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Gubas A, Attridge E, Jefferies HB, Nishimura T, Razi M, Kunzelmann S, Gilad Y, Mercer TJ, Wilson MM, Kimchi A, Tooze SA. WIPI2b recruitment to phagophores and ATG16L1 binding are regulated by ULK1 phosphorylation. EMBO Rep 2024; 25:3789-3811. [PMID: 39152217 PMCID: PMC11387628 DOI: 10.1038/s44319-024-00215-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/21/2024] [Accepted: 07/04/2024] [Indexed: 08/19/2024] Open
Abstract
One of the key events in autophagy is the formation of a double-membrane phagophore, and many regulatory mechanisms underpinning this remain under investigation. WIPI2b is among the first proteins to be recruited to the phagophore and is essential for stimulating autophagy flux by recruiting the ATG12-ATG5-ATG16L1 complex, driving LC3 and GABARAP lipidation. Here, we set out to investigate how WIPI2b function is regulated by phosphorylation. We studied two phosphorylation sites on WIPI2b, S68 and S284. Phosphorylation at these sites plays distinct roles, regulating WIPI2b's association with ATG16L1 and the phagophore, respectively. We confirm WIPI2b is a novel ULK1 substrate, validated by the detection of endogenous phosphorylation at S284. Notably, S284 is situated within an 18-amino acid stretch, which, when in contact with liposomes, forms an amphipathic helix. Phosphorylation at S284 disrupts the formation of the amphipathic helix, hindering the association of WIPI2b with membranes and autophagosome formation. Understanding these intricacies in the regulatory mechanisms governing WIPI2b's association with its interacting partners and membranes, holds the potential to shed light on these complex processes, integral to phagophore biogenesis.
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Affiliation(s)
- Andrea Gubas
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Muscular Dystrophy UK, London, SE1 8QD, UK
| | - Eleanor Attridge
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Harold Bj Jefferies
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Taki Nishimura
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
- PRESTO, Japan Science and Technology Agency, Chiyoda-ku, Tokyo, Japan
| | - Minoo Razi
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Yuval Gilad
- The Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Adi Kimchi
- The Weizmann Institute of Science, Rehovot, Israel
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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2
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Welch LG, Muschalik N, Munro S. The FAM114A proteins are adaptors for the recycling of Golgi enzymes. J Cell Sci 2024; 137:jcs262160. [PMID: 39129673 PMCID: PMC11441981 DOI: 10.1242/jcs.262160] [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: 03/27/2024] [Accepted: 08/01/2024] [Indexed: 08/13/2024] Open
Abstract
Golgi-resident enzymes remain in place while their substrates flow through from the endoplasmic reticulum to elsewhere in the cell. COPI-coated vesicles bud from the Golgi to recycle Golgi residents to earlier cisternae. Different enzymes are present in different parts of the stack, and one COPI adaptor protein, GOLPH3, acts to recruit enzymes into vesicles in part of the stack. Here, we used proximity biotinylation to identify further components of intra-Golgi vesicles and found FAM114A2, a cytosolic protein. Affinity chromatography with FAM114A2, and its paralogue FAM114A1, showed that they bind to Golgi-resident membrane proteins, with membrane-proximal basic residues in the cytoplasmic tail being sufficient for the interaction. Deletion of both proteins from U2OS cells did not cause substantial defects in Golgi function. However, a Drosophila orthologue of these proteins (CG9590/FAM114A) is also localised to the Golgi and binds directly to COPI. Drosophila mutants lacking FAM114A have defects in glycosylation of glue proteins in the salivary gland. Thus, the FAM114A proteins bind Golgi enzymes and are candidate adaptors to contribute specificity to COPI vesicle recycling in the Golgi stack.
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Affiliation(s)
- Lawrence G. Welch
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Nadine Muschalik
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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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: 2] [Impact Index Per Article: 2.0] [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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Arab M, Chen T, Lowe M. Mechanisms governing vesicle traffic at the Golgi apparatus. Curr Opin Cell Biol 2024; 88:102365. [PMID: 38705050 DOI: 10.1016/j.ceb.2024.102365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024]
Abstract
Vesicle transport at the Golgi apparatus is a well-described process, and the major protein components involved have been identified. This includes the coat proteins that function in cargo sorting and vesicle formation, and the proteins that mediate the downstream events of vesicle tethering and membrane fusion. However, despite this knowledge, there remain significant gaps in our mechanistic understanding of these processes which includes how they are coordinated in space and time. In this review we discuss recent advances that have provided new insights into the mechanisms of Golgi trafficking, focussing on vesicle formation and cargo sorting, and vesicle tethering and fusion. These studies point to a high degree of spatial organisation of trafficking components at the Golgi and indicate an inherent plasticity of trafficking. Going forward, further advancements in technology and more sophisticated functional assays are expected to yield greater understanding of the mechanisms that govern Golgi trafficking events.
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Affiliation(s)
- Maryam Arab
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Tong Chen
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Martin Lowe
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK.
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5
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Johnson DH, Kou OH, Bouzos N, Zeno WF. Protein-membrane interactions: sensing and generating curvature. Trends Biochem Sci 2024; 49:401-416. [PMID: 38508884 PMCID: PMC11069444 DOI: 10.1016/j.tibs.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/22/2024]
Abstract
Biological membranes are integral cellular structures that can be curved into various geometries. These curved structures are abundant in cells as they are essential for various physiological processes. However, curved membranes are inherently unstable, especially on nanometer length scales. To stabilize curved membranes, cells can utilize proteins that sense and generate membrane curvature. In this review, we summarize recent research that has advanced our understanding of interactions between proteins and curved membrane surfaces, as well as work that has expanded our ability to study curvature sensing and generation. Additionally, we look at specific examples of cellular processes that require membrane curvature, such as neurotransmission, clathrin-mediated endocytosis (CME), and organelle biogenesis.
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Affiliation(s)
- David H Johnson
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Orianna H Kou
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Nicoletta Bouzos
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Wade F Zeno
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90089, USA.
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6
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van Hilten N, Methorst J, Verwei N, Risselada HJ. Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders. SCIENCE ADVANCES 2023; 9:eade8839. [PMID: 36930719 PMCID: PMC10022891 DOI: 10.1126/sciadv.ade8839] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Proteins can specifically bind to curved membranes through curvature-induced hydrophobic lipid packing defects. The chemical diversity among such curvature "sensors" challenges our understanding of how they differ from general membrane "binders" that bind without curvature selectivity. Here, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations (Evo-MD) to resolve the peptide sequences that optimally recognize the curvature of lipid membranes. We subsequently demonstrate how a synergy between Evo-MD and a neural network (NN) can enhance the identification and discovery of curvature sensing peptides and proteins. To this aim, we benchmark a physics-trained NN model against experimental data and show that we can correctly identify known sensors and binders. We illustrate that sensing and binding are phenomena that lie on the same thermodynamic continuum, with only subtle but explainable differences in membrane binding free energy, consistent with the serendipitous discovery of sensors.
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Affiliation(s)
- Niek van Hilten
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Jeroen Methorst
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Nino Verwei
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
| | - Herre Jelger Risselada
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden, 2333 CC, Netherlands
- Department of Physics, Technical University Dortmund, Otto-Hahn-Strasse 4, Dortmund, 44227, Germany
- Institute of Theoretical Physics, Georg-August-University Göttingen, Friedrich-Hund-Platz 1, Göttingen, 37077, Germany
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7
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Sokoya T, Parolek J, Foged MM, Danylchuk DI, Bozan M, Sarkar B, Hilderink A, Philippi M, Botto LD, Terhal PA, Mäkitie O, Piehler J, Kim Y, Burd CG, Klymchenko AS, Maeda K, Holthuis JCM. Pathogenic variants of sphingomyelin synthase SMS2 disrupt lipid landscapes in the secretory pathway. eLife 2022; 11:e79278. [PMID: 36102623 PMCID: PMC9531943 DOI: 10.7554/elife.79278] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Sphingomyelin is a dominant sphingolipid in mammalian cells. Its production in the trans-Golgi traps cholesterol synthesized in the ER to promote formation of a sphingomyelin/sterol gradient along the secretory pathway. This gradient marks a fundamental transition in physical membrane properties that help specify organelle identify and function. We previously identified mutations in sphingomyelin synthase SMS2 that cause osteoporosis and skeletal dysplasia. Here, we show that SMS2 variants linked to the most severe bone phenotypes retain full enzymatic activity but fail to leave the ER owing to a defective autonomous ER export signal. Cells harboring pathogenic SMS2 variants accumulate sphingomyelin in the ER and display a disrupted transbilayer sphingomyelin asymmetry. These aberrant sphingomyelin distributions also occur in patient-derived fibroblasts and are accompanied by imbalances in cholesterol organization, glycerophospholipid profiles, and lipid order in the secretory pathway. We postulate that pathogenic SMS2 variants undermine the capacity of osteogenic cells to uphold nonrandom lipid distributions that are critical for their bone forming activity.
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Affiliation(s)
- Tolulope Sokoya
- Molecular Cell Biology Division, Department of Biology and Center of Cellular Nanoanalytics, Osnabrück UniversityOsnabrückGermany
| | - Jan Parolek
- Molecular Cell Biology Division, Department of Biology and Center of Cellular Nanoanalytics, Osnabrück UniversityOsnabrückGermany
| | - Mads Møller Foged
- Cell Death and Metabolism Group, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research CenterCopenhagenDenmark
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, Université de StrasbourgStrasbourgFrance
| | - Manuel Bozan
- Molecular Cell Biology Division, Department of Biology and Center of Cellular Nanoanalytics, Osnabrück UniversityOsnabrückGermany
| | - Bingshati Sarkar
- Molecular Cell Biology Division, Department of Biology and Center of Cellular Nanoanalytics, Osnabrück UniversityOsnabrückGermany
| | - Angelika Hilderink
- Molecular Cell Biology Division, Department of Biology and Center of Cellular Nanoanalytics, Osnabrück UniversityOsnabrückGermany
| | - Michael Philippi
- Biophysics Division, Department of Biology and Center of Cellular Nanoanalytics, Osnabrück UniversityOsnabrückGermany
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of UtahSalt Lake CityUnited States
| | - Paulien A Terhal
- Department of Genetics, University Medical Center UtrechtUtrechtNetherlands
| | - Outi Mäkitie
- Children’s Hospital, University of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Jacob Piehler
- Biophysics Division, Department of Biology and Center of Cellular Nanoanalytics, Osnabrück UniversityOsnabrückGermany
| | - Yeongho Kim
- Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | - Christopher G Burd
- Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, Université de StrasbourgStrasbourgFrance
| | - Kenji Maeda
- Cell Death and Metabolism Group, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research CenterCopenhagenDenmark
| | - Joost CM Holthuis
- Molecular Cell Biology Division, Department of Biology and Center of Cellular Nanoanalytics, Osnabrück UniversityOsnabrückGermany
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8
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Tumor protein D54 binds intracellular nanovesicles via an extended amphipathic region. J Biol Chem 2022; 298:102136. [PMID: 35714773 PMCID: PMC9270247 DOI: 10.1016/j.jbc.2022.102136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Tumor Protein D54 (TPD54) is an abundant cytosolic protein that belongs to the TPD52 family, a family of four proteins (TPD52, 53, 54 and 55) that are overexpressed in several cancer cells. Even though the functions of these proteins remain elusive, recent investigations indicate that TPD54 binds to very small cytosolic vesicles with a diameter of ca. 30 nm, half the size of classical (e.g. COPI and COPII) transport vesicles. Here, we investigated the mechanism of intracellular nanovesicle capture by TPD54. Bioinformatical analysis suggests that TPD54 contains a small coiled-coil followed by four amphipathic helices (AH1-4), which could fold upon binding to lipid membranes. Limited proteolysis, circular dichroism (CD) spectroscopy, tryptophan fluorescence, and cysteine mutagenesis coupled to covalent binding of a membrane sensitive probe showed that binding of TPD54 to small liposomes is accompanied by large structural changes in the amphipathic helix region. Furthermore, site-directed mutagenesis indicated that AH2 and AH3 have a predominant role in TPD54 binding to membranes both in cells and using model liposomes. We found that AH3 has the physicochemical features of an Amphipathic Lipid Packing Sensor (ALPS) motif, which, in other proteins, enables membrane binding in a curvature-dependent manner. Accordingly, we observed that binding of TPD54 to liposomes is very sensitive to membrane curvature and lipid unsaturation. We conclude that TPD54 recognizes nanovesicles through a combination of ALPS-dependent and -independent mechanisms.
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9
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Scott JS, Nassar ZD, Swinnen JV, Butler LM. Monounsaturated fatty acids: key regulators of cell viability and intracellular signalling in cancer. Mol Cancer Res 2022; 20:1354-1364. [PMID: 35675039 DOI: 10.1158/1541-7786.mcr-21-1069] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/29/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]
Abstract
Cancer cells feature increased macromolecular biosynthesis to support the formation of new organelles and membranes for cell division. In particular, lipids are key macromolecules that comprise cellular membrane components, substrates for energy generation and mediators of inter- and intracellular signalling. The emergence of more sensitive and accurate technology for profiling the "lipidome" of cancer cells has led to unprecedented leaps in understanding the complexity of cancer metabolism, but also highlighted promising therapeutic vulnerabilities. Notably, fatty acids, as lipid building blocks, are critical players in all stages of cancer development and progression and the importance of fatty acid desaturation and its impact on cancer cell biology has been well established. Recent years have seen the reports of new mechanistic insights into the role of monounsaturated fatty acids (MUFAs) in cancer, as regulators of cell death and lipid-related cellular signalling. This commentary aims to highlight these diverse roles of MUFAs in cancer cells which may yield new directions for therapeutic interventions involving these important fatty acids.
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Affiliation(s)
| | | | | | - Lisa M Butler
- University of Adelaide, School of Medicine and Freemasons Foundation Centre for Men's Health, Adelaide, SA, Australia
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10
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Milanini J, Magdeleine M, Fuggetta N, Ikhlef S, Brau F, Abelanet S, Alpy F, Tomasetto C, Drin G. In situ artificial contact sites (ISACS) between synthetic and endogenous organelle membranes allow for quantification of protein-tethering activities. J Biol Chem 2022; 298:101780. [PMID: 35231443 PMCID: PMC9052148 DOI: 10.1016/j.jbc.2022.101780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 11/16/2022] Open
Abstract
Membrane contact sites are specialized areas where the membranes of two distinct organelles are physically connected and allow for the exchange of molecules and for signaling processes. Understanding the mechanisms whereby proteins localize to and function in these structures is of special interest; however, methods allowing for reconstitution of these contact sites are few and only based on synthetic membranes and recombinant proteins. Here, we devised a strategy to create in situ artificial contact sites between synthetic and endogenous organelle membranes. Liposomes functionalized with a peptide containing a two phenylalanines in an acidic tract (FFAT) motif were added to adherent cells whose plasma membrane was perforated. Confocal and super-resolution microscopy revealed that these liposomes associated with the endoplasmic reticulum via the specific interaction of the FFAT motif with endoplasmic reticulum–resident vesicle-associated membrane protein–associated proteins. This approach allowed for quantification of the attachment properties of peptides corresponding to FFAT motifs derived from distinct proteins and of a protein construct derived from steroidogenic acute regulatory protein–related lipid transfer domain-3. Collectively, these data indicate that the creation of in situ artificial contact sites represents an efficient approach for studying the membrane-tethering activity of proteins and for designing membrane contact site reconstitution assays in cellular contexts.
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Affiliation(s)
- Julie Milanini
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Maud Magdeleine
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Nicolas Fuggetta
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Souade Ikhlef
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Frédéric Brau
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Sophie Abelanet
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France
| | - Fabien Alpy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U1258, Université de Strasbourg, Illkirch, France
| | - Catherine Tomasetto
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U1258, Université de Strasbourg, Illkirch, France
| | - Guillaume Drin
- Université Côte d'Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), Valbonne, France.
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11
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Prieto J, García-Cañaveras JC, León M, Sendra R, Ponsoda X, Izpisúa Belmonte JC, Lahoz A, Torres J. c-MYC Triggers Lipid Remodelling During Early Somatic Cell Reprogramming to Pluripotency. Stem Cell Rev Rep 2021; 17:2245-2261. [PMID: 34476741 PMCID: PMC8599373 DOI: 10.1007/s12015-021-10239-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 11/30/2022]
Abstract
Metabolic rewiring and mitochondrial dynamics remodelling are hallmarks of cell reprogramming, but the roles of the reprogramming factors in these changes are not fully understood. Here we show that c-MYC induces biosynthesis of fatty acids and increases the rate of pentose phosphate pathway. Time-course profiling of fatty acids and complex lipids during cell reprogramming using lipidomics revealed a profound remodelling of the lipid content, as well as the saturation and length of their acyl chains, in a c-MYC-dependent manner. Pluripotent cells displayed abundant cardiolipins and scarce phosphatidylcholines, with a prevalence of monounsaturated acyl chains. Cells undergoing cell reprogramming showed an increase in mitochondrial membrane potential that paralleled that of mitochondrial-specific cardiolipins. We conclude that c-MYC controls the rewiring of somatic cell metabolism early in cell reprogramming by orchestrating cell proliferation, synthesis of macromolecular components and lipid remodelling, all necessary processes for a successful phenotypic transition to pluripotency.
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Affiliation(s)
- Javier Prieto
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, 46100, Burjassot, Valencia, Spain.,Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Marian León
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Ramón Sendra
- Departamento de Bioquímica y Biología Molecular, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Xavier Ponsoda
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, 46100, Burjassot, Valencia, Spain
| | | | - Agustín Lahoz
- Biomarkers and Precision Medicine Unit, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain.
| | - Josema Torres
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, 46100, Burjassot, Valencia, Spain. .,Instituto de Investigación Sanitaria (INCLIVA), 46010, Valencia, Spain.
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12
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Intrinsically disordered proteins and membranes: a marriage of convenience for cell signalling? Biochem Soc Trans 2021; 48:2669-2689. [PMID: 33155649 PMCID: PMC7752083 DOI: 10.1042/bst20200467] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023]
Abstract
The structure-function paradigm has guided investigations into the molecules involved in cellular signalling for decades. The peripheries of this paradigm, however, start to unravel when considering the co-operation between proteins and the membrane in signalling processes. Intrinsically disordered regions hold distinct advantages over folded domains in terms of their binding promiscuity, sensitivity to their particular environment and their ease of modulation through post-translational modifications. Low sequence complexity and bias towards charged residues are also favourable for the multivalent electrostatic interactions that occur at the surfaces of lipid bilayers. This review looks at the principles behind the successful marriage between protein disorder and membranes in addition to the role of this partnership in modifying and regulating signalling in cellular processes. The HVR (hypervariable region) of small GTPases is highlighted as a well-studied example of the nuanced role a short intrinsically disordered region can play in the fine-tuning of signalling pathways.
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13
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Jamecna D, Antonny B. Intrinsically disordered protein regions at membrane contact sites. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:159020. [PMID: 34352388 DOI: 10.1016/j.bbalip.2021.159020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022]
Abstract
Membrane contact sites (MCS) are regions of close apposition between membrane-bound organelles. Proteins that occupy MCS display various domain organisation. Among them, lipid transfer proteins (LTPs) frequently contain both structured domains as well as regions of intrinsic disorder. In this review, we discuss the various roles of intrinsically disordered protein regions (IDPRs) in LTPs as well as in other proteins that are associated with organelle contact sites. We distinguish the following functions: (i) to act as flexible tethers between two membranes; (ii) to act as entropic barriers to prevent protein crowding and regulate membrane tethering geometry; (iii) to define the action range of catalytic domains. These functions are added to other functions of IDPRs in membrane environments, such as mediating protein-protein and protein-membrane interactions. We suggest that the overall efficiency and fidelity of contact sites might require fine coordination between all these IDPR activities.
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Affiliation(s)
- Denisa Jamecna
- Université Côte d'Azur et CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France; Biochemistry Center (BZH), Heidelberg, Germany
| | - Bruno Antonny
- Université Côte d'Azur et CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, 660 route des lucioles, 06560 Valbonne, France.
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14
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Saez JJ, Dogniaux S, Shafaq-Zadah M, Johannes L, Hivroz C, Zucchetti AE. Retrograde and Anterograde Transport of Lat-Vesicles during the Immunological Synapse Formation: Defining the Finely-Tuned Mechanism. Cells 2021; 10:cells10020359. [PMID: 33572370 PMCID: PMC7916135 DOI: 10.3390/cells10020359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
LAT is an important player of the signaling cascade induced by TCR activation. This adapter molecule is present at the plasma membrane of T lymphocytes and more abundantly in intracellular compartments. Upon T cell activation the intracellular pool of LAT is recruited to the immune synapse (IS). We previously described two pathways controlling LAT trafficking: retrograde transport from endosomes to the TGN, and anterograde traffic from the Golgi to the IS. We address the specific role of four proteins, the GTPase Rab6, the t-SNARE syntaxin-16, the v-SNARE VAMP7 and the golgin GMAP210, in each pathway. Using different methods (endocytosis and Golgi trap assays, confocal and TIRF microscopy, TCR-signalosome pull down) we show that syntaxin-16 is regulating the retrograde transport of LAT whereas VAMP7 is regulating the anterograde transport. Moreover, GMAP210 and Rab6, known to contribute to both pathways, are in our cellular context, specifically and respectively, involved in anterograde and retrograde transport of LAT. Altogether, our data describe how retrograde and anterograde pathways coordinate LAT enrichment at the IS and point to the Golgi as a central hub for the polarized recruitment of LAT to the IS. The role that this finely-tuned transport of signaling molecules plays in T-cell activation is discussed.
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Affiliation(s)
- Juan José Saez
- Institut Curie, Université PSL, U932 INSERM, Integrative Analysis of T Cell Activation Team, 26 Rue d’Ulm, 75248 Paris CEDEX 05, France; (J.J.S.); (S.D.)
| | - Stephanie Dogniaux
- Institut Curie, Université PSL, U932 INSERM, Integrative Analysis of T Cell Activation Team, 26 Rue d’Ulm, 75248 Paris CEDEX 05, France; (J.J.S.); (S.D.)
| | - Massiullah Shafaq-Zadah
- Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team, 75005 Paris, France; (M.S.-Z.); (L.J.)
| | - Ludger Johannes
- Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team, 75005 Paris, France; (M.S.-Z.); (L.J.)
| | - Claire Hivroz
- Institut Curie, Université PSL, U932 INSERM, Integrative Analysis of T Cell Activation Team, 26 Rue d’Ulm, 75248 Paris CEDEX 05, France; (J.J.S.); (S.D.)
- Correspondence: (C.H.); (A.E.Z.); Tel.: +33-156-246-438 (A.E.Z.)
| | - Andrés Ernesto Zucchetti
- Institut Curie, Université PSL, U932 INSERM, Integrative Analysis of T Cell Activation Team, 26 Rue d’Ulm, 75248 Paris CEDEX 05, France; (J.J.S.); (S.D.)
- Correspondence: (C.H.); (A.E.Z.); Tel.: +33-156-246-438 (A.E.Z.)
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15
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Chaudhary R, Mishra S, Kota S, Misra H. Molecular interactions and their predictive roles in cell pole determination in bacteria. Crit Rev Microbiol 2021; 47:141-161. [PMID: 33423591 DOI: 10.1080/1040841x.2020.1857686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacterial cell cycle is divided into well-coordinated phases; chromosome duplication and segregation, cell elongation, septum formation, and cytokinesis. The temporal separation of these phases depends upon the growth rates and doubling time in different bacteria. The entire process of cell division starts with the assembly of divisome complex at mid-cell position followed by constriction of the cell wall and septum formation. In the mapping of mid-cell position for septum formation, the gradient of oscillating Min proteins across the poles plays a pivotal role in several bacteria genus. The cues in the cell that defines the poles and plane of cell division are not fully characterized in cocci. Recent studies have shed some lights on molecular interactions at the poles and the underlying mechanisms involved in pole determination in non-cocci. In this review, we have brought forth recent findings on these aspects together, which would suggest a model to explain the mechanisms of pole determination in rod shaped bacteria and could be extrapolated as a working model in cocci.
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Affiliation(s)
- Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Hari Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
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16
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Tripathy M, Thangamani S, Srivastava A. Three-Dimensional Packing Defects in Lipid Membrane as a Function of Membrane Order. J Chem Theory Comput 2020; 16:7800-7816. [PMID: 33226805 DOI: 10.1021/acs.jctc.0c00609] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Lipid membrane packing defects are considered to be an essential parameter that regulates specific membrane binding of several peripheral proteins. In the absence of direct experimental characterization, lipid packing defects and their role in the binding of peripheral proteins are generally investigated through computational studies, which have been immensely successful in unraveling the key steps of the membrane-binding process. However, packing defects are calculated using two-dimensional (2D) projections and the crucial information on their depths is generally overlooked. Here, we present a simple yet computationally efficient algorithm, which identifies these defects in three dimensions. We validate the algorithm on a number of model membrane systems that are previously studied using 2D defect calculations and find that the defect size and the defect depth may not always be directly correlated. We employ the algorithm to understand the nature of packing defects in flat bilayer membranes exhibiting liquid-ordered (Lo), liquid-disordered (Ld), and co-existing (Lo/Ld) phases. Our results indicate the presence of shallower, smaller, and spatially localized defects in the Lo phase membranes as compared to the defects in Ld and mixed Lo/Ld phase membranes. Such analyses can elucidate the molecular-scale mechanisms that drive the preferential localization of certain proteins to either of the liquid phases or their interface. We also analyze the membrane sensing and anchoring process of a peptide in terms of the three-dimensional defects, which provides additional insights into the process with respect to depth distributions across the bilayer leaflets.
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Affiliation(s)
- Madhusmita Tripathy
- Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C.V. Raman Road, Bangalore, Karnataka 560012, India
| | - Subasini Thangamani
- Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C.V. Raman Road, Bangalore, Karnataka 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science-Bangalore, C.V. Raman Road, Bangalore, Karnataka 560012, India
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17
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Kawano K, Yokoyama F, Kawamoto J, Ogawa T, Kurihara T, Futaki S. Development of a Simple and Rapid Method for In Situ Vesicle Detection in Cultured Media. J Mol Biol 2020; 432:5876-5888. [PMID: 32931802 DOI: 10.1016/j.jmb.2020.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023]
Abstract
Extracellular membrane vesicles (EMVs) are biogenic secretory lipidic vesicles that play significant roles in intercellular communication related to human diseases and bacterial pathogenesis. They are being investigated for their possible use in diagnosis, vaccines, and biotechnology. However, the existing methods suffer from a number of issues. High-speed centrifugation, a widely used method to collect EMVs, may cause structural artifacts. Immunostaining methods require several steps and thus the separation and detection of EMVs from the secretory cells is time-consuming. Furthermore, detection of EMVs using these methods requires specific and costly antibodies. To tackle these problems, development of a simple and rapid detection method for the EMVs in the cultured medium without separation from the secretory cells is a pressing task. In this study, we focused on the Gram-negative bacterium Shewanella vesiculosa HM13, which produces a large amount of EMVs including a cargo protein with high purity, as a model. Curvature-sensing peptides were used for EMV-detection tools. FAAV, a peptide derived from sorting nexin protein 1, selectively binds to the EMVs even in the presence of the secretory cells in the complex cultured medium. FAAV can fully detect the EMVs within a few minutes, and the resistance of FAAV to proteases enables it to withstand prolonged use in the cultured medium. Fluorescence/Förster resonance energy transfer was used to develop a method to detect changes in the amount of the EMVs with high sensitivity. Overall, our results indicate the potential applicability of FAAV for in situ EMV detection in cultured media.
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Affiliation(s)
- Kenichi Kawano
- Laboratory of Biofunctional Design Chemistry, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan.
| | - Fumiaki Yokoyama
- Laboratory of Molecular Microbial Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan.
| | - Jun Kawamoto
- Laboratory of Molecular Microbial Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Takuya Ogawa
- Laboratory of Molecular Microbial Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Tatsuo Kurihara
- Laboratory of Molecular Microbial Science, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
| | - Shiroh Futaki
- Laboratory of Biofunctional Design Chemistry, Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Japan
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18
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Triacylglycerols sequester monotopic membrane proteins to lipid droplets. Nat Commun 2020; 11:3944. [PMID: 32769983 PMCID: PMC7414839 DOI: 10.1038/s41467-020-17585-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/08/2020] [Indexed: 01/05/2023] Open
Abstract
Triacylglycerols (TG) are synthesized at the endoplasmic reticulum (ER) bilayer and packaged into organelles called lipid droplets (LDs). LDs are covered by a single phospholipid monolayer contiguous with the ER bilayer. This connection is used by several monotopic integral membrane proteins, with hydrophobic membrane association domains (HDs), to diffuse between the organelles. However, how proteins partition between ER and LDs is not understood. Here, we employed synthetic model systems and found that HD-containing proteins strongly prefer monolayers and returning to the bilayer is unfavorable. This preference for monolayers is due to a higher affinity of HDs for TG over membrane phospholipids. Protein distribution is regulated by PC/PE ratio via alterations in monolayer packing and HD-TG interaction. Thus, HD-containing proteins appear to non-specifically accumulate to the LD surface. In cells, protein editing mechanisms at the ER membrane would be necessary to prevent unspecific relocation of HD-containing proteins to LDs. Triacylglycerols (TG) are synthesized at the endoplasmic reticulum (ER) bilayer and packaged into monolayer lipid droplets (LDs), but how proteins partition between ER and LDs is poorly understood. Here authors use synthetic model systems and find that proteins containing hydrophobic membrane association domains strongly prefer monolayers and that returning to the bilayer is unfavorable.
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19
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Harayama T, Shimizu T. Roles of polyunsaturated fatty acids, from mediators to membranes. J Lipid Res 2020; 61:1150-1160. [PMID: 32487545 PMCID: PMC7397749 DOI: 10.1194/jlr.r120000800] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
PUFAs, such as AA and DHA, are recognized as important biomolecules, but understanding their precise roles and modes of action remains challenging. PUFAs are precursors for a plethora of signaling lipids, for which knowledge about synthetic pathways and receptors has accumulated. However, due to their extreme diversity and the ambiguity concerning the identity of their cognate receptors, the roles of PUFA-derived signaling lipids require more investigation. In addition, PUFA functions cannot be explained just as lipid mediator precursors because they are also critical for the regulation of membrane biophysical properties. The presence of PUFAs in membrane lipids also affects the functions of transmembrane proteins and peripheral membrane proteins. Although the roles of PUFAs as membrane lipid building blocks were difficult to analyze, the discovery of lysophospholipid acyltransferases (LPLATs), which are critical for their incorporation, advanced our understanding. Recent studies unveiled how LPLATs affect PUFA levels in membrane lipids, and their genetic manipulation became an excellent strategy to study the roles of PUFA-containing lipids. In this review, we will provide an overview of metabolic pathways regulating PUFAs as lipid mediator precursors and membrane components and update recent progress about their functions. Some issues to be solved for future research will also be discussed.
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Affiliation(s)
- Takeshi Harayama
- Department of Biochemistry and National Centre of Competence in Research in Chemical Biology, University of Geneva, CH-1211 Geneva, Switzerland
| | - Takao Shimizu
- Department of Lipid Signaling, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo 162-8655, Japan and Department of Lipidomics, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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20
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Vanni S, Riccardi L, Palermo G, De Vivo M. Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids. Acc Chem Res 2019; 52:3087-3096. [PMID: 31364837 DOI: 10.1021/acs.accounts.9b00134] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The regulatory chemical mechanisms of lipid trafficking and degradation are involved in many pathophysiological processes, being implicated in severe pain, inflammation, and cancer. In addition, the processing of lipids is also relevant for industrial and environmental applications. However, there is poor understanding of the chemical features that control lipid membrane trafficking and allow lipid-degrading enzymes to efficiently select and hydrolyze specific fatty acids from a complex cellular milieu of bioactive lipids. This is particularly true for lipid acyl chains, which have diverse structures that can critically affect the many complex reactions needed to elongate, desaturate, or transport fatty acids. Building upon our own contributions in this field, we will discuss how molecular simulations, integrated with experimental evidence, have revealed that the structure and dynamics of the lipid tail are actively involved in modulating membrane trafficking at cellular organelles, and enzymatic reactions at cell membranes. Further evidence comes from recent crystal structures of lipid receptors and remodeling enzymes. Taken together, these recent works have identified those structural features of the lipid acyl chain that are crucial for the regioselectivity and stereospecificity of essential desaturation reactions. In this context, we will first illustrate how atomistic and coarse-grained simulations have elucidated the structure-function relationships between the chemical composition of the lipid's acyl chains and the molecular properties of lipid bilayers. Particular emphasis will be given to the prominent chemical role of the number of double carbon-carbon bonds along the lipid acyl chain, that is, discriminating between saturated, monounsaturated, and polyunsaturated lipids. Different levels of saturation in fatty acid molecules dramatically influence the biophysical properties of lipid assemblies and their interaction with proteins. We will then discuss the processing of lipids by membrane-bound enzymes. Our focus will be on lipids such as anandamide and 2-arachidonoylglycerol. These are the main molecules that act as neurotransmitters in the endocannabinoid system. Specifically, recent findings indicate a crucial interplay between the level of saturation of the lipid tail, its energetically and sterically favored conformations, and the hydrophobic accessory cavities in lipid-degrading enzymes, which help form catalytically active conformations of the selected substrate. This Account will emphasize how the specific chemical structure of acyl chains affects the molecular mechanisms for modulating membrane trafficking and selective hydrolysis. The results examined here show that, by using molecular simulations to investigate lipid plasticity and substrate flexibility, researchers can enrich their interpretation of experimental results about the structure-function relationships of lipids. This could positively impact chemical and biological studies in the field and ultimately support protein engineering studies and structure-based drug discovery to target lipid-processing enzymes.
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Affiliation(s)
- Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
- Université Côte d’Azur, CNRS, IPMC, 06560 Valbonne, France
| | - Laura Riccardi
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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21
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Abstract
Muschalik and Munro introduce golgins and their roles as vesicle tethers and scaffolds at the Golgi.
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22
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Abstract
Lipid droplets (LDs), important organelles for energy storage and involved in the development of metabolic disorders, are extremely dynamic and interact with many other cellular compartments to orchestrate lipid metabolism. Little is known about how these organelle contacts are changed according to cellular needs and functions under different metabolic and pathological conditions and which proteins regulate this. Here, we summarize recent exciting discoveries about the reorganization of organelle contacts in steatotic liver, including the identification of novel LD contact site proteins in cell lines and in animals. We also discuss state of the art proteomics workflows that enable the characterization of LD-organelle contacts and tethering proteins and give an outlook how this can inform obesity research.
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Affiliation(s)
- Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich-Neuherberg, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Denmark
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23
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Zucchetti AE, Bataille L, Carpier JM, Dogniaux S, San Roman-Jouve M, Maurin M, Stuck MW, Rios RM, Baldari CT, Pazour GJ, Hivroz C. Tethering of vesicles to the Golgi by GMAP210 controls LAT delivery to the immune synapse. Nat Commun 2019; 10:2864. [PMID: 31253807 PMCID: PMC6599081 DOI: 10.1038/s41467-019-10891-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 06/08/2019] [Indexed: 01/06/2023] Open
Abstract
The T cell immune synapse is a site of intense vesicular trafficking. Here we show that the golgin GMAP210, known to capture vesicles and organize membrane traffic at the Golgi, is involved in the vesicular transport of LAT to the immune synapse. Upon activation, more GMAP210 interact with LAT-containing vesicles and go together with LAT to the immune synapse. Regulating LAT recruitment and LAT-dependent signaling, GMAP210 controls T cell activation. Using a rerouting and capture assay, we show that GMAP210 captures VAMP7-decorated vesicles. Overexpressing different domains of GMAP210, we also show that GMAP210 allows their specific delivery to the immune synapse by tethering LAT-vesicles to the Golgi. Finally, in a model of ectopic expression of LAT in ciliated cells, we show that GMAP210 tethering activity controls the delivery of LAT to the cilium. Hence, our results reveal a function for the golgin GMAP210 conveying specific vesicles to the immune synapse.
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Affiliation(s)
- Andres Ernesto Zucchetti
- Institut Curie, PSL Research University, INSERM U932, Integrative analysis of T cell activation team, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Laurence Bataille
- Institut Curie, PSL Research University, INSERM U932, Integrative analysis of T cell activation team, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Jean-Marie Carpier
- Institut Curie, PSL Research University, INSERM U932, Integrative analysis of T cell activation team, 26 rue d'Ulm, 75248, Paris Cedex 05, France.,Immunobiology Department, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Stéphanie Dogniaux
- Institut Curie, PSL Research University, INSERM U932, Integrative analysis of T cell activation team, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Mabel San Roman-Jouve
- Institut Curie, PSL Research University, INSERM U932, Integrative analysis of T cell activation team, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Mathieu Maurin
- Institut Curie, PSL Research University, INSERM U932, Integrative analysis of T cell activation team, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Michael W Stuck
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Rosa M Rios
- Cell Dynamics and Signaling Department, CABIMER-CSIC/US/UPO, 41092, Seville, Spain
| | - Cosima T Baldari
- Department of Life Sciences, University of Siena, 53100 Siena, Italy
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Claire Hivroz
- Institut Curie, PSL Research University, INSERM U932, Integrative analysis of T cell activation team, 26 rue d'Ulm, 75248, Paris Cedex 05, France.
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24
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Gillingham AK, Munro S. Transport carrier tethering - how vesicles are captured by organelles. Curr Opin Cell Biol 2019; 59:140-146. [PMID: 31154044 DOI: 10.1016/j.ceb.2019.04.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 12/20/2022]
Abstract
All cells contain numerous membrane-bound organelles that carry out specific functions. These compartments do not, however, act in isolation. Some are in direct contact via membrane contact sites, while others exchange material via specific vesicles or tubular carriers laden with cargo. The term tethering in the context of this review is used to describe the primary recognition and docking of transport carriers with acceptor organelles that occurs before SNARE engagement and membrane fusion. However, it is important to note that other tethering events occur, for example, between organelles in direct contact, which do not lead to fusion.
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Affiliation(s)
- Alison K Gillingham
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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25
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Anderson NS, Barlowe C. Conserved juxtamembrane domains in the yeast golgin Coy1 drive assembly of a megadalton-sized complex and mediate binding to tethering and SNARE proteins. J Biol Chem 2019; 294:9690-9705. [PMID: 31073031 DOI: 10.1074/jbc.ra119.008107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/26/2019] [Indexed: 12/13/2022] Open
Abstract
The architecture and organization of the Golgi complex depend on a family of coiled-coil proteins called golgins. Golgins are thought to form extended homodimers that are C-terminally anchored to Golgi membranes, whereas their N termini extend into the cytoplasm to initiate vesicle capture. Previously, we reported that the Saccharomyces cerevisiae golgin Coy1 contributes to intra-Golgi retrograde transport and binds to the conserved oligomeric Golgi (COG) complex and multiple retrograde Golgi Q-SNAREs (where SNARE is soluble NSF-attachment protein receptor). Here, using various engineered yeast strains, membrane protein extraction and fractionation methods, and in vitro binding assays, we mapped the Coy1 regions responsible for these activities. We also report that Coy1 assembles into a megadalton-size complex and that assembly of this complex depends on the most C-terminal coiled-coil and a conserved region between this coiled-coil and the transmembrane domain of Coy1. We found that this conserved region is necessary and sufficient for binding the SNARE protein Sed5 and the COG complex. Mutagenesis of conserved arginine residues within the C-terminal coiled-coil disrupted oligomerization, binding, and function of Coy1. Our findings indicate that the stable incorporation of Coy1 into a higher-order oligomer is required for its interactions and role in maintaining Golgi homeostasis. We propose that Coy1 assembles into a docking platform that directs COG-bound vesicles toward cognate SNAREs on the Golgi membrane.
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Affiliation(s)
- Nadine S Anderson
- From the Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - Charles Barlowe
- From the Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
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26
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Lipid exchange and signaling at ER–Golgi contact sites. Curr Opin Cell Biol 2019; 57:8-15. [DOI: 10.1016/j.ceb.2018.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/14/2018] [Accepted: 10/16/2018] [Indexed: 01/24/2023]
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27
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Bore SL, Kolli HB, Kawakatsu T, Milano G, Cascella M. Mesoscale Electrostatics Driving Particle Dynamics in Nonhomogeneous Dielectrics. J Chem Theory Comput 2019; 15:2033-2041. [DOI: 10.1021/acs.jctc.8b01201] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sigbjørn Løland Bore
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Hima Bindu Kolli
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
| | - Toshihiro Kawakatsu
- Department of Physics, Tohoku University, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Miyagi, Japan
| | - Giuseppe Milano
- Department of Organic Materials Science, Yamagata University, 4-3-16 Jonan ,Yonezawa, Yamagata-ken 992-8510, Japan
| | - Michele Cascella
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, PO Box 1033 Blindern, 0315 Oslo, Norway
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28
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Abstract
The Golgi apparatus is a central intracellular membrane-bound organelle with key functions in trafficking, processing, and sorting of newly synthesized membrane and secretory proteins and lipids. To best perform these functions, Golgi membranes form a unique stacked structure. The Golgi structure is dynamic but tightly regulated; it undergoes rapid disassembly and reassembly during the cell cycle of mammalian cells and is disrupted under certain stress and pathological conditions. In the past decade, significant amount of effort has been made to reveal the molecular mechanisms that regulate the Golgi membrane architecture and function. Here we review the major discoveries in the mechanisms of Golgi structure formation, regulation, and alteration in relation to its functions in physiological and pathological conditions to further our understanding of Golgi structure and function in health and diseases.
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Affiliation(s)
- Jie Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Erpan Ahat
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Neurology, University of Michigan School of Medicine, Ann Arbor, MI, USA.
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A Single Point Mutation in the Rhinovirus 2B Protein Reduces the Requirement for Phosphatidylinositol 4-Kinase Class III Beta in Viral Replication. J Virol 2018; 92:JVI.01462-18. [PMID: 30209171 DOI: 10.1128/jvi.01462-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/31/2018] [Indexed: 01/31/2023] Open
Abstract
Rhinoviruses (RVs) replicate on cytoplasmic membranes derived from the Golgi apparatus. They encode membrane-targeted proteins 2B, 2C, and 3A, which control trafficking and lipid composition of the replication membrane. The virus recruits host factors for replication, such as phosphatidylinositol 4 (PI4)-kinase 3beta (PI4K3b), which boosts PI4-phosphate (PI4P) levels and drives lipid countercurrent exchange of PI4P against cholesterol at endoplasmic reticulum-Golgi membrane contact sites through the lipid shuttling protein oxysterol binding protein 1 (OSBP1). We identified a PI4K3b inhibitor-resistant RV-A16 variant with a single point mutation in the conserved 2B protein near the cytosolic carboxy terminus, isoleucine 92 to threonine (termed 2B[I92T]). The mutation did not confer resistance to cholesterol-sequestering compounds or OSBP1 inhibition, suggesting invariant dependency on the PI4P/cholesterol lipid countercurrents. In the presence of PI4K3b inhibitor, Golgi reorganization and PI4P lipid induction occurred in RV-A16 2B[I92] but not in wild-type infection. The knockout of PI4K3b abolished the replication of both the 2B[I92T] mutant and the wild type. Doxycycline-inducible expression of PI4K3b in PI4K3b knockout cells efficiently rescued the 2B[I92T] mutant and, less effectively, wild-type virus infection. Ectopic expression of 2B[I92T] or 2B was less efficient than that of 3A in recruiting PI4K3b to perinuclear membranes, suggesting a supportive rather than decisive role of 2B in recruiting PI4K3b. The data suggest that 2B tunes the recruitment of PI4K3b to the replication membrane and allows the virus to adapt to cells with low levels of PI4K3b while still maintaining the PI4P/cholesterol countercurrent for establishing Golgi-derived RV replication membranes.IMPORTANCE Human rhinoviruses (RVs) are the major cause of the common cold worldwide. They cause asthmatic exacerbations and chronic obstructive pulmonary disease. Despite recent advances, the development of antivirals and vaccines has proven difficult due to the high number and variability of RV types. The identification of critical host factors and their interactions with viral proteins and membrane lipids for the establishment of viral replication is a basis for drug development strategies. Our findings here shed new light on the interactions between nonstructural viral membrane proteins and class III phosphatidylinositol 4 kinases from the host and highlight the importance of phosphatidylinositol 4 phosphate for RV replication.
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30
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Gautier R, Bacle A, Tiberti ML, Fuchs PF, Vanni S, Antonny B. PackMem: A Versatile Tool to Compute and Visualize Interfacial Packing Defects in Lipid Bilayers. Biophys J 2018; 115:436-444. [PMID: 30055754 DOI: 10.1016/j.bpj.2018.06.025] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 06/15/2018] [Accepted: 06/26/2018] [Indexed: 11/18/2022] Open
Abstract
The analysis of the structural organization of lipid bilayers is generally performed across the direction normal to the bilayer/water interface, whereas the surface properties of the bilayer at the interface with water are often neglected. Here, we present PackMem, a bioinformatic tool that performs a topographic analysis of the bilayer surface from various molecular dynamics simulations. PackMem unifies and rationalizes previous analyses based on a Cartesian grid. The grid allows identification of surface regions defined as lipid-packing defects where lipids are loosely packed, leading to cavities in which aliphatic carbons are exposed to the solvent, either deep inside or close to the membrane surface. Examples are provided to show that the abundance of lipid-packing defects varies according to the temperature and to the bilayer composition. Because lipid-packing defects control the adsorption of peripheral proteins with hydrophobic insertions, PackMem is instrumental for us to understand and quantify the adhesive properties of biological membranes as well as their response to mechanical perturbations such as membrane deformation.
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Affiliation(s)
- Romain Gautier
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France.
| | - Amélie Bacle
- Institut Jacques Monod, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Patrick F Fuchs
- Institut Jacques Monod, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France; Laboratoire des biomolécules, Sorbonne Université, École normale supérieure, PSL University, CNRS, Paris, France
| | - Stefano Vanni
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France; Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Bruno Antonny
- Université Côte d'Azur, CNRS, IPMC, Sophia-Antipolis, France
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31
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The Many Faces of Amphipathic Helices. Biomolecules 2018; 8:biom8030045. [PMID: 29976879 PMCID: PMC6164224 DOI: 10.3390/biom8030045] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/02/2018] [Accepted: 07/02/2018] [Indexed: 12/14/2022] Open
Abstract
Amphipathic helices (AHs), a secondary feature found in many proteins, are defined by their structure and by the segregation of hydrophobic and polar residues between two faces of the helix. This segregation allows AHs to adsorb at polar⁻apolar interfaces such as the lipid surfaces of cellular organelles. Using various examples, we discuss here how variations within this general scheme impart membrane-interacting AHs with different interfacial properties. Among the key parameters are: (i) the size of hydrophobic residues and their density per helical turn; (ii) the nature, the charge, and the distribution of polar residues; and (iii) the length of the AH. Depending on how these parameters are tuned, AHs can deform lipid bilayers, sense membrane curvature, recognize specific lipids, coat lipid droplets, or protect membranes from stress. Via these diverse mechanisms, AHs play important roles in many cellular processes.
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32
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Morriswood B, Hoeller O. Resurrection science. EMBO Rep 2018; 19:embr.201846577. [PMID: 29950517 DOI: 10.15252/embr.201846577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Brooke Morriswood
- Department of Cell & Developmental Biology, University of Würzburg, Würzburg, Germany
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33
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Hofbauer HF, Gecht M, Fischer SC, Seybert A, Frangakis AS, Stelzer EHK, Covino R, Hummer G, Ernst R. The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1. J Cell Biol 2018; 217:3109-3126. [PMID: 29941475 PMCID: PMC6122994 DOI: 10.1083/jcb.201802027] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/28/2018] [Accepted: 06/18/2018] [Indexed: 01/09/2023] Open
Abstract
Phosphatidic acid (PA) lipids have a dual role as building blocks for membrane biogenesis and as active signaling molecules. This study establishes the molecular details of selective PA recognition by the transcriptional regulator Opi1 from baker’s yeast. A key event in cellular physiology is the decision between membrane biogenesis and fat storage. Phosphatidic acid (PA) is an important intermediate at the branch point of these pathways and is continuously monitored by the transcriptional repressor Opi1 to orchestrate lipid metabolism. In this study, we report on the mechanism of membrane recognition by Opi1 and identify an amphipathic helix (AH) for selective binding of PA over phosphatidylserine (PS). The insertion of the AH into the membrane core renders Opi1 sensitive to the lipid acyl chain composition and provides a means to adjust membrane biogenesis. By rational design of the AH, we tune the membrane-binding properties of Opi1 and control its responsiveness in vivo. Using extensive molecular dynamics simulations, we identify two PA-selective three-finger grips that tightly bind the PA phosphate headgroup while interacting less intimately with PS. This work establishes lipid headgroup selectivity as a new feature in the family of AH-containing membrane property sensors.
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Affiliation(s)
- Harald F Hofbauer
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany .,Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany.,Institute of Medical Biochemistry and Molecular Biology, School of Medicine, University of Saarland, Homburg, Germany
| | - Michael Gecht
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Sabine C Fischer
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Physical Biology, Interdisciplinary Center for Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Anja Seybert
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Ernst H K Stelzer
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Physical Biology, Interdisciplinary Center for Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Roberto Covino
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Ernst
- Institute of Medical Biochemistry and Molecular Biology, School of Medicine, University of Saarland, Homburg, Germany
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34
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Haider A, Wei YC, Lim K, Barbosa AD, Liu CH, Weber U, Mlodzik M, Oras K, Collier S, Hussain MM, Dong L, Patel S, Alvarez-Guaita A, Saudek V, Jenkins BJ, Koulman A, Dymond MK, Hardie RC, Siniossoglou S, Savage DB. PCYT1A Regulates Phosphatidylcholine Homeostasis from the Inner Nuclear Membrane in Response to Membrane Stored Curvature Elastic Stress. Dev Cell 2018; 45:481-495.e8. [PMID: 29754800 PMCID: PMC5971203 DOI: 10.1016/j.devcel.2018.04.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/27/2018] [Accepted: 04/11/2018] [Indexed: 12/19/2022]
Abstract
Cell and organelle membranes consist of a complex mixture of phospholipids (PLs) that determine their size, shape, and function. Phosphatidylcholine (PC) is the most abundant phospholipid in eukaryotic membranes, yet how cells sense and regulate its levels in vivo remains unclear. Here we show that PCYT1A, the rate-limiting enzyme of PC synthesis, is intranuclear and re-locates to the nuclear membrane in response to the need for membrane PL synthesis in yeast, fly, and mammalian cells. By aligning imaging with lipidomic analysis and data-driven modeling, we demonstrate that yeast PCYT1A membrane association correlates with membrane stored curvature elastic stress estimates. Furthermore, this process occurs inside the nucleus, although nuclear localization signal mutants can compensate for the loss of endogenous PCYT1A in yeast and in fly photoreceptors. These data suggest an ancient mechanism by which nucleoplasmic PCYT1A senses surface PL packing defects on the inner nuclear membrane to control PC homeostasis.
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Affiliation(s)
- Afreen Haider
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Yu-Chen Wei
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Koini Lim
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Antonio D Barbosa
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Che-Hsiung Liu
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Ursula Weber
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marek Mlodzik
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Kadri Oras
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Simon Collier
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - M Mahmood Hussain
- Departments of Cell Biology and Pediatrics, State University of New York Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Liang Dong
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Satish Patel
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Anna Alvarez-Guaita
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Vladimir Saudek
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Benjamin J Jenkins
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Albert Koulman
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Marcus K Dymond
- Division of Chemistry, School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton BN2 4GJ, UK
| | - Roger C Hardie
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Symeon Siniossoglou
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK.
| | - David B Savage
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
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35
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Čopič A, Antoine-Bally S, Giménez-Andrés M, La Torre Garay C, Antonny B, Manni MM, Pagnotta S, Guihot J, Jackson CL. A giant amphipathic helix from a perilipin that is adapted for coating lipid droplets. Nat Commun 2018; 9:1332. [PMID: 29626194 PMCID: PMC5889406 DOI: 10.1038/s41467-018-03717-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 03/05/2018] [Indexed: 11/21/2022] Open
Abstract
How proteins are targeted to lipid droplets (LDs) and distinguish the LD surface from the surfaces of other organelles is poorly understood, but many contain predicted amphipathic helices (AHs) that are involved in targeting. We have focused on human perilipin 4 (Plin4), which contains an AH that is exceptional in terms of length and repetitiveness. Using model cellular systems, we show that AH length, hydrophobicity, and charge are important for AH targeting to LDs and that these properties can compensate for one another, albeit at a loss of targeting specificity. Using synthetic lipids, we show that purified Plin4 AH binds poorly to lipid bilayers but strongly interacts with pure triglycerides, acting as a coat and forming small oil droplets. Because Plin4 overexpression alleviates LD instability under conditions where their coverage by phospholipids is limiting, we propose that the Plin4 AH replaces the LD lipid monolayer, for example during LD growth. Lipid droplets are cellular organelles important for cellular homeostasis and their disruption has been implicated in many diseases. Here the authors use a large amphipathic helix from perilipin 4 to uncover parameters important for specific lipid droplet targeting and stabilization of the oil core.
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Affiliation(s)
- Alenka Čopič
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France.
| | - Sandra Antoine-Bally
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France
| | - Manuel Giménez-Andrés
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France.,Université Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - César La Torre Garay
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France
| | - Bruno Antonny
- Université Côte d'Azur, CNRS, IPMC, 06560, Valbonne, France
| | - Marco M Manni
- Université Côte d'Azur, CNRS, IPMC, 06560, Valbonne, France
| | | | - Jeanne Guihot
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France
| | - Catherine L Jackson
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013, Paris, France
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36
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37
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Boncompain G, Weigel AV. Transport and sorting in the Golgi complex: multiple mechanisms sort diverse cargo. Curr Opin Cell Biol 2018; 50:94-101. [DOI: 10.1016/j.ceb.2018.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/28/2018] [Accepted: 03/05/2018] [Indexed: 01/22/2023]
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38
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Bird IM, Kim SH, Schweppe DK, Caetano-Lopes J, Robling AG, Charles JF, Gygi SP, Warman ML, Smits PJ. The skeletal phenotype of achondrogenesis type 1A is caused exclusively by cartilage defects. Development 2018; 145:dev.156588. [PMID: 29180569 PMCID: PMC5825869 DOI: 10.1242/dev.156588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/16/2017] [Indexed: 12/12/2022]
Abstract
Inactivating mutations in the ubiquitously expressed membrane trafficking component GMAP-210 (encoded by Trip11) cause achondrogenesis type 1A (ACG1A). ACG1A is surprisingly tissue specific, mainly affecting cartilage development. Bone development is also abnormal, but as chondrogenesis and osteogenesis are closely coupled, this could be a secondary consequence of the cartilage defect. A possible explanation for the tissue specificity of ACG1A is that cartilage and bone are highly secretory tissues with a high use of the membrane trafficking machinery. The perinatal lethality of ACG1A prevents investigating this hypothesis. We therefore generated mice with conditional Trip11 knockout alleles and inactivated Trip11 in chondrocytes, osteoblasts, osteoclasts and pancreas acinar cells, all highly secretory cell types. We discovered that the ACG1A skeletal phenotype is solely due to absence of GMAP-210 in chondrocytes. Mice lacking GMAP-210 in osteoblasts, osteoclasts and acinar cells were normal. When we inactivated Trip11 in primary chondrocyte cultures, GMAP-210 deficiency affected trafficking of a subset of chondrocyte-expressed proteins rather than globally impairing membrane trafficking. Thus, GMAP-210 is essential for trafficking specific cargoes in chondrocytes but is dispensable in other highly secretory cells. Summary: Conditional inactivation of the cis-Golgin GMAP-210 reveals that the skeletal phenotype in achondrogenesis type-1A, which is caused by mutations in GMAP-210, is solely due to impaired protein trafficking by chondrocytes.
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Affiliation(s)
- Ian M Bird
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Susie H Kim
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Devin K Schweppe
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joana Caetano-Lopes
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alexander G Robling
- Department of Anatomy and Cell Biology, Indiana University, Indianapolis, IN 46202, USA
| | - Julia F Charles
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew L Warman
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Patrick J Smits
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, Boston Children's Hospital, Boston, MA 02115, USA
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At the ends of their tethers! How coiled-coil proteins capture vesicles at the Golgi. Biochem Soc Trans 2017; 46:43-50. [PMID: 29273618 DOI: 10.1042/bst20170188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 12/20/2022]
Abstract
Cells face a complex problem: how to transfer lipids and proteins between membrane compartments in an organized, timely fashion. Indeed, many thousands of membrane and secretory proteins must traffic out of the ER to different organelles to function, while others are retrieved from the plasma membrane having fulfilled their roles [Nat. Rev. Mol. Cell Biol. (2013) 14, 382-392]. This process is highly dynamic and failure to target cargo accurately leads to catastrophic consequences for the cell, as is clear from the numerous human diseases associated with defects in membrane trafficking [Int. J. Mol. Sci. (2013) 14, 18670-18681; Traffic (2000) 1, 836-851]. How then does the cell organize this enormous transfer of material in its crowded internal environment? And how specifically do vesicles carrying proteins and lipids recognize and fuse with the correct compartment?
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40
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Vanni S. Intracellular Lipid Droplets: From Structure to Function. Lipid Insights 2017; 10:1178635317745518. [PMID: 29270019 PMCID: PMC5731618 DOI: 10.1177/1178635317745518] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/03/2017] [Indexed: 12/13/2022] Open
Abstract
Lipid droplets (LDs) are unique intracellular organelles that are mainly constituted by neutral lipids (triglycerides, sterol esters). As such they serve as the main site of energy storage in the cell and they are akin to oil emulsions in water. To prevent the direct exposure of the hydrophobic neutral lipids to the aqueous environment of the cytosol, LDs are surrounded by a monolayer of phospholipids that thus behave as a natural surfactant. This interfacial structure is rather unique inside the cell, but a molecular understanding of how the LD structure modulates its functions is still lacking, mainly due to technical challenges in both experimental and computational approaches to investigate oil-in-water emulsions. Recently, we have investigated the structure of LDs using a combination of existing and newly developed computational approaches that are optimized to study oil-water interfaces.1 Our simulations provide a comprehensive molecular characterization of the unique surface properties of LDs, suggesting structure-function relationship in several LD-related metabolic processes.
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Affiliation(s)
- Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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41
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Probing and manipulating intracellular membrane traffic by microinjection of artificial vesicles. Proc Natl Acad Sci U S A 2017; 114:E9883-E9892. [PMID: 29087339 PMCID: PMC5699080 DOI: 10.1073/pnas.1713524114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
There is still a large gap in our understanding between the functional complexity of cells and the reconstruction of partial cellular functions in vitro from purified or engineered parts. Here we have introduced artificial vesicles of defined composition into living cells to probe the capacity of the cellular cytoplasm in dealing with foreign material and to develop tools for the directed manipulation of cellular functions. Our data show that protein-free liposomes, after variable delay times, are captured by the Golgi apparatus that is reached either by random diffusion or, in the case of large unilamellar vesicles, by microtubule-dependent transport via a dynactin/dynein motor complex. However, insertion of early endosomal SNARE proteins suffices to convert liposomes into trafficking vesicles that dock and fuse with early endosomes, thus overriding the default pathway to the Golgi. Moreover, such liposomes can be directed to mitochondria expressing simple artificial affinity tags, which can also be employed to divert endogenous trafficking vesicles. In addition, fusion or subsequent acidification of liposomes can be monitored by incorporation of appropriate chemical sensors. This approach provides an opportunity for probing and manipulating cellular functions that cannot be addressed by conventional genetic approaches. We conclude that the cellular cytoplasm has a remarkable capacity for self-organization and that introduction of such macromolecular complexes may advance nanoengineering of eukaryotic cells.
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42
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Soares TA, Vanni S, Milano G, Cascella M. Toward Chemically Resolved Computer Simulations of Dynamics and Remodeling of Biological Membranes. J Phys Chem Lett 2017; 8:3586-3594. [PMID: 28707901 DOI: 10.1021/acs.jpclett.7b00493] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cellular membranes are fundamental constituents of living organisms. Apart from defining the boundaries of the cells, they are involved in a wide range of biological functions, associated with both their structural and the dynamical properties. Biomembranes can undergo large-scale transformations when subject to specific environmental changes, including gel-liquid phase transitions, change of aggregation structure, formation of microtubules, or rupture into vesicles. All of these processes are dependent on a delicate interplay between intermolecular forces, molecular crowding, and entropy, and their understanding requires approaches that are able to capture and rationalize the details of all of the involved interactions. Molecular dynamics-based computational models at atom-level resolution are, in principle, the best way to perform such investigations. Unfortunately, the relevant spatial and time dimensionalities involved in membrane remodeling phenomena would require computational costs that are today unaffordable on a routinely basis. Such hurdles can be removed by coarse-graining the representations of the individual molecular components of the systems. This procedure anyway reduces the possibility of describing the chemical variations in the lipid mixtures composing biological membranes. New hybrid particle field multiscale approaches offer today a promising alternative to the more traditional particle-based simulations methods. By combining chemically distinguishable molecular representations with mesoscale-based computationally affordable potentials, they appear as one of the most promising ways to keep an accurate description of the chemical complexity of biological membranes and, at the same time, cover the required scales to describe remodeling events.
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Affiliation(s)
- Thereza A Soares
- Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária , Recife PE 50740-560, Brazil
| | - Stefano Vanni
- Department of Biology, University of Fribourg , 1700 Fribourg, Switzerland
| | - Giuseppe Milano
- Dipartimento di Chimica e Biologia, Università di Salerno , Via Giovanni Paolo II, 132, I-84084 Fisciano, Italy
| | - Michele Cascella
- Department of Chemistry and Centre for Theoretical and Computational Chemistry (CTCC) , Sem Saelands vei 26, 0371 Oslo, Norway
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Witkos TM, Lowe M. Recognition and tethering of transport vesicles at the Golgi apparatus. Curr Opin Cell Biol 2017; 47:16-23. [DOI: 10.1016/j.ceb.2017.02.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/02/2017] [Accepted: 02/08/2017] [Indexed: 12/15/2022]
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44
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Teis D, Kukulski W. Meeting report - Emerging Concepts in Cell Organization. J Cell Sci 2017; 130:2229-2233. [PMID: 28738320 DOI: 10.1242/jcs.206219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
New concepts in cell organization emerged in a medieval castle during a snowy week in January 2017 in the middle of the Austrian Alps. The occasion was the 10th Annaberg EMBO workshop in Goldegg am See; organized by Gabriele Seethaler, Catherine Rabouille and Marino Zerial. There were 95 participants, including many who gave talks and presented posters, enjoying a familial and trusting atmosphere that stimulated lively exchange of (unpublished) results, new ideas and thoughts.
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Affiliation(s)
- David Teis
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Wanda Kukulski
- Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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45
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Bacle A, Gautier R, Jackson CL, Fuchs PFJ, Vanni S. Interdigitation between Triglycerides and Lipids Modulates Surface Properties of Lipid Droplets. Biophys J 2017; 112:1417-1430. [PMID: 28402884 DOI: 10.1016/j.bpj.2017.02.032] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/07/2017] [Accepted: 02/23/2017] [Indexed: 12/12/2022] Open
Abstract
Intracellular lipid droplets (LDs) are the main cellular site of metabolic energy storage. Their structure is unique inside the cell, with a core of esterified fatty acids and sterols, mainly triglycerides and sterol esters, surrounded by a single monolayer of phospholipids. Numerous peripheral proteins, including several that were previously associated with intracellular compartments surrounded by a lipid bilayer, have been recently shown to target the surface of LDs, but how they are able to selectively target this organelle remains largely unknown. Here, we use atomistic and coarse-grained molecular dynamics simulations to investigate the molecular properties of the LD surface and to characterize how it differs from that of a lipid bilayer. Our data suggest that although several surface properties are remarkably similar between the two structures, key differences originate from the interdigitation between surface phospholipids and core neutral lipids that occurs in LDs. This property is extremely sensitive to membrane undulations, unlike in lipid bilayers, and it strongly affects both lipid-packing defects and the lateral pressure profile. We observed a marked change in overall surface properties for surface tensions >10 mN/m, indicative of a bimodal behavior. Our simulations provide a comprehensive molecular characterization of the unique surface properties of LDs and suggest how the molecular properties of the surface lipid monolayer can be modulated by the underlying neutral lipids.
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Affiliation(s)
- Amélie Bacle
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Romain Gautier
- Université Cote d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France
| | - Catherine L Jackson
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Patrick F J Fuchs
- Institut Jacques Monod, UMR 7592, CNRS Université Paris-Diderot, Sorbonne Paris Cité, Paris, France.
| | - Stefano Vanni
- Université Cote d'Azur, Centre National de la Recherche Scientifique, Institut de Pharmacologie Moléculaire et Cellulaire, Sophia Antipolis, France.
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46
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Burr R, Stewart EV, Espenshade PJ. Coordinate Regulation of Yeast Sterol Regulatory Element-binding Protein (SREBP) and Mga2 Transcription Factors. J Biol Chem 2017; 292:5311-5324. [PMID: 28202541 DOI: 10.1074/jbc.m117.778209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Indexed: 11/06/2022] Open
Abstract
The Mga2 and Sre1 transcription factors regulate oxygen-responsive lipid homeostasis in the fission yeast Schizosaccharomyces pombe in a manner analogous to the mammalian sterol regulatory element-binding protein (SREBP)-1 and SREBP-2 transcription factors. Mga2 and SREBP-1 regulate triacylglycerol and glycerophospholipid synthesis, whereas Sre1 and SREBP-2 regulate sterol synthesis. In mammals, a shared activation mechanism allows for coordinate regulation of SREBP-1 and SREBP-2. In contrast, distinct pathways activate fission yeast Mga2 and Sre1. Therefore, it is unclear whether and how these two related pathways are coordinated to maintain lipid balance in fission yeast. Previously, we showed that Sre1 cleavage is defective in the absence of mga2 Here, we report that this defect is due to deficient unsaturated fatty acid synthesis, resulting in aberrant membrane transport. This defect is recapitulated by treatment with the fatty acid synthase inhibitor cerulenin and is rescued by addition of exogenous unsaturated fatty acids. Furthermore, sterol synthesis inhibition blocks Mga2 pathway activation. Together, these data demonstrate that Sre1 and Mga2 are each regulated by the lipid product of the other transcription factor pathway, providing a source of coordination for these two branches of lipid synthesis.
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Affiliation(s)
- Risa Burr
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Emerson V Stewart
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Peter J Espenshade
- From the Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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47
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Recursive Alterations of the Relationship between Simple Membrane Geometry and Insertion of Amphiphilic Motifs. MEMBRANES 2017; 7:membranes7010006. [PMID: 28208740 PMCID: PMC5371967 DOI: 10.3390/membranes7010006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 11/30/2022]
Abstract
The shape and composition of a membrane directly regulate the localization, activity, and signaling properties of membrane associated proteins. Proteins that both sense and generate membrane curvature, e.g., through amphiphilic insertion motifs, potentially engage in recursive binding dynamics, where the recruitment of the protein itself changes the properties of the membrane substrate. Simple geometric models of membrane curvature interactions already provide prediction tools for experimental observations, however these models are treating curvature sensing and generation as separated phenomena. Here, we outline a model that applies both geometric and basic thermodynamic considerations. This model allows us to predict the consequences of recursive properties in such interaction schemes and thereby integrate the membrane as a dynamic substrate. We use this combined model to hypothesize the origin and properties of tubular carrier systems observed in cells. Furthermore, we pinpoint the coupling to a membrane reservoir as a factor that influences the membrane curvature sensing and generation properties of local curvatures in the cell in line with classic determinants such as lipid composition and membrane geometry.
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48
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Wong M, Gillingham AK, Munro S. The golgin coiled-coil proteins capture different types of transport carriers via distinct N-terminal motifs. BMC Biol 2017; 15:3. [PMID: 28122620 PMCID: PMC5267433 DOI: 10.1186/s12915-016-0345-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/21/2016] [Indexed: 12/13/2022] Open
Abstract
Background The internal organization of cells depends on mechanisms to ensure that transport carriers, such as vesicles, fuse only with the correct destination organelle. Several types of proteins have been proposed to confer specificity to this process, and we have recently shown that a set of coiled-coil proteins on the Golgi, called golgins, are able to capture specific classes of carriers when relocated to an ectopic location. Results Mapping of six different golgins reveals that, in each case, a short 20–50 residue region is necessary and sufficient to capture specific carriers. In all six of GMAP-210, golgin-84, TMF, golgin-97, golgin-245, and GCC88, this region is located at the extreme N-terminus of the protein. The vesicle-capturing regions of GMAP-210, golgin-84, and TMF capture intra-Golgi vesicles and share some sequence features, suggesting that they act in a related, if distinct, manner. In the case of GMAP-210, this shared feature is in addition to a previously characterized “amphipathic lipid-packing sensor” motif that can capture highly curved membranes, with the two motifs being apparently involved in capturing distinct types of vesicles. Of the three GRIP domain golgins that capture endosome-to-Golgi carriers, golgin-97 and golgin-245 share a closely related capture motif, whereas that in GCC88 is distinct, suggesting that it works by a different mechanism and raising the possibility that the three golgins capture different classes of endosome-derived carriers that share many cargos but have distinct features for recognition at the Golgi. Conclusions For six different golgins, the capture of carriers is mediated by a short region at the N-terminus of the protein. There appear to be at least four different types of motif, consistent with specific golgins capturing specific classes of carrier and implying the existence of distinct receptors present on each of these different carrier classes.
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Affiliation(s)
- Mie Wong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alison K Gillingham
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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Updegrove TB, Ramamurthi KS. Geometric protein localization cues in bacterial cells. Curr Opin Microbiol 2017; 36:7-13. [PMID: 28110195 DOI: 10.1016/j.mib.2016.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/15/2016] [Accepted: 12/17/2016] [Indexed: 10/20/2022]
Abstract
Bacterial cells are highly organized at a molecular level. Understanding how specific proteins localize to their proper subcellular address has been a major challenge in bacterial cell biology. One mechanism, which appears to be increasingly more common, is the use of 'geometric cues' for protein localization. In this model, certain shape-sensing proteins recognize, and preferentially embed into, either negatively or positively curved (concave or convex, respectively) membranes. Here, we review examples of bacterial proteins that reportedly localize by sensing geometric cues and highlight emerging mechanistic understandings of how proteins may recognize subtle differences in membrane curvature.
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Affiliation(s)
- Taylor B Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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50
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Ranftler C, Meisslitzer-Ruppitsch C, Neumüller J, Ellinger A, Pavelka M. Golgi apparatus dis- and reorganizations studied with the aid of 2-deoxy-D-glucose and visualized by 3D-electron tomography. Histochem Cell Biol 2016; 147:415-438. [PMID: 27975144 PMCID: PMC5359389 DOI: 10.1007/s00418-016-1515-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2016] [Indexed: 12/31/2022]
Abstract
We studied Golgi apparatus disorganizations and reorganizations in human HepG2 hepatoblastoma cells by using the nonmetabolizable glucose analogue 2-deoxy-d-glucose (2DG) and analyzing the changes in Golgi stack architectures by 3D-electron tomography. Golgi stacks remodel in response to 2DG-treatment and are replaced by tubulo-glomerular Golgi bodies, from which mini-Golgi stacks emerge again after removal of 2DG. The Golgi stack changes correlate with the measured ATP-values. Our findings indicate that the classic Golgi stack architecture is impeded, while cells are under the influence of 2DG at constantly low ATP-levels, but the Golgi apparatus is maintained in forms of the Golgi bodies and Golgi stacks can be rebuilt as soon as 2DG is removed. The 3D-electron microscopic results highlight connecting regions that interlink membrane compartments in all phases of Golgi stack reorganizations and show that the compact Golgi bodies mainly consist of continuous intertwined tubules. Connections and continuities point to possible new transport pathways that could substitute for other modes of traffic. The changing architectures visualized in this work reflect Golgi stack dynamics that may be essential for basic cell physiologic and pathologic processes and help to learn, how cells respond to conditions of stress.
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Affiliation(s)
- Carmen Ranftler
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | | | - Josef Neumüller
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Adolf Ellinger
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria
| | - Margit Pavelka
- Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstraße 17, 1090, Vienna, Austria.
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