1
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Nixon-Abell J, Ruggeri FS, Qamar S, Herling TW, Czekalska MA, Shen Y, Wang G, King C, Fernandopulle MS, Sneideris T, Watson JL, Pillai VVS, Meadows W, Henderson JW, Chambers JE, Wagstaff JL, Williams SH, Coyle H, Šneiderienė G, Lu Y, Zhang S, Marciniak SJ, Freund SMV, Derivery E, Ward ME, Vendruscolo M, Knowles TPJ, St George-Hyslop P. ANXA11 biomolecular condensates facilitate protein-lipid phase coupling on lysosomal membranes. Nat Commun 2025; 16:2814. [PMID: 40118863 PMCID: PMC11928461 DOI: 10.1038/s41467-025-58142-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 03/12/2025] [Indexed: 03/24/2025] Open
Abstract
Phase transitions of cellular proteins and lipids play a key role in governing the organisation and coordination of intracellular biology. Recent work has raised the intriguing prospect that phase transitions in proteins and lipids can be co-regulated. Here we investigate this possibility in the ribonucleoprotein (RNP) granule-ANXA11-lysosome ensemble, where ANXA11 tethers RNP granules to lysosomal membranes to enable their co-trafficking. We show that changes to the protein phase state within this system, driven by the low complexity ANXA11 N-terminus, induces a coupled phase state change in the lipids of the underlying membrane. We identify the ANXA11 interacting proteins ALG2 and CALC as potent regulators of ANXA11-based phase coupling and demonstrate their influence on the nanomechanical properties of the ANXA11-lysosome ensemble and its capacity to engage RNP granules. The phenomenon of protein-lipid phase coupling we observe within this system serves as a potential regulatory mechanism in RNA trafficking and offers an important template to understand other examples across the cell whereby biomolecular condensates closely juxtapose organellar membranes.
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Grants
- Wellcome Trust
- F30 AG060722 NIA NIH HHS
- FC001029 Arthritis Research UK
- Canadian Institutes of Health Research (406915 Foundation Grant and Canadian Consortium on Neurodegeneration in Aging); Wellcome Career Development Award 227745/Z/23/Z (JNA), Wellcome Trust Collaborative Award 203249/Z/16/Z (PStGH, MEV, TPK), a US Alzheimer Society Zenith Grant ZEN-18-529769 (PStGH), a National Institute on Aging grant F30AG060722 (MEW), the NIH-Oxford-Cambridge Scholars Program (MSF), the El-Hibri Foundation (MSF), the Dutch Ministry of Education – Sector Plan Beta for science and technology (FSR), an Ernest Oppenheimer Early Career Research Fellowship (TWH), the Polish Ministry of Science and Higher Education (by Mobilnosc Plus V, decision number 1623/MOB/V/2017/0, MAC), and the Medical Research Council as part of UKRI (MC_UP_1201/13 to ED & MC_U105184326 to LMB NMR facility), and the Human Frontier Science Program (Career Development Award CDA00034/2017-C to ED). The CIMR microscopy core is supported by a Wellcome Trust Strategic Award 100140, and a Wellcome Trust equipment grant 093026. The Francis Crick Institute receives its core funding from Cancer Research UK (FC001029), the UK Medical Research Council (FC001029), and the Wellcome Trust (FC001029).
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Affiliation(s)
- Jonathon Nixon-Abell
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK.
| | - Francesco S Ruggeri
- Physical Chemistry and Soft matter, Wageningen University & Research, Stippeneng, The Netherlands
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Seema Qamar
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
| | - Therese W Herling
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Magdalena A Czekalska
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Yi Shen
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
| | - Guozhen Wang
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Christopher King
- National institute for Neurological Disorder and Stroke, NIH, Bethesda, MD, USA
| | - Michael S Fernandopulle
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
- National institute for Neurological Disorder and Stroke, NIH, Bethesda, MD, USA
- Medical Scientist Training Program, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Joseph L Watson
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Visakh V S Pillai
- Physical Chemistry and Soft matter, Wageningen University & Research, Stippeneng, The Netherlands
| | - William Meadows
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
| | - James W Henderson
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
| | - Joseph E Chambers
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
| | - Jane L Wagstaff
- Structure Studies Division, NMR Facility, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Sioned H Williams
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
| | - Helena Coyle
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
| | - Greta Šneiderienė
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Yuqian Lu
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Shuyuan Zhang
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Stefan J Marciniak
- Department of Clinical Neurosciences, Cambridge Institute for Medical Research, Clinical School, University of Cambridge, Cambridge, UK
| | - Stefan M V Freund
- Structure Studies Division, NMR Facility, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Emmanuel Derivery
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Michael E Ward
- National institute for Neurological Disorder and Stroke, NIH, Bethesda, MD, USA
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Peter St George-Hyslop
- Department of Medicine (Division of Neurology), Temerty Faculty of Medicine, University Health Network, University of Toronto, Toronto, ON, Canada.
- Carol and Gene Ludwig Center for Research on Neurodegeneration, Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University Irvine Medical Center, New York, NY, USA.
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2
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Torun A, Tuğral H, Banerjee S. Crosstalk Between Phase-Separated Membraneless Condensates and Membrane-Bound Organelles in Cellular Function and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2025. [PMID: 40095243 DOI: 10.1007/5584_2025_852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Compartmentalization in eukaryotic cells allows the spatiotemporal regulation of biochemical processes, in addition to allowing specific sets of proteins to interact in a regulated as well as stochastic manner. Although membrane-bound organelles are thought to be the key players of cellular compartmentalization, membraneless biomolecular condensates such as stress granules, P bodies, and many others have recently emerged as key players that are also thought to bring order to a highly chaotic environment. Here, we have evaluated the latest studies on biomolecular condensates, specifically focusing on how they interact with membrane-bound organelles and modulate each other's functions. We also highlight the importance of this interaction in neurodegenerative and cardiovascular diseases as well as in cancer.
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Affiliation(s)
- Aydan Torun
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Türkiye
| | - Hoşnaz Tuğral
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Türkiye
| | - Sreeparna Banerjee
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Türkiye.
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3
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Jennrich J, Farkas Á, Urlaub H, Schwappach B, Bohnsack KE. The formation of chaperone-rich GET bodies depends on the tetratricopeptide repeat region of Sgt2 and is reversed by NADH. J Cell Sci 2025; 138:jcs263616. [PMID: 39976550 PMCID: PMC11959614 DOI: 10.1242/jcs.263616] [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: 10/18/2024] [Accepted: 01/30/2025] [Indexed: 03/21/2025] Open
Abstract
The guided-entry of tail-anchored proteins (GET) pathway is a post-translational targeting route to the endoplasmic reticulum (ER). Upon glucose withdrawal, the soluble GET proteins re-localize to dynamic cytosolic foci, here termed GET bodies. Our data reveal that the pre-targeting complex components, Sgt2 and the Get4-Get5 heterodimer, and the Get3 ATPase play important roles in the assembly of these structures in Saccharomyces cerevisiae. More specifically, the TPR region of Sgt2 is required as a GET body scaffold. Systematic compositional analyses of GET bodies reveal their chaperone-rich nature and the presence of numerous proteins involved in metabolic processes. Temporal analyses of GET body assembly demonstrate the sequential recruitment of different chaperones, and we discover the requirement of Sis1 and Sti1 for maintaining the dynamic properties of these structures. In vivo, NADH derived from the oxidation of ethanol to acetaldehyde can induce GET body disassembly in a reaction depending on the alcohol dehydrogenase Adh2 and in vitro, addition of NADH resolves GET bodies. This suggests a mechanistic basis for their formation and disassembly in response to the metabolic shift caused by glucose withdrawal and re-addition.
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Affiliation(s)
- Jonas Jennrich
- Department of Molecular Biology, University Medical Centre Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Ákos Farkas
- Department of Molecular Biology, University Medical Centre Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Faßberg 11, 37077 Göttingen, Germany
- Institute for Clinical Chemistry, University Medical Centre Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Centre Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Katherine E. Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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4
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Kim Y, Parolek J, Burd CG. Cholesterol depletion activates trafficking-coupled sphingolipid synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.12.637879. [PMID: 39990424 PMCID: PMC11844529 DOI: 10.1101/2025.02.12.637879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Within cellular membranes, sphingomyelin is associated with cholesterol and this complex facilitates homeostatic regulation of membrane viscosity. Acute cholesterol depletion increases the synthesis of very-long-chain (VLC) sphingomyelin, but a link between lipid sensing and sphingolipid synthesis is lacking. Using sphingolipid metabolic flux analysis, we observed that VLC-ceramide, the precursor to VLC complex sphingolipids that are produced in the Golgi apparatus, was rapidly consumed after cholesterol depletion, while synthesis of long-chain sphingolipids was unaffected. Sphingolipid trafficking assays showed that cholesterol depletion enhances VLC-Ceramide trafficking from the endoplasmic reticulum to the Golgi apparatus. Changes in the sizes of coatomer II ER exit sites were correlated with increased VLC-Ceramide trafficking and concomitant increase in sphingomyelin. Depletion of Sec16A, a component of the COPII network, abolished VLC-SM synthesis. This study reveals ER-to-Golgi trafficking of VLC-Ceramide as a key regulatory node in organelle membrane homeostasis pathways. Summary In cellular membranes, sphingomyelin is associated with cholesterol. Metabolic flux analysis of sphingolipid metabolism showed that synthesis rate of sphingomyelin, but not ceramide, was increased after depletion of cholesterol due increased rate of COPII-dependent ER-to-Golgi transport of ceramide.
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5
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Bollen C, Louwagie S, Deroover F, Duverger W, Khodaparast L, Khodaparast L, Hofkens D, Schymkowitz J, Rousseau F, Dewachter L, Michiels J. Composition and liquid-to-solid maturation of protein aggregates contribute to bacterial dormancy development and recovery. Nat Commun 2025; 16:1046. [PMID: 39865082 PMCID: PMC11770139 DOI: 10.1038/s41467-025-56387-8] [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] [Received: 03/06/2024] [Accepted: 01/16/2025] [Indexed: 01/28/2025] Open
Abstract
Recalcitrant bacterial infections can be caused by various types of dormant bacteria, including persisters and viable but nonculturable (VBNC) cells. Despite their clinical importance, we know fairly little about bacterial dormancy development and recovery. Previously, we established a correlation between protein aggregation and dormancy in Escherichia coli. Here, we present further support for a direct relationship between both. Our experiments demonstrate that aggregates progressively sequester proteins involved in energy production, thereby likely causing ATP depletion and dormancy. Furthermore, we demonstrate that structural features of protein aggregates determine the cell's ability to exit dormancy and resume growth. Proteins were shown to first assemble in liquid-like condensates that solidify over time. This liquid-to-solid phase transition impedes aggregate dissolution, thereby preventing growth resumption. Our data support a model in which aggregate structure, rather than cellular activity, marks the transition from the persister to the VBNC state.
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Affiliation(s)
- Celien Bollen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Sofie Louwagie
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Femke Deroover
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Wouter Duverger
- Switch Laboratory, Center for Brain and Disease Research, VIB-KU Leuven, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, Center for Brain and Disease Research, VIB-KU Leuven, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Laleh Khodaparast
- Switch Laboratory, Center for Brain and Disease Research, VIB-KU Leuven, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Dieter Hofkens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, Center for Brain and Disease Research, VIB-KU Leuven, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, Center for Brain and Disease Research, VIB-KU Leuven, Leuven, Belgium
- Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium
- de Duve institute, Université catholique de Louvain, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.
- Center for Microbiology, VIB-KU Leuven, Leuven, Belgium.
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6
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Milano SN, Bayer LV, Ko JJ, Casella CE, Bratu DP. The role of ER exit sites in maintaining P-body organization and integrity during Drosophila melanogaster oogenesis. EMBO Rep 2025; 26:494-520. [PMID: 39653851 PMCID: PMC11772875 DOI: 10.1038/s44319-024-00344-x] [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: 07/13/2024] [Revised: 11/08/2024] [Accepted: 11/15/2024] [Indexed: 12/12/2024] Open
Abstract
Processing bodies (P-bodies) are cytoplasmic membrane-less organelles which host multiple mRNA processing events. While the fundamental principles of P-body organization are beginning to be elucidated in vitro, a nuanced understanding of how their assembly is regulated in vivo remains elusive. Here, we investigate the potential link between ER exit sites and P-bodies in Drosophila melanogaster egg chambers. Employing a combination of live and super-resolution imaging, we find that P-bodies associated with ER exit sites are larger and less mobile than cytoplasmic P-bodies, indicating that they constitute a distinct class of P-bodies. Moreover, we demonstrate that altering the composition of ER exit sites has differential effects on core P-body proteins (Me31B, Cup, and Trailer Hitch), suggesting a potential role for ER exit sites in P-body organization. Furthermore, we show that in the absence of ER exit sites, P-body integrity is compromised and the stability and translational repression efficiency of the maternal mRNA, oskar, are reduced. Together, our data highlights the crucial role of ER exit sites in governing P-body organization.
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Affiliation(s)
- Samantha N Milano
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, 10065, USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Livia V Bayer
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, 10065, USA
| | - Julie J Ko
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, 10065, USA
| | - Caroline E Casella
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, 10065, USA
| | - Diana P Bratu
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, 10065, USA.
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, New York, NY, 10016, USA.
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7
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Chen K, Cao X. Biomolecular condensates: phasing in regulated host-pathogen interactions. Trends Immunol 2025; 46:29-45. [PMID: 39672748 DOI: 10.1016/j.it.2024.11.010] [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] [Received: 08/09/2024] [Revised: 11/12/2024] [Accepted: 11/19/2024] [Indexed: 12/15/2024]
Abstract
Biomolecular condensates are membraneless organelles formed through liquid-liquid phase separation. Innate immunity is essential to host defense against infections, but pathogens also harbor sophisticated mechanisms to evade host defense. The formation of biomolecular condensates emerges as a key biophysical mechanism in host-pathogen interactions, playing pivotal roles in regulating immune responses and pathogen life cycles within the host. In this review we summarize recent advances in our understanding of how biomolecular condensates remodel membrane-bound organelles, influence infection-induced cell death, and are hijacked by pathogens for survival, as well as how they modulate mammalian innate immunity. We discuss the implications of dysregulated formation of biomolecular condensates during host-pathogen interactions and infectious diseases and propose future directions for developing potential treatments against such infections.
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Affiliation(s)
- Kun Chen
- State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200127, China; Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Xuetao Cao
- Department of Immunology, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, 100005 Beijing, China.
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8
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Kim N, Yun H, Lee H, Yoo JY. Interplay between membranes and biomolecular condensates in the regulation of membrane-associated cellular processes. Exp Mol Med 2024; 56:2357-2364. [PMID: 39482532 PMCID: PMC11612285 DOI: 10.1038/s12276-024-01337-5] [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: 02/19/2024] [Revised: 08/04/2024] [Accepted: 08/11/2024] [Indexed: 11/03/2024] Open
Abstract
Liquid‒liquid phase separation (LLPS) has emerged as a key mechanism for organizing cellular spaces independent of membranes. Biomolecular condensates, which assemble through LLPS, exhibit distinctive liquid droplet-like behavior and can exchange constituents with their surroundings. The regulation of condensate phases, including transitions from a liquid state to gel or irreversible aggregates, is important for their physiological functions and for controlling pathological progression, as observed in neurodegenerative diseases and cancer. While early studies on biomolecular condensates focused primarily on those in fluidic environments such as the cytosol, recent discoveries have revealed their existence in close proximity to, on, or even comprising membranes. The aim of this review is to provide an overview of the properties of membrane-associated condensates in a cellular context and their biological functions in relation to membranes.
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Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
| | - Hyeri Yun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Hojin Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
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9
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Wu H, Wang LC, Sow BM, Leow D, Zhu J, Gallo KM, Wilsbach K, Gupta R, Ostrow LW, Yeo CJJ, Sobota RM, Li R. TDP43 aggregation at ER-exit sites impairs ER-to-Golgi transport. Nat Commun 2024; 15:9026. [PMID: 39424779 PMCID: PMC11489672 DOI: 10.1038/s41467-024-52706-7] [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: 04/28/2024] [Accepted: 09/18/2024] [Indexed: 10/21/2024] Open
Abstract
Protein aggregation plays key roles in age-related degenerative diseases, but how different proteins coalesce to form inclusions that vary in composition, morphology, molecular dynamics and confer physiological consequences is poorly understood. Here we employ a general reporter based on mutant Hsp104 to identify proteins forming aggregates in human cells under common proteotoxic stress. We identify over 300 proteins that form different inclusions containing subsets of aggregating proteins. In particular, TDP43, implicated in Amyotrophic Lateral Sclerosis (ALS), partitions dynamically between two distinct types of aggregates: stress granule and a previously unknown non-dynamic (solid-like) inclusion at the ER exit sites (ERES). TDP43-ERES co-aggregation is induced by diverse proteotoxic stresses and observed in the motor neurons of ALS patients. Such aggregation causes retention of secretory cargos at ERES and therefore delays ER-to-Golgi transport, providing a link between TDP43 aggregation and compromised cellular function in ALS patients.
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Affiliation(s)
- Hongyi Wu
- Mechanobiology Institute, National University of Singapore (NUS), Singapore, Singapore
| | - Loo Chien Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Belle M Sow
- Mechanobiology Institute, National University of Singapore (NUS), Singapore, Singapore
| | - Damien Leow
- Department of Anatomy, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jin Zhu
- Mechanobiology Institute, National University of Singapore (NUS), Singapore, Singapore
| | - Kathryn M Gallo
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Kathleen Wilsbach
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Roshni Gupta
- Mechanobiology Institute, National University of Singapore (NUS), Singapore, Singapore
| | - Lyle W Ostrow
- Department of Neurology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Neurology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Crystal J J Yeo
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- National Neuroscience Institute, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, Scotland, UK
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Rong Li
- Mechanobiology Institute, National University of Singapore (NUS), Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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10
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Suda Y, Tachikawa H, Suda T, Kurokawa K, Nakano A, Irie K. Remodeling of the secretory pathway is coordinated with de novo membrane formation in budding yeast gametogenesis. iScience 2024; 27:110855. [PMID: 39319263 PMCID: PMC11419814 DOI: 10.1016/j.isci.2024.110855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 07/01/2024] [Accepted: 08/28/2024] [Indexed: 09/26/2024] Open
Abstract
Gametogenesis in budding yeast involves a large-scale rearrangement of membrane traffic to allow the de novo formation of a membrane, called the prospore membrane (PSM). However, the mechanism underlying this event is not fully elucidated. Here, we show that the number of endoplasmic reticulum exit sites (ERES) per cell fluctuates and switches from decreasing to increasing upon the onset of PSM formation. Reduction in ERES number, presumably accompanying a transient stall in membrane traffic, resulting in the loss of preexisting Golgi apparatus from the cell, was followed by local ERES regeneration, leading to Golgi reassembly in nascent spores. We have revealed that protein phosphatase-1 (PP-1) and its development-specific subunit, Gip1, promote ERES regeneration through Sec16 foci formation. Furthermore, sed4Δ, a mutant with impaired ERES formation, showed defects in PSM growth and spore formation. Thus, ERES regeneration in nascent spores facilitates the segregation of membrane traffic organelles, leading to PSM growth.
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Affiliation(s)
- Yasuyuki Suda
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Hiroyuki Tachikawa
- Department of Sport and Wellness, College of Sport and Wellness, Rikkyo University, Niiza, Saitama, Japan
| | - Tomomi Suda
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, Japan
| | - Kenji Irie
- Department of Molecular Cell Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
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11
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Malhotra V. Tailored assemblies of COPII proteins in secretion. J Cell Biol 2024; 223:e202404013. [PMID: 38958655 PMCID: PMC11222725 DOI: 10.1083/jcb.202404013] [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] [Indexed: 07/04/2024] Open
Abstract
Export of secretory cargoes from the endoplasmic reticulum (ER) requires COPII proteins, which were first identified for their ability to coat small vesicles that bud from the ER. Recent data indicate that COPII proteins can also organize into a collar at the necks of tubules, as well as phase-separate into liquid-like condensates. Thus, COPII assemblies seem to be tailored to accommodate variations in the size and quantities of cargo secreted.
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Affiliation(s)
- Vivek Malhotra
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
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12
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Madan A, Kelly KP, Bahk P, Sullivan CE, Poling ME, Brent AE, Alassaf M, Dubrulle J, Rajan A. Atg8/LC3 controls systemic nutrient surplus signaling in flies and humans. Curr Biol 2024; 34:3327-3341.e9. [PMID: 38955177 PMCID: PMC11303106 DOI: 10.1016/j.cub.2024.06.005] [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] [Revised: 04/26/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024]
Abstract
Organisms experience constant nutritional flux. Mechanisms at the interface of opposing nutritional states-scarcity and surplus-enable organismal energy homeostasis. Contingent on nutritional stores, adipocytes secrete adipokines, such as the fat hormone leptin, to signal nutrient status to the central brain. Increased leptin secretion underlies metabolic dysregulation during common obesity, but the molecular mechanisms regulating leptin secretion from human adipocytes are poorly understood. Here, we report that Atg8/LC3 family proteins, best known for their role in autophagy during nutrient scarcity, play an evolutionarily conserved role during nutrient surplus by promoting adipokine secretion. We show that in a well-fed state, Atg8/LC3 promotes the secretion of the Drosophila functional leptin ortholog unpaired 2 (Upd2) and leptin from human adipocytes. Proteomic analyses reveal that LC3 directs leptin to a secretory pathway in human cells. We identified LC3-dependent extracellular vesicle (EV) loading and secretion (LDELS) as a required step for leptin release, highlighting a unique secretory route adopted by leptin in human adipocytes. In Drosophila, mutations to Upd2's Atg8 interaction motif (AIM) result in constitutive adipokine retention. Atg8-mediated Upd2 retention alters lipid storage and hunger response and rewires the bulk organismal transcriptome in a manner conducive to starvation survival. Thus, Atg8/LC3's bidirectional role in nutrient sensing-conveying nutrient surplus and responding to nutrient deprivation-enables organisms to manage nutrient flux effectively. We posit that decoding how bidirectional molecular switches-such as Atg8/LC3-operate at the nexus of nutritional scarcity and surplus will inform therapeutic strategies to tackle chronic metabolic disorders.
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Affiliation(s)
- Aditi Madan
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | - Kevin P Kelly
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | - Patrick Bahk
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | | | | | - Ava E Brent
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | - Mroj Alassaf
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA
| | - Julien Dubrulle
- Cellular Imaging Core, Shared Resources, Fred Hutch, Seattle, WA 98109, USA
| | - Akhila Rajan
- Basic Sciences Division, Fred Hutch, Seattle, WA 98109, USA.
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13
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Kasberg W, Luong P, Minushkin K, Pustova I, Swift KA, Zhao M, Audhya A. TFG regulates inner COPII coat recruitment to facilitate anterograde secretory protein transport. Mol Biol Cell 2024; 35:ar113. [PMID: 38985515 PMCID: PMC11321049 DOI: 10.1091/mbc.e24-06-0282] [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: 06/27/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
Coat protein complex II (COPII) governs the initial steps of biosynthetic secretory protein transport from the endoplasmic reticulum (ER), facilitating the movement of a wide variety of cargoes. Here, we demonstrate that Trk-fused gene (TFG) regulates the rate at which inner COPII coat proteins are concentrated at ER subdomains. Specifically, in cells lacking TFG, the GTPase-activating protein (GAP) Sec23 accumulates more rapidly at budding sites on the ER as compared with control cells, potentially altering the normal timing of GTP hydrolysis on Sar1. Under these conditions, anterograde trafficking of several secretory cargoes is delayed, irrespective of their predicted size. We propose that TFG controls the local, freely available pool of Sec23 during COPII coat formation and limits its capacity to prematurely destabilize COPII complexes on the ER. This function of TFG enables it to act akin to a rheostat, promoting the ordered recruitment of Sec23, which is critical for efficient secretory cargo export.
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Affiliation(s)
- William Kasberg
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Peter Luong
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Kayla Minushkin
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Iryna Pustova
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Kevin A. Swift
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Meixian Zhao
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53706
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14
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Ravindran R, Michnick SW. Biomolecular condensates as drivers of membrane trafficking and remodelling. Curr Opin Cell Biol 2024; 89:102393. [PMID: 38936257 DOI: 10.1016/j.ceb.2024.102393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024]
Abstract
Membrane remodelling is essential for the trafficking of macromolecules throughout the cell, a process that regulates various aspects of cellular health and pathology. Recent studies implicate the role of biomolecular condensates in regulating multiple steps of the membrane trafficking pathway including but not limited to the organization of the trafficking machinery, dynamic remodeling of membranes, spatial and functional regulation, and response to cellular signals. The implicated proteins contain key structural elements, most notably prion-like domains within intrinsically disordered regions that are necessary for biomolecular condensate formation at fusion sites in processes like endocytic assembly, autophagy, organelle biosynthesis and synaptic vesicle fusion. Experimental and theoretical advances in the field continue to demonstrate that protein condensates can perform mechanical work, the implications of which can be extrapolated to diverse areas of membrane biology.
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Affiliation(s)
- Rini Ravindran
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada
| | - Stephen W Michnick
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada.
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15
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Milano SN, Bayer LV, Ko JJ, Casella CE, Bratu DP. The role of ER exit sites in maintaining P-body organization and transmitting ER stress response during Drosophila melanogaster oogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.03.601952. [PMID: 39005311 PMCID: PMC11245038 DOI: 10.1101/2024.07.03.601952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Processing bodies (P-bodies) are cytoplasmic membrane-less organelles which host multiple mRNA processing events. While the fundamental principles of P-body organization are beginning to be elucidated in vitro, a nuanced understanding of how their assembly is regulated in vivo remains elusive. Here, we investigate the potential link between ER exit sites and P-bodies in Drosophila melanogaster egg chambers. Employing a combination of live and super-resolution imaging, we found that P-bodies associated with ER exit sites are larger and less mobile than cytoplasmic P-bodies, indicating that they constitute a distinct class of P-bodies which are more mature than their cytoplasmic counterparts. Moreover, we demonstrate that altering the composition of ER exit sites has differential effects on core P-body proteins (Me31B, Cup, and Trailer Hitch) suggesting a potential role for ER exit sites in P-body organization. We further show that in the absence of ER exit sites, P-body integrity is compromised and the stability and translational repression efficiency of the maternal mRNA, oskar, are reduced. Finally, we show that ER stress is communicated to P-bodies via ER exit sites, highlighting the pivotal role of ER exit sites as a bridge between membrane-bound and membrane-less organelles in ER stress response. Together, our data unveils the significance of ER exit sites not only in governing P-body organization, but also in facilitating inter-organellar communication during stress, potentially bearing implications for a variety of disease pathologies.
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Affiliation(s)
- Samantha N. Milano
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, NY, 10016 USA
| | - Livia V. Bayer
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Julie J. Ko
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Caroline E. Casella
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
| | - Diana P. Bratu
- Department of Biological Sciences, Hunter College, City University of New York, NY, 10065 USA
- Program in Molecular, Cellular, and Developmental Biology, The Graduate Center, City University of New York, NY, 10016 USA
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16
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Campelo F, Lillo JV, von Blume J. Protein condensates in the the secretory pathway: Unraveling biophysical interactions and function. Biophys J 2024; 123:1531-1541. [PMID: 38698644 PMCID: PMC11214006 DOI: 10.1016/j.bpj.2024.04.031] [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: 01/19/2024] [Revised: 03/23/2024] [Accepted: 04/30/2024] [Indexed: 05/05/2024] Open
Abstract
The emergence of phase separation phenomena among macromolecules has identified biomolecular condensates as fundamental cellular organizers. These condensates concentrate specific components and accelerate biochemical reactions without relying on membrane boundaries. Although extensive studies have revealed a large variety of nuclear and cytosolic membraneless organelles, we are witnessing a surge in the exploration of protein condensates associated with the membranes of the secretory pathway, such as the endoplasmic reticulum and the Golgi apparatus. This review focuses on protein condensates in the secretory pathway and discusses their impact on the organization and functions of this cellular process. Moreover, we explore the modes of condensate-membrane association and the biophysical and cellular consequences of protein condensate interactions with secretory pathway membranes.
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Affiliation(s)
- Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain.
| | - Javier Vera Lillo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Julia von Blume
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut.
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17
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Wang B, Pareek G, Kundu M. ULK/Atg1: phasing in and out of autophagy. Trends Biochem Sci 2024; 49:494-505. [PMID: 38565496 PMCID: PMC11162330 DOI: 10.1016/j.tibs.2024.03.004] [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: 12/15/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Autophagy - a highly regulated intracellular degradation process - is pivotal in maintaining cellular homeostasis. Liquid-liquid phase separation (LLPS) is a fundamental mechanism regulating the formation and function of membrane-less compartments. Recent research has unveiled connections between LLPS and autophagy, suggesting that phase separation events may orchestrate the spatiotemporal organization of autophagic machinery and cargo sequestration. The Unc-51-like kinase (ULK)/autophagy-related 1 (Atg1) family of proteins is best known for its regulatory role in initiating autophagy, but there is growing evidence that the functional spectrum of ULK/Atg1 extends beyond autophagy regulation. In this review, we explore the spatial and temporal regulation of the ULK/Atg1 family of kinases, focusing on their recruitment to LLPS-driven compartments, and highlighting their multifaceted functions beyond their traditional role.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, 518057, China
| | - Gautam Pareek
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mondira Kundu
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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18
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Arab M, Chen T, Lowe M. Mechanisms governing vesicle traffic at the Golgi apparatus. Curr Opin Cell Biol 2024; 88:102365. [PMID: 38705050 DOI: 10.1016/j.ceb.2024.102365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024]
Abstract
Vesicle transport at the Golgi apparatus is a well-described process, and the major protein components involved have been identified. This includes the coat proteins that function in cargo sorting and vesicle formation, and the proteins that mediate the downstream events of vesicle tethering and membrane fusion. However, despite this knowledge, there remain significant gaps in our mechanistic understanding of these processes which includes how they are coordinated in space and time. In this review we discuss recent advances that have provided new insights into the mechanisms of Golgi trafficking, focussing on vesicle formation and cargo sorting, and vesicle tethering and fusion. These studies point to a high degree of spatial organisation of trafficking components at the Golgi and indicate an inherent plasticity of trafficking. Going forward, further advancements in technology and more sophisticated functional assays are expected to yield greater understanding of the mechanisms that govern Golgi trafficking events.
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Affiliation(s)
- Maryam Arab
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Tong Chen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Martin Lowe
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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19
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Nguyen DTM, Koppers M, Farías GG. Endoplasmic reticulum - condensate interactions in protein synthesis and secretion. Curr Opin Cell Biol 2024; 88:102357. [PMID: 38626704 DOI: 10.1016/j.ceb.2024.102357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/18/2024]
Abstract
In the past decade, a growing amount of evidence has demonstrated that organelles do not act autonomously and independently but rather communicate with each other to coordinate different processes for proper cellular function. With a highly extended network throughout the cell, the endoplasmic reticulum (ER) plays a central role in interorganelle communication through membrane contact sites. Here, we highlight recent evidence indicating that the ER also forms contacts with membrane-less organelles. These interactions contribute to the dynamic assembly and disassembly of condensates and controlled protein secretion. Additionally, emerging evidence suggests their involvement in mRNA localization and localized translation. We further explore exciting future directions of this emerging theme in the organelle contact site field.
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Affiliation(s)
- Dan T M Nguyen
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Max Koppers
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Ginny G Farías
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
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20
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Dzaki N, Alenius M. A cilia-bound unconventional secretory pathway for Drosophila odorant receptors. BMC Biol 2024; 22:84. [PMID: 38610043 PMCID: PMC11015608 DOI: 10.1186/s12915-024-01877-2] [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: 02/03/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Post-translational transport is a vital process which ensures that each protein reaches its site of function. Though most do so via an ordered ER-to-Golgi route, an increasing number of proteins are now shown to bypass this conventional secretory pathway. RESULTS In the Drosophila olfactory sensory neurons (OSNs), odorant receptors (ORs) are trafficked from the ER towards the cilia. Here, we show that Or22a, a receptor of various esters and alcoholic compounds, reaches the cilia partially through unconventional means. Or22a frequently present as puncta at the somatic cell body exit and within the dendrite prior to the cilia base. These rarely coincide with markers of either the intermediary ER-Golgi-intermediate-compartment (ERGIC) or Golgi structures. ERGIC and Golgi also displayed axonal localization biases, a further indication that at least some measure of OR transport may occur independently of their involvement. Additionally, neither the loss of several COPII genes involved in anterograde trafficking nor ERGIC itself affected puncta formation or Or22a transport to the cilium. Instead, we observed the consistent colocalization of Or22a puncta with Grasp65, the sole Drosophila homolog of mammalian GRASP55/Grh1, a marker of the unconventional pathway. The numbers of both Or22a and Grasp65-positive puncta were furthermore increased upon nutritional starvation, a condition known to enhance Golgi-bypassing secretory activity. CONCLUSIONS Our results demonstrate an alternative route of Or22a transport, thus expanding the repertoire of unconventional secretion mechanisms in neurons.
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Affiliation(s)
- Najat Dzaki
- Department of Molecular Biology, Umeå University, Umeå, 901 87, SE, Sweden
| | - Mattias Alenius
- Department of Molecular Biology, Umeå University, Umeå, 901 87, SE, Sweden.
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21
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Marijan D, Momchilova EA, Burns D, Chandhok S, Zapf R, Wille H, Potoyan DA, Audas TE. Protein thermal sensing regulates physiological amyloid aggregation. Nat Commun 2024; 15:1222. [PMID: 38336721 PMCID: PMC10858206 DOI: 10.1038/s41467-024-45536-0] [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: 05/24/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
To survive, cells must respond to changing environmental conditions. One way that eukaryotic cells react to harsh stimuli is by forming physiological, RNA-seeded subnuclear condensates, termed amyloid bodies (A-bodies). The molecular constituents of A-bodies induced by different stressors vary significantly, suggesting this pathway can tailor the cellular response by selectively aggregating a subset of proteins under a given condition. Here, we identify critical structural elements that regulate heat shock-specific amyloid aggregation. Our data demonstrates that manipulating structural pockets in constituent proteins can either induce or restrict their A-body targeting at elevated temperatures. We propose a model where selective aggregation within A-bodies is mediated by the thermal stability of a protein, with temperature-sensitive structural regions acting as an intrinsic form of post-translational regulation. This system would provide cells with a rapid and stress-specific response mechanism, to tightly control physiological amyloid aggregation or other cellular stress response pathways.
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Affiliation(s)
- Dane Marijan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Evgenia A Momchilova
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Daniel Burns
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sahil Chandhok
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Richard Zapf
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Davit A Potoyan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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22
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Sun S, Zhao G, Jia M, Jiang Q, Li S, Wang H, Li W, Wang Y, Bian X, Zhao YG, Huang X, Yang G, Cai H, Pastor-Pareja JC, Ge L, Zhang C, Hu J. Stay in touch with the endoplasmic reticulum. SCIENCE CHINA. LIFE SCIENCES 2024; 67:230-257. [PMID: 38212460 DOI: 10.1007/s11427-023-2443-9] [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: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 01/13/2024]
Abstract
The endoplasmic reticulum (ER), which is composed of a continuous network of tubules and sheets, forms the most widely distributed membrane system in eukaryotic cells. As a result, it engages a variety of organelles by establishing membrane contact sites (MCSs). These contacts regulate organelle positioning and remodeling, including fusion and fission, facilitate precise lipid exchange, and couple vital signaling events. Here, we systematically review recent advances and converging themes on ER-involved organellar contact. The molecular basis, cellular influence, and potential physiological functions for ER/nuclear envelope contacts with mitochondria, Golgi, endosomes, lysosomes, lipid droplets, autophagosomes, and plasma membrane are summarized.
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Affiliation(s)
- Sha Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gan Zhao
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Mingkang Jia
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haibin Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjing Li
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yan G Zhao
- Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ge Yang
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jose C Pastor-Pareja
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Institute of Neurosciences, Consejo Superior de Investigaciones Cientfflcas-Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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23
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Wang F, Zhang Y. Physiology and pharmacological targeting of phase separation. J Biomed Sci 2024; 31:11. [PMID: 38245749 PMCID: PMC10800077 DOI: 10.1186/s12929-024-00993-z] [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: 08/30/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) in biology describes a process by which proteins form membraneless condensates within a cellular compartment when conditions are met, including the concentration and posttranslational modifications of the protein components, the condition of the aqueous solution (pH, ionic strength, pressure, and temperature), and the existence of assisting factors (such as RNAs or other proteins). In these supramolecular liquid droplet-like inclusion bodies, molecules are held together through weak intermolecular and/or intramolecular interactions. With the aid of LLPS, cells can assemble functional sub-units within a given cellular compartment by enriching or excluding specific factors, modulating cellular function, and rapidly responding to environmental or physiological cues. Hence, LLPS is emerging as an important means to regulate biology and physiology. Yet, excessive inclusion body formation by, for instance, higher-than-normal concentrations or mutant forms of the protein components could result in the conversion from dynamic liquid condensates into more rigid gel- or solid-like aggregates, leading to the disruption of the organelle's function followed by the development of human disorders like neurodegenerative diseases. In summary, well-controlled formation and de-formation of LLPS is critical for normal biology and physiology from single cells to individual organisms, whereas abnormal LLPS is involved in the pathophysiology of human diseases. In turn, targeting these aggregates or their formation represents a promising approach in treating diseases driven by abnormal LLPS including those neurodegenerative diseases that lack effective therapies.
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Affiliation(s)
- Fangfang Wang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA.
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24
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Wilfling F, Kaksonen M, Stachowiak J. Protein condensates as flexible platforms for membrane traffic. Curr Opin Cell Biol 2023; 85:102258. [PMID: 37832166 PMCID: PMC11165926 DOI: 10.1016/j.ceb.2023.102258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023]
Abstract
With an essential role in nearly every physiological process and disease state, trafficking vesicles are fundamental to cell biology. Canonical understanding of membrane traffic has been driven by key achievements in structural biology. Nonetheless, discoveries over the past few years progressively point to the critical role of intrinsically disordered domains and proteins, which lack a well-defined secondary structure. From the initiation of endocytosis and the sequestration of synaptic vesicles to the stabilization of endoplasmic reticulum exit sites and the extension of the autophagic cup, flexible protein condensates, rich in intrinsic disorder, are increasingly implicated. While important debates about the physical nature and mechanistic interpretation of these findings remain, the significance of transient, multivalent protein assemblies in membrane traffic is increasingly clear.
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Affiliation(s)
- Florian Wilfling
- Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, Frankfurt a. M., Germany.
| | - Marko Kaksonen
- University of Geneva, Department of Biochemistry, Geneva, Switzerland.
| | - Jeanne Stachowiak
- University of Texas at Austin, Department of Biomedical Engineering, USA; University of Texas at Austin, Department of Chemical Engineering, USA.
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25
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Kim N, Kim TH, Kim C, Lee JE, Kang MG, Shin S, Jung M, Kim JS, Mun JY, Rhee HW, Park SY, Shin Y, Yoo JY. Intrinsically disordered region-mediated condensation of IFN-inducible SCOTIN/SHISA-5 inhibits ER-to-Golgi vesicle transport. Dev Cell 2023; 58:1950-1966.e8. [PMID: 37816329 DOI: 10.1016/j.devcel.2023.08.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023]
Abstract
Newly synthesized proteins in the endoplasmic reticulum (ER) are sorted by coat protein complex II (COPII) at the ER exit site en route to the Golgi. Under cellular stresses, COPII proteins become targets of regulation to control the transport. Here, we show that the COPII outer coat proteins Sec31 and Sec13 are selectively sequestered into the biomolecular condensate of SCOTIN/SHISA-5, which interferes with COPII vesicle formation and inhibits ER-to-Golgi transport. SCOTIN is an ER transmembrane protein with a cytosolic intrinsically disordered region (IDR), which is required and essential for the formation of condensates. Upon IFN-γ stimulation, which is a cellular condition that induces SCOTIN expression and condensation, ER-to-Golgi transport was inhibited in a SCOTIN-dependent manner. Furthermore, cancer-associated mutations of SCOTIN perturb its ability to form condensates and control transport. Together, we propose that SCOTIN impedes the ER-to-Golgi transport through its ability to form biomolecular condensates at the ER membrane.
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Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
| | - Tae-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jee-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sanghee Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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26
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Gallo R, Rai AK, McIntyre ABR, Meyer K, Pelkmans L. DYRK3 enables secretory trafficking by maintaining the liquid-like state of ER exit sites. Dev Cell 2023; 58:1880-1897.e11. [PMID: 37643612 DOI: 10.1016/j.devcel.2023.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/16/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
The dual-specificity kinase DYRK3 controls the formation and dissolution of multiple biomolecular condensates, regulating processes including stress recovery and mitotic progression. Here, we report that DYRK3 functionally interacts with proteins associated with endoplasmic reticulum (ER) exit sites (ERESs) and that inhibition of DYRK3 perturbs the organization of the ERES-Golgi interface and secretory trafficking. DYRK3-mediated regulation of ERES depends on the N-terminal intrinsically disordered region (IDR) of the peripheral membrane protein SEC16A, which co-phase separates with ERES components to form liquid-like condensates on the surface of the ER. By modulating the liquid-like properties of ERES, we show that their physical state is essential for functional cargo trafficking through the early secretory pathway. Our findings support a mechanism whereby phosphorylation by DYRK3 and its reversal by serine-threonine phosphatases regulate the material properties of ERES to create a favorable physicochemical environment for directional membrane traffic in eukaryotic cells.
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Affiliation(s)
- Raffaella Gallo
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Arpan Kumar Rai
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
| | - Alexa B R McIntyre
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Katrina Meyer
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8046 Zurich, Switzerland.
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27
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Dragwidge JM, Van Damme D. Protein phase separation in plant membrane biology: more than just a compartmentalization strategy. THE PLANT CELL 2023; 35:3162-3172. [PMID: 37352127 PMCID: PMC10473209 DOI: 10.1093/plcell/koad177] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
The formation of biomolecular condensates through phase separation is an important strategy to compartmentalize cellular functions. While it is now well established that condensates exist throughout eukaryotic cells, how condensates assemble and function on lipid membranes is only beginning to be understood. In this perspective, we highlight work from plant, animal, and yeast model systems showing that condensates assemble on many endomembrane surfaces to carry out diverse functions. In vesicle trafficking, condensation has reported roles in the formation of endocytic vesicles and autophagosomes and in the inactivation of secretory COPII vesicles. We briefly discuss how membranes and membrane lipids regulate the formation and function of membrane-associated condensates. This includes how membranes act as surfaces for condensate assembly, with lipids mediating the nucleation of condensates during endocytosis and other processes. Additionally, membrane-condensate interactions give rise to the biophysical property of "wetting", which has functional importance in shaping autophagosomal and vacuolar membranes. We also speculate on the existence of membrane-associated condensates during cell polarity in plants and discuss how condensation may help to establish functional plasma membrane domains. Lastly, we provide advice on relevant in vitro and in vivo approaches and techniques to study membrane-associated phase separation.
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Affiliation(s)
- Jonathan Michael Dragwidge
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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28
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Kasberg W, Luong P, Hanna MG, Minushkin K, Tsao A, Shankar R, Block S, Audhya A. The Sar1 GTPase is dispensable for COPII-dependent cargo export from the ER. Cell Rep 2023; 42:112635. [PMID: 37300835 PMCID: PMC10592460 DOI: 10.1016/j.celrep.2023.112635] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 04/21/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Coat protein complex II (COPII) plays an integral role in the packaging of secretory cargoes within membrane-enclosed transport carriers that leave the endoplasmic reticulum (ER) from discrete subdomains. Lipid bilayer remodeling necessary for this process is driven initially by membrane penetration mediated by the Sar1 GTPase and further stabilized by assembly of a multilayered complex of several COPII proteins. However, the relative contributions of these distinct factors to transport carrier formation and protein trafficking remain unclear. Here, we demonstrate that anterograde cargo transport from the ER continues in the absence of Sar1, although the efficiency of this process is dramatically reduced. Specifically, secretory cargoes are retained nearly five times longer at ER subdomains when Sar1 is depleted, but they ultimately remain capable of being translocated to the perinuclear region of cells. Taken together, our findings highlight alternative mechanisms by which COPII promotes transport carrier biogenesis.
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Affiliation(s)
- William Kasberg
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Peter Luong
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Michael G Hanna
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Kayla Minushkin
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Annabelle Tsao
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Raakhee Shankar
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Samuel Block
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA.
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29
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Jin G, Lin L, Li K, Li J, Yu C, Wei Z. Structural basis of ELKS/Rab6B interaction and its role in vesicle capturing enhanced by liquid-liquid phase separation. J Biol Chem 2023:104808. [PMID: 37172719 DOI: 10.1016/j.jbc.2023.104808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
ELKS proteins play a key role in organizing intracellular vesicle trafficking and targeting in both neurons and non-neuronal cells. While it is known that ELKS interacts with the vesicular traffic regulator, the Rab6 GTPase, the molecular basis governing ELKS-mediated trafficking of Rab6-coated vesicles has remained unclear. In this study, we solved the Rab6B structure in complex with the Rab6-binding domain of ELKS1, revealing that a C-terminal segment of ELKS1 forms a helical hairpin to recognize Rab6B through a unique binding mode. We further showed that liquid-liquid phase separation (LLPS) of ELKS1 allows it to compete with other Rab6 effectors for binding to Rab6B and accumulate Rab6B-coated liposomes to the protein condensate formed by ELKS1. We also found that the ELKS1 condensate recruits Rab6B-coated vesicles to vesicle releasing sites and promotes vesicle exocytosis. Together, our structural, biochemical, and cellular analyses suggest that ELKS1, via the LLPS-enhanced interaction with Rab6, captures Rab6-coated vesicles from the cargo transport machine for efficient vesicle releasing at exocytotic sites. These findings shed new light on the understanding of spatiotemporal regulation of vesicle trafficking through the interplay between membranous structures and membraneless condensates.
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Affiliation(s)
- Gaowei Jin
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Leishu Lin
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Kaiyue Li
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jiashan Li
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Cong Yu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, Guangdong, China 518055.
| | - Zhiyi Wei
- Brain Research Center, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China; School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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30
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Zhang C, Kalaitsidou E, Damen JMA, Grond R, Rabouille C, Wu W. Novel Components of the Stress Assembly Sec Body Identified by Proximity Labeling. Cells 2023; 12:cells12071055. [PMID: 37048128 PMCID: PMC10093351 DOI: 10.3390/cells12071055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Sec bodies are membraneless stress-induced assemblies that form by the coalescence of endoplasmic reticulum exit sites (ERES). Through APEX2 tagging of Sec24AB, we biotinylated and identified the full complement of Sec body proteins. In the presence of biotin-phenol and H2O2 (APEX on), APEX2 facilitates the transfer of a biotin moiety to nearby interactors of chimeric Sec24AB. Using this unbiased approach comparing APEX on and off (−H2O2) conditions, we identified 52 proteins specifically enriched in Sec bodies. These include a large proportion of ER and Golgi proteins, packaged without defined stoichiometry, which we could selectively verify by imaging. Interestingly, Sec body components are neither transcriptionally nor translationally regulated under the conditions that induce Sec body formation, suggesting that incorporation of these proteins into granules may be driven instead by the aggregation of nucleating proteins with a high content of intrinsically disordered regions. This reinforces the notion that Sec bodies may act as storage for ERES, ER and Golgi components during stress.
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31
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Suzuki K, Hirata E. Liquid droplet formation and cytoplasm to vacuole targeting of aminopeptidase I are temperature sensitive in Saccharomyces cerevisiae. FEBS Lett 2023; 597:631-642. [PMID: 36217212 DOI: 10.1002/1873-3468.14509] [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] [Received: 07/07/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 11/10/2022]
Abstract
Aminopeptidase I (Ape1) is one of the major cargoes of the cytoplasm-to-vacuole targeting (Cvt) pathway, which is a kind of selective autophagy, in Saccharomyces cerevisiae. After synthesis, the Ape1 precursor (prApe1) undergoes phase separation to form liquid droplets, termed Ape1 droplets, in the cytoplasm. In this study, we found that cells expressing prApe1-GFP exhibited temperature-sensitive formation of Ape1 droplets, which affected its transport. Moreover, we showed that endogenous Ape1 transport was defective at high temperatures in various laboratory strains due to the defect in the formation of Ape1 droplets at these temperatures. Finally, we found that gene disruptants showing heat-tolerant growth suppressed the temperature sensitivity of the Ape1 transport. The formation of Ape1 droplets might be an indicator of cytoplasmic integrity at high temperature.
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Affiliation(s)
- Kuninori Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Life Science Data Research Center, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Japan
| | - Eri Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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32
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Zhang K, Huang M, Li A, Wen J, Yan L, Li Y, Guo L, Senthil KS, Zhou Y, Chen G, Liu Y, Zhang X, Yao X, Qin D, Su H. DIAPH3 condensates formed by liquid-liquid phase separation act as a regulatory hub for stress-induced actin cytoskeleton remodeling. Cell Rep 2023; 42:111986. [PMID: 36640348 DOI: 10.1016/j.celrep.2022.111986] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/24/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
Membraneless condensates, such as stress granules (SGs) and processing bodies (P-bodies), have attracted wide attention due to their unique feature of rapid response to stress without first requiring nuclear feedback. In this study, we identify diaphanous-related formin 3 (DIAPH3), an actin nucleator, as a scaffold protein to initiate liquid-liquid phase separation (LLPS) and form abundant cytosolic phase-separated DIAPH3 granules (D-granules) in mammalian cells such as HeLa, HEK293, and fibroblasts under various stress conditions. Neither mRNAs nor known stress-associated condensate markers, such as G3BP1, G3BP2, and TIA1 for SGs and DCP1A for P-bodies, are detected in D-granules. Using overexpression and knockout of DIAPH3, pharmacological interventions, and optogenetics, we further demonstrate that stress-induced D-granules spatially sequester DIAPH3 within the condensation to inhibit the assembly of actin filaments in filopodia. This study reveals that D-granules formed by LLPS act as a regulatory hub for actin cytoskeletal remodeling in response to stress.
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Affiliation(s)
- Ke Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Miaodan Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Ang Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Jing Wen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Lingli Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yunhao Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Liman Guo
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Kumaran Satyanarayanan Senthil
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yangyang Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Guobing Chen
- Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, China
| | - Yong Liu
- Laboratory of Neuroscience in Health and Disease Institute, Guangzhou First People's Hospital School of Medicine, South China University of Technology, Guangzhou, China
| | - Xiaofei Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaoli Yao
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Dajiang Qin
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huanxing Su
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
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33
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Kim-Holzapfel DM, Dey R, Richardson BC, Arachchige D, Reddy K, De Vitto H, Bhandari J, French JB. Human uridine 5'-monophosphate synthase stores metabolic potential in inactive biomolecular condensates. J Biol Chem 2023; 299:102949. [PMID: 36708921 PMCID: PMC9978035 DOI: 10.1016/j.jbc.2023.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/02/2023] [Accepted: 01/06/2023] [Indexed: 01/27/2023] Open
Abstract
Human uridine 5'-monophosphate synthase (HsUMPS) is a bifunctional enzyme that catalyzes the final two steps in de novo pyrimidine biosynthesis. The individual orotate phosphoribosyl transferase and orotidine monophosphate domains have been well characterized, but little is known about the overall structure of the protein and how the organization of domains impacts function. Using a combination of chromatography, electron microscopy, and complementary biophysical methods, we report herein that HsUMPS can be observed in two structurally distinct states, an enzymatically active dimeric form and a nonactive multimeric form. These two states readily interconvert to reach an equilibrium that is sensitive to perturbations of the active site and the presence of substrate. We determined that the smaller molecular weight form of HsUMPS is an S-shaped dimer that can self-assemble into relatively well-ordered globular condensates. Our analysis suggests that the transition between dimer and multimer is driven primarily by oligomerization of the orotate phosphoribosyl transferase domain. While the cellular distribution of HsUMPS is unaffected, quantification by mass spectrometry revealed that de novo pyrimidine biosynthesis is dysregulated when this protein is unable to assemble into inactive condensates. Taken together, our data suggest that HsUMPS self-assembles into biomolecular condensates as a means to store metabolic potential for the regulation of metabolic rates.
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Affiliation(s)
- Deborah M Kim-Holzapfel
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA; Molecular and Cellular Biology PhD Program, Stony Brook University, Stony Brook, New York, USA
| | - Raja Dey
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | | | | | - Kanamata Reddy
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Humberto De Vitto
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Janarjan Bhandari
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Jarrod B French
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA.
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34
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Konietzny A, Wegmann S, Mikhaylova M. The endoplasmic reticulum puts a new spin on synaptic tagging. Trends Neurosci 2023; 46:32-44. [PMID: 36428191 DOI: 10.1016/j.tins.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/12/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
The heterogeneity of the endoplasmic reticulum (ER) makes it a versatile platform for a broad range of homeostatic processes, ranging from calcium regulation to synthesis and trafficking of proteins and lipids. It is not surprising that neurons use this organelle to fine-tune synaptic properties and thereby provide specificity to synaptic inputs. In this review, we discuss the mechanisms that enable activity-dependent ER recruitment into dendritic spines, with a focus on molecular mechanisms that mediate transport and retention of the ER in spines. The role of calcium signaling in spine ER, synaptopodin 'tagging' of active synapses, and the formation of the spine apparatus (SA) are highlighted. Finally, we discuss the role of liquid-liquid phase separation as a possible driving force in these processes.
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Affiliation(s)
- Anja Konietzny
- AG Optobiology, Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany; Guest Group 'Neuronal Protein Transport', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Marina Mikhaylova
- AG Optobiology, Institute of Biology, Humboldt Universität zu Berlin, Berlin, Germany; Guest Group 'Neuronal Protein Transport', Center for Molecular Neurobiology, ZMNH, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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35
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van Leeuwen W, Nguyen DTM, Grond R, Veenendaal T, Rabouille C, Farías GG. Stress-induced phase separation of ERES components into Sec bodies precedes ER exit inhibition in mammalian cells. J Cell Sci 2022; 135:jcs260294. [PMID: 36325988 PMCID: PMC10112967 DOI: 10.1242/jcs.260294] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Phase separation of components of ER exit sites (ERES) into membraneless compartments, the Sec bodies, occurs in Drosophila cells upon exposure to specific cellular stressors, namely, salt stress and amino acid starvation, and their formation is linked to the early secretory pathway inhibition. Here, we show Sec bodies also form in secretory mammalian cells upon the same stress. These reversible and membraneless structures are positive for ERES components, including both Sec16A and Sec16B isoforms and COPII subunits. We find that Sec16A, but not Sec16B, is a driver for Sec body formation, and that the coalescence of ERES components into Sec bodies occurs by fusion. Finally, we show that the stress-induced coalescence of ERES components into Sec bodies precedes ER exit inhibition, leading to their progressive depletion from ERES that become non-functional. Stress relief causes an immediate dissolution of Sec bodies and the concomitant restoration of ER exit. We propose that the dynamic conversion between ERES and Sec body assembly, driven by Sec16A, regulates protein exit from the ER during stress and upon stress relief in mammalian cells, thus providing a conserved pro-survival mechanism in response to stress.
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Affiliation(s)
- Wessel van Leeuwen
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht 3584 CT, The Netherlands
| | - Dan T. M. Nguyen
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Rianne Grond
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht 3584 CT, The Netherlands
| | - Tineke Veenendaal
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht 3584 CT, The Netherlands
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
- Department of Biomedical Sciences in Cells and Systems, UMC Groningen, Groningen 9713 AV, The Netherlands
| | - Ginny G. Farías
- Cell Biology, Neurobiology and Biophysics. Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
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36
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Bejan DS, Sundalam S, Jin H, Morgan RK, Kirby IT, Siordia IR, Tivon B, London N, Cohen MS. Structure-guided design and characterization of a clickable, covalent PARP16 inhibitor. Chem Sci 2022; 13:13898-13906. [PMID: 36544740 PMCID: PMC9710212 DOI: 10.1039/d2sc04820e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/06/2022] [Indexed: 11/18/2022] Open
Abstract
PARP16-the sole ER-resident PARP family member-is gaining attention as a potential therapeutic target for cancer treatment. Nevertheless, the precise function of the catalytic activity of PARP16 is poorly understood. This is primarily due to the lack of inhibitors that are selective for PARP16 over other PARP family members. Herein, we describe a structure-guided strategy for generating a selective PARP16 inhibitor by incorporating two selectivity determinants into a phthalazinone pan-PARP inhibitor scaffold: (i) an acrylamide-based inhibitor (DB008) designed to covalently react with a non-conserved cysteine (Cys169, human numbering) in the NAD+ binding pocket of PARP16 and (ii) a dual-purpose ethynyl group designed to bind in a unique hydrophobic cavity adjacent to the NAD+ binding pocket as well as serve as a click handle. DB008 exhibits good selectivity for PARP16 versus other PARP family members. Copper-catalyzed azide-alkyne cycloaddition (CuAAC) confirmed that covalent labeling of PARP16 by DB008 in cells is dependent on Cys169. DB008 exhibits excellent proteome-wide selectivity at concentrations required to achieve saturable labeling of endogenous PARP16. In-cell competition labeling experiments using DB008 provided a facile strategy for evaluating putative PARP16 inhibitors. Lastly, we found that PARP16 is sequestered into a detergent-insoluble fraction under prolonged amino acid starvation, and surprisingly, treatment with PARP16 inhibitors prevented this effect. These results suggest that the catalytic activity of PARP16 regulates its solubility in response to nutrient stress.
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Affiliation(s)
- Daniel S Bejan
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland OR 97239 USA
| | - Sunil Sundalam
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland OR 97239 USA
| | - Haihong Jin
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland OR 97239 USA
| | - Rory K Morgan
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland OR 97239 USA
| | - Ilsa T Kirby
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland OR 97239 USA
| | - Ivan R Siordia
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland OR 97239 USA
| | - Barr Tivon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Rehovot 7610001 Israel
| | - Nir London
- Department of Chemical and Structural Biology, The Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University Portland OR 97239 USA
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Ren J, Zhang Z, Zong Z, Zhang L, Zhou F. Emerging Implications of Phase Separation in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202855. [PMID: 36117111 PMCID: PMC9631093 DOI: 10.1002/advs.202202855] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Indexed: 05/19/2023]
Abstract
In eukaryotic cells, biological activities are executed in distinct cellular compartments or organelles. Canonical organelles with membrane-bound structures are well understood. Cells also inherently contain versatile membrane-less organelles (MLOs) that feature liquid or gel-like bodies. A biophysical process termed liquid-liquid phase separation (LLPS) elucidates how MLOs form through dynamic biomolecule assembly. LLPS-related molecules often have multivalency, which is essential for low-affinity inter- or intra-molecule interactions to trigger phase separation. Accumulating evidence shows that LLPS concentrates and organizes desired molecules or segregates unneeded molecules in cells. Thus, MLOs have tunable functional specificity in response to environmental stimuli and metabolic processes. Aberrant LLPS is widely associated with several hallmarks of cancer, including sustained proliferative signaling, growth suppressor evasion, cell death resistance, telomere maintenance, DNA damage repair, etc. Insights into the molecular mechanisms of LLPS provide new insights into cancer therapeutics. Here, the current understanding of the emerging concepts of LLPS and its involvement in cancer are comprehensively reviewed.
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Affiliation(s)
- Jiang Ren
- School of MedicineZhejiang University City CollegeHangzhou215123China
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Long Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- International Biomed‐X Research Center, Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhou215123China
| | - Fangfang Zhou
- School of MedicineZhejiang University City CollegeHangzhou215123China
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China
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38
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Cheng S, Altmeppen G, So C, Welp LM, Penir S, Ruhwedel T, Menelaou K, Harasimov K, Stützer A, Blayney M, Elder K, Möbius W, Urlaub H, Schuh M. Mammalian oocytes store mRNAs in a mitochondria-associated membraneless compartment. Science 2022; 378:eabq4835. [PMID: 36264786 DOI: 10.1126/science.abq4835] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Full-grown oocytes are transcriptionally silent and must stably maintain the messenger RNAs (mRNAs) needed for oocyte meiotic maturation and early embryonic development. However, where and how mammalian oocytes store maternal mRNAs is unclear. Here, we report that mammalian oocytes accumulate mRNAs in a mitochondria-associated ribonucleoprotein domain (MARDO). MARDO assembly around mitochondria was promoted by the RNA-binding protein ZAR1 and directed by an increase in mitochondrial membrane potential during oocyte growth. MARDO foci coalesced into hydrogel-like matrices that clustered mitochondria. Maternal mRNAs stored in the MARDO were translationally repressed. Loss of ZAR1 disrupted the MARDO, dispersed mitochondria, and caused a premature loss of MARDO-localized mRNAs. Thus, a mitochondria-associated membraneless compartment controls mitochondrial distribution and regulates maternal mRNA storage, translation, and decay to ensure fertility in mammals.
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Affiliation(s)
- Shiya Cheng
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gerrit Altmeppen
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Chun So
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sarah Penir
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Torben Ruhwedel
- Electron Microscopy City Campus, Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Katerina Menelaou
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Bourn Hall Clinic, Cambridge, UK
| | - Katarina Harasimov
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexandra Stützer
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | | | | | - Wiebke Möbius
- Electron Microscopy City Campus, Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Melina Schuh
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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39
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Fefilova AS, Antifeeva IA, Gavrilova AA, Turoverov KK, Kuznetsova IM, Fonin AV. Reorganization of Cell Compartmentalization Induced by Stress. Biomolecules 2022; 12:1441. [PMID: 36291650 PMCID: PMC9599104 DOI: 10.3390/biom12101441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/17/2022] Open
Abstract
The discovery of intrinsically disordered proteins (IDPs) that do not have an ordered structure and nevertheless perform essential functions has opened a new era in the understanding of cellular compartmentalization. It threw the bridge from the mostly mechanistic model of the organization of the living matter to the idea of highly dynamic and functional "soft matter". This paradigm is based on the notion of the major role of liquid-liquid phase separation (LLPS) of biopolymers in the spatial-temporal organization of intracellular space. The LLPS leads to the formation of self-assembled membrane-less organelles (MLOs). MLOs are multicomponent and multifunctional biological condensates, highly dynamic in structure and composition, that allow them to fine-tune the regulation of various intracellular processes. IDPs play a central role in the assembly and functioning of MLOs. The LLPS importance for the regulation of chemical reactions inside the cell is clearly illustrated by the reorganization of the intracellular space during stress response. As a reaction to various types of stresses, stress-induced MLOs appear in the cell, enabling the preservation of the genetic and protein material during unfavourable conditions. In addition, stress causes structural, functional, and compositional changes in the MLOs permanently present inside the cells. In this review, we describe the assembly of stress-induced MLOs and the stress-induced modification of existing MLOs in eukaryotes, yeasts, and prokaryotes in response to various stress factors.
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Affiliation(s)
| | | | | | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of RAS, 194064 St. Petersburg, Russia
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Somasundaram K, Gupta B, Jain N, Jana S. LncRNAs divide and rule: The master regulators of phase separation. Front Genet 2022; 13:930792. [PMID: 36035193 PMCID: PMC9399341 DOI: 10.3389/fgene.2022.930792] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Most of the human genome, except for a small region that transcribes protein-coding RNAs, was considered junk. With the advent of RNA sequencing technology, we know that much of the genome codes for RNAs with no protein-coding potential. Long non-coding RNAs (lncRNAs) that form a significant proportion are dynamically expressed and play diverse roles in physiological and pathological processes. Precise spatiotemporal control of their expression is essential to carry out various biochemical reactions inside the cell. Intracellular organelles with membrane-bound compartments are known for creating an independent internal environment for carrying out specific functions. The formation of membrane-free ribonucleoprotein condensates resulting in intracellular compartments is documented in recent times to execute specialized tasks such as DNA replication and repair, chromatin remodeling, transcription, and mRNA splicing. These liquid compartments, called membrane-less organelles (MLOs), are formed by liquid–liquid phase separation (LLPS), selectively partitioning a specific set of macromolecules from others. While RNA binding proteins (RBPs) with low complexity regions (LCRs) appear to play an essential role in this process, the role of RNAs is not well-understood. It appears that short nonspecific RNAs keep the RBPs in a soluble state, while longer RNAs with unique secondary structures promote LLPS formation by specifically binding to RBPs. This review will update the current understanding of phase separation, physio-chemical nature and composition of condensates, regulation of phase separation, the role of lncRNA in the phase separation process, and the relevance to cancer development and progression.
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41
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van Leeuwen W, VanInsberghe M, Battich N, Salmén F, van Oudenaarden A, Rabouille C. Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo. CELL REPORTS METHODS 2022; 2:100235. [PMID: 35784648 PMCID: PMC9243631 DOI: 10.1016/j.crmeth.2022.100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/24/2022] [Accepted: 05/20/2022] [Indexed: 11/09/2022]
Abstract
Stress granules are phase-separated assemblies formed around RNAs. So far, the techniques available to identify these RNAs are not suitable for single cells and small tissues displaying cell heterogeneity. Here, we used TRIBE (target of RNA-binding proteins identified by editing) to profile stress granule RNAs. We used an RNA-binding protein (FMR1) fused to the catalytic domain of an RNA-editing enzyme (ADAR), which coalesces into stress granules upon oxidative stress. RNAs colocalized with this fusion are edited, producing mutations that are detectable by VASA sequencing. Using single-molecule FISH, we validated that this purification-free method can reliably identify stress granule RNAs in bulk and single S2 cells and in Drosophila neurons. Similar to mammalian cells, we find that stress granule mRNAs encode ATP binding, cell cycle, and transcription factors. This method opens the possibility to identify stress granule RNAs and other RNA-based assemblies in other single cells and tissues.
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Affiliation(s)
| | | | - Nico Battich
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
| | - Fredrik Salmén
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
| | | | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, the Netherlands
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Biomedical Sciences in Cells and Systems, UMC Groningen, Groningen, the Netherlands
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42
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Antifeeva IA, Fonin AV, Fefilova AS, Stepanenko OV, Povarova OI, Silonov SA, Kuznetsova IM, Uversky VN, Turoverov KK. Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept. Cell Mol Life Sci 2022; 79:251. [PMID: 35445278 PMCID: PMC11073196 DOI: 10.1007/s00018-022-04276-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 12/14/2022]
Abstract
At the turn of the twenty-first century, fundamental changes took place in the understanding of the structure and function of proteins and then in the appreciation of the intracellular space organization. A rather mechanistic model of the organization of living matter, where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional "soft matter" lies at the heart of all living things. According this "new view", the most important role in the spatio-temporal organization of the intracellular space is played by liquid-liquid phase transitions of biopolymers. These self-organizing cellular compartments are open dynamic systems existing at the edge of chaos. They are characterized by the exceptional structural and compositional dynamics, and their multicomponent nature and polyfunctionality provide means for the finely tuned regulation of various intracellular processes. Changes in the external conditions can cause a disruption of the biogenesis of these cellular bodies leading to the irreversible aggregation of their constituent proteins, followed by the transition to a gel-like state and the emergence of amyloid fibrils. This work represents a historical overview of changes in our understanding of the intracellular space compartmentalization. It also reflects methodological breakthroughs that led to a change in paradigms in this area of science and discusses modern ideas about the organization of the intracellular space. It is emphasized here that the membrane-less organelles have to combine a certain resistance to the changes in their environment and, at the same time, show high sensitivity to the external signals, which ensures the normal functioning of the cell.
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Affiliation(s)
- Iuliia A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olga I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Sergey A Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia.
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43
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Distributed synthesis of sarcolemmal and sarcoplasmic reticulum membrane proteins in cardiac myocytes. Basic Res Cardiol 2021; 116:63. [PMID: 34713358 PMCID: PMC8553722 DOI: 10.1007/s00395-021-00895-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/30/2021] [Accepted: 09/11/2021] [Indexed: 02/05/2023]
Abstract
It is widely assumed that synthesis of membrane proteins, particularly in the heart, follows the classical secretory pathway with mRNA translation occurring in perinuclear regions followed by protein trafficking to sites of deployment. However, this view is based on studies conducted in less-specialized cells, and has not been experimentally addressed in cardiac myocytes. Therefore, we undertook direct experimental investigation of protein synthesis in cardiac tissue and isolated myocytes using single-molecule visualization techniques and a novel proximity-ligated in situ hybridization approach for visualizing ribosome-associated mRNA molecules for a specific protein species, indicative of translation sites. We identify here, for the first time, that the molecular machinery for membrane protein synthesis occurs throughout the cardiac myocyte, and enables distributed synthesis of membrane proteins within sub-cellular niches where the synthesized protein functions using local mRNA pools trafficked, in part, by microtubules. We also observed cell-wide distribution of membrane protein mRNA in myocardial tissue from both non-failing and hypertrophied (failing) human hearts, demonstrating an evolutionarily conserved distributed mechanism from mouse to human. Our results identify previously unanticipated aspects of local control of cardiac myocyte biology and highlight local protein synthesis in cardiac myocytes as an important potential determinant of the heart’s biology in health and disease.
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44
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Bisnett BJ, Condon BM, Linhart NA, Lamb CH, Huynh DT, Bai J, Smith TJ, Hu J, Georgiou GR, Boyce M. Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation. Glycobiology 2021; 31:1102-1120. [PMID: 34142147 PMCID: PMC8457363 DOI: 10.1093/glycob/cwab055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) is a dynamic form of intracellular glycosylation common in animals, plants and other organisms. O-GlcNAcylation is essential in mammalian cells and is dysregulated in myriad human diseases, such as cancer, neurodegeneration and metabolic syndrome. Despite this pathophysiological significance, key aspects of O-GlcNAc signaling remain incompletely understood, including its impact on fundamental cell biological processes. Here, we investigate the role of O-GlcNAcylation in the coat protein II complex (COPII), a system universally conserved in eukaryotes that mediates anterograde vesicle trafficking from the endoplasmic reticulum. We identify new O-GlcNAcylation sites on Sec24C, Sec24D and Sec31A, core components of the COPII system, and provide evidence for potential nutrient-sensitive pathway regulation through site-specific glycosylation. Our work suggests a new connection between metabolism and trafficking through the conduit of COPII protein O-GlcNAcylation.
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Affiliation(s)
- Brittany J Bisnett
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Brett M Condon
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Noah A Linhart
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Caitlin H Lamb
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Duc T Huynh
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jingyi Bai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Timothy J Smith
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jimin Hu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - George R Georgiou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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45
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Zhang C, van Leeuwen W, Blotenburg M, Aguilera-Gomez A, Brussee S, Grond R, Kampinga HH, Rabouille C. Activation of salt Inducible Kinases, IRE1 and PERK leads to Sec bodies formation in Drosophila S2 cells. J Cell Sci 2021; 134:272062. [PMID: 34350957 PMCID: PMC8445602 DOI: 10.1242/jcs.258685] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
The phase separation of the non-membrane bound Sec bodies occurs in Drosophila S2 cells by coalescence of components of the endoplasmic reticulum (ER) exit sites under the stress of amino acid starvation. Here, we address which signaling pathways cause Sec body formation and find that two pathways are critical. The first is the activation of the salt-inducible kinases (SIKs; SIK2 and SIK3) by Na+ stress, which, when it is strong, is sufficient. The second is activation of IRE1 and PERK (also known as PEK in flies) downstream of ER stress induced by the absence of amino acids, which needs to be combined with moderate salt stress to induce Sec body formation. SIK, and IRE1 and PERK activation appear to potentiate each other through the stimulation of the unfolded protein response, a key parameter in Sec body formation. This work shows the role of SIKs in phase transition and re-enforces the role of IRE1 and PERK as a metabolic sensor for the level of circulating amino acids and salt. This article has an associated First Person interview with the first author of the paper. Summary: In S2 cells, the phase-separated Sec bodies form upon the combined activation of salt-inducible kinases, IRE1 and PERK.
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Affiliation(s)
- Chujun Zhang
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | | | | | | | - Sem Brussee
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | - Rianne Grond
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands
| | - Harm H Kampinga
- Department of Biomedical Sciences in Cells and Systems, UMC Groningen, The Netherlands
| | - Catherine Rabouille
- Hubrecht Institute of the KNAW & UMC Utrecht, Utrecht, The Netherlands.,Department of Biomedical Sciences in Cells and Systems, UMC Groningen, The Netherlands.,Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, The Netherlands
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Nüchel J, Tauber M, Nolte JL, Mörgelin M, Türk C, Eckes B, Demetriades C, Plomann M. An mTORC1-GRASP55 signaling axis controls unconventional secretion to reshape the extracellular proteome upon stress. Mol Cell 2021; 81:3275-3293.e12. [PMID: 34245671 PMCID: PMC8382303 DOI: 10.1016/j.molcel.2021.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/21/2021] [Accepted: 06/14/2021] [Indexed: 01/13/2023]
Abstract
Cells communicate with their environment via surface proteins and secreted factors. Unconventional protein secretion (UPS) is an evolutionarily conserved process, via which distinct cargo proteins are secreted upon stress. Most UPS types depend upon the Golgi-associated GRASP55 protein. However, its regulation and biological role remain poorly understood. Here, we show that the mechanistic target of rapamycin complex 1 (mTORC1) directly phosphorylates GRASP55 to maintain its Golgi localization, thus revealing a physiological role for mTORC1 at this organelle. Stimuli that inhibit mTORC1 cause GRASP55 dephosphorylation and relocalization to UPS compartments. Through multiple, unbiased, proteomic analyses, we identify numerous cargoes that follow this unconventional secretory route to reshape the cellular secretome and surfactome. Using MMP2 secretion as a proxy for UPS, we provide important insights on its regulation and physiological role. Collectively, our findings reveal the mTORC1-GRASP55 signaling hub as the integration point in stress signaling upstream of UPS and as a key coordinator of the cellular adaptation to stress. mTORC1 phosphorylates GRASP55 directly at the Golgi in non-stressed cells mTORC1 inactivation by stress leads to GRASP55 dephosphorylation and relocalization GRASP55 relocalization to autophagosomes and MVBs drives UPS of selected cargo mTORC1-GRASP55 link cellular stress to changes in the extracellular proteome via UPS
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Affiliation(s)
- Julian Nüchel
- Max Planck Institute for Biology of Ageing (MPI-AGE), 50931 Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Biochemistry, 50931 Cologne, Germany
| | - Marina Tauber
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Biochemistry, 50931 Cologne, Germany
| | - Janica L Nolte
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | | | - Clara Türk
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Beate Eckes
- University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Translational Matrix Biology, 50931 Cologne, Germany
| | - Constantinos Demetriades
- Max Planck Institute for Biology of Ageing (MPI-AGE), 50931 Cologne, Germany; University of Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany.
| | - Markus Plomann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Biochemistry, 50931 Cologne, Germany.
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Pancsa R, Vranken W, Mészáros B. Computational resources for identifying and describing proteins driving liquid-liquid phase separation. Brief Bioinform 2021; 22:6124912. [PMID: 33517364 PMCID: PMC8425267 DOI: 10.1093/bib/bbaa408] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/23/2020] [Accepted: 12/12/2020] [Indexed: 01/06/2023] Open
Abstract
One of the most intriguing fields emerging in current molecular biology is the study of membraneless organelles formed via liquid–liquid phase separation (LLPS). These organelles perform crucial functions in cell regulation and signalling, and recent years have also brought about the understanding of the molecular mechanism of their formation. The LLPS field is continuously developing and optimizing dedicated in vitro and in vivo methods to identify and characterize these non-stoichiometric molecular condensates and the proteins able to drive or contribute to LLPS. Building on these observations, several computational tools and resources have emerged in parallel to serve as platforms for the collection, annotation and prediction of membraneless organelle-linked proteins. In this survey, we showcase recent advancements in LLPS bioinformatics, focusing on (i) available databases and ontologies that are necessary to describe the studied phenomena and the experimental results in an unambiguous way and (ii) prediction methods to assess the potential LLPS involvement of proteins. Through hands-on application of these resources on example proteins and representative datasets, we give a practical guide to show how they can be used in conjunction to provide in silico information on LLPS.
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Affiliation(s)
- Rita Pancsa
- Enzymology Institute of the Research Centre for Natural Sciences, Budapest, Hungary
| | - Wim Vranken
- Computer Science, chemistry and biomedical sciences at the Vrije Universiteit Brussel
| | - Bálint Mészáros
- Structural and Computational Biology Unit at the European Molecular Biology Laboratory, Heidelberg 69117, Germany
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Bisnett BJ, Condon BM, Lamb CH, Georgiou GR, Boyce M. Export Control: Post-transcriptional Regulation of the COPII Trafficking Pathway. Front Cell Dev Biol 2021; 8:618652. [PMID: 33511128 PMCID: PMC7835409 DOI: 10.3389/fcell.2020.618652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
The coat protein complex II (COPII) mediates forward trafficking of protein and lipid cargoes from the endoplasmic reticulum. COPII is an ancient and essential pathway in all eukaryotes and COPII dysfunction underlies a range of human diseases. Despite this broad significance, major aspects of COPII trafficking remain incompletely understood. For example, while the biochemical features of COPII vesicle formation are relatively well characterized, much less is known about how the COPII system dynamically adjusts its activity to changing physiologic cues or stresses. Recently, post-transcriptional mechanisms have emerged as a major mode of COPII regulation. Here, we review the current literature on how post-transcriptional events, and especially post-translational modifications, govern the COPII pathway.
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Affiliation(s)
- Brittany J Bisnett
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Brett M Condon
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Caitlin H Lamb
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - George R Georgiou
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
| | - Michael Boyce
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States
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Koppers M, Özkan N, Farías GG. Complex Interactions Between Membrane-Bound Organelles, Biomolecular Condensates and the Cytoskeleton. Front Cell Dev Biol 2020; 8:618733. [PMID: 33409284 PMCID: PMC7779554 DOI: 10.3389/fcell.2020.618733] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/03/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane-bound and membraneless organelles/biomolecular condensates ensure compartmentalization into functionally distinct units enabling proper organization of cellular processes. Membrane-bound organelles form dynamic contacts with each other to enable the exchange of molecules and to regulate organelle division and positioning in coordination with the cytoskeleton. Crosstalk between the cytoskeleton and dynamic membrane-bound organelles has more recently also been found to regulate cytoskeletal organization. Interestingly, recent work has revealed that, in addition, the cytoskeleton and membrane-bound organelles interact with cytoplasmic biomolecular condensates. The extent and relevance of these complex interactions are just beginning to emerge but may be important for cytoskeletal organization and organelle transport and remodeling. In this review, we highlight these emerging functions and emphasize the complex interplay of the cytoskeleton with these organelles. The crosstalk between membrane-bound organelles, biomolecular condensates and the cytoskeleton in highly polarized cells such as neurons could play essential roles in neuronal development, function and maintenance.
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Affiliation(s)
| | | | - Ginny G. Farías
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
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Bagamery LE, Justman QA, Garner EC, Murray AW. A Putative Bet-Hedging Strategy Buffers Budding Yeast against Environmental Instability. Curr Biol 2020; 30:4563-4578.e4. [PMID: 32976801 DOI: 10.1016/j.cub.2020.08.092] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/20/2020] [Accepted: 08/26/2020] [Indexed: 12/19/2022]
Abstract
To grow and divide, cells must extract resources from dynamic and unpredictable environments. Many organisms use different metabolic strategies for distinct contexts. Budding yeast can produce ATP from carbon sources by mechanisms that prioritize either speed (fermentation) or yield (respiration). Withdrawing glucose from exponentially growing cells reveals variability in their ability to switch from fermentation to respiration. We observe two subpopulations of glucose-starved cells: recoverers, which rapidly adapt and resume growth, and arresters, which enter a shock state characterized by deformation of many cellular structures, including mitochondria. These states are heritable, and on high glucose, arresters grow and divide faster than recoverers. Recoverers have a fitness advantage during a carbon source shift but are less fit in a constant, high-glucose environment, and we observe natural variation in the frequency of the two states across wild yeast strains. These experiments suggest that bet hedging has evolved in budding yeast.
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Affiliation(s)
- Laura E Bagamery
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Quincey A Justman
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
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