51
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Clemens L, Kutuzov M, Bayer KV, Goyette J, Allard J, Dushek O. Determination of the molecular reach of the protein tyrosine phosphatase SHP-1. Biophys J 2021; 120:2054-2066. [PMID: 33781765 PMCID: PMC8204385 DOI: 10.1016/j.bpj.2021.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/05/2021] [Accepted: 03/23/2021] [Indexed: 12/26/2022] Open
Abstract
Immune receptors signal by recruiting (or tethering) enzymes to their cytoplasmic tails to catalyze reactions on substrates within reach. This is the case for the phosphatase SHP-1, which, upon tethering to inhibitory receptors, dephosphorylates diverse substrates to control T cell activation. Precisely how tethering regulates SHP-1 activity is incompletely understood. Here, we measure binding, catalysis, and molecular reach for tethered SHP-1 reactions. We determine the molecular reach of SHP-1 to be 13.0 nm, which is longer than the estimate from the allosterically active structure (5.3 nm), suggesting that SHP-1 can achieve a longer reach by exploring multiple active conformations. Using modeling, we show that when uniformly distributed, receptor-SHP-1 complexes can only reach 15% of substrates, but this increases to 90% when they are coclustered. When within reach, we show that membrane recruitment increases the activity of SHP-1 by a 1000-fold increase in local concentration. The work highlights how molecular reach regulates the activity of membrane-recruited SHP-1 with insights applicable to other membrane-tethered reactions.
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Affiliation(s)
- Lara Clemens
- Center for Complex Biological Systems, University of California Irvine, Irvine, California
| | - Mikhail Kutuzov
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences University of New South Wales, Sydney, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Jun Allard
- Center for Complex Biological Systems, University of California Irvine, Irvine, California.
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom.
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52
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Goetz SK, Mahamid J. Visualizing Molecular Architectures of Cellular Condensates: Hints of Complex Coacervation Scenarios. Dev Cell 2021; 55:97-107. [PMID: 33049214 DOI: 10.1016/j.devcel.2020.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/15/2020] [Accepted: 09/05/2020] [Indexed: 02/09/2023]
Abstract
In the last decade, liquid-liquid phase separation has emerged as a fundamental principle in the organization of crowded cellular environments into functionally distinct membraneless compartments. It is now established that biomolecules can condense into various physical phases, traditionally defined for simple polymer systems, and more recently elucidated by techniques employed in life sciences. We review pioneering cryo-electron tomography studies that have begun to unravel a wide spectrum of molecular architectures, ranging from amorphous to crystalline assemblies, that underlie cellular condensates. These observations bring into question current interpretations of microscopic phase behavior. Furthermore, by examining emerging concepts of non-classical phase separation pathways in small-molecule crystallization, we draw parallels with biomolecular condensation that highlight aspects not yet fully explored. In particular, transient and metastable intermediates that might be challenging to capture experimentally inside cells could be probed through computational simulations and enable a multi-scale understanding of the subcellular organization governed by distinct phases.
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Affiliation(s)
- Sara Kathrin Goetz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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53
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Wiegand T, Hyman AA. Drops and fibers - how biomolecular condensates and cytoskeletal filaments influence each other. Emerg Top Life Sci 2020; 4:247-261. [PMID: 33048111 PMCID: PMC7733666 DOI: 10.1042/etls20190174] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
The cellular cytoskeleton self-organizes by specific monomer-monomer interactions resulting in the polymerization of filaments. While we have long thought about the role of polymerization in cytoskeleton formation, we have only begun to consider the role of condensation in cytoskeletal organization. In this review, we highlight how the interplay between polymerization and condensation leads to the formation of the cytoskeleton.
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Affiliation(s)
- Tina Wiegand
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
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54
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A framework for understanding the functions of biomolecular condensates across scales. Nat Rev Mol Cell Biol 2020; 22:215-235. [PMID: 33169001 DOI: 10.1038/s41580-020-00303-z] [Citation(s) in RCA: 378] [Impact Index Per Article: 94.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes. They are also implicated in a wide range of cellular functions, organizing molecules that act in processes ranging from RNA metabolism to signalling to gene regulation. Early work in the field focused on identifying condensates and understanding how their physical properties and regulation arise from molecular constituents. Recent years have brought a focus on understanding condensate functions. Studies have revealed functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating localization of cellular materials and homeostatic responses). In this Roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the recent literature and organize these functions into a series of non-exclusive classes across the different length scales. We conclude with a discussion of areas of current interest and challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology.
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55
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Borowicz P, Chan H, Hauge A, Spurkland A. Adaptor proteins: Flexible and dynamic modulators of immune cell signalling. Scand J Immunol 2020; 92:e12951. [DOI: 10.1111/sji.12951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Paweł Borowicz
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Hanna Chan
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anette Hauge
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
| | - Anne Spurkland
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Oslo Norway
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56
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How the T cell signaling network processes information to discriminate between self and agonist ligands. Proc Natl Acad Sci U S A 2020; 117:26020-26030. [PMID: 33020303 DOI: 10.1073/pnas.2008303117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
T cells exhibit remarkable sensitivity and selectivity in detecting and responding to agonist peptides (p) bound to MHC molecules in a sea of self pMHC molecules. Despite much work, understanding of the underlying mechanisms of distinguishing such ligands remains incomplete. Here, we quantify T cell discriminatory capacity using channel capacity, a direct measure of the signaling network's ability to discriminate between antigen-presenting cells (APCs) displaying either self ligands or a mixture of self and agonist ligands. This metric shows how differences in information content between these two types of peptidomes are decoded by the topology and rates of kinetic proofreading signaling steps inside T cells. Using channel capacity, we constructed numerically substantiated hypotheses to explain the discriminatory role of a recently identified slow LAT Y132 phosphorylation step. Our results revealed that in addition to the number and kinetics of sequential signaling steps, a key determinant of discriminatory capability is spatial localization of a minimum number of these steps to the engaged TCR. Biochemical and imaging experiments support these findings. Our results also reveal the discriminatory role of early negative feedback and necessary amplification conferred by late positive feedback.
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57
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Dodson AE, Kennedy S. Phase Separation in Germ Cells and Development. Dev Cell 2020; 55:4-17. [PMID: 33007213 DOI: 10.1016/j.devcel.2020.09.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/28/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022]
Abstract
The animal germline is an immortal cell lineage that gives rise to eggs and/or sperm each generation. Fusion of an egg and sperm, or fertilization, sets off a cascade of developmental events capable of producing an array of different cell types and body plans. How germ cells develop, function, and eventually give rise to entirely new organisms is an important question in biology. A growing body of evidence suggests that phase separation events likely play a significant and multifaceted role in germ cells and development. Here, we discuss the organization, dynamics, and potential functions of phase-separated compartments in germ cells and examine the various ways in which phase separation might contribute to the development of multicellular organisms.
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Affiliation(s)
- Anne E Dodson
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
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58
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Chung JK, Huang WYC, Carbone CB, Nocka LM, Parikh AN, Vale RD, Groves JT. Coupled membrane lipid miscibility and phosphotyrosine-driven protein condensation phase transitions. Biophys J 2020; 120:1257-1265. [PMID: 33080222 DOI: 10.1016/j.bpj.2020.09.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/18/2022] Open
Abstract
Lipid miscibility phase separation has long been considered to be a central element of cell membrane organization. More recently, protein condensation phase transitions, into three-dimensional droplets or in two-dimensional lattices on membrane surfaces, have emerged as another important organizational principle within cells. Here, we reconstitute the linker for activation of T cells (LAT):growth-factor-receptor-bound protein 2 (Grb2):son of sevenless (SOS) protein condensation on the surface of giant unilamellar vesicles capable of undergoing lipid phase separations. Our results indicate that the assembly of the protein condensate on the membrane surface can drive lipid phase separation. This phase transition occurs isothermally and is governed by tyrosine phosphorylation on LAT. Furthermore, we observe that the induced lipid phase separation drives localization of the SOS substrate, K-Ras, into the LAT:Grb2:SOS protein condensate.
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Affiliation(s)
- Jean K Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, California; The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - William Y C Huang
- Department of Chemistry, University of California, Berkeley, Berkeley, California; The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Catherine B Carbone
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California; The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Laura M Nocka
- Department of Chemistry, University of California, Berkeley, Berkeley, California
| | - Atul N Parikh
- Department of Biomedical Engineering, University of California, Davis, Davis, California
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California; The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, California; The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory, Woods Hole, Massachusetts.
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59
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Abstract
Many critical biological events, including biochemical signaling, membrane traffic, and cell motility, originate at membrane surfaces. Each such event requires that members of a specific group of proteins and lipids rapidly assemble together at a specific site on the membrane surface. Understanding the biophysical mechanisms that stabilize these assemblies is critical to decoding and controlling cellular functions. In this article, we review progress toward a quantitative biophysical understanding of the mechanisms that drive membrane heterogeneity and organization. We begin from a physical perspective, reviewing the fundamental principles and key experimental evidence behind each proposed mechanism. We then shift to a biological perspective, presenting key examples of the role of heterogeneity in biology and asking which physical mechanisms may be responsible. We close with an applied perspective, noting that membrane heterogeneity provides a novel therapeutic target that is being exploited by a growing number of studies at the interface of biology, physics, and engineering.
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Affiliation(s)
- Wade F Zeno
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Kasey J Day
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
| | - Vernita D Gordon
- Department of Physics, The University of Texas at Austin, Austin, Texas 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Center for Nonlinear Dynamics, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA;
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
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60
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Hui E. Understanding T cell signaling using membrane reconstitution. Immunol Rev 2020; 291:44-56. [PMID: 31402497 DOI: 10.1111/imr.12767] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/31/2022]
Abstract
T cells are central players of our immune system, as their functions range from killing tumorous and virus-infected cells to orchestrating the entire immune response. In order for T cells to divide and execute their functions, they must be activated by antigen-presenting cells (APCs) through a cell-cell junction. Extracellular interactions between receptors on T cells and their ligands on APCs trigger signaling cascades comprised of protein-protein interactions, enzymatic reactions, and spatial reorganization events, to either stimulate or repress T cell activation. Plasma membrane is the major platform for T cell signaling. Recruitment of cytosolic proteins to membrane-bound receptors is a common critical step in many signaling pathways. Membranes decrease the dimensionality of protein-protein interactions to enable weak yet biologically important interactions. Membrane resident proteins can phase separate into micro-islands that promote signaling by enriching or excluding signal regulators. Moreover, some membrane lipids can either mediate or regulate cell signaling by interacting with signaling proteins. While it is critical to investigate T cell signaling in a cellular environment, the large number of signaling pathways involved and potential crosstalk have made it difficult to obtain precise, quantitative information on T cell signaling. Reconstitution of purified proteins to model membranes provides a complementary avenue for T cell signaling research. Here, I review recent progress in studying T cell signaling using membrane reconstitution approaches.
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Affiliation(s)
- Enfu Hui
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California
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61
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Martinez-Fabregas J, Wilmes S, Wang L, Hafer M, Pohler E, Lokau J, Garbers C, Cozzani A, Fyfe PK, Piehler J, Kazemian M, Mitra S, Moraga I. Kinetics of cytokine receptor trafficking determine signaling and functional selectivity. eLife 2019; 8:e49314. [PMID: 31774398 PMCID: PMC6914340 DOI: 10.7554/elife.49314] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/24/2019] [Indexed: 12/27/2022] Open
Abstract
Cytokines activate signaling via assembly of cell surface receptors, but it is unclear whether modulation of cytokine-receptor binding parameters can modify biological outcomes. We have engineered IL-6 variants with different affinities to gp130 to investigate how cytokine receptor binding dwell-times influence functional selectivity. Engineered IL-6 variants showed a range of signaling amplitudes and induced biased signaling, with changes in receptor binding dwell-times affecting more profoundly STAT1 than STAT3 phosphorylation. We show that this differential signaling arises from defective translocation of ligand-gp130 complexes to the endosomal compartment and competitive STAT1/STAT3 binding to phospho-tyrosines in gp130, and results in unique patterns of STAT3 binding to chromatin. This leads to a graded gene expression response and differences in ex vivo differentiation of Th17, Th1 and Treg cells. These results provide a molecular understanding of signaling biased by cytokine receptors, and demonstrate that manipulation of signaling thresholds is a useful strategy to decouple cytokine functional pleiotropy.
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Affiliation(s)
- Jonathan Martinez-Fabregas
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Stephan Wilmes
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Luopin Wang
- Department Computer SciencePurdue UniversityWest LafayetteUnited States
| | | | - Elizabeth Pohler
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Juliane Lokau
- Department of Pathology, Medical FacultyOtto-von-Guericke-University MagdeburgMagdeburgGermany
| | - Christoph Garbers
- Department of Pathology, Medical FacultyOtto-von-Guericke-University MagdeburgMagdeburgGermany
| | - Adeline Cozzani
- INSERM UMR-S-11721, Centre de Recherche Jean-Pierre Aubert (JPARC), Institut pour la Recherche sur le Cancer de Lille (IRCL), Université de LilleLilleFrance
| | - Paul K Fyfe
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Jacob Piehler
- Department of BiologyUniversity of OsnabrückOsnabrückGermany
| | - Majid Kazemian
- Department Computer SciencePurdue UniversityWest LafayetteUnited States
| | - Suman Mitra
- INSERM UMR-S-11721, Centre de Recherche Jean-Pierre Aubert (JPARC), Institut pour la Recherche sur le Cancer de Lille (IRCL), Université de LilleLilleFrance
| | - Ignacio Moraga
- Division of Cell Signaling and Immunology, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
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62
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The Control Centers of Biomolecular Phase Separation: How Membrane Surfaces, PTMs, and Active Processes Regulate Condensation. Mol Cell 2019; 76:295-305. [PMID: 31604601 DOI: 10.1016/j.molcel.2019.09.016] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/30/2022]
Abstract
Biomolecular condensation is emerging as an essential process for cellular compartmentalization. The formation of biomolecular condensates can be driven by liquid-liquid phase separation, which arises from weak, multivalent interactions among proteins and nucleic acids. A substantial body of recent work has revealed that diverse cellular processes rely on biomolecular condensation and that aberrant phase separation may cause disease. Many proteins display an intrinsic propensity to undergo phase separation. However, the mechanisms by which cells regulate phase separation to build functional condensates at the appropriate time and location are only beginning to be understood. Here, we review three key cellular mechanisms that enable the control of biomolecular phase separation: membrane surfaces, post-translational modifications, and active processes. We discuss how these mechanisms may function in concert to provide robust control over biomolecular condensates and suggest new research avenues that will elucidate how cells build and maintain these key centers of cellular compartmentalization.
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63
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Case LB, Zhang X, Ditlev JA, Rosen MK. Stoichiometry controls activity of phase-separated clusters of actin signaling proteins. Science 2019; 363:1093-1097. [PMID: 30846599 DOI: 10.1126/science.aau6313] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022]
Abstract
Biomolecular condensates concentrate macromolecules into foci without a surrounding membrane. Many condensates appear to form through multivalent interactions that drive liquid-liquid phase separation (LLPS). LLPS increases the specific activity of actin regulatory proteins toward actin assembly by the Arp2/3 complex. We show that this increase occurs because LLPS of the Nephrin-Nck-N-WASP signaling pathway on lipid bilayers increases membrane dwell time of N-WASP and Arp2/3 complex, consequently increasing actin assembly. Dwell time varies with relative stoichiometry of the signaling proteins in the phase-separated clusters, rendering N-WASP and Arp2/3 activity stoichiometry dependent. This mechanism of controlling protein activity is enabled by the stoichiometrically undefined nature of biomolecular condensates. Such regulation should be a general feature of signaling systems that assemble through multivalent interactions and drive nonequilibrium outputs.
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Affiliation(s)
- Lindsay B Case
- The HHMI Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA.,Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xu Zhang
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jonathon A Ditlev
- The HHMI Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA.,Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michael K Rosen
- The HHMI Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA. .,Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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64
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Mclaurin JD, Weiner OD. Multiple sources of signal amplification within the B-cell Ras/MAPK pathway. Mol Biol Cell 2019; 30:1610-1620. [PMID: 31042097 PMCID: PMC6727637 DOI: 10.1091/mbc.e18-09-0560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Ras-Map kinase (MAPK) cascade underlies functional decisions in a wide range of cell types and organisms. In B-cells, positive feedback-driven Ras activation is the proposed source of the digital (all or none) MAPK responses following antigen stimulation. However, an inability to measure endogenous Ras activity in living cells has hampered our ability to test this model directly. Here we leverage biosensors of endogenous Ras and ERK activity to revisit this question. We find that B-cell receptor (BCR) ligation drives switch-like Ras activation and that lower BCR signaling output is required for the maintenance versus the initiation of Ras activation. Surprisingly, digital ERK responses persist in the absence of positive feedback-mediated Ras activation, and digital ERK is observed at a threshold level of Ras activation. These data suggest an independent analogue-to-digital switch downstream of Ras activation and reveal that multiple sources of signal amplification exist within the Ras-ERK module of the BCR pathway.
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Affiliation(s)
- Justin D Mclaurin
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
| | - Orion D Weiner
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158
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65
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Lee IH, Imanaka MY, Modahl EH, Torres-Ocampo AP. Lipid Raft Phase Modulation by Membrane-Anchored Proteins with Inherent Phase Separation Properties. ACS OMEGA 2019; 4:6551-6559. [PMID: 31179407 PMCID: PMC6547621 DOI: 10.1021/acsomega.9b00327] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/29/2019] [Indexed: 05/11/2023]
Abstract
Cell plasma membranes are a heterogeneous mixture of lipids and membrane proteins. The importance of heterogeneous lipid domains (also called lipid rafts) as a molecular sorting platform has been implicated in many physiological processes. Cell plasma membranes that are detached from the cytoskeletal structure spontaneously phase separate into distinct domains at equilibrium, which show their inherent demixing properties. Recently, researchers have discovered that proteins with strong interprotein interactions also spontaneously phase separate into distinct protein domains, thus enabling the maintenance of many membraneless organelles. Protein phase separation may also take place on the lipid membranes via lipid-anchored proteins, which suggests another potential molecular sorting platform for physiological processes on the cell membrane. When two-phase separation properties coexist physiologically, they may change the resulting phase behavior or serve as independent sorting platforms. In this paper, we used in vitro reconstitution and fluorescence imaging to systematically quantify the phase behavior that arises when proteins with inherent phase separation properties interact with raft mixture lipid membranes. Our observations and simulations show both that the proteins may enhance lipid phase separation and that this is a general property of phase-separating protein systems with a diverse number of components involved. This suggests that we should consider the overall effect of the properties of both membrane-anchored proteins and lipids when interpreting molecular sorting phenomena on the membranes.
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Affiliation(s)
- Il-Hyung Lee
- Department
of Chemistry and Department of Biology, University of Puget
Sound, Tacoma, Washington 98416, United States
- E-mail:
| | - Matthew Y. Imanaka
- Department
of Chemistry and Department of Biology, University of Puget
Sound, Tacoma, Washington 98416, United States
| | - Emmi H. Modahl
- Department
of Chemistry and Department of Biology, University of Puget
Sound, Tacoma, Washington 98416, United States
| | - Ana P. Torres-Ocampo
- Department
of Biochemistry and Molecular Biology, University
of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
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66
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Abstract
Cell surface transmembrane receptors often form nanometer- to micrometer-scale clusters to initiate signal transduction in response to environmental cues. Extracellular ligand oligomerization, domain-domain interactions, and binding to multivalent proteins all contribute to cluster formation. Here we review the current understanding of mechanisms driving cluster formation in a series of representative receptor systems: glycosylated receptors, immune receptors, cell adhesion receptors, Wnt receptors, and receptor tyrosine kinases. We suggest that these clusters share properties of systems that undergo liquid-liquid phase separation and could be investigated in this light.
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Affiliation(s)
- Lindsay B Case
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , ,
| | - Jonathon A Ditlev
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , ,
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; , ,
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67
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Tischer DK, Weiner OD. Light-based tuning of ligand half-life supports kinetic proofreading model of T cell signaling. eLife 2019; 8:42498. [PMID: 30947808 PMCID: PMC6488292 DOI: 10.7554/elife.42498] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 04/03/2019] [Indexed: 11/30/2022] Open
Abstract
T cells are thought to discriminate self from foreign peptides by converting small differences in ligand binding half-life into large changes in cell signaling. Such a kinetic proofreading model has been difficult to test directly, as existing methods of altering ligand binding half-life also change other potentially important biophysical parameters, most notably the mechanical stability of the receptor-ligand interaction. Here we develop an optogenetic approach to specifically tune the binding half-life of a chimeric antigen receptor without changing other binding parameters and provide direct evidence of kinetic proofreading in T cell signaling. This half-life discrimination is executed in the proximal signaling pathway, downstream of ZAP70 recruitment and upstream of diacylglycerol accumulation. Our methods represent a general tool for temporal and spatial control of T cell signaling and extend the reach of optogenetics to probe pathways where the individual molecular kinetics, rather than the ensemble average, gates downstream signaling.
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Affiliation(s)
- Doug K Tischer
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Orion David Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, United States
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68
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Affiliation(s)
- Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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69
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Huang WYC, Alvarez S, Kondo Y, Lee YK, Chung JK, Lam HYM, Biswas KH, Kuriyan J, Groves JT. A molecular assembly phase transition and kinetic proofreading modulate Ras activation by SOS. Science 2019; 363:1098-1103. [PMID: 30846600 PMCID: PMC6563836 DOI: 10.1126/science.aau5721] [Citation(s) in RCA: 208] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022]
Abstract
The guanine nucleotide exchange factor (GEF) Son of Sevenless (SOS) is a key Ras activator that is autoinhibited in the cytosol and activates upon membrane recruitment. Autoinhibition release involves structural rearrangements of the protein at the membrane and thus introduces a delay between initial recruitment and activation. In this study, we designed a single-molecule assay to resolve the time between initial receptor-mediated membrane recruitment and the initiation of GEF activity of individual SOS molecules on microarrays of Ras-functionalized supported membranes. The rise-and-fall shape of the measured SOS activation time distribution and the long mean time scale to activation (~50 seconds) establish a basis for kinetic proofreading in the receptor-mediated activation of Ras. We further demonstrate that this kinetic proofreading is modulated by the LAT (linker for activation of T cells)-Grb2-SOS phosphotyrosine-driven phase transition at the membrane.
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Affiliation(s)
- William Y C Huang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Steven Alvarez
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - Yasushi Kondo
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Young Kwang Lee
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jean K Chung
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | - Kabir H Biswas
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - John Kuriyan
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Divisions of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Divisions of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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70
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Ganzinger KA, Schwille P. More from less - bottom-up reconstitution of cell biology. J Cell Sci 2019; 132:132/4/jcs227488. [PMID: 30718262 DOI: 10.1242/jcs.227488] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ultimate goal of bottom-up synthetic biology is recreating life in its simplest form. However, in its quest to find the minimal functional units of life, this field contributes more than its main aim by also offering a range of tools for asking, and experimentally approaching, biological questions. This Review focusses on how bottom-up reconstitution has furthered our understanding of cell biology. Studying cell biological processes in vitro has a long tradition, but only recent technological advances have enabled researchers to reconstitute increasingly complex biomolecular systems by controlling their multi-component composition and their spatiotemporal arrangements. We illustrate this progress using the example of cytoskeletal processes. Our understanding of these has been greatly enhanced by reconstitution experiments, from the first in vitro experiments 70 years ago to recent work on minimal cytoskeleton systems (including this Special Issue of Journal of Cell Science). Importantly, reconstitution approaches are not limited to the cytoskeleton field. Thus, we also discuss progress in other areas, such as the shaping of biomembranes and cellular signalling, and prompt the reader to add their subfield of cell biology to this list in the future.
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Affiliation(s)
- Kristina A Ganzinger
- Physics of Cellular Interactions Group, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Petra Schwille
- Department Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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71
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Bandaru P, Kondo Y, Kuriyan J. The Interdependent Activation of Son-of-Sevenless and Ras. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031534. [PMID: 29610148 DOI: 10.1101/cshperspect.a031534] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The guanine-nucleotide exchange factor (GEF) Son-of-Sevenless (SOS) plays a critical role in metazoan signaling by converting Ras•GDP (guanosine diphosphate) to Ras•GTP (guanosine triphosphate) in response to tyrosine kinase activation. Structural studies have shown that SOS differs from other Ras-specific GEFs in that SOS is itself activated by Ras•GTP binding to an allosteric site, distal to the site of nucleotide exchange. The activation of SOS involves membrane recruitment and conformational changes, triggered by lipid binding, that open the allosteric binding site for Ras•GTP. This is in contrast to other Ras-specific GEFs, which are activated by second messengers that more directly affect the active site. Allosteric Ras•GTP binding stabilizes SOS at the membrane, where it can turn over other Ras molecules processively, leading to an ultrasensitive response that is distinct from that of other Ras-specific GEFs.
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Affiliation(s)
- Pradeep Bandaru
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| | - Yasushi Kondo
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| | - John Kuriyan
- Departments of Molecular and Cell Biology and of Chemistry, California Institute for Quantitative Biosciences, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
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72
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Lin JJY, Low-Nam ST, Alfieri KN, McAffee DB, Fay NC, Groves JT. Mapping the stochastic sequence of individual ligand-receptor binding events to cellular activation: T cells act on the rare events. Sci Signal 2019; 12:12/564/eaat8715. [PMID: 30647147 DOI: 10.1126/scisignal.aat8715] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
T cell receptor (TCR) binding to agonist peptide major histocompatibility complex (pMHC) triggers signaling events that initiate T cell responses. This system is remarkably sensitive, requiring only a few binding events to successfully activate a cellular response. On average, activating pMHC ligands exhibit mean dwell times of at least a few seconds when bound to the TCR. However, a T cell accumulates pMHC-TCR interactions as a stochastic series of discrete, single-molecule binding events whose individual dwell times are broadly distributed. With activation occurring in response to only a handful of such binding events, individual cells are unlikely to experience the average binding time. Here, we mapped the ensemble of pMHC-TCR binding events in space and time while simultaneously monitoring cellular activation. Our findings revealed that T cell activation hinges on rare, long-dwell time binding events that are an order of magnitude longer than the average agonist pMHC-TCR dwell time. Furthermore, we observed that short pMHC-TCR binding events that were spatially correlated and temporally sequential led to cellular activation. These observations indicate that T cell antigen discrimination likely occurs by sensing the tail end of the pMHC-TCR binding dwell time distribution rather than its average properties.
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Affiliation(s)
- Jenny J Y Lin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shalini T Low-Nam
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katherine N Alfieri
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Darren B McAffee
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicole C Fay
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA.
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73
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74
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Ditlev JA, Case LB, Rosen MK. Who's In and Who's Out-Compositional Control of Biomolecular Condensates. J Mol Biol 2018; 430:4666-4684. [PMID: 30099028 PMCID: PMC6204295 DOI: 10.1016/j.jmb.2018.08.003] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 02/06/2023]
Abstract
Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid-liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.
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Affiliation(s)
- Jonathon A Ditlev
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Lindsay B Case
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Michael K Rosen
- Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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75
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Biswas KH, Cho NJ, Groves JT. Fabrication of Multicomponent, Spatially Segregated DNA and Protein-Functionalized Supported Membrane Microarray. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9781-9788. [PMID: 30032610 DOI: 10.1021/acs.langmuir.8b01364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Deoxyribonucleic acid (DNA) has been used as a material for a variety of applications, including surface functionalization for cell biological or in vitro reconstitution studies. Use of DNA-based surface functionalization eliminates limitations of multiplexing posed by traditionally used methods in applications requiring spatially segregated surface functionalization. Recently, we have reported a stochastic, membrane fusion-based strategy to fabricate multicomponent membrane array substrates displaying spatially segregated protein ligands using biotin-streptavidin and Ni-NTA-polyhistidine interactions. Here, we report the delivery of DNA oligonucleotide-conjugated lipid molecules to membrane corrals, allowing spatially segregated membrane corral functionalization in a membrane microarray. Incubation of microbeads coated with the supported membrane resulted in an exchange of lipid contents with planar membrane corrals present on a micropatterned substrate. Increases in the system temperature and membrane corral size resulted in alterations in the rate constant of lipid exchange, which are in agreement with our previously developed analytical model and further confirm that lipid exchange is a diffusion-based process that takes place after the formation of a long "fusion-stalk" between the two membranes. We take advantage of the physical dimensions of the fusion-stalk with a large aspect ratio to deliver DNA oligonucleotide-conjugated lipid molecules to membrane corrals. We believe that the ability to functionalize membrane corrals with DNA oligonucleotides significantly increases the utility of the stochastic fusion-mediated lipid delivery strategy in the functionalization of biomolecules such as DNA or DNA-conjugated protein ligands.
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Affiliation(s)
- Kabir H Biswas
- Mechanobiology Institute , National University of Singapore , Singapore 117411 , Singapore
- School of Materials Science and Engineering , Nanyang Technological University , Singapore 639798 , Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering , Nanyang Technological University , Singapore 639798 , Singapore
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive , Singapore 637459 , Singapore
| | - Jay T Groves
- School of Materials Science and Engineering , Nanyang Technological University , Singapore 639798 , Singapore
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
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76
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Protein Clusters in Phosphotyrosine Signal Transduction. J Mol Biol 2018; 430:4547-4556. [PMID: 29870724 DOI: 10.1016/j.jmb.2018.05.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/08/2018] [Accepted: 05/28/2018] [Indexed: 11/20/2022]
Abstract
Signal transduction systems based on tyrosine phosphorylation are central to cell-cell communication in multicellular organisms. Typically, in such a system, the signal is initiated by activating tyrosine kinases associated with transmembrane receptors, which induces tyrosine phosphorylation of the receptor and/or associated proteins. The phosphorylated tyrosines then serve as docking sites for the binding of various downstream effector proteins. It has long been observed that the cooperative association of the receptors and effectors produces higher-order protein assemblies (clusters) following signal activation in virtually all phosphotyrosine signal transduction systems. However, mechanistic studies on how such clustering processes affect signal transduction outcomes have only emerged recently. Here we review current progress in decoding the biophysical consequences of clustering on the behavior of the system, and how clustering affects how these receptors process information.
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77
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78
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Biswas KH, Zhongwen C, Dubey AK, Oh D, Groves JT. Multicomponent Supported Membrane Microarray for Monitoring Spatially Resolved Cellular Signaling Reactions. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Kabir H. Biswas
- Mechanobiology Institute; National University of Singapore; Singapore 117411 Singapore
| | - Chen Zhongwen
- Mechanobiology Institute; National University of Singapore; Singapore 117411 Singapore
| | - Alok Kumar Dubey
- Mechanobiology Institute; National University of Singapore; Singapore 117411 Singapore
| | - Dongmyung Oh
- Mechanobiology Institute; National University of Singapore; Singapore 117411 Singapore
| | - Jay T. Groves
- Department of Chemistry; University of California; Berkeley CA 94720 USA
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79
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Courtney AH, Lo WL, Weiss A. TCR Signaling: Mechanisms of Initiation and Propagation. Trends Biochem Sci 2017; 43:108-123. [PMID: 29269020 DOI: 10.1016/j.tibs.2017.11.008] [Citation(s) in RCA: 315] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
The mechanisms by which a T cell detects antigen using its T cell antigen receptor (TCR) are crucial to our understanding of immunity and the harnessing of T cells therapeutically. A hallmark of the T cell response is the ability of T cells to quantitatively respond to antigenic ligands derived from pathogens while remaining inert to similar ligands derived from host tissues. Recent studies have revealed exciting properties of the TCR and the behaviors of its signaling effectors that are used to detect and discriminate between antigens. Here we highlight these recent findings, focusing on the proximal TCR signaling molecules Zap70, Lck, and LAT, to provide mechanistic models and insights into the exquisite sensitivity and specificity of the TCR.
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Affiliation(s)
- Adam H Courtney
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute (HHMI), San Francisco, CA 94143, USA
| | - Wan-Lin Lo
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute (HHMI), San Francisco, CA 94143, USA
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute (HHMI), San Francisco, CA 94143, USA.
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80
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Huang WYC, Chiang HK, Groves JT. Dynamic Scaling Analysis of Molecular Motion within the LAT:Grb2:SOS Protein Network on Membranes. Biophys J 2017; 113:1807-1813. [PMID: 29045874 DOI: 10.1016/j.bpj.2017.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/27/2017] [Accepted: 08/14/2017] [Indexed: 01/29/2023] Open
Abstract
Biochemical signaling pathways often involve proteins with multiple, modular interaction domains. Signaling activates binding sites, such as by tyrosine phosphorylation, which enables protein recruitment and growth of networked protein assemblies. Although widely observed, the physical properties of the assemblies, as well as the mechanisms by which they function, remain largely unknown. Here we examine molecular mobility within LAT:Grb2:SOS assemblies on supported membranes by single-molecule tracking. Trajectory analysis reveals a discrete temporal transition to subdiffusive motion below a characteristic timescale, indicating that the LAT:Grb2:SOS assembly has the dynamical structure of a loosely entangled polymer. Such dynamical analysis is also applicable in living cells, where it offers another dimension on the characteristics of cellular signaling assemblies.
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Affiliation(s)
- William Y C Huang
- Department of Chemistry, University of California, Berkeley, Berkeley, California
| | - Han-Kuei Chiang
- Department of Chemistry, University of California, Berkeley, Berkeley, California
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, California.
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81
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Huang WYC, Ditlev JA, Chiang HK, Rosen MK, Groves JT. Allosteric Modulation of Grb2 Recruitment to the Intrinsically Disordered Scaffold Protein, LAT, by Remote Site Phosphorylation. J Am Chem Soc 2017; 139:18009-18015. [PMID: 29182244 DOI: 10.1021/jacs.7b09387] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tyrosine phosphorylation of membrane receptors and scaffold proteins followed by recruitment of SH2 domain-containing adaptor proteins constitutes a central mechanism of intracellular signal transduction. During early T-cell receptor (TCR) activation, phosphorylation of linker for activation of T cells (LAT) leading to recruitment of adaptor proteins, including Grb2, is one prototypical example. LAT contains multiple modifiable sites, and this multivalency may provide additional layers of regulation, although this is not well understood. Here, we quantitatively analyze the effects of multivalent phosphorylation of LAT by reconstituting the initial reactions of the TCR signaling pathway on supported membranes. Results from a series of LAT constructs with combinatorial mutations of tyrosine residues reveal a previously unidentified allosteric mechanism in which the binding affinity of LAT:Grb2 depends on the phosphorylation at remote tyrosine sites. Additionally, we find that LAT:Grb2 binding affinity is altered by membrane localization. This allostery mainly regulates the kinetic on-rate, not off-rate, of LAT:Grb2 interactions. LAT is an intrinsically disordered protein, and these data suggest that phosphorylation changes the overall ensemble of configurations to modulate the accessibility of other phosphorylated sites to Grb2. Using Grb2 as a phosphorylation reporter, we further monitored LAT phosphorylation by TCR ζ chain-recruited ZAP-70, which suggests a weakly processive catalysis on membranes. Taken together, these results suggest that signal transmission through LAT is strongly gated and requires multiple phosphorylation events before efficient signal transmission is achieved.
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Affiliation(s)
- William Y C Huang
- The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory , Woods Hole, Massachusetts 02543, United States.,Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Jonathon A Ditlev
- The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory , Woods Hole, Massachusetts 02543, United States.,Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Han-Kuei Chiang
- Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
| | - Michael K Rosen
- The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory , Woods Hole, Massachusetts 02543, United States.,Department of Biophysics and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Jay T Groves
- The Howard Hughes Medical Institute Summer Institute, Marine Biological Laboratory , Woods Hole, Massachusetts 02543, United States.,Department of Chemistry, University of California, Berkeley , Berkeley, California 94720, United States
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82
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Abstract
Signaling breakthroughs of 2016 clustered mainly in the areas of neuroscience, immunology, and metabolism, with excursions into plant hormone signaling and bacterial manipulation of host signaling pathways. Perhaps reflecting the growing maturity of the discipline of cell signaling, many of this year's breakthroughs have implications for the pathogenesis or treatment of human disease.
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83
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Changede R, Sheetz M. Integrin and cadherin clusters: A robust way to organize adhesions for cell mechanics. Bioessays 2016; 39:1-12. [PMID: 27930828 DOI: 10.1002/bies.201600123] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent studies at the nanometer scale have revealed that relatively uniform clusters of adhesion proteins (50-100 nm) constitute the modular units of cell adhesion sites in both cell-matrix and cell-cell adhesions. Super resolution microscopy and membrane protein diffusion studies both suggest that even large focal adhesions are formed of 100 nm clusters that are loosely aggregated. Clusters of 20-50 adhesion molecules (integrins or cadherins) can support large forces through avidity binding interactions but can also be disassembled or endocytosed rapidly. Assembly of the clusters of integrins is force-independent and involves gathering integrins at ligand binding sites where they are stabilized by cytoplasmic adhesion proteins that crosslink the integrin cytoplasmic tails plus connect the clusters to the cell cytoskeleton. Cooperative-signaling events can occur in a single cluster without cascading to other clusters. Thus, the clusters appear to be very important elements in many cellular processes and can be considered as a critical functional module.
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Affiliation(s)
- Rishita Changede
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Michael Sheetz
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
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