1
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Du Y, Fan X, Song C, Chang W, Xiong J, Deng L, Ji WK. Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation. J Cell Biol 2024; 223:e202402083. [PMID: 39352497 PMCID: PMC11457499 DOI: 10.1083/jcb.202402083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/25/2024] [Accepted: 08/07/2024] [Indexed: 10/09/2024] Open
Abstract
VPS13B/COH1 is the only known causative factor for Cohen syndrome, an early-onset autosomal recessive developmental disorder with intellectual inability, developmental delay, joint hypermobility, myopia, and facial dysmorphism as common features, but the molecular basis of VPS13B/COH1 in pathogenesis remains largely unclear. Here, we identify Sec23 interacting protein (Sec23IP) at the ER exit site (ERES) as a VPS13B adaptor that recruits VPS13B to ERES-Golgi interfaces. VPS13B interacts directly with Sec23IP via the VPS13 adaptor binding domain (VAB), and the interaction promotes the association between ERES and the Golgi. Disease-associated missense mutations of VPS13B-VAB impair the interaction with Sec23IP. Knockout of VPS13B or Sec23IP blocks the formation of tubular ERGIC, an unconventional cargo carrier that expedites ER-to-Golgi transport. In addition, depletion of VPS13B or Sec23IP delays ER export of procollagen, suggesting a link between procollagen secretion and joint laxity in patients with Cohen disease. Together, our study reveals a crucial role of VPS13B-Sec23IP interaction at the ERES-Golgi interface in the pathogenesis of Cohen syndrome.
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Affiliation(s)
- Yuanjiao Du
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Xinyu Fan
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | | | | | - Juan Xiong
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Deng
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China
- Shenzhen Bay Laboratory, Shenzhen, China
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2
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Ugur B, Schueder F, Shin J, Hanna MG, Wu Y, Leonzino M, Su M, McAdow AR, Wilson C, Postlethwait J, Solnica-Krezel L, Bewersdorf J, De Camilli P. VPS13B is localized at the interface between Golgi cisternae and is a functional partner of FAM177A1. J Cell Biol 2024; 223:e202311189. [PMID: 39331042 PMCID: PMC11451052 DOI: 10.1083/jcb.202311189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/31/2024] [Accepted: 08/05/2024] [Indexed: 09/28/2024] Open
Abstract
Mutations in VPS13B, a member of a protein family implicated in bulk lipid transport between adjacent membranes, cause Cohen syndrome. VPS13B is known to be concentrated in the Golgi complex, but its precise location within this organelle and thus the site(s) where it achieves lipid transport remains unclear. Here, we show that VPS13B is localized at the interface between proximal and distal Golgi subcompartments and that Golgi complex reformation after Brefeldin A (BFA)-induced disruption is delayed in VPS13B KO cells. This delay is phenocopied by the loss of FAM177A1, a Golgi complex protein of unknown function reported to be a VPS13B interactor and whose mutations also result in a developmental disorder. In zebrafish, the vps13b ortholog, not previously annotated in this organism, genetically interacts with fam177a1. Collectively, these findings raise the possibility that bulk lipid transport by VPS13B may play a role in the dynamics of Golgi membranes and that VPS13B may be assisted in this function by FAM177A1.
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Affiliation(s)
- Berrak Ugur
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Florian Schueder
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jimann Shin
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael G. Hanna
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Yumei Wu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Marianna Leonzino
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Maohan Su
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anthony R. McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Catherine Wilson
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Lilianna Solnica-Krezel
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
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3
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Srinivasan S, Álvarez D, John Peter AT, Vanni S. Unbiased MD simulations identify lipid binding sites in lipid transfer proteins. J Cell Biol 2024; 223:e202312055. [PMID: 39105757 PMCID: PMC11303870 DOI: 10.1083/jcb.202312055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/29/2024] [Accepted: 07/16/2024] [Indexed: 08/07/2024] Open
Abstract
The characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to understand their molecular mechanism. However, several structures of LTPs, and notably those proposed to act as bridges between membranes, do not provide the precise location of their endogenous lipid ligands. To address this limitation, computational approaches are a powerful alternative methodology, but they are often limited by the high flexibility of lipid substrates. Here, we develop a protocol based on unbiased coarse-grain molecular dynamics simulations in which lipids placed away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the lipid entry pathway. We apply this approach to characterize lipid binding to bridge LTPs of the Vps13-Atg2 family, for which the lipid localization inside the protein is currently unknown. Overall, our work paves the way to determine binding pockets and entry pathways for several LTPs in an inexpensive, fast, and accurate manner.
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Affiliation(s)
| | - Daniel Álvarez
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, España
| | - Arun T John Peter
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research Bio-inspired Materials, University of Fribourg , Fribourg, Switzerland
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4
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Kang Y, Pogany J, Nagy PD. Proviral role of ATG2 autophagy related protein in tomato bushy stunt virus replication through bulk phospholipid transfer into the viral replication organelle. Mol Biol Cell 2024; 35:ar124. [PMID: 39110527 PMCID: PMC11481700 DOI: 10.1091/mbc.e24-05-0236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/30/2024] [Indexed: 09/21/2024] Open
Abstract
Subversion of cellular membranes and membrane proliferation are used by positive-strand RNA viruses to build viral replication organelles (VROs) that support virus replication. The biogenesis of the membranous VROs requires major changes in lipid metabolism and lipid transfer in infected cells. In this work, we show that tomato bushy stunt virus (TBSV) hijacks Atg2 autophagy related protein with bulk lipid transfer activity into VROs via interaction with TBSV p33 replication protein. Deletion of Atg2 in yeast and knockdown of Atg2 in Nicotiana benthamiana resulted in decreased TBSV replication. We found that subversion of Atg2 by TBSV was important to enrich VRO membranes with phosphatidylethanolamine (PE), phosphatidylserine (PS) and PI(3)P phosphoinositide. Interestingly, inhibition of autophagy did not affect the efficient recruitment of Atg2 into VROs, and overexpression of Atg2 enhanced TBSV replication, indicating autophagy-independent subversion of Atg2 by TBSV. These findings suggest that the proviral function of Atg2 lipid transfer protein is in VRO membrane proliferation. In addition, we find that Atg2 interacting partner Atg9 with membrane lipid-scramblase activity is also coopted for tombusvirus replication. Altogether, the subversion of Atg2 bridge-type lipid transfer protein provides a new mechanism for tombusviruses to greatly expand VRO membranes to support robust viral replication.
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Affiliation(s)
- Yuanrong Kang
- Department of Plant Pathology, University of Kentucky, Plant Science Building, Lexington, KY 40546
| | - Judit Pogany
- Department of Plant Pathology, University of Kentucky, Plant Science Building, Lexington, KY 40546
| | - Peter D. Nagy
- Department of Plant Pathology, University of Kentucky, Plant Science Building, Lexington, KY 40546
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5
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Hanna MG, Rodriguez Cruz HO, Fujise K, Li Z, Monetti M, De Camilli P. Bridge-like lipid transfer protein 3A (BLTP3A) is associated with membranes of the late endocytic pathway and is an effector of CASM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.28.615015. [PMID: 39386594 PMCID: PMC11463362 DOI: 10.1101/2024.09.28.615015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Recent studies have identified a family of rod-shaped proteins which includes VPS13 and ATG2 and are thought to mediate unidirectional lipid transport at intracellular membrane contacts by a bridge-like mechanism. Here, we show that one such protein, BLTP3A/UHRF1BP1, associates with VAMP7-positive vesicles via its C-terminal region and anchors them to lysosomes via the binding of its chorein domain containing N-terminal region to Rab7. Upon damage of lysosomal membranes and resulting mATG8 recruitment to their surface by CASM, BLTP3A first dissociates from lysosomes but then reassociates with them via an interaction of its LIR motif with mATG8. Such interaction is mutually exclusive to the binding of BLTP3A to vesicles and leaves its N-terminal chorein domain, i.e. the proposed entry site of lipids into this family of proteins, available for binding to another membrane, possibly the ER. Our findings reveal that BLTP3A is an effector CASM, potentially as part of a mechanism to help repair or minimize lysosome damage by delivering lipids.
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6
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Hamaï A, Drin G. Specificity of lipid transfer proteins: An in vitro story. Biochimie 2024:S0300-9084(24)00217-7. [PMID: 39304019 DOI: 10.1016/j.biochi.2024.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 09/06/2024] [Accepted: 09/17/2024] [Indexed: 09/22/2024]
Abstract
Lipids, which are highly diverse, are finely distributed between organelle membranes and the plasma membrane (PM) of eukaryotic cells. As a result, each compartment has its own lipid composition and molecular identity, which is essential for the functional fate of many proteins. This distribution of lipids depends on two main processes: lipid synthesis, which takes place in different subcellular regions, and the transfer of these lipids between and across membranes. This review will discuss the proteins that carry lipids throughout the cytosol, called LTPs (Lipid Transfer Proteins). More than the modes of action or biological roles of these proteins, we will focus on the in vitro strategies employed during the last 60 years to address a critical question: What are the lipid ligands of these LTPs? We will describe the extent to which these strategies, combined with structural data and investigations in cells, have made it possible to discover proteins, namely ORPs, Sec14, PITPs, STARDs, Ups/PRELIs, START-like, SMP-domain containing proteins, and bridge-like LTPs, which compose some of the main eukaryotic LTP families, and their lipid ligands. We will see how these approaches have played a central role in cell biology, showing that LTPs can connect distant metabolic branches, modulate the composition of cell membranes, and even create new subcellular compartments.
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Affiliation(s)
- Amazigh Hamaï
- Université Côte d'Azur, CNRS and Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660 route des lucioles, 06560, Valbonne Sophia Antipolis, France
| | - Guillaume Drin
- Université Côte d'Azur, CNRS and Inserm, Institut de Pharmacologie Moléculaire et Cellulaire, UMR 7275, 660 route des lucioles, 06560, Valbonne Sophia Antipolis, France.
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7
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Isola D, Elazar Z. Phospholipid Supply for Autophagosome Biogenesis. J Mol Biol 2024; 436:168691. [PMID: 38944336 DOI: 10.1016/j.jmb.2024.168691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/10/2024] [Accepted: 06/24/2024] [Indexed: 07/01/2024]
Abstract
Autophagy is a cellular degradation pathway where double-membrane autophagosomes form de novo to engulf cytoplasmic material destined for lysosomal degradation. This process requires regulated membrane remodeling, beginning with the initial autophagosomal precursor and progressing to its elongation and maturation into a fully enclosed, fusion-capable vesicle. While the core protein machinery involved in autophagosome formation has been extensively studied over the past two decades, the role of phospholipids in this process has only recently been studied. This review focuses on the phospholipid composition of the phagophore membrane and the mechanisms that supply lipids to expand this unique organelle.
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Affiliation(s)
- Damilola Isola
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zvulun Elazar
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
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8
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Vacca F, Yalcin B, Ansar M. Exploring the pathological mechanisms underlying Cohen syndrome. Front Neurosci 2024; 18:1431400. [PMID: 39010945 PMCID: PMC11247020 DOI: 10.3389/fnins.2024.1431400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 06/18/2024] [Indexed: 07/17/2024] Open
Abstract
Cohen Syndrome (CS) is a rare autosomal recessive disorder caused by biallelic mutations in the VPS13B gene. It is characterized by multiple clinical features, including acquired microcephaly, developmental delay, intellectual disability, neutropenia, and retinal degeneration. VPS13B is part of the bridge-like lipid transport (BLTP) protein family, which in mammals also includes VPS13A, -C, and -D. The proteins of this family are peripheral membrane proteins with different sub-cellular localization, but all share similar structural features and have been proposed to act as lipid transport proteins at organellar membrane contact sites. VPS13B is localized at the Golgi apparatus and is essential for the maintenance of organelle architecture. Here we present a review of the experimental data on the function of the protein at the cellular level, discussing the potential link with disease phenotype and review the studies on animal models recapitulating features of the human disease.
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Affiliation(s)
- Fabrizio Vacca
- Department of Ophthalmology, University of Lausanne, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, Lausanne, Switzerland
| | - Binnaz Yalcin
- Inserm UMR1231, Université de Bourgogne, Dijon, France
| | - Muhammad Ansar
- Department of Ophthalmology, University of Lausanne, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, Lausanne, Switzerland
- Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
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9
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Kang Y, Lehmann KS, Vanegas J, Long H, Jefferson A, Freeman M, Clark S. Structural basis of bulk lipid transfer by bridge-like lipid transfer protein LPD-3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600134. [PMID: 38948693 PMCID: PMC11213131 DOI: 10.1101/2024.06.21.600134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Bridge-like lipid transport proteins (BLTPs) are an evolutionarily conserved family of proteins that localize to membrane contact sites and are thought to mediate the bulk transfer of lipids from a donor membrane, typically the endoplasmic reticulum (ER), to an acceptor membrane, such as a that of the cell or an organelle 1 . Despite the fundamental importance of BLTPs for cellular function, the architecture, composition, and lipid transfer mechanisms remain poorly characterized. Here, we present the subunit composition and the cryo-electron microscopy structure of the native LPD-3 BLTP complex isolated from transgenic C. elegans . LPD-3 folds into an elongated, rod-shaped tunnel whose interior is filled with ordered lipid molecules that are coordinated by a track of ionizable residues that line one side of the tunnel. LPD-3 forms a complex with two previously uncharacterized proteins, here named "Intake" and "Spigot", both of which interact with the N-terminal end of LPD-3 where lipids enter the tunnel. Intake has three transmembrane helices, one of which borders the entrance to the tunnel; Spigot has one transmembrane helix and extends 80 Å along the cytosolic surface of LPD-3. Experiments in multiple model systems indicate that Spigot plays a conserved role in ER-PM contact site formation. Our LPD-3 complex structural data, together with molecular dynamics simulations of the transmembrane region in a lipid bilayer, reveal protein-lipid interactions that suggest a model for how the native LPD-3-complex mediates bulk lipid transport and provide a foundation for mechanistic studies of BLTPs.
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10
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Zhang Y, Lin C. Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow. Curr Opin Cell Biol 2024; 88:102377. [PMID: 38823338 PMCID: PMC11193448 DOI: 10.1016/j.ceb.2024.102377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/12/2024] [Accepted: 05/13/2024] [Indexed: 06/03/2024]
Abstract
Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area, resulting in a membrane tension difference called osmotic membrane tension. We examine the thermodynamic basis and experimental evidence of lipid osmosis and osmotic membrane tension. We predict that lipid osmosis can drive bulk lipid flows between different membrane regions through lipid transfer proteins, scramblases, or similar barriers that selectively pass lipids but not membrane proteins. We also speculate on the biological functions of lipid osmosis. Finally, we explore other driving forces for lipid transfer and describe potential methods and systems to further test our theory.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA; Nanobiology Institute, Yale University, West Haven, CT 06516, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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11
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John Peter AT, Kornmann B. Uncovering mechanisms of interorganelle lipid transport by enzymatic mass tagging. FEBS Lett 2024; 598:1292-1298. [PMID: 38268324 DOI: 10.1002/1873-3468.14810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Lipid trafficking is critical for the biogenesis and expansion of organelle membranes. Lipid transport proteins (LTPs) have been proposed to facilitate lipid transport at contact sites between organelles. Despite the fundamental importance of LTPs in cell physiology, our knowledge on the mechanisms of interorganelle lipid distribution remains poor due to the scarcity of assays to monitor lipid flux in vivo. In this review, we highlight the recent development of a versatile method named METALIC (Mass tagging-Enabled Tracking of Lipids in Cells), which uses a combination of enzymatic mass tagging and mass spectrometry to track lipid flux between organelles inside living cells. We discuss the methodology, its distinct advantages, limitations as well as its potential to unearth the pipelines of lipid transport and LTP function in vivo.
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12
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Enkler L, Spang A. Functional interplay of lipid droplets and mitochondria. FEBS Lett 2024; 598:1235-1251. [PMID: 38268392 DOI: 10.1002/1873-3468.14809] [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: 10/12/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Our body stores energy mostly in form of fatty acids (FAs) in lipid droplets (LDs). From there the FAs can be mobilized and transferred to peroxisomes and mitochondria. This transfer is dependent on close opposition of LDs and mitochondria and peroxisomes and happens at membrane contact sites. However, the composition and the dynamics of these contact sites is not well understood, which is in part due to the dependence on the metabolic state of the cell and on the cell- and tissue-type. Here, we summarize the current knowledge on the contacts between lipid droplets and mitochondria both in mammals and in the yeast Saccharomyces cerevisiae, in which various contact sites are well studied. We discuss possible functions of the contact site and their implication in disease.
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Affiliation(s)
| | - Anne Spang
- Biozentrum, University of Basel, Switzerland
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13
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Dudka W, Salo VT, Mahamid J. Zooming into lipid droplet biology through the lens of electron microscopy. FEBS Lett 2024; 598:1127-1142. [PMID: 38726814 DOI: 10.1002/1873-3468.14899] [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: 01/26/2024] [Revised: 04/08/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Electron microscopy (EM), in its various flavors, has significantly contributed to our understanding of lipid droplets (LD) as central organelles in cellular metabolism. For example, EM has illuminated that LDs, in contrast to all other cellular organelles, are uniquely enclosed by a single phospholipid monolayer, revealed the architecture of LD contact sites with different organelles, and provided near-atomic resolution maps of key enzymes that regulate neutral lipid biosynthesis and LD biogenesis. In this review, we first provide a brief history of pivotal findings in LD biology unveiled through the lens of an electron microscope. We describe the main EM techniques used in the context of LD research and discuss their current capabilities and limitations, thereby providing a foundation for utilizing suitable EM methodology to address LD-related questions with sufficient level of structural preservation, detail, and resolution. Finally, we highlight examples where EM has recently been and is expected to be instrumental in expanding the frontiers of LD biology.
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Affiliation(s)
- Wioleta Dudka
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Veijo T Salo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
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14
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Zhang Y, Lin C. Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574656. [PMID: 38260424 PMCID: PMC10802412 DOI: 10.1101/2024.01.08.574656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area, resulting in a membrane tension difference called osmotic membrane tension. We examine the thermodynamic basis and experimental evidence of lipid osmosis and osmotic membrane tension. We predict that lipid osmosis can drive bulk lipid flows between different membrane regions through lipid transfer proteins, scramblases, or other similar barriers that selectively pass lipids but not membrane proteins. We also speculate on the biological functions of lipid osmosis. Finally, we explore other driving forces for lipid transfer and describe potential methods and systems to further test our theory.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
- Nanobiology Institute, Yale University, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
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15
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Schmid M, Fischer P, Engl M, Widder J, Kerschbaum-Gruber S, Slade D. The interplay between autophagy and cGAS-STING signaling and its implications for cancer. Front Immunol 2024; 15:1356369. [PMID: 38660307 PMCID: PMC11039819 DOI: 10.3389/fimmu.2024.1356369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Autophagy is an intracellular process that targets various cargos for degradation, including members of the cGAS-STING signaling cascade. cGAS-STING senses cytosolic double-stranded DNA and triggers an innate immune response through type I interferons. Emerging evidence suggests that autophagy plays a crucial role in regulating and fine-tuning cGAS-STING signaling. Reciprocally, cGAS-STING pathway members can actively induce canonical as well as various non-canonical forms of autophagy, establishing a regulatory network of feedback mechanisms that alter both the cGAS-STING and the autophagic pathway. The crosstalk between autophagy and the cGAS-STING pathway impacts a wide variety of cellular processes such as protection against pathogenic infections as well as signaling in neurodegenerative disease, autoinflammatory disease and cancer. Here we provide a comprehensive overview of the mechanisms involved in autophagy and cGAS-STING signaling, with a specific focus on the interactions between the two pathways and their importance for cancer.
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Affiliation(s)
- Maximilian Schmid
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Patrick Fischer
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Joachim Widder
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Sylvia Kerschbaum-Gruber
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- MedAustron Ion Therapy Center, Wiener Neustadt, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
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16
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Wang J, Xiong J, Zhang S, Li D, Chu Q, Chang W, Deng L, Ji WK. Biogenesis of Rab14-positive endosome buds at Golgi-endosome contacts by the RhoBTB3-SHIP164-Vps26B complex. Cell Discov 2024; 10:38. [PMID: 38565878 PMCID: PMC10987540 DOI: 10.1038/s41421-024-00651-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/25/2024] [Indexed: 04/04/2024] Open
Abstract
Early endosomes (EEs) are crucial in cargo sorting within vesicular trafficking. While cargoes destined for degradation are retained in EEs and eventually transported to lysosomes, recycled cargoes for the plasma membrane (PM) or the Golgi undergo segregation into specialized membrane structures known as EE buds during cargo sorting. Despite this significance, the molecular basis of the membrane expansion during EE bud formation has been poorly understood. In this study, we identify a protein complex comprising SHIP164, an ATPase RhoBTB3, and a retromer subunit Vps26B, which promotes the formation of EE buds at Golgi-EE contacts. Our findings reveal that Vps26B acts as a novel Rab14 effector, and Rab14 activity regulates the association of SHIP164 with EEs. Depletion of SHIP164 leads to enlarged Rab14+ EEs without buds, a phenotype rescued by wild-type SHIP164 but not the lipid transfer-defective mutants. Suppression of RhoBTB3 or Vps26B mirrors the effects of SHIP164 depletion. Together, we propose a lipid transport-dependent pathway mediated by the RhoBTB3-SHIP164-Vps26B complex at Golgi-EE contacts, which is essential for EE budding.
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Affiliation(s)
- Jingru Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Department of Ultrasound Medicine, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Juan Xiong
- Department of Anesthesiology and Pain Medicine, Hubei Key Laboratory of Geriatric Anesthesia and Perioperative Brain Health, and Wuhan Clinical Research Center for Geriatric Anesthesia, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuhan Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | - Dongchen Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Qingzhu Chu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China
| | | | - Lin Deng
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, China.
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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17
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Suzuki SW, West M, Zhang Y, Fan JS, Roberts RT, Odorizzi G, Emr SD. A role for Vps13-mediated lipid transfer at the ER-endosome contact site in ESCRT-mediated sorting. J Cell Biol 2024; 223:e202307094. [PMID: 38319250 PMCID: PMC10847051 DOI: 10.1083/jcb.202307094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Endosomes are specialized organelles that function in the secretory and endocytic protein sorting pathways. Endocytosed cell surface receptors and transporters destined for lysosomal degradation are sorted into intraluminal vesicles (ILVs) at endosomes by endosomal sorting complexes required for transport (ESCRT) proteins. The endosomes (multivesicular bodies, MVBs) then fuse with the lysosome. During endosomal maturation, the number of ILVs increases, but the size of endosomes does not decrease despite the consumption of the limiting membrane during ILV formation. Vesicle-mediated trafficking is thought to provide lipids to support MVB biogenesis. However, we have uncovered an unexpected contribution of a large bridge-like lipid transfer protein, Vps13, in this process. Here, we reveal that Vps13-mediated lipid transfer at ER-endosome contact sites is required for the ESCRT pathway. We propose that Vps13 may play a critical role in supplying lipids to the endosome, ensuring continuous ESCRT-mediated sorting during MVB biogenesis.
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Affiliation(s)
- Sho W. Suzuki
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Matthew West
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Yichen Zhang
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jenny S. Fan
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Rachel T. Roberts
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Greg Odorizzi
- Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Scott D. Emr
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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18
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Durant M, Mucelli X, Huang LS. Meiotic Cytokinesis in Saccharomyces cerevisiae: Spores That Just Need Closure. J Fungi (Basel) 2024; 10:132. [PMID: 38392804 PMCID: PMC10890087 DOI: 10.3390/jof10020132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
In the budding yeast Saccharomyces cerevisiae, sporulation occurs during starvation of a diploid cell and results in the formation of four haploid spores forming within the mother cell ascus. Meiosis divides the genetic material that is encapsulated by the prospore membrane that grows to surround the haploid nuclei; this membrane will eventually become the plasma membrane of the haploid spore. Cellularization of the spores occurs when the prospore membrane closes to capture the haploid nucleus along with some cytoplasmic material from the mother cell, and thus, closure of the prospore membrane is the meiotic cytokinetic event. This cytokinetic event involves the removal of the leading-edge protein complex, a complex of proteins that localizes to the leading edge of the growing prospore membrane. The development and closure of the prospore membrane must be coordinated with other meiotic exit events such as spindle disassembly. Timing of the closure of the prospore membrane depends on the meiotic exit pathway, which utilizes Cdc15, a Hippo-like kinase, and Sps1, an STE20 family GCKIII kinase, acting in parallel to the E3 ligase Ama1-APC/C. This review describes the sporulation process and focuses on the development of the prospore membrane and the regulation of prospore membrane closure.
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Affiliation(s)
- Matthew Durant
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Xheni Mucelli
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Linda S Huang
- Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
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19
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Sun S, Zhao G, Jia M, Jiang Q, Li S, Wang H, Li W, Wang Y, Bian X, Zhao YG, Huang X, Yang G, Cai H, Pastor-Pareja JC, Ge L, Zhang C, Hu J. Stay in touch with the endoplasmic reticulum. SCIENCE CHINA. LIFE SCIENCES 2024; 67:230-257. [PMID: 38212460 DOI: 10.1007/s11427-023-2443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 01/13/2024]
Abstract
The endoplasmic reticulum (ER), which is composed of a continuous network of tubules and sheets, forms the most widely distributed membrane system in eukaryotic cells. As a result, it engages a variety of organelles by establishing membrane contact sites (MCSs). These contacts regulate organelle positioning and remodeling, including fusion and fission, facilitate precise lipid exchange, and couple vital signaling events. Here, we systematically review recent advances and converging themes on ER-involved organellar contact. The molecular basis, cellular influence, and potential physiological functions for ER/nuclear envelope contacts with mitochondria, Golgi, endosomes, lysosomes, lipid droplets, autophagosomes, and plasma membrane are summarized.
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Affiliation(s)
- Sha Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gan Zhao
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Mingkang Jia
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Jiang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Shulin Li
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Haibin Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenjing Li
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunyun Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xin Bian
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Yan G Zhao
- Brain Research Center, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ge Yang
- Laboratory of Computational Biology & Machine Intelligence, School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jose C Pastor-Pareja
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Institute of Neurosciences, Consejo Superior de Investigaciones Cientfflcas-Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain.
| | - Liang Ge
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Ronayne CT, Latorre-Muro P. Navigating the landscape of mitochondrial-ER communication in health and disease. Front Mol Biosci 2024; 11:1356500. [PMID: 38323074 PMCID: PMC10844478 DOI: 10.3389/fmolb.2024.1356500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/10/2024] [Indexed: 02/08/2024] Open
Abstract
Intracellular organelle communication enables the maintenance of tissue homeostasis and health through synchronized adaptive processes triggered by environmental cues. Mitochondrial-Endoplasmic Reticulum (ER) communication sustains cellular fitness by adjusting protein synthesis and degradation, and metabolite and protein trafficking through organelle membranes. Mitochondrial-ER communication is bidirectional and requires that the ER-components of the Integrated Stress Response signal to mitochondria upon activation and, likewise, mitochondria signal to the ER under conditions of metabolite and protein overload to maintain proper functionality and ensure cellular survival. Declines in the mitochondrial-ER communication occur upon ageing and correlate with the onset of a myriad of heterogeneous age-related diseases such as obesity, type 2 diabetes, cancer, or neurodegenerative pathologies. Thus, the exploration of the molecular mechanisms of mitochondrial-ER signaling and regulation will provide insights into the most fundamental cellular adaptive processes with important therapeutical opportunities. In this review, we will discuss the pathways and mechanisms of mitochondrial-ER communication at the mitochondrial-ER interface and their implications in health and disease.
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Affiliation(s)
- Conor T. Ronayne
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
| | - Pedro Latorre-Muro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
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21
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Voeltz GK, Sawyer EM, Hajnóczky G, Prinz WA. Making the connection: How membrane contact sites have changed our view of organelle biology. Cell 2024; 187:257-270. [PMID: 38242082 DOI: 10.1016/j.cell.2023.11.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/13/2023] [Accepted: 11/29/2023] [Indexed: 01/21/2024]
Abstract
The view of organelles and how they operate together has changed dramatically over the last two decades. The textbook view of organelles was that they operated largely independently and were connected by vesicular trafficking and the diffusion of signals through the cytoplasm. We now know that all organelles make functional close contacts with one another, often called membrane contact sites. The study of these sites has moved to center stage in cell biology as it has become clear that they play critical roles in healthy and developing cells and during cell stress and disease states. Contact sites have important roles in intracellular signaling, lipid metabolism, motor-protein-mediated membrane dynamics, organelle division, and organelle biogenesis. Here, we summarize the major conceptual changes that have occurred in cell biology as we have come to appreciate how contact sites integrate the activities of organelles.
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Affiliation(s)
- G K Voeltz
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - E M Sawyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - G Hajnóczky
- MitoCare Center, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - W A Prinz
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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22
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Ching C, Maufront J, di Cicco A, Lévy D, Dezi M. C ool-contacts: Cryo-Electron Microscopy of Membrane Contact Sites and Their Components. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241231364. [PMID: 38410695 PMCID: PMC10895918 DOI: 10.1177/25152564241231364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Electron microscopy has played a pivotal role in elucidating the ultrastructure of membrane contact sites between cellular organelles. The advent of cryo-electron microscopy has ushered in the ability to determine atomic models of constituent proteins or protein complexes within sites of membrane contact through single particle analysis. Furthermore, it enables the visualization of the three-dimensional architecture of membrane contact sites, encompassing numerous copies of proteins, whether in vitro reconstituted or directly observed in situ using cryo-electron tomography. Nevertheless, there exists a scarcity of cryo-electron microscopy studies focused on the site of membrane contact and their constitutive proteins. This review provides an overview of the contributions made by cryo-electron microscopy to our understanding of membrane contact sites, outlines the associated limitations, and explores prospects in this field.
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Affiliation(s)
- Cyan Ching
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Julien Maufront
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Aurélie di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Manuela Dezi
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
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23
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Mann D, Fromm SA, Martinez-Sanchez A, Gopaldass N, Choy R, Mayer A, Sachse C. Atg18 oligomer organization in assembled tubes and on lipid membrane scaffolds. Nat Commun 2023; 14:8086. [PMID: 38057304 DOI: 10.1038/s41467-023-43460-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
Autophagy-related protein 18 (Atg18) participates in the elongation of early autophagosomal structures in concert with Atg2 and Atg9 complexes. How Atg18 contributes to the structural coordination of Atg2 and Atg9 at the isolation membrane remains to be understood. Here, we determined the cryo-EM structures of Atg18 organized in helical tubes, Atg18 oligomers in solution as well as on lipid membrane scaffolds. The helical assembly is composed of Atg18 tetramers forming a lozenge cylindrical lattice with remarkable structural similarity to the COPII outer coat. When reconstituted with lipid membranes, using subtomogram averaging we determined tilted Atg18 dimer structures bridging two juxtaposed lipid membranes spaced apart by 80 Å. Moreover, lipid reconstitution experiments further delineate the contributions of Atg18's FRRG motif and the amphipathic helical extension in membrane interaction. The observed structural plasticity of Atg18's oligomeric organization and membrane binding properties provide a molecular framework for the positioning of downstream components of the autophagy machinery.
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Affiliation(s)
- Daniel Mann
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
| | - Simon A Fromm
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Martinez-Sanchez
- Department of Information and Communications Engineering, Faculty of Computers Sciences, University of Murcia, Murcia, Spain
| | - Navin Gopaldass
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Ramona Choy
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
| | - Andreas Mayer
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Carsten Sachse
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
- Department of Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, Germany.
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24
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Shnaider TA, Khabarova AA, Morozova KN, Yunusova AM, Yakovleva SA, Chvileva AS, Wolf ER, Kiseleva EV, Grigor'eva EV, Voinova VY, Lagarkova MA, Pomerantseva EA, Musatova EV, Smirnov AV, Smirnova AV, Stoklitskaya DS, Arefieva TI, Larina DA, Nikitina TV, Pristyazhnyuk IE. Ultrastructural Abnormalities in Induced Pluripotent Stem Cell-Derived Neural Stem Cells and Neurons of Two Cohen Syndrome Patients. Cells 2023; 12:2702. [PMID: 38067130 PMCID: PMC10705360 DOI: 10.3390/cells12232702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/12/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Cohen syndrome is an autosomal recessive disorder caused by VPS13B (COH1) gene mutations. This syndrome is significantly underdiagnosed and is characterized by intellectual disability, microcephaly, autistic symptoms, hypotension, myopia, retinal dystrophy, neutropenia, and obesity. VPS13B regulates intracellular membrane transport and supports the Golgi apparatus structure, which is critical for neuron formation. We generated induced pluripotent stem cells from two patients with pronounced manifestations of Cohen syndrome and differentiated them into neural stem cells and neurons. Using transmission electron microscopy, we documented multiple new ultrastructural changes associated with Cohen syndrome in the neuronal cells. We discovered considerable disturbances in the structure of some organelles: Golgi apparatus fragmentation and swelling, endoplasmic reticulum structural reorganization, mitochondrial defects, and the accumulation of large autophagosomes with undigested contents. These abnormalities underline the ultrastructural similarity of Cohen syndrome to many neurodegenerative diseases. The cell models that we developed based on patient-specific induced pluripotent stem cells can serve to uncover not only neurodegenerative processes, but the causes of intellectual disability in general.
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Affiliation(s)
- Tatiana A Shnaider
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna A Khabarova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ksenia N Morozova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anastasia M Yunusova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Sophia A Yakovleva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anastasia S Chvileva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina R Wolf
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena V Kiseleva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Grigor'eva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Viktori Y Voinova
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
- The Mental Health Research Center, Moscow 115522, Russia
| | - Maria A Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia
| | | | | | - Alexander V Smirnov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anna V Smirnova
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
| | | | - Tatiana I Arefieva
- National Medical Research Centre of Cardiology Named after Academician E. I. Chazov., Moscow 121552, Russia
| | - Daria A Larina
- Clinical Research Institute of Pediatrics Named after Acad. Y.E. Veltischev, Moscow 125412, Russia
| | - Tatiana V Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk 634050, Russia
| | - Inna E Pristyazhnyuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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25
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Hanna M, Guillén-Samander A, De Camilli P. RBG Motif Bridge-Like Lipid Transport Proteins: Structure, Functions, and Open Questions. Annu Rev Cell Dev Biol 2023; 39:409-434. [PMID: 37406299 DOI: 10.1146/annurev-cellbio-120420-014634] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The life of eukaryotic cells requires the transport of lipids between membranes, which are separated by the aqueous environment of the cytosol. Vesicle-mediated traffic along the secretory and endocytic pathways and lipid transfer proteins (LTPs) cooperate in this transport. Until recently, known LTPs were shown to carry one or a few lipids at a time and were thought to mediate transport by shuttle-like mechanisms. Over the last few years, a new family of LTPs has been discovered that is defined by a repeating β-groove (RBG) rod-like structure with a hydrophobic channel running along their entire length. This structure and the localization of these proteins at membrane contact sites suggest a bridge-like mechanism of lipid transport. Mutations in some of these proteins result in neurodegenerative and developmental disorders. Here we review the known properties and well-established or putative physiological roles of these proteins, and we highlight the many questions that remain open about their functions.
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Affiliation(s)
- Michael Hanna
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrés Guillén-Samander
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA;
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut, USA
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
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26
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Cooper BF, Clark R, Kudhail A, Bhabha G, Ekiert DC, Khalid S, Isom GL. Phospholipid transport to the bacterial outer membrane through an envelope-spanning bridge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561070. [PMID: 37873249 PMCID: PMC10592960 DOI: 10.1101/2023.10.05.561070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The outer membrane of Gram-negative bacteria provides a formidable barrier, essential for both pathogenesis and antimicrobial resistance. Biogenesis of the outer membrane requires the transport of phospholipids across the cell envelope. Recently, YhdP was implicated as a major protagonist in the transport of phospholipids from the inner membrane to the outer membrane however the molecular mechanism of YhdP mediated transport remains elusive. Here, utilising AlphaFold, we observe YhdP to form an elongated assembly of 60 β strands that curve to form a continuous hydrophobic groove. This architecture is consistent with our negative stain electron microscopy data which reveals YhdP to be approximately 250 Å in length and thus sufficient to span the bacterial cell envelope. Furthermore, molecular dynamics simulations and in vivo bacterial growth assays indicate essential helical regions at the N- and C-termini of YhdP, that may embed into the inner and outer membranes respectively, reinforcing its envelope spanning nature. Our in vivo crosslinking data reveal phosphate-containing substrates captured along the length of the YhdP groove, providing direct evidence that YhdP transports phospholipids. This finding is congruent with our molecular dynamics simulations which demonstrate the propensity for inner membrane lipids to spontaneously enter the groove of YhdP. Collectively, our results support a model in which YhdP bridges the cell envelope, providing a hydrophobic environment for the transport of phospholipids to the outer membrane.
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Affiliation(s)
- Benjamin F. Cooper
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Robert Clark
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Anju Kudhail
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016
| | - Damian C. Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Georgia L. Isom
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
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27
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Korfhage JL, Wan N, Elhan H, Kauffman L, Pineda M, Fuller DM, Thiam AR, Reinisch KM, Melia TJ. ATG2A-mediated bridge-like lipid transport regulates lipid droplet accumulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553257. [PMID: 37645754 PMCID: PMC10461963 DOI: 10.1101/2023.08.14.553257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
ATG2 proteins facilitate bulk lipid transport between membranes. ATG2 is an essential autophagy protein, but ATG2 also localizes to lipid droplets (LDs), and genetic depletion of ATG2 increases LD numbers while impairing fatty acid transport from LDs to mitochondria. How ATG2 supports LD homeostasis and whether lipid transport regulates this homeostasis remains unknown. Here we demonstrate that ATG2 is preferentially recruited to phospholipid monolayers such as those surrounding LDs rather than to phospholipid bilayers. In vitro, ATG2 can drive phospholipid transport from artificial LDs with rates that correlate with the binding affinities, such that phospholipids are moved much more efficiently when one of the ATG2-interacting structures is an artificial LD. ATG2 is thought to exhibit 'bridge-like" lipid transport, with lipids flowing across the protein between membranes. We mutated key amino acids within the bridge to form a transport-dead ATG2 mutant (TD-ATG2A) which we show specifically blocks bridge-like, but not shuttle-like, lipid transport in vitro. TD-ATG2A still localizes to LDs, but is unable to rescue LD accumulation in ATG2 knockout cells. Thus, ATG2 has a natural affinity for, and an enhanced activity upon LD surfaces and uses bridge-like lipid transport to support LD dynamics in cells.
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Affiliation(s)
- Justin L. Korfhage
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
| | - Neng Wan
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
| | - Helin Elhan
- Laboratoire de Physique de l’École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, 75005 Paris, France
| | - Lisa Kauffman
- Laboratoire de Physique de l’École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, 75005 Paris, France
| | - Mia Pineda
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
| | - Devin M. Fuller
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
| | - Abdou Rachid Thiam
- Laboratoire de Physique de l’École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, 75005 Paris, France
| | - Karin M. Reinisch
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
| | - Thomas J. Melia
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
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28
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Dabrowski R, Tulli S, Graef M. Parallel phospholipid transfer by Vps13 and Atg2 determines autophagosome biogenesis dynamics. J Cell Biol 2023; 222:e202211039. [PMID: 37115156 PMCID: PMC10148235 DOI: 10.1083/jcb.202211039] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/30/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
During autophagy, rapid membrane assembly expands small phagophores into large double-membrane autophagosomes. Theoretical modeling predicts that the majority of autophagosomal phospholipids are derived from highly efficient non-vesicular phospholipid transfer (PLT) across phagophore-ER contacts (PERCS). Currently, the phagophore-ER tether Atg2 is the only PLT protein known to drive phagophore expansion in vivo. Here, our quantitative live-cell imaging analysis reveals a poor correlation between the duration and size of forming autophagosomes and the number of Atg2 molecules at PERCS of starving yeast cells. Strikingly, we find that Atg2-mediated PLT is non-rate limiting for autophagosome biogenesis because membrane tether and the PLT protein Vps13 localizes to the rim and promotes the expansion of phagophores in parallel with Atg2. In the absence of Vps13, the number of Atg2 molecules at PERCS determines the duration and size of forming autophagosomes with an apparent in vivo transfer rate of ∼200 phospholipids per Atg2 molecule and second. We propose that conserved PLT proteins cooperate in channeling phospholipids across organelle contact sites for non-rate-limiting membrane assembly during autophagosome biogenesis.
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Affiliation(s)
- Rahel Dabrowski
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Susanna Tulli
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Martin Graef
- Max Planck Research Group of Autophagy and Cellular Ageing, Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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29
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Tornero-Écija A, Zapata-Del-Baño A, Antón-Esteban L, Vincent O, Escalante R. The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5. Life Sci Alliance 2023; 6:e202201852. [PMID: 36977596 PMCID: PMC10053439 DOI: 10.26508/lsa.202201852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Human VPS13 proteins are implicated in severe neurological diseases. These proteins play an important role in lipid transport at membrane contact sites between different organelles. Identification of adaptors that regulate the subcellular localization of these proteins at specific membrane contact sites is essential to understand their function and role in disease. We have identified the sorting nexin SNX5 as an interactor of VPS13A that mediates its association with endosomal subdomains. As for the yeast sorting nexin and Vps13 endosomal adaptor Ypt35, this association involves the VPS13 adaptor-binding (VAB) domain in VPS13A and a PxP motif in SNX5. Notably, this interaction is impaired by mutation of a conserved asparagine residue in the VAB domain, which is also required for Vps13-adaptor binding in yeast and is pathogenic in VPS13D. VPS13A fragments containing the VAB domain co-localize with SNX5, whereas the more C-terminal part of VPS13A directs its localization to the mitochondria. Overall, our results suggest that a fraction of VPS13A localizes to junctions between the endoplasmic reticulum, mitochondria, and SNX5-containing endosomes.
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Affiliation(s)
- Alba Tornero-Écija
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | | | - Laura Antón-Esteban
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols, C.S.I.C./U.A.M., Madrid, Spain
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30
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Henne WM. The (social) lives, deaths, and biophysical phases of lipid droplets. Curr Opin Cell Biol 2023; 82:102178. [PMID: 37295067 PMCID: PMC10782554 DOI: 10.1016/j.ceb.2023.102178] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023]
Abstract
Lipid droplets (LDs) are major lipid storage organelles, sequestering energy-rich triglycerides and serving as nutrient sinks for cellular homeostasis. Observed for over a century but generally ignored, LDs are now appreciated to play key roles in organismal physiology and disease. They also form numerous functional contacts with other organelles. Here, we highlight recent studies examining LDs from distinct perspectives of their life cycle: their biogenesis, "social" life as they interact with other organelles, and deaths via lipolysis or lipophagy. We also discuss recent work showing how changes in LD lipid content alter the biophysical phases of LD lipids, and how this may fine-tune the LD protein landscape and ultimately LD function.
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Affiliation(s)
- W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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31
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Wozny MR, Di Luca A, Morado DR, Picco A, Khaddaj R, Campomanes P, Ivanović L, Hoffmann PC, Miller EA, Vanni S, Kukulski W. In situ architecture of the ER-mitochondria encounter structure. Nature 2023:10.1038/s41586-023-06050-3. [PMID: 37165187 DOI: 10.1038/s41586-023-06050-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis that rely on lipid exchange via membrane contact sites1-3, but the underpinning mechanisms remain poorly understood. In yeast, tethering and lipid transfer between the two organelles is mediated by the endoplasmic reticulum-mitochondria encounter structure (ERMES), a four-subunit complex of unresolved stoichiometry and architecture4-6. Here we determined the molecular organization of ERMES within Saccharomyces cerevisiae cells using integrative structural biology by combining quantitative live imaging, cryo-correlative microscopy, subtomogram averaging and molecular modelling. We found that ERMES assembles into approximately 25 discrete bridge-like complexes distributed irregularly across a contact site. Each bridge consists of three synaptotagmin-like mitochondrial lipid binding protein domains oriented in a zig-zag arrangement. Our molecular model of ERMES reveals a pathway for lipids. These findings resolve the in situ supramolecular architecture of a major inter-organelle lipid transfer machinery and provide a basis for the mechanistic understanding of lipid fluxes in eukaryotic cells.
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Affiliation(s)
- Michael R Wozny
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Dustin R Morado
- MRC Laboratory of Molecular Biology, Cambridge, UK
- SciLifeLab, Solna, Sweden
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrea Picco
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Rasha Khaddaj
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Lazar Ivanović
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Patrick C Hoffmann
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| | - Wanda Kukulski
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
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32
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Guillén-Samander A, De Camilli P. Endoplasmic Reticulum Membrane Contact Sites, Lipid Transport, and Neurodegeneration. Cold Spring Harb Perspect Biol 2023; 15:a041257. [PMID: 36123033 PMCID: PMC10071438 DOI: 10.1101/cshperspect.a041257] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Endoplasmic Reticulum (ER) is an endomembrane system that plays a multiplicity of roles in cell physiology and populates even the most distal cell compartments, including dendritic tips and axon terminals of neurons. Some of its functions are achieved by a cross talk with other intracellular membranous organelles and with the plasma membrane at membrane contacts sites (MCSs). As the ER synthesizes most membrane lipids, lipid exchanges mediated by lipid transfer proteins at MCSs are a particularly important aspect of this cross talk, which synergizes with the cross talk mediated by vesicular transport. Several mutations of genes that encode proteins localized at ER MCSs result in familial neurodegenerative diseases, emphasizing the importance of the normal lipid traffic within cells for a healthy brain. Here, we provide an overview of such diseases, with a specific focus on proteins that directly or indirectly impact lipid transport.
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Affiliation(s)
- Andrés Guillén-Samander
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA
| | - Pietro De Camilli
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland 20815, USA
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33
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Dall'Armellina F, Stagi M, Swan LE. In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms. Proteins 2023; 91:439-455. [PMID: 36404287 PMCID: PMC10953354 DOI: 10.1002/prot.26446] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/14/2022] [Accepted: 11/03/2022] [Indexed: 11/22/2022]
Abstract
The VPS13 protein family constitutes a novel class of bridge-like lipid transferases. Autosomal recessive inheritance of mutations in VPS13 genes is associated with the development of neurodegenerative diseases in humans. Bioinformatic approaches previously recognized the domain architecture of these proteins. In this study, we model the first ever full-length structures of the four human homologs VPS13A, VPS13B, VPS13C, and VPS13D in association with model membranes, to investigate their lipid transfer ability and potential structural association with membrane leaflets. We analyze the evolutionary conservation and physicochemical properties of these proteins, focusing on conserved C-terminal amphipathic helices that disturb organelle surfaces and that, adjoined, resemble a traditional Venetian gondola. The gondola domains share significant structural homology with lipid droplet surface-binding proteins. We introduce in silico protein-membrane models displaying the mode of association of VPS13A, VPS13B, VPS13C, and VPS13D to donor and target membranes, and present potential models of action for protein-mediated lipid transfer.
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Affiliation(s)
- Filippo Dall'Armellina
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
| | - Massimiliano Stagi
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
| | - Laura E. Swan
- Department of Biochemistry and Systems BiologyInstitute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUK
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34
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Li M, Tripathi-Giesgen I, Schulman BA, Baumeister W, Wilfling F. In situ snapshots along a mammalian selective autophagy pathway. Proc Natl Acad Sci U S A 2023; 120:e2221712120. [PMID: 36917659 PMCID: PMC10041112 DOI: 10.1073/pnas.2221712120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/08/2023] [Indexed: 03/16/2023] Open
Abstract
Selective macroautophagy (hereafter referred to as autophagy) describes a process in which cytosolic material is engulfed in a double membrane organelle called an autophagosome. Autophagosomes are carriers responsible for delivering their content to a lytic compartment for destruction. The cargo can be of diverse origin, ranging from macromolecular complexes to protein aggregates, organelles, and even invading pathogens. Each cargo is unique in composition and size, presenting different challenges to autophagosome biogenesis. Among the largest cargoes targeted by the autophagy machinery are intracellular bacteria, which can, in the case of Salmonella, range from 2 to 5 μm in length and 0.5 to 1.5 μm in width. How phagophores form and expand on such a large cargo remains mechanistically unclear. Here, we used HeLa cells infected with an auxotrophic Salmonella to study the process of phagophore biogenesis using in situ correlative cryo-ET. We show that host cells generate multiple phagophores at the site of damaged Salmonella-containing vacuoles (SCVs). The observed double membrane structures range from disk-shaped to expanded cup-shaped phagophores, which have a thin intermembrane lumen with a dilating rim region and expand using the SCV, the outer membrane of Salmonella, or existing phagophores as templates. Phagophore rims establish different forms of contact with the endoplasmic reticulum (ER) via structurally distinct molecular entities for membrane formation and expansion. Early omegasomes correlated with the marker Double-FYVE domain-Containing Protein 1 (DFCP1) are observed in close association with the ER without apparent membrane continuity. Our study provides insights into the formation of phagophores around one of the largest selective cargoes.
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Affiliation(s)
- Meijing Li
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry,82152Martinsried, Germany
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry,82152Martinsried, Germany
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry,82152Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry,82152Martinsried, Germany
| | - Florian Wilfling
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry,82152Martinsried, Germany
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, 60438Frankfurt a. M., Germany
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35
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Cai W, Li P, Gu M, Xu H. Lysosomal Ion Channels and Lysosome-Organelle Interactions. Handb Exp Pharmacol 2023; 278:93-108. [PMID: 36882602 DOI: 10.1007/164_2023_640] [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: 03/09/2023]
Abstract
Intracellular organelles exchange their luminal contents with each other via both vesicular and non-vesicular mechanisms. By forming membrane contact sites (MCSs) with ER and mitochondria, lysosomes mediate bidirectional transport of metabolites and ions between lysosomes and organelles that regulate lysosomal physiology, movement, membrane remodeling, and membrane repair. In this chapter, we will first summarize the current knowledge of lysosomal ion channels and then discuss the molecular and physiological mechanisms that regulate lysosome-organelle MCS formation and dynamics. We will also discuss the roles of lysosome-ER and lysosome-mitochondria MCSs in signal transduction, lipid transport, Ca 2+ transfer, membrane trafficking, and membrane repair, as well as their roles in lysosome-related pathologies.
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Affiliation(s)
- Weijie Cai
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Ping Li
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Mingxue Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dun Neurological Research Institute, Houston, TX, USA
| | - Haoxing Xu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dun Neurological Research Institute, Houston, TX, USA. .,Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Department of Cardiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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36
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Du Y, Chang W, Gao L, Deng L, Ji WK. Tex2 is required for lysosomal functions at TMEM55-dependent ER membrane contact sites. J Cell Biol 2023; 222:213838. [PMID: 36705603 PMCID: PMC9930140 DOI: 10.1083/jcb.202205133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 10/17/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023] Open
Abstract
ER tubules form and maintain membrane contact sites (MCSs) with late endosomes/lysosomes (LE/lys). The molecular composition and cellular functions of these MCSs are poorly understood. Here, we find that Tex2, an SMP domain-containing lipid transfer protein conserved in metazoan and yeast, is a tubular ER protein and is recruited to ER-LE/lys MCSs by TMEM55, phosphatases that convert PI(4,5)P2 to PI5P on LE/lys. We show that the Tex2-TMEM55 interaction occurs between an N-terminal region of Tex2 and a catalytic motif in the PTase domain of TMEM55. The Tex2-TMEM55 interaction can be regulated by endosome-resident type 2 PI4K activities. Functionally, Tex2 knockout results in defects in lysosomal trafficking, digestive capacity, and lipid composition of LE/lys membranes. Together, our data identify Tex2 as a tubular ER protein that resides at TMEM55-dependent ER-LE/lys MCSs required for lysosomal functions.
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Affiliation(s)
- Yuanjiao Du
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Wuhan, China,https://ror.org/00p991c53Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China,https://ror.org/00sdcjz77Shenzhen Bay Laboratory, Shenzhen, China
| | - Weiping Chang
- https://ror.org/00sdcjz77Shenzhen Bay Laboratory, Shenzhen, China
| | - Lei Gao
- https://ror.org/05hfa4n20Microscopy Core Facility, Westlake University, Hangzhou, Zhejiang, China
| | - Lin Deng
- https://ror.org/00sdcjz77Shenzhen Bay Laboratory, Shenzhen, China
| | - Wei-Ke Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Wuhan, China,https://ror.org/00p991c53Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China,https://ror.org/00sdcjz77Shenzhen Bay Laboratory, Shenzhen, China,Correspondence to Wei-Ke Ji:
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37
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Subra M, Dezi M, Bigay J, Lacas-Gervais S, Di Cicco A, Araújo ARD, Abélanet S, Fleuriot L, Debayle D, Gautier R, Patel A, Roussi F, Antonny B, Lévy D, Mesmin B. VAP-A intrinsically disordered regions enable versatile tethering at membrane contact sites. Dev Cell 2023; 58:121-138.e9. [PMID: 36693319 DOI: 10.1016/j.devcel.2022.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/21/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023]
Abstract
Membrane contact sites (MCSs) are heterogeneous in shape, composition, and dynamics. Despite this diversity, VAP proteins act as receptors for multiple FFAT motif-containing proteins and drive the formation of most MCSs that involve the endoplasmic reticulum (ER). Although the VAP-FFAT interaction is well characterized, no model explains how VAP adapts to its partners in various MCSs. We report that VAP-A localization to different MCSs depends on its intrinsically disordered regions (IDRs) in human cells. VAP-A interaction with PTPIP51 and VPS13A at ER-mitochondria MCS conditions mitochondria fusion by promoting lipid transfer and cardiolipin buildup. VAP-A also enables lipid exchange at ER-Golgi MCS by interacting with oxysterol-binding protein (OSBP) and CERT. However, removing IDRs from VAP-A restricts its distribution and function to ER-mitochondria MCS. Our data suggest that IDRs do not modulate VAP-A preference toward specific partners but do adjust their geometry to MCS organization and lifetime constraints. Thus, IDR-mediated VAP-A conformational flexibility ensures membrane tethering plasticity and efficiency.
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Affiliation(s)
- Mélody Subra
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Manuela Dezi
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005 Paris, France
| | - Joëlle Bigay
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Sandra Lacas-Gervais
- Université Côte d'Azur, Centre Commun de Microscopie Appliquée, Parc Valrose, 06000 Nice, France
| | - Aurélie Di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005 Paris, France
| | - Ana Rita Dias Araújo
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Sophie Abélanet
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Lucile Fleuriot
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Delphine Debayle
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Romain Gautier
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Amanda Patel
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Fanny Roussi
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Bruno Antonny
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, 75005 Paris, France
| | - Bruno Mesmin
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France.
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Renne MF, Bao X, Hokken MWJ, Bierhuizen AS, Hermansson M, Sprenger RR, Ewing TA, Ma X, Cox RC, Brouwers JF, De Smet CH, Ejsing CS, de Kroon AIPM. Molecular species selectivity of lipid transport creates a mitochondrial sink for di-unsaturated phospholipids. EMBO J 2022; 41:e106837. [PMID: 34873731 PMCID: PMC8762554 DOI: 10.15252/embj.2020106837] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondria depend on the import of phospholipid precursors for the biosynthesis of phosphatidylethanolamine (PE) and cardiolipin, yet the mechanism of their transport remains elusive. A dynamic lipidomics approach revealed that mitochondria preferentially import di-unsaturated phosphatidylserine (PS) for subsequent conversion to PE by the mitochondrial PS decarboxylase Psd1p. Several protein complexes tethering mitochondria to the endomembrane system have been implicated in lipid transport in yeast, including the endoplasmic reticulum (ER)-mitochondrial encounter structure (ERMES), ER-membrane complex (EMC), and the vacuole and mitochondria patch (vCLAMP). By limiting the availability of unsaturated phospholipids, we created conditions to investigate the mechanism of lipid transfer and the contributions of the tethering complexes in vivo. Under these conditions, inactivation of ERMES components or of the vCLAMP component Vps39p exacerbated accumulation of saturated lipid acyl chains, indicating that ERMES and Vps39p contribute to the mitochondrial sink for unsaturated acyl chains by mediating transfer of di-unsaturated phospholipids. These results support the concept that intermembrane lipid flow is rate-limited by molecular species-dependent lipid efflux from the donor membrane and driven by the lipid species' concentration gradient between donor and acceptor membrane.
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Affiliation(s)
- Mike F Renne
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Xue Bao
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Margriet WJ Hokken
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Department of Medical MicrobiologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
| | - Adolf S Bierhuizen
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Martin Hermansson
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Tom A Ewing
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Wageningen Food & Biobased ResearchWageningen University & ResearchWageningenThe Netherlands
| | - Xiao Ma
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Ruud C Cox
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Jos F Brouwers
- Biochemistry and Cell BiologyDepartment of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
- Present address:
Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Cedric H De Smet
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Christer S Ejsing
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Anton IPM de Kroon
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
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Braschi B, Bruford EA, Cavanagh AT, Neuman SD, Bashirullah A. The bridge-like lipid transfer protein (BLTP) gene group: introducing new nomenclature based on structural homology indicating shared function. Hum Genomics 2022; 16:66. [PMID: 36461115 PMCID: PMC9719229 DOI: 10.1186/s40246-022-00439-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
The HUGO Gene Nomenclature Committee assigns unique symbols and names to human genes. The use of approved nomenclature enables effective communication between researchers, and there are multiple examples of how the usage of unapproved alias symbols can lead to confusion. We discuss here a recent nomenclature update (May 2022) for a set of genes that encode proteins with a shared repeating β-groove domain. Some of the proteins encoded by genes in this group have already been shown to function as lipid transporters. By working with researchers in the field, we have been able to introduce a new root symbol (BLTP, which stands for "bridge-like lipid transfer protein") for this domain-based gene group. This new nomenclature not only reflects the shared domain in these proteins, but also takes into consideration the mounting evidence of a shared lipid transport function.
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Affiliation(s)
- Bryony Braschi
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, Cambridgeshire, CB2 0AW, UK
| | - Amy T Cavanagh
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI, 53705-2222, USA
| | - Sarah D Neuman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI, 53705-2222, USA
| | - Arash Bashirullah
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI, 53705-2222, USA
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40
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Weng X, Wang H. Apical vesicles: Social networking at the pollen tube tip. REPRODUCTION AND BREEDING 2022. [DOI: 10.1016/j.repbre.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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41
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Castro IG, Shortill SP, Dziurdzik SK, Cadou A, Ganesan S, Valenti R, David Y, Davey M, Mattes C, Thomas FB, Avraham RE, Meyer H, Fadel A, Fenech EJ, Ernst R, Zaremberg V, Levine TP, Stefan C, Conibear E, Schuldiner M. Systematic analysis of membrane contact sites in Saccharomyces cerevisiae uncovers modulators of cellular lipid distribution. eLife 2022; 11:74602. [DOI: 10.7554/elife.74602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Actively maintained close appositions between organelle membranes, also known as contact sites, enable the efficient transfer of biomolecules between cellular compartments. Several such sites have been described as well as their tethering machineries. Despite these advances we are still far from a comprehensive understanding of the function and regulation of most contact sites. To systematically characterize contact site proteomes, we established a high-throughput screening approach in Saccharomyces cerevisiae based on co-localization imaging. We imaged split fluorescence reporters for six different contact sites, several of which are poorly characterized, on the background of 1165 strains expressing a mCherry-tagged yeast protein that has a cellular punctate distribution (a hallmark of contact sites), under regulation of the strong TEF2 promoter. By scoring both co-localization events and effects on reporter size and abundance, we discovered over 100 new potential contact site residents and effectors in yeast. Focusing on several of the newly identified residents, we identified three homologs of Vps13 and Atg2 that are residents of multiple contact sites. These proteins share their lipid transport domain, thus expanding this family of lipid transporters. Analysis of another candidate, Ypr097w, which we now call Lec1 (Lipid-droplet Ergosterol Cortex 1), revealed that this previously uncharacterized protein dynamically shifts between lipid droplets and the cell cortex, and plays a role in regulation of ergosterol distribution in the cell. Overall, our analysis expands the universe of contact site residents and effectors and creates a rich database to mine for new functions, tethers, and regulators.
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Affiliation(s)
| | - Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Samantha Katarzyna Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Angela Cadou
- Laboratory for Molecular Cell Biology, University College London
| | | | - Rosario Valenti
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Yotam David
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
| | - Carsten Mattes
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | - Ffion B Thomas
- Laboratory for Molecular Cell Biology, University College London
| | | | - Hadar Meyer
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Emma J Fenech
- Department of Molecular Genetics, Weizmann Institute of Science
| | - Robert Ernst
- Medical Biochemistry and Molecular Biology, PZMS, Medical Faculty, Saarland University
| | | | - Tim P Levine
- UCL Institute of Ophthalmology, University College London
| | | | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia
- Department of Medical Genetics, University of British Columbia
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science
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42
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McEwan DG, Ryan KM. ATG2 and VPS13 proteins: molecular highways transporting lipids to drive membrane expansion and organelle communication. FEBS J 2022; 289:7113-7127. [PMID: 34783437 DOI: 10.1111/febs.16280] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 01/13/2023]
Abstract
Communication between organelles is an essential process that helps maintain cellular homeostasis and organelle contact sites have recently emerged as crucial mediators of this communication. The emergence of a class of molecular bridges that span the inter-organelle gaps has now been shown to direct the flow of lipid traffic from one lipid bilayer to another. One of the key components of these molecular bridges is the presence of an N-terminal Chorein/VPS13 domain. This is an evolutionarily conserved domain present in multiple proteins within the endocytic and autophagy trafficking pathways. Herein, we discuss the current state-of-the-art of this class of proteins, focusing on the role of these lipid transporters in the autophagy and endocytic pathways. We discuss the recent biochemical and structural advances that have highlighted the essential role Chorein-N domain containing ATG2 proteins play in driving the formation of the autophagosome and how lipids are transported from the endoplasmic reticulum to the growing phagophore. We also consider the VPS13 proteins, their role in organelle contacts and the endocytic pathway and highlight how disease-causing mutations disrupt these contact sites. Finally, we open the door to discuss other Chorein_N domain containing proteins, for instance, UHRF1BP1/1L, their role in disease and look towards prokaryote examples of Chorein_N-like domains. Taken together, recent advances have highlighted an exciting opportunity to delve deeper into inter-organelle communication and understand how lipids are transported between membrane bilayers and how this process is disrupted in multiple diseases.
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Affiliation(s)
| | - Kevin M Ryan
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
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43
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Fujiki Y, Okumoto K, Honsho M, Abe Y. Molecular insights into peroxisome homeostasis and peroxisome biogenesis disorders. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119330. [PMID: 35917894 DOI: 10.1016/j.bbamcr.2022.119330] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Peroxisomes are single-membrane organelles essential for cell metabolism including the β-oxidation of fatty acids, synthesis of etherlipid plasmalogens, and redox homeostasis. Investigations into peroxisome biogenesis and the human peroxisome biogenesis disorders (PBDs) have identified 14 PEX genes encoding peroxins involved in peroxisome biogenesis and the mutation of PEX genes is responsible for the PBDs. Many recent findings have further advanced our understanding of the biology, physiology, and consequences of a functional deficit of peroxisomes. In this Review, we discuss cell defense mechanisms that counteract oxidative stress by 1) a proapoptotic Bcl-2 factor BAK-mediated release to the cytosol of H2O2-degrading catalase from peroxisomes and 2) peroxisomal import suppression of catalase by Ser232-phosphorylation of Pex14, a docking protein for the Pex5-PTS1 complex. With respect to peroxisome division, the important issue of how the energy-rich GTP is produced and supplied for the division process was recently addressed by the discovery of a nucleoside diphosphate kinase-like protein, termed DYNAMO1 in a lower eukaryote, which has a mammalian homologue NME3. In regard to the mechanisms underlying the pathogenesis of PBDs, a new PBD model mouse defective in Pex14 manifests a dysregulated brain-derived neurotrophic factor (BDNF)-TrkB pathway, an important signaling pathway for cerebellar morphogenesis. Communications between peroxisomes and other organelles are also addressed.
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Affiliation(s)
- Yukio Fujiki
- Medical Institute of Bioregulation, Institute of Rheological Functions of Food, Collaboration Program, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan.
| | - Kanji Okumoto
- Department of Biology and Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Masanori Honsho
- Medical Institute of Bioregulation, Institute of Rheological Functions of Food, Collaboration Program, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan
| | - Yuichi Abe
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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44
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Neuman SD, Levine TP, Bashirullah A. A novel superfamily of bridge-like lipid transfer proteins. Trends Cell Biol 2022; 32:962-974. [PMID: 35491307 PMCID: PMC9588498 DOI: 10.1016/j.tcb.2022.03.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 01/21/2023]
Abstract
Lipid transfer proteins mediate nonvesicular transport of lipids at membrane contact sites to regulate the lipid composition of organelle membranes. Recently, a new type of bridge-like lipid transfer protein has emerged; these proteins contain a long hydrophobic groove and can mediate bulk transport of lipids between organelles. Here, we review recent insights into the structure of these proteins and identify a repeating modular unit that we propose to name the repeating β-groove (RBG) domain. This new structural understanding conceptually unifies all the RBG domain-containing lipid transfer proteins as members of an RBG protein superfamily. We also examine the biological functions of these lipid transporters in normal physiology and disease and speculate on the evolutionary origins of RBG proteins in bacteria.
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Affiliation(s)
- Sarah D Neuman
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA
| | - Tim P Levine
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK.
| | - Arash Bashirullah
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, Madison, WI 53705-2222, USA.
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45
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Giacometti SI, MacRae MR, Dancel-Manning K, Bhabha G, Ekiert DC. Lipid Transport Across Bacterial Membranes. Annu Rev Cell Dev Biol 2022; 38:125-153. [PMID: 35850151 DOI: 10.1146/annurev-cellbio-120420-022914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport.
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Affiliation(s)
- Sabrina I Giacometti
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Kristen Dancel-Manning
- Office of Science and Research, New York University School of Medicine, New York, NY, USA;
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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46
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Zhang Y, Ge J, Bian X, Kumar A. Quantitative Models of Lipid Transfer and Membrane Contact Formation. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:1-21. [PMID: 36120532 DOI: 10.1177/25152564221096024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lipid transfer proteins (LTPs) transfer lipids between different organelles, and thus play key roles in lipid homeostasis and organelle dynamics. The lipid transfer often occurs at the membrane contact sites (MCS) where two membranes are held within 10-30 nm. While most LTPs act as a shuttle to transfer lipids, recent experiments reveal a new category of eukaryotic LTPs that may serve as a bridge to transport lipids in bulk at MCSs. However, the molecular mechanisms underlying lipid transfer and MCS formation are not well understood. Here, we first review two recent studies of extended synaptotagmin (E-Syt)-mediated membrane binding and lipid transfer using novel approaches. Then we describe mathematical models to quantify the kinetics of lipid transfer by shuttle LTPs based on a lipid exchange mechanism. We find that simple lipid mixing among membranes of similar composition and/or lipid partitioning among membranes of distinct composition can explain lipid transfer against a concentration gradient widely observed for LTPs. We predict that selective transport of lipids, but not membrane proteins, by bridge LTPs leads to osmotic membrane tension by analogy to the osmotic pressure across a semipermeable membrane. A gradient of such tension and the conventional membrane tension may drive bulk lipid flow through bridge LTPs at a speed consistent with the fast membrane expansion observed in vivo. Finally, we discuss the implications of membrane tension and lipid transfer in organelle biogenesis. Overall, the quantitative models may help clarify the mechanisms of LTP-mediated MCS formation and lipid transfer.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jinghua Ge
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Xin Bian
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA.,Present address: State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Avinash Kumar
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
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47
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Tan JX, Finkel T. A phosphoinositide signalling pathway mediates rapid lysosomal repair. Nature 2022; 609:815-821. [PMID: 36071159 PMCID: PMC9450835 DOI: 10.1038/s41586-022-05164-4] [Citation(s) in RCA: 116] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 07/29/2022] [Indexed: 12/23/2022]
Abstract
Lysosomal dysfunction has been increasingly linked to disease and normal ageing1,2. Lysosomal membrane permeabilization (LMP), a hallmark of lysosome-related diseases, can be triggered by diverse cellular stressors3. Given the damaging contents of lysosomes, LMP must be rapidly resolved, although the underlying mechanisms are poorly understood. Here, using an unbiased proteomic approach, we show that LMP stimulates a phosphoinositide-initiated membrane tethering and lipid transport (PITT) pathway for rapid lysosomal repair. Upon LMP, phosphatidylinositol-4 kinase type 2α (PI4K2A) accumulates rapidly on damaged lysosomes, generating high levels of the lipid messenger phosphatidylinositol-4-phosphate. Lysosomal phosphatidylinositol-4-phosphate in turn recruits multiple oxysterol-binding protein (OSBP)-related protein (ORP) family members, including ORP9, ORP10, ORP11 and OSBP, to orchestrate extensive new membrane contact sites between damaged lysosomes and the endoplasmic reticulum. The ORPs subsequently catalyse robust endoplasmic reticulum-to-lysosome transfer of phosphatidylserine and cholesterol to support rapid lysosomal repair. Finally, the lipid transfer protein ATG2 is also recruited to damaged lysosomes where its activity is potently stimulated by phosphatidylserine. Independent of macroautophagy, ATG2 mediates rapid membrane repair through direct lysosomal lipid transfer. Together, our findings identify that the PITT pathway maintains lysosomal membrane integrity, with important implications for numerous age-related diseases characterized by impaired lysosomal function.
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Affiliation(s)
- Jay Xiaojun Tan
- Aging Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Toren Finkel
- Aging Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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48
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Park JS, Hu Y, Hollingsworth NM, Miltenberger-Miltenyi G, Neiman AM. Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans. J Cell Sci 2022; 135:jcs260227. [PMID: 35950506 PMCID: PMC9482346 DOI: 10.1242/jcs.260227] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
VPS13 family proteins form conduits between the membranes of different organelles through which lipids are transferred. In humans, there are four VPS13 paralogs, and mutations in the genes encoding each of them are associated with different inherited disorders. VPS13 proteins contain multiple conserved domains. The Vps13 adaptor-binding (VAB) domain binds to adaptor proteins that recruit VPS13 to specific membrane contact sites. This work demonstrates the importance of a different domain in VPS13A function. The pleckstrin homology (PH) domain at the C-terminal region of VPS13A is required to form a complex with the XK scramblase and for the co-localization of VPS13A with XK within the cell. Alphafold modeling was used to predict an interaction surface between VPS13A and XK. Mutations in this region disrupt both complex formation and co-localization of the two proteins. Mutant VPS13A alleles found in patients with VPS13A disease truncate the PH domain. The phenotypic similarities between VPS13A disease and McLeod syndrome caused by mutations in VPS13A and XK, respectively, argue that loss of the VPS13A-XK complex is the basis of both diseases.
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Affiliation(s)
- Jae-Sook Park
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Yiying Hu
- Fish Core Unit, German Center for Neurodegenerative Diseases München (DZNE), 81377 Munich, Germany
- Munich Medical Research School (MMRS), 80336 Munich, Germany
| | - Nancy M. Hollingsworth
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | | | - Aaron M. Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane. Proc Natl Acad Sci U S A 2022; 119:e2205425119. [PMID: 35994651 PMCID: PMC9436381 DOI: 10.1073/pnas.2205425119] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chorea-acanthocytosis (ChAc) and McLeod syndrome are diseases with shared clinical manifestations caused by mutations in VPS13A and XK, respectively. Key features of these conditions are the degeneration of caudate neurons and the presence of abnormally shaped erythrocytes. XK belongs to a family of plasma membrane (PM) lipid scramblases whose action results in exposure of PtdSer at the cell surface. VPS13A is an endoplasmic reticulum (ER)-anchored lipid transfer protein with a putative role in the transport of lipids at contacts of the ER with other membranes. Recently VPS13A and XK were reported to interact by still unknown mechanisms. So far, however, there is no evidence for a colocalization of the two proteins at contacts of the ER with the PM, where XK resides, as VPS13A was shown to be localized at contacts between the ER and either mitochondria or lipid droplets. Here we show that VPS13A can also localize at ER-PM contacts via the binding of its PH domain to a cytosolic loop of XK, that such interaction is regulated by an intramolecular interaction within XK, and that both VPS13A and XK are highly expressed in the caudate neurons. Binding of the PH domain of VPS13A to XK is competitive with its binding to intracellular membranes that mediate other tethering functions of VPS13A. Our findings support a model according to which VPS13A-dependent lipid transfer between the ER and the PM is coupled to lipid scrambling within the PM. They raise the possibility that defective cell surface exposure of PtdSer may be responsible for neurodegeneration.
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Cai S, Wu Y, Guillén-Samander A, Hancock-Cerutti W, Liu J, De Camilli P. In situ architecture of the lipid transport protein VPS13C at ER-lysosome membrane contacts. Proc Natl Acad Sci U S A 2022; 119:e2203769119. [PMID: 35858323 PMCID: PMC9303930 DOI: 10.1073/pnas.2203769119] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023] Open
Abstract
VPS13 is a eukaryotic lipid transport protein localized at membrane contact sites. Previous studies suggested that it may transfer lipids between adjacent bilayers by a bridge-like mechanism. Direct evidence for this hypothesis from a full-length structure and from electron microscopy (EM) studies in situ is still missing, however. Here, we have capitalized on AlphaFold predictions to complement the structural information already available about VPS13 and to generate a full-length model of human VPS13C, the Parkinson's disease-linked VPS13 paralog localized at contacts between the endoplasmic reticulum (ER) and endo/lysosomes. Such a model predicts an ∼30-nm rod with a hydrophobic groove that extends throughout its length. We further investigated whether such a structure can be observed in situ at ER-endo/lysosome contacts. To this aim, we combined genetic approaches with cryo-focused ion beam (cryo-FIB) milling and cryo-electron tomography (cryo-ET) to examine HeLa cells overexpressing this protein (either full length or with an internal truncation) along with VAP, its anchoring binding partner at the ER. Using these methods, we identified rod-like densities that span the space separating the two adjacent membranes and that match the predicted structures of either full-length VPS13C or its shorter truncated mutant, thus providing in situ evidence for a bridge model of VPS13 in lipid transport.
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Affiliation(s)
- Shujun Cai
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- HHMI, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Yumei Wu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- HHMI, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Andrés Guillén-Samander
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- HHMI, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - William Hancock-Cerutti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- HHMI, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Jun Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- HHMI, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
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