1
|
Sánchez-Costa M, Urigoitia A, Comino N, Arnaiz B, Khatami N, Ruiz-Hernandez R, Diamanti E, Abarrategi A, López-Gallego F. In-Hydrogel Cell-Free Protein Expression System as Biocompatible and Implantable Biomaterial. ACS APPLIED MATERIALS & INTERFACES 2024; 16:15993-16002. [PMID: 38509001 DOI: 10.1021/acsami.4c01388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Biomaterials capable of delivering therapeutic proteins are relevant in biomedicine, yet their manufacturing relies on centralized manufacturing chains that pose challenges to their remote implementation at the point of care. This study explores the viability of confined cell-free protein synthesis within porous hydrogels as biomaterials that dynamically produce and deliver proteins to in vitro and in vivo biological microenvironments. These functional biomaterials have the potential to be assembled as implants at the point of care. To this aim, we first entrap cell-free extracts (CFEs) from Escherichia coli containing the transcription-translation machinery, together with plasmid DNA encoding the super folded green fluorescence protein (sGFP) as a model protein, into hydrogels using various preparation methods. Agarose hydrogels result in the most suitable biomaterials to confine the protein synthesis system, demonstrating efficient sGFP production and diffusion from the core to the surface of the hydrogel. Freeze-drying (FD) of agarose hydrogels still allows for the synthesis and diffusion of sGFP, yielding a more attractive biomaterial for its reconstitution and implementation at the point of care. FD-agarose hydrogels are biocompatible in vitro, allowing for the colonization of cell microenvironments along with cell proliferation. Implantation assays of this biomaterial in a preclinical mouse model proved the feasibility of this protein synthesis approach in an in vivo context and indicated that the physical properties of the biomaterials influence their immune responses. This work introduces a promising avenue for biomaterial fabrication, enabling the in vivo synthesis and targeted delivery of proteins and opening new paths for advanced protein therapeutic approaches based on biocompatible biomaterials.
Collapse
Affiliation(s)
| | - Ane Urigoitia
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
| | - Natalia Comino
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
| | - Blanca Arnaiz
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
| | - Neda Khatami
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
- Polymat, University of Basque Country UPV/EHU, Donostia/San Sebastián 20018, Gipuzkoa, Spain
| | | | - Eleftheria Diamanti
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
| | - Ander Abarrategi
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, 48013Bilbao, Spain
| | - Fernando López-Gallego
- CIC biomaGUNE, Edificio Empresarial "C", Paseo de Miramón 182, 20009Donostia, Spain
- IKERBASQUE, Basque Foundation for Science, 48013Bilbao, Spain
| |
Collapse
|
2
|
Yanagisawa M. Cell-size space effects on phase separation of binary polymer blends. Biophys Rev 2022; 14:1093-1103. [PMID: 36345284 PMCID: PMC9636348 DOI: 10.1007/s12551-022-01001-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2022] [Indexed: 12/22/2022] Open
Abstract
Within living cells, a diverse array of biomolecules is present at high concentrations. To better understand how molecular behavior differs under such conditions (collectively described as macromolecular crowding), the crowding environment has been reproduced inside artificial cells. We have previously shown that the combination of macromolecular crowding and microscale geometries imposed by the artificial cells can alter the molecular behaviors induced by macromolecular crowding in bulk solutions. We have named the effect that makes such a difference the cell-size space effect (CSE). Here, we review the underlying biophysics of CSE for phase separation of binary polymer blends. We discuss how the cell-size space can initiate phase separation, unlike nano-sized spaces, which are known to hinder nucleation and phase separation. Additionally, we discuss how the dimensions of the artificial cell and its membrane characteristics can significantly impact phase separation dynamics and equilibrium composition. Although these findings are, of themselves, very interesting, their real significance may lie in helping to clarify the functions of the cell membrane and space size in the regulation of intracellular phase separation.
Collapse
Affiliation(s)
- Miho Yanagisawa
- Graduate School of Arts and Sciences, Komaba Institute for Science, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo, 153-8902 Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo, 113-0033 Japan
- Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo, 153-8902 Japan
| |
Collapse
|
3
|
Natsume Y. Thermo-Statistical Effects of Inclusions on Vesicles: Division into Multispheres and Polyhedral Deformation. MEMBRANES 2022; 12:membranes12060608. [PMID: 35736315 PMCID: PMC9229943 DOI: 10.3390/membranes12060608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022]
Abstract
The construction of simple cellular models has attracted much attention as a way to explore the origin of life or elucidate the mechanisms of cell division. In the absence of complex regulatory systems, some bacteria spontaneously divide through thermostatistically elucidated mechanisms, and incorporating these simple physical principles could help to construct primitive or artificial cells. Because thermodynamic interactions play an essential role in such mechanisms, this review discusses the thermodynamic aspects of spontaneous division models of vesicles that contain a high density of inclusions, with their membrane serving as a boundary. Vesicles with highly dense inclusions are deformed according to the volume-to-area ratio. The phase separation of beads at specific intermediate volume fractions and the associated polyhedral deformation of the membrane are considered in relation to the Alder transition. Current advances in the development of a membrane-growth vesicular model are summarized. The thermostatistical understanding of these mechanisms could become a cornerstone for the construction of vesicular models that display spontaneous cell division.
Collapse
Affiliation(s)
- Yuno Natsume
- Schoolteacher Training Course/Natural Sciences, Cooperative Faculty of Education, Utsunomiya University, Mine-machi 350, Utsunomiya 321-8505, Japan;
- Institute for Promotion of Research Center for Bioscience Research and Education, Utsunomiya University, Mine-machi 350, Utsunomiya 321-8505, Japan
| |
Collapse
|
4
|
Deyama T, Matsui Y, Chadani Y, Sekine Y, Doi N, Fujiwara K. Transcription-translation of the Escherichia coli genome within artificial cells. Chem Commun (Camb) 2021; 57:10367-10370. [PMID: 34541593 DOI: 10.1039/d1cc04401j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we created artificial cells in which information of the genome of living cells is expressed by the elements encoded in the genome. We confirmed that the system works normally within artificial cells, which paves the way for reconstructing living cells from biomolecules.
Collapse
Affiliation(s)
- Tatsuki Deyama
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Yukino Matsui
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Yuhei Chadani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| |
Collapse
|
5
|
System concentration shift as a regulator of transcription-translation system within liposomes. iScience 2021; 24:102859. [PMID: 34386726 PMCID: PMC8346668 DOI: 10.1016/j.isci.2021.102859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
Biochemical systems in living cells have their optimum concentration ratio among each constituent element to maintain their functionality. However, in the case of the biochemical system with complex interactions and feedbacks among elements, their activity as a system greatly changes by the concentration shift of the entire system irrespective of the concentration ratio among elements. In this study, by using a transcription-translation (TX-TL) system as the subject, we illustrate the principle of the nonlinear relationship between the system concentration and the activity of the system. Our experiment and simulation showed that shifts of the system concentration of TX-TL by dilution and concentration works as a switch of activity and demonstrated its ability to induce a biochemical system to confer the permeability of small molecules to liposomes. These results contribute to the creation of artificial cells with the switch and provide an insight into the emergence of protocells.
Collapse
|
6
|
Uwaguchi Y, Fujiwara K, Doi N. Switching ON of Transcription-Translation System Using GUV Fusion by Co-supplementation of Calcium with Long-Chain Polyethylene Glycol. Chembiochem 2021; 22:2319-2324. [PMID: 33971077 DOI: 10.1002/cbic.202100100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/28/2021] [Indexed: 11/09/2022]
Abstract
Giant unilamellar vesicles (GUVs) have been used as a material for bottom-up synthetic biology. However, due to the semi-permeability of the membrane, the need for methods to fuse GUVs has increased. To this aim, methods that are simple and show low leakage during fusion are important. In this study, we report a method of GUV fusion by a divalent cation (Ca2+ ) enhanced with a long chain polyethylene glycol (PEG20k). The methods showed significant GUV fusion without leakage of internal components of GUVs and maintained cell-free transcription-translation ability inside the GUVs without external supplementation of macromolecules. We demonstrate that the Ca-PEG method can be applied for switching ON of transcription-translation in GUVs in a fusion-dependent manner. The method developed here can be applied to extend bottom-up synthetic biology and molecular robotics that use GUVs as a chassis.
Collapse
Affiliation(s)
- Yusuke Uwaguchi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| |
Collapse
|
7
|
A Relationship between NTP and Cell Extract Concentration for Cell-Free Protein Expression. Life (Basel) 2021; 11:life11030237. [PMID: 33805612 PMCID: PMC7999496 DOI: 10.3390/life11030237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/29/2023] Open
Abstract
The cell-free protein synthesis (CFPS) that synthesizes mRNA and protein from a template DNA has been featured as an important tool to emulate living systems in vitro. However, an obstacle to emulate living cells by CFPS is the loss of activity in the case of usage of high concentration cell extracts. In this study, we found that a high concentration of NTP which inhibits in the case of lower concentration cell extract restored the loss of CFPS activity using high concentration cell extracts. The NTP restoration was independent of the energy regeneration system used, and NTP derivatives also restored the levels of CFPS using a high concentration cell extract. Experiments using dialysis mode of CFPS showed that continuous exchange of small molecule reduced levels of NTP requirement and improved reaction speed of CFPS using the high concentration of cell extract. These findings contribute to the development of a method to understand the condition of living cells by in vitro emulation, and are expected to lead to the achievement of the reconstitution of living cells from biomolecule mixtures.
Collapse
|
8
|
Li A, Pazzi J, Xu M, Subramaniam AB. Cellulose Abetted Assembly and Temporally Decoupled Loading of Cargo into Vesicles Synthesized from Functionally Diverse Lamellar Phase Forming Amphiphiles. Biomacromolecules 2018; 19:849-859. [DOI: 10.1021/acs.biomac.7b01645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Alexander Li
- Department of Bioengineering, University of California, Merced, Merced, California 95343, United States
| | - Joseph Pazzi
- Department of Bioengineering, University of California, Merced, Merced, California 95343, United States
| | - Melissa Xu
- Department of Bioengineering, University of California, Merced, Merced, California 95343, United States
| | - Anand Bala Subramaniam
- Department of Bioengineering, University of California, Merced, Merced, California 95343, United States
| |
Collapse
|
9
|
Fujiwara K, Adachi T, Doi N. Artificial Cell Fermentation as a Platform for Highly Efficient Cascade Conversion. ACS Synth Biol 2018; 7:363-370. [PMID: 29258304 DOI: 10.1021/acssynbio.7b00365] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Because of its high specificity and stereoselectivity, cascade reactions using enzymes have been attracting attention as a platform for chemical synthesis. However, the sensitivity of enzymes outside their optimum conditions and their rapid decrease of activity upon dilution are drawbacks of the system. In this study, we developed a system for cascade enzymatic conversion in bacteria-shaped liposomes formed by hypertonic treatment, and demonstrated that the system can overcome the drawbacks of the enzymatic cascade reactions in bulk. This system produced final products at a level equivalent to the maximum concentration of the bulk system (0.10 M, e.g., 4.6 g/L), and worked even under conditions where enzymes normally lose their function. Under diluted conditions, the conversion rate of the artificial cell system was remarkably higher than that in the bulk system. Our results indicate that artificial cells can behave as a platform to perform fermentative production like microorganisms.
Collapse
Affiliation(s)
- Kei Fujiwara
- Department of Biosciences
and Informatics, Faculty of Science and Technology, Keio University, Yokohama 223−8522, Japan
| | - Takuma Adachi
- Department of Biosciences
and Informatics, Faculty of Science and Technology, Keio University, Yokohama 223−8522, Japan
| | - Nobuhide Doi
- Department of Biosciences
and Informatics, Faculty of Science and Technology, Keio University, Yokohama 223−8522, Japan
| |
Collapse
|
10
|
Fujiwara K, Yanagisawa M. Liposomal internal viscosity affects the fate of membrane deformation induced by hypertonic treatment. SOFT MATTER 2017; 13:9192-9198. [PMID: 29184957 DOI: 10.1039/c7sm01421j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Artificial lipid membranes have been utilized to understand the physical mechanisms of the deformation patterns of live cells. However, typical artificial membrane systems contain only dilute components compared to those in the cytoplasm of live cells. By using giant unilamellar liposomes containing dense protein solutions similar to those in live cells, we here reveal that viscosity derived from internal crowding affects the deformation patterns of lipid membranes. After hypertonic treatment, liposome deformation patterns transitioned from budding to tubing when the initial internal macromolecular concentrations were increased. Remarkably, instead of observing different transition concentrations between two species of macromolecules, the viscosity at the transition concentration was found to be similar. Further analyses clearly demonstrated that the internal viscosity affects the deformation patterns of lipid membranes induced by hypertonic treatment. These results indicate that the viscosity of the cytoplasm is a key factor in determining cell deformation, and suggest the association of a process involving dynamic instability, such as a viscous fingering phenomenon, during the determination of deformation patterns by hypertonic treatment.
Collapse
Affiliation(s)
- Kei Fujiwara
- Department of Biosciences and Informatics, Faculty of Science and Technology Keio University, Yokohama 223-8522, Japan.
| | | |
Collapse
|
11
|
Fujiwara K, Sawamura T, Niwa T, Deyama T, Nomura SIM, Taguchi H, Doi N. In vitro transcription-translation using bacterial genome as a template to reconstitute intracellular profile. Nucleic Acids Res 2017; 45:11449-11458. [PMID: 28977538 PMCID: PMC5737407 DOI: 10.1093/nar/gkx776] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
In vitro transcription–translation systems (TX–TL) can synthesize most of individual genes encoded in genomes by using strong promoters and translation initiation sequences. This fact raises a possibility that TX–TL using genome as a template can reconstitute the profile of RNA and proteins in living cells. By using cell extracts and genome prepared from different organisms, here we developed a system for in vitro genome transcription–translation (iGeTT) using bacterial genome and cell extracts, and surveyed de novo synthesis of RNA and proteins. Two-dimensional electrophoresis and nano LC–MS/MS showed that proteins were actually expressed by iGeTT. Quantitation of transcription levels of 50 genes for intracellular homeostasis revealed that the levels of RNA synthesis by iGeTT are highly correlated with those in growth phase cells. Furthermore, activity of iGeTT was influenced by transcription derived from genome structure and gene location in genome. These results suggest that intracellular profiles and characters of genome can be emulated by TX–TL using genome as a template.
Collapse
Affiliation(s)
- Kei Fujiwara
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama 223-8522, Japan
- To whom correspondence should be addressed. Tel: +81 45 566 1533;
| | - Tsunehito Sawamura
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama 223-8522, Japan
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Tatsuki Deyama
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama 223-8522, Japan
| | - Shin-ichiro M. Nomura
- Department of Robotics, School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama 223-8522, Japan
| |
Collapse
|
12
|
Fujiwara K, Doi N. Biochemical Preparation of Cell Extract for Cell-Free Protein Synthesis without Physical Disruption. PLoS One 2016; 11:e0154614. [PMID: 27128597 PMCID: PMC4851396 DOI: 10.1371/journal.pone.0154614] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/17/2016] [Indexed: 12/31/2022] Open
Abstract
Cell-free protein synthesis (CFPS) is a powerful tool for the preparation of toxic proteins, directed protein evolution, and bottom-up synthetic biology. The transcription-translation machinery for CFPS is provided by cell extracts, which usually contain 20–30 mg/mL of proteins. In general, these cell extracts are prepared by physical disruption; however, this requires technical experience and special machinery. Here, we report a method to prepare cell extracts for CFPS using a biochemical method, which disrupts cells through the combination of lysozyme treatment, osmotic shock, and freeze-thaw cycles. The resulting cell extracts showed similar features to those obtained by physical disruption, and was able to synthesize active green fluorescent proteins in the presence of appropriate chemicals to a concentration of 20 μM (0.5 mg/mL).
Collapse
Affiliation(s)
- Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223–8522, Japan
- * E-mail:
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223–8522, Japan
| |
Collapse
|