizing reaction environments for NRPS CFE is described. This strategy is demonstrated in E. coli lysate reactions using blue pigment synthetase A (BpsA), a model NRPS, carrying a C-terminal tetracysteine (TC) tag which forms a fluorescent complex with the biarsenical dye, FlAsH. A colorimetric assay was adapted for lysate reactions to detect the blue pigment product, indigoidine, of cell-free expressed BpsA-TC, confirming that the tagged enzyme is catalytically active. An optimized protocol for end point TC/FlAsH complex measurements in reactions enables quick comparisons of full-length BpsA-TC expressed under different reaction conditions, defining unique requirements for NRPS expression that are related to the protein's catalytic activity and size. Importantly, these protein-dependent CFE conditions enable higher indigoidine titer and improve the expression of other monomodular NRPSs. Notably, these conditions differ from those used for the expression of superfolder GFP (sfGFP), a common reporter for optimizing lysate-based CFE systems, indicating the necessity for tailored reporters to optimize expression for specific enzyme classes. The reporter system is anticipated to advance lysate-based CFE systems for complex enzyme synthesis, enabling natural product discovery.
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Affiliation(s)
- Jaime Lorenzo N Dinglasan
- Graduate School of Genome Science & Technology, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Tien T Sword
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - J William Barker
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Constance B Bailey
- Department of Chemistry, University of Tennessee-Knoxville, Knoxville, Tennessee 37996, United States
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5
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De Capitani J, Mutschler H. The Long Road to a Synthetic Self-Replicating Central Dogma. Biochemistry 2023; 62:1221-1232. [PMID: 36944355 PMCID: PMC10077596 DOI: 10.1021/acs.biochem.3c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.
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Affiliation(s)
- Jacopo De Capitani
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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Ye Q, Lin X, Wang T, Cui Y, Jiang H, Lu Y. Programmable protein topology via
SpyCatcher‐SpyTag
chemistry in one‐pot cell‐free expression system. Protein Sci 2022; 31:e4335. [DOI: 10.1002/pro.4335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Qingning Ye
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
- College of New Energy and Materials China University of Petroleum Beijing China
| | - Xiaomei Lin
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
| | - Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
| | - Yuntao Cui
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
| | - Hao Jiang
- School of Materials Science and Engineering Beijing Institute of Technology Beijing China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering Tsinghua University Beijing China
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7
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Development of a robust Escherichia coli-based cell-free protein synthesis application platform. Biochem Eng J 2020; 165:107830. [PMID: 33100890 PMCID: PMC7568173 DOI: 10.1016/j.bej.2020.107830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/30/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
A robust cell-free protein synthesis platform has been developed. Engineering strategies were explored to improve the synthesis efficiency. The platform has been applied in prototyping, screening and on-demand synthesis.
Since the cell-free protein synthesis system is not limited by the cell growth, all the substrates are used to produce the protein of interest, and the reaction environment can be flexibly controlled. All the advantages allow it to synthesize toxic proteins, membrane proteins, and unnatural proteins that are difficult to make in vivo. However, one typical reason why the cell-free system has not been widely accepted as a practical alternative, is its expression efficiency problem. The Escherichia coli-based system was chosen in this study, and the model protein deGFP was expressed to explore a more efficient cell-free system. The results showed that Mg2+ with a concentration of 15 mM in the cell-free system with BL21 Star (DE3) as the extract could better synthesize protein. The smaller the vectors, the lighter the burden, the higher the protein synthesis. Simulating the crowding effect in the cell does not improve the protein expression efficiency of the optimized cell-free protein synthesis system. Based on the optimized system, the cell-free fundamental research platform, primary screening platform, and portable biomolecular synthesis platform were established. This study provides a robust cell-free protein synthesis toolbox with easy extract preparation and high protein yield. It also enables more researchers to reap the benefits from the cell-free biosynthesis platform.
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