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Banerjee T, Matsuoka S, Biswas D, Miao Y, Pal DS, Kamimura Y, Ueda M, Devreotes PN, Iglesias PA. A dynamic partitioning mechanism polarizes membrane protein distribution. Nat Commun 2023; 14:7909. [PMID: 38036511 PMCID: PMC10689845 DOI: 10.1038/s41467-023-43615-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023] Open
Abstract
The plasma membrane is widely regarded as the hub of the numerous signal transduction activities. Yet, the fundamental biophysical mechanisms that spatiotemporally compartmentalize different classes of membrane proteins remain unclear. Using multimodal live-cell imaging, here we first show that several lipid-anchored membrane proteins are consistently depleted from the membrane regions where the Ras/PI3K/Akt/F-actin network is activated. The dynamic polarization of these proteins does not depend upon the F-actin-based cytoskeletal structures, recurring shuttling between membrane and cytosol, or directed vesicular trafficking. Photoconversion microscopy and single-molecule measurements demonstrate that these lipid-anchored molecules have substantially dissimilar diffusion profiles in different regions of the membrane which enable their selective segregation. When these diffusion coefficients are incorporated into an excitable network-based stochastic reaction-diffusion model, simulations reveal that the altered affinity mediated selective partitioning is sufficient to drive familiar propagating wave patterns. Furthermore, normally uniform integral and lipid-anchored membrane proteins partition successfully when membrane domain-specific peptides are optogenetically recruited to them. We propose "dynamic partitioning" as a new mechanism that can account for large-scale compartmentalization of a wide array of lipid-anchored and integral membrane proteins during various physiological processes where membrane polarizes.
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Affiliation(s)
- Tatsat Banerjee
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Satomi Matsuoka
- Laboratory for Cell Signaling Dynamics, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Laboratory of Single Molecule Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Debojyoti Biswas
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yuchuan Miao
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Dhiman Sankar Pal
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yoichiro Kamimura
- Laboratory for Cell Signaling Dynamics, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
| | - Masahiro Ueda
- Laboratory for Cell Signaling Dynamics, RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan
- Laboratory of Single Molecule Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Peter N Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Pablo A Iglesias
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
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Takebayashi K, Kamimura Y, Ueda M. Field model for multistate lateral diffusion of various transmembrane proteins observed in living Dictyostelium cells. J Cell Sci 2023; 136:286715. [PMID: 36655427 PMCID: PMC10022678 DOI: 10.1242/jcs.260280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
The lateral diffusion of transmembrane proteins on plasma membranes is a fundamental process for various cellular functions. Diffusion properties specific for individual protein species have been extensively studied, but the common features among protein species are poorly understood. Here, we systematically studied the lateral diffusion of various transmembrane proteins in the lower eukaryote Dictyostelium discoideum cells using a hidden Markov model for single-molecule trajectories obtained experimentally. As common features, all membrane proteins that had from one to ten transmembrane regions adopted three free diffusion states with similar diffusion coefficients regardless of their structural variability. All protein species reduced their mobility similarly upon the inhibition of microtubule or actin cytoskeleton dynamics, or myosin II. The relationship between protein size and the diffusion coefficient was consistent with the Saffman-Delbrück model, meaning that membrane viscosity is a major determinant of lateral diffusion, but protein size is not. These protein species-independent properties of multistate free diffusion were explained simply and quantitatively by free diffusion on the three membrane regions with different viscosities, which is in sharp contrast to the complex diffusion behavior of transmembrane proteins in higher eukaryotes.
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Affiliation(s)
- Kazutoshi Takebayashi
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.,Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Yoichiro Kamimura
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Masahiro Ueda
- Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.,Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
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3
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Banerjee T, Matsuoka S, Biswas D, Miao Y, Pal DS, Kamimura Y, Ueda M, Devreotes PN, Iglesias PA. A dynamic partitioning mechanism polarizes membrane protein distribution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522496. [PMID: 36712016 PMCID: PMC9881856 DOI: 10.1101/2023.01.03.522496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The plasma membrane is widely regarded as the hub of the signal transduction network activities that drives numerous physiological responses, including cell polarity and migration. Yet, the symmetry breaking process in the membrane, that leads to dynamic compartmentalization of different proteins, remains poorly understood. Using multimodal live-cell imaging, here we first show that multiple endogenous and synthetic lipid-anchored proteins, despite maintaining stable tight association with the inner leaflet of the plasma membrane, were unexpectedly depleted from the membrane domains where the signaling network was spontaneously activated such as in the new protrusions as well as within the propagating ventral waves. Although their asymmetric patterns resembled those of standard peripheral "back" proteins such as PTEN, unlike the latter, these lipidated proteins did not dissociate from the membrane upon global receptor activation. Our experiments not only discounted the possibility of recurrent reversible translocation from membrane to cytosol as it occurs for weakly bound peripheral membrane proteins, but also ruled out the necessity of directed vesicular trafficking and cytoskeletal supramolecular structure-based restrictions in driving these dynamic symmetry breaking events. Selective photoconversion-based protein tracking assays suggested that these asymmetric patterns instead originate from the inherent ability of these membrane proteins to "dynamically partition" into distinct domains within the plane of the membrane. Consistently, single-molecule measurements showed that these lipid-anchored molecules have substantially dissimilar diffusion profiles in different regions of the membrane. When these profiles were incorporated into an excitable network-based stochastic reaction-diffusion model of the system, simulations revealed that our proposed "dynamic partitioning" mechanism is sufficient to give rise to familiar asymmetric propagating wave patterns. Moreover, we demonstrated that normally uniform integral and lipid-anchored membrane proteins in Dictyostelium and mammalian neutrophil cells can be induced to partition spatiotemporally to form polarized patterns, by optogenetically recruiting membrane domain-specific peptides to these proteins. Together, our results indicate "dynamic partitioning" as a new mechanism of plasma membrane organization, that can account for large-scale compartmentalization of a wide array of lipid-anchored and integral membrane proteins in different physiological processes.
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Yoshioka D, Fukushima S, Koteishi H, Okuno D, Ide T, Matsuoka S, Ueda M. Single-molecule imaging of PI(4,5)P 2 and PTEN in vitro reveals a positive feedback mechanism for PTEN membrane binding. Commun Biol 2020; 3:92. [PMID: 32111929 PMCID: PMC7048775 DOI: 10.1038/s42003-020-0818-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/10/2020] [Indexed: 01/21/2023] Open
Abstract
PTEN, a 3-phosphatase of phosphoinositide, regulates asymmetric PI(3,4,5)P3 signaling for the anterior-posterior polarization and migration of motile cells. PTEN acts through posterior localization on the plasma membrane, but the mechanism for this accumulation is poorly understood. Here we developed an in vitro single-molecule imaging assay with various lipid compositions and use it to demonstrate that the enzymatic product, PI(4,5)P2, stabilizes PTEN's membrane-binding. The dissociation kinetics and lateral mobility of PTEN depended on the PI(4,5)P2 density on artificial lipid bilayers. The basic residues of PTEN were responsible for electrostatic interactions with anionic PI(4,5)P2 and thus the PI(4,5)P2-dependent stabilization. Single-molecule imaging in living Dictyostelium cells revealed that these interactions were indispensable for the stabilization in vivo, which enabled efficient cell migration by accumulating PTEN posteriorly to restrict PI(3,4,5)P3 distribution to the anterior. These results suggest that PI(4,5)P2-mediated positive feedback and PTEN-induced PI(4,5)P2 clustering may be important for anterior-posterior polarization.
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Affiliation(s)
- Daisuke Yoshioka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Seiya Fukushima
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hiroyasu Koteishi
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Daichi Okuno
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Toru Ide
- Graduate School of Natural Science and Technology, Okayama University, Okayama-shi, Okayama, 700-8530, Japan
| | - Satomi Matsuoka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan.
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Masahiro Ueda
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 565-0043, Japan.
- Center for Biosystems Dynamics Research (BDR), RIKEN, Suita, Osaka, 565-0874, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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Miyanaga Y, Kamimura Y, Kuwayama H, Devreotes PN, Ueda M. Chemoattractant receptors activate, recruit and capture G proteins for wide range chemotaxis. Biochem Biophys Res Commun 2018; 507:304-310. [PMID: 30454895 DOI: 10.1016/j.bbrc.2018.11.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 11/19/2022]
Abstract
The wide range sensing of extracellular signals is a common feature of various sensory cells. Eukaryotic chemotactic cells driven by GPCRs and their cognate G proteins are one example. This system endows the cells directional motility towards their destination over long distances. There are several mechanisms to achieve the long dynamic range, including negative regulation of the receptors upon ligand interaction and spatial regulation of G proteins, as we found recently. However, these mechanisms are insufficient to explain the 105-fold range of chemotaxis seen in Dictyostelium. Here, we reveal that the receptor-mediated activation, recruitment, and capturing of G proteins mediate chemotactic signaling at the lower, middle and higher concentration ranges, respectively. These multiple mechanisms of G protein dynamics can successfully cover distinct ranges of ligand concentrations, resulting in seamless and broad chemotaxis. Furthermore, single-molecule imaging analysis showed that the activated Gα subunit forms an unconventional complex with the agonist-bound receptor. This complex formation of GPCR-Gα increased the membrane-binding time of individual Gα molecules and therefore resulted in the local accumulation of Gα. Our findings provide an additional chemotactic dynamic range mechanism in which multiple G protein dynamics positively contribute to the production of gradient information.
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Affiliation(s)
- Yukihiro Miyanaga
- Laboratory for Single Molecular Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yoichiro Kamimura
- Laboratory for Cell Signaling Dynamics, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, 565-0874, Japan
| | - Hidekazu Kuwayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan
| | - Peter N Devreotes
- Department of Cell Biology, Johns Hopkins University School of Medicine, 725 N. Wolfe St., 114 WBSB, Baltimore, MD, 21205, USA
| | - Masahiro Ueda
- Laboratory for Single Molecular Biology, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, 565-0874, Japan.
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Matsuoka S, Ueda M. Mutual inhibition between PTEN and PIP3 generates bistability for polarity in motile cells. Nat Commun 2018; 9:4481. [PMID: 30367048 PMCID: PMC6203803 DOI: 10.1038/s41467-018-06856-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/02/2018] [Indexed: 12/13/2022] Open
Abstract
Phosphatidylinositol 3,4,5-trisphosphate (PIP3) and PIP3 phosphatase (PTEN) are enriched mutually exclusively on the anterior and posterior membranes of eukaryotic motile cells. However, the mechanism that causes this spatial separation between the two molecules is unknown. Here we develop a method to manipulate PIP3 levels in living cells and used it to show PIP3 suppresses the membrane localization of PTEN. Single-molecule measurements of membrane-association and -dissociation kinetics and of lateral diffusion reveal that PIP3 suppresses the PTEN binding site required for stable PTEN membrane binding. Mutual inhibition between PIP3 and PTEN provides a mechanistic basis for bistability that creates a PIP3-enriched/PTEN-excluded state and a PTEN-enriched/PIP3-excluded state underlying the strict spatial separation between PIP3 and PTEN. The PTEN binding site also mediates the suppression of PTEN membrane localization in chemotactic signaling. These results illustrate that the PIP3-PTEN bistable system underlies a cell's decision-making for directional movement irrespective of the environment.
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Affiliation(s)
- Satomi Matsuoka
- Laboratory for Cell Signaling Dynamics, RIKEN QBiC, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan.
- Laboratory of Single Molecule Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Laboratory for Cell Signaling Dynamics, RIKEN BDR, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Masahiro Ueda
- Laboratory for Cell Signaling Dynamics, RIKEN QBiC, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
- Laboratory of Single Molecule Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Laboratory of Single Molecule Biology, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
- Laboratory for Cell Signaling Dynamics, RIKEN BDR, 6-2-3, Furuedai, Suita, Osaka, 565-0874, Japan
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