1
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Pan S, Gries K, Engel BD, Schroda M, Haselwandter CA, Scheuring S. The cyanobacterial protein VIPP1 forms ESCRT-III-like structures on lipid bilayers. Nat Struct Mol Biol 2024:10.1038/s41594-024-01367-7. [PMID: 39060677 DOI: 10.1038/s41594-024-01367-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 07/03/2024] [Indexed: 07/28/2024]
Abstract
The biogenesis and maintenance of thylakoid membranes require vesicle-inducing protein in plastids 1 (VIPP1). VIPP1 is a member of the endosomal sorting complex required for transport-III (ESCRT-III) superfamily, whose members form diverse filament-based supramolecular structures that facilitate membrane deformation and fission. VIPP1 cryo-electron microscopy (EM) structures in solution revealed helical rods and baskets of stacked rings, with amphipathic membrane-binding domains in the lumen. However, how VIPP1 interacts with membranes remains largely unknown. Here, using high-speed atomic force microscopy (HS-AFM), we show that VIPP1 assembles into right-handed chiral spirals and regular polygons on supported lipid bilayers via ESCRT-III-like filament assembly and dynamics. VIPP1 filaments grow clockwise into spirals through polymerization at a ring-shaped central polymerization hub, and into polygons through clockwise polymerization at the sector peripheries. Interestingly, VIPP1 initially forms Archimedean spirals, which upon maturation transform into logarithmic spirals through lateral annealing of strands to the outermore low-curvature spiral turns.
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Affiliation(s)
- Sichen Pan
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA
| | - Karin Gries
- Molecular Biotechnology and Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
| | | | - Michael Schroda
- Molecular Biotechnology and Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Christoph A Haselwandter
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Simon Scheuring
- Weill Cornell Medicine, Department of Anesthesiology, New York, NY, USA.
- Weill Cornell Medicine, Department of Physiology and Biophysics, New York, NY, USA.
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2
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Bragulat-Teixidor H, Ishihara K, Szücs GM, Otsuka S. The endoplasmic reticulum connects to the nucleus by constricted junctions that mature after mitosis. EMBO Rep 2024; 25:3137-3159. [PMID: 38877171 PMCID: PMC11239909 DOI: 10.1038/s44319-024-00175-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024] Open
Abstract
Junctions between the endoplasmic reticulum (ER) and the outer membrane of the nuclear envelope (NE) physically connect both organelles. These ER-NE junctions are essential for supplying the NE with lipids and proteins synthesized in the ER. However, little is known about the structure of these ER-NE junctions. Here, we systematically study the ultrastructure of ER-NE junctions in cryo-fixed mammalian cells staged in anaphase, telophase, and interphase by correlating live cell imaging with three-dimensional electron microscopy. Our results show that ER-NE junctions in interphase cells have a pronounced hourglass shape with a constricted neck of 7-20 nm width. This morphology is significantly distinct from that of junctions within the ER network, and their morphology emerges as early as telophase. The highly constricted ER-NE junctions are seen in several mammalian cell types, but not in budding yeast. We speculate that the unique and highly constricted ER-NE junctions are regulated via novel mechanisms that contribute to ER-to-NE lipid and protein traffic in higher eukaryotes.
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Affiliation(s)
- Helena Bragulat-Teixidor
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria.
- Vienna BioCenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria.
| | - Keisuke Ishihara
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gréta Martina Szücs
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria
| | - Shotaro Otsuka
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.
- Medical University of Vienna, Max Perutz Labs, Vienna, Austria.
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3
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Liu M, Liu Y, Song T, Yang L, Qi L, Zhang YZ, Wang Y, Shen QT. Three-dimensional architecture of ESCRT-III flat spirals on the membrane. Proc Natl Acad Sci U S A 2024; 121:e2319115121. [PMID: 38709931 PMCID: PMC11098116 DOI: 10.1073/pnas.2319115121] [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: 11/01/2023] [Accepted: 04/01/2024] [Indexed: 05/08/2024] Open
Abstract
The endosomal sorting complexes required for transport (ESCRTs) are responsible for membrane remodeling in many cellular processes, such as multivesicular body biogenesis, viral budding, and cytokinetic abscission. ESCRT-III, the most abundant ESCRT subunit, assembles into flat spirals as the primed state, essential to initiate membrane invagination. However, the three-dimensional architecture of ESCRT-III flat spirals remained vague for decades due to highly curved filaments with a small diameter and a single preferred orientation on the membrane. Here, we unveiled that yeast Snf7, a component of ESCRT-III, forms flat spirals on the lipid monolayers using cryogenic electron microscopy. We developed a geometry-constrained Euler angle-assigned reconstruction strategy and obtained moderate-resolution structures of Snf7 flat spirals with varying curvatures. Our analyses showed that Snf7 subunits recline on the membrane with N-terminal motifs α0 as anchors, adopt an open state with fused α2/3 helices, and bend α2/3 gradually from the outer to inner parts of flat spirals. In all, we provide the orientation and conformations of ESCRT-III flat spirals on the membrane and unveil the underlying assembly mechanism, which will serve as the initial step in understanding how ESCRTs drive membrane abscission.
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Affiliation(s)
- Mingdong Liu
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen518055, China
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Yunhui Liu
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen518055, China
| | - Tiefeng Song
- College of Life Sciences, Zhejiang University, Hangzhou310058, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining314400, China
| | - Liuyan Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao266237, China
| | - Lei Qi
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao266237, China
- Biomedical Research Center for Structural Analysis, Shandong University, Jinan250012, China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao266237, China
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou310058, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining314400, China
| | - Qing-Tao Shen
- School of Life Sciences, Department of Chemical Biology, Southern University of Science and Technology, Shenzhen518055, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao266237, China
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen518055, China
- iHuman Institute and School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
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4
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Knyazeva A, Li S, Corkery DP, Shankar K, Herzog LK, Zhang X, Singh B, Niggemeyer G, Grill D, Gilthorpe JD, Gaetani M, Carlson LA, Waldmann H, Wu YW. A chemical inhibitor of IST1-CHMP1B interaction impairs endosomal recycling and induces noncanonical LC3 lipidation. Proc Natl Acad Sci U S A 2024; 121:e2317680121. [PMID: 38635626 PMCID: PMC11047075 DOI: 10.1073/pnas.2317680121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 04/20/2024] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) machinery constitutes multisubunit protein complexes that play an essential role in membrane remodeling and trafficking. ESCRTs regulate a wide array of cellular processes, including cytokinetic abscission, cargo sorting into multivesicular bodies (MVBs), membrane repair, and autophagy. Given the versatile functionality of ESCRTs, and the intricate organizational structure of the ESCRT machinery, the targeted modulation of distinct ESCRT complexes is considerably challenging. This study presents a pseudonatural product targeting IST1-CHMP1B within the ESCRT-III complexes. The compound specifically disrupts the interaction between IST1 and CHMP1B, thereby inhibiting the formation of IST1-CHMP1B copolymers essential for normal-topology membrane scission events. While the compound has no impact on cytokinesis, MVB sorting, or biogenesis of extracellular vesicles, it rapidly inhibits transferrin receptor recycling in cells, resulting in the accumulation of transferrin in stalled sorting endosomes. Stalled endosomes become decorated by lipidated LC3, suggesting a link between noncanonical LC3 lipidation and inhibition of the IST1-CHMP1B complex.
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Affiliation(s)
- Anastasia Knyazeva
- Department of Chemistry, Umeå University, 901 87Umeå, Sweden
- Science for Life Laboratory, Umeå University, 901 87Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, 901 87Umeå, Sweden
| | - Shuang Li
- Department of Chemistry, Umeå University, 901 87Umeå, Sweden
- Science for Life Laboratory, Umeå University, 901 87Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, 901 87Umeå, Sweden
| | - Dale P. Corkery
- Department of Chemistry, Umeå University, 901 87Umeå, Sweden
- Science for Life Laboratory, Umeå University, 901 87Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, 901 87Umeå, Sweden
| | - Kasturika Shankar
- Umeå Centre for Microbial Research, Umeå University, 901 87Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, 901 87Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, 901 87, Umeå, Sweden
| | - Laura K. Herzog
- Department of Chemistry, Umeå University, 901 87Umeå, Sweden
- Science for Life Laboratory, Umeå University, 901 87Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, 901 87Umeå, Sweden
| | - Xuepei Zhang
- Chemical Proteomics Core Facility, Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77Stockholm, Sweden
- Chemical Proteomics Unit, Science for Life Laboratory, 171 77Stockholm, Sweden
- Chemical Proteomics, Swedish National Infrastructure for Biological Mass Spectrometry, 171 77Stockholm, Sweden
| | - Birendra Singh
- Department of Surgical and Perioperative Sciences, Unit of Anesthesiology and Intensive Care Medicine, Umeå University, 901 87Umeå, Sweden
| | - Georg Niggemeyer
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - David Grill
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | | | - Massimiliano Gaetani
- Chemical Proteomics Core Facility, Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77Stockholm, Sweden
- Chemical Proteomics Unit, Science for Life Laboratory, 171 77Stockholm, Sweden
- Chemical Proteomics, Swedish National Infrastructure for Biological Mass Spectrometry, 171 77Stockholm, Sweden
| | - Lars-Anders Carlson
- Umeå Centre for Microbial Research, Umeå University, 901 87Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, 901 87Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, 901 87, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, 901 87, Umeå, Sweden
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, 44227, Dortmund, Germany
| | - Yao-Wen Wu
- Department of Chemistry, Umeå University, 901 87Umeå, Sweden
- Science for Life Laboratory, Umeå University, 901 87Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, 901 87Umeå, Sweden
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5
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Peng R, Rochon K, Stagg SM, Mears JA. The Structure of the Drp1 Lattice on Membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588123. [PMID: 38617273 PMCID: PMC11014616 DOI: 10.1101/2024.04.04.588123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanism. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. Additionally, we observed contact between Drp1 and membrane that can be assigned to variable domain sequence. We identified two states of the Drp1 lattice representing conformational changes related to membrane curvature differences. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.
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Affiliation(s)
- Ruizhi Peng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
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6
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Clippinger AK, Naismith TV, Yoo W, Jansen S, Kast DJ, Hanson PI. IST1 regulates select recycling pathways. Traffic 2024; 25:e12921. [PMID: 37926552 PMCID: PMC11027954 DOI: 10.1111/tra.12921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 08/21/2023] [Accepted: 09/23/2023] [Indexed: 11/07/2023]
Abstract
ESCRTs (Endosomal Sorting Complex Required for Transports) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intraluminal vesicles (ILVs) to generate multivesicular endosomes. While most of the 12 ESCRT-III proteins are known to play roles in ILV formation, IST1 has been associated with a wider range of endosomal remodeling events. Here, we extend previous studies of IST1 function in endosomal trafficking and confirm that IST1, along with its binding partner CHMP1B, contributes to scission of early endosomal carriers. Functionally, depleting IST1 impaired delivery of transferrin receptor from early/sorting endosomes to the endocytic recycling compartment and instead increased its rapid recycling to the plasma membrane via peripheral endosomes enriched in the clathrin adaptor AP-1. IST1 is also important for export of mannose 6-phosphate receptor from early/sorting endosomes. Examination of IST1 binding partners on endosomes revealed that IST1 interacts with the MIT domain-containing sorting nexin SNX15, a protein previously reported to regulate endosomal recycling. Our kinetic and spatial analyses establish that SNX15 and IST1 occupy a clathrin-containing subdomain on the endosomal perimeter distinct from those previously implicated in cargo retrieval or degradation. Using live-cell microscopy, we see that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or the base of endosomal tubules. These findings indicate that IST1 contributes to a subset of recycling pathways from the early/sorting endosome.
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Affiliation(s)
- Amy K Clippinger
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Teresa V Naismith
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Wonjin Yoo
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Silvia Jansen
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - David J Kast
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Phyllis I Hanson
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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7
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Pfitzner AK, Zivkovic H, Bernat-Silvestre C, West M, Peltier T, Humbert F, Odorizzi G, Roux A. Vps60 initiates alternative ESCRT-III filaments. J Cell Biol 2023; 222:e202206028. [PMID: 37768378 PMCID: PMC10538557 DOI: 10.1083/jcb.202206028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 03/08/2023] [Accepted: 06/12/2023] [Indexed: 09/29/2023] Open
Abstract
Endosomal sorting complex required for transport-III (ESCRT-III) participates in essential cellular functions, from cell division to endosome maturation. The remarkable increase of its subunit diversity through evolution may have enabled the acquisition of novel functions. Here, we characterize a novel ESCRT-III copolymer initiated by Vps60. Membrane-bound Vps60 polymers recruit Vps2, Vps24, Did2, and Ist1, as previously shown for Snf7. Snf7- and Vps60-based filaments can coexist on membranes without interacting as their polymerization and recruitment of downstream subunits remain spatially and biochemically separated. In fibroblasts, Vps60/CHMP5 and Snf7/CHMP4 are both recruited during endosomal functions and cytokinesis, but their localization is segregated and their recruitment dynamics are different. Contrary to Snf7/CHMP4, Vps60/CHMP5 is not recruited during nuclear envelope reformation. Taken together, our results show that Vps60 and Snf7 form functionally distinct ESCRT-III polymers, supporting the notion that diversification of ESCRT-III subunits through evolution is linked to the acquisition of new cellular functions.
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Affiliation(s)
| | - Henry Zivkovic
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | | | - Matt West
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Tanner Peltier
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Frédéric Humbert
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Greg Odorizzi
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
- National Center of Competence in Research in Chemical Biology, University of Geneva, Geneva, Switzerland
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8
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Hermosilla Aguayo V, Martin P, Tian N, Zheng J, Aho R, Losa M, Selleri L. ESCRT-dependent control of craniofacial morphogenesis with concomitant perturbation of NOTCH signaling. Dev Biol 2023; 503:25-42. [PMID: 37573008 DOI: 10.1016/j.ydbio.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
Craniofacial development is orchestrated by transcription factor-driven regulatory networks, epigenetic modifications, and signaling pathways. Signaling molecules and their receptors rely on endo-lysosomal trafficking to prevent accumulation on the plasma membrane. ESCRT (Endosomal Sorting Complexes Required for Transport) machinery is recruited to endosomal membranes enabling degradation of such endosomal cargoes. Studies in vitro and in invertebrate models established the requirements of the ESCRT machinery in membrane remodeling, endosomal trafficking, and lysosomal degradation of activated membrane receptors. However, investigations during vertebrate development have been scarce. By ENU-induced mutagenesis, we isolated a mouse line, Vps25ENU/ENU, carrying a hypomorphic allele of the ESCRT-II component Vps25, with craniofacial anomalies resembling features of human congenital syndromes. Here, we assessed the spatiotemporal dynamics of Vps25 and additional ESCRT-encoding genes during murine development. We show that these genes are ubiquitously expressed although enriched in discrete domains of the craniofacial complex, heart, and limbs. ESCRT-encoding genes, including Vps25, are expressed in both cranial neural crest-derived mesenchyme and epithelium. Unlike constitutive ESCRT mutants, Vps25ENU/ENU embryos display late lethality. They exhibit hypoplastic lower jaw, stunted snout, dysmorphic ear pinnae, and secondary palate clefting. Thus, we provide the first evidence for critical roles of ESCRT-II in craniofacial morphogenesis and report perturbation of NOTCH signaling in craniofacial domains of Vps25ENU/ENU embryos. Given the known roles of NOTCH signaling in the developing cranium, and notably the lower jaw, we propose that the NOTCH pathway partly mediates the craniofacial defects of Vps25ENU/ENU mouse embryos.
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Affiliation(s)
- Viviana Hermosilla Aguayo
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, Dept of Orofacial Sciences and Dept of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Peter Martin
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, Dept of Orofacial Sciences and Dept of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nuo Tian
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, Dept of Orofacial Sciences and Dept of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - James Zheng
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, Dept of Orofacial Sciences and Dept of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert Aho
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, Dept of Orofacial Sciences and Dept of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marta Losa
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, Dept of Orofacial Sciences and Dept of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Institute for Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, Dept of Orofacial Sciences and Dept of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
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9
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Schlösser L, Sachse C, Low HH, Schneider D. Conserved structures of ESCRT-III superfamily members across domains of life. Trends Biochem Sci 2023; 48:993-1004. [PMID: 37718229 DOI: 10.1016/j.tibs.2023.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 09/19/2023]
Abstract
Structural and evolutionary studies of cyanobacterial phage shock protein A (PspA) and inner membrane-associated protein of 30 kDa (IM30) have revealed that these proteins belong to the endosomal sorting complex required for transport-III (ESCRT-III) superfamily, which is conserved across all three domains of life. PspA and IM30 share secondary and tertiary structures with eukaryotic ESCRT-III proteins, whilst also oligomerizing via conserved interactions. Here, we examine the structures of bacterial ESCRT-III-like proteins and compare the monomeric and oligomerized forms with their eukaryotic counterparts. We discuss conserved interactions used for self-assembly and highlight key hinge regions that mediate oligomer ultrastructure versatility. Finally, we address the differences in nomenclature assigned to equivalent structural motifs in both the bacterial and eukaryotic fields and suggest a common nomenclature applicable across the ESCRT-III superfamily.
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Affiliation(s)
- Lukas Schlösser
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institute for Biological Information Processing/IBI-6 Cellular Structural Biology, Jülich, Germany; Department of Biology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Harry H Low
- Department of Infectious Disease, Imperial College, London, UK
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany.
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10
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Ader NR, Chen L, Surovtsev IV, Chadwick WL, Rodriguez EC, King MC, Lusk CP. An ESCRT grommet cooperates with a diffusion barrier to maintain nuclear integrity. Nat Cell Biol 2023; 25:1465-1477. [PMID: 37783794 DOI: 10.1038/s41556-023-01235-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The molecular mechanisms by which the endosomal sorting complexes required for transport (ESCRT) proteins contribute to the integrity of the nuclear envelope (NE) barrier are not fully defined. We leveraged the single NE hole generated by mitotic extrusion of the Schizosaccharomyces pombe spindle pole body to reveal two modes of ESCRT function executed by distinct complements of ESCRT-III proteins, both dependent on CHMP7/Cmp7. A grommet-like function is required to restrict the NE hole in anaphase B, whereas replacement of Cmp7 by a sealing module ultimately closes the NE in interphase. Without Cmp7, nucleocytoplasmic compartmentalization remains intact despite NE discontinuities of up to 540 nm, suggesting mechanisms to limit diffusion through these holes. We implicate spindle pole body proteins as key components of a diffusion barrier acting with Cmp7 in anaphase B. Thus, NE remodelling mechanisms cooperate with proteinaceous diffusion barriers beyond nuclear pore complexes to maintain the nuclear compartment.
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Affiliation(s)
- Nicholas R Ader
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Linda Chen
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Ivan V Surovtsev
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
- Department of Physics, Yale University, New Haven, CT, USA
| | | | - Elisa C Rodriguez
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, CT, USA.
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.
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11
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Paine EL, Skalicky JJ, Whitby FG, Mackay DR, Ullman KS, Hill CP, Sundquist WI. The Calpain-7 protease functions together with the ESCRT-III protein IST1 within the midbody to regulate the timing and completion of abscission. eLife 2023; 12:e84515. [PMID: 37772788 PMCID: PMC10586806 DOI: 10.7554/elife.84515] [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: 11/08/2022] [Accepted: 09/28/2023] [Indexed: 09/30/2023] Open
Abstract
The Endosomal Sorting Complexes Required for Transport (ESCRT) machinery mediates the membrane fission step that completes cytokinetic abscission and separates dividing cells. Filaments composed of ESCRT-III subunits constrict membranes of the intercellular bridge midbody to the abscission point. These filaments also bind and recruit cofactors whose activities help execute abscission and/or delay abscission timing in response to mitotic errors via the NoCut/Abscission checkpoint. We previously showed that the ESCRT-III subunit IST1 binds the cysteine protease Calpain-7 (CAPN7) and that CAPN7 is required for both efficient abscission and NoCut checkpoint maintenance (Wenzel et al., 2022). Here, we report biochemical and crystallographic studies showing that the tandem microtubule-interacting and trafficking (MIT) domains of CAPN7 bind simultaneously to two distinct IST1 MIT interaction motifs. Structure-guided point mutations in either CAPN7 MIT domain disrupted IST1 binding in vitro and in cells, and depletion/rescue experiments showed that the CAPN7-IST1 interaction is required for (1) CAPN7 recruitment to midbodies, (2) efficient abscission, and (3) NoCut checkpoint arrest. CAPN7 proteolytic activity is also required for abscission and checkpoint maintenance. Hence, IST1 recruits CAPN7 to midbodies, where its proteolytic activity is required to regulate and complete abscission.
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Affiliation(s)
- Elliott L Paine
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Frank G Whitby
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Douglas R Mackay
- Department of Oncological Sciences, Huntsman Cancer Institute, University of UtahSalt Lake CityUnited States
| | - Katharine S Ullman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of UtahSalt Lake CityUnited States
| | - Christopher P Hill
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
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12
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S Cannon K, Sarsam RD, Tedamrongwanish T, Zhang K, Baker RW. Lipid nanodiscs as a template for high-resolution cryo-EM structures of peripheral membrane proteins. J Struct Biol 2023; 215:107989. [PMID: 37364761 DOI: 10.1016/j.jsb.2023.107989] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/05/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Peripheral membrane proteins are ubiquitous throughout cell biology and are required for a variety of cellular processes such as signal transduction, membrane trafficking, and autophagy. Transient binding to the membrane has a profound impact on protein function, serving to induce conformational changes and alter biochemical and biophysical parameters by increasing the local concentration of factors and restricting diffusion to two dimensions. Despite the centrality of the membrane in serving as a template for cell biology, there are few reported high-resolution structures of peripheral membrane proteins bound to the membrane. We analyzed the utility of lipid nanodiscs to serve as a template for cryo-EM analysis of peripheral membrane proteins. We tested a variety of nanodiscs and we report a 3.3 Å structure of the AP2 clathrin adaptor complex bound to a 17-nm nanodisc, with sufficient resolution to visualize a bound lipid head group. Our data demonstrate that lipid nanodiscs are amenable to high-resolution structure determination of peripheral membrane proteins and provide a framework for extending this analysis to other systems.
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Affiliation(s)
- Kevin S Cannon
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Reta D Sarsam
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Tanita Tedamrongwanish
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Kevin Zhang
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA
| | - Richard W Baker
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA; UNC Lineberger Comprehensive Cancer Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA.
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13
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Clippinger AK, Naismith TV, Yoo W, Jansen S, Kast D, Hanson PI. IST1 regulates select endosomal recycling pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551359. [PMID: 37577466 PMCID: PMC10418098 DOI: 10.1101/2023.07.31.551359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
ESCRTs (Endosomal Sorting Complex Required for Transport) are a modular set of protein complexes with membrane remodeling activities that include the formation and release of intralumenal vesicles (ILVs) to generate multivesicular endosomes. While most of the 12 ESCRT-III proteins are known to play roles in ILV formation, IST1 has been associated with a wider range of endosomal remodeling events. Here, we extend previous studies of IST1 function in endosomal trafficking and confirm that IST1, along with its binding partner CHMP1B, contributes to scission of early endosomal carriers. Depleting IST1 impaired delivery of transferrin receptor from early/sorting endosomes to the endocytic recycling compartment and instead increased its rapid recycling to the plasma membrane via peripheral endosomes enriched in the clathrin adaptor AP-1. IST1 is also important for export of mannose 6-phosphate receptor from early/sorting endosomes. Examination of IST1 binding partners on endosomes revealed that IST1 interacts with the MIT domain-containing sorting nexin SNX15, a protein previously reported to regulate endosomal recycling. Our kinetic and spatial analyses establish that SNX15 and IST1 occupy a clathrin-containing subdomain on the endosomal perimeter distinct from those previously implicated in cargo retrieval or degradation. Using live-cell microscopy we see that SNX15 and CHMP1B alternately recruit IST1 to this subdomain or the base of endosomal tubules. These findings indicate that IST1 contributes to a subset of recycling pathways from the early/sorting endosome.
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14
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Pan W, Chen H, Wang A, Wang F, Zhang X. Challenges and strategies: Scalable and efficient production of mesenchymal stem cells-derived exosomes for cell-free therapy. Life Sci 2023; 319:121524. [PMID: 36828131 DOI: 10.1016/j.lfs.2023.121524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/10/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023]
Abstract
Exosomes are small membrane vesicles secreted by most cell types, and widely exist in cell supernatants and various body fluids. They can transmit numerous bioactive elements, such as proteins, nucleic acids, and lipids, to affect the gene expression and function of recipient cells. Mesenchymal stem cells (MSCs) have been confirmed to be a potentially promising therapy for tissue repair and regeneration. Accumulating studies demonstrated that the predominant regenerative paradigm of MSCs transplantation was the paracrine effect but not the differentiation effect. Exosomes secreted by MSCs also showed similar therapeutic effects as their parent cells and were considered to be used for cell-free regenerative medicine. However, the inefficient and limited production has hampered their development for clinical translation. In this review, we summarize potential methods to efficiently promote the yield of exosomes. We mainly focus on engineering the process of exosome biogenesis and secretion, altering the cell culture conditions, cell expansion through 3D dynamic culture and the isolation of exosomes. In addition, we also discuss the application of MSCs-derived exosomes as therapeutics in disease treatment.
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Affiliation(s)
- Wei Pan
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-based Medicine, Institute of Biochemical and Biotechnological Drug, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Hongyuan Chen
- Department of General Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324 Jingwuweiqi Road 324, Jinan 250021, China
| | - Aijun Wang
- Surgical Bioengineering Laboratory, Department of Surgery, UC Davis Health Medical Center, 4625 2nd Avenue, Sacramento, CA 95817, USA
| | - Fengshan Wang
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), NMPA Key Laboratory for Quality Research and Evaluation of Carbohydrate-based Medicine, Institute of Biochemical and Biotechnological Drug, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China; National Glycoengineering Research Center, Shandong University, Jinan, Shandong 250012, China.
| | - Xinke Zhang
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China.
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15
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Moss FR, Lincoff J, Tucker M, Mohammed A, Grabe M, Frost A. Brominated lipid probes expose structural asymmetries in constricted membranes. Nat Struct Mol Biol 2023; 30:167-175. [PMID: 36624348 PMCID: PMC9935397 DOI: 10.1038/s41594-022-00898-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/11/2022] [Indexed: 01/11/2023]
Abstract
Lipids in biological membranes are thought to be functionally organized, but few experimental tools can probe nanoscale membrane structure. Using brominated lipids as contrast probes for cryo-EM and a model ESCRT-III membrane-remodeling system composed of human CHMP1B and IST1, we observed leaflet-level and protein-localized structural lipid patterns within highly constricted and thinned membrane nanotubes. These nanotubes differed markedly from protein-free, flat bilayers in leaflet thickness, lipid diffusion rates and lipid compositional and conformational asymmetries. Simulations and cryo-EM imaging of brominated stearoyl-docosahexanenoyl-phosphocholine showed how a pair of phenylalanine residues scored the outer leaflet with a helical hydrophobic defect where polyunsaturated docosahexaenoyl tails accumulated at the bilayer surface. Combining cryo-EM of halogenated lipids with molecular dynamics thus enables new characterizations of the composition and structure of membranes on molecular length scales.
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Affiliation(s)
- Frank R Moss
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - James Lincoff
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Maxwell Tucker
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Arshad Mohammed
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- University of California Berkeley, Berkeley, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Michael Grabe
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Cardiovascular Research Institute, University of California San Francisco (UCSF), San Francisco, CA, USA.
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
- Altos Labs, Redwood City, CA, USA.
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16
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Azad K, Guilligay D, Boscheron C, Maity S, De Franceschi N, Sulbaran G, Effantin G, Wang H, Kleman JP, Bassereau P, Schoehn G, Roos WH, Desfosses A, Weissenhorn W. Structural basis of CHMP2A-CHMP3 ESCRT-III polymer assembly and membrane cleavage. Nat Struct Mol Biol 2023; 30:81-90. [PMID: 36604498 DOI: 10.1038/s41594-022-00867-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/12/2022] [Indexed: 01/07/2023]
Abstract
The endosomal sorting complex required for transport (ESCRT) is a highly conserved protein machinery that drives a divers set of physiological and pathological membrane remodeling processes. However, the structural basis of ESCRT-III polymers stabilizing, constricting and cleaving negatively curved membranes is yet unknown. Here we present cryo-EM structures of membrane-coated CHMP2A-CHMP3 filaments from Homo sapiens of two different diameters at 3.3 and 3.6 Å resolution. The structures reveal helical filaments assembled by CHMP2A-CHMP3 heterodimers in the open ESCRT-III conformation, which generates a partially positive charged membrane interaction surface, positions short N-terminal motifs for membrane interaction and the C-terminal VPS4 target sequence toward the tube interior. Inter-filament interactions are electrostatic, which may facilitate filament sliding upon VPS4-mediated polymer remodeling. Fluorescence microscopy as well as high-speed atomic force microscopy imaging corroborate that VPS4 can constrict and cleave CHMP2A-CHMP3 membrane tubes. We therefore conclude that CHMP2A-CHMP3-VPS4 act as a minimal membrane fission machinery.
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Affiliation(s)
- Kimi Azad
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Delphine Guilligay
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Cecile Boscheron
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Nicola De Franceschi
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.,Curie Institute, Laboratory of Physical Chemistry Curie, University of PSL, Sorbonne University, CNRS, Paris, France
| | - Guidenn Sulbaran
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Gregory Effantin
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Haiyan Wang
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jean-Philippe Kleman
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Patricia Bassereau
- Curie Institute, Laboratory of Physical Chemistry Curie, University of PSL, Sorbonne University, CNRS, Paris, France
| | - Guy Schoehn
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Institute, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Ambroise Desfosses
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Winfried Weissenhorn
- Institute of Structural Biology (IBS), University Grenoble Alpes, CEA, CNRS, Grenoble, France.
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17
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Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical Rules for Shape-Shifting Filaments that Remodel Membranes. PHYSICAL REVIEW LETTERS 2022; 129:268101. [PMID: 36608212 DOI: 10.1103/physrevlett.129.268101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein-membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation.
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Affiliation(s)
- Billie Meadowcroft
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Ivan Palaia
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | | | - Aurélien Roux
- Biochemistry Department, University of Geneva, CH-1211 Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, CH-1211 Geneva, Switzerland
| | - Buzz Baum
- MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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18
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Cryo-electron tomography reveals structural insights into the membrane remodeling mode of dynamin-like EHD filaments. Nat Commun 2022; 13:7641. [PMID: 36496453 PMCID: PMC9741607 DOI: 10.1038/s41467-022-35164-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Eps15-homology domain containing proteins (EHDs) are eukaryotic, dynamin-related ATPases involved in cellular membrane trafficking. They oligomerize on membranes into filaments that induce membrane tubulation. While EHD crystal structures in open and closed conformations were previously reported, little structural information is available for the membrane-bound oligomeric form. Consequently, mechanistic insights into the membrane remodeling mechanism have remained sparse. Here, by using cryo-electron tomography and subtomogram averaging, we determined structures of nucleotide-bound EHD4 filaments on membrane tubes of various diameters at an average resolution of 7.6 Å. Assembly of EHD4 is mediated via interfaces in the G-domain and the helical domain. The oligomerized EHD4 structure resembles the closed conformation, where the tips of the helical domains protrude into the membrane. The variation in filament geometry and tube radius suggests a spontaneous filament curvature of approximately 1/70 nm-1. Combining the available structural and functional data, we suggest a model for EHD-mediated membrane remodeling.
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19
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Avalos-Padilla Y, Georgiev VN, Ewins E, Robinson T, Orozco E, Lipowsky R, Dimova R. Stepwise remodeling and subcompartment formation in individual vesicles by three ESCRT-III proteins. iScience 2022; 26:105765. [PMID: 36590172 PMCID: PMC9800321 DOI: 10.1016/j.isci.2022.105765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) is a multi-protein machinery involved in several membrane remodeling processes. Different approaches have been used to resolve how ESCRT proteins scission membranes. However, the underlying mechanisms generating membrane deformations are still a matter of debate. Here, giant unilamellar vesicles, microfluidic technology, and micropipette aspiration are combined to continuously follow the ESCRT-III-mediated membrane remodeling on the single-vesicle level for the first time. With this approach, we identify different mechanisms by which a minimal set of three ESCRT-III proteins from Entamoeba histolytica reshape the membrane. These proteins modulate the membrane stiffness and spontaneous curvature to regulate bud size and generate intraluminal vesicles even in the absence of ATP. We demonstrate that the bud stability depends on the protein concentration and membrane tension. The approaches introduced here should open the road to diverse applications in synthetic biology for establishing artificial cells with several membrane compartments.
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Affiliation(s)
- Yunuen Avalos-Padilla
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, ES-08028 Barcelona, Spain,Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, ES-08036 Barcelona, Spain
| | - Vasil N. Georgiev
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Eleanor Ewins
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Tom Robinson
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV IPN, 07360 Ciudad de México, México
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany,Corresponding author
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20
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Laidlaw KME, Calder G, MacDonald C. Recycling of cell surface membrane proteins from yeast endosomes is regulated by ubiquitinated Ist1. J Cell Biol 2022; 221:213481. [PMID: 36125415 PMCID: PMC9491851 DOI: 10.1083/jcb.202109137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/28/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
Upon internalization, many surface membrane proteins are recycled back to the plasma membrane. Although these endosomal trafficking pathways control surface protein activity, the precise regulatory features and division of labor between interconnected pathways are poorly defined. In yeast, we show recycling back to the surface occurs through distinct pathways. In addition to retrograde recycling pathways via the late Golgi, used by synaptobrevins and driven by cargo ubiquitination, we find nutrient transporter recycling bypasses the Golgi in a pathway driven by cargo deubiquitination. Nutrient transporters rapidly internalize to, and recycle from, endosomes marked by the ESCRT-III associated factor Ist1. This compartment serves as both “early” and “recycling” endosome. We show Ist1 is ubiquitinated and that this is required for proper endosomal recruitment and cargo recycling to the surface. Additionally, the essential ATPase Cdc48 and its adaptor Npl4 are required for recycling, potentially through regulation of ubiquitinated Ist1. This collectively suggests mechanistic features of recycling from endosomes to the plasma membrane are conserved.
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Affiliation(s)
- Kamilla M E Laidlaw
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Grant Calder
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
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21
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Jani RA, Di Cicco A, Keren-Kaplan T, Vale-Costa S, Hamaoui D, Hurbain I, Tsai FC, Di Marco M, Macé AS, Zhu Y, Amorim MJ, Bassereau P, Bonifacino JS, Subtil A, Marks MS, Lévy D, Raposo G, Delevoye C. PI4P and BLOC-1 remodel endosomal membranes into tubules. J Biophys Biochem Cytol 2022; 221:213508. [PMID: 36169638 PMCID: PMC9524204 DOI: 10.1083/jcb.202110132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 07/25/2022] [Accepted: 08/31/2022] [Indexed: 12/11/2022] Open
Abstract
Intracellular trafficking is mediated by transport carriers that originate by membrane remodeling from donor organelles. Tubular carriers contribute to the flux of membrane lipids and proteins to acceptor organelles, but how lipids and proteins impose a tubular geometry on the carriers is incompletely understood. Using imaging approaches on cells and in vitro membrane systems, we show that phosphatidylinositol-4-phosphate (PI4P) and biogenesis of lysosome-related organelles complex 1 (BLOC-1) govern the formation, stability, and functions of recycling endosomal tubules. In vitro, BLOC-1 binds and tubulates negatively charged membranes, including those containing PI4P. In cells, endosomal PI4P production by type II PI4-kinases is needed to form and stabilize BLOC-1-dependent recycling endosomal tubules. Decreased PI4KIIs expression impairs the recycling of endosomal cargoes and the life cycles of intracellular pathogens such as Chlamydia bacteria and influenza virus that exploit the membrane dynamics of recycling endosomes. This study demonstrates how a phospholipid and a protein complex coordinate the remodeling of cellular membranes into functional tubules.
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Affiliation(s)
- Riddhi Atul Jani
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Aurélie Di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Tal Keren-Kaplan
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Silvia Vale-Costa
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Daniel Hamaoui
- Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Cellular biology of microbial infection, Paris, France
| | - Ilse Hurbain
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Feng-Ching Tsai
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Mathilde Di Marco
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France
| | - Anne-Sophie Macé
- Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Yueyao Zhu
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, Oeiras, Portugal.,Universidade Católica Portuguesa, Católica Medical School, Católica Biomedical Research Centre, Palma de Cima, Lisboa, Portugal
| | - Patricia Bassereau
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Agathe Subtil
- Institut Pasteur, Université de Paris Cité, CNRS UMR3691, Cellular biology of microbial infection, Paris, France
| | - Michael S Marks
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico-Chimie Curie, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Graça Raposo
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
| | - Cédric Delevoye
- Institut Curie, Université PSL, CNRS, UMR144, Structure and Membrane Compartments, Paris, France.,Institut Curie, Université PSL, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), Paris, France
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22
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Wenzel EM, Elfmark LA, Stenmark H, Raiborg C. ER as master regulator of membrane trafficking and organelle function. J Cell Biol 2022; 221:213468. [PMID: 36108241 PMCID: PMC9481738 DOI: 10.1083/jcb.202205135] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 12/13/2022] Open
Abstract
The endoplasmic reticulum (ER), which occupies a large portion of the cytoplasm, is the cell’s main site for the biosynthesis of lipids and carbohydrate conjugates, and it is essential for folding, assembly, and biosynthetic transport of secreted proteins and integral membrane proteins. The discovery of abundant membrane contact sites (MCSs) between the ER and other membrane compartments has revealed that, in addition to its biosynthetic and secretory functions, the ER plays key roles in the regulation of organelle dynamics and functions. In this review, we will discuss how the ER regulates endosomes, lysosomes, autophagosomes, mitochondria, peroxisomes, and the Golgi apparatus via MCSs. Such regulation occurs via lipid and Ca2+ transfer and also via control of in trans dephosphorylation reactions and organelle motility, positioning, fusion, and fission. The diverse controls of other organelles via MCSs manifest the ER as master regulator of organelle biology.
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Affiliation(s)
- Eva Maria Wenzel
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway 1
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway 2
| | - Liv Anker Elfmark
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway 1
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway 2
| | - Harald Stenmark
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway 1
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway 2
| | - Camilla Raiborg
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Oslo, Norway 1
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway 2
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23
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Jiang X, Harker-Kirschneck L, Vanhille-Campos C, Pfitzner AK, Lominadze E, Roux A, Baum B, Šarić A. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLoS Comput Biol 2022; 18:e1010586. [PMID: 36251703 PMCID: PMC9612822 DOI: 10.1371/journal.pcbi.1010586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/27/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022] Open
Abstract
ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.
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Affiliation(s)
- Xiuyun Jiang
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Lena Harker-Kirschneck
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Christian Vanhille-Campos
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Elene Lominadze
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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24
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Wenzel DM, Mackay DR, Skalicky JJ, Paine EL, Miller MS, Ullman KS, Sundquist WI. Comprehensive analysis of the human ESCRT-III-MIT domain interactome reveals new cofactors for cytokinetic abscission. eLife 2022; 11:e77779. [PMID: 36107470 PMCID: PMC9477494 DOI: 10.7554/elife.77779] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
The 12 related human ESCRT-III proteins form filaments that constrict membranes and mediate fission, including during cytokinetic abscission. The C-terminal tails of polymerized ESCRT-III subunits also bind proteins that contain Microtubule-Interacting and Trafficking (MIT) domains. MIT domains can interact with ESCRT-III tails in many different ways to create a complex binding code that is used to recruit essential cofactors to sites of ESCRT activity. Here, we have comprehensively and quantitatively mapped the interactions between all known ESCRT-III tails and 19 recombinant human MIT domains. We measured 228 pairwise interactions, quantified 60 positive interactions, and discovered 18 previously unreported interactions. We also report the crystal structure of the SPASTIN MIT domain in complex with the IST1 C-terminal tail. Three MIT enzymes were studied in detail and shown to: (1) localize to cytokinetic midbody membrane bridges through interactions with their specific ESCRT-III binding partners (SPASTIN-IST1, KATNA1-CHMP3, and CAPN7-IST1), (2) function in abscission (SPASTIN, KATNA1, and CAPN7), and (3) function in the 'NoCut' abscission checkpoint (SPASTIN and CAPN7). Our studies define the human MIT-ESCRT-III interactome, identify new factors and activities required for cytokinetic abscission and its regulation, and provide a platform for analyzing ESCRT-III and MIT cofactor interactions in all ESCRT-mediated processes.
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Affiliation(s)
- Dawn M Wenzel
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Douglas R Mackay
- Department of Oncological Sciences, Huntsman Cancer Institute, University of UtahSalt Lake CityUnited States
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Elliott L Paine
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Matthew S Miller
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
| | - Katharine S Ullman
- Department of Oncological Sciences, Huntsman Cancer Institute, University of UtahSalt Lake CityUnited States
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of MedicineSalt Lake CityUnited States
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25
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Gros M, Segura E, Rookhuizen DC, Baudon B, Heurtebise-Chrétien S, Burgdorf N, Maurin M, Kapp EA, Simpson RJ, Kozik P, Villadangos JA, Bertrand MJM, Burbage M, Amigorena S. Endocytic membrane repair by ESCRT-III controls antigen export to the cytosol during antigen cross-presentation. Cell Rep 2022; 40:111205. [PMID: 35977488 PMCID: PMC9396532 DOI: 10.1016/j.celrep.2022.111205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/10/2022] [Accepted: 07/22/2022] [Indexed: 11/03/2022] Open
Abstract
Despite its crucial role in initiation of cytotoxic immune responses, the molecular pathways underlying antigen cross-presentation remain incompletely understood. The mechanism of antigen exit from endocytic compartments into the cytosol is a long-standing matter of controversy, confronting two main models: transfer through specific channels/transporters or rupture of endocytic membranes and leakage of luminal content. By monitoring the occurrence of intracellular damage in conventional dendritic cells (cDCs), we show that cross-presenting cDC1s display more frequent endomembrane injuries and increased recruitment of endosomal sorting complex required for transport (ESCRT)-III, the main repair system for intracellular membranes, relative to cDC2s. Silencing of CHMP2a or CHMP4b, two effector subunits of ESCRT-III, enhances cytosolic antigen export and cross-presentation. This phenotype is partially reversed by chemical inhibition of RIPK3, suggesting that endocytic damage is related to basal activation of the necroptosis pathway. Membrane repair therefore proves crucial in containing antigen export to the cytosol and cross-presentation in cDCs.
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Affiliation(s)
- Marine Gros
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France.
| | - Elodie Segura
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France; Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Molecular Biology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Derek C Rookhuizen
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Blandine Baudon
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | | | - Nina Burgdorf
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Mathieu Maurin
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
| | - Eugene A Kapp
- Walter & Eliza Hall Institute of Medical Research, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Richard J Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, VIC 3086, Australia
| | - Patrycja Kozik
- Protein & Nucleic Acid Chemistry Division, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jose A Villadangos
- Department of Microbiology and Immunology at the Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Biochemistry and Molecular Biology at the Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mathieu J M Bertrand
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark-Zwinjaarde 71, 9052 Zwinaarde-Ghent, Belgium; VIB Center for Inflammation Research, Technologiepark-Zwinjaarde 71, 9052 Zwinaarde-Ghent, Belgium
| | - Marianne Burbage
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France.
| | - Sebastian Amigorena
- Institut Curie, PSL University, INSERM U932, Immunity and Cancer, 75005 Paris, France
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26
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Bevilacqua G. The Viral Origin of Human Breast Cancer: From the Mouse Mammary Tumor Virus (MMTV) to the Human Betaretrovirus (HBRV). Viruses 2022; 14:v14081704. [PMID: 36016325 PMCID: PMC9412291 DOI: 10.3390/v14081704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 02/04/2023] Open
Abstract
A Human Betaretrovirus (HBRV) has been identified in humans, dating as far back as about 4500 years ago, with a high probability of it being acquired by our species around 10,000 years ago, following a species jump from mice to humans. HBRV is the human homolog of the MMTV (mouse mammary tumor virus), which is the etiological agent of murine mammary tumors. The hypothesis of a HMTV (human mammary tumor virus) was proposed about 50 years ago, and has acquired a solid scientific basis during the last 30 years, with the demonstration of a robust link with breast cancer and with PBC, primary biliary cholangitis. This article summarizes most of what is known about MMTV/HMTV/HBRV since the discovery of MMTV at the beginning of last century, to make evident both the quantity and the quality of the research supporting the existence of HBRV and its pathogenic role. Here, it is sufficient to mention that scientific evidence includes that viral sequences have been identified in breast-cancer samples in a worldwide distribution, that the complete proviral genome has been cloned from breast cancer and patients with PBC, and that saliva contains HBRV, as a possible route of inter-human infection. Controversies that have arisen concerning results obtained from human tissues, many of them outdated by new scientific evidence, are critically discussed and confuted.
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27
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Cada AK, Pavlin MR, Castillo JP, Tong AB, Larsen KP, Ren X, Yokom AL, Tsai FC, Shiah JV, Bassereau PM, Bustamante CJ, Hurley JH. Friction-driven membrane scission by the human ESCRT-III proteins CHMP1B and IST1. Proc Natl Acad Sci U S A 2022; 119:e2204536119. [PMID: 35858336 PMCID: PMC9303997 DOI: 10.1073/pnas.2204536119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/31/2022] [Indexed: 12/15/2022] Open
Abstract
The endosomal sorting complexes required for transport (ESCRT) system is an ancient and ubiquitous membrane scission machinery that catalyzes the budding and scission of membranes. ESCRT-mediated scission events, exemplified by those involved in the budding of HIV-1, are usually directed away from the cytosol ("reverse topology"), but they can also be directed toward the cytosol ("normal topology"). The ESCRT-III subunits CHMP1B and IST1 can coat and constrict positively curved membrane tubes, suggesting that these subunits could catalyze normal topology membrane severing. CHMP1B and IST1 bind and recruit the microtubule-severing AAA+ ATPase spastin, a close relative of VPS4, suggesting that spastin could have a VPS4-like role in normal-topology membrane scission. Here, we reconstituted the process in vitro using membrane nanotubes pulled from giant unilamellar vesicles using an optical trap in order to determine whether CHMP1B and IST1 are capable of membrane severing on their own or in concert with VPS4 or spastin. CHMP1B and IST1 copolymerize on membrane nanotubes, forming stable scaffolds that constrict the tubes, but do not, on their own, lead to scission. However, CHMP1B-IST1 scaffolded tubes were severed when an additional extensional force was applied, consistent with a friction-driven scission mechanism. We found that spastin colocalized with CHMP1B-enriched sites but did not disassemble the CHMP1B-IST1 coat from the membrane. VPS4 resolubilized CHMP1B and IST1 without leading to scission. These observations show that the CHMP1B-IST1 ESCRT-III combination is capable of severing membranes by a friction-driven mechanism that is independent of VPS4 and spastin.
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Affiliation(s)
- A. King Cada
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Mark R. Pavlin
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
| | - Juan P. Castillo
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Alexander B. Tong
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kevin P. Larsen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Adam L. Yokom
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Feng-Ching Tsai
- Laboratoire Physico-Chimie Curie, Institut Curie, Université Paris Sciences & Letters, CNRS UMR168, Sorbonne Université, Paris, 75005 France
| | - Jamie V. Shiah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Patricia M. Bassereau
- Laboratoire Physico-Chimie Curie, Institut Curie, Université Paris Sciences & Letters, CNRS UMR168, Sorbonne Université, Paris, 75005 France
| | - Carlos J. Bustamante
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Physics, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
- Kavli Energy Nanoscience Institute, University of California, Berkeley, CA 94720
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
- Helen Wills Institute of Neuroscience, University of California, Berkeley, CA 94720
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28
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Ohnishi N, Sugimoto M, Kondo H, Shioya KI, Zhang L, Sakamoto W. Distinctive in vitro ATP Hydrolysis Activity of AtVIPP1, a Chloroplastic ESCRT-III Superfamily Protein in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:949578. [PMID: 35903241 PMCID: PMC9315428 DOI: 10.3389/fpls.2022.949578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Vesicle-inducing protein in plastid 1 (VIPP1), characteristic to oxygenic photosynthetic organisms, is a membrane-remodeling factor that forms homo-oligomers and functions in thylakoid membrane formation and maintenance. The cyanobacterial VIPP1 structure revealed a monomeric folding pattern similar to that of endosomal sorting complex required for transport (ESCRT) III. Characteristic to VIPP1, however, is its own GTP and ATP hydrolytic activity without canonical domains. In this study, we found that histidine-tagged Arabidopsis VIPP1 (AtVIPP1) hydrolyzed GTP and ATP to produce GDP and ADP in vitro, respectively. Unexpectedly, the observed GTPase and ATPase activities were biochemically distinguishable, because the ATPase was optimized for alkaline conditions and dependent on Ca2+ as well as Mg2+, with a higher affinity for ATP than GTP. We found that a version of AtVIPP1 protein with a mutation in its nucleotide-binding site, as deduced from the cyanobacterial structure, retained its hydrolytic activity, suggesting that Arabidopsis and cyanobacterial VIPP1s have different properties. Negative staining particle analysis showed that AtVIPP1 formed particle or rod structures that differed from those of cyanobacteria and Chlamydomonas. These results suggested that the nucleotide hydrolytic activity and oligomer formation of VIPP1 are common in photosynthetic organisms, whereas their properties differ among species.
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Affiliation(s)
- Norikazu Ohnishi
- Institute for Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Manabu Sugimoto
- Institute for Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Hideki Kondo
- Institute for Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Ken-ichi Shioya
- Institute for Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Lingang Zhang
- School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Wataru Sakamoto
- Institute for Plant Science and Resources, Okayama University, Kurashiki, Japan
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29
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The ESCRT Machinery: Remodeling, Repairing, and Sealing Membranes. MEMBRANES 2022; 12:membranes12060633. [PMID: 35736340 PMCID: PMC9229795 DOI: 10.3390/membranes12060633] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023]
Abstract
The ESCRT machinery is an evolutionarily conserved membrane remodeling complex that is used by the cell to perform reverse membrane scission in essential processes like protein degradation, cell division, and release of enveloped retroviruses. ESCRT-III, together with the AAA ATPase VPS4, harbors the main remodeling and scission function of the ESCRT machinery, whereas early-acting ESCRTs mainly contribute to protein sorting and ESCRT-III recruitment through association with upstream targeting factors. Here, we review recent advances in our understanding of the molecular mechanisms that underlie membrane constriction and scission by ESCRT-III and describe the involvement of this machinery in the sealing and repairing of damaged cellular membranes, a key function to preserve cellular viability and organellar function.
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30
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Migliano SM, Wenzel EM, Stenmark H. Biophysical and molecular mechanisms of ESCRT functions, and their implications for disease. Curr Opin Cell Biol 2022; 75:102062. [DOI: 10.1016/j.ceb.2022.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/14/2022] [Accepted: 01/22/2022] [Indexed: 12/31/2022]
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31
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Nadeem A, Berg A, Pace H, Alam A, Toh E, Ådén J, Zlatkov N, Myint SL, Persson K, Gröbner G, Sjöstedt A, Bally M, Barandun J, Uhlin BE, Wai SN. Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae. eLife 2022; 11:73439. [PMID: 35131030 PMCID: PMC8824476 DOI: 10.7554/elife.73439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/19/2022] [Indexed: 12/29/2022] Open
Abstract
The α-pore-forming toxins (α-PFTs) from pathogenic bacteria damage host cell membranes by pore formation. We demonstrate a remarkable, hitherto unknown mechanism by an α-PFT protein from Vibrio cholerae. As part of the MakA/B/E tripartite toxin, MakA is involved in membrane pore formation similar to other α-PFTs. In contrast, MakA in isolation induces tube-like structures in acidic endosomal compartments of epithelial cells in vitro. The present study unravels the dynamics of tubular growth, which occurs in a pH-, lipid-, and concentration-dependent manner. Within acidified organelle lumens or when incubated with cells in acidic media, MakA forms oligomers and remodels membranes into high-curvature tubes leading to loss of membrane integrity. A 3.7 Å cryo-electron microscopy structure of MakA filaments reveals a unique protein-lipid superstructure. MakA forms a pinecone-like spiral with a central cavity and a thin annular lipid bilayer embedded between the MakA transmembrane helices in its active α-PFT conformation. Our study provides insights into a novel tubulation mechanism of an α-PFT protein and a new mode of action by a secreted bacterial toxin.
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Affiliation(s)
- Aftab Nadeem
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Hudson Pace
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Athar Alam
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Eric Toh
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Jörgen Ådén
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Nikola Zlatkov
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Si Lhyam Myint
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Karina Persson
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Gerhard Gröbner
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Anders Sjöstedt
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Marta Bally
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Jonas Barandun
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
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32
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Shankar R, Lettman MM, Whisler W, Frankel EB, Audhya A. The ESCRT machinery directs quality control over inner nuclear membrane architecture. Cell Rep 2022; 38:110263. [PMID: 35045304 PMCID: PMC8801257 DOI: 10.1016/j.celrep.2021.110263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 11/21/2021] [Accepted: 12/21/2021] [Indexed: 11/20/2022] Open
Abstract
The late-acting endosomal sorting complex required for transport (ESCRT) machinery has been implicated in facilitating the resealing of the nuclear envelope (NE) after mitosis, enabling compartmentalization of the genome away from the cytoplasm. Here, we leverage the stereotypic first division of the C. elegans embryo to identify additional functions of the ESCRT machinery in maintaining the structure of the inner nuclear membrane. Specifically, impaired ESCRT function results in a defect in the pruning of inner nuclear membrane invaginations, which arise normally during NE reformation and expansion. Additionally, in combination with a hypomorphic mutation that interferes with assembly of the underlying nuclear lamina, inhibition of ESCRT function significantly perturbs NE architecture and increases chromosome segregation defects, resulting in penetrant embryonic lethality. Our findings highlight links between ESCRT-mediated inner nuclear membrane remodeling, maintenance of nuclear envelope morphology, and the preservation of the genome during early development. In this study, Shankar et al. demonstrate that defects in ESCRT machinery functions impair pruning of inner nuclear membrane invaginations that form normally after mitotic exit as the nuclear envelope undergoes expansion. These findings highlight a critical role for the ESCRT machinery in the maintenance of inner nuclear membrane morphology.
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Affiliation(s)
- Raakhee Shankar
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Molly M Lettman
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - William Whisler
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Elisa B Frankel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA.
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33
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Rheinemann L, Downhour DM, Bredbenner K, Mercenne G, Davenport KA, Schmitt PT, Necessary CR, McCullough J, Schmitt AP, Simon SM, Sundquist WI, Elde NC. RetroCHMP3 blocks budding of enveloped viruses without blocking cytokinesis. Cell 2021; 184:5419-5431.e16. [PMID: 34597582 PMCID: PMC8929533 DOI: 10.1016/j.cell.2021.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/03/2021] [Accepted: 09/03/2021] [Indexed: 11/26/2022]
Abstract
Many enveloped viruses require the endosomal sorting complexes required for transport (ESCRT) pathway to exit infected cells. This highly conserved pathway mediates essential cellular membrane fission events, which restricts the acquisition of adaptive mutations to counteract viral co-option. Here, we describe duplicated and truncated copies of the ESCRT-III factor CHMP3 that block ESCRT-dependent virus budding and arose independently in New World monkeys and mice. When expressed in human cells, these retroCHMP3 proteins potently inhibit release of retroviruses, paramyxoviruses, and filoviruses. Remarkably, retroCHMP3 proteins have evolved to reduce interactions with other ESCRT-III factors and have little effect on cellular ESCRT processes, revealing routes for decoupling cellular ESCRT functions from viral exploitation. The repurposing of duplicated ESCRT-III proteins thus provides a mechanism to generate broad-spectrum viral budding inhibitors without blocking highly conserved essential cellular ESCRT functions.
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Affiliation(s)
- Lara Rheinemann
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Diane Miller Downhour
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kate Bredbenner
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY 10065, USA
| | - Gaelle Mercenne
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kristen A Davenport
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Phuong Tieu Schmitt
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christina R Necessary
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - John McCullough
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Anthony P Schmitt
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, Rockefeller University, New York, NY 10065, USA.
| | - Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - Nels C Elde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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34
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Pashkova N, Yu L, Schnicker NJ, Tseng CC, Gakhar L, Katzmann DJ, Piper RC. Interactions of ubiquitin and CHMP5 with the V domain of HD-PTP reveals role for regulation of Vps4 ATPase. Mol Biol Cell 2021; 32:ar42. [PMID: 34586919 PMCID: PMC8694081 DOI: 10.1091/mbc.e21-04-0219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The family of Bro1 proteins coordinates the activity of the Endosomal Sorting Complexes Required for Transport (ESCRTs) to mediate a number of membrane remodeling events. These events culminate in membrane scission catalyzed by ESCRT-III, whose polymerization and disassembly is controlled by the AAA-ATPase, Vps4. Bro1-family members Alix and HD-PTP as well as yeast Bro1 have central “V” domains that noncovalently bind Ub and connect ubiquitinated proteins to ESCRT-driven functions such as the incorporation of ubiquitinated membrane proteins into intralumenal vesicles of multivesicular bodies. Recently, it was discovered that the V domain of yeast Bro1 binds the MIT domain of Vps4 to stimulate its ATPase activity. Here we determine the structural basis for how the V domain of human HD-PTP binds ubiquitin. The HD-PTP V domain also binds the MIT domain of Vps4, and ubiquitin binding to the HD-PTP V domain enhances its ability to stimulate Vps4 ATPase activity. Additionally, we found that V domains of both HD-PTP and Bro1 bind CHMP5 and Vps60, respectively, providing another potential molecular mechanism to alter Vps4 activity. These data support a model whereby contacts between ubiquitin, ESCRT-III, and Vps4 by V domains of the Bro1 family may coordinate late events in ESCRT-driven membrane remodeling events.
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Affiliation(s)
- Natalya Pashkova
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
| | - Liping Yu
- NMR facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242.,Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
| | | | - Chun-Che Tseng
- Biochemistry and Molecular Biology Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, 55905.,Protein Crystallography Facility, University of Iowa, Iowa City, IA, 52242
| | - Lokesh Gakhar
- Protein Crystallography Facility, University of Iowa, Iowa City, IA, 52242
| | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905
| | - Robert C Piper
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242
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35
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Thorsen MK, Lai A, Lee MW, Hoogerheide DP, Wong GCL, Freed JH, Heldwein EE. Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering. mBio 2021; 12:e0154821. [PMID: 34425706 PMCID: PMC8406295 DOI: 10.1128/mbio.01548-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/28/2021] [Indexed: 02/01/2023] Open
Abstract
During replication of herpesviruses, capsids escape from the nucleus into the cytoplasm by budding at the inner nuclear membrane. This unusual process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid by oligomerizing into a hexagonal, membrane-bound scaffold. Here, we found that highly basic membrane-proximal regions (MPRs) of the NEC alter lipid order by inserting into the lipid headgroups and promote negative Gaussian curvature. We also find that the electrostatic interactions between the MPRs and the membranes are essential for membrane deformation. One of the MPRs is phosphorylated by a viral kinase during infection, and the corresponding phosphomimicking mutations block capsid nuclear egress. We show that the same phosphomimicking mutations disrupt the NEC-membrane interactions and inhibit NEC-mediated budding in vitro, providing a biophysical explanation for the in vivo phenomenon. Our data suggest that the NEC generates negative membrane curvature by both lipid ordering and protein scaffolding and that phosphorylation acts as an off switch that inhibits the membrane-budding activity of the NEC to prevent capsid-less budding. IMPORTANCE Herpesviruses are large viruses that infect nearly all vertebrates and some invertebrates and cause lifelong infections in most of the world's population. During replication, herpesviruses export their capsids from the nucleus into the cytoplasm by an unusual mechanism in which the viral nuclear egress complex (NEC) deforms the nuclear membrane around the capsid. However, how membrane deformation is achieved is unclear. Here, we show that the NEC from herpes simplex virus 1, a prototypical herpesvirus, uses clusters of positive charges to bind membranes and order membrane lipids. Reducing the positive charge or introducing negative charges weakens the membrane deforming ability of the NEC. We propose that the virus employs electrostatics to deform nuclear membrane around the capsid and can control this process by changing the NEC charge through phosphorylation. Blocking NEC-membrane interactions could be exploited as a therapeutic strategy.
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Affiliation(s)
- Michael K. Thorsen
- Department of Molecular Biology and Microbiology, Graduate Program in Cellular, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Alex Lai
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York, USA
| | - Michelle W. Lee
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Gerard C. L. Wong
- Department of Bioengineering, Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Jack H. Freed
- Department of Chemistry and Chemical Biology and National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York, USA
| | - Ekaterina E. Heldwein
- Department of Molecular Biology and Microbiology, Graduate Program in Cellular, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts, USA
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36
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Liu J, Tassinari M, Souza DP, Naskar S, Noel JK, Bohuszewicz O, Buck M, Williams TA, Baum B, Low HH. Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily. Cell 2021; 184:3660-3673.e18. [PMID: 34166615 PMCID: PMC8281802 DOI: 10.1016/j.cell.2021.05.041] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/24/2020] [Accepted: 05/25/2021] [Indexed: 12/31/2022]
Abstract
Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life.
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Affiliation(s)
- Jiwei Liu
- Department of Infectious Disease, Imperial College, London, UK
| | | | - Diorge P Souza
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Souvik Naskar
- Department of Infectious Disease, Imperial College, London, UK
| | - Jeffrey K Noel
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Martin Buck
- Department of Life Sciences, Imperial College, London, UK
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Buzz Baum
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK; Division of Cell Biology, MRC Laboratory of Molecular Biology, Cambridge, UK; Institute for the Physics of Living Systems, University College London, London, UK.
| | - Harry H Low
- Department of Infectious Disease, Imperial College, London, UK.
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37
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Gupta TK, Klumpe S, Gries K, Heinz S, Wietrzynski W, Ohnishi N, Niemeyer J, Spaniol B, Schaffer M, Rast A, Ostermeier M, Strauss M, Plitzko JM, Baumeister W, Rudack T, Sakamoto W, Nickelsen J, Schuller JM, Schroda M, Engel BD. Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity. Cell 2021; 184:3643-3659.e23. [PMID: 34166613 DOI: 10.1016/j.cell.2021.05.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/16/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022]
Abstract
Vesicle-inducing protein in plastids 1 (VIPP1) is essential for the biogenesis and maintenance of thylakoid membranes, which transform light into life. However, it is unknown how VIPP1 performs its vital membrane-remodeling functions. Here, we use cryo-electron microscopy to determine structures of cyanobacterial VIPP1 rings, revealing how VIPP1 monomers flex and interweave to form basket-like assemblies of different symmetries. Three VIPP1 monomers together coordinate a non-canonical nucleotide binding pocket on one end of the ring. Inside the ring's lumen, amphipathic helices from each monomer align to form large hydrophobic columns, enabling VIPP1 to bind and curve membranes. In vivo mutations in these hydrophobic surfaces cause extreme thylakoid swelling under high light, indicating an essential role of VIPP1 lipid binding in resisting stress-induced damage. Using cryo-correlative light and electron microscopy (cryo-CLEM), we observe oligomeric VIPP1 coats encapsulating membrane tubules within the Chlamydomonas chloroplast. Our work provides a structural foundation for understanding how VIPP1 directs thylakoid biogenesis and maintenance.
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Affiliation(s)
- Tilak Kumar Gupta
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Sven Klumpe
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Karin Gries
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Steffen Heinz
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Wojciech Wietrzynski
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Justus Niemeyer
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Benjamin Spaniol
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Anna Rast
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Matthias Ostermeier
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Mike Strauss
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC H3A 17C, Canada
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Till Rudack
- Biospectroscopy, Center for Protein Diagnostics (PRODI), Ruhr University Bochum, 44801 Bochum, Germany; Department of Biophysics, Faculty of Biology & Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Jörg Nickelsen
- Department of Molecular Plant Sciences, LMU Munich, 82152 Martinsried, Germany
| | - Jan M Schuller
- SYNMIKRO Research Center and Department of Chemistry, Philipps-University Marburg, 35032 Marburg, Germany.
| | - Michael Schroda
- Molecular Biotechnology and Systems Biology, Technische Universität Kaiserslautern, 67663 Kaiserslautern, Germany.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Department of Chemistry, Technical University of Munich, 85748 Garching, Germany.
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38
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Junglas B, Huber ST, Heidler T, Schlösser L, Mann D, Hennig R, Clarke M, Hellmann N, Schneider D, Sachse C. PspA adopts an ESCRT-III-like fold and remodels bacterial membranes. Cell 2021; 184:3674-3688.e18. [PMID: 34166616 DOI: 10.1016/j.cell.2021.05.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/01/2021] [Accepted: 05/26/2021] [Indexed: 12/31/2022]
Abstract
PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 Å resolution cryoelectron microscopy (cryo-EM) structure of PspA assembled in helical rods. PspA monomers adopt a canonical ESCRT-III fold in an extended open conformation. PspA rods are capable of enclosing lipids and generating positive membrane curvature. Using cryo-EM, we visualized how PspA remodels membrane vesicles into μm-sized structures and how it mediates the formation of internalized vesicular structures. Hotspots of these activities are zones derived from PspA assemblies, serving as lipid transfer platforms and linking previously separated lipid structures. These membrane fusion and fission activities are in line with the described functional properties of bacterial PspA/IM30/LiaH proteins. Our structural and functional analyses reveal that bacterial PspA belongs to the evolutionary ancestry of ESCRT-III proteins involved in membrane remodeling.
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Affiliation(s)
- Benedikt Junglas
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Stefan T Huber
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Thomas Heidler
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lukas Schlösser
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Daniel Mann
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Raoul Hennig
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Mairi Clarke
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; Institute of Molecular Physiology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany.
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Department of Biology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany.
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39
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Banjade S, Shah YH, Tang S, Emr SD. Design principles of the ESCRT-III Vps24-Vps2 module. eLife 2021; 10:67709. [PMID: 34028356 PMCID: PMC8143795 DOI: 10.7554/elife.67709] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/11/2021] [Indexed: 12/16/2022] Open
Abstract
ESCRT-III polymerization is required for all endosomal sorting complex required for transport (ESCRT)-dependent events in the cell. However, the relative contributions of the eight ESCRT-III subunits differ between each process. The minimal features of ESCRT-III proteins necessary for function and the role for the multiple ESCRT-III subunits remain unclear. To identify essential features of ESCRT-III subunits, we previously studied the polymerization mechanisms of two ESCRT-III subunits Snf7 and Vps24, identifying the association of the helix-4 region of Snf7 with the helix-1 region of Vps24 (Banjade et al., 2019a). Here, we find that mutations in the helix-1 region of another ESCRT-III subunit Vps2 can functionally replace Vps24 in Saccharomyces cerevisiae. Engineering and genetic selections revealed the required features of both subunits. Our data allow us to propose three minimal features required for ESCRT-III function – spiral formation, lateral association of the spirals through heteropolymerization, and binding to the AAA + ATPase Vps4 for dynamic remodeling.
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Affiliation(s)
- Sudeep Banjade
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Yousuf H Shah
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Shaogeng Tang
- Department of Biochemistry, Stanford University, Stanford, United States
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
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40
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Pfitzner AK, Moser von Filseck J, Roux A. Principles of membrane remodeling by dynamic ESCRT-III polymers. Trends Cell Biol 2021; 31:856-868. [PMID: 33980463 DOI: 10.1016/j.tcb.2021.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Endosomal protein complex required for transport-III (ESCRT-III) polymers are involved in many crucial cellular functions, from cell division to endosome-lysosome dynamics. As a eukaryotic membrane remodeling machinery, ESCRT-III is unique in its ability to catalyze fission of membrane necks from their luminal side and to participate in membrane remodeling processes of essentially all cellular organelles. Found in Archaea, it is also the most evolutionary ancient membrane remodeling machinery. The simple protein structure shared by all of its subunits assembles into a large variety of filament shapes, limiting our understanding of how these filaments achieve membrane remodeling. Here, we review recent findings that discovered unpredicted properties of ESCRT-III polymers, which enable us to define general principles of the mechanism by which ESCRT-III filaments remodel membranes.
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Affiliation(s)
| | | | - Aurélien Roux
- Biochemistry Department, University of Geneva, CH-1211 Geneva, Switzerland; Swiss National Centre for Competence in Research Programme Chemical Biology, CH-1211 Geneva, Switzerland.
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41
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Alqabandi M, de Franceschi N, Maity S, Miguet N, Bally M, Roos WH, Weissenhorn W, Bassereau P, Mangenot S. The ESCRT-III isoforms CHMP2A and CHMP2B display different effects on membranes upon polymerization. BMC Biol 2021; 19:66. [PMID: 33832485 PMCID: PMC8033747 DOI: 10.1186/s12915-021-00983-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/16/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND ESCRT-III proteins are involved in many membrane remodeling processes including multivesicular body biogenesis as first discovered in yeast. In humans, ESCRT-III CHMP2 exists as two isoforms, CHMP2A and CHMP2B, but their physical characteristics have not been compared yet. RESULTS Here, we use a combination of techniques on biomimetic systems and purified proteins to study their affinity and effects on membranes. We establish that CHMP2B binding is enhanced in the presence of PI(4,5)P2 lipids. In contrast, CHMP2A does not display lipid specificity and requires CHMP3 for binding significantly to membranes. On the micrometer scale and at moderate bulk concentrations, CHMP2B forms a reticular structure on membranes whereas CHMP2A (+CHMP3) binds homogeneously. Thus, CHMP2A and CHMP2B unexpectedly induce different mechanical effects to membranes: CHMP2B strongly rigidifies them while CHMP2A (+CHMP3) has no significant effect. CONCLUSIONS We therefore conclude that CHMP2B and CHMP2A exhibit different mechanical properties and might thus contribute differently to the diverse ESCRT-III-catalyzed membrane remodeling processes.
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Affiliation(s)
- Maryam Alqabandi
- Laboratoire Physico Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Nicola de Franceschi
- Laboratoire Physico Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nolwenn Miguet
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Marta Bally
- Umeå University, Department of Clinical Microbiology & Wallenberg Centre for Molecular Medicine, 90185, Umeå, Sweden
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Winfried Weissenhorn
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, 75005, Paris, France
| | - Stéphanie Mangenot
- Laboratoire Physico Chimie Curie, Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, 75005, Paris, France.
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Nguyen HC, Melo AA, Kruk J, Frost A, Gabruk M. Photocatalytic LPOR forms helical lattices that shape membranes for chlorophyll synthesis. NATURE PLANTS 2021; 7:437-444. [PMID: 33875834 DOI: 10.1038/s41477-021-00885-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/19/2021] [Indexed: 05/21/2023]
Abstract
Chlorophyll biosynthesis, crucial to life on Earth, is tightly regulated because its precursors are phototoxic1. In flowering plants, the enzyme light-dependent protochlorophyllide oxidoreductase (LPOR) captures photons to catalyse the penultimate reaction: the reduction of a double bond within protochlorophyllide (Pchlide) to generate chlorophyllide (Chlide)2,3. In darkness, LPOR oligomerizes to facilitate photon energy transfer and catalysis4,5. However, the complete three-dimensional structure of LPOR, the higher-order architecture of LPOR oligomers and the implications of these self-assembled states for catalysis, including how LPOR positions Pchlide and the co-factor NADPH, remain unknown. Here, we report the atomic structure of LPOR assemblies by electron cryo-microscopy. LPOR polymerizes with its substrates into helical filaments around constricted lipid bilayer tubes. Portions of LPOR and Pchlide insert into the outer membrane leaflet, targeting the product, Chlide, to the membrane for the final reaction site of chlorophyll biosynthesis. In addition to its crucial photocatalytic role, we show that in darkness LPOR filaments directly shape membranes into high-curvature tubules with the spectral properties of the prolamellar body, whose light-triggered disassembly provides lipids for thylakoid assembly. Moreover, our structure of the catalytic site challenges previously proposed reaction mechanisms6. Together, our results reveal a new and unexpected synergy between photosynthetic membrane biogenesis and chlorophyll synthesis in plants, orchestrated by LPOR.
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Affiliation(s)
- Henry C Nguyen
- Department of Biochemistry & Biophysics, Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.
- Asher Biotherapeutics, South San Francisco, CA, USA.
| | - Arthur A Melo
- Department of Biochemistry & Biophysics, Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
| | - Jerzy Kruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Adam Frost
- Department of Biochemistry & Biophysics, Quantitative Biosciences Institute, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Michal Gabruk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
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Davis OB, Shin HR, Lim CY, Wu EY, Kukurugya M, Maher CF, Perera RM, Ordonez MP, Zoncu R. NPC1-mTORC1 Signaling Couples Cholesterol Sensing to Organelle Homeostasis and Is a Targetable Pathway in Niemann-Pick Type C. Dev Cell 2020; 56:260-276.e7. [PMID: 33308480 DOI: 10.1016/j.devcel.2020.11.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/05/2020] [Accepted: 11/17/2020] [Indexed: 01/22/2023]
Abstract
Lysosomes promote cellular homeostasis through macromolecular hydrolysis within their lumen and metabolic signaling by the mTORC1 kinase on their limiting membranes. Both hydrolytic and signaling functions require precise regulation of lysosomal cholesterol content. In Niemann-Pick type C (NPC), loss of the cholesterol exporter, NPC1, causes cholesterol accumulation within lysosomes, leading to mTORC1 hyperactivation, disrupted mitochondrial function, and neurodegeneration. The compositional and functional alterations in NPC lysosomes and nature of aberrant cholesterol-mTORC1 signaling contribution to organelle pathogenesis are not understood. Through proteomic profiling of NPC lysosomes, we find pronounced proteolytic impairment compounded with hydrolase depletion, enhanced membrane damage, and defective mitophagy. Genetic and pharmacologic mTORC1 inhibition restores lysosomal proteolysis without correcting cholesterol storage, implicating aberrant mTORC1 as a pathogenic driver downstream of cholesterol accumulation. Consistently, mTORC1 inhibition ameliorates mitochondrial dysfunction in a neuronal model of NPC. Thus, cholesterol-mTORC1 signaling controls organelle homeostasis and is a targetable pathway in NPC.
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Affiliation(s)
- Oliver B Davis
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hijai R Shin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Chun-Yan Lim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Emma Y Wu
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Pediatric Gastroenterology, Hepatology, and Nutrition, University of California, San Diego, La Jolla, CA 92037, USA
| | - Matthew Kukurugya
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Claire F Maher
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rushika M Perera
- Department of Anatomy and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - M Paulina Ordonez
- Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Department of Pediatric Gastroenterology, Hepatology, and Nutrition, University of California, San Diego, La Jolla, CA 92037, USA.
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA 94720, USA.
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44
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McCullough J, Sundquist WI. Membrane Remodeling: ESCRT-III Filaments as Molecular Garrotes. Curr Biol 2020; 30:R1425-R1428. [DOI: 10.1016/j.cub.2020.09.086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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45
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Horváth P, Müller-Reichert T. A Structural View on ESCRT-Mediated Abscission. Front Cell Dev Biol 2020; 8:586880. [PMID: 33240884 PMCID: PMC7680848 DOI: 10.3389/fcell.2020.586880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/16/2020] [Indexed: 11/25/2022] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) mediates cellular processes that are related to membrane remodeling, such as multivesicular body (MVB) formation, viral budding and cytokinesis. Abscission is the final stage of cytokinesis that results in the physical separation of the newly formed two daughter cells. Although abscission has been investigated for decades, there are still fundamental open questions related to the spatio-temporal organization of the molecular machinery involved in this process. Reviewing knowledge obtained from in vitro as well as in vivo experiments, we give a brief overview on the role of ESCRT components in abscission mainly focussing on mammalian cells.
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Affiliation(s)
- Péter Horváth
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Thomas Müller-Reichert
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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46
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Abstract
The endosomal sorting complexes required for transport (ESCRTs) I, -II and -III, and their associated factors are a collection of ∼20 proteins in yeast and ∼30 in mammals, responsible for severing membrane necks in processes that range from multivesicular body formation, HIV release and cytokinesis, to plasma and lysosomal membrane repair. ESCRTs are best known for 'reverse-topology' membrane scission, where they act on the inner surface of membrane necks, often when membranes are budded away from the cytosol. These events are driven by membrane-associated assemblies of dozens to hundreds of ESCRT molecules. ESCRT-III proteins form filaments with a variety of geometries and ESCRT-I has now been shown to also form helical structures. The complex nature of the system and the unusual topology of its action has made progress challenging, and led to controversies with regard to its underlying mechanism. This Review will focus on recent advances obtained by structural in vitro reconstitution and in silico mechanistic studies, and places them in their biological context. The field is converging towards a consensus on the broad outlines of a mechanism that is driven by a progressive ATP-dependent treadmilling exchange of ESCRT subunits, as well as compositional change and geometric transitions in ESCRT filaments.
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Affiliation(s)
- Mark Remec Pavlin
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James H Hurley
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA .,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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47
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Pfitzner AK, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission. Cell 2020; 182:1140-1155.e18. [PMID: 32814015 PMCID: PMC7479521 DOI: 10.1016/j.cell.2020.07.021] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/04/2020] [Accepted: 07/15/2020] [Indexed: 01/02/2023]
Abstract
The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity.
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Affiliation(s)
| | - Vincent Mercier
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland; National Center of Competence in Research in Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Xiuyun Jiang
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Buzz Baum
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland; National Center of Competence in Research in Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.
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Abstract
During viral replication, herpesviruses utilize a unique strategy, termed nuclear egress, to translocate capsids from the nucleus into the cytoplasm. This initial budding step transfers a newly formed capsid from within the nucleus, too large to fit through nuclear pores, through the inner nuclear membrane to the perinuclear space. The perinuclear enveloped virion must then fuse with the outer nuclear membrane to be released into the cytoplasm for further maturation, undergoing budding once again at the trans-Golgi network or early endosomes, and ultimately exit the cell non-lytically to spread infection. This first budding process is mediated by two conserved viral proteins, UL31 and UL34, that form a heterodimer called the nuclear egress complex (NEC). This review focuses on what we know about how the NEC mediates capsid transport to the perinuclear space, including steps prior to and after this budding event. Additionally, we discuss the involvement of other viral proteins in this process and how NEC-mediated budding may be regulated during infection.
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Affiliation(s)
- Elizabeth B Draganova
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Michael K Thorsen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Ekaterina E Heldwein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
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Bertin A, de Franceschi N, de la Mora E, Maity S, Alqabandi M, Miguet N, di Cicco A, Roos WH, Mangenot S, Weissenhorn W, Bassereau P. Human ESCRT-III polymers assemble on positively curved membranes and induce helical membrane tube formation. Nat Commun 2020; 11:2663. [PMID: 32471988 PMCID: PMC7260177 DOI: 10.1038/s41467-020-16368-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
Endosomal sorting complexes for transport-III (ESCRT-III) assemble in vivo onto membranes with negative Gaussian curvature. How membrane shape influences ESCRT-III polymerization and how ESCRT-III shapes membranes is yet unclear. Human core ESCRT-III proteins, CHMP4B, CHMP2A, CHMP2B and CHMP3 are used to address this issue in vitro by combining membrane nanotube pulling experiments, cryo-electron tomography and AFM. We show that CHMP4B filaments preferentially bind to flat membranes or to tubes with positive mean curvature. Both CHMP2B and CHMP2A/CHMP3 assemble on positively curved membrane tubes. Combinations of CHMP4B/CHMP2B and CHMP4B/CHMP2A/CHMP3 are recruited to the neck of pulled membrane tubes and reshape vesicles into helical "corkscrew-like" membrane tubes. Sub-tomogram averaging reveals that the ESCRT-III filaments assemble parallel and locally perpendicular to the tube axis, highlighting the mechanical stresses imposed by ESCRT-III. Our results underline the versatile membrane remodeling activity of ESCRT-III that may be a general feature required for cellular membrane remodeling processes.
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Affiliation(s)
- Aurélie Bertin
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France.
- Sorbonne Université, 75005, Paris, France.
| | - Nicola de Franceschi
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France.
- Sorbonne Université, 75005, Paris, France.
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, avenue des Martyrs, 38000, Grenoble, France.
| | - Eugenio de la Mora
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France
- Sorbonne Université, 75005, Paris, France
| | - Sourav Maity
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands
| | - Maryam Alqabandi
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France
- Sorbonne Université, 75005, Paris, France
| | - Nolwen Miguet
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, avenue des Martyrs, 38000, Grenoble, France
| | - Aurélie di Cicco
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France
- Sorbonne Université, 75005, Paris, France
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Nijenborgh 4, 9747, AG Groningen, The Netherlands
| | - Stéphanie Mangenot
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France
- Sorbonne Université, 75005, Paris, France
| | - Winfried Weissenhorn
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 71, avenue des Martyrs, 38000, Grenoble, France.
| | - Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France.
- Sorbonne Université, 75005, Paris, France.
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