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Zhu M, Li Z, Li J, Lin Y, Chen H, Qiao X, Wang X, Liu X, Huang X. Organelle-like structural evolution of coacervate droplets induced by photopolymerization. Nat Commun 2025; 16:1783. [PMID: 39971992 DOI: 10.1038/s41467-025-57069-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 02/11/2025] [Indexed: 02/21/2025] Open
Abstract
The dynamic study of coacervates in vitro contributes our understanding of phase separation mechanisms in cells due to complex intracellular physiology. However, current researches mainly involve the use of exogenous auxiliary agents to form multi-compartmental coacervates with short-term stability. Herein, we report the endogenous self-organizing of multi-component coacervates (HA/PDDA/BSA/DMAEMA) induced by a dynamic stimulation process of protein-mediated photopolymerization. As polymerization proceeds, the cycled structural evolution and maturation from coacervate droplets into multi-compartmental coacervates, coacervate vesicles and coacervate droplets are revealed, which are driven by electrostatic interaction and osmotic pressure difference supported by dynamic and thermodynamic control. Specially, by regulating the light stimulation time, a type of multi-compartmental coacervates can be widely obtained with high structural stability over 300 days. Being a promising artificial cell model, it shows the special characteristic of compartmentalized encapsulation of substrates, efficiently improving enzymatic interfacial catalytic efficiency of organelle-like communication. Our study holds great potential for advancing the understanding of the structural evolution mechanism of membraneless organelles and provides an instructive technique for constructing multi-compartmental coacervates with long-term stability.
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Affiliation(s)
- Mei Zhu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Zhenhui Li
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Junbo Li
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Youping Lin
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Haixu Chen
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Xin Qiao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Xiaoliang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Xiaoman Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China.
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China.
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2
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Song S, Ivanov T, Doan-Nguyen TP, da Silva LC, Xie J, Landfester K, Cao S. Synthetic Biomolecular Condensates: Phase-Separation Control, Cytomimetic Modelling and Emerging Biomedical Potential. Angew Chem Int Ed Engl 2025; 64:e202418431. [PMID: 39575859 DOI: 10.1002/anie.202418431] [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: 09/24/2024] [Indexed: 01/24/2025]
Abstract
Liquid-liquid phase separation towards the formation of synthetic coacervate droplets represents a rapidly advancing frontier in the fields of synthetic biology, material science, and biomedicine. These artificial constructures mimic the biophysical principles and dynamic features of natural biomolecular condensates that are pivotal for cellular regulation and organization. Via adapting biological concepts, synthetic condensates with dynamic phase-separation control provide crucial insights into the fundamental cell processes and regulation of complex biological pathways. They are increasingly designed with the ability to display more complex and ambitious cell-like features and behaviors, which offer innovative solutions for cytomimetic modeling and engineering active materials with sophisticated functions. In this minireview, we highlight recent advancements in the design and construction of synthetic coacervate droplets; including their biomimicry structure and organization to replicate life-like properties and behaviors, and the dynamic control towards engineering active coacervates. Moreover, we highlight the unique applications of synthetic coacervates as catalytic centers and promising delivery vehicles, so that these biomimicry assemblies can be translated into practical applications.
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Affiliation(s)
- Siyu Song
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, 55128, Mainz, Germany
| | - Tsvetomir Ivanov
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Thao P Doan-Nguyen
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- International Center for Young Scientists, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, Ibaraki, 305-0047, Japan
| | - Lucas Caire da Silva
- Max Planck Institute for Polymer Research, 55128, Mainz, Germany
- Department of Chemistry, McGill University, Montreal, H3A 0B8, Canada
| | - Jing Xie
- Institute of Biomedical Engineering, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, PR China
| | | | - Shoupeng Cao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, PR China
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3
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Apuzzo E, Cathcarth M, Picco AS, von Bilderling C, Azzaroni O, Agazzi ML, Herrera SE. Insights into the Mechanism of Protein Loading by Chain-Length Asymmetric Complex Coacervates. Biomacromolecules 2025; 26:1171-1183. [PMID: 39807630 DOI: 10.1021/acs.biomac.4c01516] [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: 01/16/2025]
Abstract
The study of the phase behavior of polyelectrolyte complex coacervates has attracted significant attention in recent years due to their potential use as membrane-less organelles, microreactors, and drug delivery platforms. In this work, we investigate the mechanism of protein loading in chain-length asymmetric complex coacervates composed of a polyelectrolyte and an oppositely charged multivalent ion. Unlike the symmetric case (polycation + polyanion), we show that protein loading is highly selective based on the protein's net charge: only proteins with charges opposite to the polyelectrolyte can be loaded. Through a series of systematic experiments, we identified that the protein loading process relies on the formation of a neutral three-component coacervate in which both the protein and the multivalent ion serve as complexing agents for the polyelectrolyte. Lastly, we demonstrated that this mechanism extends to the sequestration of other charged small molecules, offering valuable insights into designing functional multicomponent coacervates.
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Affiliation(s)
- Eugenia Apuzzo
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, CONICET, Universidad Nacional de La Plata, Diagonal 113 y 64, La Plata (Buenos Aires) 1900, Argentina
| | - Marilina Cathcarth
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, CONICET, Universidad Nacional de La Plata, Diagonal 113 y 64, La Plata (Buenos Aires) 1900, Argentina
| | - Agustín S Picco
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, CONICET, Universidad Nacional de La Plata, Diagonal 113 y 64, La Plata (Buenos Aires) 1900, Argentina
| | - Catalina von Bilderling
- Departamento de Tecnología y Administración, CONICET, Universidad Nacional de Avellaneda, Avellaneda, Mario Bravo 1460, Avellaneda (Buenos Aires) B1868, Argentina
| | - Omar Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, CONICET, Universidad Nacional de La Plata, Diagonal 113 y 64, La Plata (Buenos Aires) 1900, Argentina
| | - Maximiliano L Agazzi
- Instituto para el Desarrollo Agroindustrial y de la Salud, CONICET, Universidad Nacional de Río Cuarto, Ruta Nacional 36 KM 601, Río Cuarto (Córdoba) 5800, Argentina
| | - Santiago E Herrera
- Instituto de Química de los Materiales, Ambiente y Energía, CONICET, Universidad de Buenos Aires, Intendente Güiraldes 2160, CABA (Buenos Aires) 1428, Argentina
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4
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Ren T, Liang D. Biphasic Coacervation Controlled by Kinetics as Studied by De Novo-Designed Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2025; 41:1756-1764. [PMID: 39811981 DOI: 10.1021/acs.langmuir.4c04114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
Abstract
Coacervation is generally treated as a liquid-liquid phase separation process and is controlled mainly by thermodynamics. However, kinetics could make a dominant contribution, especially in systems containing multiple interactions. In this work, using peptides of (XXLY)6SSSGSS to tune the charge density and the degree of hydrophobicity, as well as to introduce secondary structures, we evaluated the effect of kinetics on biphasic coacervates formed by peptides with single-stranded oligonucleotides and quaternized dextran at varying pH values. Only in the case where the charge density is constant and the electrostatic interaction is the major driving force for Coacervation is the effect of kinetics negligible. When pH-dependent electrostatic interaction and hydrophobic interaction are involved or the peptides form secondary structures, the Coacervation process is then path-dependent, indicating that the kinetics controls the phase separation process. The Coacervation by combining two different peptides suggests that the peptide with a higher charge density plays a leading role in the early stage, while the cooperation of both peptides takes over afterward. Our work demonstrates that it is normal to observe coacervates with different morphologies and functions due to kinetic control, especially in living cells. Peptides with minimized sequences are a practical approach to reveal the mechanism of Coacervation processes controlled by kinetics.
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Affiliation(s)
- Tianhao Ren
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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5
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Lambert GS, Maldonado RJK, Parent LJ. Role of the Psi Packaging Signal and Dimerization Initiation Sequence in the Organization of Rous Sarcoma Virus Gag-gRNA Co-Condensates. Viruses 2025; 17:97. [PMID: 39861886 PMCID: PMC11769450 DOI: 10.3390/v17010097] [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: 12/04/2024] [Revised: 12/31/2024] [Accepted: 01/08/2025] [Indexed: 01/27/2025] Open
Abstract
Retroviral genome selection and virion assembly remain promising targets for novel therapeutic intervention. Recent studies have demonstrated that the Gag proteins of Rous sarcoma virus (RSV) and human immunodeficiency virus type-1 (HIV-1) undergo nuclear trafficking, colocalize with nascent genomic viral RNA (gRNA) at transcription sites, may interact with host transcription factors, and display biophysical properties characteristic of biomolecular condensates. In the present work, we utilized a controlled in vitro condensate assay and advanced imaging approaches to investigate the effects of interactions between RSV Gag condensates and viral and nonviral RNAs on condensate abundance and organization. We observed that the psi (Ψ) packaging signal and the dimerization initiation sequence (DIS) had stabilizing effects on RSV Gag condensates, while RNAs lacking these features promoted or antagonized condensation, depending on local protein concentration and condensate architecture. An RNA containing Ψ, DIS, and the dimerization linkage structure (DLS) that is capable of stable dimer formation was observed to act as a bridge between RSV Gag condensates. These observations suggest additional, condensate-related roles for Gag-Ψ binding, gRNA dimerization, and Gag dimerization/multimerization in gRNA selection and packaging, representing a significant step forward in our understanding of how these interactions collectively facilitate efficient genome packaging.
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Affiliation(s)
- Gregory S. Lambert
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; (G.S.L.); (R.J.K.M.)
| | - Rebecca J. Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; (G.S.L.); (R.J.K.M.)
- Department of Microbiology and Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Leslie J. Parent
- Department of Medicine, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA; (G.S.L.); (R.J.K.M.)
- Department of Microbiology and Immunology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA
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6
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Sekar N, Sahu P, Sudhakar S, Kotamarthi HC. Electrostatic interactions drive phase separation in Pup protein. Chem Commun (Camb) 2024; 60:14980-14983. [PMID: 39588871 DOI: 10.1039/d4cc04264f] [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: 11/27/2024]
Abstract
The similarities in the liquid-liquid phase separation (LLPS) phenomenon between membrane-less organelles (MLOs) and coacervates make them an ideal platform for studying the nature of life. Herein, we have developed a peptide-protein coacervative system between the positively charged poly-L-lysine peptide and negatively charged intrinsically disordered Pup protein to model the electrostatic nature of MLOs, providing insights into their in vivo mechanisms and potential therapeutic targets. We have constructed a phase diagram for coacervate formation at different concentrations of the Pup-PLL system, determined by turbidity measurements and optical microscopy. Fluorescence microscopy confirms the presence of both the polymers in the coacervates and the pH dependent studies confirm the role of electrostatics and emphasize the significance of charge density during coacervation.
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Affiliation(s)
- Narendran Sekar
- Department of Applied Mechanics and Biomedical Engineering, IIT Madras, India.
| | | | - Swathi Sudhakar
- Department of Applied Mechanics and Biomedical Engineering, IIT Madras, India.
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7
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Wang H, Zhuang H, Tang W, Zhu J, Zhu W, Jiang L. Coacervate-pore complexes for selective molecular transport and dynamic reconfiguration. Nat Commun 2024; 15:10069. [PMID: 39567561 PMCID: PMC11579452 DOI: 10.1038/s41467-024-54510-9] [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: 04/10/2024] [Accepted: 11/13/2024] [Indexed: 11/22/2024] Open
Abstract
Despite surging interests on liquid-state coacervates and condensates, confinement within solid-state pores for selective permeation remains an unexplored area. Drawing inspiration from nuclear pore complexes (NPCs), we design and construct coacervate-pore complexes (CPCs) with regulatable permeability. We demonstrate universal CPC formation across 19 coacervate systems and 5 pore types, where capillarity drives the spontaneous imbibition of coacervate droplets into dispersed or interconnected pores. CPCs regulate through-pore transport by forming a fluidic network that modulates guest molecule permeability based on guest-coacervate affinity, mimicking NPC selectivity. While solid constructs of NPC mimicries are limited by spatial fixation of polymer chains, CPCs of a liquid nature feature dynamic healing and rapid phase transitioning for permeability recovery and regulation, respectively. Looking forward, we expect the current work to establish a basis for developing liquid-based NPC analogs using a large pool of synthetic coacervates and biomolecular condensates.
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Affiliation(s)
- Hao Wang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, Guangdong Basic Research Center of Excellence for Energy & Information Polymer Materials, South China University of Technology, Guangzhou, 510640, China
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Hui Zhuang
- Experimental Basis and Practical Training Center, South China Agricultural University, Guangzhou, 510642, China
| | - Wenjing Tang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jun Zhu
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, Guangdong Basic Research Center of Excellence for Energy & Information Polymer Materials, South China University of Technology, Guangzhou, 510640, China
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
| | - Lingxiang Jiang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China.
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, Guangdong Basic Research Center of Excellence for Energy & Information Polymer Materials, South China University of Technology, Guangzhou, 510640, China.
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640, China.
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8
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Wei M, Wang X, Qiao Y. Multiphase coacervates: mimicking complex cellular structures through liquid-liquid phase separation. Chem Commun (Camb) 2024; 60:13169-13178. [PMID: 39439431 DOI: 10.1039/d4cc04533e] [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: 10/25/2024]
Abstract
Coacervate microdroplets, arising from liquid-liquid phase separation, have emerged as promising models for primary cells, demonstrating the ability to regulate biomolecular enrichment, create chemical gradients, accelerate confined reactions, and even express proteins. Notably, multiphase coacervation provides a robust framework to replicate hierarchically complex cellular structures, offering valuable insights into cellular organization and function. In this review, we explore the recent advancements in the study of multiphase coacervates, focusing on design strategies, underlying mechanisms, structural control, and their applications in biomimetics. These developments highlight the potential of multiphase coacervates as powerful tools in the field of synthetic biology and material science.
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Affiliation(s)
- Minghao Wei
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaokang Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Chawla R, Tom JKA, Boyd T, Tu NH, Bai T, Grotjahn DA, Park D, Deniz AA, Racki LR. Reentrant DNA shells tune polyphosphate condensate size. Nat Commun 2024; 15:9258. [PMID: 39462120 PMCID: PMC11513989 DOI: 10.1038/s41467-024-53469-x] [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: 11/15/2023] [Accepted: 10/11/2024] [Indexed: 10/28/2024] Open
Abstract
The inorganic biopolymer polyphosphate (polyP) occurs in all domains of life and affects myriad cellular processes. A longstanding observation is polyP's frequent proximity to chromatin, and, in many bacteria, its occurrence as magnesium (Mg2+)-enriched condensates embedded in the nucleoid region, particularly in response to stress. The physical basis of the interaction between polyP, DNA and Mg2+, and the resulting effects on the organization of the nucleoid and polyP condensates, remain poorly understood. Here, using a minimal system of polyP, Mg2+, and DNA, we find that DNA can form shells around polyP-Mg2+ condensates. These shells show reentrant behavior, that is, they form within a window of Mg2+ concentrations, representing a tunable architecture with potential relevance in other multicomponent condensates. This surface association tunes condensate size and DNA morphology in a manner dependent on DNA length and concentration, even at DNA concentrations orders of magnitude lower than found in the cell. Our work also highlights the remarkable capacity of two primordial inorganic species to organize DNA.
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Affiliation(s)
- Ravi Chawla
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Chakra Techworks Inc., San Diego, CA, USA
| | - Jenna K A Tom
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tumara Boyd
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nicholas H Tu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tanxi Bai
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Donghyun Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashok A Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Lisa R Racki
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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10
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Song S, Ivanov T, Yuan D, Wang J, da Silva LC, Xie J, Cao S. Peptide-Based Biomimetic Condensates via Liquid-Liquid Phase Separation as Biomedical Delivery Vehicles. Biomacromolecules 2024; 25:5468-5488. [PMID: 39178343 DOI: 10.1021/acs.biomac.4c00814] [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: 08/25/2024]
Abstract
Biomolecular condensates are dynamic liquid droplets through intracellular liquid-liquid phase separation that function as membraneless organelles, which are highly involved in various complex cellular processes and functions. Artificial analogs formed via similar pathways that can be integrated with biological complexity and advanced functions have received tremendous research interest in the field of synthetic biology. The coacervate droplet-based compartments can partition and concentrate a wide range of solutes, which are regarded as attractive candidates for mimicking phase-separation behaviors and biophysical features of biomolecular condensates. The use of peptide-based materials as phase-separating components has advantages such as the diversity of amino acid residues and customized sequence design, which allows for programming their phase-separation behaviors and the physicochemical properties of the resulting compartments. In this Perspective, we highlight the recent advancements in the design and construction of biomimicry condensates from synthetic peptides relevant to intracellular phase-separating protein, with specific reference to their molecular design, self-assembly via phase separation, and biorelated applications, to envisage the use of peptide-based droplets as emerging biomedical delivery vehicles.
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Affiliation(s)
- Siyu Song
- Life-Like Materials and Systems, Department of Chemistry, University of Mainz, Mainz 55128, Germany
| | | | - Dandan Yuan
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | - Jianqiang Wang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
| | | | - Jing Xie
- Institute of Biomedical Engineering, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shoupeng Cao
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu 610065, China
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11
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Agrawal A, Radakovic A, Vonteddu A, Rizvi S, Huynh VN, Douglas JF, Tirrell MV, Karim A, Szostak JW. Did the exposure of coacervate droplets to rain make them the first stable protocells? SCIENCE ADVANCES 2024; 10:eadn9657. [PMID: 39167649 PMCID: PMC11338219 DOI: 10.1126/sciadv.adn9657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/17/2024] [Indexed: 08/23/2024]
Abstract
Membraneless coacervate microdroplets have long been proposed as model protocells as they can grow, divide, and concentrate RNA by natural partitioning. However, the rapid exchange of RNA between these compartments, along with their rapid fusion, both within minutes, means that individual droplets would be unable to maintain their separate genetic identities. Hence, Darwinian evolution would not be possible, and the population would be vulnerable to collapse due to the rapid spread of parasitic RNAs. In this study, we show that distilled water, mimicking rain/freshwater, leads to the formation of electrostatic crosslinks on the interface of coacervate droplets that not only suppress droplet fusion indefinitely but also allow the spatiotemporal compartmentalization of RNA on a timescale of days depending on the length and structure of RNA. We suggest that these nonfusing membraneless droplets could potentially act as protocells with the capacity to evolve compartmentalized ribozymes in prebiotic environments.
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Affiliation(s)
- Aman Agrawal
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Aleksandar Radakovic
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Anusha Vonteddu
- Materials Science and Engineering Program, University of Houston, Houston, TX 77204, USA
| | - Syed Rizvi
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Vivian N. Huynh
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Jack F. Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Matthew V. Tirrell
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
- Argonne National Laboratory, Lemont, IL, 60439 USA
| | - Alamgir Karim
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
- Materials Science and Engineering Program, University of Houston, Houston, TX 77204, USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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12
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Zhou Y, Zhang K, Moreno S, Temme A, Voit B, Appelhans D. Continuous Transformation from Membrane-Less Coacervates to Membranized Coacervates and Giant Vesicles: Toward Multicompartmental Protocells with Complex (Membrane) Architectures. Angew Chem Int Ed Engl 2024; 63:e202407472. [PMID: 38847278 DOI: 10.1002/anie.202407472] [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: 04/19/2024] [Indexed: 07/25/2024]
Abstract
The membranization of membrane-less coacervates paves the way for the exploitation of complex protocells with regard to structural and cell-like functional behaviors. However, the controlled transformation from membranized coacervates to vesicles remains a challenge. This can provide stable (multi)phase and (multi)compartmental architectures through the reconfiguration of coacervate droplets in the presence of (bioactive) polymers, bio(macro)molecules and/or nanoobjects. Herein, we present a continuous protocell transformation from membrane-less coacervates to membranized coacervates and, ultimately, to giant hybrid vesicles. This transformation process is orchestrated by altering the balance of non-covalent interactions through varying concentrations of an anionic terpolymer, leading to dynamic processes such as spontaneous membranization of terpolymer nanoparticles at the coacervate surface, disassembly of the coacervate phase mediated by the excess anionic charge, and the redistribution of coacervate components in membrane. The diverse protocells during the transformation course provide distinct structural features and molecular permeability. Notably, the introduction of multiphase coacervates in this continuous transformation process signifies advancements toward the creation of synthetic cells with different diffusible compartments. Our findings emphasize the highly controlled continuous structural reorganization of coacervate protocells and represents a novel step toward the development of advanced and sophisticated synthetic protocells with more precise compositions and complex (membrane) structures.
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Affiliation(s)
- Yang Zhou
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Organic Chemistry of Polymers, TUD Dresden University of Technology, Dresden, 01062, Germany
| | - Kehu Zhang
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Organic Chemistry of Polymers, TUD Dresden University of Technology, Dresden, 01062, Germany
| | - Silvia Moreno
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
| | - Achim Temme
- Department of Neurosurgery, Section Experimental Neurosurgery/Tumor Immunology, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, 01307, Germany
- German Cancer Consortium (DKTK), partner site Dresden, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany, National Center for Tumor Diseases (NCT), Fetscherstraße 74, Dresden, 01307, Germany
| | - Brigitte Voit
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Organic Chemistry of Polymers, TUD Dresden University of Technology, Dresden, 01062, Germany
| | - Dietmar Appelhans
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
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13
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Chew PY, Joseph JA, Collepardo-Guevara R, Reinhardt A. Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures. Biophys J 2024; 123:1342-1355. [PMID: 37408305 PMCID: PMC11163273 DOI: 10.1016/j.bpj.2023.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023] Open
Abstract
Multiphasic architectures are found ubiquitously in biomolecular condensates and are thought to have important implications for the organization of multiple chemical reactions within the same compartment. Many of these multiphasic condensates contain RNA in addition to proteins. Here, we investigate the importance of different interactions in multiphasic condensates comprising two different proteins and RNA using computer simulations with a residue-resolution coarse-grained model of proteins and RNA. We find that in multilayered condensates containing RNA in both phases, protein-RNA interactions dominate, with aromatic residues and arginine forming the key stabilizing interactions. The total aromatic and arginine content of the two proteins must be appreciably different for distinct phases to form, and we show that this difference increases as the system is driven toward greater multiphasicity. Using the trends observed in the different interaction energies of this system, we demonstrate that we can also construct multilayered condensates with RNA preferentially concentrated in one phase. The "rules" identified can thus enable the design of synthetic multiphasic condensates to facilitate further study of their organization and function.
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Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jerelle A Joseph
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Physics, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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14
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Song Y. Liquid-liquid phase separation-inspired design of biomaterials. Biomater Sci 2024; 12:1943-1949. [PMID: 38465963 DOI: 10.1039/d3bm02008h] [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: 03/12/2024]
Abstract
Liquid-liquid phase separation (LLPS) is a crucial biological process that governs biomolecular condensation, assembly, and functionality within phase-separated aqueous environments. This phenomenon serves as a source of inspiration for the creation of artificial designs in both structured and functional biomaterials, presenting novel strategies for manipulating the structures of functional protein aggregates in a wide range of biomedical applications. This mini review summarizes my past research endeavors, offering a panoramic overview of LLPS-inspired biomaterials utilized in the design of structured materials, the development of cell mimetics, and the advancement of intelligent biomaterials.
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Affiliation(s)
- Yang Song
- State Key Laboratory of Metal Matrix Composites, School of Material Science & Engineering, Shanghai Jiao Tong University, China.
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15
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Roy PS. Complex Coacervate-Based Materials for Biomedicine: Recent Advancements and Future Prospects. Ind Eng Chem Res 2024; 63:5414-5487. [DOI: 10.1021/acs.iecr.3c03830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
Affiliation(s)
- Partha Sarathi Roy
- Division of Pharmaceutical Sciences, Health Sciences Building, University of Missouri─Kansas City, 2464 Charlotte St., Kansas City, Missouri 64108-2718, United States
- Department of Pharmaceutics/Medicinal Chemistry, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, 751 Brookside Rd., Stockton, California 95211, United States
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16
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Green CM, Sementa D, Mathur D, Melinger JS, Deshpande P, Elbaum-Garfinkle S, Medintz IL, Ulijn RV, Díaz SA. Sequestration within peptide coacervates improves the fluorescence intensity, kinetics, and limits of detection of dye-based DNA biosensors. Commun Chem 2024; 7:49. [PMID: 38424154 PMCID: PMC10904739 DOI: 10.1038/s42004-024-01124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Peptide-based liquid-liquid phase separated domains, or coacervates, are a biomaterial gaining new interest due to their exciting potential in fields ranging from biosensing to drug delivery. In this study, we demonstrate that coacervates provide a simple and biocompatible medium to improve nucleic acid biosensors through the sequestration of both the biosensor and target strands within the coacervate, thereby increasing their local concentration. Using the well-established polyarginine (R9) - ATP coacervate system and an energy transfer-based DNA molecular beacon we observed three key improvements: i) a greater than 20-fold reduction of the limit of detection within coacervates when compared to control buffer solutions; ii) an increase in the kinetics, equilibrium was reached more than 4-times faster in coacervates; and iii) enhancement in the dye fluorescent quantum yields within the coacervates, resulting in greater signal-to-noise. The observed benefits translate into coacervates greatly improving bioassay functionality.
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Affiliation(s)
- Christopher M Green
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Deborah Sementa
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Joseph S Melinger
- Electronics Sciences and Technology Division Code 6816, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Priyasha Deshpande
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center, Graduate Center of the City University of New York, New York, NY, 10031, USA
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
- Department of Chemistry Hunter College, City University of New York, New York, NY, 10065, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, DC, 20375, USA.
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17
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Shono M, Aburatani K, Yanagisawa M, Yoshikawa K, Shioi A. Periodic Alignment of Binary Droplets via a Microphase Separation of a Tripolymer Solution under Tubular Confinement. ACS Macro Lett 2024:207-211. [PMID: 38265017 PMCID: PMC10883045 DOI: 10.1021/acsmacrolett.3c00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
We report the spontaneous formation of a characteristic periodic pattern through the phase separation of a tripolymer solution comprising polyethylene-glycol (PEG)/dextran (DEX)/gelatin. When this tripolymer solution is introduced into a glass capillary with a PEG-coated inner surface, we observe the time-dependent growth of microphase separation. Remarkably, a self-organized, periodic alignment of DEX- and gelatin-rich microdroplets ensues, surrounded by a PEG-rich phase. This pattern demonstrates considerable stability, enduring for at least 8 h. The fundamental characteristics of the experimentally observed periodic alignment are successfully replicated via numerical simulations using a Cahn-Hilliard model underpinned by a set of simple, theoretically derived equations. We propose that this type of kinetically stabilized periodic patterning can be produced across a broad range of phase-separation systems by selecting appropriate boundary conditions such as at the surface within a narrow channel.
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Affiliation(s)
- Mayu Shono
- Department of Chemical Engineering and Materials Science, Doshisha University, Kyoto 610-0321, Japan
| | - Koki Aburatani
- Department of Chemical Engineering and Materials Science, Doshisha University, Kyoto 610-0321, Japan
| | - Miho Yanagisawa
- Komaba Institute for Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
| | - Akihisa Shioi
- Department of Chemical Engineering and Materials Science, Doshisha University, Kyoto 610-0321, Japan
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18
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Cook AB, Gonzalez BD, van Hest JCM. Tuning of Cationic Polymer Functionality in Complex Coacervate Artificial Cells for Optimized Enzyme Activity. Biomacromolecules 2024; 25:425-435. [PMID: 38064593 PMCID: PMC10777345 DOI: 10.1021/acs.biomac.3c01063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024]
Abstract
Complex coacervates are a versatile platform to mimic the structure of living cells. In both living systems and artificial cells, a macromolecularly crowded condensate phase has been shown to be able to modulate enzyme activity. Yet, how enzyme activity is affected by interactions (particularly with cationic charges) inside coacervates is not well studied. Here, we synthesized a series of amino-functional polymers to investigate the effect of the type of amine and charge density on coacervate formation, stability, protein partitioning, and enzyme function. The polymers were prepared by RAFT polymerization using as monomers aminoethyl methacrylate (AEAM), 2-(dimethylamino)ethyl methacrylate (DMAEMA), imidazolepropyl methacrylamide (IPMAm), and [2-(methacryloyloxy)ethyl] trimethylammonium chloride (TMAEMA). Membranized complex coacervate artificial cells were formed with these polycations and an anionic amylose derivative. Results show that polycations with reduced charge density result in higher protein mobility in the condensates and also higher enzyme activity. Insights described here could help guide the use of coacervate artificial cells in applications such as sensing, catalysis, and therapeutic formulations.
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Affiliation(s)
- Alexander B Cook
- Bio-Organic
Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, Netherlands
| | - Bruno Delgado Gonzalez
- Departamento
de Química Orgánica, Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Santiago de Compostela 15782, Spain
| | - Jan C M van Hest
- Bio-Organic
Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, Netherlands
- Biomedical
Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, Netherlands
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19
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Wang J, Abbas M, Wang J, Spruijt E. Selective amide bond formation in redox-active coacervate protocells. Nat Commun 2023; 14:8492. [PMID: 38129391 PMCID: PMC10739716 DOI: 10.1038/s41467-023-44284-x] [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: 08/26/2021] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Coacervate droplets are promising protocell models because they sequester a wide range of guest molecules and may catalyze their conversion. However, it remains unclear how life's building blocks, including peptides, could be synthesized from primitive precursor molecules inside such protocells. Here, we develop a redox-active protocell model formed by phase separation of prebiotically relevant ferricyanide (Fe(CN)63-) molecules and cationic peptides. Their assembly into coacervates can be regulated by redox chemistry and the coacervates act as oxidizing hubs for sequestered metabolites, like NAD(P)H and gluthathione. Interestingly, the oxidizing potential of Fe(CN)63- inside coacervates can be harnessed to drive the formation of new amide bonds between prebiotically relevant amino acids and α-amidothioacids. Aminoacylation is enhanced in Fe(CN)63-/peptide coacervates and selective for amino acids that interact less strongly with the coacervates. We finally use Fe(CN)63--containing coacervates to spatially control assembly of fibrous networks inside and at the surface of coacervate protocells. These results provide an important step towards the prebiotically relevant integration of redox chemistry in primitive cell-like compartments.
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Affiliation(s)
- Jiahua Wang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Department of Radiology, Shanghai Jiao Tong University School of Medicine Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Manzar Abbas
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Junyou Wang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
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20
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Perin GB, Moreno S, Zhou Y, Günther M, Boye S, Voit B, Felisberti MI, Appelhans D. Construction of Membraneless and Multicompartmentalized Coacervate Protocells Controlling a Cell Metabolism-like Cascade Reaction. Biomacromolecules 2023; 24:5807-5822. [PMID: 37984848 DOI: 10.1021/acs.biomac.3c00828] [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: 11/22/2023]
Abstract
In recent years, there has been growing attention to designing synthetic protocells, capable of mimicking micrometric and multicompartmental structures and highly complex physicochemical and biological processes with spatiotemporal control. Controlling metabolism-like cascade reactions in coacervate protocells is still challenging since signal transduction has to be involved in sequential and parallelized actions mediated by a pH change. Herein, we report the hierarchical construction of membraneless and multicompartmentalized protocells composed of (i) a cytosol-like scaffold based on complex coacervate droplets stable under flow conditions, (ii) enzyme-active artificial organelles and a substrate nanoreservoir capable of triggering a cascade reaction between them in response to a pH increase, and (iii) a signal transduction component based on the urease enzyme capable of the conversion of an exogenous biological fuel (urea) into an endogenous signal (ammonia and pH increase). Overall, this strategy allows a synergistic communication between their components within the membraneless and multicompartment protocells and, thus, metabolism-like enzymatic cascade reactions. This signal communication is transmitted through a scaffold protocell from an "inactive state" (nonfluorescent protocell) to an "active state" (fluorescent protocell capable of consuming stored metabolites).
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Affiliation(s)
- Giovanni B Perin
- Institute of Chemistry, University of Campinas, 13083-970 Campinas, São Paulo, Brazil
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, D-01069 Dresden, Germany
| | - Silvia Moreno
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, D-01069 Dresden, Germany
| | - Yang Zhou
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, D-01069 Dresden, Germany
- Organic Chemistry of Polymers, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Markus Günther
- Institute of Botany, Faculty of Biology, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Susanne Boye
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, D-01069 Dresden, Germany
| | - Brigitte Voit
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, D-01069 Dresden, Germany
- Organic Chemistry of Polymers, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Maria I Felisberti
- Institute of Chemistry, University of Campinas, 13083-970 Campinas, São Paulo, Brazil
| | - Dietmar Appelhans
- Leibniz-Institut für Polymerforschung Dresden, Hohe Straße 6, D-01069 Dresden, Germany
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21
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Lin T, Zhou Y, Dadmohammadi Y, Yaghoobi M, Meletharayil G, Kapoor R, Abbaspourrad A. Encapsulation and stabilization of lactoferrin in polyelectrolyte ternary complexes. Food Hydrocoll 2023; 145:109064. [PMID: 37545760 PMCID: PMC10399645 DOI: 10.1016/j.foodhyd.2023.109064] [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] [Indexed: 08/08/2023]
Abstract
Effective delivery of the bioactive protein, lactoferrin (LF), remains a challenge as it is sensitive to environmental changes and easily denatured during heating, restricting its application in functional food products. To overcome these challenges, we formulated novel polyelectrolyte ternary complexes of LF with gelatin (G) and negatively charged polysaccharides, to improve the thermal stability of LF with retained antibacterial activity. Linear, highly charged polysaccharides were able to form interpolymeric complexes with LF and G, while coacervates were formed with branched polysaccharides. A unique multiphase coacervate was observed in the gum Arabic GA-LF-G complex, where a special coacervate-in-coacervate structure was found. The ternary complexes made with GA, soy soluble polysaccharide (SSP), or high methoxyl pectin (HMP) preserved the protein structures and demonstrated enhanced thermal stability of LF. The GA-LF-G complex was especially stable with >90% retention of the native LF after treatment at 90 °C for 2 min in a water bath or at 145 °C for 30 s, while the LF control had only ~ 7% undenatured LF under both conditions. In comparison to untreated LF, LF in ternary complex retained significant antibacterial activity on both Gram-positive and Gram-negative bacteria, even after heat treatment. These ternary complexes of LF maintain the desired functionality of LF, thermal stability and antibacterial activity, in the final products. The ternary complex structure, particularly the multiphase coacervate, may serve as a template for the encapsulation and stabilization of other bioactives and peptides.
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Affiliation(s)
- Tiantian Lin
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Yufeng Zhou
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Younas Dadmohammadi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Mohammad Yaghoobi
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | | | | | - Alireza Abbaspourrad
- Department of Food Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
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22
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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.
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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
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23
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Wang X, Qiao X, Chen H, Wang L, Liu X, Huang X. Synthetic-Cell-Based Multi-Compartmentalized Hierarchical Systems. SMALL METHODS 2023; 7:e2201712. [PMID: 37069779 DOI: 10.1002/smtd.202201712] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/14/2023] [Indexed: 06/19/2023]
Abstract
In the extant lifeforms, the self-sustaining behaviors refer to various well-organized biochemical reactions in spatial confinement, which rely on compartmentalization to integrate and coordinate the molecularly crowded intracellular environment and complicated reaction networks in living/synthetic cells. Therefore, the biological phenomenon of compartmentalization has become an essential theme in the field of synthetic cell engineering. Recent progress in the state-of-the-art of synthetic cells has indicated that multi-compartmentalized synthetic cells should be developed to obtain more advanced structures and functions. Herein, two ways of developing multi-compartmentalized hierarchical systems, namely interior compartmentalization of synthetic cells (organelles) and integration of synthetic cell communities (synthetic tissues), are summarized. Examples are provided for different construction strategies employed in the above-mentioned engineering ways, including spontaneous compartmentalization in vesicles, host-guest nesting, phase separation mediated multiphase, adhesion-mediated assembly, programmed arrays, and 3D printing. Apart from exhibiting advanced structures and functions, synthetic cells are also applied as biomimetic materials. Finally, key challenges and future directions regarding the development of multi-compartmentalized hierarchical systems are summarized; these are expected to lay the foundation for the creation of a "living" synthetic cell as well as provide a larger platform for developing new biomimetic materials in the future.
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Affiliation(s)
- Xiaoliang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Xin Qiao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Haixu Chen
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Lei Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Xiaoman Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, P. R. China
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24
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Lin Z, Beneyton T, Baret JC, Martin N. Coacervate Droplets for Synthetic Cells. SMALL METHODS 2023; 7:e2300496. [PMID: 37462244 DOI: 10.1002/smtd.202300496] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/15/2023] [Indexed: 12/24/2023]
Abstract
The design and construction of synthetic cells - human-made microcompartments that mimic features of living cells - have experienced a real boom in the past decade. While many efforts have been geared toward assembling membrane-bounded compartments, coacervate droplets produced by liquid-liquid phase separation have emerged as an alternative membrane-free compartmentalization paradigm. Here, the dual role of coacervate droplets in synthetic cell research is discussed: encapsulated within membrane-enclosed compartments, coacervates act as surrogates of membraneless organelles ubiquitously found in living cells; alternatively, they can be viewed as crowded cytosol-like chassis for constructing integrated synthetic cells. After introducing key concepts of coacervation and illustrating the chemical diversity of coacervate systems, their physicochemical properties and resulting bioinspired functions are emphasized. Moving from suspensions of free floating coacervates, the two nascent roles of these droplets in synthetic cell research are highlighted: organelle-like modules and cytosol-like templates. Building the discussion on recent studies from the literature, the potential of coacervate droplets to assemble integrated synthetic cells capable of multiple life-inspired functions is showcased. Future challenges that are still to be tackled in the field are finally discussed.
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Affiliation(s)
- Zi Lin
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France
| | - Thomas Beneyton
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France
| | - Jean-Christophe Baret
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France
| | - Nicolas Martin
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France
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25
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Barriales K, Kassem S, Sementa D, Vidal Ceballos A, Wang T, Khandaker S, Abzalimov RR, Jain A, Elbaum-Garfinkle S, Ulijn RV. Localized and regulated peptide pigment formation inside liquid droplets through confined enzymatic oxidation. Chem Commun (Camb) 2023; 59:14138-14141. [PMID: 37955166 DOI: 10.1039/d3cc04231f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Melanin pigments are found in most life forms, where they are responsible for coloration and ultraviolet (UV) light protection. Natural melanin is a poorly soluble and complex biosynthesis product produced through confined and templated enzymatic oxidation of tyrosine. It has been challenging to create water-soluble synthetic mimics. This study demonstrates the enzymatic synthesis of oxidized phenols confined inside liquid droplets. We use an amphiphilic, bifunctional peptide, DYFR9, that combines a tyrosine tripeptide previously shown to undergo enzymatic oxidation to form peptide pigments with broad absorbance, and polyarginine to facilitate complex coacervation in the presence of ATP. When ATP, DYFR9 are mixed and exposed to tyrosinase, pigmented liquid droplets result, while no appreciable oxidation is observed in the bulk.
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Affiliation(s)
- Kenny Barriales
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, New York 10065, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
| | - Salma Kassem
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
| | - Deborah Sementa
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
| | - Alfredo Vidal Ceballos
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, 10016, USA
| | - Tong Wang
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
| | - Shadman Khandaker
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
| | - Rinat R Abzalimov
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
| | - Ankit Jain
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
- Department of Chemistry and Biochemistry, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Brooklyn College Cancer Center, Brooklyn College, The City University of New York, 2900 Beford Ave, Brooklyn, NY 11210, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, 10016, USA
| | - Shana Elbaum-Garfinkle
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, 10016, USA
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center, City University of New York (CUNY), 85 St Nicholas Terrace, New York, New York 10031, USA.
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, New York 10065, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, 10016, USA
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26
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Osmanović D, Franco E. Chemical reaction motifs driving non-equilibrium behaviours in phase separating materials. J R Soc Interface 2023; 20:20230117. [PMID: 37907095 PMCID: PMC10618056 DOI: 10.1098/rsif.2023.0117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/11/2023] [Indexed: 11/02/2023] Open
Abstract
Chemical reactions that couple to systems that phase separate have been implicated in diverse contexts from biology to materials science. However, how a particular set of chemical reactions (chemical reaction network, CRN) would affect the behaviours of a phase separating system is difficult to fully predict theoretically. In this paper, we analyse a mean field theory coupling CRNs to a combined system of phase separating and non-phase separating materials and analyse how the properties of the CRNs affect different classes of non-equilibrium behaviour: microphase separation or temporally oscillating patterns. We examine the problem of achieving microphase separated condensates by statistical analysis of the Jacobians, of which the most important motifs are negative feedback of the phase separating component and combined inhibition/activation by the non-phase separating components. We then identify CRN motifs that are likely to yield microphase by examining randomly generated networks and parameters. Molecular sequestration of the phase separating motif is shown to be the most robust towards yielding microphase separation. Subsequently, we find that dynamics of the phase separating species is promoted most easily by inducing oscillations in the diffusive components coupled to the phase separating species. Our results provide guidance towards the design of CRNs that manage the formation, dissolution and organization of compartments.
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Affiliation(s)
- Dino Osmanović
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles 90095, CA, USA
| | - Elisa Franco
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles 90095, CA, USA
- Department of Bioengineering, University of California, Los Angeles 90095, CA, USA
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27
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Shelby SA, Veatch SL. The Membrane Phase Transition Gives Rise to Responsive Plasma Membrane Structure and Function. Cold Spring Harb Perspect Biol 2023; 15:a041395. [PMID: 37553204 PMCID: PMC10626261 DOI: 10.1101/cshperspect.a041395] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Several groups have recently reported evidence for the emergence of domains in cell plasma membranes when membrane proteins are organized by ligand binding or assembly of membrane proximal scaffolds. These domains recruit and retain components that favor the liquid-ordered phase, adding to a decades-old literature interrogating the contribution of membrane phase separation in plasma membrane organization and function. Here we propose that both past and present observations are consistent with a model in which membranes have a high compositional susceptibility, arising from their thermodynamic state in a single phase that is close to a miscibility phase transition. This rigorous framework naturally allows for both transient structure in the form of composition fluctuations and long-lived structure in the form of induced domains. In this way, the biological tuning of plasma membrane composition enables a responsive compositional landscape that facilitates and augments cellular biochemistry vital to plasma membrane functions.
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Affiliation(s)
- Sarah A Shelby
- Biochemistry & Cellular and Molecular Biology, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
| | - Sarah L Veatch
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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28
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Liu X, Mokarizadeh AH, Narayanan A, Mane P, Pandit A, Tseng YM, Tsige M, Joy A. Multiphasic Coacervates Assembled by Hydrogen Bonding and Hydrophobic Interactions. J Am Chem Soc 2023; 145:23109-23120. [PMID: 37820374 DOI: 10.1021/jacs.3c06675] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Coacervation has emerged as a prevalent mechanism to compartmentalize biomolecules in living cells. Synthetic coacervates help in understanding the assembly process and mimic the functions of biological coacervates as simplified artificial systems. Though the molecular mechanism and mesoscopic properties of coacervates formed from charged coacervates have been well investigated, the details of the assembly and stabilization of nonionic coacervates remain largely unknown. Here, we describe a library of coacervate-forming polyesteramides and show that the water-tertiary amide bridging hydrogen bonds and hydrophobic interactions stabilize these nonionic, single-component coacervates. Analogous to intracellular biological coacervates, these coacervates exhibit "liquid-like" features with low viscosity and low interfacial energy, and form coacervates with as few as five repeating units. By controlling the temperature and engineering the molar ratio between hydrophobic interaction sites and bridging hydrogen bonding sites, we demonstrate the tuneability of the viscosity and interfacial tension of polyesteramide-based coacervates. Taking advantage of the differences in the mesoscopic properties of these nonionic coacervates, we engineered multiphasic coacervates with core-shell architectures similar to those of intracellular biological coacervates, such as nucleoli and stress granule-p-body complexes. The multiphasic structures produced from these synthetic nonionic polyesteramide coacervates may serve as a valuable tool for investigating physicochemical principles deployed by living cells to spatiotemporally control cargo partitioning, biochemical reaction rates, and interorganellar signal transport.
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Affiliation(s)
- Xinhao Liu
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Abdol Hadi Mokarizadeh
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Amal Narayanan
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Prathamesh Mane
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Avanti Pandit
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Yen-Ming Tseng
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Mesfin Tsige
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Abraham Joy
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
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29
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Chawla R, Tom JKA, Boyd T, Grotjahn DA, Park D, Deniz AA, Racki LR. Reentrant DNA shells tune polyphosphate condensate size. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557044. [PMID: 37745474 PMCID: PMC10515899 DOI: 10.1101/2023.09.13.557044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The ancient, inorganic biopolymer polyphosphate (polyP) occurs in all three domains of life and affects myriad cellular processes. An intriguing feature of polyP is its frequent proximity to chromatin, and in the case of many bacteria, its occurrence in the form of magnesium-enriched condensates embedded in the nucleoid, particularly in response to stress. The physical basis of the interaction between polyP and DNA, two fundamental anionic biopolymers, and the resulting effects on the organization of both the nucleoid and polyP condensates remain poorly understood. Given the essential role of magnesium ions in the coordination of polymeric phosphate species, we hypothesized that a minimal system of polyP, magnesium ions, and DNA (polyP-Mg2+-DNA) would capture key features of the interplay between the condensates and bacterial chromatin. We find that DNA can profoundly affect polyP-Mg2+ coacervation even at concentrations several orders of magnitude lower than found in the cell. The DNA forms shells around polyP-Mg2+ condensates and these shells show reentrant behavior, primarily forming in the concentration range close to polyP-Mg2+ charge neutralization. This surface association tunes both condensate size and DNA morphology in a manner dependent on DNA properties, including length and concentration. Our work identifies three components that could form the basis of a central and tunable interaction hub that interfaces with cellular interactors. These studies will inform future efforts to understand the basis of polyP granule composition and consolidation, as well as the potential capacity of these mesoscale assemblies to remodel chromatin in response to diverse stressors at different length and time scales.
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Affiliation(s)
| | | | - Tumara Boyd
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Donghyun Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lisa R. Racki
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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30
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Kubota R, Hiroi T, Ikuta Y, Liu Y, Hamachi I. Visualizing Formation and Dynamics of a Three-Dimensional Sponge-like Network of a Coacervate in Real Time. J Am Chem Soc 2023; 145:18316-18328. [PMID: 37562059 DOI: 10.1021/jacs.3c03793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Coacervates, which are formed by liquid-liquid phase separation, have been extensively explored as models for synthetic cells and membraneless organelles, so their in-depth structural analysis is crucial. However, both the inner structure dynamics and formation mechanism of coacervates remain elusive. Herein, we demonstrate real-time confocal observation of a three-dimensional sponge-like network in a dipeptide-based coacervate. In situ generation of the dipeptide allowed us to capture the emergence of the sponge-like network via unprecedented membrane folding of vesicle-shaped intermediates. We also visualized dynamic fluctuation of the network, including reversible engagement/disengagement of cross-links and a stochastic network kissing event. Photoinduced transient formation of a multiphase coacervate was achieved with a thermally responsive phase transition. Our findings expand the fundamental understanding of synthetic coacervates and provide opportunities to manipulate their physicochemical properties by engineering the inner network for potential applications in development of artificial cells and life-like material fabrication.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Taro Hiroi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuriki Ikuta
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuchong Liu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Nishikyo-ku, Katsura 615-8530, Japan
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31
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Kojima K, Tomita S, Kamimura M. Fluorescence Imaging of Nanoparticle Uptake into Liquid-Liquid Phase-Separated Droplets. Chempluschem 2023; 88:e202300207. [PMID: 37310764 DOI: 10.1002/cplu.202300207] [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: 04/30/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/14/2023]
Abstract
Liquid-liquid phase separation (LLPS) in living cells has received considerable attention in the biomedical research field. This study is the first to report nanoparticle (NP) uptake into LLPS droplets. Fluorescent dye, Nile red loaded polystyrene NPs (NR-PSt NPs) uptake into model LLPS droplets consisting of adenosine triphosphate (ATP) and poly-L-lysine (PLL) was visualized using fluorescence imaging. Fluorescence imaging showed that the LLPS droplets had a quick NP uptake behavior. Furthermore, temperature changes (4-37 °C) significantly affected the NP uptake behavior of the LLPS droplets. Moreover, the NP-incorporated droplets displayed high stability under strong ionic strength conditions (1 M NaCl). ATP measurements displayed that ATP was released from the NP-incorporated droplets, indicating that the weakly negatively charged ATP molecules and strongly negatively charged NPs were exchanged, which resulted in the high stability of the LLPS droplets. These fundamental findings will contribute to the LLPS studies using various NPs.
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Affiliation(s)
- Keitaro Kojima
- Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo, 125-8585, Japan
| | - Shunsuke Tomita
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Masao Kamimura
- Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika, Tokyo, 125-8585, Japan
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32
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Fraccia TP, Martin N. Non-enzymatic oligonucleotide ligation in coacervate protocells sustains compartment-content coupling. Nat Commun 2023; 14:2606. [PMID: 37160869 PMCID: PMC10169843 DOI: 10.1038/s41467-023-38163-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/18/2023] [Indexed: 05/11/2023] Open
Abstract
Modern cells are complex chemical compartments tightly regulated by an underlying DNA-encoded program. Achieving a form of coupling between molecular content, chemical reactions, and chassis in synthetic compartments represents a key step to the assembly of evolvable protocells but remains challenging. Here, we design coacervate droplets that promote non-enzymatic oligonucleotide polymerization and that restructure as a result of the reaction dynamics. More specifically, we rationally exploit complexation between end-reactive oligonucleotides able to stack into long physical polymers and a cationic azobenzene photoswitch to produce three different phases-soft solids, liquid crystalline or isotropic coacervates droplets-each of them having a different impact on the reaction efficiency. Dynamical modulation of coacervate assembly and dissolution via trans-cis azobenzene photo-isomerization is used to demonstrate cycles of light-actuated oligonucleotide ligation. Remarkably, changes in the population of polynucleotides during polymerization induce phase transitions due to length-based DNA self-sorting to produce multiphase coacervates. Overall, by combining a tight reaction-structure coupling and environmental responsiveness, our reactive coacervates provide a general route to the non-enzymatic synthesis of polynucleotides and pave the way to the emergence of a primitive compartment-content coupling in membrane-free protocells.
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Affiliation(s)
- Tommaso P Fraccia
- Institut Pierre-Gilles de Gennes, Chimie Biologie et Innovation, UMR 8231, ESPCI Paris, PSL University, CNRS, 6 rue Jean Calvin, 75005, Paris, France.
- Department of Pharmacological and Biomolecular Sciences, University of Milano, 20133, Milano, Italy.
| | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, 115 avenue du Dr. Schweitzer, 33600, Pessac, France.
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33
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Illmann MD, Schäfl L, Drees F, Hartmann L, Schmidt S. Glycan-Presenting Coacervates Derived from Charged Poly(active esters): Preparation, Phase Behavior, and Lectin Capture. Biomacromolecules 2023. [PMID: 37133885 DOI: 10.1021/acs.biomac.3c00046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This study presents the preparation and phase behavior of glycan-functionalized polyelectrolytes for capturing carbohydrate-binding proteins and bacteria in liquid condensate droplets. The droplets are formed by complex coacervation of poly(active ester)-derived polyanions and polycations. This approach allows for a straightforward modular introduction of charged motifs and specifically interacting units; mannose and galactose oligomers are used here as first examples. The introduction of carbohydrates has a notable effect on the phase separation and the critical salt concentration, potentially by reducing the charge density. Two mannose binding species, concanavalin A (ConA) and Escherichia coli, are shown to not only specifically bind to mannose-functionalized coacervates but also to some degree to unfunctionalized, carbohydrate-free coacervates. This suggests non-carbohydrate-specific charge-charge interactions between the protein/bacteria and the droplets. However, when mannose interactions are inhibited or when non-binding galactose-functionalized polymers are used, interactions are significantly weakened. This confirms specific mannose-mediated binding functionalization and suggests that introducing carbohydrates reduces non-specific charge-charge interactions by a so far unidentified mechanism. Overall, the presented route toward glycan-presenting polyelectrolytes enables new functional liquid condensate droplets with specific biomolecular interactions.
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Affiliation(s)
- Michele Denise Illmann
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Lea Schäfl
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Felicitas Drees
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
- Institute of Macromolecular Chemistry, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 31, 79104 Freiburg, Germany
| | - Laura Hartmann
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
- Institute of Macromolecular Chemistry, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 31, 79104 Freiburg, Germany
| | - Stephan Schmidt
- Institute of Organic Chemistry and Macromolecular Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
- Institute of Macromolecular Chemistry, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Str. 31, 79104 Freiburg, Germany
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34
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Sakuta H, Nakatani N, Torisawa T, Sumino Y, Tsumoto K, Oiwa K, Yoshikawa K. Self-emergent vortex flow of microtubule and kinesin in cell-sized droplets under water/water phase separation. Commun Chem 2023; 6:80. [PMID: 37100870 PMCID: PMC10133263 DOI: 10.1038/s42004-023-00879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 04/11/2023] [Indexed: 04/28/2023] Open
Abstract
By facilitating a water/water phase separation (w/wPS), crowded biopolymers in cells form droplets that contribute to the spatial localization of biological components and their biochemical reactions. However, their influence on mechanical processes driven by protein motors has not been well studied. Here, we show that the w/wPS droplet spontaneously entraps kinesins as well as microtubules (MTs) and generates a micrometre-scale vortex flow inside the droplet. Active droplets with a size of 10-100 µm are generated through w/wPS of dextran and polyethylene glycol mixed with MTs, molecular-engineered chimeric four-headed kinesins and ATP after mechanical mixing. MTs and kinesin rapidly created contractile network accumulated at the interface of the droplet and gradually generated vortical flow, which can drive translational motion of a droplet. Our work reveals that the interface of w/wPS contributes not only to chemical processes but also produces mechanical motion by assembling species of protein motors in a functioning manner.
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Affiliation(s)
- Hiroki Sakuta
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Organization for Research Initiatives and Development, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro, Tokyo, 153-8902, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, 153-8902, Japan
| | - Naoki Nakatani
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
| | - Takayuki Torisawa
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Yutaka Sumino
- Department of Applied Physics, Faculty of Advanced Engineering, WaTUS and DCIS, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan.
| | - Kanta Tsumoto
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Mie, 514-8507, Japan
| | - Kazuhiro Oiwa
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, 651-2492, Japan.
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako, Hyogo, 678-1297, Japan.
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
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35
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Chen J, Bai Q, Li Y, Liu Z, Li Y, Liang D. Coacervates Forming Coexisting Phases on a Mineral Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:5814-5824. [PMID: 37053474 DOI: 10.1021/acs.langmuir.3c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Minerals played a crucial role in the chemical evolution of small molecules into biopolymers. Yet, it is still not clear how the minerals are related to the formation and the evolution of protocells on early Earth. In this work, using the coacervate formed by quaternized dextran (Q-dextran) and single-stranded oligonucleotides (ss-oligo) as the protocell model, we systematically studied the phase separation of Q-dextran and ss-oligo on the muscovite surface. Serving as rigid and 2D polyelectrolytes, the muscovite surface can be treated by Q-dextran to become negatively charged, neutral, or positively charged. We observed that Q-dextran and ss-oligo form uniform coacervates on naked and neutral muscovite surfaces, while they form biphasic coacervates containing Q-dextran-rich phases and ss-oligo-rich phases on positively or negatively charged muscovite surfaces that were pretreated by Q-dextran. The evolution of the phases is caused by the redistribution of the components as the coacervate touches the surface. Our study indicates that the mineral surface could be a potential driving force for the formation of protocells with hierarchical structures and desirable functions on prebiotic Earth.
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Affiliation(s)
- Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yanzhang Li
- Beijing Key Laboratory of Mineral Environmental Function, and the Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing 100871, China
| | - Zhijun Liu
- Beijing National Laboratory for Molecular Sciences, and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yan Li
- Beijing Key Laboratory of Mineral Environmental Function, and the Key Laboratory of Orogenic Belts and Crustal Evolution, School of Earth and Space Science, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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36
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Huang Y, Huang J, Yin W, Xie F, Coleman B, Cao Y, Aya S, Zhu W, Yang Z, Jiang L. Encoding Coacervate Droplets with Paramagnetism for Dynamical Reconfigurability and Spatial Addressability. ACS NANO 2023; 17:6234-6246. [PMID: 36951305 DOI: 10.1021/acsnano.2c09617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
It is an ongoing endeavor in chemistry and materials science to regulate coacervate droplets on a physiologically relevant spatiotemporal scale to ultimately match or even surpass living cells' precision, complexity, and functionality. Herein, we develop a magnetic strategy orthogonal to the thermal, pH, light, or chemical counterparts that are commonly employed by biotic or artificial systems; its successful implementation thus adds a missing piece to the current arsenal of manipulative methodologies. Specifically, we paramagnetize the otherwise diamagnetic coacervate droplets by cooperatively combining paramagnetic ingredients (including organic radicals, metal ions, and Fe3O4 nanoparticles) and coacervate ingredients to obtain "MagCoa" droplets. A simple model is derived theoretically to account for migration and division of MagCoa droplets in an uneven magnetic field. Experimentally, we produce an array of compartmentalized and monodispersed droplets using microfluidics and magnetically steer them with uniformity and synchronicity. We design and fabricate spatial magnetic modulators to engineer the landscape of a magnetic field that, in turn, directs the MagCoa droplets into predesigned patterns in a reconfigurable fashion. These programmable liquid patterns can be potentially extended to dynamic assembly and information encryption. We envision that the toolbox established here is of generality and multitudes to serve as a practical guide to control droplets magnetically.
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Affiliation(s)
- Yangkun Huang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
| | - Jinpeng Huang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Wenxiang Yin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Fei Xie
- Institute of Information Technology, Handan University, Handan 056005, China
| | - Benjamin Coleman
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005-1892, United States
| | - Yaoyu Cao
- Guangdong Provincial Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 511443, China
| | - Satoshi Aya
- College of Chemistry and Materials Science, Jinan University, Guangzhou 510632, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Wei Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Zhijie Yang
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China
| | - Lingxiang Jiang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou 510640, China
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37
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Chen M, Liu G, Zhang M, Li Y, Hong X, Yang H. Programmatically Dynamic Microcompartmentation in Coacervate-in-Pickering Emulsion Protocell. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206437. [PMID: 36564366 DOI: 10.1002/smll.202206437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The desire for exploration of cellular functional mechanisms has substantially increased the rapid development of artificial cells. However, the construction of synthetic cells with high organizational complexity remains challenging due to the lack of facile approaches ensuring dynamic multi-compartments of cytoplasm and stability of membranes in protocells. Herein, a stable coacervate-in-Pickering emulsion protocell model comprising a membraneless coacervate phase formed by poly-l-lysine (PLys) and adenosine triphosphate (ATP) encapsulated in Pickering emulsion is put forward only through simple one-step emulsification. The dynamic distribution of intracellular components (coacervates in this protocell model) can be manipulated by changes in temperature or pH. This coacervate-in-Pickering emulsion protocell system exhibits repeatable cycle stability in response to external stimuli (at least 24 cycles for temperature and 3 cycles for pH). By encapsulating antagonistic enzymes into coacervates, glucose oxidase (GOx) and urease as an example, the control of local enzyme concentration is achieved by introducing glucose and urea to adjust the pH value in Pickering emulsion droplets. This hybrid protocell model with programmatically dynamic microcompartmentation and sufficient stability is expected to be further studied and applied in cellular biology, facilitating the development of lifelike systems with potential in practical applications.
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Affiliation(s)
- Mengqing Chen
- College of Chemistry and Molecule Sciences, Wuhan University, Wuhan, 430072, China
| | - Guoliang Liu
- College of Chemistry and Molecule Sciences, Wuhan University, Wuhan, 430072, China
| | - Ming Zhang
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
| | - Yanyan Li
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
| | - Xinlin Hong
- College of Chemistry and Molecule Sciences, Wuhan University, Wuhan, 430072, China
| | - Hengquan Yang
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan, 030006, China
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38
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Chew PY, Joseph JA, Collepardo-Guevara R, Reinhardt A. Thermodynamic origins of two-component multiphase condensates of proteins. Chem Sci 2023; 14:1820-1836. [PMID: 36819870 PMCID: PMC9931050 DOI: 10.1039/d2sc05873a] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
Intracellular condensates are highly multi-component systems in which complex phase behaviour can ensue, including the formation of architectures comprising multiple immiscible condensed phases. Relying solely on physical intuition to manipulate such condensates is difficult because of the complexity of their composition, and systematically learning the underlying rules experimentally would be extremely costly. We address this challenge by developing a computational approach to design pairs of protein sequences that result in well-separated multilayered condensates and elucidate the molecular origins of these compartments. Our method couples a genetic algorithm to a residue-resolution coarse-grained protein model. We demonstrate that we can design protein partners to form multiphase condensates containing naturally occurring proteins, such as the low-complexity domain of hnRNPA1 and its mutants, and show how homo- and heterotypic interactions must differ between proteins to result in multiphasicity. We also show that in some cases the specific pattern of amino-acid residues plays an important role. Our findings have wide-ranging implications for understanding and controlling the organisation, functions and material properties of biomolecular condensates.
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Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
| | - Jerelle A Joseph
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
- Department of Physics, University of Cambridge Cambridge CB3 0HE UK
- Department of Genetics, University of Cambridge Cambridge CB2 3EH UK
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
- Department of Physics, University of Cambridge Cambridge CB3 0HE UK
- Department of Genetics, University of Cambridge Cambridge CB2 3EH UK
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge CB2 1EW UK
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39
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Zhorabek F, Abesekara MS, Liu J, Dai X, Huang J, Chau Y. Construction of multiphasic membraneless organelles towards spontaneous spatial segregation and directional flow of biochemical reactions. Chem Sci 2023; 14:801-811. [PMID: 36755726 PMCID: PMC9890938 DOI: 10.1039/d2sc05438h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/29/2022] [Indexed: 01/15/2023] Open
Abstract
Many intracellular membraneless organelles (MLOs) appear to adapt a hierarchical multicompartment organization for efficient coordination of highly complex reaction networks. Recapitulating such an internal architecture in biomimetic platforms is, therefore, an important step to facilitate the functional understanding of MLOs and to enable the design of advanced microreactors. Herein, we present a modular bottom-up approach for building synthetic multiphasic condensates using a set of engineered multivalent polymer-oligopeptide hybrids. These hybrid constructs exhibit dynamic phase separation behaviour generating membraneless droplets with a subdivided interior featuring distinct chemical and physical properties, whereby a range of functional biomolecules can be spontaneously enriched and spatially segregated. The platform also attains separated confinement of transcription and translation reactions in proximal compartments, while allowing inter-compartment communication via a directional flow of reactants. With advanced structural and functional features attained, this system can be of great value as a MLO model and as a cell-free system for multiplex chemical biosynthesis.
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Affiliation(s)
- Fariza Zhorabek
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong SAR China
| | - Manisha Sandupama Abesekara
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong SAR China
| | - Jianhui Liu
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong SAR China
| | - Xin Dai
- Department of Chemistry, Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong SARChina
| | - Jinqing Huang
- Department of Chemistry, Hong Kong University of Science and TechnologyClear Water Bay, KowloonHong Kong SARChina
| | - Ying Chau
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology Clear Water Bay, Kowloon Hong Kong SAR China
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40
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Ma L, Fang X, Wang C. Peptide-based coacervates in therapeutic applications. Front Bioeng Biotechnol 2023; 10:1100365. [PMID: 36686257 PMCID: PMC9845597 DOI: 10.3389/fbioe.2022.1100365] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.
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Affiliation(s)
- Lilusi Ma
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaocui Fang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Xiaocui Fang, ; Chen Wang,
| | - Chen Wang
- CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China,University of Chinese Academy of Sciences, Beijing, China,*Correspondence: Xiaocui Fang, ; Chen Wang,
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41
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Alshareedah I, Banerjee PR. Measurement of Protein and Nucleic Acid Diffusion Coefficients Within Biomolecular Condensates Using In-Droplet Fluorescence Correlation Spectroscopy. Methods Mol Biol 2023; 2563:199-213. [PMID: 36227474 PMCID: PMC9884114 DOI: 10.1007/978-1-0716-2663-4_9] [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: 11/06/2022]
Abstract
Liquid-liquid phase separation of protein and RNA complexes into biomolecular condensates has emerged as a ubiquitous phenomenon in living systems. These protein-RNA condensates are thought to be involved in many biological functions in all forms of life. One of the most sought-after properties of these condensates is their dynamical properties, as they are a major determinant of condensate physiological function and disease processes. Measurement of the diffusion dynamics of individual components in a multicomponent biomolecular condensate is therefore routinely performed. Here, we outline the experimental procedure for performing in-droplet fluorescence correlation spectroscopy (FCS) measurements to extract the diffusion coefficient of individual molecules within a biomolecular condensate in vitro. Unlike more common experiments such as fluorescence recovery after photobleaching (FRAP), where data interpretation is not straightforward and strictly model dependent, FCS offers a robust and more accurate way to quantify biomolecular diffusion rates in the dense phase. The small observation volume allows FCS experiments to report on the local diffusion coefficient within a spatial resolution of <1 μm, making it ideal for probing spatial inhomogeneities within condensates as well as variable dynamics within subcompartments of multiphasic condensates.
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Affiliation(s)
| | - Priya R Banerjee
- Department of Physics, University at Buffalo SUNY, Buffalo, NY, USA.
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42
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Chen X, Chen EQ, Yang S. Multiphase Coacervation of Polyelectrolytes Driven by Asymmetry of Charged Sequence. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Er-Qiang Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Shuang Yang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
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43
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Latham AP, Zhang B. Molecular Determinants for the Layering and Coarsening of Biological Condensates. AGGREGATE (HOBOKEN, N.J.) 2022; 3:e306. [PMID: 37065433 PMCID: PMC10101022 DOI: 10.1002/agt2.306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Many membraneless organelles, or biological condensates, form through phase separation, and play key roles in signal sensing and transcriptional regulation. While the functional importance of these condensates has inspired many studies to characterize their stability and spatial organization, the underlying principles that dictate these emergent properties are still being uncovered. In this review, we examine recent work on biological condensates, especially multicomponent systems. We focus on connecting molecular factors such as binding energy, valency, and stoichiometry with the interfacial tension, explaining the nontrivial interior organization in many condensates. We further discuss mechanisms that arrest condensate coalescence by lowering the surface tension or introducing kinetic barriers to stabilize the multidroplet state.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94143
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139
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44
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Tom JA, Onuchic PL, Deniz AA. Short PolyA RNA Homopolymers Undergo Mg 2+-Mediated Kinetically Arrested Condensation. J Phys Chem B 2022; 126:9715-9725. [PMID: 36378781 PMCID: PMC9706566 DOI: 10.1021/acs.jpcb.2c05935] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RNA-RNA interactions have increasingly been recognized for their potential to shape the mesoscale properties of biomolecular condensates, influencing morphology, organization, and material state through networking interactions. While most studies have focused on networking via Watson-Crick base pairing interactions, previous work has suggested a potential for noncanonical RNA-RNA interactions to also give rise to condensation and alter overall material state. Here, we test the phase separation of short polyA RNA (polyrA) homopolymers. We discover and characterize the potential for short polyrA sequences to form RNA condensates at lower Mg2+ concentrations than previously observed, which appear as internally arrested droplets with slow polyrA diffusion despite continued fusion. Our work also reveals a negative cooperativity effect between the effects of Mg2+ and Na+ on polyrA condensation. Finally, we observe that polyrA sequences can act as promoters of phase separation in mixed sequences. These results demonstrate the potential for noncanonical interactions to act as networking stickers, leading to specific condensation properties inherent to polyrA composition and structure, with implications for the fundamental physical chemistry of the system and function of polyA RNA in biology.
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45
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Donau C, Späth F, Stasi M, Bergmann AM, Boekhoven J. Phase Transitions in Chemically Fueled, Multiphase Complex Coacervate Droplets. Angew Chem Int Ed Engl 2022; 61:e202211905. [PMID: 36067054 PMCID: PMC9828839 DOI: 10.1002/anie.202211905] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 01/12/2023]
Abstract
Membraneless organelles are droplets in the cytosol that are regulated by chemical reactions. Increasing studies suggest that they are internally organized. However, how these subcompartments are regulated remains elusive. Herein, we describe a complex coacervate-based model composed of two polyanions and a short peptide. With a chemical reaction cycle, we control the affinity of the peptide for the polyelectrolytes leading to distinct regimes inside the phase diagram. We study the transitions from one regime to another and identify new transitions that can only occur under kinetic control. Finally, we show that the chemical reaction cycle controls the liquidity of the droplets offering insights into how active processes inside cells play an important role in tuning the liquid state of membraneless organelles. Our work demonstrates that not only thermodynamic properties but also kinetics should be considered in the organization of multiple phases in droplets.
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Affiliation(s)
- Carsten Donau
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
| | - Fabian Späth
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
| | - Michele Stasi
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
| | - Alexander M. Bergmann
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
| | - Job Boekhoven
- Department of ChemistryTechnical University of MunichLichtenbergstrasse 485748GarchingGermany
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46
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Johnston AR, Pitch GM, Minckler ED, Mora IG, Balasco Serrão VH, Dailing EA, Ayzner AL. Excitonically Coupled Simple Coacervates via Liquid/Liquid Phase Separation. J Phys Chem Lett 2022; 13:10275-10281. [PMID: 36305559 PMCID: PMC9661528 DOI: 10.1021/acs.jpclett.2c02466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Viscoelastic liquid coacervate phases that are highly enriched in nonconjugated polyelectrolytes are currently the subject of highly active research from biological and soft-materials perspectives. However, formation of a liquid, electronically active coacervate has proved highly elusive, since extended π-electron interactions strongly favor the solid state. Herein we show that a conjugated polyelectrolyte can be rationally designed to undergo aqueous liquid/liquid phase separation to form a liquid coacervate phase. This result is significant both because it adds to the fundamental understanding of liquid/liquid phase separation but also because it opens intriguing applications in light harvesting and beyond. We find that the semiconducting coacervate is intrinsically excitonically coupled, allowing for long-range exciton diffusion in a strongly correlated, fluctuating environment. The emergent excitonic states are comprised of both excimers and H-aggregates.
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Affiliation(s)
- Anna R. Johnston
- Department
of Chemistry and Biochemistry, University
of California—Santa Cruz, Santa Cruz, California95064, United States
| | - Gregory M. Pitch
- Department
of Chemistry and Biochemistry, University
of California—Santa Cruz, Santa Cruz, California95064, United States
| | - Eris D. Minckler
- Department
of Chemistry and Biochemistry, University
of California—Santa Cruz, Santa Cruz, California95064, United States
| | - Ivette G. Mora
- Department
of Chemistry and Biochemistry, University
of California—Santa Cruz, Santa Cruz, California95064, United States
| | - Vitor H. Balasco Serrão
- Department
of Chemistry and Biochemistry, University
of California—Santa Cruz, Santa Cruz, California95064, United States
- Biomolecular
cryo-Electron Microscopy Facility, University
of California—Santa Cruz, Santa Cruz, California95064, United States
| | - Eric A. Dailing
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California94720, United States
| | - Alexander L. Ayzner
- Department
of Chemistry and Biochemistry, University
of California—Santa Cruz, Santa Cruz, California95064, United States
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47
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Kamal M, Tokmakjian L, Knox J, Mastrangelo P, Ji J, Cai H, Wojciechowski JW, Hughes MP, Takács K, Chu X, Pei J, Grolmusz V, Kotulska M, Forman-Kay JD, Roy PJ. A spatiotemporal reconstruction of the C. elegans pharyngeal cuticle reveals a structure rich in phase-separating proteins. eLife 2022; 11:e79396. [PMID: 36259463 PMCID: PMC9629831 DOI: 10.7554/elife.79396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
How the cuticles of the roughly 4.5 million species of ecdysozoan animals are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. Forty-eight percent of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families whose transcripts are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs, which are introduced for the first time here. All four families have sequence properties that drive phase separation and we demonstrate phase separation for one exemplar in vitro. This systematic analysis represents the first blueprint for cuticle construction and highlights the massive contribution that phase-separating materials make to the structure.
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Affiliation(s)
- Muntasir Kamal
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Levon Tokmakjian
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Pharmacology and Toxicology, University of TorontoTorontoCanada
| | - Jessica Knox
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Peter Mastrangelo
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Jingxiu Ji
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Hao Cai
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
| | - Jakub W Wojciechowski
- Wroclaw University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical EngineeringWroclawPoland
| | - Michael P Hughes
- Department of Cell and Molecular Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös UniversityBudapestHungary
| | - Xiaoquan Chu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Jianfeng Pei
- Department of Computer Science and Technology, Tsinghua UniversityBeijingChina
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös UniversityBudapestHungary
| | - Malgorzata Kotulska
- Wroclaw University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical EngineeringWroclawPoland
| | - Julie Deborah Forman-Kay
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Peter J Roy
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Pharmacology and Toxicology, University of TorontoTorontoCanada
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48
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Saha A, Yi R, Fahrenbach AC, Wang A, Jia TZ. A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry. Life (Basel) 2022; 12:1595. [PMID: 36295030 PMCID: PMC9604842 DOI: 10.3390/life12101595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022] Open
Abstract
The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.
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Affiliation(s)
- Arpita Saha
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Amity Institute of Applied Sciences, Amity University, Kolkata 700135, India
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Albert C. Fahrenbach
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Tony Z. Jia
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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49
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Slootbeek AD, van Haren MHI, Smokers IBA, Spruijt E. Growth, replication and division enable evolution of coacervate protocells. Chem Commun (Camb) 2022; 58:11183-11200. [PMID: 36128910 PMCID: PMC9536485 DOI: 10.1039/d2cc03541c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022]
Abstract
Living and proliferating cells undergo repeated cycles of growth, replication and division, all orchestrated by complex molecular networks. How a minimal cell cycle emerged and helped primitive cells to evolve remains one of the biggest mysteries in modern science, and is an active area of research in chemistry. Protocells are cell-like compartments that recapitulate features of living cells and may be seen as the chemical ancestors of modern life. While compartmentalization is not strictly required for primitive, open-ended evolution of self-replicating systems, it gives such systems a clear identity by setting the boundaries and it can help them overcome three major obstacles of dilution, parasitism and compatibility. Compartmentalization is therefore widely considered to be a central hallmark of primitive life, and various types of protocells are actively investigated, with the ultimate goal of developing a protocell capable of autonomous proliferation by mimicking the well-known cell cycle of growth, replication and division. We and others have found that coacervates are promising protocell candidates in which chemical building blocks required for life are naturally concentrated, and chemical reactions can be selectively enhanced or suppressed. This feature article provides an overview of how growth, replication and division can be realized with coacervates as protocells and what the bottlenecks are. Considerations are given for designing chemical networks in coacervates that can lead to sustained growth, selective replication and controlled division, in a way that they are linked together like in the cell cycle. Ultimately, such a system may undergo evolution by natural selection of certain phenotypes, leading to adaptation and the gain of new functions, and we end with a brief discussion of the opportunities for coacervates to facilitate this.
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Affiliation(s)
- Annemiek D Slootbeek
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Iris B A Smokers
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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50
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Zhou S, Cai X, Zhang Y, Chen Q, Yang X, Wang K, Jian L, Liu J. DNA nanotubes in coacervate microdroplets as biomimetic cytoskeletons modulate the liquid fluidic properties of protocells. J Mater Chem B 2022; 10:8322-8329. [PMID: 36168959 DOI: 10.1039/d2tb01451c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coacervate microdroplets, formed via liquid-liquid phase separation, have been proposed as a compartment model for the construction of artificial cells or organelles. However, these microsystems are very fragile and demonstrate liquid-like fluidity. Here, an artificial cytoskeleton based on DNA nanotubes was constructed in coacervate microdroplets to modulate the liquid fluidic properties of the microdroplets. The coacervate microdroplets were obtained from the association of oppositely charged polyelectrolytes through liquid-liquid phase separation, and DNA nanotubes were constructed by molecular tile self-assembly from six clip sequences. The DNA nanotubes were efficiently sequestered in the liquid coacervate microdroplets, and the rigid structure of the DNA nanotubes was capable of modulating the liquid fluidic properties of the coacervate protocell models, as indicated by coalescence imaging and atomic force microscopy analysis. Therefore, artificial cytoskeletons made from DNA nanotubes worked in modulating the liquid fluidic properties of coacervate microdroplets, in a manner akin to the cytoskeleton in the cell. DNA cytoskeletons have the potential to become an ideal platform with which how the liquid fluidic properties of cells are modulated by their cytoskeletons can be investigated, and the cell-sized coacervate microdroplets containing artificial cytoskeletons might be critical in developing a stable liquid-phase protocell model.
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Affiliation(s)
- Shaohong Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
| | - Xueer Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
| | - Yanwen Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
| | - Qiaoshu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
| | - Lixin Jian
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, P. R. China.
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