1
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Geng Q, Keya JJ, Hotta T, Verhey KJ. The kinesin-3 KIF1C undergoes liquid-liquid phase separation for accumulation of specific transcripts at the cell periphery. EMBO J 2024; 43:3192-3213. [PMID: 38898313 PMCID: PMC11294625 DOI: 10.1038/s44318-024-00147-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/30/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
In cells, mRNAs are transported to and positioned at subcellular areas to locally regulate protein production. Recent studies have identified the kinesin-3 family member motor protein KIF1C as an RNA transporter. However, it is not clear how KIF1C interacts with RNA molecules. Here, we show that the KIF1C C-terminal tail domain contains an intrinsically disordered region (IDR) that drives liquid-liquid phase separation (LLPS). KIF1C forms dynamic puncta in cells that display physical properties of liquid condensates and incorporate RNA molecules in a sequence-selective manner. Endogenous KIF1C forms condensates in cellular protrusions, where mRNAs are enriched in an IDR-dependent manner. Purified KIF1C tail constructs undergo LLPS in vitro at near-endogenous nM concentrations and in the absence of crowding agents and can directly recruit RNA molecules. Overall, our work uncovers an intrinsic correlation between the LLPS activity of KIF1C and its role in mRNA positioning. In addition, the LLPS activity of KIF1C's tail represents a new mode of motor-cargo interaction that extends our current understanding of cytoskeletal motor proteins.
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Affiliation(s)
- Qi Geng
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jakia Jannat Keya
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
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2
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Bharti, Carlson A, Chan TS. Plateau-Rayleigh instability of a soft layer coated on a rigid cylinder. SOFT MATTER 2024; 20:5456-5463. [PMID: 38952171 DOI: 10.1039/d4sm00061g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
We study the Plateau-Rayleigh instability of a soft viscoelastic solid layer coated on a rigid cylinder i.e., a soft fibre with a rigid core. The onset of instability is examined using a linear stability analysis. We find that increasing the rigid cylinder radius or the stiffness of the layer reduces the growth rate of the fastest growing mode. For each rigid cylinder radius, a critical elastocapillary number is found below which all wavelengths of disturbances are stable. The critical value for a soft fibre with a thick rigid cylindrical core can be several orders of magnitudes larger than that for a totally soft fibre (no rigid core). This highlights the strong stabilizing effect of the rigid core on the system. Increasing the relaxation timescale of the viscoelastic material also slows down the growth of disturbances, but has no effect on the critical elastocapillary number. Interestingly, the wavelength of the fastest growing mode is independent of the rigid cylinder radius for the purely elastic case.
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Affiliation(s)
- Bharti
- Mechanics Division, Department of Mathematics, University of Oslo, 0316 Oslo, Norway.
| | - Andreas Carlson
- Mechanics Division, Department of Mathematics, University of Oslo, 0316 Oslo, Norway.
| | - Tak Shing Chan
- Mechanics Division, Department of Mathematics, University of Oslo, 0316 Oslo, Norway.
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3
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Lee CT, Bell M, Bonilla-Quintana M, Rangamani P. Biophysical Modeling of Synaptic Plasticity. Annu Rev Biophys 2024; 53:397-426. [PMID: 38382115 DOI: 10.1146/annurev-biophys-072123-124954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Miriam Bell
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Mayte Bonilla-Quintana
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, California, USA;
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4
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Roggeveen JV, Wang H, Shi Z, Stone HA. A calibration-free model of micropipette aspiration for measuring properties of protein condensates. Biophys J 2024; 123:1393-1403. [PMID: 37789618 PMCID: PMC11163300 DOI: 10.1016/j.bpj.2023.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/13/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023] Open
Abstract
There is growing evidence that biological condensates, which are also referred to as membraneless organelles, and liquid-liquid phase separation play critical roles regulating many important cellular processes. Understanding the roles these condensates play in biology is predicated on understanding the material properties of these complex substances. Recently, micropipette aspiration (MPA) has been proposed as a tool to assay the viscosity and surface tension of condensates. This tool allows the measurement of both material properties in one relatively simple experiment, in contrast to many other techniques that only provide one or a ratio of parameters. While this technique has been commonly used in the literature to determine the material properties of membrane-bound objects dating back decades, the model describing the dynamics of MPA for objects with an external membrane does not correctly capture the hydrodynamics of unbounded fluids, leading to a calibration parameter several orders of magnitude larger than predicted. In this work we derive a new model for MPA of biological condensates that does not require any calibration and is consistent with the hydrodynamics of the MPA geometry. We validate the predictions of this model by conducting MPA experiments on a standard silicone oil of known material properties and are able to predict the viscosity and surface tension using MPA. Finally, we reanalyze with this new model the MPA data presented in previous works for condensates formed from LAF-1 RGG domains.
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Affiliation(s)
- James V Roggeveen
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey
| | - Huan Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - Zheng Shi
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey.
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey.
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5
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Ma Q, Surya W, He D, Yang H, Han X, Nai MH, Lim CT, Torres J, Miao Y. Spa2 remodels ADP-actin via molecular condensation under glucose starvation. Nat Commun 2024; 15:4491. [PMID: 38802374 PMCID: PMC11130202 DOI: 10.1038/s41467-024-48863-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/15/2024] [Indexed: 05/29/2024] Open
Abstract
Actin nucleotide-dependent actin remodeling is essential to orchestrate signal transduction and cell adaptation. Rapid energy starvation requires accurate and timely reorganization of the actin network. Despite distinct treadmilling mechanisms of ADP- and ATP-actin filaments, their filament structures are nearly identical. How other actin-binding proteins regulate ADP-actin filament assembly is unclear. Here, we show that Spa2 which is the polarisome scaffold protein specifically remodels ADP-actin upon energy starvation in budding yeast. Spa2 triggers ADP-actin monomer nucleation rapidly through a dimeric core of Spa2 (aa 281-535). Concurrently, the intrinsically disordered region (IDR, aa 1-281) guides Spa2 undergoing phase separation and wetting on the surface of ADP-G-actin-derived F-actin and bundles the filaments. Both ADP-actin-specific nucleation and bundling activities of Spa2 are actin D-loop dependent. The IDR and nucleation core of Spa2 are evolutionarily conserved by coexistence in the fungus kingdom, suggesting a universal adaptation mechanism in the fungal kingdom in response to glucose starvation, regulating ADP-G-actin and ADP-F-actin with high nucleotide homogeneity.
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Affiliation(s)
- Qianqian Ma
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Wahyu Surya
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Danxia He
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Hanmeng Yang
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Xiao Han
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Mui Hoon Nai
- Department of Biomedical Engineering, National University of Singapore, 117583, Singapore, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, 117583, Singapore, Singapore
- Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, 119276, Singapore, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921, Singapore, Singapore.
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6
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Phua DY, Sun X, Alushin GM. Force-activated zyxin assemblies coordinate actin nucleation and crosslinking to orchestrate stress fiber repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594765. [PMID: 38798419 PMCID: PMC11118565 DOI: 10.1101/2024.05.17.594765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
As the cytoskeleton sustains cell and tissue forces, it incurs physical damage that must be repaired to maintain mechanical homeostasis. The LIM-domain protein zyxin detects force-induced ruptures in actin-myosin stress fibers, coordinating downstream repair factors to restore stress fiber integrity through unclear mechanisms. Here, we reconstitute stress fiber repair with purified proteins, uncovering detailed links between zyxin's force-regulated binding interactions and cytoskeletal dynamics. In addition to binding individual tensed actin filaments (F-actin), zyxin's LIM domains form force-dependent assemblies that bridge broken filament fragments. Zyxin assemblies engage repair factors through multi-valent interactions, coordinating nucleation of new F-actin by VASP and its crosslinking into aligned bundles by ɑ-actinin. Through these combined activities, stress fiber repair initiates within the cores of micron-scale damage sites in cells, explaining how these F-actin depleted regions are rapidly restored. Thus, zyxin's force-dependent organization of actin repair machinery inherently operates at the network scale to maintain cytoskeletal integrity.
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Affiliation(s)
- Donovan Y.Z. Phua
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Xiaoyu Sun
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Gregory M. Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
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7
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Sun S, Zhou J, Liu P. Liquid-liquid phase separation of microtubule-binding proteins in the regulation of spindle assembly. Cell Prolif 2024:e13649. [PMID: 38736355 DOI: 10.1111/cpr.13649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/19/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024] Open
Abstract
Cell division is a highly regulated process essential for the accurate segregation of chromosomes. Central to this process is the assembly of a bipolar mitotic spindle, a highly dynamic microtubule (MT)-based structure responsible for chromosome movement. The nucleation and dynamics of MTs are intricately regulated by MT-binding proteins. Over the recent years, various MT-binding proteins have been reported to undergo liquid-liquid phase separation, forming either single- or multi-component condensates on MTs. Herein, we provide a comprehensive summary of the phase separation characteristics of these proteins. We underscore their critical roles in MT nucleation, spindle assembly and kinetochore-MT attachment during the cell division process. Furthermore, we discuss the current challenges and various remaining unsolved problems, highlights the ongoing research efforts aimed at a deeper understanding of the role of the phase separation process during spindle assembly and orientation. Our review aims to contribute to the collective knowledge in this area and stimulate further investigations that will enhance our comprehension of the intricate mechanisms governing cell division.
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Affiliation(s)
- Shuang Sun
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| | - Peiwei Liu
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, Jinan, China
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8
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Rouches MN, Machta BB. Polymer Collapse & Liquid-Liquid Phase-Separation are Coupled in a Generalized Prewetting Transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591767. [PMID: 38746247 PMCID: PMC11092468 DOI: 10.1101/2024.04.29.591767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with particular sequences of DNA. At unphysiological concentrations many of these nuclear proteins can phase-separate in the absence of DNA, and it has been hypothesized that, in vivo, the thermodynamic forces driving these phases help determine chromosomal organization. However it is unclear how DNA, itself a long polymer subject to configurational transitions, interacts with three-dimensional protein phases. Here we show that a long compressible polymer can be coupled to interacting protein mixtures, leading to a generalized prewetting transition where polymer collapse is coincident with a locally stabilized liquid droplet. We use lattice Monte-Carlo simulations and a mean-field theory to show that these phases can be stable even in regimes where both polymer collapse and coexisting liquid phases are unstable in isolation, and that these new transitions can be either abrupt or continuous. For polymers with internal linear structure we further show that changes in the concentration of bulk components can lead to changes in three-dimensional polymer structure. In the nucleus there are many distinct proteins that interact with many different regions of chromatin, potentially giving rise to many different Prewet phases. The simple systems we consider here highlight chromatin's role as a lower-dimensional surface whose interactions with proteins are required for these novel phases.
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Affiliation(s)
- Mason N. Rouches
- Department of Molecular Biophysics & Biochemistry, Yale University and Quantitative Biology Institute, Yale University
| | - Benjamin B. Machta
- Department of Physics, Yale University and Quantitative Biology Institute, Yale University
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9
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Rouches MN, Machta BB. Polymer Collapse & Liquid-Liquid Phase-Separation are Coupled in a Generalized Prewetting Transition. ARXIV 2024:arXiv:2404.19158v1. [PMID: 38745698 PMCID: PMC11092872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with particular sequences of DNA. At unphysiological concentrations many of these nuclear proteins can phase-separate in the absence of DNA, and it has been hypothesized that, in vivo, the thermodynamic forces driving these phases help determine chromosomal organization. However it is unclear how DNA, itself a long polymer subject to configurational transitions, interacts with three-dimensional protein phases. Here we show that a long compressible polymer can be coupled to interacting protein mixtures, leading to a generalized prewetting transition where polymer collapse is coincident with a locally stabilized liquid droplet. We use lattice Monte-Carlo simulations and a mean-field theory to show that these phases can be stable even in regimes where both polymer collapse and coexisting liquid phases are unstable in isolation, and that these new transitions can be either abrupt or continuous. For polymers with internal linear structure we further show that changes in the concentration of bulk components can lead to changes in three-dimensional polymer structure. In the nucleus there are many distinct proteins that interact with many different regions of chromatin, potentially giving rise to many different Prewet phases. The simple systems we consider here highlight chromatin's role as a lower-dimensional surface whose interactions with proteins are required for these novel phases.
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Affiliation(s)
- Mason N. Rouches
- Department of Molecular Biophysics & Biochemistry, Yale University and Quantitative Biology Institute, Yale University
| | - Benjamin B. Machta
- Department of Physics, Yale University and Quantitative Biology Institute, Yale University
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10
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Graham K, Chandrasekaran A, Wang L, Yang N, Lafer EM, Rangamani P, Stachowiak JC. Liquid-like condensates mediate competition between actin branching and bundling. Proc Natl Acad Sci U S A 2024; 121:e2309152121. [PMID: 38207079 PMCID: PMC10801869 DOI: 10.1073/pnas.2309152121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
Cellular remodeling of actin networks underlies cell motility during key morphological events, from embryogenesis to metastasis. In these transformations, there is an inherent competition between actin branching and bundling, because steric clashes among branches create a mechanical barrier to bundling. Recently, liquid-like condensates consisting purely of proteins involved in either branching or bundling of the cytoskeleton have been found to catalyze their respective functions. Yet in the cell, proteins that drive branching and bundling are present simultaneously. In this complex environment, which factors determine whether a condensate drives filaments to branch or become bundled? To answer this question, we added the branched actin nucleator, Arp2/3, to condensates composed of VASP, an actin bundling protein. At low actin to VASP ratios, branching activity, mediated by Arp2/3, robustly inhibited VASP-mediated bundling of filaments, in agreement with agent-based simulations. In contrast, as the actin to VASP ratio increased, addition of Arp2/3 led to formation of aster-shaped structures, in which bundled filaments emerged from a branched actin core, analogous to filopodia emerging from a branched lamellipodial network. These results demonstrate that multi-component, liquid-like condensates can modulate the inherent competition between bundled and branched actin morphologies, leading to organized, higher-order structures, similar to those found in motile cells.
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Affiliation(s)
- Kristin Graham
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX78712
| | - Aravind Chandrasekaran
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA92093
| | - Liping Wang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX78229
| | - Noel Yang
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX78712
| | - Eileen M. Lafer
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX78229
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA92093
| | - Jeanne C. Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX78712
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX78712
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11
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Volkov VA, Akhmanova A. Phase separation on microtubules: from droplet formation to cellular function? Trends Cell Biol 2024; 34:18-30. [PMID: 37453878 DOI: 10.1016/j.tcb.2023.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Microtubules are cytoskeletal polymers that play important roles in numerous cellular processes, ranging from the control of cell shape and polarity to cell division and intracellular transport. Many of these roles rely on proteins that bind to microtubule ends and shafts, carry intrinsically disordered regions, and form complex multivalent interaction networks. A flurry of recent studies demonstrated that these properties allow diverse microtubule-binding proteins to undergo liquid-liquid phase separation (LLPS) in vitro. It is proposed that LLPS could potentially affect multiple microtubule-related processes, such as microtubule nucleation, control of microtubule dynamics and organization, and microtubule-based transport. Here, we discuss the evidence in favor and against the occurrence of LLPS and its functional significance for microtubule-based processes in cells.
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Affiliation(s)
- Vladimir A Volkov
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.
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12
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Lawrence EJ, Chatterjee S, Zanic M. More is different: Reconstituting complexity in microtubule regulation. J Biol Chem 2023; 299:105398. [PMID: 37898404 PMCID: PMC10694663 DOI: 10.1016/j.jbc.2023.105398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023] Open
Abstract
Microtubules are dynamic cytoskeletal filaments that undergo stochastic switching between phases of polymerization and depolymerization-a behavior known as dynamic instability. Many important cellular processes, including cell motility, chromosome segregation, and intracellular transport, require complex spatiotemporal regulation of microtubule dynamics. This coordinated regulation is achieved through the interactions of numerous microtubule-associated proteins (MAPs) with microtubule ends and lattices. Here, we review the recent advances in our understanding of microtubule regulation, focusing on results arising from biochemical in vitro reconstitution approaches using purified multiprotein ensembles. We discuss how the combinatory effects of MAPs affect both the dynamics of individual microtubule ends, as well as the stability and turnover of the microtubule lattice. In addition, we highlight new results demonstrating the roles of protein condensates in microtubule regulation. Our overall intent is to showcase how lessons learned from reconstitution approaches help unravel the regulatory mechanisms at play in complex cellular environments.
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Affiliation(s)
- Elizabeth J Lawrence
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Saptarshi Chatterjee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Marija Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA.
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13
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Crabtree MD, Holland J, Pillai AS, Kompella PS, Babl L, Turner NN, Eaton JT, Hochberg GKA, Aarts DGAL, Redfield C, Baldwin AJ, Nott TJ. Ion binding with charge inversion combined with screening modulates DEAD box helicase phase transitions. Cell Rep 2023; 42:113375. [PMID: 37980572 PMCID: PMC10935546 DOI: 10.1016/j.celrep.2023.113375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/14/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023] Open
Abstract
Membraneless organelles, or biomolecular condensates, enable cells to compartmentalize material and processes into unique biochemical environments. While specific, attractive molecular interactions are known to stabilize biomolecular condensates, repulsive interactions, and the balance between these opposing forces, are largely unexplored. Here, we demonstrate that repulsive and attractive electrostatic interactions regulate condensate stability, internal mobility, interfaces, and selective partitioning of molecules both in vitro and in cells. We find that signaling ions, such as calcium, alter repulsions between model Ddx3 and Ddx4 condensate proteins by directly binding to negatively charged amino acid sidechains and effectively inverting their charge, in a manner fundamentally dissimilar to electrostatic screening. Using a polymerization model combined with generalized stickers and spacers, we accurately quantify and predict condensate stability over a wide range of pH, salt concentrations, and amino acid sequences. Our model provides a general quantitative treatment for understanding how charge and ions reversibly control condensate stability.
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Affiliation(s)
- Michael D Crabtree
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jack Holland
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Arvind S Pillai
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Purnima S Kompella
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Leon Babl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Noah N Turner
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - James T Eaton
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK; Kavli Insititute of Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Rd, Oxford, OX1 3QU, UK
| | - Georg K A Hochberg
- Department of Chemistry, Philipps University Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; Center for Synthetic Microbiology, Philipps University Marburg, Karl-von-Frisch-Straße 14, 35032 Marburg, Germany
| | - Dirk G A L Aarts
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew J Baldwin
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK; Kavli Insititute of Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, Sherrington Rd, Oxford, OX1 3QU, UK.
| | - Timothy J Nott
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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14
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Holland J, Castrejón-Pita AA, Tuinier R, Aarts DGAL, Nott TJ. Surface tension measurement and calculation of model biomolecular condensates. SOFT MATTER 2023; 19:8706-8716. [PMID: 37791635 PMCID: PMC10663989 DOI: 10.1039/d3sm00820g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]
Abstract
The surface tension of liquid-like protein-rich biomolecular condensates is an emerging physical principle governing the mesoscopic interior organisation of biological cells. In this study, we present a method to evaluate the surface tension of model biomolecular condensates, through straighforward sessile drop measurements of capillary lengths and condensate densities. Our approach bypasses the need for characterizing condensate viscosities, which was required in previously reported techniques. We demonstrate this method using model condensates comprising two mutants of the intrinsically disordered protein Ddx4N. Notably, we uncover a detrimental impact of increased protein net charge on the surface tension of Ddx4N condensates. Furthermore, we explore the application of Scheutjens-Fleer theory, calculating condensate surface tensions through a self-consistent mean-field framework using Flory-Huggins interaction parameters. This relatively simple theory provides semi-quantitative accuracy in predicting Ddx4N condensate surface tensions and enables the evaluation of molecular organisation at condensate surfaces. Our findings shed light on the molecular details of fluid-fluid interfaces in biomolecular condensates.
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Affiliation(s)
- Jack Holland
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.
- Dept. of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | | | - Remco Tuinier
- Laboratory of Physical Chemistry, Department of Chemical Engineering and Chemistry & Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Dirk G A L Aarts
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.
| | - Timothy J Nott
- Dept. of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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15
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Tayar AM, Caballero F, Anderberg T, Saleh OA, Cristina Marchetti M, Dogic Z. Controlling liquid-liquid phase behaviour with an active fluid. NATURE MATERIALS 2023; 22:1401-1408. [PMID: 37679525 DOI: 10.1038/s41563-023-01660-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
Demixing binary liquids is a ubiquitous transition explained using a well-established thermodynamic formalism that requires the equality of intensive thermodynamics parameters across phase boundaries. Demixing transitions also occur when binary fluid mixtures are driven away from equilibrium, but predicting and designing such out-of-equilibrium transitions remains a challenge. Here we study the liquid-liquid phase separation of attractive DNA nanostars driven away from equilibrium using a microtubule-based active fluid. We find that activity lowers the critical temperature and narrows the range of coexistence concentrations, but only in the presence of mechanical bonds between the liquid droplets and reconfiguring active fluid. Similar behaviours are observed in numerical simulations, suggesting that the activity suppression of the critical point is a generic feature of active liquid-liquid phase separation. Our work describes a versatile platform for building soft active materials with feedback control and providing an insight into self-organization in cell biology.
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Affiliation(s)
- Alexandra M Tayar
- Department of Physics, University of California, Santa Barbara, CA, USA.
| | | | - Trevor Anderberg
- Department of Physics, University of California, Santa Barbara, CA, USA
| | - Omar A Saleh
- Department of Physics, University of California, Santa Barbara, CA, USA
- Materials Department, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - M Cristina Marchetti
- Department of Physics, University of California, Santa Barbara, CA, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Zvonimir Dogic
- Department of Physics, University of California, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA.
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16
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Geng Q, Keya JJ, Hotta T, Verhey KJ. KIF1C, an RNA transporting kinesin-3, undergoes liquid-liquid phase separation through its C-terminal disordered domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563538. [PMID: 37961614 PMCID: PMC10634753 DOI: 10.1101/2023.10.23.563538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The spatial distribution of mRNA is critical for local control of protein production. Recent studies have identified the kinesin-3 family member KIF1C as an RNA transporter. However, it is not clear how KIF1C interacts with RNA molecules. Here, we show that KIF1C's C-terminal tail domain is an intrinsically disordered region (IDR) containing a prion-like domain (PLD) that is unique compared to the C-terminal tails of other kinesin family members. In cells, KIF1C constructs undergo reversible formation of dynamic puncta that display physical properties of liquid condensates and incorporate RNA molecules in a sequence-selective manner. The IDR is necessary and sufficient for driving liquid-liquid phase separation (LLPS) but the condensate properties can be modulated by adjacent coiled-coil segments. The purified KIF1C IDR domain undergoes LLPS in vitro at near-endogenous nM concentrations in a salt-dependent manner. Deletion of the IDR abolished the ability of KIF1C to undergo LLPS and disrupted the distribution of mRNA cargoes to the cell periphery. Our work thus uncovers an intrinsic correlation between the LLPS activity of KIF1C and its role as an RNA transporter. In addition, as the first kinesin motor reported to undergo LLPS, our work reveals a previously uncharacterized mode of motor-cargo interaction that extends our understanding of the behavior of cytoskeletal motor proteins.
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Affiliation(s)
- Qi Geng
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jakia Jannat Keya
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
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17
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Kraus J, Alfaro-Aco R, Gouveia B, Petry S. Microtubule nucleation for spindle assembly: one molecule at a time. Trends Biochem Sci 2023; 48:761-775. [PMID: 37482516 PMCID: PMC10789498 DOI: 10.1016/j.tibs.2023.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023]
Abstract
The cell orchestrates the dance of chromosome segregation with remarkable speed and fidelity. The mitotic spindle is built from scratch after interphase through microtubule (MT) nucleation, which is dependent on the γ-tubulin ring complex (γ-TuRC), the universal MT template. Although several MT nucleation pathways build the spindle framework, the question of when and how γ-TuRC is targeted to these nucleation sites in the spindle and subsequently activated remains an active area of investigation. Recent advances facilitated the discovery of new MT nucleation effectors and their mechanisms of action. In this review, we illuminate each spindle assembly pathway and subsequently consider how the pathways are merged to build a spindle.
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Affiliation(s)
- Jodi Kraus
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Bernardo Gouveia
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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18
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Valdez VA, Neahring L, Petry S, Dumont S. Mechanisms underlying spindle assembly and robustness. Nat Rev Mol Cell Biol 2023; 24:523-542. [PMID: 36977834 PMCID: PMC10642710 DOI: 10.1038/s41580-023-00584-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 03/30/2023]
Abstract
The microtubule-based spindle orchestrates chromosome segregation during cell division. Following more than a century of study, many components and pathways contributing to spindle assembly have been described, but how the spindle robustly assembles remains incompletely understood. This process involves the self-organization of a large number of molecular parts - up to hundreds of thousands in vertebrate cells - whose local interactions give rise to a cellular-scale structure with emergent architecture, mechanics and function. In this Review, we discuss key concepts in our understanding of spindle assembly, focusing on recent advances and the new approaches that enabled them. We describe the pathways that generate the microtubule framework of the spindle by driving microtubule nucleation in a spatially controlled fashion and present recent insights regarding the organization of individual microtubules into structural modules. Finally, we discuss the emergent properties of the spindle that enable robust chromosome segregation.
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Affiliation(s)
| | - Lila Neahring
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA, USA
- Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA, USA
| | - Sabine Petry
- Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Sophie Dumont
- Department of Bioengineering & Therapeutic Sciences, UCSF, San Francisco, CA, USA.
- Developmental & Stem Cell Biology Graduate Program, UCSF, San Francisco, CA, USA.
- Department of Biochemistry & Biophysics, UCSF, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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19
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Abstract
Multivalent proteins and nucleic acids, collectively referred to as multivalent associative biomacromolecules, provide the driving forces for the formation and compositional regulation of biomolecular condensates. Here, we review the key concepts of phase transitions of aqueous solutions of associative biomacromolecules, specifically proteins that include folded domains and intrinsically disordered regions. The phase transitions of these systems come under the rubric of coupled associative and segregative transitions. The concepts underlying these processes are presented, and their relevance to biomolecular condensates is discussed.
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Affiliation(s)
- Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Samuel R Cohen
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
- Center of Regenerative Medicine, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Furqan Dar
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307 Dresden, Germany
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20
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Gordon SG, Rog O. Building the synaptonemal complex: Molecular interactions between the axis and the central region. PLoS Genet 2023; 19:e1010822. [PMID: 37471284 PMCID: PMC10359014 DOI: 10.1371/journal.pgen.1010822] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
The successful delivery of genetic material to gametes requires tightly regulated interactions between the parental chromosomes. Central to this regulation is a conserved chromosomal interface called the synaptonemal complex (SC), which brings the parental chromosomes in close proximity along their length. While many of its components are known, the interfaces that mediate the assembly of the SC remain a mystery. Here, we survey findings from different model systems while focusing on insight gained in the nematode C. elegans. We synthesize our current understanding of the structure, dynamics, and biophysical properties of the SC and propose mechanisms for SC assembly.
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Affiliation(s)
- Spencer G. Gordon
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Ofer Rog
- School of Biological Sciences and Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah, United States of America
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21
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Ramm B, Schumacher D, Harms A, Heermann T, Klos P, Müller F, Schwille P, Søgaard-Andersen L. Biomolecular condensate drives polymerization and bundling of the bacterial tubulin FtsZ to regulate cell division. Nat Commun 2023; 14:3825. [PMID: 37380708 DOI: 10.1038/s41467-023-39513-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
Cell division is spatiotemporally precisely regulated, but the underlying mechanisms are incompletely understood. In the social bacterium Myxococcus xanthus, the PomX/PomY/PomZ proteins form a single megadalton-sized complex that directly positions and stimulates cytokinetic ring formation by the tubulin homolog FtsZ. Here, we study the structure and mechanism of this complex in vitro and in vivo. We demonstrate that PomY forms liquid-like biomolecular condensates by phase separation, while PomX self-assembles into filaments generating a single large cellular structure. The PomX structure enriches PomY, thereby guaranteeing the formation of precisely one PomY condensate per cell through surface-assisted condensation. In vitro, PomY condensates selectively enrich FtsZ and nucleate GTP-dependent FtsZ polymerization and bundle FtsZ filaments, suggesting a cell division site positioning mechanism in which the single PomY condensate enriches FtsZ to guide FtsZ-ring formation and division. This mechanism shares features with microtubule nucleation by biomolecular condensates in eukaryotes, supporting this mechanism's ancient origin.
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Affiliation(s)
- Beatrice Ramm
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
- Department of Physics, Princeton University, Princeton, NJ, 08544, USA.
| | - Dominik Schumacher
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
| | - Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Tamara Heermann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Philipp Klos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Franziska Müller
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
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22
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Graham K, Chandrasekaran A, Wang L, Yang N, Lafer EM, Rangamani P, Stachowiak JC. Liquid-like condensates mediate competition between actin branching and bundling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.23.546267. [PMID: 37425724 PMCID: PMC10327076 DOI: 10.1101/2023.06.23.546267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Cellular remodeling of actin networks underlies cell motility during key morphological events, from embryogenesis to metastasis. In these transformations there is an inherent competition between actin branching and bundling, because steric clashes among branches create a mechanical barrier to bundling. Recently, liquid-like condensates consisting purely of proteins involved in either branching or bundling of the cytoskeleton have been found to catalyze their respective functions. Yet in the cell, proteins that drive branching and bundling are present simultaneously. In this complex environment, which factors determine whether a condensate drives filaments to branch versus becoming bundled? To answer this question, we added the branched actin nucleator, Arp2/3, to condensates composed of VASP, an actin bundling protein. At low actin to VASP ratios, branching activity, mediated by Arp2/3, robustly inhibited VASP-mediated bundling of filaments, in agreement with agent-based simulations. In contrast, as the actin to VASP ratio increased, addition of Arp2/3 led to formation of aster-shaped structures, in which bundled filaments emerged from a branched actin core, analogous to filopodia emerging from a branched lamellipodial network. These results demonstrate that multi-component, liquid-like condensates can modulate the inherent competition between bundled and branched actin morphologies, leading to organized, higher-order structures, similar to those found in motile cells.
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Affiliation(s)
- Kristin Graham
- University of Texas at Austin, Department of Biomedical Engineering
| | | | - Liping Wang
- University of Texas Health Science Center at San Antonio, Department of Biochemistry and Structural Biology
| | - Noel Yang
- University of Texas at Austin, Department of Biomedical Engineering
| | - Eileen M. Lafer
- University of Texas Health Science Center at San Antonio, Department of Biochemistry and Structural Biology
| | - Padmini Rangamani
- University of California San Diego, Department of Mechanical and Aerospace Engineering
| | - Jeanne C. Stachowiak
- University of Texas at Austin, Department of Biomedical Engineering
- University of Texas at Austin, Department of Chemical Engineering
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23
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Guo C, Alfaro-Aco R, Zhang C, Russell RW, Petry S, Polenova T. Structural basis of protein condensation on microtubules underlying branching microtubule nucleation. Nat Commun 2023; 14:3682. [PMID: 37344496 PMCID: PMC10284871 DOI: 10.1038/s41467-023-39176-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 06/01/2023] [Indexed: 06/23/2023] Open
Abstract
Targeting protein for Xklp2 (TPX2) is a key factor that stimulates branching microtubule nucleation during cell division. Upon binding to microtubules (MTs), TPX2 forms condensates via liquid-liquid phase separation, which facilitates recruitment of microtubule nucleation factors and tubulin. We report the structure of the TPX2 C-terminal minimal active domain (TPX2α5-α7) on the microtubule lattice determined by magic-angle-spinning NMR. We demonstrate that TPX2α5-α7 forms a co-condensate with soluble tubulin on microtubules and binds to MTs between two adjacent protofilaments and at the intersection of four tubulin heterodimers. These interactions stabilize the microtubules and promote the recruitment of tubulin. Our results reveal that TPX2α5-α7 is disordered in solution and adopts a folded structure on MTs, indicating that TPX2α5-α7 undergoes structural changes from unfolded to folded states upon binding to microtubules. The aromatic residues form dense interactions in the core, which stabilize folding of TPX2α5-α7 on microtubules. This work informs on how the phase-separated TPX2α5-α7 behaves on microtubules and represents an atomic-level structural characterization of a protein that is involved in a condensate on cytoskeletal filaments.
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Affiliation(s)
- Changmiao Guo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Raymundo Alfaro-Aco
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Chunting Zhang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Ryan W Russell
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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24
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Lin WJ, Shi WP, Ge WY, Chen LL, Guo WH, Shang P, Yin DC. Magnetic Fields Reduce Apoptosis by Suppressing Phase Separation of Tau-441. RESEARCH (WASHINGTON, D.C.) 2023; 6:0146. [PMID: 37228640 PMCID: PMC10204748 DOI: 10.34133/research.0146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
The biological effects of magnetic fields (MFs) have been a controversial issue. Fortunately, in recent years, there has been increasing evidence that MFs do affect biological systems. However, the physical mechanism remains unclear. Here, we show that MFs (16 T) reduce apoptosis in cell lines by inhibiting liquid-liquid phase separation (LLPS) of Tau-441, suggesting that the MF effect on LLPS may be one of the mechanisms for understanding the "mysterious" magnetobiological effects. The LLPS of Tau-441 occurred in the cytoplasm after induction with arsenite. The phase-separated droplets of Tau-441 recruited hexokinase (HK), resulting in a decrease in the amount of free HK in the cytoplasm. In cells, HK and Bax compete to bind to the voltage-dependent anion channel (VDAC I) on the mitochondrial membrane. A decrease in the number of free HK molecules increased the chance of Bax binding to VDAC I, leading to increased Bax-mediated apoptosis. In the presence of a static MF, LLPS was marked inhibited and HK recruitment was reduced, resulting in an increased probability of HK binding to VDAC I and a decreased probability of Bax binding to VDAC I, thus reducing Bax-mediated apoptosis. Our findings revealed a new physical mechanism for understanding magnetobiological effects from the perspective of LLPS. In addition, these results show the potential applications of physical environments, such as MFs in this study, in the treatment of LLPS-related diseases.
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25
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Liu H, Shima T. Preference of CAMSAP3 for expanded microtubule lattice contributes to stabilization of the minus end. Life Sci Alliance 2023; 6:e202201714. [PMID: 36894175 PMCID: PMC9998277 DOI: 10.26508/lsa.202201714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/11/2023] Open
Abstract
CAMSAPs are proteins that show microtubule minus-end-specific localization, decoration, and stabilization. Although the mechanism for minus-end recognition via their C-terminal CKK domain has been well described in recent studies, it is unclear how CAMSAPs stabilize microtubules. Our several binding assays revealed that the D2 region of CAMSAP3 specifically binds to microtubules with the expanded lattice. To investigate the relationship between this preference and the stabilization effect of CAMSAP3, we precisely measured individual microtubule lengths and found that D2 binding expanded the microtubule lattice by ∼3%. Consistent with the notion that the expanded lattice is a common feature of stable microtubules, the presence of D2 slowed the microtubule depolymerization rate to ∼1/20, suggesting that the D2-triggered lattice expansion stabilizes microtubules. Combining these results, we propose that CAMSAP3 stabilizes microtubules by lattice expansion upon D2 binding, which further accelerates the recruitment of other CAMSAP3 molecules. Because only CAMSAP3 has D2 and the highest microtubule-stabilizing effect among mammalian CAMSAPs, our model also explains the molecular basis for the functional diversity of CAMSAP family members.
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Affiliation(s)
- Hanjin Liu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Shima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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26
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Biomolecular condensation involving the cytoskeleton. Brain Res Bull 2023; 194:105-117. [PMID: 36690162 DOI: 10.1016/j.brainresbull.2023.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/07/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023]
Abstract
Biomolecular condensation of proteins contributes to the organization of the cytoplasm and nucleoplasm. A number of condensation processes appear to be directly involved in regulating the structure, function and dynamics of the cytoskeleton. Liquid-liquid phase separation of cytoskeleton proteins, together with polymerization modulators, promotes cytoskeletal fiber nucleation and branching. Furthermore, the attachment of protein condensates to the cytoskeleton can contribute to cytoskeleton stability and organization, regulate transport, create patterns of functional reaction containers, and connect the cytoskeleton with membranes. Surface-bound condensates can exert and buffer mechanical forces that give stability and flexibility to the cytoskeleton, thus, may play a large role in cell biology. In this review, we introduce the concept and role of cellular biomolecular condensation, explain its special function on cytoskeletal fiber surfaces, and point out potential definition and experimental caveats. We review the current literature on protein condensation processes related to the actin, tubulin, and intermediate filament cytoskeleton, and discuss some of them in the context of neurobiology. In summary, we provide an overview about biomolecular condensation in relation to cytoskeleton structure and function, which offers a base for the exploration and interpretation of cytoskeletal condensates in neurobiology.
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27
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Tsukita K, Kitamata M, Kashihara H, Yano T, Fujiwara I, Day TF, Katsuno T, Kim J, Takenaga F, Tanaka H, Park S, Miyata M, Watanabe H, Kondoh G, Takahashi R, Tamura A, Tsukita S. Phase separation of an actin nucleator by junctional microtubules regulates epithelial function. SCIENCE ADVANCES 2023; 9:eadf6358. [PMID: 36791197 PMCID: PMC9931218 DOI: 10.1126/sciadv.adf6358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Liquid-liquid phase separation (LLPS) is involved in various dynamic biological phenomena. In epithelial cells, dynamic regulation of junctional actin filaments tethered to the apical junctional complex (AJC) is critical for maintaining internal homeostasis against external perturbations; however, the role of LLPS in this process remains unknown. Here, after identifying a multifunctional actin nucleator, cordon bleu (Cobl), as an AJC-enriched microtubule-associated protein, we conducted comprehensive in vitro and in vivo analyses. We found that apical microtubules promoted LLPS of Cobl at the AJC, and Cobl actin assembly activity increased upon LLPS. Thus, microtubules spatiotemporally regulated junctional actin assembly for epithelial morphogenesis and paracellular barriers. Collectively, these findings established that LLPS of the actin nucleator Cobl mediated dynamic microtubule-actin cross-talk in junctions, which fine-tuned the epithelial barrier.
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Affiliation(s)
- Kazuto Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Itabashi-ku, Tokyo 173-0003, Japan
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Neurology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Manabu Kitamata
- Advanced Comprehensive Research Organization, Teikyo University, Itabashi-ku, Tokyo 173-0003, Japan
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroka Kashihara
- Advanced Comprehensive Research Organization, Teikyo University, Itabashi-ku, Tokyo 173-0003, Japan
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoki Yano
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Ikuko Fujiwara
- Departments of Materials Science and Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Timothy F. Day
- Advanced Comprehensive Research Organization, Teikyo University, Itabashi-ku, Tokyo 173-0003, Japan
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tatsuya Katsuno
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
- Center for Anatomical, Pathological and Forensic Medical Researches, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Jaewon Kim
- Graduate School of Mechanical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Korea
| | - Fumiko Takenaga
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroo Tanaka
- Advanced Comprehensive Research Organization, Teikyo University, Itabashi-ku, Tokyo 173-0003, Japan
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Pharmacology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Sungsu Park
- Graduate School of Mechanical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Korea
| | - Makoto Miyata
- Graduate School of Science, Osaka Metropolitan University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Hitomi Watanabe
- Laboratory of Integrative Biological Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Gen Kondoh
- Laboratory of Integrative Biological Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Atsushi Tamura
- Advanced Comprehensive Research Organization, Teikyo University, Itabashi-ku, Tokyo 173-0003, Japan
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Pharmacology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Sachiko Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Itabashi-ku, Tokyo 173-0003, Japan
- Laboratory of Barriology and Cell Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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28
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Kulkarni A, Vidal-Henriquez E, Zwicker D. Effective simulations of interacting active droplets. Sci Rep 2023; 13:733. [PMID: 36639416 PMCID: PMC9839783 DOI: 10.1038/s41598-023-27630-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional approaches, like solving the Cahn-Hilliard equation. To overcome this challenge, we here present an alternative, efficient method. The main idea is to focus on the relevant degrees of freedom, like droplet positions and sizes. We derive dynamical equations for these quantities using approximate analytical solutions obtained from a sharp interface limit and linearized equations in the bulk phases. We verify our method against fully-resolved simulations and show that it can describe interacting droplets under the influence of chemical reactions and external gradients using only a fraction of the computational costs of traditional methods. Our method can be extended to include other processes in the future and will thus serve as a relevant platform for understanding the dynamics of droplets in cells.
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Affiliation(s)
- Ajinkya Kulkarni
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | | | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany.
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29
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+TIPs condense on microtubule plus-ends. Nat Cell Biol 2023; 25:12-14. [PMID: 36650376 DOI: 10.1038/s41556-022-01068-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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30
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Maan R, Reese L, Volkov VA, King MR, van der Sluis EO, Andrea N, Evers WH, Jakobi AJ, Dogterom M. Multivalent interactions facilitate motor-dependent protein accumulation at growing microtubule plus-ends. Nat Cell Biol 2023; 25:68-78. [PMID: 36536175 PMCID: PMC9859754 DOI: 10.1038/s41556-022-01037-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Growing microtubule ends organize end-tracking proteins into comets of mixed composition. Here using a reconstituted fission yeast system consisting of end-binding protein Mal3, kinesin Tea2 and cargo Tip1, we found that these proteins can be driven into liquid-phase droplets both in solution and at microtubule ends under crowding conditions. In the absence of crowding agents, cryo-electron tomography revealed that motor-dependent comets consist of disordered networks where multivalent interactions may facilitate non-stoichiometric accumulation of cargo Tip1. We found that two disordered protein regions in Mal3 are required for the formation of droplets and motor-dependent accumulation of Tip1, while autonomous Mal3 comet formation requires only one of them. Using theoretical modelling, we explore possible mechanisms by which motor activity and multivalent interactions may lead to the observed enrichment of Tip1 at microtubule ends. We conclude that microtubule ends may act as platforms where multivalent interactions condense microtubule-associated proteins into large multi-protein complexes.
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Affiliation(s)
- Renu Maan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Louis Reese
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.,Physiology Course 2017, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Vladimir A Volkov
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.,Physiology Course 2017, Marine Biological Laboratory, Woods Hole, MA, USA.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Matthew R King
- Physiology Course 2017, Marine Biological Laboratory, Woods Hole, MA, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St Louis, MO, USA
| | - Eli O van der Sluis
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nemo Andrea
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Wiel H Evers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Arjen J Jakobi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands. .,Physiology Course 2017, Marine Biological Laboratory, Woods Hole, MA, USA.
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31
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The augmin complex architecture reveals structural insights into microtubule branching. Nat Commun 2022; 13:5635. [PMID: 36163468 PMCID: PMC9512787 DOI: 10.1038/s41467-022-33228-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
In mitosis, the augmin complex binds to spindle microtubules to recruit the γ-tubulin ring complex (γ-TuRC), the principal microtubule nucleator, for the formation of branched microtubules. Our understanding of augmin-mediated microtubule branching is hampered by the lack of structural information on the augmin complex. Here, we elucidate the molecular architecture and conformational plasticity of the augmin complex using an integrative structural biology approach. The elongated structure of the augmin complex is characterised by extensive coiled-coil segments and comprises two structural elements with distinct but complementary functions in γ-TuRC and microtubule binding, linked by a flexible hinge. The augmin complex is recruited to microtubules via a composite microtubule binding site comprising a positively charged unordered extension and two calponin homology domains. Our study provides the structural basis for augmin function in branched microtubule formation, decisively fostering our understanding of spindle formation in mitosis. The formation of branched microtubule networks in mitotic spindles depends on the augmin complex. Zupa, Würtz et al. elucidate the molecular architecture and conformational plasticity of the augmin complex using integrative structural biology, providing structural insights into microtubule branching.
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32
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Inaba H, Sueki Y, Ichikawa M, Kabir AMR, Iwasaki T, Shigematsu H, Kakugo A, Sada K, Tsukazaki T, Matsuura K. Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside. SCIENCE ADVANCES 2022; 8:eabq3817. [PMID: 36070375 PMCID: PMC9451167 DOI: 10.1126/sciadv.abq3817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/22/2022] [Indexed: 05/24/2023]
Abstract
Microtubules play important roles in biological functions by forming superstructures, such as doublets and branched structures, in vivo. Despite the importance, it is challenging to construct these superstructures in vitro. Here, we designed a tetrameric fluorescent protein Azami-Green (AG) fused with His-tag and Tau-derived peptide (TP), TP-AG, to generate the superstructures. Main binding sites of TP-AG can be controlled to the inside and outside of microtubules by changing the polymerization conditions. The binding of TP-AG to the inside promoted microtubule formation and generated rigid and stable microtubules. The binding of TP-AG to the outside induced various microtubule superstructures, including doublets, multiplets, branched structures, and extremely long microtubules by recruiting tubulins to microtubules. Motile microtubule aster structures were also constructed by TP-AG. The generation of various microtubule superstructures by a single type of exogenous protein is a new concept for understanding the functions of microtubules and constructing microtubule-based nanomaterials.
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Affiliation(s)
- Hiroshi Inaba
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
| | - Yurina Sueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
| | - Muneyoshi Ichikawa
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | | | - Takashi Iwasaki
- Department of Bioresources Science, Graduate School of Agricultural Sciences, Tottori University, Tottori 680-8553, Japan
| | | | - Akira Kakugo
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomoya Tsukazaki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Kazunori Matsuura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori 680-8552, Japan
- Centre for Research on Green Sustainable Chemistry, Tottori University, Tottori 680-8552, Japan
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33
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Gouveia B, Kim Y, Shaevitz JW, Petry S, Stone HA, Brangwynne CP. Capillary forces generated by biomolecular condensates. Nature 2022; 609:255-264. [PMID: 36071192 DOI: 10.1038/s41586-022-05138-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 07/25/2022] [Indexed: 12/21/2022]
Abstract
Liquid-liquid phase separation and related phase transitions have emerged as generic mechanisms in living cells for the formation of membraneless compartments or biomolecular condensates. The surface between two immiscible phases has an interfacial tension, generating capillary forces that can perform work on the surrounding environment. Here we present the physical principles of capillarity, including examples of how capillary forces structure multiphase condensates and remodel biological substrates. As with other mechanisms of intracellular force generation, for example, molecular motors, capillary forces can influence biological processes. Identifying the biomolecular determinants of condensate capillarity represents an exciting frontier, bridging soft matter physics and cell biology.
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Affiliation(s)
- Bernardo Gouveia
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Yoonji Kim
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, USA.
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,The Howard Hughes Medical Institute, Princeton, NJ, USA.
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34
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Chen X, Wu T, Huang D, Zhou J, Zhou F, Tu M, Zhang Y, Li B, Li Y, Jiang L. Optothermally Programmable Liquids with Spatiotemporal Precision and Functional Complexity. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2205563. [PMID: 35918709 DOI: 10.1002/adma.202205563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Due to the intrinsic lack of spatial order and self-supported shape, liquids are often incompatible with precision manufacturing/processing and are potentially limited for advanced functionality. Herein, an optothermal strategy is developed to fully command phase-separated liquids with unprecedented spatiotemporal addressability. Specifically, a laser is focused onto an Au film to create a hot spot that locally demixes a temperature-responsive solution to produce a single optothermal droplet. Spatial precision is assured by the well-defined thermal field and temporal accuracy guaranteed by the fast heating and response rate. Time-multiplexed laser foci are deployed to engineer the thermal landscape as desired, which in turn dictates the formation/dissolution, positioning, shaping, and dynamic reconfiguration of the phase-separated liquids. Further, laser foci are programmed to orchestrate the liquid patterns in a time-continuous manner to produce liquid animations on the microscale with high fidelity. While focused lasers are routinely used to manipulate solid particles or to microfabricate solid materials, the current strategy embraces the merits of liquids and features functional complexity in information encryption, payload transportation, and reaction localization. The strategy is further applicable in scenarios such as subcellular organization of biomolecular condensates and programmable modulation of non-equilibrium systems.
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Affiliation(s)
- Xixi Chen
- Institute of Nanophotonics, Jinan University, Guangzhou, 511443, China
| | - Tianli Wu
- Institute of Nanophotonics, Jinan University, Guangzhou, 511443, China
| | - Danmin Huang
- College of Chemistry and Materials Science, Jinan University, Guangzhou, 510632, China
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China
| | - Jiajia Zhou
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, 510640, China
| | - Fengxiang Zhou
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, 510640, China
| | - Mei Tu
- College of Chemistry and Materials Science, Jinan University, Guangzhou, 510632, China
| | - Yao Zhang
- Institute of Nanophotonics, Jinan University, Guangzhou, 511443, China
| | - Baojun Li
- Institute of Nanophotonics, Jinan University, Guangzhou, 511443, China
| | - Yuchao Li
- Institute of Nanophotonics, Jinan University, Guangzhou, 511443, China
| | - Lingxiang Jiang
- South China Advanced Institute for Soft Matter Science and Technology, School of Emergent Soft Matter, South China University of Technology, Guangzhou, 510640, China
- Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, South China University of Technology, Guangzhou, 510640, China
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35
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Abstract
The interplay between phase separation and wetting of multicomponent mixtures is ubiquitous in nature and technology and recently gained significant attention across scientific disciplines, due to the discovery of biomolecular condensates. It is well understood that sessile droplets, undergoing phase separation in a static wetting configuration, exhibit microdroplet nucleation at their contact lines, forming an oil ring during later stages. However, very little is known about the dynamic counterpart, when phase separation occurs in a nonequilibrium wetting configuration, i.e., spreading droplets. Here we show that liquid-liquid phase separation strongly couples to the spreading motion of three-phase contact lines. Thus, the classical Cox-Voinov law is not applicable anymore, because phase separation adds an active spreading force beyond the capillary driving. Intriguingly, we observe that spreading starts well before any visible nucleation of microdroplets in the main droplet. Using high-speed ellipsometry, we further demonstrate that the evaporation-induced enrichment, together with surface forces, causes an even earlier nucleation in the wetting precursor film around the droplet, initiating the observed wetting transition. We expect our findings to improve the fundamental understanding of phase separation processes that involve dynamical contact lines and/or surface forces, with implications in a wide range of applications, from oil recovery or inkjet printing to material synthesis and biomolecular condensates.
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36
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Surface tension and super-stoichiometric surface enrichment in two-component biomolecular condensates. iScience 2022; 25:103852. [PMID: 35198903 PMCID: PMC8851291 DOI: 10.1016/j.isci.2022.103852] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/28/2021] [Accepted: 01/26/2022] [Indexed: 11/24/2022] Open
Abstract
Cells can achieve internal organization by exploiting liquid-liquid phase separation to form biomolecular condensates. Here we focus on the surface properties of condensates composed of two multivalent associative polymers held together by one-to-one “sticker” bonds. Using coarse-grained molecular-dynamics simulations, we study the influence of component stoichiometry on condensate surface properties. We find that unequal stoichiometry results in enrichment of the majority species at the interface and a sharp reduction of surface tension. To relate these two effects, we show that the reduction in surface tension scales linearly with the excess concentration of free binding sites at the interface. Our results imply that each excess free site contributes an approximately fixed additional energy and entropy to the interface, with the latter dominating such that enrichment of free majority sites lowers the surface tension. Our work provides insight into novel physical mechanisms by which cells can regulate condensate surface properties. Stoichiometry controls the surface tension of two-component biomolecular condensates Unequal stoichiometry leads to enrichment of the majority species at the interface Enrichment of the free majority binding sites increases the interfacial entropy Surface tension is drastically reduced at unequal stoichiometry
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37
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Chin AF, Zheng Y, Hilser VJ. Phylogenetic convergence of phase separation and mitotic function in the disordered protein BuGZ. Protein Sci 2022; 31:822-834. [PMID: 34984754 DOI: 10.1002/pro.4270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 11/05/2022]
Abstract
Intrinsically disordered proteins (IDPs) effect biological function despite their sequence-encoded lack of preference for stable three-dimensional structure. Among their many functions, IDPs form membraneless cellular compartments through liquid-liquid phase separation (LLPS), also termed biomolecular condensation. The extent to which LLPS has been evolutionarily selected remains largely unknown, as the complexities of IDP evolution hamper progress. Unlike structured proteins, rapid sequence divergence typical of IDPs confounds inference of their biophysical or biological functions from comparative sequence analyses. Here, we leverage mitosis as a universal eukaryotic feature to interrogate condensate evolutionary history. We observe that evolution has conserved the ability for six homologs of the mitotic IDP BuGZ to undergo LLPS and to serve the same mitotic function, despite low sequence conservation. We also observe that cellular context may tune LLPS. The phylogenetic correlation of LLPS and mitotic function in one protein raises the possibility of an ancient evolutionary interplay between LLPS and biological function, dating back at least 1.6 billion years to the last common ancestor of plants and animals. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Alexander F Chin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Yixian Zheng
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, Maryland, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.,T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland, USA
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38
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Böddeker TJ, Rosowski KA, Berchtold D, Emmanouilidis L, Han Y, Allain FHT, Style RW, Pelkmans L, Dufresne ER. Non-specific adhesive forces between filaments and membraneless organelles. NATURE PHYSICS 2022; 18:571-578. [PMID: 35582428 PMCID: PMC9106579 DOI: 10.1038/s41567-022-01537-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/04/2022] [Indexed: 05/07/2023]
Abstract
Many membraneless organelles are liquid-like domains that form inside the active, viscoelastic environment of living cells through phase separation. To investigate the potential coupling of phase separation with the cytoskeleton, we quantify the structural correlations of membraneless organelles (stress granules) and cytoskeletal filaments (microtubules) in a human-derived epithelial cell line. We find that microtubule networks are substantially denser in the vicinity of stress granules. When microtubules are depolymerized, the sub-units localize near the surface of the stress granules. We interpret these data using a thermodynamic model of partitioning of particles to the surface and bulk of the droplets. In this framework, our data are consistent with a weak (≲k B T) affinity of the microtubule sub-units for stress granule interfaces. As microtubules polymerize, their interfacial affinity increases, providing sufficient adhesion to deform droplets and/or the network. Our work suggests that proteins and other objects in the cell have a non-specific affinity for droplet interfaces that increases with the contact area and becomes most apparent when they have no preference for the interior of a droplet over the rest of the cytoplasm. We validate this basic physical phenomenon in vitro through the interaction of a simple protein-RNA condensate with microtubules.
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Affiliation(s)
| | | | - Doris Berchtold
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Yaning Han
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | | | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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39
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Wang H, Kelley FM, Milovanovic D, Schuster BS, Shi Z. Surface tension and viscosity of protein condensates quantified by micropipette aspiration. BIOPHYSICAL REPORTS 2021; 1:100011. [PMID: 36247368 PMCID: PMC9563586 DOI: 10.1016/j.bpr.2021.100011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022]
Abstract
The material properties of biomolecular condensates have been suggested to play important biological and pathological roles. Despite the rapid increase in the number of biomolecules identified that undergo liquid-liquid phase separation, quantitative studies and direct measurements of the material properties of the resulting condensates have been severely lagging behind. Here, we develop a micropipette-based technique that uniquely, to our knowledge, allows quantifications of both the surface tension and viscosity of biomolecular condensates, independent of labeling and surface-wetting effects. We demonstrate the accuracy and versatility of this technique by measuring condensates of LAF-1 RGG domains and a polymer-based aqueous two-phase system. We further confirm our measurements using established condensate fusion and fluorescence recovery after photobleaching assays. We anticipate the micropipette-based technique will be widely applicable to biomolecular condensates and will resolve several limitations regarding current approaches.
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Affiliation(s)
- Huan Wang
- Department of Chemistry and Chemical Biology
| | - Fleurie M. Kelley
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Benjamin S. Schuster
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, New Jersey
| | - Zheng Shi
- Department of Chemistry and Chemical Biology
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40
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Kato S, Garenne D, Noireaux V, Maeda YT. Phase Separation and Protein Partitioning in Compartmentalized Cell-Free Expression Reactions. Biomacromolecules 2021; 22:3451-3459. [PMID: 34258998 DOI: 10.1021/acs.biomac.1c00546] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Liquid-liquid phase separation (LLPS) is important to control a wide range of reactions from gene expression to protein degradation in a cell-sized space. To bring a better understanding of the compatibility of such phase-separated structures with protein synthesis, we study emergent LLPS in a cell-free transcription-translation (TXTL) reaction. When the TXTL reaction composed of many proteins is concentrated, the uniformly mixed state becomes unstable, and membrane-less phases form spontaneously. This LLPS droplet formation is induced when the TXTL reaction is enclosed in water-in-oil emulsion droplets, in which water evaporates from the surface. As the emulsion droplets shrink, smaller LLPS droplets appear inside the emulsion droplets and coalesce into large phase-separated domains that partition the localization of synthesized reporter proteins. The presence of PEG in the TXTL reaction is important not only for versatile cell-free protein synthesis but also for the formation of two large domains capable of protein partitioning. Our results may shed light on the dynamic interplay of LLPS formation and cell-free protein synthesis toward the construction of synthetic organelles.
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Affiliation(s)
- Shuzo Kato
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
| | - David Garenne
- School of Physics and Astronomy, University of Minnesota, 115 Union Street Se, Minneapolis, Minnesota 55455, United States
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, 115 Union Street Se, Minneapolis, Minnesota 55455, United States
| | - Yusuke T Maeda
- Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan
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41
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Kirschbaum J, Zwicker D. Controlling biomolecular condensates via chemical reactions. J R Soc Interface 2021; 18:20210255. [PMID: 34186016 PMCID: PMC8241490 DOI: 10.1098/rsif.2021.0255] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
Biomolecular condensates are small droplets forming spontaneously in biological cells through phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on post-translational modifications of proteins. For biomolecular condensates, such chemical modifications could alter the molecular interaction of key condensate components. Here, we test this idea using a theoretical model based on non-equilibrium thermodynamics. In particular, we describe the chemical reactions using transition-state theory, which accounts for the non-ideality of phase separation. We identify that fast control, as in cell signalling, is only possible when external energy input drives the reaction out of equilibrium. If this reaction differs inside and outside the droplet, it is even possible to control droplet sizes. Such an imbalance in the reaction could be created by enzymes localizing to the droplet. Since this situation is typical inside cells, we speculate that our proposed mechanism is used to stabilize multiple droplets with independently controlled size and count. Our model provides a novel and thermodynamically consistent framework for describing droplets subject to non-equilibrium chemical reactions.
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Affiliation(s)
- Jan Kirschbaum
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - David Zwicker
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
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42
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Jambon-Puillet E, Piéchaud MR, Brun PT. Elastic amplification of the Rayleigh-Taylor instability in solidifying melts. Proc Natl Acad Sci U S A 2021; 118:e2020701118. [PMID: 33619177 PMCID: PMC7958244 DOI: 10.1073/pnas.2020701118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The concomitant mechanical deformation and solidification of melts are relevant to a broad range of phenomena. Examples include the preparation of cotton candy, the atomization of metals, the manufacture of glass fibers, and the formation of elongated structures in volcanic eruptions known as Pele's hair. Usually, solid-like deformations during solidification are neglected as the melt is much more malleable in its initial liquid-like form. Here we demonstrate how elastic deformations in the midst of solidification, i.e., while the melt responds as a very soft solid ([Formula: see text] Pa), can lead to the formation of previously unknown periodic structures. Namely, we generate an array of droplets on a thin layer of liquid elastomer melt coated on the outside of a rotating cylinder through the Rayleigh-Taylor instability. Then, as the melt cures and goes through its gelation point, the rotation speed is increased and the drops stretch into hairs. The ongoing solidification eventually hardens the material, permanently "freezing" these elastic deformations into a patterned solid. Using experiments, simulation, and theory, we demonstrate that the formation of our two-step patterns can be rationalized when combining the tools from fluid mechanics, elasticity, and statistics. Our study therefore provides a framework to analyze multistep pattern formation processes and harness them to assemble complex materials.
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Affiliation(s)
- Etienne Jambon-Puillet
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
| | - Matthieu Royer Piéchaud
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
| | - P-T Brun
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08540
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