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Wang L, Yang Z, Satoshi F, Prasanna X, Yan Z, Vihinen H, Chen Y, Zhao Y, He X, Bu Q, Li H, Zhao Y, Jiang L, Qin F, Dai Y, Zhang N, Qin M, Kuang W, Zhao Y, Jokitalo E, Vattulainen I, Kajander T, Zhao H, Cen X. Membrane remodeling by FAM92A1 during brain development regulates neuronal morphology, synaptic function, and cognition. Nat Commun 2024; 15:6209. [PMID: 39043703 PMCID: PMC11266426 DOI: 10.1038/s41467-024-50565-w] [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: 09/18/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
The Bin/Amphiphysin/Rvs (BAR) domain protein FAM92A1 is a multifunctional protein engaged in regulating mitochondrial ultrastructure and ciliogenesis, but its physiological role in the brain remains unclear. Here, we show that FAM92A1 is expressed in neurons starting from embryonic development. FAM92A1 knockout in mice results in altered brain morphology and age-associated cognitive deficits, potentially due to neuronal degeneration and disrupted synaptic plasticity. Specifically, FAM92A1 deficiency impairs diverse neuronal membrane morphology, including the mitochondrial inner membrane, myelin sheath, and synapses, indicating its roles in membrane remodeling and maintenance. By determining the crystal structure of the FAM92A1 BAR domain, combined with atomistic molecular dynamics simulations, we uncover that FAM92A1 interacts with phosphoinositide- and cardiolipin-containing membranes to induce lipid-clustering and membrane curvature. Altogether, these findings reveal the physiological role of FAM92A1 in the brain, highlighting its impact on synaptic plasticity and neural function through the regulation of membrane remodeling and endocytic processes.
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Affiliation(s)
- Liang Wang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Ziyun Yang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Fudo Satoshi
- Helsinki Institute of Life Science - Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Xavier Prasanna
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Ziyi Yan
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Helena Vihinen
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Yaxing Chen
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yue Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Xiumei He
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
- School of Life Sciences, Guangxi Normal University, Guilin, China
- Guangxi Universities Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, 541004, China
| | - Qian Bu
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Hongchun Li
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Ying Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Linhong Jiang
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Feng Qin
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yanping Dai
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Ni Zhang
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Meng Qin
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Weihong Kuang
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yinglan Zhao
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Eija Jokitalo
- Helsinki Institute of Life Science (HiLIFE) - Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Tommi Kajander
- Helsinki Institute of Life Science - Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hongxia Zhao
- Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
- School of Life Sciences, Guangxi Normal University, Guilin, China.
- Guangxi Universities Key Laboratory of Stem Cell and Biopharmaceutical Technology, Guangxi Normal University, Guilin, 541004, China.
| | - Xiaobo Cen
- Mental Health Center and National Chengdu Center for Safety Evaluation of Drugs, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China.
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2
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Overduin M, Bhat R. Recognition and remodeling of endosomal zones by sorting nexins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184305. [PMID: 38408696 DOI: 10.1016/j.bbamem.2024.184305] [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: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
The proteolipid code determines how cytosolic proteins find and remodel membrane surfaces. Here, we investigate how this process works with sorting nexins Snx1 and Snx3. Both proteins form sorting machines by recognizing membrane zones enriched in phosphatidylinositol 3-phosphate (PI3P), phosphatidylserine (PS) and cholesterol. This co-localized combination forms a unique "lipid codon" or lipidon that we propose is responsible for endosomal targeting, as revealed by structures and interactions of their PX domain-based readers. We outline a membrane recognition and remodeling mechanism for Snx1 and Snx3 involving this code element alongside transmembrane pH gradients, dipole moment-guided docking and specific protein-protein interactions. This generates an initial membrane-protein assembly (memtein) that then recruits retromer and additional PX proteins to recruit cell surface receptors for sorting to the trans-Golgi network (TGN), lysosome and plasma membranes. Post-translational modification (PTM) networks appear to regulate how the sorting machines form and operate at each level. The commonalities and differences between these sorting nexins show how the proteolipid code orchestrates parallel flows of molecular information from ribosome emergence to organelle genesis, and illuminates a universally applicable model of the membrane.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
| | - Rakesh Bhat
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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3
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Liao Z, Si T, Kai JJ, Fan J. Mechanism of Membrane Curvature Induced by SNX1: Insights from Molecular Dynamics Simulations. J Phys Chem B 2024; 128:2144-2153. [PMID: 38408890 DOI: 10.1021/acs.jpcb.3c07009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
SNX proteins have been found to induce membrane remodeling to facilitate the generation of transport carriers in endosomal pathways. However, the molecular mechanism of membrane bending and the role of lipids in the bending process remain elusive. Here, we conducted coarse-grained molecular dynamics simulations to investigate the role of the three structural modules (PX, BAR, and AH) of SNX1 and the PI3P lipids in membrane deformation. We observed that the presence of all three domains is essential for SNX1 to achieve a stable membrane deformation. BAR is capable of remodeling the membrane through the charged residues on its concave surface, but it requires PX and AH to establish stable membrane binding. AH penetrates into the lipid membrane, thereby promoting the induction of membrane curvature; however, it is inadequate on its own to maintain membrane bending. PI3P lipids are also indispensable for membrane remodeling, as they play a dominant role in the interactions of lipids with the BAR domain. Our results enhance the comprehension of the molecular mechanism underlying SNX1-induced membrane curvature and help future studies of curvature-inducing proteins.
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Affiliation(s)
- Zhenyu Liao
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
| | - Ting Si
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
- Department of Physics, City University of Hong Kong, Kowloon 999077 Hong Kong, China
| | - Ji-Jung Kai
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
- Centre for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon 999077 Hong Kong, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
- Centre for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon 999077 Hong Kong, China
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4
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Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A. Architecture of the ESCPE-1 membrane coat. Nat Struct Mol Biol 2023; 30:958-969. [PMID: 37322239 PMCID: PMC10352136 DOI: 10.1038/s41594-023-01014-7] [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: 10/13/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.
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Affiliation(s)
| | | | | | - Morié Ishida
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - David Gil-Carton
- CIC bioGUNE, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- BREM Basque Resource for Electron Microscopy, Leioa, Spain
| | - Miguel Romero-Durana
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan Fernandez-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Daniel Castaño-Díez
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland.
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain.
| | - Aitor Hierro
- CIC bioGUNE, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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5
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Zhao Y, Caron C, Chan YY, Lee CK, Xu X, Zhang J, Masubuchi T, Wu C, Bui JD, Hui E. cis-B7:CD28 interactions at invaginated synaptic membranes provide CD28 co-stimulation and promote CD8 + T cell function and anti-tumor immunity. Immunity 2023; 56:1187-1203.e12. [PMID: 37160118 PMCID: PMC10330546 DOI: 10.1016/j.immuni.2023.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/30/2023] [Accepted: 04/07/2023] [Indexed: 05/11/2023]
Abstract
B7 ligands (CD80 and CD86), expressed by professional antigen-presenting cells (APCs), activate the main co-stimulatory receptor CD28 on T cells in trans. However, in peripheral tissues, APCs expressing B7 ligands are relatively scarce. This raises the questions of whether and how CD28 co-stimulation occurs in peripheral tissues. Here, we report that CD8+ T cells displayed B7 ligands that interacted with CD28 in cis at membrane invaginations of the immunological synapse as a result of membrane remodeling driven by phosphoinositide-3-kinase (PI3K) and sorting-nexin-9 (SNX9). cis-B7:CD28 interactions triggered CD28 signaling through protein kinase C theta (PKCθ) and promoted CD8+ T cell survival, migration, and cytokine production. In mouse tumor models, loss of T cell-intrinsic cis-B7:CD28 interactions decreased intratumoral T cells and accelerated tumor growth. Thus, B7 ligands on CD8+ T cells can evoke cell-autonomous CD28 co-stimulation in cis in peripheral tissues, suggesting cis-signaling as a general mechanism for boosting T cell functionality.
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Affiliation(s)
- Yunlong Zhao
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Christine Caron
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ya-Yuan Chan
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Calvin K Lee
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Xiaozheng Xu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jibin Zhang
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Takeya Masubuchi
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jack D Bui
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Enfu Hui
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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6
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Simonetti B, Daly JL, Cullen PJ. Out of the ESCPE room: Emerging roles of endosomal SNX-BARs in receptor transport and host-pathogen interaction. Traffic 2023; 24:234-250. [PMID: 37089068 PMCID: PMC10768393 DOI: 10.1111/tra.12885] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/22/2023] [Accepted: 03/28/2023] [Indexed: 04/25/2023]
Abstract
Several functions of the human cell, such as sensing nutrients, cell movement and interaction with the surrounding environment, depend on a myriad of transmembrane proteins and their associated proteins and lipids (collectively termed "cargoes"). To successfully perform their tasks, cargo must be sorted and delivered to the right place, at the right time, and in the right amount. To achieve this, eukaryotic cells have evolved a highly organized sorting platform, the endosomal network. Here, a variety of specialized multiprotein complexes sort cargo into itineraries leading to either their degradation or their recycling to various organelles for further rounds of reuse. A key sorting complex is the Endosomal SNX-BAR Sorting Complex for Promoting Exit (ESCPE-1) that promotes the recycling of an array of cargos to the plasma membrane and/or the trans-Golgi network. ESCPE-1 recognizes a hydrophobic-based sorting motif in numerous cargoes and orchestrates their packaging into tubular carriers that pinch off from the endosome and travel to the target organelle. A wide range of pathogens mimic this sorting motif to hijack ESCPE-1 transport to promote their invasion and survival within infected cells. In other instances, ESCPE-1 exerts restrictive functions against pathogens by limiting their replication and infection. In this review, we discuss ESCPE-1 assembly and functions, with a particular focus on recent advances in the understanding of its role in membrane trafficking, cellular homeostasis and host-pathogen interaction.
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Affiliation(s)
- Boris Simonetti
- Charles River Laboratories, Discovery House, Quays Office ParkConference Avenue, PortisheadBristolUK
| | - James L. Daly
- Department of Infectious DiseasesSchool of Immunology and Microbial Sciences, Guy's Hospital, King's College LondonLondonUK
| | - Peter J. Cullen
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences BuildingUniversity of BristolBristolUK
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7
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Overduin M, Tran A, Eekels DM, Overduin F, Kervin TA. Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes. MEMBRANES 2022; 12:1161. [PMID: 36422153 PMCID: PMC9692390 DOI: 10.3390/membranes12111161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Membrane proteins are broadly classified as transmembrane (TM) or peripheral, with functions that pertain to only a single bilayer at a given time. Here, we explicate a class of proteins that contain both transmembrane and peripheral domains, which we dub transmembrane membrane readers (TMMRs). Their transmembrane and peripheral elements anchor them to one bilayer and reversibly attach them to another section of bilayer, respectively, positioning them to tether and fuse membranes while recognizing signals such as phosphoinositides (PIs) and modifying lipid chemistries in proximity to their transmembrane domains. Here, we analyze full-length models from AlphaFold2 and Rosetta, as well as structures from nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, using the Membrane Optimal Docking Area (MODA) program to map their membrane-binding surfaces. Eukaryotic TMMRs include phospholipid-binding C1, C2, CRAL-TRIO, FYVE, GRAM, GTPase, MATH, PDZ, PH, PX, SMP, StART and WD domains within proteins including protrudin, sorting nexins and synaptotagmins. The spike proteins of SARS-CoV-2 as well as other viruses are also TMMRs, seeing as they are anchored into the viral membrane while mediating fusion with host cell membranes. As such, TMMRs have key roles in cell biology and membrane trafficking, and include drug targets for diseases such as COVID-19.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Anh Tran
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | | | - Finn Overduin
- Institute of Nutritional Science, University of Potsdam, 14476 Potsdam, Germany
| | - Troy A. Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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8
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Solinger JA, Spang A. Sorting of cargo in the tubular endosomal network. Bioessays 2022; 44:e2200158. [DOI: 10.1002/bies.202200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Affiliation(s)
| | - Anne Spang
- Biozentrum University of Basel Basel Switzerland
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9
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Mallik B, Bhat S, Kumar V. Role of Bin‐Amphiphysin‐Rvs (BAR) domain proteins in mediating neuronal signaling and disease. Synapse 2022; 76:e22248. [DOI: 10.1002/syn.22248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Bhagaban Mallik
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Bhopal Indore Bypass Road Bhopal Madhya Pradesh 462 066 India
| | - Sajad Bhat
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Bhopal Indore Bypass Road Bhopal Madhya Pradesh 462 066 India
| | - Vimlesh Kumar
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Bhopal Indore Bypass Road Bhopal Madhya Pradesh 462 066 India
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10
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Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions. J Membr Biol 2022; 255:237-259. [PMID: 35451616 PMCID: PMC9028910 DOI: 10.1007/s00232-022-00237-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022]
Abstract
Cellular membranes are highly dynamic in shape. They can rapidly and precisely regulate their shape to perform various cellular functions. The protein’s ability to sense membrane curvature is essential in various biological events such as cell signaling and membrane trafficking. As they are bound, these curvature-sensing proteins may also change the local membrane shape by one or more curvature driving mechanisms. Established curvature-sensing/driving mechanisms rely on proteins with specific structural features such as amphipathic helices and intrinsically curved shapes. However, the recent discovery and characterization of many proteins have shattered the protein structure–function paradigm, believing that the protein functions require a unique structural feature. Typically, such structure-independent functions are carried either entirely by intrinsically disordered proteins or hybrid proteins containing disordered regions and structured domains. It is becoming more apparent that disordered proteins and regions can be potent sensors/inducers of membrane curvatures. In this article, we outline the basic features of disordered proteins and regions, the motifs in such proteins that encode the function, membrane remodeling by disordered proteins and regions, and assays that may be employed to investigate curvature sensing and generation by ordered/disordered proteins.
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11
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Allen JR, Wilkinson EG, Strader LC. Creativity comes from interactions: modules of protein interactions in plants. FEBS J 2022; 289:1492-1514. [PMID: 33774929 PMCID: PMC8476656 DOI: 10.1111/febs.15847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/06/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023]
Abstract
Protein interactions are the foundation of cell biology. For robust signal transduction to occur, proteins interact selectively and modulate their behavior to direct specific biological outcomes. Frequently, modular protein interaction domains are central to these processes. Some of these domains bind proteins bearing post-translational modifications, such as phosphorylation, whereas other domains recognize and bind to specific amino acid motifs. Other modules act as diverse protein interaction scaffolds or can be multifunctional, forming head-to-head homodimers and binding specific peptide sequences or membrane phospholipids. Additionally, the so-called head-to-tail oligomerization domains (SAM, DIX, and PB1) can form extended polymers to regulate diverse aspects of biology. Although the mechanism and structures of these domains are diverse, they are united by their modularity. Together, these domains are versatile and facilitate the evolution of complex protein interaction networks. In this review, we will highlight the role of select modular protein interaction domains in various aspects of plant biology.
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Affiliation(s)
- Jeffrey R. Allen
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Edward G. Wilkinson
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Lucia C. Strader
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
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12
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Ecker M, Schregle R, Kapoor-Kaushik N, Rossatti P, Betzler VM, Kempe D, Biro M, Ariotti N, Redpath GMI, Rossy J. SNX9-induced membrane tubulation regulates CD28 cluster stability and signalling. eLife 2022; 11:e67550. [PMID: 35050850 PMCID: PMC8786313 DOI: 10.7554/elife.67550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 01/12/2022] [Indexed: 12/12/2022] Open
Abstract
T cell activation requires engagement of a cognate antigen by the T cell receptor (TCR) and the co-stimulatory signal of CD28. Both TCR and CD28 aggregate into clusters at the plasma membrane of activated T cells. While the role of TCR clustering in T cell activation has been extensively investigated, little is known about how CD28 clustering contributes to CD28 signalling. Here, we report that upon CD28 triggering, the BAR-domain protein sorting nexin 9 (SNX9) is recruited to CD28 clusters at the immunological synapse. Using three-dimensional correlative light and electron microscopy, we show that SNX9 generates membrane tubulation out of CD28 clusters. Our data further reveal that CD28 clusters are in fact dynamic structures and that SNX9 regulates their stability as well as CD28 phosphorylation and the resulting production of the cytokine IL-2. In summary, our work suggests a model in which SNX9-mediated tubulation generates a membrane environment that promotes CD28 triggering and downstream signalling events.
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Affiliation(s)
- Manuela Ecker
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
| | - Richard Schregle
- Biotechnology Institute Thurgau (BITg) at the University of KonstanzKreuzlingenSwitzerland
- Department of Biology, University of KonstanzKonstanzGermany
| | - Natasha Kapoor-Kaushik
- Electron Microscopy Unit, Mark Wainwright Analytical Centre, University of New South WalesSydneyAustralia
| | - Pascal Rossatti
- Biotechnology Institute Thurgau (BITg) at the University of KonstanzKreuzlingenSwitzerland
| | - Verena M Betzler
- Biotechnology Institute Thurgau (BITg) at the University of KonstanzKreuzlingenSwitzerland
| | - Daryan Kempe
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
| | - Maté Biro
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
| | - Nicholas Ariotti
- Electron Microscopy Unit, Mark Wainwright Analytical Centre, University of New South WalesSydneyAustralia
- Institute for Molecular Bioscience (IMB), University of QueenslandBrisbaneAustralia
| | - Gregory MI Redpath
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
| | - Jeremie Rossy
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
- Biotechnology Institute Thurgau (BITg) at the University of KonstanzKreuzlingenSwitzerland
- Department of Biology, University of KonstanzKonstanzGermany
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13
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Ford MGJ, Ramachandran R. Light Scattering Techniques to Assess Self-Assembly and Hydrodynamics of Membrane Trafficking Proteins. Methods Mol Biol 2022; 2473:259-284. [PMID: 35819771 DOI: 10.1007/978-1-0716-2209-4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Light scattering methods permit the determination of molar mass and hydrodynamic radius for a protein from first principles. They are, therefore, particularly useful for the biophysical characterization of any protein. Molar mass and hydrodynamic radius determinations may be used to demonstrate that the protein of interest multimerizes. In the endomembrane system, reversible and regulated assembly and multimerization of proteins is critical for building coats required for vesicle budding, for the function of membrane remodeling machines, for fission and fusion and for assembling and disassembling trafficking intermediates. Light scattering methods have therefore significantly contributed to the understanding of the underlying trafficking processes. Herein, we describe methods to express and purify the recombinant fungal SNX-BAR Mvp1, a membrane remodeling protein required for retrograde trafficking at the endosome. Using Mvp1 as an example, we provide protocols for determining its molar mass and hydrodynamic radius by multiangle static light scattering and dynamic light scattering, respectively. These methods can be applied directly to the study of other membrane trafficking proteins, yielding a wealth of biophysical and biochemical information.
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Affiliation(s)
- Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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Lysine acetylation regulates the interaction between proteins and membranes. Nat Commun 2021; 12:6466. [PMID: 34753925 PMCID: PMC8578602 DOI: 10.1038/s41467-021-26657-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
Abstract
Lysine acetylation regulates the function of soluble proteins in vivo, yet it remains largely unexplored whether lysine acetylation regulates membrane protein function. Here, we use bioinformatics, biophysical analysis of recombinant proteins, live-cell fluorescent imaging and genetic manipulation of Drosophila to explore lysine acetylation in peripheral membrane proteins. Analysis of 50 peripheral membrane proteins harboring BAR, PX, C2, or EHD membrane-binding domains reveals that lysine acetylation predominates in membrane-interaction regions. Acetylation and acetylation-mimicking mutations in three test proteins, amphiphysin, EHD2, and synaptotagmin1, strongly reduce membrane binding affinity, attenuate membrane remodeling in vitro and alter subcellular localization. This effect is likely due to the loss of positive charge, which weakens interactions with negatively charged membranes. In Drosophila, acetylation-mimicking mutations of amphiphysin cause severe disruption of T-tubule organization and yield a flightless phenotype. Our data provide mechanistic insights into how lysine acetylation regulates membrane protein function, potentially impacting a plethora of membrane-related processes. Lysine acetylation regulates the function of soluble proteins in vivo, yet it remains largely unexplored whether lysine acetylation regulates the function of membrane proteins. Here, the authors map lysine acetylation predominantly in membrane-interaction regions in peripheral membrane proteins and show with three candidate proteins how lysine acetylation is a regulator of membrane protein function.
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15
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Sechi S, Karimpour-Ghahnavieh A, Frappaolo A, Di Francesco L, Piergentili R, Schininà E, D’Avino PP, Giansanti MG. Identification of GOLPH3 Partners in Drosophila Unveils Potential Novel Roles in Tumorigenesis and Neural Disorders. Cells 2021; 10:cells10092336. [PMID: 34571985 PMCID: PMC8468827 DOI: 10.3390/cells10092336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/28/2022] Open
Abstract
Golgi phosphoprotein 3 (GOLPH3) is a highly conserved peripheral membrane protein localized to the Golgi apparatus and the cytosol. GOLPH3 binding to Golgi membranes depends on phosphatidylinositol 4-phosphate [PI(4)P] and regulates Golgi architecture and vesicle trafficking. GOLPH3 overexpression has been correlated with poor prognosis in several cancers, but the molecular mechanisms that link GOLPH3 to malignant transformation are poorly understood. We recently showed that PI(4)P-GOLPH3 couples membrane trafficking with contractile ring assembly during cytokinesis in dividing Drosophila spermatocytes. Here, we use affinity purification coupled with mass spectrometry (AP-MS) to identify the protein-protein interaction network (interactome) of Drosophila GOLPH3 in testes. Analysis of the GOLPH3 interactome revealed enrichment for proteins involved in vesicle-mediated trafficking, cell proliferation and cytoskeleton dynamics. In particular, we found that dGOLPH3 interacts with the Drosophila orthologs of Fragile X mental retardation protein and Ataxin-2, suggesting a potential role in the pathophysiology of disorders of the nervous system. Our findings suggest novel molecular targets associated with GOLPH3 that might be relevant for therapeutic intervention in cancers and other human diseases.
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Affiliation(s)
- Stefano Sechi
- Istituto di Biologia e Patologia Molecolari del CNR, c/o Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy; (S.S.); (A.K.-G.); (A.F.); (R.P.)
| | - Angela Karimpour-Ghahnavieh
- Istituto di Biologia e Patologia Molecolari del CNR, c/o Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy; (S.S.); (A.K.-G.); (A.F.); (R.P.)
| | - Anna Frappaolo
- Istituto di Biologia e Patologia Molecolari del CNR, c/o Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy; (S.S.); (A.K.-G.); (A.F.); (R.P.)
| | - Laura Di Francesco
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy; (L.D.F.); (E.S.)
| | - Roberto Piergentili
- Istituto di Biologia e Patologia Molecolari del CNR, c/o Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy; (S.S.); (A.K.-G.); (A.F.); (R.P.)
| | - Eugenia Schininà
- Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy; (L.D.F.); (E.S.)
| | - Pier Paolo D’Avino
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK;
| | - Maria Grazia Giansanti
- Istituto di Biologia e Patologia Molecolari del CNR, c/o Dipartimento di Biologia e Biotecnologie, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy; (S.S.); (A.K.-G.); (A.F.); (R.P.)
- Correspondence: ; Tel.: +39-064-991-2555
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16
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Overduin M, Kervin TA. The phosphoinositide code is read by a plethora of protein domains. Expert Rev Proteomics 2021; 18:483-502. [PMID: 34351250 DOI: 10.1080/14789450.2021.1962302] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The proteins that decipher nucleic acid- and protein-based information are well known, however, those that read membrane-encoded information remain understudied. Here we report 70 different human, microbial and viral protein folds that recognize phosphoinositides (PIs), comprising the readers of a vast membrane code. AREAS COVERED Membrane recognition is best understood for FYVE, PH and PX domains, which exemplify hundreds of PI code readers. Comparable lipid interaction mechanisms may be mediated by kinases, adjacent C1 and C2 domains, trafficking arrestin, GAT and VHS modules, membrane-perturbing annexin, BAR, CHMP, ENTH, HEAT, syntaxin and Tubby helical bundles, multipurpose FERM, EH, MATH, PHD, PDZ, PROPPIN, PTB and SH2 domains, as well as systems that regulate receptors, GTPases and actin filaments, transfer lipids and assembled bacterial and viral particles. EXPERT OPINION The elucidation of how membranes are recognized has extended the genetic code to the PI code. Novel discoveries include PIP-stop and MET-stop residues to which phosphates and metabolites are attached to block phosphatidylinositol phosphate (PIP) recognition, memteins as functional membrane protein apparatuses, and lipidons as lipid "codons" recognized by membrane readers. At least 5% of the human proteome senses such membrane signals and allows eukaryotic organelles and pathogens to operate and replicate.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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17
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Recent developments in membrane curvature sensing and induction by proteins. Biochim Biophys Acta Gen Subj 2021; 1865:129971. [PMID: 34333084 DOI: 10.1016/j.bbagen.2021.129971] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/11/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Membrane-bound intracellular organelles have characteristic shapes attributed to different local membrane curvatures, and these attributes are conserved across species. Over the past decade, it has been confirmed that specific proteins control the large curvatures of the membrane, whereas many others due to their specific structural features can sense the curvatures and bind to the specific geometrical cues. Elucidating the interplay between sensing and induction is indispensable to understand the mechanisms behind various biological processes such as vesicular trafficking and budding. SCOPE OF REVIEW We provide an overview of major classes of membrane proteins and the mechanisms of curvature sensing and induction. We then discuss the importance of membrane elastic characteristics to induce the membrane shapes similar to intracellular organelles. Finally, we survey recently available assays developed for studying the curvature sensing and induction by many proteins. MAJOR CONCLUSIONS Recent theoretical/computational modeling along with experimental studies have uncovered fascinating connections between lipid membrane and protein interactions. However, the phenomena of protein localization and synchronization to generate spatiotemporal dynamics in membrane morphology are yet to be fully understood. GENERAL SIGNIFICANCE The understanding of protein-membrane interactions is essential to shed light on various biological processes. This further enables the technological applications of many natural proteins/peptides in therapeutic treatments. The studies of membrane dynamic shapes help to understand the fundamental functions of membranes, while the medicinal roles of various macromolecules (such as proteins, peptides, etc.) are being increasingly investigated.
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18
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Kervin TA, Wiseman BC, Overduin M. Phosphoinositide Recognition Sites Are Blocked by Metabolite Attachment. Front Cell Dev Biol 2021; 9:690461. [PMID: 34368138 PMCID: PMC8340361 DOI: 10.3389/fcell.2021.690461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Membrane readers take part in trafficking and signaling processes by localizing proteins to organelle surfaces and transducing molecular information. They accomplish this by engaging phosphoinositides (PIs), a class of lipid molecules which are found in different proportions in various cellular membranes. The prototypes are the PX domains, which exhibit a range of specificities for PIs. Our meta-analysis indicates that recognition of membranes by PX domains is specifically controlled by modification of lysine and arginine residues including acetylation, hydroxyisobutyrylation, glycation, malonylation, methylation and succinylation of sidechains that normally bind headgroups of phospholipids including organelle-specific PI signals. Such metabolite-modulated residues in lipid binding elements are named MET-stops here to highlight their roles as erasers of membrane reader functions. These modifications are concentrated in the membrane binding sites of half of all 49 PX domains in the human proteome and correlate with phosphoregulatory sites, as mapped using the Membrane Optimal Docking Area (MODA) algorithm. As these motifs are mutated and modified in various cancers and the responsible enzymes serve as potential drug targets, the discovery of MET-stops as a widespread inhibitory mechanism may aid in the development of diagnostics and therapeutics aimed at the readers, writers and erasers of the PI code.
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Affiliation(s)
- Troy A Kervin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Brittany C Wiseman
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,Molecular and Cellular Biology, MacEwan University, Edmonton, AB, Canada.,SMALP Network, Edmonton, AB, Canada
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.,SMALP Network, Edmonton, AB, Canada
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19
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Kervin TA, Overduin M. Regulation of the Phosphoinositide Code by Phosphorylation of Membrane Readers. Cells 2021; 10:cells10051205. [PMID: 34069055 PMCID: PMC8156045 DOI: 10.3390/cells10051205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 02/07/2023] Open
Abstract
The genetic code that dictates how nucleic acids are translated into proteins is well known, however, the code through which proteins recognize membranes remains mysterious. In eukaryotes, this code is mediated by hundreds of membrane readers that recognize unique phosphatidylinositol phosphates (PIPs), which demark organelles to initiate localized trafficking and signaling events. The only superfamily which specifically detects all seven PIPs are the Phox homology (PX) domains. Here, we reveal that throughout evolution, these readers are universally regulated by the phosphorylation of their PIP binding surfaces based on our analysis of existing and modelled protein structures and phosphoproteomic databases. These PIP-stops control the selective targeting of proteins to organelles and are shown to be key determinants of high-fidelity PIP recognition. The protein kinases responsible include prominent cancer targets, underscoring the critical role of regulated membrane readership.
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20
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Chandra M, Kendall AK, Jackson LP. Toward Understanding the Molecular Role of SNX27/Retromer in Human Health and Disease. Front Cell Dev Biol 2021; 9:642378. [PMID: 33937239 PMCID: PMC8083963 DOI: 10.3389/fcell.2021.642378] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/22/2021] [Indexed: 11/30/2022] Open
Abstract
Aberrations in membrane trafficking pathways have profound effects in cellular dynamics of cellular sorting processes and can drive severe physiological outcomes. Sorting nexin 27 (SNX27) is a metazoan-specific sorting nexin protein from the PX-FERM domain family and is required for endosomal recycling of many important transmembrane receptors. Multiple studies have shown SNX27-mediated recycling requires association with retromer, one of the best-known regulators of endosomal trafficking. SNX27/retromer downregulation is strongly linked to Down's Syndrome (DS) via glutamate receptor dysfunction and to Alzheimer's Disease (AD) through increased intracellular production of amyloid peptides from amyloid precursor protein (APP) breakdown. SNX27 is further linked to addiction via its role in potassium channel trafficking, and its over-expression is linked to tumorigenesis, cancer progression, and metastasis. Thus, the correct sorting of multiple receptors by SNX27/retromer is vital for normal cellular function to prevent human diseases. The role of SNX27 in regulating cargo recycling from endosomes to the cell surface is firmly established, but how SNX27 assembles with retromer to generate tubulovesicular carriers remains elusive. Whether SNX27/retromer may be a putative therapeutic target to prevent neurodegenerative disease is now an emerging area of study. This review will provide an update on our molecular understanding of endosomal trafficking events mediated by the SNX27/retromer complex on endosomes.
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Affiliation(s)
- Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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21
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Abstract
The sorting nexin (SNX) family of proteins deform the membrane to generate transport carriers in endosomal pathways. Here, we elucidate how a prototypic member, SNX1, acts in this process. Performing cryoelectron microscopy, we find that SNX1 assembles into a protein lattice that consists of helical rows of SNX1 dimers wrapped around tubular membranes in a crosslinked fashion. We also visualize the details of this structure, which provides a molecular understanding of how various parts of SNX1 contribute to its ability to deform the membrane. Moreover, we have compared the SNX1 structure with a previously elucidated structure of an endosomal coat complex formed by retromer coupled to a SNX, which reveals how the molecular organization of the SNX in this coat complex is affected by retromer. The comparison also suggests insight into intermediary stages of assembly that results in the formation of the retromer-SNX coat complex on the membrane.
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22
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The Protein Kinase A-Dependent Phosphoproteome of the Human Pathogen Aspergillus fumigatus Reveals Diverse Virulence-Associated Kinase Targets. mBio 2020; 11:mBio.02880-20. [PMID: 33323509 PMCID: PMC7773993 DOI: 10.1128/mbio.02880-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PKA is essential for the virulence of eukaryotic human pathogens. Understanding PKA signaling mechanisms is therefore fundamental to deciphering pathogenesis and developing novel therapies. Protein kinase A (PKA) signaling plays a critical role in the growth and development of all eukaryotic microbes. However, few direct targets have been characterized in any organism. The fungus Aspergillus fumigatus is a leading infectious cause of death in immunocompromised patients, but the specific molecular mechanisms responsible for its pathogenesis are poorly understood. We used this important pathogen as a platform for a comprehensive and multifaceted interrogation of both the PKA-dependent whole proteome and phosphoproteome in order to elucidate the mechanisms through which PKA signaling regulates invasive microbial disease. Employing advanced quantitative whole-proteomic and phosphoproteomic approaches with two complementary phosphopeptide enrichment strategies, coupled to an independent PKA interactome analysis, we defined distinct PKA-regulated pathways and identified novel direct PKA targets contributing to pathogenesis. We discovered three previously uncharacterized virulence-associated PKA effectors, including an autophagy-related protein, Atg24; a CCAAT-binding transcriptional regulator, HapB; and a CCR4-NOT complex-associated ubiquitin ligase, Not4. Targeted mutagenesis, combined with in vitro kinase assays, multiple murine infection models, structural modeling, and molecular dynamics simulations, was employed to characterize the roles of these new PKA targets in growth, environmental and antimicrobial stress responses, and pathogenesis in a mammalian system. We also elucidated the molecular mechanisms of PKA regulation for these effectors by defining the functionality of phosphorylation at specific PKA target sites. We have comprehensively characterized the PKA-dependent phosphoproteome and validated PKA targets as direct regulators of infectious disease for the first time in any pathogen, providing new insights into PKA signaling and control over microbial pathogenesis.
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23
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Yang L, Tan W, Yang X, You Y, Wang J, Wen G, Zhong J. Sorting nexins: A novel promising therapy target for cancerous/neoplastic diseases. J Cell Physiol 2020; 236:3317-3335. [PMID: 33090492 DOI: 10.1002/jcp.30093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022]
Abstract
Sorting nexins (SNXs) are a diverse group of cytoplasmic- and membrane-associated phosphoinositide-binding proteins containing the PX domain proteins. The function of SNX proteins in regulating intracellular protein trafficking consists of endocytosis, endosomal sorting, and endosomal signaling. Dysfunctions of SNX proteins are demonstrated to be involved in several cancerous/neoplastic diseases. Here, we review the accumulated evidence of the molecular structure and biological function of SNX proteins and discuss the regulatory role of SNX proteins in distinct cancerous/neoplastic diseases. SNX family proteins may be a valuable potential biomarker and therapeutic strategy for diagnostics and treatment of cancerous/neoplastic diseases.
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Affiliation(s)
- Lu Yang
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan, China
- Institute of Clinical Medicine, the First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Weihua Tan
- Institute of Clinical Medicine, the First Affiliated Hospital of University of South China, Hengyang, Hunan, China
- Emergency Department, the First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Xinzhi Yang
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan, China
- Institute of Clinical Medicine, the First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Yong You
- Research Lab of Translational Medicine, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Jing Wang
- Research Lab of Translational Medicine, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Gebo Wen
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan, China
- Institute of Clinical Medicine, the First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Jing Zhong
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan, China
- Institute of Clinical Medicine, the First Affiliated Hospital of University of South China, Hengyang, Hunan, China
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24
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Antón Z, Betin VMS, Simonetti B, Traer CJ, Attar N, Cullen PJ, Lane JD. A heterodimeric SNX4--SNX7 SNX-BAR autophagy complex coordinates ATG9A trafficking for efficient autophagosome assembly. J Cell Sci 2020; 133:jcs246306. [PMID: 32513819 PMCID: PMC7375690 DOI: 10.1242/jcs.246306] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/02/2020] [Indexed: 11/24/2022] Open
Abstract
The sorting nexins (SNXs) are a family of peripheral membrane proteins that direct protein trafficking decisions within the endocytic network. Emerging evidence in yeast and mammalian cells implicates a subgroup of SNXs in selective and non-selective forms of autophagy. Using siRNA and CRISPR-Cas9, we demonstrate that the SNX-BAR protein SNX4 is needed for efficient LC3 (also known as MAP1LC3) lipidation and autophagosome assembly in mammalian cells. SNX-BARs exist as homo- and hetero-dimers, and we show that SNX4 forms functional heterodimers with either SNX7 or SNX30 that associate with tubulovesicular endocytic membranes. Detailed image-based analysis during the early stages of autophagosome assembly reveals that SNX4-SNX7 is an autophagy-specific SNX-BAR heterodimer, required for efficient recruitment and/or retention of core autophagy regulators at the nascent isolation membrane. SNX4 partially colocalises with juxtanuclear ATG9A-positive membranes, with our data linking the autophagy defect upon SNX4 disruption to the mis-trafficking and/or retention of ATG9A in the Golgi region. Taken together, our findings show that the SNX4-SNX7 heterodimer coordinates ATG9A trafficking within the endocytic network to establish productive autophagosome assembly sites, thus extending knowledge of SNXs as positive regulators of autophagy.
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Affiliation(s)
- Zuriñe Antón
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Virginie M S Betin
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Boris Simonetti
- Henry Wellcome Integrated Signalling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Colin J Traer
- Henry Wellcome Integrated Signalling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Naomi Attar
- Henry Wellcome Integrated Signalling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Peter J Cullen
- Henry Wellcome Integrated Signalling Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Jon D Lane
- Cell Biology Laboratories, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
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25
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Molecular Basis for PI(3,5)P2 Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation. J Mol Biol 2020; 432:4750-4761. [DOI: 10.1016/j.jmb.2020.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 11/23/2022]
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26
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González-Mancha N, Mérida I. Interplay Between SNX27 and DAG Metabolism in the Control of Trafficking and Signaling at the IS. Int J Mol Sci 2020; 21:ijms21124254. [PMID: 32549284 PMCID: PMC7352468 DOI: 10.3390/ijms21124254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
Recognition of antigens displayed on the surface of an antigen-presenting cell (APC) by T-cell receptors (TCR) of a T lymphocyte leads to the formation of a specialized contact between both cells named the immune synapse (IS). This highly organized structure ensures cell–cell communication and sustained T-cell activation. An essential lipid regulating T-cell activation is diacylglycerol (DAG), which accumulates at the cell–cell interface and mediates recruitment and activation of proteins involved in signaling and polarization. Formation of the IS requires rearrangement of the cytoskeleton, translocation of the microtubule-organizing center (MTOC) and vesicular compartments, and reorganization of signaling and adhesion molecules within the cell–cell junction. Among the multiple players involved in this polarized intracellular trafficking, we find sorting nexin 27 (SNX27). This protein translocates to the T cell–APC interface upon TCR activation, and it is suggested to facilitate the transport of cargoes toward this structure. Furthermore, its interaction with diacylglycerol kinase ζ (DGKζ), a negative regulator of DAG, sustains the precise modulation of this lipid and, thus, facilitates IS organization and signaling. Here, we review the role of SNX27, DAG metabolism, and their interplay in the control of T-cell activation and establishment of the IS.
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27
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Liu Y, McDonald NA, Naegele SM, Gould KL, Wu JQ. The F-BAR Domain of Rga7 Relies on a Cooperative Mechanism of Membrane Binding with a Partner Protein during Fission Yeast Cytokinesis. Cell Rep 2020; 26:2540-2548.e4. [PMID: 30840879 PMCID: PMC6425953 DOI: 10.1016/j.celrep.2019.01.112] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/03/2019] [Accepted: 01/30/2019] [Indexed: 12/17/2022] Open
Abstract
F-BAR proteins bind the plasma membrane (PM) to scaffold and organize the actin cytoskeleton. To understand how F-BAR proteins achieve their PM association, we studied the localization of a Schizosaccharomyces pombe F-BAR protein Rga7, which requires the coiled-coil protein Rng10 for targeting to the division site during cytokinesis. We find that the Rga7 F-BAR domain directly binds a motif in Rng10 simultaneously with the PM, and that an adjacent Rng10 motif independently binds the PM. Together, these multivalent interactions significantly enhance Rga7 F-BAR avidity for membranes at physiological protein concentrations, ensuring the division site localization of Rga7. Moreover, the requirement for the F-BAR domain in Rga7 localization and function in cytokinesis is bypassed by tethering an Rga7 construct lacking its F-BAR to Rng10, indicating that at least some F-BAR domains are necessary but not sufficient for PM targeting and are stably localized to specific cortical positions through adaptor proteins. Liu et al. show that the Rga7 F-BAR domain binds an adaptor protein Rng10, which contains a second membrane-binding module, to enhance Rga7 membrane avidity and stabilize its membrane association. The authors reveal a mechanism by which F-BAR domains can achieve high-avidity binding with the plasma membrane.
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Affiliation(s)
- Yajun Liu
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Nathan A McDonald
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Shelby M Naegele
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Kathleen L Gould
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA.
| | - Jian-Qiu Wu
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA.
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Sun D, Varlakhanova NV, Tornabene BA, Ramachandran R, Zhang P, Ford MGJ. The cryo-EM structure of the SNX-BAR Mvp1 tetramer. Nat Commun 2020; 11:1506. [PMID: 32198400 PMCID: PMC7083883 DOI: 10.1038/s41467-020-15110-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 02/11/2020] [Indexed: 12/22/2022] Open
Abstract
Sorting nexins (SNX) are a family of PX domain-containing proteins with pivotal roles in trafficking and signaling. SNX-BARs, which also have a curvature-generating Bin/Amphiphysin/Rvs (BAR) domain, have membrane-remodeling functions, particularly at the endosome. The minimal PX-BAR module is a dimer mediated by BAR-BAR interactions. Many SNX-BAR proteins, however, additionally have low-complexity N-terminal regions of unknown function. Here, we present the cryo-EM structure of the full-length SNX-BAR Mvp1, which is an autoinhibited tetramer. The tetramer is a dimer of dimers, wherein the membrane-interacting BAR surfaces are sequestered and the PX lipid-binding sites are occluded. The N-terminal low-complexity region of Mvp1 is essential for tetramerization. Mvp1 lacking its N-terminus is dimeric and exhibits enhanced membrane association. Membrane binding and remodeling by Mvp1 therefore requires unmasking of the PX and BAR domain lipid-interacting surfaces. This work reveals a tetrameric configuration of a SNX-BAR protein that provides critical insight into SNX-BAR function and regulation.
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Affiliation(s)
- Dapeng Sun
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Natalia V Varlakhanova
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Bryan A Tornabene
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
| | - Rajesh Ramachandran
- Department of Physiology & Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA.
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Larsson E, Hubert M, Lundmark R. Analysis of Protein and Lipid Interactions Using Liposome Co-sedimentation Assays. Methods Mol Biol 2020; 2169:119-127. [PMID: 32548824 DOI: 10.1007/978-1-0716-0732-9_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The dynamic assembly of proteins at the membrane interphase is key to many cell biological processes such as the generation and stabilization of caveolae at the cell surface via coat proteins. The liposome co-sedimentation assay has been widely used for studies of protein and lipid interactions and has provided important information about binding mechanisms, lipid-binding specificity, and curvature preference of proteins. Here, we describe this technique in detail and how it can be used as a tool to address the membrane-binding ability and lipid specificity of caveolae-associated proteins.
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Affiliation(s)
- Elin Larsson
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Madlen Hubert
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Richard Lundmark
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden.
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30
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Ma M, Burd CG. Retrograde trafficking and plasma membrane recycling pathways of the budding yeast Saccharomyces cerevisiae. Traffic 2019; 21:45-59. [PMID: 31471931 DOI: 10.1111/tra.12693] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
The endosomal system functions as a network of protein and lipid sorting stations that receives molecules from endocytic and secretory pathways and directs them to the lysosome for degradation, or exports them from the endosome via retrograde trafficking or plasma membrane recycling pathways. Retrograde trafficking pathways describe endosome-to-Golgi transport while plasma membrane recycling pathways describe trafficking routes that return endocytosed molecules to the plasma membrane. These pathways are crucial for lysosome biogenesis, nutrient acquisition and homeostasis and for the physiological functions of many types of specialized cells. Retrograde and recycling sorting machineries of eukaryotic cells were identified chiefly through genetic screens using the budding yeast Saccharomyces cerevisiae system and discovered to be highly conserved in structures and functions. In this review, we discuss advances regarding retrograde trafficking and recycling pathways, including new discoveries that challenge existing ideas about the organization of the endosomal system, as well as how these pathways intersect with cellular homeostasis pathways.
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Affiliation(s)
- Mengxiao Ma
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
| | - Christopher G Burd
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
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31
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Wang S, Zhao Z, Rodal AA. Higher-order assembly of Sorting Nexin 16 controls tubulation and distribution of neuronal endosomes. J Cell Biol 2019; 218:2600-2618. [PMID: 31253649 PMCID: PMC6683739 DOI: 10.1083/jcb.201811074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/25/2019] [Accepted: 06/05/2019] [Indexed: 01/01/2023] Open
Abstract
Endosomal maturation and distribution, driven by membrane remodeling, are critical for receptor traffic and signaling. Using both in vitro and in vivo approaches, Wang et al. reveal an unexpected coiled-coil–mediated membrane remodeling activity of SNX16 that controls neuronal endosomal tubulation, distribution, and receptor traffic. The activities of neuronal signaling receptors depend heavily on the maturation state of the endosomal compartments in which they reside. However, it remains unclear how the distribution of these compartments within the uniquely complex morphology of neurons is regulated and how this distribution itself affects signaling. Here, we identified mechanisms by which Sorting Nexin 16 (SNX16) controls neuronal endosomal maturation and distribution. We found that higher-order assembly of SNX16 via its coiled-coil (CC) domain drives membrane tubulation in vitro and endosome association in cells. In Drosophila melanogaster motor neurons, activation of Rab5 and CC-dependent self-association of SNX16 lead to its endosomal enrichment, accumulation in Rab5- and Rab7-positive tubulated compartments in the cell body, and concomitant depletion of SNX16-positive endosomes from the synapse. This results in accumulation of synaptic growth–promoting bone morphogenetic protein receptors in the cell body and correlates with increased synaptic growth. Our results indicate that Rab regulation of SNX16 assembly controls the endosomal distribution and signaling activities of receptors in neurons.
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Affiliation(s)
- ShiYu Wang
- Department of Biology, Brandeis University, Waltham, MA
| | - Zechuan Zhao
- Department of Biology, Brandeis University, Waltham, MA
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32
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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33
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Overduin M, Esmaili M. Memtein: The fundamental unit of membrane-protein structure and function. Chem Phys Lipids 2019; 218:73-84. [DOI: 10.1016/j.chemphyslip.2018.11.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 11/24/2018] [Accepted: 11/28/2018] [Indexed: 12/14/2022]
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34
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Osawa T, Alam JM, Noda NN. Membrane-binding domains in autophagy. Chem Phys Lipids 2019; 218:1-9. [DOI: 10.1016/j.chemphyslip.2018.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
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35
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Wasserman SS, Shteiman-Kotler A, Harris K, Iliadi KG, Persaud A, Zhong Y, Zhang Y, Fang X, Boulianne GL, Stewart B, Rotin D. Regulation of SH3PX1 by dNedd4-long at the Drosophila neuromuscular junction. J Biol Chem 2018; 294:1739-1752. [PMID: 30518551 DOI: 10.1074/jbc.ra118.005161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/12/2018] [Indexed: 11/06/2022] Open
Abstract
Drosophila Nedd4 (dNedd4) is a HECT E3 ubiquitin ligase present in two major isoforms: short (dNedd4S) and long (dNedd4Lo), with the latter containing two unique regions (N terminus and Middle). Although dNedd4S promotes neuromuscular synaptogenesis (NMS), dNedd4Lo inhibits it and impairs larval locomotion. To explain how dNedd4Lo inhibits NMS, MS analysis was performed to find its binding partners and identified SH3PX1, which binds dNedd4Lo unique Middle region. SH3PX1 contains SH3, PX, and BAR domains and is present at neuromuscular junctions, where it regulates active zone ultrastructure and presynaptic neurotransmitter release. Here, we demonstrate direct binding of SH3PX1 to the dNedd4Lo Middle region (which contains a Pro-rich sequence) in vitro and in cells, via the SH3PX1-SH3 domain. In Drosophila S2 cells, dNedd4Lo overexpression reduces SH3PX1 levels at the cell periphery. In vivo overexpression of dNedd4Lo post-synaptically, but not pre-synaptically, reduces SH3PX1 levels at the subsynaptic reticulum and impairs neurotransmitter release. Unexpectedly, larvae that overexpress dNedd4Lo post-synaptically and are heterozygous for a null mutation in SH3PX1 display increased neurotransmission compared with dNedd4Lo or SH3PX1 mutant larvae alone, suggesting a compensatory effect from the remaining SH3PX1 allele. These results suggest a post-synaptic-specific regulation of SH3PX1 by dNedd4Lo.
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Affiliation(s)
- Samantha S Wasserman
- Hospital for Sick Children, Cell Biology and Developmental and Stem Cell Biology programs, University of Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Ontario M5G 0A4, Canada
| | - Alina Shteiman-Kotler
- Hospital for Sick Children, Cell Biology and Developmental and Stem Cell Biology programs, University of Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Ontario M5G 0A4, Canada
| | - Kathryn Harris
- Department of Cell and System Biology, University of Toronto, Ontario M5G 0A4, Canada
| | - Konstantin G Iliadi
- Hospital for Sick Children, Cell Biology and Developmental and Stem Cell Biology programs, University of Toronto, Ontario M5G 0A4, Canada
| | - Avinash Persaud
- Hospital for Sick Children, Cell Biology and Developmental and Stem Cell Biology programs, University of Toronto, Ontario M5G 0A4, Canada
| | - Yvonne Zhong
- Hospital for Sick Children, Cell Biology and Developmental and Stem Cell Biology programs, University of Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Ontario M5G 0A4, Canada
| | - Yi Zhang
- Department of Gastrointestinal Surgery, Jilin University, Changchun 130033, China
| | - Xuedong Fang
- Department of Gastrointestinal Surgery, Jilin University, Changchun 130033, China
| | - Gabrielle L Boulianne
- Hospital for Sick Children, Cell Biology and Developmental and Stem Cell Biology programs, University of Toronto, Ontario M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Ontario M5G 0A4, Canada
| | - Bryan Stewart
- Department of Cell and System Biology, University of Toronto, Ontario M5G 0A4, Canada
| | - Daniela Rotin
- Hospital for Sick Children, Cell Biology and Developmental and Stem Cell Biology programs, University of Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Ontario M5G 0A4, Canada.
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36
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BAR domain proteins-a linkage between cellular membranes, signaling pathways, and the actin cytoskeleton. Biophys Rev 2018; 10:1587-1604. [PMID: 30456600 DOI: 10.1007/s12551-018-0467-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/17/2018] [Indexed: 12/23/2022] Open
Abstract
Actin filament assembly typically occurs in association with cellular membranes. A large number of proteins sit at the interface between actin networks and membranes, playing diverse roles such as initiation of actin polymerization, modulation of membrane curvature, and signaling. Bin/Amphiphysin/Rvs (BAR) domain proteins have been implicated in all of these functions. The BAR domain family of proteins comprises a diverse group of multi-functional effectors, characterized by their modular architecture. In addition to the membrane-curvature sensing/inducing BAR domain module, which also mediates antiparallel dimerization, most contain auxiliary domains implicated in protein-protein and/or protein-membrane interactions, including SH3, PX, PH, RhoGEF, and RhoGAP domains. The shape of the BAR domain itself varies, resulting in three major subfamilies: the classical crescent-shaped BAR, the more extended and less curved F-BAR, and the inverse curvature I-BAR subfamilies. Most members of this family have been implicated in cellular functions that require dynamic remodeling of the actin cytoskeleton, such as endocytosis, organelle trafficking, cell motility, and T-tubule biogenesis in muscle cells. Here, we review the structure and function of mammalian BAR domain proteins and the many ways in which they are interconnected with the actin cytoskeleton.
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37
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Itai N, Shimazu T, Kimura T, Ibe I, Yamashita R, Kaburagi Y, Dohi T, Tonozuka T, Takao T, Nishikawa A. The phosphorylation of sorting nexin 5 at serine 226 regulates retrograde transport and macropinocytosis. PLoS One 2018; 13:e0207205. [PMID: 30419003 PMCID: PMC6231649 DOI: 10.1371/journal.pone.0207205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/26/2018] [Indexed: 11/30/2022] Open
Abstract
Sorting nexin 5 (SNX5), a member of sorting nexin family, plays an important role in membrane trafficking, including the retrograde trafficking of the cation independent mannose 6-phosphate receptor (CI-M6PR) and macropinocytosis. Using ESI-LCMS/MS analysis, we confirmed that SNX5 serine 226 is phosphorylated. Since SNX5 forms heterodimers with SNX1 or SNX2, we examined the effect of phosphorylation at S226 on the heterodimer formations. Wild-type and mutants of SNX5, in which S226 was mutated to a glutamic acid or an alanine, were expressed in 8505C cells. In pull-down assays using SNX5 as bait, only the S226E mutant failed to precipitate both SNX1 and SNX2. Confocal microscopy data indicated that the wild type and S226A mutant were colocalized with SNX1 and SNX2 in endosomes, but the S226E was not. SNX5 and SNX6 support each other's functions and are involved with CI-M6PR retrograde trafficking. In SNX5 and SNX6 double knockdown cells, CI-M6PR was dispersed and colocalized with the endosomal marker EEA1. In a rescue experiment using SNX5 mutants, the S226A rescued CI-M6PR localization, similar to control cells, but S226E did not. Furthermore, the decrease in the uptake of dextran by macropinocytosis in SNX5 knockdown cells was recovered by the expression of rescue-wild type or S226A mutant, but not by the rescue-S226E mutant. These observations indicate that SNX5 constitutive phosphorylation that mimics the mutant S226E decreases the active SNX5 in these cells. The phosphorylation of SNX5 regulates the dimerization with SNX1 or SNX2, and this suggests that it controls membrane trafficking and protein sorting.
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Affiliation(s)
- Nao Itai
- Division of Applied Biological Chemistry, United graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Tsukasa Shimazu
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Takayuki Kimura
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Issei Ibe
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Ryo Yamashita
- Department of Diabetic Complications, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Yasushi Kaburagi
- Department of Diabetic Complications, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Taeko Dohi
- Department of Gastroenterology, Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba, Japan
| | - Takashi Tonozuka
- Division of Applied Biological Chemistry, United graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
| | - Toshifumi Takao
- Laboratory of Protein Profiling and Functional Proteomics, Institute for Protein Research, Osaka University, 3–2 Yamadaoka, Suita, Osaka, Japan
| | - Atsushi Nishikawa
- Division of Applied Biological Chemistry, United graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, Japan
- * E-mail:
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38
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McGough IJ, de Groot REA, Jellett AP, Betist MC, Varandas KC, Danson CM, Heesom KJ, Korswagen HC, Cullen PJ. SNX3-retromer requires an evolutionary conserved MON2:DOPEY2:ATP9A complex to mediate Wntless sorting and Wnt secretion. Nat Commun 2018; 9:3737. [PMID: 30213940 PMCID: PMC6137200 DOI: 10.1038/s41467-018-06114-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/13/2018] [Indexed: 12/28/2022] Open
Abstract
Wntless transports Wnt morphogens to the cell surface and is required for Wnt secretion and morphogenic gradients formation. Recycling of endocytosed Wntless requires the sorting nexin-3 (SNX3)-retromer-dependent endosome-to-Golgi transport pathway. Here we demonstrate the essential role of SNX3-retromer assembly for Wntless transport and report that SNX3 associates with an evolutionary conserved endosome-associated membrane re-modelling complex composed of MON2, DOPEY2 and the putative aminophospholipid translocase, ATP9A. In vivo suppression of Ce-mon-2, Ce-pad-1 or Ce-tat-5 (respective MON2, DOPEY2 and ATP9A orthologues) phenocopy a loss of SNX3-retromer function, leading to enhanced lysosomal degradation of Wntless and a Wnt phenotype. Perturbed Wnt signalling is also observed upon overexpression of an ATPase-inhibited TAT-5(E246Q) mutant, suggesting a role for phospholipid flippase activity during SNX3-retromer-mediated Wntless sorting. Together, these findings provide in vitro and in vivo mechanistic details to describe SNX3-retromer-mediated transport during Wnt secretion and the formation of Wnt-morphogenic gradients.
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Affiliation(s)
- Ian J McGough
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
- The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Reinoud E A de Groot
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Adam P Jellett
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Marco C Betist
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Katherine C Varandas
- Program in Cell Biology, University of California, San Francisco, 16th Street, San Francisco, CA, 94158, USA
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Chris M Danson
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Kate J Heesom
- Proteomics Facility, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Hendrik C Korswagen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands.
| | - Peter J Cullen
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
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Purushothaman LK, Ungermann C. Cargo induces retromer-mediated membrane remodeling on membranes. Mol Biol Cell 2018; 29:2709-2719. [PMID: 30188774 PMCID: PMC6249844 DOI: 10.1091/mbc.e18-06-0339] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Endosomes serve as a central sorting station of lipids and proteins that arrive via vesicular carrier from the plasma membrane and the Golgi complex. At the endosome, retromer complexes sort selected receptors and membrane proteins into tubules or vesicles that bud off the endosome. The mature endosome finally fuses with the lysosome. Retromer complexes consist of a cargo selection complex (CSC) and a membrane remodeling part (sorting nexin [SNX]-Bin/amphiphysin/Rvs [BAR], or Snx3 in yeast) and different assemblies of retromer mediate recycling of different cargoes. Due to this complexity, the exact order of events that results in carrier formation is not yet understood. Here, we reconstituted this process on giant unilamellar vesicles together with purified retromer complexes from yeast and selected cargoes. Our data reveal that the membrane remodeling activity of both Snx3 and the SNX-BAR complex is strongly reduced at low concentrations, which can be reactivated by CSC. At even lower concentrations, these complexes still associate with membranes, but only remodel membranes in the presence of their specific cargoes. Our data thus favor a simple model, where cargo functions as a specific trigger of retromer-mediated sorting on endosomes.
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Affiliation(s)
- Latha Kallur Purushothaman
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Christian Ungermann
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.,Center of Cellular Nanoanalytics Osnabrück (CellNanOs), University of Osnabrück, 49076 Osnabrück, Germany
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40
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Structure of the membrane-assembled retromer coat determined by cryo-electron tomography. Nature 2018; 561:561-564. [PMID: 30224749 PMCID: PMC6173284 DOI: 10.1038/s41586-018-0526-z] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/08/2018] [Indexed: 02/02/2023]
Abstract
Eukaryotic cells traffic proteins and lipids between different compartments using protein-coated vesicles and tubules. The retromer complex is required to generate cargo-selective tubulovesicular carriers from endosomal membranes1-3. Conserved in eukaryotes, retromer controls the cellular localization and homeostasis of hundreds of transmembrane proteins, and its disruption is associated with major neurodegenerative disorders4-7. How retromer is assembled and how it is recruited to form coated tubules is not known. Here we describe the structure of the retromer complex (Vps26-Vps29-Vps35) assembled on membrane tubules with the bin/amphiphysin/rvs-domain-containing sorting nexin protein Vps5, using cryo-electron tomography and subtomogram averaging. This reveals a membrane-associated Vps5 array, from which arches of retromer extend away from the membrane surface. Vps35 forms the 'legs' of these arches, and Vps29 resides at the apex where it is free to interact with regulatory factors. The bases of the arches connect to each other and to Vps5 through Vps26, and the presence of the same arches on coated tubules within cells confirms their functional importance. Vps5 binds to Vps26 at a position analogous to the previously described cargo- and Snx3-binding site, which suggests the existence of distinct retromer-sorting nexin assemblies. The structure provides insight into the architecture of the coat and its mechanism of assembly, and suggests that retromer promotes tubule formation by directing the distribution of sorting nexin proteins on the membrane surface while providing a scaffold for regulatory-protein interactions.
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Yong X, Hu W, Zhou X, Wang J, Burstein E, Jia D. Expression and purification of the SNX1/SNX6 complex. Protein Expr Purif 2018; 151:93-98. [PMID: 29908913 DOI: 10.1016/j.pep.2018.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/31/2018] [Accepted: 06/13/2018] [Indexed: 12/29/2022]
Abstract
The sorting nexin (SNX) family proteins play an essential role in vesicular transport, cell signaling, and membrane remodeling. The SNX members SNX1/2 and SNX5/6 form dimers, and mediate endosome-to-trans Golgi network (TGN) transport through coordinating cargo selection and membrane remodeling. It is well-known how a SNX-BAR protein forms a homodimer; however, it is less clear how a heterodimer is formed. Here a detailed expression and purification protocol of the SNX1/SNX6 complex, from both worm and human, is described. Keys to the successful protein production include co-expression of both genes, and inclusion of glycerol in the protein buffer. Solution studies suggest that SNX1 and SNX6 form a 1:1 heterodimer. The production of a large amount, high quality of the SNX1/SNX6 complex provides a basis for future biochemical and structural studies of the complex, and in vitro reconstitution of SNX1/SNX6-mediated transport.
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Affiliation(s)
- Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Drug Clinical Trial Institute, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Wenfeng Hu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Drug Clinical Trial Institute, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xue Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Drug Clinical Trial Institute, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Drug Clinical Trial Institute, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ezra Burstein
- Department of Internal Medicine and Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Drug Clinical Trial Institute, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
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Liu C, Zhai X, Du H, Cao Y, Cao H, Wang Y, Yu X, Gao J, Xu Z. Sorting nexin 9 (SNX9) is not essential for development and auditory function in mice. Oncotarget 2018; 7:68921-68932. [PMID: 27655699 PMCID: PMC5356600 DOI: 10.18632/oncotarget.12040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/02/2016] [Indexed: 12/20/2022] Open
Abstract
Sorting nexins are a large family of evolutionarily conserved proteins that play fundamental roles in endocytosis, endosomal sorting and signaling. As an important member of sorting nexin family, sorting nexin 9 (SNX9) has been shown to participate in coordinating actin polymerization with membrane tubulation and vesicle formation. We previously showed that SNX9 is expressed in mouse auditory hair cells and might regulate actin polymerization in those cells. To further examine the physiological role of SNX9, we generated Snx9 knockout mice using homologous recombination method. Unexpectedly, Snx9 knockout mice have normal viability and fertility, and are morphologically and behaviorally indistinguishable from control mice. Further investigation revealed that the morphology and function of auditory hair cells are not affected by Snx9 inactivation, and Snx9 knockout mice have normal hearing threshold. In conclusion, our data revealed that Snx9-deficient mice do not show defects in development as well as auditory function, suggesting that SNX9 is not essential for mice development and hearing.
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Affiliation(s)
- Chengcheng Liu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Xiaoyan Zhai
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Haibo Du
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Yujie Cao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Huiren Cao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Yanfei Wang
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Xiao Yu
- Department of Physiology, Shandong University School of Medicine, Jinan, Shandong 250012, P. R. China
| | - Jiangang Gao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
| | - Zhigang Xu
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Jinan, Shandong 250100, P. R. China
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Abstract
Sorting nexins anchor trafficking machines to membranes by binding phospholipids. The paradigm of the superfamily is sorting nexin 3 (SNX3), which localizes to early endosomes by recognizing phosphatidylinositol 3-phosphate (PI3P) to initiate retromer-mediated segregation of cargoes to the trans-Golgi network (TGN). Here we report the solution structure of full length human SNX3, and show that PI3P recognition is accompanied by bilayer insertion of a proximal loop in its extended Phox homology (PX) domain. Phosphoinositide (PIP) binding is completely blocked by cancer-linked phosphorylation of a conserved serine beside the stereospecific PI3P pocket. This “PIP-stop” releases endosomal SNX3 to the cytosol, and reveals how protein kinases control membrane assemblies. It constitutes a widespread regulatory element found across the PX superfamily and throughout evolution including of fungi and plants. This illuminates the mechanism of a biological switch whereby structured PIP sites are phosphorylated to liberate protein machines from organelle surfaces. Sorting nexin 3 (SNX3) is a phosphatidylinositol 3-phosphate binding protein that localizes to early endosomes. Here the authors use NMR to resolve SNX3′s membrane interactions, revealing that membrane binding is regulated through phosphorylation of a conserved serine by its lipid recognition site.
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Abstract
The phox-homology (PX) domain is a phosphoinositide-binding domain conserved in all eukaryotes and present in 49 human proteins. Proteins containing PX domains, many of which are also known as sorting nexins (SNXs), have a large variety of functions in membrane trafficking, cell signaling, and lipid metabolism in association with membranes of the secretory and endocytic system. In this review we discuss the structural basis for both canonical lipid interactions with the endosome-enriched lipid phosphatidylinositol-3-phosphate (PtdIns3P) as well as non-canonical lipids that promote membrane association. We also describe recent advances in defining the diverse mechanisms by which PX domains interact with other proteins including the retromer trafficking complex and proteins secreted by bacterial pathogens. Like other membrane interacting domains, the attachment of PX domain proteins to specific membranes is often facilitated by additional interactions that contribute to binding avidity, and we discuss this coincidence detection for several known examples.
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45
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Lo WT, Vujičić Žagar A, Gerth F, Lehmann M, Puchkov D, Krylova O, Freund C, Scapozza L, Vadas O, Haucke V. A Coincidence Detection Mechanism Controls PX-BAR Domain-Mediated Endocytic Membrane Remodeling via an Allosteric Structural Switch. Dev Cell 2017; 43:522-529.e4. [PMID: 29161595 DOI: 10.1016/j.devcel.2017.10.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/14/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
Abstract
Clathrin-mediated endocytosis occurs by bending and remodeling of the membrane underneath the coat. Bin-amphiphysin-rvs (BAR) domain proteins are crucial for endocytic membrane remodeling, but how their activity is spatiotemporally controlled is largely unknown. We demonstrate that the membrane remodeling activity of sorting nexin 9 (SNX9), a late-acting endocytic PX-BAR domain protein required for constriction of U-shaped endocytic intermediates, is controlled by an allosteric structural switch involving coincident detection of the clathrin adaptor AP2 and phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) at endocytic sites. Structural, biochemical, and cell biological data show that SNX9 is autoinhibited in solution. Binding to PI(3,4)P2 via its PX-BAR domain, and concomitant association with AP2 via sequences in the linker region, releases SNX9 autoinhibitory contacts to enable membrane constriction. Our results reveal a mechanism for restricting the latent membrane remodeling activity of BAR domain proteins to allow spatiotemporal coupling of membrane constriction to the progression of the endocytic pathway.
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Affiliation(s)
- Wen-Ting Lo
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany
| | | | - Fabian Gerth
- Freie Universität Berlin, Faculty of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Dymtro Puchkov
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Oxana Krylova
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Christian Freund
- Freie Universität Berlin, Faculty of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany
| | - Leonardo Scapozza
- University of Geneva, Section of Pharmaceutical Sciences, 1206 Geneva, Switzerland
| | - Oscar Vadas
- University of Geneva, Section of Pharmaceutical Sciences, 1206 Geneva, Switzerland.
| | - Volker Haucke
- Department of Molecular Pharmacology & Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry and Pharmacy, 14195 Berlin, Germany.
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46
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Structure and function of yeast Atg20, a sorting nexin that facilitates autophagy induction. Proc Natl Acad Sci U S A 2017; 114:E10112-E10121. [PMID: 29114050 DOI: 10.1073/pnas.1708367114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Atg20 and Snx4/Atg24 proteins have been identified in a screen for mutants defective in a type of selective macroautophagy/autophagy. Both proteins are connected to the Atg1 kinase complex, which is involved in autophagy initiation, and bind phosphatidylinositol-3-phosphate. Atg20 and Snx4 contain putative BAR domains, suggesting a possible role in membrane deformation, but they have been relatively uncharacterized. Here we demonstrate that, in addition to its function in selective autophagy, Atg20 plays a critical role in the efficient induction of nonselective autophagy. Atg20 is a dynamic posttranslationally modified protein that engages both structurally stable (PX and BAR) and intrinsically disordered domains for its function. In addition to its PX and BAR domains, Atg20 uses a third membrane-binding module, a membrane-inducible amphipathic helix present in a previously undescribed location in Atg20 within the putative BAR domain. Taken together, these findings yield insights into the molecular mechanism of the autophagy machinery.
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47
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Daste F, Walrant A, Holst MR, Gadsby JR, Mason J, Lee JE, Brook D, Mettlen M, Larsson E, Lee SF, Lundmark R, Gallop JL. Control of actin polymerization via the coincidence of phosphoinositides and high membrane curvature. J Cell Biol 2017; 216:3745-3765. [PMID: 28923975 PMCID: PMC5674896 DOI: 10.1083/jcb.201704061] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/06/2017] [Accepted: 08/04/2017] [Indexed: 12/26/2022] Open
Abstract
How the membrane environment informs when and where actin is polymerized in clathrin-mediated endocytosis is unclear. Daste et al. show that high membrane curvature stimulates PI(3,4)P2 dephosphorylation by INPP4A and that PI(3)P recruits SNX9 in conjunction with both PI(4,5)P2 and high membrane curvature. Furthermore, they find that Lowe syndrome mimics this membrane microenvironment with the aberrant formation of a PI(4,5)P2/PI(3)P intermediate, giving rise to actin comets. The conditional use of actin during clathrin-mediated endocytosis in mammalian cells suggests that the cell controls whether and how actin is used. Using a combination of biochemical reconstitution and mammalian cell culture, we elucidate a mechanism by which the coincidence of PI(4,5)P2 and PI(3)P in a curved vesicle triggers actin polymerization. At clathrin-coated pits, PI(3)P is produced by the INPP4A hydrolysis of PI(3,4)P2, and this is necessary for actin-driven endocytosis. Both Cdc42⋅guanosine triphosphate and SNX9 activate N-WASP–WIP- and Arp2/3-mediated actin nucleation. Membrane curvature, PI(4,5)P2, and PI(3)P signals are needed for SNX9 assembly via its PX–BAR domain, whereas signaling through Cdc42 is activated by PI(4,5)P2 alone. INPP4A activity is stimulated by high membrane curvature and synergizes with SNX9 BAR domain binding in a process we call curvature cascade amplification. We show that the SNX9-driven actin comets that arise on human disease–associated oculocerebrorenal syndrome of Lowe (OCRL) deficiencies are reduced by inhibiting PI(3)P production, suggesting PI(3)P kinase inhibitors as a therapeutic strategy in Lowe syndrome.
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Affiliation(s)
- Frederic Daste
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Astrid Walrant
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Mikkel R Holst
- Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Jonathan R Gadsby
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Julia Mason
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Ji-Eun Lee
- Department of Chemistry, University of Cambridge, Cambridge, England, UK
| | - Daniel Brook
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, England, UK
| | - Marcel Mettlen
- University of Texas Southwestern Medical Center, Dallas, TX
| | - Elin Larsson
- Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge, England, UK
| | | | - Jennifer L Gallop
- Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, England, UK
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Xu J, Zhang L, Ye Y, Shan Y, Wan C, Wang J, Pei D, Shu X, Liu J. SNX16 Regulates the Recycling of E-Cadherin through a Unique Mechanism of Coordinated Membrane and Cargo Binding. Structure 2017; 25:1251-1263.e5. [PMID: 28712807 DOI: 10.1016/j.str.2017.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/28/2017] [Accepted: 06/15/2017] [Indexed: 10/19/2022]
Abstract
E-Cadherin is a major component of adherens junctions on cell surfaces. SNX16 is a unique member of sorting nexins that contains a coiled-coil (CC) domain downstream of the PX domain. We report here that SNX16 regulates the recycling trafficking of E-cadherin. We solved the crystal structure of PX-CC unit of SNX16 and revealed a unique shear shaped homodimer. We identified a novel PI3P binding pocket in SNX16 that consists of both the PX and the CC domains. Surprisingly, we showed that the PPII/α2 loop, which is generally regarded as a membrane insertion loop in PX family proteins, is involved in the E-cadherin binding with SNX16. We then proposed a multivalent membrane binding model for SNX16. Our study postulates a new mechanism for coordinated membrane binding and cargo binding for SNX family proteins in general, and provide novel insights into recycling trafficking of E-cadherin.
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Affiliation(s)
- Jinxin Xu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Leilei Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Medical University Joint School of Biological Sciences, South China Institute of Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yinghua Ye
- CAS Key Laboratory of Regenerative Biology, Guangdong Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Medical University Joint School of Biological Sciences, South China Institute of Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yongli Shan
- CAS Key Laboratory of Regenerative Biology, Guangdong Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Medical University Joint School of Biological Sciences, South China Institute of Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chanjuan Wan
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Guangdong Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Medical University Joint School of Biological Sciences, South China Institute of Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaodong Shu
- CAS Key Laboratory of Regenerative Biology, Guangdong Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Medical University Joint School of Biological Sciences, South China Institute of Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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49
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Schöneberg J, Lehmann M, Ullrich A, Posor Y, Lo WT, Lichtner G, Schmoranzer J, Haucke V, Noé F. Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat Commun 2017. [PMID: 28627515 PMCID: PMC5481832 DOI: 10.1038/ncomms15873] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) involves membrane-associated scaffolds of the bin-amphiphysin-rvs (BAR) domain protein family as well as the GTPase dynamin, and is accompanied and perhaps triggered by changes in local lipid composition. How protein recruitment, scaffold assembly and membrane deformation is spatiotemporally controlled and coupled to fission is poorly understood. We show by computational modelling and super-resolution imaging that phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2] synthesis within the clathrin-coated area of endocytic intermediates triggers selective recruitment of the PX-BAR domain protein SNX9, as a result of complex interactions of endocytic proteins competing for phospholipids. The specific architecture induces positioning of SNX9 at the invagination neck where its self-assembly regulates membrane constriction, thereby providing a template for dynamin fission. These data explain how lipid conversion at endocytic pits couples local membrane constriction to fission. Our work demonstrates how computational modelling and super-resolution imaging can be combined to unravel function and mechanisms of complex cellular processes. The spatiotemporal regulation of membrane scaffolds recruitment and coupling between membrane deformation and fission in endocytosis are unclear. Here the authors show that lipid conversion at endocytic pits recruits SNX9, which couples local membrane constriction to fission in endocytosis.
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Affiliation(s)
- Johannes Schöneberg
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| | - Martin Lehmann
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.,Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Alexander Ullrich
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
| | - York Posor
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.,Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Wen-Ting Lo
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany
| | - Gregor Lichtner
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany.,Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany
| | - Jan Schmoranzer
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.,Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Volker Haucke
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.,Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin 14195, Germany.,NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Virchowweg 6, Berlin 10117, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin 14195, Germany
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50
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Liebl D, Qi X, Zhe Y, Barnett TC, Teasdale RD. SopB-Mediated Recruitment of SNX18 Facilitates Salmonella Typhimurium Internalization by the Host Cell. Front Cell Infect Microbiol 2017; 7:257. [PMID: 28664153 PMCID: PMC5471308 DOI: 10.3389/fcimb.2017.00257] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/31/2017] [Indexed: 11/16/2022] Open
Abstract
To invade epithelial cells, Salmonella enterica serovar Typhimurium (S. Typhimurium) induces macropinocytosis through the action of virulence proteins delivered across the host cell membrane via a type III secretion system. We show that after docking at the plasma membrane S. Typhimurium triggers rapid recruitment of cytosolic SNX18, a SH3-PX-BAR domain sorting nexin protein, to the bacteria-induced membrane ruffles and to the nascent Salmonella-containing vacuole. SNX18 recruitment required the inositol-phosphatase activity of the Salmonella effector SopB and an intact phosphoinositide-binding site within the PX domain of SNX18, but occurred independently of Rho-GTPases Rac1 and Cdc42 activation. SNX18 promotes formation of the SCV from the plasma membrane by acting as a scaffold to recruit Dynamin-2 and N-WASP in a process dependent on the SH3 domain of SNX18. Quantification of bacteria uptake revealed that overexpression of SNX18 increased bacteria internalization, whereas a decrease was detected in cells overexpressing the phosphoinositide-binding mutant R303Q, the ΔSH3 mutant, and in cells where endogenous levels of SNX18 were knocked-down. This study identifies SNX18 as a novel target of SopB and suggests a mechanism where S. Typhimurium engages host factors via local manipulation of phosphoinositide composition at the site of invasion to orchestrate the internalization process.
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Affiliation(s)
- David Liebl
- Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
| | - Xiaying Qi
- Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
| | - Yang Zhe
- Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia
| | - Timothy C Barnett
- Australian Infectious Diseases Research Centre, The University of QueenslandBrisbane, QLD, Australia.,School of Chemistry and Molecular Biosciences, The University of QueenslandBrisbane, QLD, Australia
| | - Rohan D Teasdale
- Institute for Molecular Bioscience, The University of QueenslandBrisbane, QLD, Australia.,Australian Infectious Diseases Research Centre, The University of QueenslandBrisbane, QLD, Australia.,School of Biomedical Sciences, The University of QueenslandBrisbane, QLD, Australia
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