1
|
Sato G, Kinoshita S, Yamada TG, Arai S, Kitaguchi T, Funahashi A, Doi N, Fujiwara K. Metabolic Tug-of-War between Glycolysis and Translation Revealed by Biochemical Reconstitution. ACS Synth Biol 2024; 13:1572-1581. [PMID: 38717981 DOI: 10.1021/acssynbio.4c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Inside cells, various biological systems work cooperatively for homeostasis and self-replication. These systems do not work independently as they compete for shared elements like ATP and NADH. However, it has been believed that such competition is not a problem in codependent biological systems such as the energy-supplying glycolysis and the energy-consuming translation system. In this study, we biochemically reconstituted the coupling system of glycolysis and translation using purified elements and found that the competition for ATP between glycolysis and protein synthesis interferes with their coupling. Both experiments and simulations revealed that this interference is derived from a metabolic tug-of-war between glycolysis and translation based on their reaction rates, which changes the threshold of the initial substrate concentration for the success coupling. By the metabolic tug-of-war, translation energized by strong glycolysis is facilitated by an exogenous ATPase, which normally inhibits translation. These findings provide chemical insights into the mechanism of competition among biological systems in living cells and provide a framework for the construction of synthetic metabolism in vitro.
Collapse
Affiliation(s)
- Gaku Sato
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Saki Kinoshita
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Takahiro G Yamada
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Department of Molecular Biology, University of California San Diego, La Jolla, California 92093, United States
| | - Satoshi Arai
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Tetsuya Kitaguchi
- Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Yokohama, Kanagawa 226-8503, Japan
| | - Akira Funahashi
- 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
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| |
Collapse
|
2
|
Nishikawa S, Sato G, Takada S, Kohyama S, Honda G, Yanagisawa M, Hori Y, Doi N, Yoshinaga N, Fujiwara K. Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308030. [PMID: 38054641 PMCID: PMC10853730 DOI: 10.1002/advs.202308030] [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: 10/24/2023] [Revised: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.
Collapse
Affiliation(s)
- Saki Nishikawa
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Gaku Sato
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Sakura Takada
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Shunshi Kohyama
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
- Present address:
Department for Cellular and Molecular BiophysicsMax Planck Institute for BiochemistryAm Klopferspitz 18D‐82152MartinsriedGermany
| | - Gen Honda
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Miho Yanagisawa
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
- Graduate School of ScienceThe University of TokyoHongo 7‐3‐1BunkyoTokyo113‐0033Japan
- Center for Complex Systems BiologyUniversal Biology InstituteThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Yutaka Hori
- Department of Applied Physics and Physico‐informaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Nobuhide Doi
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Natsuhiko Yoshinaga
- WPI Advanced Institute for Materials Research (WPI‐AIMR)Tohoku UniversityKatahira 2‐1‐1, Aoba‐KuSendai980‐8577Japan
- MathAM‐OILAISTSendai980‐8577Japan
| | - Kei Fujiwara
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| |
Collapse
|
3
|
Nobeyama T, Yoshida T, Shiraki K. Interfacial and intrinsic molecular effects on the phase separation/transition of heteroprotein condensates. Int J Biol Macromol 2024; 254:128095. [PMID: 37972831 DOI: 10.1016/j.ijbiomac.2023.128095] [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: 09/14/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Liquid-liquid phase separation (LLPS) and droplet formation by LLPS are key concepts used to explain compartmentalization in living cells. Protein contact to a membrane surface is considered an important process for protein organization in a liquid phase or during transition to a solid or liquid dispersion state. The direct experimental comprehensive investigation is; however, not performed on the surface-droplet interaction and phase transition. In the present study, we constructed simple and reproducible experiments to analyze the structural transition of aggregates and droplets in an ovalbumin (OVA) and lysozyme (LYZ) complex on glass slides with various coatings. The difference in droplet-surface interaction may only be important in the boundary region between aggregates and droplets of a protein mixture, as shown in the phase diagram. Co-aggregates of OVA-LYZ changed to droplet-like circular forms during incubation. In contrast, free l-lysine resulted in the uniform droplet-to-solid phase separation at lower concentrations and dissolved any structures at higher concentrations. These results represent the first phase-diagram-based analysis of the phase transition of droplets in a protein mixture and a comparison of surface-surface and small molecular-droplet structure interactions.
Collapse
Affiliation(s)
- Tomohiro Nobeyama
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan.
| | - Toya Yoshida
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kentaro Shiraki
- Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| |
Collapse
|
4
|
Gao R, Yu X, Kumar BVVSP, Tian L. Hierarchical Structuration in Protocellular System. SMALL METHODS 2023; 7:e2300422. [PMID: 37438327 DOI: 10.1002/smtd.202300422] [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: 03/31/2023] [Revised: 06/12/2023] [Indexed: 07/14/2023]
Abstract
Spatial control is one of the ubiquitous features in biological systems and the key to the functional complexity of living cells. The strategies to achieve such precise spatial control in protocellular systems are crucial to constructing complex artificial living systems with functional collective behavior. Herein, the authors review recent advances in the spatial control within a single protocell or between different protocells and discuss how such hierarchical structured protocellular system can be used to understand complex living systems or to advance the development of functional microreactors with the programmable release of various biomacromolecular payloads, or smart protocell-biological cell hybrid system.
Collapse
Affiliation(s)
- Rui Gao
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xinran Yu
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | | | - Liangfei Tian
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Department of Ultrasound, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310027, China
- Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
| |
Collapse
|
5
|
Stano P, Gentili PL, Damiano L, Magarini M. A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things? Molecules 2023; 28:5564. [PMID: 37513436 PMCID: PMC10385758 DOI: 10.3390/molecules28145564] [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: 05/14/2023] [Revised: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT.
Collapse
Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
| | - Pier Luigi Gentili
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Luisa Damiano
- Department of Communication, Arts and Media, IULM University, 20143 Milan, Italy
| | - Maurizio Magarini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| |
Collapse
|