51
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Yewdall NA, André AA, Lu T, Spruijt E. Coacervates as models of membraneless organelles. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2020.101416] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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52
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Wang X, Zhang P, Tian L. Spatiotemporal organization of coacervate microdroplets. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2021.101420] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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53
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Jin Y, Kotler JLM, Wang S, Huang B, Halpin JC, Street TO. The ER Chaperones BiP and Grp94 Regulate the Formation of Insulin-Like Growth Factor 2 (IGF2) Oligomers. J Mol Biol 2021; 433:166963. [PMID: 33811917 DOI: 10.1016/j.jmb.2021.166963] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 01/05/2023]
Abstract
While cytosolic Hsp90 chaperones have been extensively studied, less is known about how the ER Hsp90 paralog Grp94 recognizes clients and influences client folding. Here, we examine how Grp94 and the ER Hsp70 paralog, BiP, influence the folding of insulin-like growth factor 2 (IGF2), an established client protein of Grp94. ProIGF2 is composed of a disulfide-bonded insulin-like hormone and a C-terminal E-peptide that has sequence characteristics of an intrinsically disordered region. BiP and Grp94 have a minimal influence on folding whereby both chaperones slow proIGF2 folding and do not substantially alter the disulfide-bonded folding intermediates, suggesting that BiP and Grp94 may have an additional influence unrelated to proIGF2 folding. Indeed, we made the unexpected discovery that the E-peptide region allows proIGF2 to form dynamic oligomers. ProIGF2 oligomers can transition from a dynamic state that is capable of exchanging monomers to an irreversibly aggregated state, providing a plausible role for BiP and Grp94 in regulating proIGF2 oligomerization. In contrast to the modest influence on folding, BiP and Grp94 have a stronger influence on proIGF2 oligomerization and these chaperones exert counteracting effects. BiP suppresses proIGF2 oligomerization while Grp94 can enhance proIGF2 oligomerization in a nucleotide-dependent manner. We propose that BiP and Grp94 regulate the assembly and dynamic behavior of proIGF2 oligomers, although the biological role of proIGF2 oligomerization is not yet known.
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Affiliation(s)
- Yi Jin
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Judy L M Kotler
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Shiyu Wang
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Bin Huang
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Jackson C Halpin
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | - Timothy O Street
- Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA.
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54
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Barbee MH, Wright ZM, Allen BP, Taylor HF, Patteson EF, Knight AS. Protein-Mimetic Self-Assembly with Synthetic Macromolecules. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02826] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Meredith H. Barbee
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Zoe M. Wright
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Benjamin P. Allen
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hailey F. Taylor
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Emily F. Patteson
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Abigail S. Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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55
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Jia TZ, Caudan M, Mamajanov I. Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution. Life (Basel) 2021; 11:154. [PMID: 33671365 PMCID: PMC7922636 DOI: 10.3390/life11020154] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Abstract
Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
- Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, WA 98154, USA
| | - Melina Caudan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
| | - Irena Mamajanov
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
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56
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Pavlovic M, Antonietti M, Zeininger L. Cascade communication in disordered networks of enzyme-loaded microdroplets. Chem Commun (Camb) 2021; 57:1631-1634. [PMID: 33459334 DOI: 10.1039/d0cc08310k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A network of aqueous emulsion droplets that exhibits programmed and directional chemical inter-droplet communication is described. A non-reciprocal transfer of substrates between enzyme-containing aqueous emulsion droplets is realized by (biochemically) induced osmolarity gradients and concomitant concentration gradients are used to direct a multistep enzymatic cascade reaction across multiple droplets.
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Affiliation(s)
- Marko Pavlovic
- Department of Colloid Chemistry, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476 Potsdam, Germany.
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57
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Karoui H, Seck MJ, Martin N. Self-programmed enzyme phase separation and multiphase coacervate droplet organization. Chem Sci 2021; 12:2794-2802. [PMID: 34164043 PMCID: PMC8179374 DOI: 10.1039/d0sc06418a] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 12/20/2022] Open
Abstract
Membraneless organelles are phase-separated droplets that are dynamically assembled and dissolved in response to biochemical reactions in cells. Complex coacervate droplets produced by associative liquid-liquid phase separation offer a promising approach to mimic such dynamic compartmentalization. Here, we present a model for membraneless organelles based on enzyme/polyelectrolyte complex coacervates able to induce their own condensation and dissolution. We show that glucose oxidase forms coacervate droplets with a cationic polysaccharide on a narrow pH range, so that enzyme-driven monotonic pH changes regulate the emergence, growth, decay and dissolution of the droplets depending on the substrate concentration. Significantly, we demonstrate that time-programmed coacervate assembly and dissolution can be achieved in a single-enzyme system. We further exploit this self-driven enzyme phase separation to produce multiphase droplets via dynamic polyion self-sorting in the presence of a secondary coacervate phase. Taken together, our results open perspectives for the realization of programmable synthetic membraneless organelles based on self-regulated enzyme/polyelectrolyte complex coacervation.
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Affiliation(s)
- Hedi Karoui
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031 115 Avenue du Dr Schweitzer 33600 Pessac France
| | - Marianne J Seck
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031 115 Avenue du Dr Schweitzer 33600 Pessac France
| | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR5031 115 Avenue du Dr Schweitzer 33600 Pessac France
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58
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Jia TZ, Wang PH, Niwa T, Mamajanov I. Connecting primitive phase separation to biotechnology, synthetic biology, and engineering. J Biosci 2021; 46:79. [PMID: 34373367 PMCID: PMC8342986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One aspect of the study of the origins of life focuses on how primitive chemistries assembled into the first cells on Earth and how these primitive cells evolved into modern cells. Membraneless droplets generated from liquid-liquid phase separation (LLPS) are one potential primitive cell-like compartment; current research in origins of life includes study of the structure, function, and evolution of such systems. However, the goal of primitive LLPS research is not simply curiosity or striving to understand one of life's biggest unanswered questions, but also the possibility to discover functions or structures useful for application in the modern day. Many applicational fields, including biotechnology, synthetic biology, and engineering, utilize similar phaseseparated structures to accomplish specific functions afforded by LLPS. Here, we briefly review LLPS applied to primitive compartment research and then present some examples of LLPS applied to biomolecule purification, drug delivery, artificial cell construction, waste and pollution management, and flavor encapsulation. Due to a significant focus on similar functions and structures, there appears to be much for origins of life researchers to learn from those working on LLPS in applicational fields, and vice versa, and we hope that such researchers can start meaningful cross-disciplinary collaborations in the future.
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Affiliation(s)
- Tony Z Jia
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan ,grid.482804.2Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, Washington 98154 USA
| | - Po-Hsiang Wang
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan ,grid.37589.300000 0004 0532 3167Graduate Institute of Environmental Engineering, National Central University, Zhongli Dist, 300 Zhongda Rd, Taoyuan City, 32001 Taiwan
| | - Tatsuya Niwa
- grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8503 Japan
| | - Irena Mamajanov
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan
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59
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Altenburg WJ, Yewdall NA, Vervoort DFM, van Stevendaal MHME, Mason AF, van Hest JCM. Programmed spatial organization of biomacromolecules into discrete, coacervate-based protocells. Nat Commun 2020; 11:6282. [PMID: 33293610 PMCID: PMC7722712 DOI: 10.1038/s41467-020-20124-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
The cell cytosol is crowded with high concentrations of many different biomacromolecules, which is difficult to mimic in bottom-up synthetic cell research and limits the functionality of existing protocellular platforms. There is thus a clear need for a general, biocompatible, and accessible tool to more accurately emulate this environment. Herein, we describe the development of a discrete, membrane-bound coacervate-based protocellular platform that utilizes the well-known binding motif between Ni2+-nitrilotriacetic acid and His-tagged proteins to exercise a high level of control over the loading of biologically relevant macromolecules. This platform can accrete proteins in a controlled, efficient, and benign manner, culminating in the enhancement of an encapsulated two-enzyme cascade and protease-mediated cargo secretion, highlighting the potency of this methodology. This versatile approach for programmed spatial organization of biologically relevant proteins expands the protocellular toolbox, and paves the way for the development of the next generation of complex yet well-regulated synthetic cells.
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Affiliation(s)
- Wiggert J Altenburg
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - N Amy Yewdall
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Daan F M Vervoort
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Marleen H M E van Stevendaal
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Alexander F Mason
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
| | - Jan C M van Hest
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, The Netherlands.
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60
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Deng J, Walther A. Programmable ATP-Fueled DNA Coacervates by Transient Liquid-Liquid Phase Separation. Chem 2020; 6:3329-3343. [DOI: 10.1016/j.chempr.2020.09.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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61
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Sakuta H, Fujita F, Hamada T, Hayashi M, Takiguchi K, Tsumoto K, Yoshikawa K. Self-Emergent Protocells Generated in an Aqueous Solution with Binary Macromolecules through Liquid-Liquid Phase Separation. Chembiochem 2020; 21:3323-3328. [PMID: 32667694 PMCID: PMC7754443 DOI: 10.1002/cbic.202000344] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/09/2020] [Indexed: 12/18/2022]
Abstract
Recently, liquid-liquid phase separation (LLPS) has attracted considerable attention among researchers in the life sciences as a plausible mechanism for the generation of microstructures inside cells. LLPS occurs through multiple nonspecific interactions and does not always require a lock-and-key interaction with a binary macromolecular solution. The remarkable features of LLPS include the non-uniform localization and concentration of solutes, resulting in the ability to isolate certain chemical systems and thereby parallelize multiple chemical reactions within the limited space of a living cell. We report that, by using the macromolecules, poly(ethylene glycol) (PEG) and dextran, that exhibit LLPS in an aqueous solution, cell-sized liposomes are spontaneously formed therein in the presence of phospholipids. In this system, LLPS is generated through the depletion effect of macromolecules. The results showed that cell-like microdroplets entrapping DNA wrapped by a phospholipid layer emerge in a self-organized manner.
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Affiliation(s)
- Hiroki Sakuta
- Graduate School of Life and Medical SciencesDoshisha UniversityTataramiyakodani 1–3Kyotanabe, Kyoto610-0394Japan
| | - Fumika Fujita
- Graduate School of Life and Medical SciencesDoshisha UniversityTataramiyakodani 1–3Kyotanabe, Kyoto610-0394Japan
| | - Tsutomu Hamada
- School of Materials ScienceJapan Advanced Institute of Science and TechnologyNomi, Ishikawa923-1292Japan
| | - Masahito Hayashi
- Department of Frontier BioscienceHosei UniversityKoganei, Tokyo184-8584Japan
| | - Kingo Takiguchi
- Graduate School of ScienceNagoya University Furo-cho, Chikusa-kuNagoya, Aichi464-8602Japan
| | - Kanta Tsumoto
- Division of Chemistry for Materials Graduate School of EngineeringMie UniversityKurimamachiya-cho 1577Tsu, Mie514-8507Japan
| | - Kenichi Yoshikawa
- Graduate School of Life and Medical SciencesDoshisha UniversityTataramiyakodani 1–3Kyotanabe, Kyoto610-0394Japan
- Center for Integrative Medicine and PhysicsInstitute for Advanced StudyKyoto UniversityKyoto606-8501Japan
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62
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Fraccia TP, Jia TZ. Liquid Crystal Coacervates Composed of Short Double-Stranded DNA and Cationic Peptides. ACS NANO 2020; 14:15071-15082. [PMID: 32852935 DOI: 10.1021/acsnano.0c05083] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Phase separation of nucleic acids and proteins is a ubiquitous phenomenon regulating subcellular compartment structure and function. While complex coacervation of flexible single-stranded nucleic acids is broadly investigated, coacervation of double-stranded DNA (dsDNA) is less studied because of its propensity to generate solid precipitates. Here, we reverse this perspective by showing that short dsDNA and poly-l-lysine coacervates can escape precipitation while displaying a surprisingly complex phase diagram, including the full set of liquid crystal (LC) mesophases observed to date in bulk dsDNA. Short dsDNA supramolecular aggregation and packing in the dense coacervate phase are the main parameters regulating the global LC-coacervate phase behavior. LC-coacervate structure was characterized upon variations in temperature and monovalent salt, DNA, and peptide concentrations, which allow continuous reversible transitions between all accessible phases. A deeper understanding of LC-coacervates can gain insights to decipher structures and phase transition mechanisms within biomolecular condensates, to design stimuli-responsive multiphase synthetic compartments with different degrees of order and to exploit self-assembly driven cooperative prebiotic evolution of nucleic acids and peptides.
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Affiliation(s)
- Tommaso P Fraccia
- Institut Pierre-Gilles de Gennes, Chimie Biologie Innovation, ESPCI Paris, CNRS, PSL Research University, 75005 Paris, France
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, 1001 Fourth Ave., Suite 3201, Seattle, Washington 98154, United States
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63
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Das S, Lin YH, Vernon RM, Forman-Kay JD, Chan HS. Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins. Proc Natl Acad Sci U S A 2020; 117:28795-28805. [PMID: 33139563 PMCID: PMC7682375 DOI: 10.1073/pnas.2008122117] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS) of proteins, we conducted multiple-chain simulations of the N-terminal intrinsically disordered region (IDR) of DEAD-box helicase Ddx4, as a test case, to assess roles of electrostatic, hydrophobic, cation-π, and aromatic interactions in amino acid sequence-dependent LLPS. We evaluated three different residue-residue interaction schemes with a shared electrostatic potential. Neither a common hydrophobicity scheme nor one augmented with arginine/lysine-aromatic cation-π interactions consistently accounted for available experimental LLPS data on the wild-type, a charge-scrambled, a phenylalanine-to-alanine (FtoA), and an arginine-to-lysine (RtoK) mutant of Ddx4 IDR. In contrast, interactions based on contact statistics among folded globular protein structures reproduce the overall experimental trend, including that the RtoK mutant has a much diminished LLPS propensity. Consistency between simulation and experiment was also found for RtoK mutants of P-granule protein LAF-1, underscoring that, to a degree, important LLPS-driving π-related interactions are embodied in classical statistical potentials. Further elucidation is necessary, however, especially of phenylalanine's role in condensate assembly because experiments on FtoA and tyrosine-to-phenylalanine mutants suggest that LLPS-driving phenylalanine interactions are significantly weaker than posited by common statistical potentials. Protein-protein electrostatic interactions are modulated by relative permittivity, which in general depends on aqueous protein concentration. Analytical theory suggests that this dependence entails enhanced interprotein interactions in the condensed phase but more favorable protein-solvent interactions in the dilute phase. The opposing trends lead to only a modest overall impact on LLPS.
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Affiliation(s)
- Suman Das
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Robert M Vernon
- Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Julie D Forman-Kay
- Molecular Medicine, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada;
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64
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Samanta A, Sabatino V, Ward TR, Walther A. Functional and morphological adaptation in DNA protocells via signal processing prompted by artificial metalloenzymes. NATURE NANOTECHNOLOGY 2020; 15:914-921. [PMID: 32895521 PMCID: PMC7610402 DOI: 10.1038/s41565-020-0761-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/03/2020] [Indexed: 05/21/2023]
Abstract
For life to emerge, the confinement of catalytic reactions within protocellular environments has been proposed to be a decisive aspect to regulate chemical activity in space1. Today, cells and organisms adapt to signals2-6 by processing them through reaction networks that ultimately provide downstream functional responses and structural morphogenesis7,8. Re-enacting such signal processing in de novo-designed protocells is a profound challenge, but of high importance for understanding the design of adaptive systems with life-like traits. We report on engineered all-DNA protocells9 harbouring an artificial metalloenzyme10 whose olefin metathesis activity leads to downstream morphogenetic protocellular responses with varying levels of complexity. The artificial metalloenzyme catalyses the uncaging of a pro-fluorescent signal molecule that generates a self-reporting fluorescent metabolite designed to weaken DNA duplex interactions. This leads to pronounced growth, intraparticular functional adaptation in the presence of a fluorescent DNA mechanosensor11 or interparticle protocell fusion. Such processes mimic chemically transduced processes found in cell adaptation and cell-to-cell adhesion. Our concept showcases new opportunities to study life-like behaviour via abiotic bioorthogonal chemical and mechanical transformations in synthetic protocells. Furthermore, it reveals a strategy for inducing complex behaviour in adaptive and communicating soft-matter microsystems, and it illustrates how dynamic properties can be upregulated and sustained in micro-compartmentalized media.
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Affiliation(s)
- Avik Samanta
- A3BMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Freiburg, Germany
- DFG Cluster of Excellence "Living, Adaptive and Energy-Autonomous Materials Systems" (livMatS)@FIT, Freiburg, Germany
- Freiburg Materials Research Center, University of Freiburg, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg, Germany
| | - Valerio Sabatino
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, Basel, Switzerland.
| | - Andreas Walther
- A3BMS Lab, Institute for Macromolecular Chemistry, University of Freiburg, Freiburg, Germany.
- DFG Cluster of Excellence "Living, Adaptive and Energy-Autonomous Materials Systems" (livMatS)@FIT, Freiburg, Germany.
- Freiburg Materials Research Center, University of Freiburg, Freiburg, Germany.
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Freiburg, Germany.
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65
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Jeon BJ, Nguyen DT, Saleh OA. Sequence-Controlled Adhesion and Microemulsification in a Two-Phase System of DNA Liquid Droplets. J Phys Chem B 2020; 124:8888-8895. [PMID: 32960601 DOI: 10.1021/acs.jpcb.0c06911] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Membrane-less organelles, the liquid droplets formed via liquid-liquid phase separation (LLPS) of biomolecules in cells, act to organize intracellular components into multiple compartments. As a model for this process, and as a potential vehicle for in vitro exploitation of its properties, we explore here a synthetic multiphase LLPS system consisting of a mixture of self-assembled DNA particles. The particles, termed "DNA nanostars" (NSs), consist of four double-stranded DNA arms that each terminate in a single-stranded overhang. NSs condense into droplets due to overhang hybridization. Using two types of NSs with orthogonal overhangs enables the creation of two types of immiscible DNA droplets. Adhesion between the droplets can be tuned by the addition of "cross-linker NSs" that have two overhang sequences of each type. We find that increasing the amount of the cross-linker NSs decreases the droplet/droplet surface tension until a microemulsion transition occurs. Controlled droplet adhesion can also be achieved, without cross-linkers, using overhangs that can weakly hybridize. Finally, we show that solutes can be specifically targeted to the DNA phases by labeling them with appropriate sticky-ends. Overall, our findings demonstrate the ability to create a multiphase LLPS system, and to control its mesoscale configuration, via sequence design of the component molecules.
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Affiliation(s)
- Byoung-Jin Jeon
- Materials Department, University of California, Santa Barbara, California 93110, United States
| | - Dan T Nguyen
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93110, United States
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, California 93110, United States.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93110, United States
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66
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Linsenmeier M, Kopp MRG, Stavrakis S, de Mello A, Arosio P. Analysis of biomolecular condensates and protein phase separation with microfluidic technology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118823. [PMID: 32800925 DOI: 10.1016/j.bbamcr.2020.118823] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022]
Abstract
An increasing body of evidence shows that membraneless organelles are key components in cellular organization. These observations open a variety of outstanding questions about the physico-chemical rules underlying their assembly, disassembly and functions. Some molecular determinants of biomolecular condensates are challenging to probe and understand in complex in vivo systems. Minimalistic in vitro reconstitution approaches can fill this gap, mimicking key biological features, while maintaining sufficient simplicity to enable the analysis of fundamental aspects of biomolecular condensates. In this context, microfluidic technologies are highly attractive tools for the analysis of biomolecular phase transitions. In addition to enabling high-throughput measurements on small sample volumes, microfluidic tools provide for exquisite control of self-assembly in both time and space, leading to accurate quantitative analysis of biomolecular phase transitions. Here, with a specific focus on droplet-based microfluidics, we describe the advantages of microfluidic technology for the analysis of several aspects of phase separation. These include phase diagrams, dynamics of assembly and disassembly, rheological and surface properties, exchange of materials with the surrounding environment and the coupling between compartmentalization and biochemical reactions. We illustrate these concepts with selected examples, ranging from simple solutions of individual proteins to more complex mixtures of proteins and RNA, which represent synthetic models of biological membraneless organelles. Finally, we discuss how this technology may impact the bottom-up fabrication of synthetic artificial cells and for the development of synthetic protein materials in biotechnology.
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Affiliation(s)
- Miriam Linsenmeier
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Marie R G Kopp
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Stavros Stavrakis
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Andrew de Mello
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich 8093, Switzerland.
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67
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Ott EJE, Freedman MA. Inhibition of Phase Separation in Aerosolized Water-Soluble Polymer–Polymer Nanoparticles at Small Sizes and the Effects of Molecular Weight. J Phys Chem B 2020; 124:7518-7523. [DOI: 10.1021/acs.jpcb.0c06535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emily-Jean E. Ott
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Miriam Arak Freedman
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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68
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Abstract
Coacervate micro-droplets produced by liquid-liquid phase separation are increasingly used to emulate the dynamical organization of membraneless organelles found in living cells. Designing synthetic coacervates able to be formed and disassembled with improved spatiotemporal control is still challenging. In this chapter, we describe the design of photoswitchable coacervate droplets produced by phase separation of short double stranded DNA in the presence of an azobenzene cation. The droplets can be reversibly dissolved with light, which provides a new approach for the spatiotemporal regulation of coacervation. Significantly, the dynamics of light-actuated droplet formation and dissolution correlates with the capture and release of guest solutes. The reported system can find applications for the dynamic photocontrol of biomolecule compartmentalization, paving the way to the light-activated regulation of signaling pathways in artificial membraneless organelles.
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69
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Rizvi A, Patel U, Ianiro A, Hurst PJ, Merham JG, Patterson JP. Nonionic Block Copolymer Coacervates. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00979] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Aoon Rizvi
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Urja Patel
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Alessandro Ianiro
- Adolphe Merkle Institute, University of Fribourg, Fribourg 1700, Switzerland
| | - Paul J. Hurst
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Jovany G. Merham
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
| | - Joseph P. Patterson
- Department of Chemistry, University of California, Irvine, Irvine, California 92697-2025, United States
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70
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Enzymatic degradation of liquid droplets of DNA is modulated near the phase boundary. Proc Natl Acad Sci U S A 2020; 117:16160-16166. [PMID: 32601183 DOI: 10.1073/pnas.2001654117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Biomolecules can undergo liquid-liquid phase separation (LLPS), forming dense droplets that are increasingly understood to be important for cellular function. Analogous systems are studied as early-life compartmentalization mechanisms, for applications as protocells, or as drug-delivery vehicles. In many of these situations, interactions between the droplet and enzymatic solutes are important to achieve certain functions. To explore this, we carried out experiments in which a model LLPS system, formed from DNA "nanostar" particles, interacted with a DNA-cleaving restriction enzyme, SmaI, whose activity degraded the droplets, causing them to shrink with time. By controlling adhesion of the DNA droplet to a glass surface, we were able to carry out time-resolved imaging of this "active dissolution" process. We found that the scaling properties of droplet shrinking were sensitive to the proximity to the dissolution ("boiling") temperature of the dense liquid: For systems far from the boiling point, enzymes acted only on the droplet surface, while systems poised near the boiling point permitted enzyme penetration. This was corroborated by the observation of enzyme-induced vacuole-formation ("bubbling") events, which can only occur through enzyme internalization, and which occurred only in systems poised near the boiling point. Overall, our results demonstrate a mechanism through which the phase stability of a liquid affects its enzymatic degradation through modulation of enzyme transport properties.
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71
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Zhao H, Ibrahimova V, Garanger E, Lecommandoux S. Dynamic Spatial Formation and Distribution of Intrinsically Disordered Protein Droplets in Macromolecularly Crowded Protocells. Angew Chem Int Ed Engl 2020; 59:11028-11036. [PMID: 32207864 DOI: 10.1002/anie.202001868] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/23/2020] [Indexed: 11/09/2022]
Abstract
Elastin-like polypeptides (ELPs) have been proposed as a simple model of intrinsically disordered proteins (IDPs) which can form membraneless organelles by liquid-liquid phase separation (LLPS) in cells. Herein, the behavior of fluorescently labeled ELP is studied in cytomimetic aqueous two-phase system (ATPS) encapsulated protocells that are formed using microfluidics, which enabled confinement, changes in temperature, and statistical analysis. The spatial organization of ELP could be observed in the ATPS. Furthermore, changes in temperature triggered the dynamic formation and distribution of ELP-rich droplets within the ATPS, resulting from changes in conformation. Proteins were encapsulated along with ELP in the synthetic protocells and distinct partitioning properties of these proteins and ELP in the ATPS were observed. Therefore, the ability of ELP to coacervate with temperature can be maintained inside a cell-mimicking system.
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Affiliation(s)
- Hang Zhao
- Univ. Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600, Pessac, France
| | - Vusala Ibrahimova
- Univ. Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600, Pessac, France
| | - Elisabeth Garanger
- Univ. Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, 33600, Pessac, France
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72
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Zhao H, Ibrahimova V, Garanger E, Lecommandoux S. Dynamic Spatial Formation and Distribution of Intrinsically Disordered Protein Droplets in Macromolecularly Crowded Protocells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001868] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hang Zhao
- Univ. BordeauxCNRSBordeaux INP, LCPO, UMR 5629 33600 Pessac France
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73
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Küffner AM, Prodan M, Zuccarini R, Capasso Palmiero U, Faltova L, Arosio P. Acceleration of an Enzymatic Reaction in Liquid Phase Separated Compartments Based on Intrinsically Disordered Protein Domains. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andreas M. Küffner
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Marc Prodan
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Remo Zuccarini
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences Institute for Chemical and Bioengineering ETH Zürich, Zürich, 8093 (Switzerland)
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74
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Moreau NG, Martin N, Gobbo P, Tang TYD, Mann S. Spontaneous membrane-less multi-compartmentalization via aqueous two-phase separation in complex coacervate micro-droplets. Chem Commun (Camb) 2020; 56:12717-12720. [DOI: 10.1039/d0cc05399f] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Multiphase coacervate droplets produced by internalised aqueous two-phase separation are used for the spatially dependent chemical transfer of sugar molecules.
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Affiliation(s)
- Nicolette G. Moreau
- Centre for Protolife Research and Centre for Organized Matter Chemistry
- School of Chemistry
- University of Bristol
- Bristol BS8 1TS
- UK
| | - Nicolas Martin
- Univ. Bordeaux
- CNRS
- Centre de Recherche Paul Pascal
- UMR5031
- 33600 Pessac
| | - Pierangelo Gobbo
- Centre for Protolife Research and Centre for Organized Matter Chemistry
- School of Chemistry
- University of Bristol
- Bristol BS8 1TS
- UK
| | - T.-Y. Dora Tang
- Max Planck Institute of Molecular Cell and Genetics
- 01307 Dresden
- Germany
| | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry
- School of Chemistry
- University of Bristol
- Bristol BS8 1TS
- UK
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75
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Mountain GA, Keating CD. Formation of Multiphase Complex Coacervates and Partitioning of Biomolecules within them. Biomacromolecules 2019; 21:630-640. [PMID: 31743027 DOI: 10.1021/acs.biomac.9b01354] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biological systems employ liquid-liquid phase separation to localize macromolecules and processes. The properties of intracellular condensates that allow for multiple, distinct liquid compartments and the impact of their coexistence on phase composition and solute partitioning are not well understood. Here, we generate two and three coexisting macromolecule-rich liquid compartments by complex coacervation based on ion pairing in mixtures that contain two or three polyanions together with one, two, or three polycations. While in some systems polyelectrolyte order-of-addition was important to achieve coexisting liquid phases, for others it was not, suggesting that the observed multiphase droplet morphologies are energetically favorable. Polyelectrolytes were distributed across all coacervate phases, depending on the relative interactions between them, which in turn impacted partitioning of oligonucleotide and oligopeptide solutes. These results show the ease of generating multiphase coacervates and the ability to tune their partitioning properties via the polyelectrolyte sharing inherent to multiphase complex coacervate systems.
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Affiliation(s)
- Gregory A Mountain
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Christine D Keating
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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76
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Nguyen DT, Jeon BJ, Abraham GR, Saleh OA. Length-Dependence and Spatial Structure of DNA Partitioning into a DNA Liquid. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14849-14854. [PMID: 31638820 DOI: 10.1021/acs.langmuir.9b02098] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cells can spatially and temporally control biochemistry using liquid-liquid phase separation to form membrane-less organelles. Synthetic biomolecular liquids offer a means to study the mechanisms of this process, as well as offering a route to the creation of functional biomimetic materials. With these goals in mind, we here examine the partitioning of long double-stranded DNA linkers into a liquid composed of small DNA particles ("nanostars") whose phase separation is driven by base pairing. We find that linker partitioning is length-dependent because of a confinement penalty of inserting long strands within the liquid's characteristic mesh size. We quantify this entropic-confinement effect using a simple partitioning theory and show that its magnitude is consistent with classic Odijk pictures of confined worm-like chains. Linker partitioning can also lead to inhomogeneous structures: long linkers excluded from the liquid interior tend to preferentially accumulate on the surface of liquid droplets (i.e., acting as surfactants), while linkers forced at high concentrations into the liquid undergo a secondary phase separation, forming metastable droplet-in-droplet structures. Altogether, our work demonstrates the ability to rationally engineer the composition and structure of a model biomolecular liquid.
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