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Frain KM, Dedic E, Nel L, Bohush A, Olesen E, Thaysen K, Wüstner D, Stokes DL, Pedersen BP. Conformational changes in the Niemann-Pick type C1 protein NCR1 drive sterol translocation. Proc Natl Acad Sci U S A 2024; 121:e2315575121. [PMID: 38568972 PMCID: PMC11009665 DOI: 10.1073/pnas.2315575121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 02/22/2024] [Indexed: 04/05/2024] Open
Abstract
The membrane protein Niemann-Pick type C1 (NPC1, named NCR1 in yeast) is central to sterol homeostasis in eukaryotes. Saccharomyces cerevisiae NCR1 is localized to the vacuolar membrane, where it is suggested to carry sterols across the protective glycocalyx and deposit them into the vacuolar membrane. However, documentation of a vacuolar glycocalyx in fungi is lacking, and the mechanism for sterol translocation has remained unclear. Here, we provide evidence supporting the presence of a glycocalyx in isolated S. cerevisiae vacuoles and report four cryo-EM structures of NCR1 in two distinct conformations, named tense and relaxed. These two conformations illustrate the movement of sterols through a tunnel formed by the luminal domains, thus bypassing the barrier presented by the glycocalyx. Based on these structures and on comparison with other members of the Resistance-Nodulation-Division (RND) superfamily, we propose a transport model that links changes in the luminal domains with a cycle of protonation and deprotonation within the transmembrane region of the protein. Our model suggests that NPC proteins work by a generalized RND mechanism where the proton motive force drives conformational changes in the transmembrane domains that are allosterically coupled to luminal/extracellular domains to promote sterol transport.
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Affiliation(s)
- Kelly M. Frain
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
| | - Emil Dedic
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
| | - Lynette Nel
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
| | - Anastasiia Bohush
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus Institute of Advanced Studies, Aarhus University, AarhusC 8000, Denmark
| | - Esben Olesen
- Department of Molecular Biology and Genetics, Aarhus University, AarhusC 8000, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, OdenseM 5230, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, OdenseM 5230, Denmark
| | - David L. Stokes
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016
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Egebjerg JM, Szomek M, Thaysen K, Juhl AD, Kozakijevic S, Werner S, Pratsch C, Schneider G, Kapishnikov S, Ekman A, Röttger R, Wüstner D. Automated quantification of vacuole fusion and lipophagy in Saccharomyces cerevisiae from fluorescence and cryo-soft X-ray microscopy data using deep learning. Autophagy 2024; 20:902-922. [PMID: 37908116 PMCID: PMC11062380 DOI: 10.1080/15548627.2023.2270378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023] Open
Abstract
During starvation in the yeast Saccharomyces cerevisiae vacuolar vesicles fuse and lipid droplets (LDs) can become internalized into the vacuole in an autophagic process named lipophagy. There is a lack of tools to quantitatively assess starvation-induced vacuole fusion and lipophagy in intact cells with high resolution and throughput. Here, we combine soft X-ray tomography (SXT) with fluorescence microscopy and use a deep-learning computational approach to visualize and quantify these processes in yeast. We focus on yeast homologs of mammalian NPC1 (NPC intracellular cholesterol transporter 1; Ncr1 in yeast) and NPC2 proteins, whose dysfunction leads to Niemann Pick type C (NPC) disease in humans. We developed a convolutional neural network (CNN) model which classifies fully fused versus partially fused vacuoles based on fluorescence images of stained cells. This CNN, named Deep Yeast Fusion Network (DYFNet), revealed that cells lacking Ncr1 (ncr1∆ cells) or Npc2 (npc2∆ cells) have a reduced capacity for vacuole fusion. Using a second CNN model, we implemented a pipeline named LipoSeg to perform automated instance segmentation of LDs and vacuoles from high-resolution reconstructions of X-ray tomograms. From that, we obtained 3D renderings of LDs inside and outside of the vacuole in a fully automated manner and additionally measured droplet volume, number, and distribution. We find that ncr1∆ and npc2∆ cells could ingest LDs into vacuoles normally but showed compromised degradation of LDs and accumulation of lipid vesicles inside vacuoles. Our new method is versatile and allows for analysis of vacuole fusion, droplet size and lipophagy in intact cells.Abbreviations: BODIPY493/503: 4,4-difluoro-1,3,5,7,8-pentamethyl-4-bora-3a,4a-diaza-s-Indacene; BPS: bathophenanthrolinedisulfonic acid disodium salt hydrate; CNN: convolutional neural network; DHE; dehydroergosterol; npc2∆, yeast deficient in Npc2; DSC, Dice similarity coefficient; EM, electron microscopy; EVs, extracellular vesicles; FIB-SEM, focused ion beam milling-scanning electron microscopy; FM 4-64, N-(3-triethylammoniumpropyl)-4-(6-[4-{diethylamino} phenyl] hexatrienyl)-pyridinium dibromide; LDs, lipid droplets; Ncr1, yeast homolog of human NPC1 protein; ncr1∆, yeast deficient in Ncr1; NPC, Niemann Pick type C; NPC2, Niemann Pick type C homolog; OD600, optical density at 600 nm; ReLU, rectifier linear unit; PPV, positive predictive value; NPV, negative predictive value; MCC, Matthews correlation coefficient; SXT, soft X-ray tomography; UV, ultraviolet; YPD, yeast extract peptone dextrose.
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Affiliation(s)
- Jacob Marcus Egebjerg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense M, Denmark
| | - Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Suzana Kozakijevic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Stephan Werner
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Christoph Pratsch
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Gerd Schneider
- Department of X‑Ray Microscopy, Helmholtz-Zentrum Berlin, Germany and Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany
| | - Sergey Kapishnikov
- SiriusXT, 9A Holly Ave. Stillorgan Industrial Park, Blackrock, Co, Dublin, Ireland
| | - Axel Ekman
- Department of Biological and Environmental Science and Nanoscience Centre, University of Jyväskylä, Jyväskylä, Finland
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense M, Denmark
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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Juhl AD, Kozakijevic S, Willms T, Egebjerg JM, Szomek M, Thaysen K, Pratsch C, Werner S, Schneider G, Müller P, Wüstner D. Direct Observation of Uptake and Dissolution of Cholesterol Crystals by Macrophages Using Combined Fluorescence and X-ray Microscopy. Microsc Microanal 2023; 29:1158-1159. [PMID: 37613485 DOI: 10.1093/micmic/ozad067.592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Alice Dupont Juhl
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Suzana Kozakijevic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tido Willms
- Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Jacob M Egebjerg
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Pratsch
- Department of X-Ray Microscopy, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Stephan Werner
- Department of X-Ray Microscopy, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Gerd Schneider
- Department of X-Ray Microscopy, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Peter Müller
- Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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Winkler MBL, Kidmose RT, Szomek M, Thaysen K, Rawson S, Muench SP, Wüstner D, Pedersen BP. Structural Insight into Eukaryotic Sterol Transport through Niemann-Pick Type C Proteins. Cell 2019; 179:485-497.e18. [PMID: 31543266 DOI: 10.1016/j.cell.2019.08.038] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/05/2019] [Accepted: 08/21/2019] [Indexed: 12/24/2022]
Abstract
Niemann-Pick type C (NPC) proteins are essential for sterol homeostasis, believed to drive sterol integration into the lysosomal membrane before redistribution to other cellular membranes. Here, using a combination of crystallography, cryo-electron microscopy, and biochemical and in vivo studies on the Saccharomyces cerevisiae NPC system (NCR1 and NPC2), we present a framework for sterol membrane integration. Sterols are transferred between hydrophobic pockets of vacuolar NPC2 and membrane-protein NCR1. NCR1 has its N-terminal domain (NTD) positioned to deliver a sterol to a tunnel connecting NTD to the luminal membrane leaflet 50 Å away. A sterol is caught inside this tunnel during transport, and a proton-relay network of charged residues in the transmembrane region is linked to this tunnel supporting a proton-driven transport mechanism. We propose a model for sterol integration that clarifies the role of NPC proteins in this essential eukaryotic pathway and that rationalizes mutations in patients with Niemann-Pick disease type C.
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Affiliation(s)
- Mikael B L Winkler
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark
| | - Rune T Kidmose
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark
| | - Maria Szomek
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Katja Thaysen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Shaun Rawson
- School of Biomedical Sciences and The Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stephen P Muench
- School of Biomedical Sciences and The Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M 5230, Denmark
| | - Bjørn Panyella Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, Aarhus C 8000, Denmark; Aarhus Institute of Advanced Studies, Aarhus University, Høegh-Guldbergs Gade 6B, Aarhus C 8000, Denmark.
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