101
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Etibor TA, Yamauchi Y, Amorim MJ. Liquid Biomolecular Condensates and Viral Lifecycles: Review and Perspectives. Viruses 2021; 13:366. [PMID: 33669141 PMCID: PMC7996568 DOI: 10.3390/v13030366] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/16/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Viruses are highly dependent on the host they infect. Their dependence triggers processes of virus-host co-adaptation, enabling viruses to explore host resources whilst escaping immunity. Scientists have tackled viral-host interplay at differing levels of complexity-in individual hosts, organs, tissues and cells-and seminal studies advanced our understanding about viral lifecycles, intra- or inter-species transmission, and means to control infections. Recently, it emerged as important to address the physical properties of the materials in biological systems; membrane-bound organelles are only one of many ways to separate molecules from the cellular milieu. By achieving a type of compartmentalization lacking membranes known as biomolecular condensates, biological systems developed alternative mechanisms of controlling reactions. The identification that many biological condensates display liquid properties led to the proposal that liquid-liquid phase separation (LLPS) drives their formation. The concept of LLPS is a paradigm shift in cellular structure and organization. There is an unprecedented momentum to revisit long-standing questions in virology and to explore novel antiviral strategies. In the first part of this review, we focus on the state-of-the-art about biomolecular condensates. In the second part, we capture what is known about RNA virus-phase biology and discuss future perspectives of this emerging field in virology.
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Affiliation(s)
- Temitope Akhigbe Etibor
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TL, UK;
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
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102
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Hazra MK, Levy Y. Biophysics of Phase Separation of Disordered Proteins Is Governed by Balance between Short- And Long-Range Interactions. J Phys Chem B 2021; 125:2202-2211. [PMID: 33629837 PMCID: PMC8028311 DOI: 10.1021/acs.jpcb.0c09975] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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Intrinsically disordered proteins
play a crucial role in cellular
phase separation, yet the diverse molecular forces driving phase separation
are not fully understood. It is of utmost importance to understand
how peptide sequence, and particularly the balance between the peptides’
short- and long-range interactions with other peptides, may affect
the stability, structure, and dynamics of liquid–liquid phase
separation in protein condensates. Here, using coarse-grained molecular
dynamics simulations, we studied the liquid properties of the condensate
in a series of polymers in which the ratio of short-range dispersion
interactions to long-range electrostatic interactions varied. As the
fraction of mutations that participate in short-range interactions
increases at the expense of long-range electrostatic interactions,
a significant decrease in the critical temperature of phase separation
is observed. Nevertheless, sequences with a high fraction of short-range
interactions exhibit stabilization, which suggests compensation for
the loss of long-range electrostatic interactions. Decreased condensate
stability is coupled with decreased translational diffusion of the
polymers in the condensate, which may result in the loss of liquid
characteristics in the presence of a high fraction of uncharged residues.
The effect of exchanging long-range electrostatic interactions for
short-range interactions can be explained by the kinetics of breaking
intermolecular contacts with neighboring polymers and the kinetics
of intramolecular fluctuations. While both time scales are coupled
and increase as electrostatic interactions are lost, for sequences
that are dominated by short-range interactions, the kinetics of intermolecular
contact breakage significantly slows down. Our study supports the
contention that different types of interactions can maintain protein
condensates, however, long-range electrostatic interactions enhance
its liquid-like behavior.
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Affiliation(s)
- Milan Kumar Hazra
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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103
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Levengood JD, Peterson J, Tolbert BS, Roche J. Thermodynamic stability of hnRNP A1 low complexity domain revealed by high-pressure NMR. Proteins 2021; 89:781-791. [PMID: 33550645 DOI: 10.1002/prot.26058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/21/2020] [Accepted: 01/31/2021] [Indexed: 11/09/2022]
Abstract
We have investigated the pressure- and temperature-induced conformational changes associated with the low complexity domain of hnRNP A1, an RNA-binding protein able to phase separate in response to cellular stress. Solution NMR spectra of the hnRNP A1 low-complexity domain fused with protein-G B1 domain were collected from 1 to 2500 bar and from 268 to 290 K. While the GB1 domain shows the typical pressure-induced and cold temperature-induced unfolding expected for small globular domains, the low-complexity domain of hnRNP A1 exhibits unusual pressure and temperature dependences. We observed that the low-complexity domain is pressure sensitive, undergoing a major conformational transition within the prescribed pressure range. Remarkably, this transition has the inverse temperature dependence of a typical folding-unfolding transition. Our results suggest the presence of a low-lying extended and fully solvated state(s) of the low-complexity domain that may play a role in phase separation. This study highlights the exquisite sensitivity of solution NMR spectroscopy to observe subtle conformational changes and illustrates how pressure perturbation can be used to determine the properties of metastable conformational ensembles.
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Affiliation(s)
- Jeffrey D Levengood
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jake Peterson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | - Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
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104
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Kaur T, Raju M, Alshareedah I, Davis RB, Potoyan DA, Banerjee PR. Sequence-encoded and composition-dependent protein-RNA interactions control multiphasic condensate morphologies. Nat Commun 2021; 12:872. [PMID: 33558506 PMCID: PMC7870978 DOI: 10.1038/s41467-021-21089-4] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Multivalent protein-protein and protein-RNA interactions are the drivers of biological phase separation. Biomolecular condensates typically contain a dense network of multiple proteins and RNAs, and their competing molecular interactions play key roles in regulating the condensate composition and structure. Employing a ternary system comprising of a prion-like polypeptide (PLP), arginine-rich polypeptide (RRP), and RNA, we show that competition between the PLP and RNA for a single shared partner, the RRP, leads to RNA-induced demixing of PLP-RRP condensates into stable coexisting phases-homotypic PLP condensates and heterotypic RRP-RNA condensates. The morphology of these biphasic condensates (non-engulfing/ partial engulfing/ complete engulfing) is determined by the RNA-to-RRP stoichiometry and the hierarchy of intermolecular interactions, providing a glimpse of the broad range of multiphasic patterns that are accessible to these condensates. Our findings provide a minimal set of physical rules that govern the composition and spatial organization of multicomponent and multiphasic biomolecular condensates.
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Affiliation(s)
- Taranpreet Kaur
- Department of Physics, University at Buffalo, Buffalo, NY, USA
| | | | | | - Richoo B Davis
- Department of Physics, University at Buffalo, Buffalo, NY, USA
| | - Davit A Potoyan
- Department of Chemistry, Iowa State University, Ames, IA, USA.
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105
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Hastings RL, Boeynaems S. Designer Condensates: A Toolkit for the Biomolecular Architect. J Mol Biol 2021; 433:166837. [PMID: 33539874 DOI: 10.1016/j.jmb.2021.166837] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/06/2021] [Accepted: 01/16/2021] [Indexed: 12/19/2022]
Abstract
Protein phase separation has emerged as a novel paradigm to explain the biogenesis of membraneless organelles and other so-called biomolecular condensates. While the implication of this physical phenomenon within cell biology is providing us with novel ways for understanding how cells compartmentalize biochemical reactions and encode function in such liquid-like assemblies, the newfound appreciation of this process also provides immense opportunities for designing and sculpting biological matter. Here, we propose that understanding the cell's instruction manual of phase separation will enable bioengineers to begin creating novel functionalized biological materials and unprecedented tools for synthetic biology. We present FASE as the synthesis of the existing sticker-spacer framework, which explains the physical driving forces underlying phase separation, with quintessential principles of Scandinavian design. FASE serves both as a designer condensates catalogue and construction manual for the aspiring (membraneless) biomolecular architect. Our approach aims to inspire a new generation of bioengineers to rethink phase separation as an opportunity for creating reactive biomaterials with unconventional properties and to encode novel biological function in living systems. Although still in its infancy, several studies highlight how designer condensates have immediate and widespread potential applications in industry and medicine.
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Affiliation(s)
- Renee L Hastings
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
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106
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Zhou HX. Viscoelasticity of biomolecular condensates conforms to the Jeffreys model. J Chem Phys 2021; 154:041103. [PMID: 33514117 PMCID: PMC7847312 DOI: 10.1063/5.0038916] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/08/2021] [Indexed: 12/20/2022] Open
Abstract
Biomolecular condensates, largely by virtue of their material properties, are revolutionizing biology, and yet, the physical understanding of these properties is lagging. Here, I show that the viscoelasticity of condensates can be captured by a simple model, comprising a component where shear relaxation is an exponential function (with time constant τ1) and a component with nearly instantaneous shear relaxation (time constant τ0 → 0). Modulation of intermolecular interactions, e.g., by adding salt, can disparately affect the two components such that the τ1 component may dominate at low salt, whereas the τ0 component may dominate at high salt. Condensates have a tendency to fuse, with the dynamics accelerated by interfacial tension and impeded by viscosity. For fast-fusion condensates, shear relaxation on the τ1 timescale may become rate-limiting such that the fusion speed is no longer in direction proportion to the interfacial tension. These insights help narrow the gap in understanding between the biology and physics of biomolecular condensates.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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107
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Regy RM, Dignon GL, Zheng W, Kim YC, Mittal J. Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations. Nucleic Acids Res 2020; 48:12593-12603. [PMID: 33264400 PMCID: PMC7736803 DOI: 10.1093/nar/gkaa1099] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/21/2020] [Accepted: 10/27/2020] [Indexed: 12/22/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid-liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA and other polynucleotides play a key role in modulating protein phase separation. There is currently a dearth of modelling techniques which allow one to delve deeper into how polynucleotides play the role of a modulator/promoter of LLPS in cells using computational methods. Here, we present a coarse-grained polynucleotide model developed to fill this gap, which together with our recently developed HPS model for protein LLPS, allows us to capture the factors driving protein-polynucleotide phase separation. We explore the capabilities of the modelling framework with the LAF-1 RGG system which has been well studied in experiments and also with the HPS model previously. Further taking advantage of the fact that the HPS model maintains sequence specificity we explore the role of charge patterning on controlling polynucleotide incorporation into condensates. With increased charge patterning we observe formation of structured or patterned condensates which suggests the possible roles of polynucleotides in not only shifting the phase boundaries but also introducing microscopic organization in MLOs.
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Affiliation(s)
- Roshan Mammen Regy
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
| | - Young C Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC 20375, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
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108
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Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments. Nat Commun 2020; 11:5949. [PMID: 33230101 PMCID: PMC7683531 DOI: 10.1038/s41467-020-19775-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/27/2020] [Indexed: 12/02/2022] Open
Abstract
Multivalent polyions can undergo complex coacervation, producing membraneless compartments that accumulate ribozymes and enhance catalysis, and offering a mechanism for functional prebiotic compartmentalization in the origins of life. Here, we evaluate the impact of lower, more prebiotically-relevant, polyion multivalency on the functional performance of coacervates as compartments. Positively and negatively charged homopeptides with 1–100 residues and adenosine mono-, di-, and triphosphate nucleotides are used as model polyions. Polycation/polyanion pairs are tested for coacervation, and resulting membraneless compartments are analyzed for salt resistance, ability to provide a distinct internal microenvironment (apparent local pH, RNA partitioning), and effect on RNA structure formation. We find that coacervates formed by phase separation of the shorter polyions more effectively generated distinct pH microenvironments, accumulated RNA, and preserved duplexes than those formed by longer polyions. Hence, coacervates formed by reduced multivalency polyions are not only viable as functional compartments for prebiotic chemistries, they can outperform higher molecular weight analogues. Short cationic peptides and nucleotides can form complex coacervates, but the influence of reduced multivalency on coacervate functionality was not investigated. Here, the authors report that coacervates formed from short polyions generate distinct pH microenvironments, accumulate RNA and preserve nucleic acid duplexes more efficiently than their longer counterparts.
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109
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Ghosh A, Zhou HX. Determinants for Fusion Speed of Biomolecular Droplets. Angew Chem Int Ed Engl 2020; 59:20837-20840. [PMID: 32767698 PMCID: PMC7877791 DOI: 10.1002/anie.202006711] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/15/2020] [Indexed: 01/12/2023]
Abstract
Biomolecular droplets formed through phase separation have a tendency to fuse. The speed with which fusion occurs is a direct indicator of condensate liquidity, which is key to both cellular functions and diseases. Using a dual-trap optical tweezers setup, we found the fusion speeds of four types of droplets to differ by two orders of magnitude. The order of fusion speed correlates with the fluorescence of thioflavin T, which in turn reflects the macromolecular packing density inside droplets. Unstructured protein or polymer chains pack loosely and readily rearrange, leading to fast fusion. In contrast, structured protein domains pack more closely and have to break extensive contacts before rearrangement, corresponding to slower fusion. This molecular interpretation for disparate fusion speeds provides mechanistic insight into the assembly and aging of biomolecular droplets.
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Affiliation(s)
- Archishman Ghosh
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607 (USA)
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607 (USA)
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607 (USA)
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110
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Affiliation(s)
- Archishman Ghosh
- Department of Chemistry University of Illinois at Chicago Chicago IL 60607 USA
| | - Huan‐Xiang Zhou
- Department of Chemistry University of Illinois at Chicago Chicago IL 60607 USA
- Department of Physics University of Illinois at Chicago Chicago IL 60607 USA
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111
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Babinchak WM, Dumm BK, Venus S, Boyko S, Putnam AA, Jankowsky E, Surewicz WK. Small molecules as potent biphasic modulators of protein liquid-liquid phase separation. Nat Commun 2020; 11:5574. [PMID: 33149109 PMCID: PMC7643064 DOI: 10.1038/s41467-020-19211-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of proteins that leads to formation of membrane-less organelles is critical to many biochemical processes in the cell. However, dysregulated LLPS can also facilitate aberrant phase transitions and lead to protein aggregation and disease. Accordingly, there is great interest in identifying small molecules that modulate LLPS. Here, we demonstrate that 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) and similar compounds are potent biphasic modulators of protein LLPS. Depending on context, bis-ANS can both induce LLPS de novo as well as prevent formation of homotypic liquid droplets. Our study also reveals the mechanisms by which bis-ANS and related compounds modulate LLPS and identify key chemical features of small molecules required for this activity. These findings may provide a foundation for the rational design of small molecule modulators of LLPS with therapeutic value.
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Affiliation(s)
- W Michael Babinchak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Benjamin K Dumm
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science & Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - Solomiia Boyko
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA
| | - Andrea A Putnam
- Center for RNA Science & Therapeutics, Case Western Reserve University, Cleveland, OH, USA
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eckhard Jankowsky
- Center for RNA Science & Therapeutics, Case Western Reserve University, Cleveland, OH, USA
| | - Witold K Surewicz
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, USA.
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112
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Dao TP, Castañeda CA. Ubiquitin-Modulated Phase Separation of Shuttle Proteins: Does Condensate Formation Promote Protein Degradation? Bioessays 2020; 42:e2000036. [PMID: 32881044 PMCID: PMC7737676 DOI: 10.1002/bies.202000036] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/29/2020] [Indexed: 12/14/2022]
Abstract
Liquid-liquid phase separation (LLPS) has recently emerged as a possible mechanism that enables ubiquitin-binding shuttle proteins to facilitate the degradation of ubiquitinated substrates via distinct protein quality control (PQC) pathways. Shuttle protein LLPS is modulated by multivalent interactions among their various domains as well as heterotypic interactions with polyubiquitin chains. Here, the properties of three different shuttle proteins (hHR23B, p62, and UBQLN2) are closely examined, unifying principles for the molecular determinants of their LLPS are identified, and how LLPS is connected to their functions is discussed. Evidence supporting LLPS of other shuttle proteins is also found. In this review, it is proposed that shuttle protein LLPS leads to spatiotemporal regulation of PQC activities by mediating the recruitment of PQC machinery (including proteasomes or autophagic components) to biomolecular condensates, assembly/disassembly of condensates, selective enrichment of client proteins, and extraction of ubiquitinated proteins from condensates in cells.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY, 13244, USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY, 13244, USA
- Bioinspired Institute, Syracuse University, Syracuse, NY, 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY, 13244, USA
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113
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Pessina F, Gioia U, Brandi O, Farina S, Ceccon M, Francia S, d'Adda di Fagagna F. DNA Damage Triggers a New Phase in Neurodegeneration. Trends Genet 2020; 37:337-354. [PMID: 33020022 DOI: 10.1016/j.tig.2020.09.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Subcellular compartmentalization contributes to the organization of a plethora of molecular events occurring within cells. This can be achieved in membraneless organelles generated through liquid-liquid phase separation (LLPS), a demixing process that separates and concentrates cellular reactions. RNA is often a critical factor in mediating LLPS. Recent evidence indicates that DNA damage response foci are membraneless structures formed via LLPS and modulated by noncoding transcripts synthesized at DNA damage sites. Neurodegeneration is often associated with DNA damage, and dysfunctional LLPS events can lead to the formation of toxic aggregates. In this review, we discuss those gene products involved in neurodegeneration that undergo LLPS and their involvement in the DNA damage response.
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Affiliation(s)
- Fabio Pessina
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Ubaldo Gioia
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Ornella Brandi
- Istituto di Genetica Molecolare 'Luigi Luca Cavalli-Sforza' CNR - Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
| | - Stefania Farina
- Istituto di Genetica Molecolare 'Luigi Luca Cavalli-Sforza' CNR - Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy; University School for Advanced Studies IUSS, 27100 Pavia, Italy
| | - Marta Ceccon
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy
| | - Sofia Francia
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy; Istituto di Genetica Molecolare 'Luigi Luca Cavalli-Sforza' CNR - Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy.
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation - FIRC Institute of Molecular Oncology Foundation, 20139 Milan, Italy; Istituto di Genetica Molecolare 'Luigi Luca Cavalli-Sforza' CNR - Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy.
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114
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Zhou HX. Determination of Condensate Material Properties from Droplet Deformation. J Phys Chem B 2020; 124:8372-8379. [PMID: 32857503 DOI: 10.1021/acs.jpcb.0c06230] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
I derive theoretical results that relate the effective spring constant, χ, of protein droplets to their material properties. χ, defined as the ratio between a uniaxial applied force and the extent of the corresponding deformation, can be measured by optical tweezers. When the deformation is static, where the applied force is balanced by the interfacial tension of the droplet, the spring constant allows for the determination of the surface tension (γ). When a sinusoidal force is applied (at frequency ω), the dynamic spring constant χ(ω) is related to both γ and the complex shear modulus, G*(ω), of the droplet. The results derived here enable accurate extraction of γ and G*(ω) from χ(ω) data.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry and Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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115
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Fisher RS, Elbaum-Garfinkle S. Tunable multiphase dynamics of arginine and lysine liquid condensates. Nat Commun 2020; 11:4628. [PMID: 32934220 PMCID: PMC7492283 DOI: 10.1038/s41467-020-18224-y] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 08/12/2020] [Indexed: 12/11/2022] Open
Abstract
Liquid phase separation into two or more coexisting phases has emerged as a new paradigm for understanding subcellular organization, prebiotic life, and the origins of disease. The design principles underlying biomolecular phase separation have the potential to drive the development of novel liquid-based organelles and therapeutics, however, an understanding of how individual molecules contribute to emergent material properties, and approaches to directly manipulate phase dynamics are lacking. Here, using microrheology, we demonstrate that droplets of poly-arginine coassembled with mono/polynucleotides have approximately 100 fold greater viscosity than comparable lysine droplets, both of which can be finer tuned by polymer length. We find that these amino acid-level differences can drive the formation of coexisting immiscible phases with tunable formation kinetics and can be further exploited to trigger the controlled release of droplet components. Together, this work provides a novel mechanism for leveraging sequence-level components in order to regulate droplet dynamics and multiphase coexistence. The design principles underlying biomolecular phase separation of membrane-less organelles remain poorly understood. Using model homopolymers, Fisher et al. show that the formation kinetics of coexisting liquid phases can be tuned by exploiting differences between arginine and lysine residues.
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Affiliation(s)
- Rachel S Fisher
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA
| | - Shana Elbaum-Garfinkle
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, USA. .,Ph.D. Programs in Biochemistry and Biology at the Graduate Center, City University of New York, New York, NY, USA.
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116
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Alshareedah I, Kaur T, Banerjee PR. Methods for characterizing the material properties of biomolecular condensates. Methods Enzymol 2020; 646:143-183. [PMID: 33453924 PMCID: PMC7849318 DOI: 10.1016/bs.mie.2020.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are membrane-less sub-cellular compartments that perform a plethora of important functions in signaling and storage. The material properties of biomolecular condensates such as viscosity, surface tension, viscoelasticity, and macromolecular diffusion play important roles in regulating their biological functions. Aberrations in these properties have been implicated in various neurodegenerative disorders and certain types of cancer. Unraveling the molecular driving forces that control the fluid structure and dynamics of biomolecular condensates across different length- and time-scales necessitates the application of innovative biophysical methodologies. In this chapter, we discuss major experimental techniques that are widely used to study the material states and dynamics of biomolecular condensates as well as their practical and conceptual limitations. We end this chapter with a discussion on more advanced tools that are currently emerging to address the complex fluid dynamics of these condensates.
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Affiliation(s)
| | - Taranpreet Kaur
- Department of Physics, University at Buffalo, Buffalo, NY, United States
| | - Priya R Banerjee
- Department of Physics, University at Buffalo, Buffalo, NY, United States.
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Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. SCIENCE CHINA. LIFE SCIENCES 2020; 63:953-985. [PMID: 32548680 DOI: 10.1007/s11427-020-1702-x] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
Cells are compartmentalized by numerous membrane-enclosed organelles and membraneless compartments to ensure that a wide variety of cellular activities occur in a spatially and temporally controlled manner. The molecular mechanisms underlying the dynamics of membrane-bound organelles, such as their fusion and fission, vesicle-mediated trafficking and membrane contactmediated inter-organelle interactions, have been extensively characterized. However, the molecular details of the assembly and functions of membraneless compartments remain elusive. Mounting evidence has emerged recently that a large number of membraneless compartments, collectively called biomacromolecular condensates, are assembled via liquid-liquid phase separation (LLPS). Phase-separated condensates participate in various biological activities, including higher-order chromatin organization, gene expression, triage of misfolded or unwanted proteins for autophagic degradation, assembly of signaling clusters and actin- and microtubule-based cytoskeletal networks, asymmetric segregations of cell fate determinants and formation of pre- and post-synaptic density signaling assemblies. Biomacromolecular condensates can transition into different material states such as gel-like structures and solid aggregates. The material properties of condensates are crucial for fulfilment of their distinct functions, such as biochemical reaction centers, signaling hubs and supporting architectures. Cells have evolved multiple mechanisms to ensure that biomacromolecular condensates are assembled and disassembled in a tightly controlled manner. Aberrant phase separation and transition are causatively associated with a variety of human diseases such as neurodegenerative diseases and cancers. This review summarizes recent major progress in elucidating the roles of LLPS in various biological pathways and diseases.
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118
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Phase transition of RNA-protein complexes into ordered hollow condensates. Proc Natl Acad Sci U S A 2020; 117:15650-15658. [PMID: 32571937 DOI: 10.1073/pnas.1922365117] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Liquid-liquid phase separation of multivalent intrinsically disordered protein-RNA complexes is ubiquitous in both natural and biomimetic systems. So far, isotropic liquid droplets are the most commonly observed topology of RNA-protein condensates in experiments and simulations. Here, by systematically studying the phase behavior of RNA-protein complexes across varied mixture compositions, we report a hollow vesicle-like condensate phase of nucleoprotein assemblies that is distinct from RNA-protein droplets. We show that these vesicular condensates are stable at specific mixture compositions and concentration regimes within the phase diagram and are formed through the phase separation of anisotropic protein-RNA complexes. Similar to membranes composed of amphiphilic lipids, these nucleoprotein-RNA vesicular membranes exhibit local ordering, size-dependent permeability, and selective encapsulation capacity without sacrificing their dynamic formation and dissolution in response to physicochemical stimuli. Our findings suggest that protein-RNA complexes can robustly create lipid-free vesicle-like enclosures by phase separation.
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119
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Mandal SS. Force Spectroscopy on Single Molecules of Life. ACS OMEGA 2020; 5:11271-11278. [PMID: 32478214 PMCID: PMC7254507 DOI: 10.1021/acsomega.0c00814] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/29/2020] [Indexed: 05/02/2023]
Abstract
Biomolecules such as nucleic acids and proteins constitute the cells and its organelles that form the crucial components in all living organisms. They are associated with a variety of cellular processes during which they undergo conformational orientations. The structural rearrangements resulting from protein-protein, protein-DNA, and protein-drug interactions vary in spatial and temporal length scales. Force is one of the important key factors which regulate these interactions. The magnitude of the force can vary from sub-piconewtons to several thousands of piconewtons. Single-molecule force spectroscopy acts as a powerful tool which is capable of investigating mechanical stability and conformational rearrangements arising in biomolecules due to the above interactions. Real-time observation of conformational dynamics including access to rare or transient states and the estimation of mean dwell times using these tools aids in the kinetic analysis of these interactions. In this review, we highlight the capabilities of common force spectroscopy techniques such as optical tweezers, magnetic tweezers, and atomic force microscopy with case studies on emerging applications.
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Affiliation(s)
- Soumit S Mandal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
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120
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Babinchak WM, Surewicz WK. Liquid-Liquid Phase Separation and Its Mechanistic Role in Pathological Protein Aggregation. J Mol Biol 2020; 432:1910-1925. [PMID: 32169484 DOI: 10.1016/j.jmb.2020.03.004] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/14/2022]
Abstract
Liquid-liquid phase separation (LLPS) of proteins underlies the formation of membrane-less organelles. While it has been recognized for some time that these organelles are of key importance for normal cellular functions, a growing number of recent observations indicate that LLPS may also play a role in disease. In particular, numerous proteins that form toxic aggregates in neurodegenerative diseases, such as amyotrophic lateral sclerosis, frontotemporal lobar degeneration, and Alzheimer's disease, were found to be highly prone to phase separation, suggesting that there might be a strong link between LLPS and the pathogenic process in these disorders. This review aims to assess the molecular basis of this link through exploration of the intermolecular interactions that underlie LLPS and aggregation and the underlying mechanisms facilitating maturation of liquid droplets into more stable assemblies, including so-called labile fibrils, hydrogels, and pathological amyloids. Recent insights into the structural basis of labile fibrils and potential mechanisms by which these relatively unstable structures could transition into more stable pathogenic amyloids are also discussed. Finally, this review explores how the environment of liquid droplets could modulate protein aggregation by altering kinetics of protein self-association, affecting folding of protein monomers, or changing aggregation pathways.
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Affiliation(s)
- W Michael Babinchak
- Department of Physiology & Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Witold K Surewicz
- Department of Physiology & Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA.
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Shapira R, Katalan S, Edrei R, Eichen Y. Chirality dependent inverse-melting and re-entrant gelation in α-cyclodextrin/1-phenylethylamine mixtures. RSC Adv 2020; 10:39195-39203. [PMID: 35518437 PMCID: PMC9057694 DOI: 10.1039/d0ra07643k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 10/16/2020] [Indexed: 01/14/2023] Open
Abstract
Solutions of cyclohexakis-(1→4)-α-d-glucopyranosyl, α-cyclodextrin, αCD, in R-(+)-1-phenylethylamine, αCD/R-PEA, and S-(−)-1-phenylethylamine, αCD/S-PEA, display abnormal phase transitions that strongly depend on supramolecular diastereomeric interactions. While αCD/R-PEA mixtures show one sol–gel inverse-melting phase transition, αCD/S-PEA mixtures show temperature dependent gel–sol–gel re-entrant behavior. NMR, Raman spectroscopy, microscopy and X-ray scattering measurements reveal that hydrogen bond weakening in solution, as well as changes in crystal composition are responsible for entropy increase and gel formation upon heating. Solutions of α-cyclodextrin in chiral 1-phenylethylamine display abnormal phase transitions. Depending on supramolecular diastereomeric interactions, inverse-melting and re-entrant gels are formed.![]()
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Affiliation(s)
- Reut Shapira
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- 3200008 Haifa
- Israel
| | - Sapir Katalan
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- 3200008 Haifa
- Israel
| | - Rachel Edrei
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- 3200008 Haifa
- Israel
| | - Yoav Eichen
- Schulich Faculty of Chemistry
- Technion – Israel Institute of Technology
- 3200008 Haifa
- Israel
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