1
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Ernst R, Renne MF, Jain A, von der Malsburg A. Endoplasmic Reticulum Membrane Homeostasis and the Unfolded Protein Response. Cold Spring Harb Perspect Biol 2024; 16:a041400. [PMID: 38253414 PMCID: PMC11293554 DOI: 10.1101/cshperspect.a041400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The endoplasmic reticulum (ER) is the key organelle for membrane biogenesis. Most lipids are synthesized in the ER, and most membrane proteins are first inserted into the ER membrane before they are transported to their target organelle. The composition and properties of the ER membrane must be carefully controlled to provide a suitable environment for the insertion and folding of membrane proteins. The unfolded protein response (UPR) is a powerful signaling pathway that balances protein and lipid production in the ER. Here, we summarize our current knowledge of how aberrant compositions of the ER membrane, referred to as lipid bilayer stress, trigger the UPR.
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Affiliation(s)
- Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Mike F Renne
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Aamna Jain
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
| | - Alexander von der Malsburg
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, 66421 Homburg, Germany
- Preclinical Center for Molecular Signaling (PZMS), Medical Faculty, Saarland University, 66421 Homburg, Germany
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2
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Castello-Serrano I, Heberle FA, Diaz-Rohrer B, Ippolito R, Shurer CR, Lujan P, Campelo F, Levental KR, Levental I. Partitioning to ordered membrane domains regulates the kinetics of secretory traffic. eLife 2024; 12:RP89306. [PMID: 38837189 PMCID: PMC11152573 DOI: 10.7554/elife.89306] [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] [Indexed: 06/06/2024] Open
Abstract
The organelles of eukaryotic cells maintain distinct protein and lipid compositions required for their specific functions. The mechanisms by which many of these components are sorted to their specific locations remain unknown. While some motifs mediating subcellular protein localization have been identified, many membrane proteins and most membrane lipids lack known sorting determinants. A putative mechanism for sorting of membrane components is based on membrane domains known as lipid rafts, which are laterally segregated nanoscopic assemblies of specific lipids and proteins. To assess the role of such domains in the secretory pathway, we applied a robust tool for synchronized secretory protein traffic (RUSH, Retention Using Selective Hooks) to protein constructs with defined affinity for raft phases. These constructs consist solely of single-pass transmembrane domains (TMDs) and, lacking other sorting determinants, constitute probes for membrane domain-mediated trafficking. We find that while raft affinity can be sufficient for steady-state PM localization, it is not sufficient for rapid exit from the endoplasmic reticulum (ER), which is instead mediated by a short cytosolic peptide motif. In contrast, we find that Golgi exit kinetics are highly dependent on raft affinity, with raft preferring probes exiting the Golgi ~2.5-fold faster than probes with minimal raft affinity. We rationalize these observations with a kinetic model of secretory trafficking, wherein Golgi export can be facilitated by protein association with raft domains. These observations support a role for raft-like membrane domains in the secretory pathway and establish an experimental paradigm for dissecting its underlying machinery.
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Affiliation(s)
- Ivan Castello-Serrano
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | | | | | - Rossana Ippolito
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Carolyn R Shurer
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States
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3
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Duan M, Plemel RL, Takenaka T, Lin A, Delgado BM, Nattermann U, Nickerson DP, Mima J, Miller EA, Merz AJ. SNARE chaperone Sly1 directly mediates close-range vesicle tethering. J Cell Biol 2024; 223:e202001032. [PMID: 38478018 PMCID: PMC10943277 DOI: 10.1083/jcb.202001032] [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: 01/16/2020] [Revised: 12/20/2023] [Accepted: 02/22/2024] [Indexed: 03/17/2024] Open
Abstract
The essential Golgi protein Sly1 is a member of the Sec1/mammalian Unc-18 (SM) family of SNARE chaperones. Sly1 was originally identified through remarkable gain-of-function alleles that bypass requirements for diverse vesicle tethering factors. Employing genetic analyses and chemically defined reconstitutions of ER-Golgi fusion, we discovered that a loop conserved among Sly1 family members is not only autoinhibitory but also acts as a positive effector. An amphipathic lipid packing sensor (ALPS)-like helix within the loop directly binds high-curvature membranes. Membrane binding is required for relief of Sly1 autoinhibition and also allows Sly1 to directly tether incoming vesicles to the Qa-SNARE on the target organelle. The SLY1-20 mutation bypasses requirements for diverse tethering factors but loses this ability if the tethering activity is impaired. We propose that long-range tethers, including Golgins and multisubunit tethering complexes, hand off vesicles to Sly1, which then tethers at close range to initiate trans-SNARE complex assembly and fusion in the early secretory pathway.
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Affiliation(s)
- Mengtong Duan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rachael L. Plemel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Ariel Lin
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Biology, California State University, San Bernardino, CA, USA
| | | | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Biophysics, Structure, and Design Graduate Program, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Joji Mima
- Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Alexey J. Merz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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4
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Feathers JR, Vignogna RC, Fromme JC. Structural basis for Rab6 activation by the Ric1-Rgp1 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592747. [PMID: 38766083 PMCID: PMC11100747 DOI: 10.1101/2024.05.06.592747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rab GTPases act as molecular switches to regulate organelle homeostasis and membrane trafficking. Rab6 plays a central role in regulating cargo flux through the Golgi and is activated via nucleotide exchange by the Ric1-Rgp1 protein complex. Ric1-Rgp1 is conserved throughout eukaryotes but the structural and mechanistic basis for its function has not been established. Here we report the cryoEM structure of a Ric1-Rgp1-Rab6 complex representing a key intermediate of the nucleotide exchange reaction. This structure reveals the overall architecture of the complex and enabled us to identify interactions critical for proper recognition and activation of Rab6 on the Golgi membrane surface. Ric1-Rgp1 interacts with the nucleotide-binding domain of Rab6 using an uncharacterized helical domain, which we establish as a novel RabGEF domain by identifying residues required for Rab6 nucleotide exchange. Unexpectedly, the complex uses an arrestin fold to interact with the Rab6 hypervariable domain, indicating that interactions with the unstructured C-terminal regions of Rab GTPases may be a common specificity mechanism used by their activators. Collectively, our findings provide a detailed mechanistic understanding of regulated Rab6 activation at the Golgi.
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Affiliation(s)
- J. Ryan Feathers
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
- Current address: 201 Schultz Laboratory, Princeton University, Princeton, NJ 08544 USA
| | - Ryan C. Vignogna
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
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5
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Moore WM, Brea RJ, Knittel C, Wrightsman E, Hui B, Lou J, Ancajas CF, Best MD, Devaraj NK, Budin I. Subcellular imaging of lipids and sugars using genetically encoded proximity sensors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592120. [PMID: 38746395 PMCID: PMC11092643 DOI: 10.1101/2024.05.01.592120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Live cell imaging of lipids and other metabolites is a long-standing challenge in cell biology. Bioorthogonal labeling tools allow for the conjugation of fluorophores to several phospholipid classes, but cannot discern their trafficking between adjacent organelles or asymmetry across individual membrane leaflets. Here we present fluorogen-activating coincidence sensing (FACES), a chemogenetic tool capable of quantitatively imaging subcellular lipid pools and reporting their transbilayer orientation in living cells. FACES combines bioorthogonal chemistry with genetically encoded fluorogen-activating proteins (FAPs) for reversible proximity sensing of conjugated molecules. We first validate this approach for quantifying discrete phosphatidylcholine pools in the ER and mitochondria that are trafficked by lipid transfer proteins. We then show that transmembrane domain-containing FAPs can be used to reveal the membrane asymmetry of multiple lipid classes that are generated in the trans-Golgi network. Lastly, we demonstrate that FACES is a generalizable tool for subcellular bioorthogonal imaging by measuring changes in mitochondrial N -acetylhexosamine levels. These results demonstrate the use of fluorogenic tags for spatially-defined molecular imaging.
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Panagiotou S, Tan KW, Nguyen PM, Müller A, Oqua AI, Tomas A, Wendt A, Eliasson L, Tengholm A, Solimena M, Idevall-Hagren O. OSBP-mediated PI(4)P-cholesterol exchange at endoplasmic reticulum-secretory granule contact sites controls insulin secretion. Cell Rep 2024; 43:113992. [PMID: 38536815 DOI: 10.1016/j.celrep.2024.113992] [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: 10/04/2023] [Revised: 02/07/2024] [Accepted: 03/07/2024] [Indexed: 04/28/2024] Open
Abstract
Insulin is packaged into secretory granules that depart the Golgi and undergo a maturation process that involves changes in the protein and lipid composition of the granules. Here, we show that insulin secretory granules form physical contacts with the endoplasmic reticulum and that the lipid exchange protein oxysterol-binding protein (OSBP) is recruited to these sites in a Ca2+-dependent manner. OSBP binding to insulin granules is positively regulated by phosphatidylinositol-4 (PI4)-kinases and negatively regulated by the PI4 phosphate (PI(4)P) phosphatase Sac2. Loss of Sac2 results in excess accumulation of cholesterol on insulin granules that is normalized when OSBP expression is reduced, and both acute inhibition and small interfering RNA (siRNA)-mediated knockdown of OSBP suppress glucose-stimulated insulin secretion without affecting insulin production or intracellular Ca2+ signaling. In conclusion, we show that lipid exchange at endoplasmic reticulum (ER)-granule contact sites is involved in the exocytic process and propose that these contacts act as reaction centers with multimodal functions during insulin granule maturation.
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Affiliation(s)
| | - Kia Wee Tan
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Phuoc My Nguyen
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Andreas Müller
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Affiong Ika Oqua
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Anna Wendt
- Department of Clinical Sciences, Lund University, Lund, Sweden; Lund University Diabetes Center (LUDC), Lund, Sweden
| | - Lena Eliasson
- Department of Clinical Sciences, Lund University, Lund, Sweden; Lund University Diabetes Center (LUDC), Lund, Sweden
| | - Anders Tengholm
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Michele Solimena
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany; Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
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7
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Fougère L, Mongrand S, Boutté Y. The function of sphingolipids in membrane trafficking and cell signaling in plants, in comparison with yeast and animal cells. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159463. [PMID: 38281556 DOI: 10.1016/j.bbalip.2024.159463] [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: 05/16/2023] [Revised: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Sphingolipids are essential membrane components involved in a wide range of cellular, developmental and signaling processes. Sphingolipids are so essential that knock-out mutation often leads to lethality. In recent years, conditional or weak allele mutants as well as the broadening of the pharmacological catalog allowed to decipher sphingolipid function more precisely in a less invasive way. This review intends to provide a discussion and point of view on the function of sphingolipids with a main focus on endomembrane trafficking, Golgi-mediated protein sorting, cell polarity, cell-to-cell communication and cell signaling at the plasma membrane. While our main angle is the plant field research, we will constantly refer to and compare with the advances made in the yeast and animal field. In this review, we will emphasize the role of sphingolipids not only as a membrane component, but also as a key player at a center of homeostatic regulatory networks involving direct or indirect interaction with other lipids, proteins and ion fluxes.
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Affiliation(s)
- Louise Fougère
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, UMR 5200 CNRS, Villenave d'Ornon, France
| | - Sebastien Mongrand
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, UMR 5200 CNRS, Villenave d'Ornon, France
| | - Yohann Boutté
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, UMR 5200 CNRS, Villenave d'Ornon, France.
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8
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Reinhard J, Starke L, Klose C, Haberkant P, Hammarén H, Stein F, Klein O, Berhorst C, Stumpf H, Sáenz JP, Hub J, Schuldiner M, Ernst R. MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress. EMBO J 2024; 43:1653-1685. [PMID: 38491296 PMCID: PMC11021466 DOI: 10.1038/s44318-024-00063-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
Biological membranes have a stunning ability to adapt their composition in response to physiological stress and metabolic challenges. Little is known how such perturbations affect individual organelles in eukaryotic cells. Pioneering work has provided insights into the subcellular distribution of lipids in the yeast Saccharomyces cerevisiae, but the composition of the endoplasmic reticulum (ER) membrane, which also crucially regulates lipid metabolism and the unfolded protein response, remains insufficiently characterized. Here, we describe a method for purifying organelle membranes from yeast, MemPrep. We demonstrate the purity of our ER membrane preparations by proteomics, and document the general utility of MemPrep by isolating vacuolar membranes. Quantitative lipidomics establishes the lipid composition of the ER and the vacuolar membrane. Our findings provide a baseline for studying membrane protein biogenesis and have important implications for understanding the role of lipids in regulating the unfolded protein response (UPR). The combined preparative and analytical MemPrep approach uncovers dynamic remodeling of ER membranes in stressed cells and establishes distinct molecular fingerprints of lipid bilayer stress.
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Affiliation(s)
- John Reinhard
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Leonhard Starke
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | | | - Per Haberkant
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | | | - Frank Stein
- EMBL Heidelberg, Proteomics Core Facility, Heidelberg, Germany
| | - Ofir Klein
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Charlotte Berhorst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - Heike Stumpf
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany
| | - James P Sáenz
- Technische Universität Dresden, B CUBE, Dresden, Germany
| | - Jochen Hub
- Saarland University, Theoretical Physics and Center for Biophysics, Saarbrücken, Germany
| | - Maya Schuldiner
- Weizmann Institute of Science, Department of Molecular Genetics, Rehovot, Israel
| | - Robert Ernst
- Saarland University, Medical Biochemistry and Molecular Biology, Homburg, Germany.
- Saarland University, Preclinical Center for Molecular Signaling (PZMS), Homburg, Germany.
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9
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Neukam M, Sala P, Brunner AD, Ganß K, Palladini A, Grzybek M, Topcheva O, Vasiljević J, Broichhagen J, Johnsson K, Kurth T, Mann M, Coskun Ü, Solimena M. Purification of time-resolved insulin granules reveals proteomic and lipidomic changes during granule aging. Cell Rep 2024; 43:113836. [PMID: 38421874 DOI: 10.1016/j.celrep.2024.113836] [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: 06/05/2023] [Revised: 12/29/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Endocrine cells employ regulated exocytosis of secretory granules to secrete hormones and neurotransmitters. Secretory granule exocytosis depends on spatiotemporal variables such as proximity to the plasma membrane and age, with newly generated granules being preferentially released. Despite recent advances, we lack a comprehensive view of the molecular composition of insulin granules and associated changes over their lifetime. Here, we report a strategy for the purification of insulin secretory granules of distinct age from insulinoma INS-1 cells. Tagging the granule-resident protein phogrin with a cleavable CLIP tag, we obtain intact fractions of age-distinct granules for proteomic and lipidomic analyses. We find that the lipid composition changes over time, along with the physical properties of the membrane, and that kinesin-1 heavy chain (KIF5b) as well as Ras-related protein 3a (RAB3a) associate preferentially with younger granules. Further, we identify the Rho GTPase-activating protein (ARHGAP1) as a cytosolic factor associated with insulin granules.
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Affiliation(s)
- Martin Neukam
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
| | - Pia Sala
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | | | - Katharina Ganß
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Alessandra Palladini
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Michal Grzybek
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Oleksandra Topcheva
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Jovana Vasiljević
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Johannes Broichhagen
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120 Heidelberg, Germany
| | - Thomas Kurth
- TU Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform, Electron Microscopy and Histology Facility, 01307 Dresden, Saxony, Germany
| | - Matthias Mann
- Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany; Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany.
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10
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Kang C, Fujioka K, Sun R. Atomistic Insight into the Lipid Nanodomains of Synaptic Vesicles. J Phys Chem B 2024; 128:2707-2716. [PMID: 38325816 DOI: 10.1021/acs.jpcb.3c07982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Membrane curvature, once regarded as a passive consequence of membrane composition and cellular architecture, has been shown to actively modulate various properties of the cellular membrane. These changes could also lead to segregation of the constituents of the membrane, generating nanodomains with precise biological properties. Proteins often linked with neurodegeneration (e.g., tau, alpha-synuclein) exhibit an unintuitive affinity for synaptic vesicles in neurons, which are reported to lack distinct, ordered nanodomains based on their composition. In this study, all-atom molecular dynamics simulations are used to study a full-scale synaptic vesicle of realistic Gaussian curvature and its effect on the membrane dynamics and lipid nanodomain organization. Compelling indicators of nanodomain formation, from the perspective of composition, surface areas per lipid, order parameter, and domain lifetime, are identified in the vesicle membrane, which are absent in a flat bilayer of the same lipid composition. Therefore, our study supports the idea that curvature may induce phase separation in an otherwise fluid, disordered membrane.
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Affiliation(s)
- Christopher Kang
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kazuumi Fujioka
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Rui Sun
- Department of Chemistry, The University of Hawai'i, Ma̅noa, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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11
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Ruturaj, Mishra M, Saha S, Maji S, Rodriguez-Boulan E, Schreiner R, Gupta A. Regulation of the apico-basolateral trafficking polarity of the homologous copper-ATPases ATP7A and ATP7B. J Cell Sci 2024; 137:jcs261258. [PMID: 38032054 PMCID: PMC10729821 DOI: 10.1242/jcs.261258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
The homologous P-type copper-ATPases (Cu-ATPases) ATP7A and ATP7B are the key regulators of copper homeostasis in mammalian cells. In polarized epithelia, upon copper treatment, ATP7A and ATP7B traffic from the trans-Golgi network (TGN) to basolateral and apical membranes, respectively. We characterized the sorting pathways of Cu-ATPases between TGN and the plasma membrane and identified the machinery involved. ATP7A and ATP7B reside on distinct domains of TGN in limiting copper conditions, and in high copper, ATP7A traffics to basolateral membrane, whereas ATP7B traverses common recycling, apical sorting and apical recycling endosomes en route to apical membrane. Mass spectrometry identified regulatory partners of ATP7A and ATP7B that include the adaptor protein-1 complex. Upon knocking out pan-AP-1, sorting of both Cu-ATPases is disrupted. ATP7A loses its trafficking polarity and localizes on both apical and basolateral surfaces in high copper. By contrast, ATP7B loses TGN retention but retained its trafficking polarity to the apical domain, which became copper independent. Using isoform-specific knockouts, we found that the AP-1A complex provides directionality and TGN retention for both Cu-ATPases, whereas the AP-1B complex governs copper-independent trafficking of ATP7B solely. Trafficking phenotypes of Wilson disease-causing ATP7B mutants that disrupts putative ATP7B-AP1 interaction further substantiates the role of AP-1 in apical sorting of ATP7B.
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Affiliation(s)
- Ruturaj
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Monalisa Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Soumyendu Saha
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Saptarshi Maji
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Enrique Rodriguez-Boulan
- Department of Ophthalmology, Margaret Dyson Vision Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Ryan Schreiner
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Arnab Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
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12
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Castello-Serrano I, Heberle FA, Diaz-Rohrer B, Ippolito R, Shurer CR, Lujan P, Campelo F, Levental KR, Levental I. Partitioning to ordered membrane domains regulates the kinetics of secretory traffic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.18.537395. [PMID: 37131599 PMCID: PMC10153169 DOI: 10.1101/2023.04.18.537395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The organelles of eukaryotic cells maintain distinct protein and lipid compositions required for their specific functions. The mechanisms by which many of these components are sorted to their specific locations remain unknown. While some motifs mediating subcellular protein localization have been identified, many membrane proteins and most membrane lipids lack known sorting determinants. A putative mechanism for sorting of membrane components is based on membrane domains known as lipid rafts, which are laterally segregated nanoscopic assemblies of specific lipids and proteins. To assess the role of such domains in the secretory pathway, we applied a robust tool for synchronized secretory protein traffic (RUSH, Retention Using Selective Hooks) to protein constructs with defined affinity for raft phases. These constructs consist solely of single-pass transmembrane domains (TMDs) and, lacking other sorting determinants, constitute probes for membrane domain-mediated trafficking. We find that while raft affinity can be sufficient for steady-state PM localization, it is not sufficient for rapid exit from the endoplasmic reticulum (ER), which is instead mediated by a short cytosolic peptide motif. In contrast, we find that Golgi exit kinetics are highly dependent on raft affinity, with raft preferring probes exiting Golgi ~2.5-fold faster than probes with minimal raft affinity. We rationalize these observations with a kinetic model of secretory trafficking, wherein Golgi export can be facilitated by protein association with raft domains. These observations support a role for raft-like membrane domains in the secretory pathway and establish an experimental paradigm for dissecting its underlying machinery.
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13
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Wang HY, Dey S, Levental KR. Applications of phase-separating multi-bilayers in protein-membrane domain interactions. Methods Enzymol 2024; 700:275-294. [PMID: 38971603 DOI: 10.1016/bs.mie.2024.04.024] [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] [Indexed: 07/08/2024]
Abstract
Synthetic model membranes are important tools to elucidate lipid domain and protein interactions due to predefined lipid compositions and characterizable biophysical properties. Here, we introduce a model membrane with multiple lipid bilayers (multi-bilayers) stacked on a mica substrate that is prepared through a spin-coating technique. The spin-coated multi-bilayers are useful in the study of phase separated membranes with a high cholesterol content, mobile lipids, microscopic and reversible phase separation, and easy conjugation with proteins, which make them a good model to study interactions between proteins and membrane domains.
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Affiliation(s)
- Hong-Yin Wang
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, United States
| | - Simli Dey
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Physics of Cells and Cancer, Paris, France
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, United States.
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14
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Kovács D, Gay AS, Debayle D, Abélanet S, Patel A, Mesmin B, Luton F, Antonny B. Lipid exchange at ER-trans-Golgi contact sites governs polarized cargo sorting. J Cell Biol 2024; 223:e202307051. [PMID: 37991810 PMCID: PMC10664280 DOI: 10.1083/jcb.202307051] [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: 07/11/2023] [Revised: 10/18/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
Oxysterol binding protein (OSBP) extracts cholesterol from the ER to deliver it to the TGN via counter exchange and subsequent hydrolysis of the phosphoinositide PI(4)P. Here, we show that this pathway is essential in polarized epithelial cells where it contributes not only to the proper subcellular distribution of cholesterol but also to the trans-Golgi sorting and trafficking of numerous plasma membrane cargo proteins with apical or basolateral localization. Reducing the expression of OSBP, blocking its activity, or inhibiting a PI4Kinase that fuels OSBP with PI(4)P abolishes the epithelial phenotype. Waves of cargo enrichment in the TGN in phase with OSBP and PI(4)P dynamics suggest that OSBP promotes the formation of lipid gradients along the TGN, which helps cargo sorting. During their transient passage through the trans-Golgi, polarized plasma membrane proteins get close to OSBP but fail to be sorted when OSBP is silenced. Thus, OSBP lipid exchange activity is decisive for polarized cargo sorting and distribution in epithelial cells.
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Affiliation(s)
- Dávid Kovács
- Université Côte d’Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Anne-Sophie Gay
- Université Côte d’Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Delphine Debayle
- Université Côte d’Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Sophie Abélanet
- Université Côte d’Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Amanda Patel
- Université Côte d’Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Bruno Mesmin
- Université Côte d’Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Frédéric Luton
- Université Côte d’Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Bruno Antonny
- Université Côte d’Azur and CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
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15
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Esch BM, Walter S, Schmidt O, Fröhlich F. Identification of distinct active pools of yeast serine palmitoyltransferase in sub-compartments of the ER. J Cell Sci 2023; 136:jcs261353. [PMID: 37982431 DOI: 10.1242/jcs.261353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
Sphingolipids (SPs) are one of the three major lipid classes in eukaryotic cells and serve as structural components of the plasma membrane. The rate-limiting step in SP biosynthesis is catalyzed by the serine palmitoyltransferase (SPT). In budding yeast (Saccharomyces cerevisiae), SPT is negatively regulated by the two proteins, Orm1 and Orm2. Regulating SPT activity enables cells to adapt SP metabolism to changing environmental conditions. Therefore, the Orm proteins are phosphorylated by two signaling pathways originating from either the plasma membrane or the lysosome (or vacuole in yeast). Moreover, uptake of exogenous serine is necessary for the regulation of SP biosynthesis, which suggests the existence of differentially regulated SPT pools based on their intracellular localization. However, measuring lipid metabolic enzyme activity in different cellular sub-compartments has been challenging. Combining a nanobody recruitment approach with SP flux analysis, we show that the nuclear endoplasmic reticulum (ER)-localized SPT and the peripheral ER localized SPT pools are differentially active. Thus, our data add another layer to the complex network of SPT regulation. Moreover, combining lipid metabolic enzyme re-localization with flux analysis serves as versatile tool to measure lipid metabolism with subcellular resolution.
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Affiliation(s)
- Bianca M Esch
- Osnabrück University, Department of Biology-Chemistry, Bioanalytical Chemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Stefan Walter
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria
| | - Florian Fröhlich
- Osnabrück University, Department of Biology-Chemistry, Bioanalytical Chemistry Section, Barbarastrasse 13, 49076 Osnabrück, Germany
- Osnabrück University, Center for Cellular Nanoanalytic Osnabrück (CellNanOs), Barbarastrasse 11, 49076 Osnabrück, Germany
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16
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Brownfield BA, Richardson BC, Halaby SL, Fromme JC. Sec7 regulatory domains scaffold autoinhibited and active conformations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568272. [PMID: 38045260 PMCID: PMC10690275 DOI: 10.1101/2023.11.22.568272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The late stages of Golgi maturation involve a series of sequential trafficking events in which cargo-laden vesicles are produced and targeted to multiple distinct subcellular destinations. Each of these vesicle biogenesis events requires activation of an Arf GTPase by the Sec7/BIG guanine nucleotide exchange factor (GEF). Sec7 localization and activity is regulated by autoinhibition, positive feedback, and interaction with other GTPases. Although these mechanisms have been characterized biochemically, we lack a clear picture of how GEF localization and activity is modulated by these signals. Here we report the cryoEM structure of full-length Sec7 in its autoinhibited form, revealing the architecture of its multiple regulatory domains. We use functional experiments to determine the basis for autoinhibition and use structural predictions to produce a model for an active conformation of the GEF that is supported empirically. This study therefore elucidates the conformational transition that Sec7 undergoes to become active on the organelle membrane surface.
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Affiliation(s)
- Bryce A. Brownfield
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - Brian C. Richardson
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
- Current address: The Hormel Institute, University of Minnesota, Austin MN 55912
| | - Steve L. Halaby
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
- Current address: Abbvie Inc., Irvine, CA 92612
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
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17
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Manzer KM, Fromme JC. The Arf-GAP Age2 localizes to the late-Golgi via a conserved amphipathic helix. Mol Biol Cell 2023; 34:ar119. [PMID: 37672345 PMCID: PMC10846627 DOI: 10.1091/mbc.e23-07-0283] [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: 07/24/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023] Open
Abstract
Arf GTPases are central regulators of the Golgi complex, which serves as the nexus of membrane-trafficking pathways in eukaryotic cells. Arf proteins recruit dozens of effectors to modify membranes, sort cargos, and create and tether transport vesicles, and are therefore essential for orchestrating Golgi trafficking. The regulation of Arf activity is controlled by the action of Arf-GEFs which activate via nucleotide exchange, and Arf-GAPs which inactivate via nucleotide hydrolysis. The localization dynamics of Arf GTPases and their Arf-GAPs during Golgi maturation have not been reported. Here we use the budding yeast model to examine the temporal localization of the Golgi Arf-GAPs. We also determine the mechanisms used by the Arf-GAP Age2 to localize to the Golgi. We find that the catalytic activity of Age2 and a conserved sequence in the unstructured C-terminal domain of Age2 are both required for Golgi localization. This sequence is predicted to form an amphipathic helix and mediates direct binding of Age2 to membranes in vitro. We also report the development of a probe for sensing active Arf1 in living cells and use this probe to characterize the temporal dynamics of Arf1 during Golgi maturation.
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Affiliation(s)
- Kaitlyn M. Manzer
- Department of Molecular Biology & Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850
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18
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Schäfer JH, Körner C, Esch BM, Limar S, Parey K, Walter S, Januliene D, Moeller A, Fröhlich F. Structure of the ceramide-bound SPOTS complex. Nat Commun 2023; 14:6196. [PMID: 37794019 PMCID: PMC10550967 DOI: 10.1038/s41467-023-41747-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023] Open
Abstract
Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. Its activity is tightly regulated through multiple binding partners, including Tsc3, Orm proteins, ceramides, and the phosphatidylinositol-4-phosphate (PI4P) phosphatase Sac1. The structural organization and regulatory mechanisms of this complex are not yet understood. Here, we report the high-resolution cryo-EM structures of the yeast SPT in complex with Tsc3 and Orm1 (SPOT) as dimers and monomers and a monomeric complex further carrying Sac1 (SPOTS). In all complexes, the tight interaction of the downstream metabolite ceramide and Orm1 reveals the ceramide-dependent inhibition. Additionally, observation of ceramide and ergosterol binding suggests a co-regulation of sphingolipid biogenesis and sterol metabolism within the SPOTS complex.
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Affiliation(s)
- Jan-Hannes Schäfer
- Osnabrück University Department of Biology/Chemistry Structural Biology section, 49076, Osnabrück, Germany
| | - Carolin Körner
- Osnabrück University Department of Biology/Chemistry Bioanalytical Chemistry section, 49076, Osnabrück, Germany
| | - Bianca M Esch
- Osnabrück University Department of Biology/Chemistry Bioanalytical Chemistry section, 49076, Osnabrück, Germany
| | - Sergej Limar
- Osnabrück University Department of Biology/Chemistry Bioanalytical Chemistry section, 49076, Osnabrück, Germany
| | - Kristian Parey
- Osnabrück University Department of Biology/Chemistry Structural Biology section, 49076, Osnabrück, Germany
- Osnabrück University Center of Cellular Nanoanalytic Osnabrück (CellNanOs), 49076, Osnabrück, Germany
| | - Stefan Walter
- Osnabrück University Center of Cellular Nanoanalytic Osnabrück (CellNanOs), 49076, Osnabrück, Germany
| | - Dovile Januliene
- Osnabrück University Department of Biology/Chemistry Structural Biology section, 49076, Osnabrück, Germany.
- Osnabrück University Center of Cellular Nanoanalytic Osnabrück (CellNanOs), 49076, Osnabrück, Germany.
| | - Arne Moeller
- Osnabrück University Department of Biology/Chemistry Structural Biology section, 49076, Osnabrück, Germany.
- Osnabrück University Center of Cellular Nanoanalytic Osnabrück (CellNanOs), 49076, Osnabrück, Germany.
| | - Florian Fröhlich
- Osnabrück University Department of Biology/Chemistry Bioanalytical Chemistry section, 49076, Osnabrück, Germany.
- Osnabrück University Center of Cellular Nanoanalytic Osnabrück (CellNanOs), 49076, Osnabrück, Germany.
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19
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Fuggetta N, Rigolli N, Magdeleine M, Seminara A, Drin G. Reconstitution of ORP-mediated lipid exchange process coupled to PI(4)P metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.551917. [PMID: 37577629 PMCID: PMC10418177 DOI: 10.1101/2023.08.04.551917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Lipid distribution in the eukaryotic cells depends on tight couplings between lipid transfer and lipid metabolism. Yet these couplings remain poorly described. Notably, it is unclear to what extent lipid exchangers of the OSBP-related proteins (ORPs) family, coupled to PI(4)P metabolism, contribute to the formation of sterol and phosphatidylserine gradient between the endoplasmic reticulum (ER) and other cell regions. To address this question, we have examined in vitro the activity of Osh4p, a representative ORP, between Golgi mimetic membranes in which PI(4)P is produced by a PI 4-kinase and ER mimetic membranes in which PI(4)P is hydrolyzed by the phosphatase Sac1p. Using quantitative, real-time assays, we demonstrate that Osh4p creates a sterol gradient between the two membranes by sterol/PI(4)P exchange as soon as a PI(4)P gradient is generated at this interface following ATP addition, and define how much PI(4)P must be synthesized for this process. Then, using a kinetic model supported by our in vitro data, we estimate to what extent PI(4)P metabolism can drive lipid transfer in cells. Finally, we show that Sec14p, by transferring phosphatidylinositol between membranes, can support the synthesis of PI(4)P and the creation of a sterol gradient by Osh4p. These results indicate to what extent ORPs, under the control of PI(4)P metabolism, can distribute lipids in the cell.
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Affiliation(s)
- Nicolas Fuggetta
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Nicola Rigolli
- Laboratoire de Physique, École Normale Supérieure (LPENS), 75005 Paris, France
| | - Maud Magdeleine
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
| | - Agnese Seminara
- Malga, Department of Civil, Chemical and Environmental Engineering, University of Genoa, Villa Cambiaso 1, 16145 Genoa, Italy
| | - Guillaume Drin
- Université Côte d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France
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20
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Manzer KM, Fromme JC. The Arf-GAP Age2 localizes to the late-Golgi via a conserved amphipathic helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550229. [PMID: 37546741 PMCID: PMC10402032 DOI: 10.1101/2023.07.23.550229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Arf GTPases are central regulators of the Golgi complex, which serves as the nexus of membrane trafficking pathways in eukaryotic cells. Arf proteins recruit dozens of effectors to modify membranes, sort cargos, and create and tether transport vesicles, and are therefore essential for orchestrating Golgi trafficking. The regulation of Arf activity is controlled by the action of Arf-GEFs, which activate via nucleotide exchange, and Arf-GAPs, which inactivate via nucleotide hydrolysis. The localization dynamics of Arf GTPases and their Arf-GAPs during Golgi maturation have not been reported. Here we use the budding yeast model to examine the temporal localization of the Golgi Arf-GAPs. We also determine the mechanisms used by the Arf-GAP Age2 to localize to the Golgi. We find that the catalytic activity of Age2 and a conserved sequence in the unstructured C-terminal domain of Age2 are both required for Golgi localization. This sequence is predicted to form an amphipathic helix and mediates direct binding of Age2 to membranes in vitro . We also report the development of a probe for sensing active Arf1 in living cells and use this probe to characterize the temporal dynamics of Arf1 during Golgi maturation.
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Affiliation(s)
- Kaitlyn M Manzer
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - J Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
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21
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Aguilera-Romero A, Lucena R, Sabido-Bozo S, Muñiz M. Impact of sphingolipids on protein membrane trafficking. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159334. [PMID: 37201864 DOI: 10.1016/j.bbalip.2023.159334] [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: 02/21/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Membrane trafficking is essential to maintain the spatiotemporal control of protein and lipid distribution within membrane systems of eukaryotic cells. To achieve their functional destination proteins are sorted and transported into lipid carriers that construct the secretory and endocytic pathways. It is an emerging theme that lipid diversity might exist in part to ensure the homeostasis of these pathways. Sphingolipids, a chemical diverse type of lipids with special physicochemical characteristics have been implicated in the selective transport of proteins. In this review, we will discuss current knowledge about how sphingolipids modulate protein trafficking through the endomembrane systems to guarantee that proteins reach their functional destination and the proposed underlying mechanisms.
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Affiliation(s)
- Auxiliadora Aguilera-Romero
- Department of Cell Biology, University of Seville, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain.
| | - Rafael Lucena
- Department of Cell Biology, University of Seville, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain
| | - Susana Sabido-Bozo
- Department of Cell Biology, University of Seville, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain
| | - Manuel Muñiz
- Department of Cell Biology, University of Seville, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Spain.
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22
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Limar S, Körner C, Martínez-Montañés F, Stancheva VG, Wolf VN, Walter S, Miller EA, Ejsing CS, Galassi VV, Fröhlich F. Yeast Svf1 binds ceramides and contributes to sphingolipid metabolism at the ER cis-Golgi interface. J Cell Biol 2023; 222:e202109162. [PMID: 36897280 PMCID: PMC10038888 DOI: 10.1083/jcb.202109162] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/21/2022] [Accepted: 02/03/2023] [Indexed: 03/11/2023] Open
Abstract
Ceramides are essential precursors of complex sphingolipids and act as potent signaling molecules. Ceramides are synthesized in the endoplasmic reticulum (ER) and receive their head-groups in the Golgi apparatus, yielding complex sphingolipids (SPs). Transport of ceramides between the ER and the Golgi is executed by the essential ceramide transport protein (CERT) in mammalian cells. However, yeast cells lack a CERT homolog, and the mechanism of ER to Golgi ceramide transport remains largely elusive. Here, we identified a role for yeast Svf1 in ceramide transport between the ER and the Golgi. Svf1 is dynamically targeted to membranes via an N-terminal amphipathic helix (AH). Svf1 binds ceramide via a hydrophobic binding pocket that is located in between two lipocalin domains. We showed that Svf1 membrane-targeting is important to maintain flux of ceramides into complex SPs. Together, our results show that Svf1 is a ceramide binding protein that contributes to sphingolipid metabolism at Golgi compartments.
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Affiliation(s)
- Sergej Limar
- Department of Biology/Chemistry Bioanalytical Chemistry Section, Osnabrück University, Osnabrück, Germany
| | - Carolin Körner
- Department of Biology/Chemistry Bioanalytical Chemistry Section, Osnabrück University, Osnabrück, Germany
| | - Fernando Martínez-Montañés
- Department of Biochemistry and Molecular Biology Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | | | - Verena N. Wolf
- Department of Biology/Chemistry Bioanalytical Chemistry Section, Osnabrück University, Osnabrück, Germany
| | - Stefan Walter
- Osnabrück University Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück, Germany
| | | | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vanesa Viviana Galassi
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
- Instituto Interdisciplinario de Ciencias Básicas (ICB), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
| | - Florian Fröhlich
- Department of Biology/Chemistry Bioanalytical Chemistry Section, Osnabrück University, Osnabrück, Germany
- Osnabrück University Center of Cellular Nanoanalytic Osnabrück (CellNanOs), Osnabrück, Germany
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23
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Abstract
The formation of membrane vesicles is a common feature in all eukaryotes. Lipid rafts are the best-studied example of membrane domains for both eukaryotes and prokaryotes, and their existence also is suggested in Archaea membranes. Lipid rafts are involved in the formation of transport vesicles, endocytic vesicles, exocytic vesicles, synaptic vesicles and extracellular vesicles, as well as enveloped viruses. Two mechanisms of how rafts are involved in vesicle formation have been proposed: first, that raft proteins and/or lipids located in lipid rafts associate with coat proteins that form a budding vesicle, and second, vesicle budding is triggered by enzymatic generation of cone-shaped ceramides and inverted cone-shaped lyso-phospholipids. In both cases, induction of curvature is also facilitated by the relaxation of tension in the raft domain. In this Review, we discuss the role of raft-derived vesicles in several intracellular trafficking pathways. We also highlight their role in different pathways of endocytosis, and in the formation of intraluminal vesicles (ILVs) through budding inwards from the multivesicular body (MVB) membrane, because rafts inside MVB membranes are likely to be involved in loading RNA into ILVs. Finally, we discuss the association of glycoproteins with rafts via the glycocalyx.
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Affiliation(s)
- Karolina Sapoń
- Institute of Biology, University of Opole, Kominka 6, 45-032 Opole, Poland
| | - Rafał Mańka
- Institute of Biology, University of Opole, Kominka 6, 45-032 Opole, Poland
| | - Teresa Janas
- Institute of Biology, University of Opole, Kominka 6, 45-032 Opole, Poland
| | - Tadeusz Janas
- Institute of Biology, University of Opole, Kominka 6, 45-032 Opole, Poland
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24
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Reinhard J, Leveille CL, Cornell CE, Merz AJ, Klose C, Ernst R, Keller SL. Remodeling of yeast vacuole membrane lipidomes from the log (one phase) to stationary stage (two phases). Biophys J 2023; 122:1043-1057. [PMID: 36635960 PMCID: PMC10111276 DOI: 10.1016/j.bpj.2023.01.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/03/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Upon nutrient limitation, budding yeast of Saccharomyces cerevisiae shift from fast growth (the log stage) to quiescence (the stationary stage). This shift is accompanied by liquid-liquid phase separation in the membrane of the vacuole, an endosomal organelle. Recent work indicates that the resulting micrometer-scale domains in vacuole membranes enable yeast to survive periods of stress. An outstanding question is which molecular changes might cause this membrane phase separation. Here, we conduct lipidomics of vacuole membranes in both the log and stationary stages. Isolation of pure vacuole membranes is challenging in the stationary stage, when lipid droplets are in close contact with vacuoles. Immuno-isolation has previously been shown to successfully purify log-stage vacuole membranes with high organelle specificity, but it was not previously possible to immuno-isolate stationary-stage vacuole membranes. Here, we develop Mam3 as a bait protein for vacuole immuno-isolation, and demonstrate low contamination by non-vacuolar membranes. We find that stationary-stage vacuole membranes contain surprisingly high fractions of phosphatidylcholine lipids (∼40%), roughly twice as much as log-stage membranes. Moreover, in the stationary stage, these lipids have higher melting temperatures, due to longer and more saturated acyl chains. Another surprise is that no significant change in sterol content is observed. These lipidomic changes, which are largely reflected on the whole-cell level, fit within the predominant view that phase separation in membranes requires at least three types of molecules to be present: lipids with high melting temperatures, lipids with low melting temperatures, and sterols.
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Affiliation(s)
- John Reinhard
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany; PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany
| | | | | | - Alexey J Merz
- Department of Biochemistry, University of Washington, Seattle, WA
| | | | - Robert Ernst
- Medical Biochemistry and Molecular Biology, Medical Faculty, Saarland University, Homburg, Germany; PZMS, Center for Molecular Signaling, Medical Faculty, Saarland University, Homburg, Germany.
| | - Sarah L Keller
- Department of Chemistry, University of Washington, Seattle, WA.
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25
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Fang R, Jiang Q, Jia X, Jiang Z. ARMH3-mediated recruitment of PI4KB directs Golgi-to-endosome trafficking and activation of the antiviral effector STING. Immunity 2023; 56:500-515.e6. [PMID: 36921576 DOI: 10.1016/j.immuni.2023.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/30/2022] [Accepted: 01/26/2023] [Indexed: 03/15/2023]
Abstract
The cGAS-STING pathway mediates cytoplasmic DNA-triggered innate immunity. STING activation is initiated by cyclic-GMP-AMP (cGAMP)-induced translocation from the endoplasmic reticulum and sulfated glycosaminoglycans-induced polymerization at the Golgi. Here, we examine the mechanisms underlying STING transport and activation beyond the Golgi. A genome-wide CRISPR-Cas9 screen identified Armadillo-like helical domain-containing protein 3 (ARMH3) as critical for STING activation. Upon cGAMP-triggered translocation, ARMH3 interacted with STING at the Golgi and recruited phosphatidylinositol 4-kinase beta (PI4KB) to synthesize PI4P, which directed STING Golgi-to-endosome trafficking via PI4P-binding proteins AP-1 and GGA2. Disrupting PI4P-dependent lipid transport through RNAi of other PI4P-binding proteins impaired STING activation. Consistently, disturbed lipid composition inhibited STING activation, whereas aberrantly elevated cellular PI4P led to cGAS-independent STING activation. Armh3fl/fllLyzCre/Cre mice were susceptible to DNA virus challenge in vivo. Thus, ARMH3 bridges STING and PIK4B to generate PI4P for STING transportation and activation, an interaction conserved in all eukaryotes.
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Affiliation(s)
- Run Fang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Qifei Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xinying Jia
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhengfan Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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26
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Diaz-Rohrer B, Castello-Serrano I, Chan SH, Wang HY, Shurer CR, Levental KR, Levental I. Rab3 mediates a pathway for endocytic sorting and plasma membrane recycling of ordered microdomains. Proc Natl Acad Sci U S A 2023; 120:e2207461120. [PMID: 36848577 PMCID: PMC10013782 DOI: 10.1073/pnas.2207461120] [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: 04/30/2022] [Accepted: 01/31/2023] [Indexed: 03/01/2023] Open
Abstract
The composition of the plasma membrane (PM) must be tightly controlled despite constant, rapid endocytosis, which requires active, selective recycling of endocytosed membrane components. For many proteins, the mechanisms, pathways, and determinants of this PM recycling remain unknown. We report that association with ordered, lipid-driven membrane microdomains (known as rafts) is sufficient for PM localization of a subset of transmembrane proteins and that abrogation of raft association disrupts their trafficking and leads to degradation in lysosomes. Using orthogonal, genetically encoded probes with tunable raft partitioning, we screened for the trafficking machinery required for efficient recycling of engineered microdomain-associated cargo from endosomes to the PM. Using this screen, we identified the Rab3 family as an important mediator of PM localization of microdomain-associated proteins. Disruption of Rab3 reduced PM localization of raft probes and led to their accumulation in Rab7-positive endosomes, suggesting inefficient recycling. Abrogation of Rab3 function also mislocalized the endogenous raft-associated protein Linker for Activation of T cells (LAT), leading to its intracellular accumulation and reduced T cell activation. These findings reveal a key role for lipid-driven microdomains in endocytic traffic and suggest Rab3 as a mediator of microdomain recycling and PM composition.
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Affiliation(s)
- Barbara Diaz-Rohrer
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA22904
| | - Ivan Castello-Serrano
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA22904
| | - Sze Ham Chan
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA22904
| | - Hong-Yin Wang
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA22904
| | - Carolyn R. Shurer
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA22904
| | - Kandice R. Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA22904
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA22904
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27
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Vos M, Klein C, Hicks AA. Role of Ceramides and Sphingolipids in Parkinson's Disease. J Mol Biol 2023:168000. [PMID: 36764358 DOI: 10.1016/j.jmb.2023.168000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/24/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Sphingolipids, including the basic ceramide, are a subset of bioactive lipids that consist of many different species. Sphingolipids are indispensable for proper neuronal function, and an increasing number of studies have emerged on the complexity and importance of these lipids in (almost) all biological processes. These include regulation of mitochondrial function, autophagy, and endosomal trafficking, which are affected in Parkinson's disease (PD). PD is the second most common neurodegenerative disorder and is characterized by the loss of dopaminergic neurons. Currently, PD cannot be cured due to the lack of knowledge of the exact pathogenesis. Nonetheless, important advances have identified molecular changes in mitochondrial function, autophagy, and endosomal function. Furthermore, recent studies have identified ceramide alterations in patients suffering from PD, and in PD models, suggesting a critical interaction between sphingolipids and related cellular processes in PD. For instance, autosomal recessive forms of PD cause mitochondrial dysfunction, including energy production or mitochondrial clearance, that is directly influenced by manipulating sphingolipids. Additionally, endo-lysosomal recycling is affected by genes that cause autosomal dominant forms of the disease, such as VPS35 and SNCA. Furthermore, endo-lysosomal recycling is crucial for transporting sphingolipids to different cellular compartments where they will execute their functions. This review will discuss mitochondrial dysfunction, defects in autophagy, and abnormal endosomal activity in PD and the role sphingolipids play in these vital molecular processes.
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Affiliation(s)
- Melissa Vos
- Institute of Neurogenetics, University of Luebeck, 23562 Luebeck, Germany.
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, 23562 Luebeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine (affiliated to the University of Luebeck, Luebeck, Germany), Eurac Research, 39100 Bolzano, Italy. https://twitter.com/andrewhicks
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28
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Kumar A, Sarkar P, Chattopadhyay A. Metabolic depletion of sphingolipids inhibits agonist-induced endocytosis of the serotonin 1A receptor. Traffic 2023; 24:95-107. [PMID: 36533718 DOI: 10.1111/tra.12879] [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: 05/11/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 12/23/2022]
Abstract
G protein-coupled receptors (GPCRs) are vital cellular signaling machinery and currently represent ~40% drug targets. Endocytosis of GPCRs is an important process that allows stringent spatiotemporal control over receptor population on the cell surface. Although the role of proteins in GPCR endocytosis is well addressed, the contribution of membrane lipids in this process is rather unexplored. Sphingolipids are essential functional lipids in higher eukaryotes and are implicated in several neurological functions. To understand the role of sphingolipids in GPCR endocytosis, we subjected cells expressing human serotonin1A receptors (an important neurotransmitter GPCR involved in cognitive and behavioral functions) to metabolic sphingolipid depletion using fumonisin B1 , an inhibitor of sphingolipid biosynthetic pathway. Our results, using flow cytometric analysis and confocal microscopic imaging, show that sphingolipid depletion inhibits agonist-induced endocytosis of the serotonin1A receptor in a concentration-dependent manner, which was restored when sphingolipid levels were replenished. We further show that there was no change in the internalization of transferrin, a marker for clathrin-mediated endocytosis, under sphingolipid-depleted condition, highlighting the specific requirement of sphingolipids for endocytosis of serotonin1A receptors. Our results reveal the regulatory role of sphingolipids in GPCR endocytosis and highlight the importance of neurotransmitter receptor trafficking in health and disease.
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Affiliation(s)
- Abhishek Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India
| | - Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Amitabha Chattopadhyay
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
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29
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Highland CM, Thomas LL, Fromme JC. Methods for Studying Membrane-Proximal GAP Activity on Prenylated Rab GTPase Substrates. Methods Mol Biol 2023; 2557:507-518. [PMID: 36512233 PMCID: PMC9851423 DOI: 10.1007/978-1-0716-2639-9_29] [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] [Indexed: 12/15/2022]
Abstract
Rab GTPases are key regulators of membrane trafficking. When GTP-bound, or "active," Rabs are anchored to membranes and recruit effector proteins that mediate vesicle formation, transport, and fusion. Rabs are inactivated by GTPase-activating proteins (Rab-GAPs), which catalyze GTP hydrolysis, rendering Rabs cytosolic. In vivo, C-terminal prenylation modifications link activated Rabs to organelle and vesicle membranes, yet historically, in vitro Rab-GAP activity assays have been performed in the absence of membranes. We have developed a method for assaying Rab-GAP activity in a physiological context, with dissociation of the Rab from the membrane serving as a readout for Rab-GAP activity. Given that membrane-binding status is a key consequence of Rab activation state, this assay will be useful for the study of a wide range of Rab/Rab-GAP pairs.
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Affiliation(s)
- Carolyn M Highland
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Laura L Thomas
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
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30
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Creating and sensing asymmetric lipid distributions throughout the cell. Emerg Top Life Sci 2022; 7:7-19. [PMID: 36373850 DOI: 10.1042/etls20220028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022]
Abstract
A key feature of eukaryotic cells is the asymmetric distribution of lipids along their secretory pathway. Because of the biological significance of these asymmetries, it is crucial to define the mechanisms which create them. Extensive studies have led to the identification of lipid transfer proteins (LTPs) that work with lipid-synthesizing enzymes to carry lipids between two distinct membranes in a directional manner, and are thus able to create asymmetries in lipid distribution throughout the cell. These networks are often in contact sites where two organelle membranes are in close proximity for reasons we have only recently started to understand. A question is whether these networks transfer lipids en masse within the cells or adjust the lipid composition of organelle membranes. Finally, recent data have confirmed that some networks organized around LTPs do not generate lipid asymmetries between membranes but sense them and rectify the lipid content of the cell.
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31
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Feng MW, Delneri D, Millar CB, O'Keefe RT. Eisosome disruption by noncoding RNA deletion increases protein secretion in yeast. PNAS NEXUS 2022; 1:pgac241. [PMID: 36712349 PMCID: PMC9802208 DOI: 10.1093/pnasnexus/pgac241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Noncoding RNAs (ncRNAs) regulate many aspects of gene expression. We investigated how ncRNAs affected protein secretion in yeast by large-scale screening for improved endogenous invertase secretion in ncRNA deletion strains with deletion of stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs), tRNAs, or snRNAs. We identified three candidate ncRNAs, SUT418, SUT390, and SUT125, that improved endogenous invertase secretion when deleted. As SUTs can affect expression of nearby genes, we quantified adjacent gene transcription and found that the PIL1 gene was down-regulated in the SUT125 deletion strain. Pil1 is a core component of eisosomes, nonmobile invaginations found throughout the plasma membrane. PIL1 knockout alone, or in combination with eisosome components LSP1 or SUR7, resulted in further increased secretion of invertase. Secretion of heterologous GFP was also increased upon PIL1 deletion, but this increase was signal sequence dependent. To reveal the potential for increased biopharmaceutical production, secretion of monoclonal antibody Pexelizumab scFv peptide was increased by PIL1 deletion. Global analysis of secreted proteins revealed that approximately 20% of secreted proteins, especially serine-enriched secreted proteins, including invertase, were increased upon eisosome disruption. Eisosomes are enriched with APC transporters and sphingolipids, which are essential components for secretory vesicle formation and protein sorting. Sphingolipid and serine biosynthesis pathways were up-regulated upon PIL1 deletion. We propose that increased secretion of endogenous and heterologous proteins upon PIL1 deletion resulted from sphingolipid redistribution in the plasma membrane and up-regulated sphingolipid biosynthesis. Overall, a new pathway to improve protein secretion in yeast via eisosome disruption has been identified.
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Affiliation(s)
- Matthew Wenjie Feng
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Daniela Delneri
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK,Manchester Institute of Biotechnology, Faculty of Biology Medicine and Health, The University of Manchester, 131 Princess street, Manchester, M1 7DN, UK
| | - Catherine B Millar
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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32
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Uemura S, Moriguchi T. Pleiotropic roles of N-glycans for enzyme activities and stabilities of MIPC synthases, Csh1 and Sur1/Csg1, in Saccharomyces cerevisiae. Glycobiology 2022; 32:778-790. [PMID: 35713525 DOI: 10.1093/glycob/cwac035] [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: 02/03/2022] [Revised: 05/12/2022] [Accepted: 05/26/2022] [Indexed: 11/15/2022] Open
Abstract
Mannosyl phosphorylceramide (MIPC) is a membrane lipid classified as a complex sphingolipid in Saccharomyces cerevisiae. MIPC is synthesized by two redundant enzymes, Sur1/Csg1 and Csh1, in the Golgi lumen. MIPC consists of five subtypes (A, B', B, C, and D-type) according to the position and number of hydroxyl groups on the ceramide moiety. Sur1 exerts higher impact on synthesis of MIPC-B and MIPC-C than Csh1. In this study, we elucidated the roles played by N-glycans attached to Sur1 and Csh1, and dissected the mechanisms underlying substrate recognition by these two enzymes. Sur1 carries an N-glycan on Asn-224, while Csh1 has N-glycans on Asn-51 and Asn-247. Although intracellular proteins usually harbor core-type N-glycans, the N-glycan on Asn-51 of Csh1 exhibited a unique mannan-like structure containing a long backbone of mannose. Sur1 N224Q and Csh1 N51Q mutants exhibited a decrease in the activity to synthesize specific MIPC subtypes for each enzyme, suggesting that these N-glycans play a role in substrate recognition through their catalytic domains. Moreover, ectopic insertion of an N-glycosylation consensus sequence (NST) at codon 51 of Sur1 (Sur1-NST51) resulted in an artificial modification with mannan, which markedly decreased protein stability. Our results suggest that the diminished stability of the Sur1-NST51 mutant protein could be attributable to potential structural alterations by the mannan. Collectively, the present study reveals essential luminal domains of Sur1 and Csh1 that dictate substrate specificity and/or the protein stabilities via mannan modification.
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Affiliation(s)
- Satoshi Uemura
- Division of Medical Biochemistry, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi 983-8536, Japan
| | - Takashi Moriguchi
- Division of Medical Biochemistry, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1, Fukumuro, Miyagino-ku, Sendai, Miyagi 983-8536, Japan
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33
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Thomas FB, Omnus DJ, Bader JM, Chung GH, Kono N, Stefan CJ. Tricalbin proteins regulate plasma membrane phospholipid homeostasis. Life Sci Alliance 2022; 5:5/8/e202201430. [PMID: 35440494 PMCID: PMC9018018 DOI: 10.26508/lsa.202201430] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 12/26/2022] Open
Abstract
The evolutionarily conserved extended synaptotagmin (E-Syt) proteins are calcium-activated lipid transfer proteins that function at contacts between the ER and plasma membrane (ER-PM contacts). However, roles of the E-Syt family members in PM lipid organisation remain incomplete. Among the E-Syt family, the yeast tricalbin (Tcb) proteins are essential for PM integrity upon heat stress, but it is not known how they contribute to PM maintenance. Using quantitative lipidomics and microscopy, we find that the Tcb proteins regulate phosphatidylserine homeostasis at the PM. Moreover, upon heat-induced membrane stress, Tcb3 co-localises with the PM protein Sfk1 that is implicated in PM phospholipid asymmetry and integrity. The Tcb proteins also control the PM targeting of the known phosphatidylserine effector Pkc1 upon heat-induced stress. Phosphatidylserine has evolutionarily conserved roles in PM organisation, integrity, and repair. We propose that phospholipid regulation is an ancient essential function of E-Syt family members required for PM integrity.
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Affiliation(s)
- Ffion B Thomas
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Deike J Omnus
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Jakob M Bader
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Gary Hc Chung
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Nozomu Kono
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Christopher J Stefan
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
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34
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Rohli KE, Boyer CK, Blom SE, Stephens SB. Nutrient Regulation of Pancreatic Islet β-Cell Secretory Capacity and Insulin Production. Biomolecules 2022; 12:335. [PMID: 35204835 PMCID: PMC8869698 DOI: 10.3390/biom12020335] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 01/27/2023] Open
Abstract
Pancreatic islet β-cells exhibit tremendous plasticity for secretory adaptations that coordinate insulin production and release with nutritional demands. This essential feature of the β-cell can allow for compensatory changes that increase secretory output to overcome insulin resistance early in Type 2 diabetes (T2D). Nutrient-stimulated increases in proinsulin biosynthesis may initiate this β-cell adaptive compensation; however, the molecular regulators of secretory expansion that accommodate the increased biosynthetic burden of packaging and producing additional insulin granules, such as enhanced ER and Golgi functions, remain poorly defined. As these adaptive mechanisms fail and T2D progresses, the β-cell succumbs to metabolic defects resulting in alterations to glucose metabolism and a decline in nutrient-regulated secretory functions, including impaired proinsulin processing and a deficit in mature insulin-containing secretory granules. In this review, we will discuss how the adaptative plasticity of the pancreatic islet β-cell's secretory program allows insulin production to be carefully matched with nutrient availability and peripheral cues for insulin signaling. Furthermore, we will highlight potential defects in the secretory pathway that limit or delay insulin granule biosynthesis, which may contribute to the decline in β-cell function during the pathogenesis of T2D.
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Affiliation(s)
- Kristen E. Rohli
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; (K.E.R.); (C.K.B.); (S.E.B.)
- Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Cierra K. Boyer
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; (K.E.R.); (C.K.B.); (S.E.B.)
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Sandra E. Blom
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; (K.E.R.); (C.K.B.); (S.E.B.)
- Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Samuel B. Stephens
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, USA; (K.E.R.); (C.K.B.); (S.E.B.)
- Division of Endocrinology and Metabolism, Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
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35
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Levic DS, Bagnat M. Self-organization of apical membrane protein sorting in epithelial cells. FEBS J 2022; 289:659-670. [PMID: 33864720 PMCID: PMC8522177 DOI: 10.1111/febs.15882] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/25/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023]
Abstract
Polarized epithelial cells are characterized by the asymmetric distribution of proteins between apical and basolateral domains of the plasma membrane. This asymmetry is highly conserved and is fundamental to epithelial cell physiology, development, and homeostasis. How proteins are segregated for apical or basolateral delivery, a process known as sorting, has been the subject of considerable investigation for decades. Despite these efforts, the rules guiding apical sorting are poorly understood and remain controversial. Here, we consider mechanisms of apical membrane protein sorting and argue that they are largely driven by self-organization and biophysical principles. The preponderance of data to date is consistent with the idea that apical sorting is not ruled by a dedicated protein-based sorting machinery and relies instead on the concerted effects of oligomerization, phase separation of lipids and proteins in membranes, and pH-dependent glycan interactions.
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Affiliation(s)
- Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC 27710, USA,Correspondence to Michel Bagnat: or Dan Levic:
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC 27710, USA,Correspondence to Michel Bagnat: or Dan Levic:
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36
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Körner C, Fröhlich F. Compartmentation and functions of sphingolipids. Curr Opin Cell Biol 2022; 74:104-111. [DOI: 10.1016/j.ceb.2022.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/08/2023]
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37
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Robinson BP, Hawbaker S, Chiang A, Jordahl EM, Anaokar S, Nikiforov A, Bowman RW, Ziegler P, McAtee CK, Patton-Vogt J, O'Donnell AF. Alpha-arrestins Aly1/Art6 and Aly2/Art3 regulate trafficking of the glycerophosphoinositol transporter Git1 and impact phospholipid homeostasis. Biol Cell 2021; 114:3-31. [PMID: 34562280 DOI: 10.1111/boc.202100007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/23/2021] [Accepted: 07/15/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND INFORMATION Phosphatidylinositol (PI) is an essential phospholipid, critical to membrane bilayers. The complete deacylation of PI by B-type phospholipases produces intracellular and extracellular glycerophosphoinositol (GPI). Extracellular GPI is transported into the cell via Git1, a member of the Major Facilitator Superfamily of transporters at the yeast plasma membrane. Internalized GPI is degraded to produce inositol, phosphate and glycerol, thereby contributing to these pools. GIT1 gene expression is controlled by nutrient balance, with phosphate or inositol starvation increasing GIT1 expression to stimulate GPI uptake. However, less is known about control of Git1 protein levels or localization. RESULTS We find that the α-arrestins, an important class of protein trafficking adaptor, regulate Git1 localization and this is dependent upon their interaction with the ubiquitin ligase Rsp5. Specifically, α-arrestin Aly2 stimulates Git1 trafficking to the vacuole under basal conditions, but in response to GPI-treatment, either Aly1 or Aly2 promote Git1 vacuole trafficking. Cell surface retention of Git1, as occurs in aly1∆ aly2∆ cells, is linked to impaired growth in the presence of exogenous GPI and results in increased uptake of radiolabeled GPI, suggesting that accumulation of GPI somehow causes cellular toxicity. Regulation of α-arrestin Aly1 by the protein phosphatase calcineurin improves steady-state and substrate-induced trafficking of Git1, however, calcineurin plays a larger role in Git1 trafficking beyond regulation of α-arrestins. Interestingly, loss of Aly1 and Aly2 increased phosphatidylinositol-3-phosphate on the limiting membrane of the vacuole, and this was further exacerbated by GPI addition, suggesting that the effect is partially linked to Git1. Loss of Aly1 and Aly2 leads to increased incorporation of inositol label from [3 H]-inositol-labelled GPI into PI, confirming that internalized GPI influences PI balance and indicating a role for the a-arrestins in this regulation. CONCLUSIONS The α-arrestins Aly1 and Aly2 are novel regulators of Git1 trafficking with previously unanticipated roles in controlling phospholipid distribution and balance. SIGNIFICANCE To our knowledge, this is the first example of α-arrestin regulation of phosphatidyliniositol-3-phosphate levels. In future studies it will be exciting to determine if other α-arrestins similarly alter PI and PIPs to change the cellular landscape.
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Affiliation(s)
- Benjamin P Robinson
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Sarah Hawbaker
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Annette Chiang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Eric M Jordahl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sanket Anaokar
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Alexiy Nikiforov
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Ray W Bowman
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Philip Ziegler
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Ceara K McAtee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jana Patton-Vogt
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Allyson F O'Donnell
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA.,Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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38
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Lujan P, Campelo F. Should I stay or should I go? Golgi membrane spatial organization for protein sorting and retention. Arch Biochem Biophys 2021; 707:108921. [PMID: 34038703 DOI: 10.1016/j.abb.2021.108921] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/12/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
The Golgi complex is the membrane-bound organelle that lies at the center of the secretory pathway. Its main functions are to maintain cellular lipid homeostasis, to orchestrate protein processing and maturation, and to mediate protein sorting and export. These functions are not independent of one another, and they all require that the membranes of the Golgi complex have a well-defined biochemical composition. Importantly, a finely-regulated spatiotemporal organization of the Golgi membrane components is essential for the correct performance of the organelle. In here, we review our current mechanistic and molecular understanding of how Golgi membranes are spatially organized in the lateral and axial directions to fulfill their functions. In particular, we highlight the current evidence and proposed models of intra-Golgi transport, as well as the known mechanisms for the retention of Golgi residents and for the sorting and export of transmembrane cargo proteins. Despite the controversies, conflicting evidence, clashes between models, and technical limitations, the field has moved forward and we have gained extensive knowledge in this fascinating topic. However, there are still many important questions that remain to be completely answered. We hope that this review will help boost future investigations on these issues.
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Affiliation(s)
- Pablo Lujan
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860, Barcelona, Spain.
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39
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Metabolic Depletion of Sphingolipids Does Not Alter Cell Cycle Progression in Chinese Hamster Ovary Cells. J Membr Biol 2021; 255:1-12. [PMID: 34392379 DOI: 10.1007/s00232-021-00198-7] [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: 07/06/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
The cell cycle is a sequential multi-step process essential for growth and proliferation of cells comprising multicellular organisms. Although a number of proteins are known to modulate the cell cycle, the role of lipids in regulation of cell cycle is still emerging. In our previous work, we monitored the role of cholesterol in cell cycle progression in CHO-K1 cells. Since sphingolipids enjoy a functionally synergistic relationship with membrane cholesterol, in this work, we explored whether sphingolipids could modulate the eukaryotic cell cycle using CHO-K1 cells. Sphingolipids are essential components of eukaryotic cell membranes and are involved in a number of important cellular functions. To comprehensively monitor the role of sphingolipids on cell cycle progression, we carried out metabolic depletion of sphingolipids in CHO-K1 cells using inhibitors (fumonisin B1, myriocin, and PDMP) that block specific steps of the sphingolipid biosynthetic pathway and examined their effect on individual cell cycle phases. Our results show that metabolic inhibitors led to significant reduction in specific sphingolipids, yet such inhibition in sphingolipid biosynthesis did not show any effect on cell cycle progression in CHO-K1 cells. We speculate that any role of sphingolipids on cell cycle progression could be context and cell-type dependent, and cancer cells could be a better choice for monitoring such regulation, since sphingolipids are differentially modulated in these cells.
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40
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Germanos M, Gao A, Taper M, Yau B, Kebede MA. Inside the Insulin Secretory Granule. Metabolites 2021; 11:metabo11080515. [PMID: 34436456 PMCID: PMC8401130 DOI: 10.3390/metabo11080515] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/19/2022] Open
Abstract
The pancreatic β-cell is purpose-built for the production and secretion of insulin, the only hormone that can remove glucose from the bloodstream. Insulin is kept inside miniature membrane-bound storage compartments known as secretory granules (SGs), and these specialized organelles can readily fuse with the plasma membrane upon cellular stimulation to release insulin. Insulin is synthesized in the endoplasmic reticulum (ER) as a biologically inactive precursor, proinsulin, along with several other proteins that will also become members of the insulin SG. Their coordinated synthesis enables synchronized transit through the ER and Golgi apparatus for congregation at the trans-Golgi network, the initiating site of SG biogenesis. Here, proinsulin and its constituents enter the SG where conditions are optimized for proinsulin processing into insulin and subsequent insulin storage. A healthy β-cell is continually generating SGs to supply insulin in vast excess to what is secreted. Conversely, in type 2 diabetes (T2D), the inability of failing β-cells to secrete may be due to the limited biosynthesis of new insulin. Factors that drive the formation and maturation of SGs and thus the production of insulin are therefore critical for systemic glucose control. Here, we detail the formative hours of the insulin SG from the luminal perspective. We do this by mapping the journey of individual members of the SG as they contribute to its genesis.
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41
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Encinar Del Dedo J, Fernández-Golbano IM, Pastor L, Meler P, Ferrer-Orta C, Rebollo E, Geli MI. Coupled sterol synthesis and transport machineries at ER-endocytic contact sites. J Cell Biol 2021; 220:212484. [PMID: 34283201 PMCID: PMC8294947 DOI: 10.1083/jcb.202010016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 05/27/2021] [Accepted: 06/29/2021] [Indexed: 12/17/2022] Open
Abstract
Sterols are unevenly distributed within cellular membranes. How their biosynthetic and transport machineries are organized to generate heterogeneity is largely unknown. We previously showed that the yeast sterol transporter Osh2 is recruited to endoplasmic reticulum (ER)–endocytic contacts to facilitate actin polymerization. We now find that a subset of sterol biosynthetic enzymes also localizes at these contacts and interacts with Osh2 and the endocytic machinery. Following the sterol dynamics, we show that Osh2 extracts sterols from these subdomains, which we name ERSESs (ER sterol exit sites). Further, we demonstrate that coupling of the sterol synthesis and transport machineries is required for endocytosis in mother cells, but not in daughters, where plasma membrane loading with accessible sterols and endocytosis are linked to secretion.
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Affiliation(s)
| | | | - Laura Pastor
- Institute for Molecular Biology of Barcelona, Spanish Research Council, Barcelona, Spain
| | - Paula Meler
- Institute for Molecular Biology of Barcelona, Spanish Research Council, Barcelona, Spain
| | - Cristina Ferrer-Orta
- Institute for Molecular Biology of Barcelona, Spanish Research Council, Barcelona, Spain
| | - Elena Rebollo
- Institute for Molecular Biology of Barcelona, Spanish Research Council, Barcelona, Spain
| | - Maria Isabel Geli
- Institute for Molecular Biology of Barcelona, Spanish Research Council, Barcelona, Spain
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42
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Ito Y, Esnay N, Platre MP, Wattelet-Boyer V, Noack LC, Fougère L, Menzel W, Claverol S, Fouillen L, Moreau P, Jaillais Y, Boutté Y. Sphingolipids mediate polar sorting of PIN2 through phosphoinositide consumption at the trans-Golgi network. Nat Commun 2021; 12:4267. [PMID: 34257291 PMCID: PMC8277843 DOI: 10.1038/s41467-021-24548-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/23/2021] [Indexed: 01/09/2023] Open
Abstract
The lipid composition of organelles acts as a landmark to define membrane identity and specify subcellular function. Phosphoinositides are anionic lipids acting in protein sorting and trafficking at the trans-Golgi network (TGN). In animal cells, sphingolipids control the turnover of phosphoinositides through lipid exchange mechanisms at endoplasmic reticulum/TGN contact sites. In this study, we discover a mechanism for how sphingolipids mediate phosphoinositide homeostasis at the TGN in plant cells. Using multiple approaches, we show that a reduction of the acyl-chain length of sphingolipids results in an increased level of phosphatidylinositol-4-phosphate (PtdIns(4)P or PI4P) at the TGN but not of other lipids usually coupled to PI4P during exchange mechanisms. We show that sphingolipids mediate Phospholipase C (PLC)-driven consumption of PI4P at the TGN rather than local PI4P synthesis and that this mechanism is involved in the polar sorting of the auxin efflux carrier PIN2 at the TGN. Together, our data identify a mode of action of sphingolipids in lipid interplay at the TGN during protein sorting. Lipid composition impacts the function of cellular membranes. Here the authors show that a reduction in sphingolipid acyl-chain length promotes phosphoinositide consumption by phospholipase C at the Arabidopsis trans-Golgi network which in turn regulates sorting of the auxin efflux carrier PIN2.
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Affiliation(s)
- Yoko Ito
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, Villenave d'Ornon, France
| | - Nicolas Esnay
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, Villenave d'Ornon, France.,BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon1, CNRS, INRAE, Lyon, France.,Plant Molecular and Cellular Biology Laboratory and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Lise C Noack
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon1, CNRS, INRAE, Lyon, France
| | - Louise Fougère
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, Villenave d'Ornon, France
| | - Wilhelm Menzel
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, Villenave d'Ornon, France.,Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | | | - Laetitia Fouillen
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, Villenave d'Ornon, France.,MetaboHub-Bordeaux Metabolome INRAE, Villenave d'Ornon, France
| | - Patrick Moreau
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, Villenave d'Ornon, France.,Bordeaux Imaging Centre, Plant Imaging Platform, UMS 3420 University of Bordeaux-CNRS, INRAE, Villenave-d'Ornon Cedex, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon1, CNRS, INRAE, Lyon, France
| | - Yohann Boutté
- Laboratoire de Biogenèse Membranaire, Univ. Bordeaux, Villenave d'Ornon, France.
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43
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The PKD-Dependent Biogenesis of TGN-to-Plasma Membrane Transport Carriers. Cells 2021; 10:cells10071618. [PMID: 34203456 PMCID: PMC8303525 DOI: 10.3390/cells10071618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/14/2021] [Accepted: 06/24/2021] [Indexed: 01/30/2023] Open
Abstract
Membrane trafficking is essential for processing and transport of proteins and lipids and to establish cell compartmentation and tissue organization. Cells respond to their needs and control the quantity and quality of protein secretion accordingly. In this review, we focus on a particular membrane trafficking route from the trans-Golgi network (TGN) to the cell surface: protein kinase D (PKD)-dependent pathway for constitutive secretion mediated by carriers of the TGN to the cell surface (CARTS). Recent findings highlight the importance of lipid signaling by organelle membrane contact sites (MCSs) in this pathway. Finally, we discuss our current understanding of multiple signaling pathways for membrane trafficking regulation mediated by PKD, G protein-coupled receptors (GPCRs), growth factors, metabolites, and mechanosensors.
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44
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Guo X, Zhang J, Li X, Xiao E, Lange JD, Rienstra CM, Burke MD, Mitchell DA. Sterol Sponge Mechanism Is Conserved for Glycosylated Polyene Macrolides. ACS CENTRAL SCIENCE 2021; 7:781-791. [PMID: 34079896 PMCID: PMC8161476 DOI: 10.1021/acscentsci.1c00148] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 05/07/2023]
Abstract
Amphotericin-like glycosylated polyene macrolides (GPMs) are a clinically and industrially important family of natural products, but the mechanisms by which they exert their extraordinary biological activities have remained unclear for more than half a century. Amphotericin B exerts fungicidal action primarily via self-assembly into an extramembranous sponge that rapidly extracts ergosterol from fungal membranes, but it has remained unclear whether this mechanism is applicable to other GPMs. Using a highly conserved polyene-hemiketal region of GPMs that we hypothesized to represent a conserved ergosterol-binding domain, we bioinformatically mapped the entirety of the GPM sequence-function space and expanded the number of GPM biosynthetic gene clusters (BGCs) by 10-fold. We further leveraged bioinformatic predictions and tetrazine-based reactivity screening targeting the electron-rich polyene region of GPMs to discover a first-in-class methyltetraene- and diepoxide-containing GPM, kineosporicin, and to assign BGCs to many new producers of previously reported members. Leveraging a range of structurally diverse known and newly discovered GPMs, we found that the sterol sponge mechanism of fungicidal action is conserved.
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Affiliation(s)
- Xiaorui Guo
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jiabao Zhang
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
| | - Xinyi Li
- Department
of Biochemistry, Roger Adams Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Emily Xiao
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Justin D. Lange
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
| | - Chad M. Rienstra
- Department
of Biochemistry and National Magnetic Resonance Facility at Madison, DeLuca Biochemistry Laboratories, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Martin D. Burke
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
- Department
of Biochemistry, Roger Adams Laboratory, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801 United States
| | - Douglas A. Mitchell
- Department
of Chemistry, Roger Adams Laboratory, University
of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Avenue, Urbana, Illinois 61801, United States
- Department
of Microbiology, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
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45
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Wakana Y, Hayashi K, Nemoto T, Watanabe C, Taoka M, Angulo-Capel J, Garcia-Parajo MF, Kumata H, Umemura T, Inoue H, Arasaki K, Campelo F, Tagaya M. The ER cholesterol sensor SCAP promotes CARTS biogenesis at ER-Golgi membrane contact sites. J Cell Biol 2021; 220:211521. [PMID: 33156328 PMCID: PMC7654440 DOI: 10.1083/jcb.202002150] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 09/15/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
In response to cholesterol deprivation, SCAP escorts SREBP transcription factors from the endoplasmic reticulum to the Golgi complex for their proteolytic activation, leading to gene expression for cholesterol synthesis and uptake. Here, we show that in cholesterol-fed cells, ER-localized SCAP interacts through Sac1 phosphatidylinositol 4-phosphate (PI4P) phosphatase with a VAP-OSBP complex, which mediates counter-transport of ER cholesterol and Golgi PI4P at ER-Golgi membrane contact sites (MCSs). SCAP knockdown inhibited the turnover of PI4P, perhaps due to a cholesterol transport defect, and altered the subcellular distribution of the VAP-OSBP complex. As in the case of perturbation of lipid transfer complexes at ER-Golgi MCSs, SCAP knockdown inhibited the biogenesis of the trans-Golgi network-derived transport carriers CARTS, which was reversed by expression of wild-type SCAP or a Golgi transport-defective mutant, but not of cholesterol sensing-defective mutants. Altogether, our findings reveal a new role for SCAP under cholesterol-fed conditions in the facilitation of CARTS biogenesis via ER-Golgi MCSs, depending on the ER cholesterol.
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Affiliation(s)
- Yuichi Wakana
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kaito Hayashi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Takumi Nemoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Chiaki Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Masato Taoka
- Faculty of Science, Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Jessica Angulo-Capel
- Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria F Garcia-Parajo
- Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Hidetoshi Kumata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Tomonari Umemura
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Hiroki Inoue
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Felix Campelo
- Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mitsuo Tagaya
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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46
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Highland CM, Fromme JC. Arf1 directly recruits the Pik1-Frq1 PI4K complex to regulate the final stages of Golgi maturation. Mol Biol Cell 2021; 32:1064-1080. [PMID: 33788598 PMCID: PMC8101487 DOI: 10.1091/mbc.e21-02-0069] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
Proper Golgi complex function depends on the activity of Arf1, a GTPase whose effectors assemble and transport outgoing vesicles. Phosphatidylinositol 4-phosphate (PI4P) generated at the Golgi by the conserved PI 4-kinase Pik1 (PI4KIIIβ) is also essential for Golgi function, although its precise roles in vesicle formation are less clear. Arf1 has been reported to regulate PI4P production, but whether Pik1 is a direct Arf1 effector is not established. Using a combination of live-cell time-lapse imaging analyses, acute PI4P depletion experiments, and in vitro protein-protein interaction assays on Golgi-mimetic membranes, we present evidence for a model in which Arf1 initiates the final stages of Golgi maturation by tightly controlling PI4P production through direct recruitment of the Pik1-Frq1 PI4-kinase complex. This PI4P serves as a critical signal for AP-1 and secretory vesicle formation, the final events at maturing Golgi compartments. This work therefore establishes the regulatory and temporal context surrounding Golgi PI4P production and its precise roles in Golgi maturation.
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Affiliation(s)
- Carolyn M. Highland
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - J. Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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47
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Kumar A, Sarkar P, Chattopadhyay A. Metabolic Depletion of Sphingolipids Reduces Cell Surface Population of the Human Serotonin 1A Receptor due to Impaired Trafficking. ACS Chem Neurosci 2021; 12:1189-1196. [PMID: 33760584 DOI: 10.1021/acschemneuro.1c00017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Sphingolipids and their metabolites are increasingly implicated in the pathogenesis of many metabolic and neurological diseases. It has been postulated that sphingolipids coalesce with cholesterol to form laterally segregated lipid domains that are involved in protein sorting and trafficking. In this work, we have explored the effect of metabolic depletion of sphingolipids on cell surface expression of the human serotonin1A receptor, a neurotransmitter G protein-coupled receptor. We used fumonisin B1 (FB1), a fungal mycotoxin, to inhibit sphingolipid biosynthesis in HEK-293 cells stably expressing the human serotonin1A receptor. Our results obtained using flow cytometric analysis and confocal microscopic imaging show that the cell surface population of the serotonin1A receptor is reduced under sphingolipid-depleted condition. Western blot analysis confirmed that there was no significant difference in total cellular level of the serotonin1A receptor upon depletion of sphingolipids. Interestingly, the effect of FB1 on serotonin1A receptor population was reversed upon replenishment with sphingolipids. These results indicate that sphingolipid depletion does not alter total cellular receptor levels, but impairs serotonin1A receptor trafficking to the cellular plasma membrane. These results could provide mechanistic insights into the role of sphingolipids in modulation of neurotransmitter receptor signaling and trafficking in health and disease.
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Affiliation(s)
- Abhishek Kumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
- Amity Institute of Biotechnology, Amity University Haryana, Amity Education Valley, Gurugram 122 413, India
| | - Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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48
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Thomas LL, Highland CM, Fromme JC. Arf1 orchestrates Rab GTPase conversion at the trans-Golgi network. Mol Biol Cell 2021; 32:1104-1120. [PMID: 33788577 PMCID: PMC8351538 DOI: 10.1091/mbc.e20-10-0664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Rab family GTPases are key organizers of membrane trafficking and function as markers of organelle identity. Accordingly, Rab GTPases often occupy specific membrane domains, and mechanisms exist to prevent the inappropriate mixing of distinct Rab domains. The yeast Golgi complex can be divided into two broad Rab domains: Ypt1 (Rab1) and Ypt6 (Rab6) are present at the early/medial Golgi and sharply transition to Ypt31/32 (Rab11) at the late Golgi/trans-Golgi network (TGN). This Rab conversion has been attributed to GTPase-activating protein (GAP) cascades in which Ypt31/32 recruits the Rab-GAPs Gyp1 and Gyp6 to inactivate Ypt1 and Ypt6, respectively. Here we report that Rab transition at the TGN involves additional layers of regulation. We provide new evidence confirming the TRAPPII complex as an important regulator of Ypt6 inactivation and uncover an unexpected role of the Arf1 GTPase in recruiting Gyp1 to drive Ypt1 inactivation at the TGN. Given its established role in directly recruiting TRAPPII to the TGN, Arf1 is therefore a master regulator of Rab conversion on maturing Golgi compartments.
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Affiliation(s)
- Laura L Thomas
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Carolyn M Highland
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Symons JL, Cho KJ, Chang JT, Du G, Waxham MN, Hancock JF, Levental I, Levental KR. Lipidomic atlas of mammalian cell membranes reveals hierarchical variation induced by culture conditions, subcellular membranes, and cell lineages. SOFT MATTER 2021; 17:288-297. [PMID: 32451522 PMCID: PMC7688498 DOI: 10.1039/d0sm00404a] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Lipid membranes are ubiquitous biological organizers, required for structural and functional compartmentalization of the cell and sub-cellular organelles. Membranes in living cells are compositionally complex, comprising hundreds of dynamically regulated, distinct lipid species. Cellular physiology requires tight regulation of these lipidomic profiles to achieve proper membrane functionality. While some general features of tissue- and organelle-specific lipid complements have been identified, less is known about detailed lipidomic variations caused by cell-intrinsic or extrinsic factors. Here, we use shotgun lipidomics to report detailed, comprehensive lipidomes of a variety of cultured and primary mammalian membrane preparations to identify trends and sources of variation. Unbiased principle component analysis (PCA) shows clear separation between cultured and primary cells, with primary erythrocytes, synaptic membranes, and other mammalian tissue lipidomes sharply diverging from all cultured cell lines and also from one other. Most broadly, cultured cell membrane preparations were distinguished by their paucity of polyunsaturated lipids. Cultured mammalian cell lines were comparatively similar to one another, although we detected clear, highly reproducible lipidomic signatures of individual cell lines and plasma membrane (PM) isolations thereof. These measurements begin to establish a comprehensive lipidomic atlas of mammalian cells and tissues, identifying some major sources of variation. These observations will allow investigation of the regulation and functional significance of mammalian lipidomes in various contexts.
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Affiliation(s)
- Jessica L Symons
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Suite 4.202, 6431 Fannin St, Houston, TX 77030, USA.
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Suite 4.202, 6431 Fannin St, Houston, TX 77030, USA.
| | - Guangwei Du
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Suite 4.202, 6431 Fannin St, Houston, TX 77030, USA.
| | - M Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Suite 4.202, 6431 Fannin St, Houston, TX 77030, USA.
| | - Ilya Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Suite 4.202, 6431 Fannin St, Houston, TX 77030, USA.
| | - Kandice R Levental
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Suite 4.202, 6431 Fannin St, Houston, TX 77030, USA.
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50
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Levic DS, Ryan S, Marjoram L, Honeycutt J, Bagwell J, Bagnat M. Distinct roles for luminal acidification in apical protein sorting and trafficking in zebrafish. J Cell Biol 2020; 219:133852. [PMID: 32328632 PMCID: PMC7147097 DOI: 10.1083/jcb.201908225] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/20/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023] Open
Abstract
Epithelial cell physiology critically depends on the asymmetric distribution of channels and transporters. However, the mechanisms targeting membrane proteins to the apical surface are still poorly understood. Here, we performed a visual forward genetic screen in the zebrafish intestine and identified mutants with defective apical targeting of membrane proteins. One of these mutants, affecting the vacuolar H+-ATPase gene atp6ap1b, revealed specific requirements for luminal acidification in apical, but not basolateral, membrane protein sorting and transport. Using a low temperature block assay combined with genetic and pharmacologic perturbation of luminal pH, we monitored transport of newly synthesized membrane proteins from the TGN to apical membrane in live zebrafish. We show that vacuolar H+-ATPase activity regulates sorting of O-glycosylated proteins at the TGN, as well as Rab8-dependent post-Golgi trafficking of different classes of apical membrane proteins. Thus, luminal acidification plays distinct and specific roles in apical membrane biogenesis.
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Affiliation(s)
| | - Sean Ryan
- Department of Cell Biology, Duke University, Durham, NC
| | | | | | | | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC
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