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Suzuki K, Okawa Y, Akter S, Ito H, Shiba Y. Arf GTPase-Activating proteins ADAP1 and ARAP1 regulate incorporation of CD63 in multivesicular bodies. Biol Open 2024; 13:bio060338. [PMID: 38682696 PMCID: PMC11103404 DOI: 10.1242/bio.060338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024] Open
Abstract
Arf GTPase-activating proteins (ArfGAPs) mediate the hydrolysis of GTP bound to ADP-ribosylation factors. ArfGAPs are critical for cargo sorting in the Golgi-to-ER traffic. However, the role of ArfGAPs in sorting into intralumenal vesicles (ILVs) in multivesicular bodies (MVBs) in post-Golgi traffic remains unclear. Exosomes are extracellular vesicles (EVs) of endosomal origin. CD63 is an EV marker. CD63 is enriched ILVs in MVBs of cells. However, the secretion of CD63 positive EVs has not been consistent with the data on CD63 localization in MVBs, and how CD63-containing EVs are formed is yet to be understood. To elucidate the mechanism of CD63 transport to ILVs, we focused on CD63 localization in MVBs and searched for the ArfGAPs involved in CD63 localization. We observed that ADAP1 and ARAP1 depletion inhibited CD63 localization to enlarged endosomes after Rab5Q79L overexpression. We tested epidermal growth factor (EGF) and CD9 localization in MVBs. We observed that ADAP1 and ARAP1 depletion inhibited CD9 localization in enlarged endosomes but not EGF. Our results indicate ADAP1 and ARAP1, regulate incorporation of CD63 and CD9, but not EGF, in overlapped and different MVBs. Our work will contribute to distinguish heterogenous ILVs and exosomes by ArfGAPs.
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Affiliation(s)
- Kasumi Suzuki
- Graduate course of Biological Sciences, Division of Science and Engineering, Graduate School of Arts and Sciences, Iwate University, 020-8551, Morioka, Japan
| | - Yoshitaka Okawa
- Graduate course of Biological Sciences, Division of Science and Engineering, Graduate School of Arts and Sciences, Iwate University, 020-8551, Morioka, Japan
| | - Sharmin Akter
- Graduate course of Biological Sciences, Division of Science and Engineering, Graduate School of Arts and Sciences, Iwate University, 020-8551, Morioka, Japan
| | - Haruki Ito
- Biological Sciences Course, Faculty of Science and Engineering, Iwate University, 020-8551, Morioka, Japan
| | - Yoko Shiba
- Graduate course of Biological Sciences, Division of Science and Engineering, Graduate School of Arts and Sciences, Iwate University, 020-8551, Morioka, Japan
- Biological Sciences Course, Faculty of Science and Engineering, Iwate University, 020-8551, Morioka, Japan
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2
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Pang X, Zhang Y, Park K, Liao Z, Li J, Xu J, Hong MT, Yin G, Zhang T, Wang Y, Egelman EH, Fan J, Park SY, Hsu VW, Sun F. Structural elucidation of how ARF small GTPases induce membrane tubulation for vesicle fission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572083. [PMID: 38187566 PMCID: PMC10769218 DOI: 10.1101/2023.12.19.572083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The ADP-Ribosylation Factor (ARF) small GTPases have been found to act in vesicle fission through a direct ability to tubulate membrane. Here, we have used cryo-electron microscopy (EM) to solve the structure of an ARF6 protein lattice assembled on tubulated membrane to 3.9 Å resolution. ARF6 forms tetramers that polymerize into helical arrays to form this lattice. We identify, and confirm functionally, protein contacts critical for this lattice formation. The solved structure also suggests how the ARF amphipathic helix is positioned in the lattice for membrane insertion, and how a GTPase-activating protein (GAP) docks onto the lattice to catalyze ARF-GTP hydrolysis in completing membrane fission. As ARF1 and ARF6 are structurally conserved, we have also modeled ARF1 onto the ARF6 lattice, which has allowed us to pursue the reconstitution of Coat Protein I (COPI) vesicles to confirm more definitively that the ARF lattice acts in vesicle fission. Our findings are notable for having achieved the first detailed glimpse of how a small GTPase bends membrane and having provided a molecular understanding of how an ARF protein acts in vesicle fission.
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Affiliation(s)
- Xiaoyun Pang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Equal contribution
| | - Yan Zhang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Equal contribution
| | - Kunyou Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
- Equal contribution
| | - Zhenyu Liao
- City University of Hong Kong, Hong Kong, China
| | - Jian Li
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Jiashu Xu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minh-Triet Hong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Guoliang Yin
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tongming Zhang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoyu Wang
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, VA 22908 USA
| | - Jun Fan
- City University of Hong Kong, Hong Kong, China
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Victor W Hsu
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Department of Medicine, Harvard Medical School, Boston, MA 02115 USA
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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3
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Dey D, Qing E, He Y, Chen Y, Jennings B, Cohn W, Singh S, Gakhar L, Schnicker NJ, Pierce BG, Whitelegge JP, Doray B, Orban J, Gallagher T, Hasan SS. A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs. Nat Commun 2023; 14:8358. [PMID: 38102143 PMCID: PMC10724246 DOI: 10.1038/s41467-023-44076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
The spike (S) protein of SARS-CoV-2 is delivered to the virion assembly site in the ER-Golgi Intermediate Compartment (ERGIC) from both the ER and cis-Golgi in infected cells. However, the relevance and modulatory mechanism of this bidirectional trafficking are unclear. Here, using structure-function analyses, we show that S incorporation into virus-like particles (VLP) and VLP fusogenicity are determined by coatomer-dependent S delivery from the cis-Golgi and restricted by S-coatomer dissociation. Although S mimicry of the host coatomer-binding dibasic motif ensures retrograde trafficking to the ERGIC, avoidance of the host-like C-terminal acidic residue is critical for S-coatomer dissociation and therefore incorporation into virions or export for cell-cell fusion. Because this C-terminal residue is the key determinant of SARS-CoV-2 assembly and fusogenicity, our work provides a framework for the export of S protein encoded in genetic vaccines for surface display and immune activation.
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Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Enya Qing
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Yanan He
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
| | - Yihong Chen
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
| | - Benjamin Jennings
- Department of Internal Medicine, Hematology Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Whitaker Cohn
- Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Suruchi Singh
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lokesh Gakhar
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Protein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- PAQ Therapeutics, Burlington, MA, 01803, USA
| | - Nicholas J Schnicker
- Protein and Crystallography Facility, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Balraj Doray
- Department of Internal Medicine, Hematology Division, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - John Orban
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, 60153, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD, 21201, USA.
- Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD, 20850, USA.
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4
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Dey D, Hasan SS. Strategies for rapid production of crystallization quality coatomer WD40 domains. Protein Expr Purif 2023; 212:106358. [PMID: 37625737 PMCID: PMC10529451 DOI: 10.1016/j.pep.2023.106358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
The vesicular secretion of soluble cargo proteins from the endoplasmic reticulum (ER) is accompanied by the export of ER-resident membrane proteins that are co-packaged in secretory vesicles. The cytosolic coatomer protein complex I (COPI) utilizes the N-terminal WD40 domains of α-COPI and β'-COPI subunits to bind these membrane protein "clients" for ER retrieval. These "αWD40" and "β'WD40" domains are structural homologs that demonstrate distinct selectivity for client proteins. However, elucidation of the atomic-level principles of coatomer-client interactions has been challenging due to the tendency of αWD40 domain to undergo aggregation during expression and purification. Here we describe a rapid recombinant production strategy from E. coli, which substantially enhances the quality of the purified αWD40 domain. The αWD40 purification and crystallization are completed within one day, which minimizes aggregation losses and yields a 1.9 Å resolution crystal structure. We demonstrate the versatility of this strategy by applying it to purify the β'WD40 domain, which yields crystal structures in the 1.2-1.3 Å resolution range. As an alternate recombinant production system, we develop a cost-effective strategy for αWD40 production in human Expi293 cells. Finally, we suggest a roadmap to simplify these protocols further, which is of significance for the production of WD40 mutants prone to rapid aggregation. The WD40 production strategies presented here are likely to have broad applications because the WD40 domain represents one of the largest families of biomolecular interaction modules in the eukaryotic proteome and is critical for trafficking of host as well as viral proteins such as the SARS-CoV-2 spike protein.
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Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, Baltimore, MD, 21201, USA; Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Rockville, MD, 20850, USA.
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5
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Manzer KM, Fromme JC. The Arf-GAP Age2 localizes to the late-Golgi via a conserved amphipathic helix. Mol Biol Cell 2023; 34:ar119. [PMID: 37672345 PMCID: PMC10846627 DOI: 10.1091/mbc.e23-07-0283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023] Open
Abstract
Arf GTPases are central regulators of the Golgi complex, which serves as the nexus of membrane-trafficking pathways in eukaryotic cells. Arf proteins recruit dozens of effectors to modify membranes, sort cargos, and create and tether transport vesicles, and are therefore essential for orchestrating Golgi trafficking. The regulation of Arf activity is controlled by the action of Arf-GEFs which activate via nucleotide exchange, and Arf-GAPs which inactivate via nucleotide hydrolysis. The localization dynamics of Arf GTPases and their Arf-GAPs during Golgi maturation have not been reported. Here we use the budding yeast model to examine the temporal localization of the Golgi Arf-GAPs. We also determine the mechanisms used by the Arf-GAP Age2 to localize to the Golgi. We find that the catalytic activity of Age2 and a conserved sequence in the unstructured C-terminal domain of Age2 are both required for Golgi localization. This sequence is predicted to form an amphipathic helix and mediates direct binding of Age2 to membranes in vitro. We also report the development of a probe for sensing active Arf1 in living cells and use this probe to characterize the temporal dynamics of Arf1 during Golgi maturation.
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Affiliation(s)
- Kaitlyn M. Manzer
- Department of Molecular Biology & Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850
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6
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Guo X, Zhang M, Liu X, Zhang Y, Wang C, Guo Y. Attachment, Entry, and Intracellular Trafficking of Classical Swine Fever Virus. Viruses 2023; 15:1870. [PMID: 37766277 PMCID: PMC10534341 DOI: 10.3390/v15091870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Classical swine fever virus (CSFV), which is a positive-sense, single-stranded RNA virus with an envelope, is a member of the Pestivirus genus in the Flaviviridae family. CSFV causes a severe and highly contagious disease in pigs and is prevalent worldwide, threatening the pig farming industry. The detailed mechanisms of the CSFV life cycle have been reported, but are still limited. Some receptors and attachment factors of CSFV, including heparan sulfate (HS), laminin receptor (LamR), complement regulatory protein (CD46), MER tyrosine kinase (MERTK), disintegrin, and metalloproteinase domain-containing protein 17 (ADAM17), were identified. After attachment, CSFV internalizes via clathrin-mediated endocytosis (CME) and/or caveolae/raft-dependent endocytosis (CavME). After internalization, CSFV moves to early and late endosomes before uncoating. During this period, intracellular trafficking of CSFV relies on components of the endosomal sorting complex required for transport (ESCRT) and Rab proteins in the endosome dynamics, with a dependence on the cytoskeleton network. This review summarizes the data on the mechanisms of CSFV attachment, internalization pathways, and intracellular trafficking, and provides a general view of the early events in the CSFV life cycle.
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Affiliation(s)
| | | | | | | | | | - Yidi Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130012, China
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7
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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] [Grants] [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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8
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O'Donoghue L, Comer SP, Hiebner DW, Schoen I, von Kriegsheim A, Smolenski A. RhoGAP6 interacts with COPI to regulate protein transport. Biochem J 2023; 480:1109-1127. [PMID: 37409526 DOI: 10.1042/bcj20230013] [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: 01/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
RhoGAP6 is the most highly expressed GTPase-activating protein (GAP) in platelets specific for RhoA. Structurally RhoGAP6 contains a central catalytic GAP domain surrounded by large, disordered N- and C-termini of unknown function. Sequence analysis revealed three conserved consecutive overlapping di-tryptophan motifs close to the RhoGAP6 C-terminus which were predicted to bind to the mu homology domain (MHD) of δ-COP, a component of the COPI vesicle complex. We confirmed an endogenous interaction between RhoGAP6 and δ-COP in human platelets using GST-CD2AP which binds an N-terminal RhoGAP6 SH3 binding motif. Next, we confirmed that the MHD of δ-COP and the di-tryptophan motifs of RhoGAP6 mediate the interaction between both proteins. Each of the three di-tryptophan motifs appeared necessary for stable δ-COP binding. Proteomic analysis of other potential RhoGAP6 di-tryptophan motif binding partners indicated that the RhoGAP6/δ-COP interaction connects RhoGAP6 to the whole COPI complex. 14-3-3 was also established as a RhoGAP6 binding partner and its binding site was mapped to serine 37. We provide evidence of potential cross-regulation between 14-3-3 and δ-COP binding, however, neither δ-COP nor 14-3-3 binding to RhoGAP6 impacted RhoA activity. Instead, analysis of protein transport through the secretory pathway demonstrated that RhoGAP6/δ-COP binding increased protein transport to the plasma membrane, as did a catalytically inactive mutant of RhoGAP6. Overall, we have identified a novel interaction between RhoGAP6 and δ-COP which is mediated by conserved C-terminal di-tryptophan motifs, and which might control protein transport in platelets.
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Affiliation(s)
- Lorna O'Donoghue
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
| | - Shane P Comer
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
| | - Dishon W Hiebner
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- UCD School of Chemical & Bioprocess Engineering, Engineering & Materials Science Centre, University College Dublin, Belfield Dublin 4, Ireland
| | - Ingmar Schoen
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St Stephen's Green, Dublin D02 YN77, Ireland
| | - Alex von Kriegsheim
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, U.K
| | - Albert Smolenski
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St Stephen's Green, Dublin D02 YN77, Ireland
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9
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Manzer KM, Fromme JC. The Arf-GAP Age2 localizes to the late-Golgi via a conserved amphipathic helix. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550229. [PMID: 37546741 PMCID: PMC10402032 DOI: 10.1101/2023.07.23.550229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Arf GTPases are central regulators of the Golgi complex, which serves as the nexus of membrane trafficking pathways in eukaryotic cells. Arf proteins recruit dozens of effectors to modify membranes, sort cargos, and create and tether transport vesicles, and are therefore essential for orchestrating Golgi trafficking. The regulation of Arf activity is controlled by the action of Arf-GEFs, which activate via nucleotide exchange, and Arf-GAPs, which inactivate via nucleotide hydrolysis. The localization dynamics of Arf GTPases and their Arf-GAPs during Golgi maturation have not been reported. Here we use the budding yeast model to examine the temporal localization of the Golgi Arf-GAPs. We also determine the mechanisms used by the Arf-GAP Age2 to localize to the Golgi. We find that the catalytic activity of Age2 and a conserved sequence in the unstructured C-terminal domain of Age2 are both required for Golgi localization. This sequence is predicted to form an amphipathic helix and mediates direct binding of Age2 to membranes in vitro . We also report the development of a probe for sensing active Arf1 in living cells and use this probe to characterize the temporal dynamics of Arf1 during Golgi maturation.
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Affiliation(s)
- Kaitlyn M Manzer
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - J Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
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10
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Tagiltsev G, Kelley R, Zhang X, Khavnekar S, Kotecha A, Plitzko JM, Briggs JAG. Structural Analysis of COPI Pathway in Chlamydomonas reinhardtii. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:895. [PMID: 37613410 DOI: 10.1093/micmic/ozad067.443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Grigory Tagiltsev
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ron Kelley
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Xianjun Zhang
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Sagar Khavnekar
- CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Jürgen M Plitzko
- CryoEM Technology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - John A G Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
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11
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Yong X, Jia G, Liu Z, Zhou C, Yi J, Tang Y, Chen L, Chen L, Wang Y, Sun Q, Billadeau D, Su Z, Jia D. Cryo-EM structure of the Mon1-Ccz1-RMC1 complex reveals molecular basis of metazoan RAB7A activation. Proc Natl Acad Sci U S A 2023; 120:e2301725120. [PMID: 37216550 PMCID: PMC10235969 DOI: 10.1073/pnas.2301725120] [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: 02/07/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
Understanding of the evolution of metazoans from their unicellular ancestors is a fundamental question in biology. In contrast to fungi which utilize the Mon1-Ccz1 dimeric complex to activate the small GTPase RAB7A, metazoans rely on the Mon1-Ccz1-RMC1 trimeric complex. Here, we report a near-atomic resolution cryogenic-electron microscopy structure of the Drosophila Mon1-Ccz1-RMC1 complex. RMC1 acts as a scaffolding subunit and binds to both Mon1 and Ccz1 on the surface opposite to the RAB7A-binding site, with many of the RMC1-contacting residues from Mon1 and Ccz1 unique to metazoans, explaining the binding specificity. Significantly, the assembly of RMC1 with Mon1-Ccz1 is required for cellular RAB7A activation, autophagic functions and organismal development in zebrafish. Our studies offer a molecular explanation for the different degree of subunit conservation across species, and provide an excellent example of how metazoan-specific proteins take over existing functions in unicellular organisms.
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Affiliation(s)
- Xin Yong
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Guowen Jia
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Zhe Liu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Chunzhuang Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Jiamin Yi
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Yingying Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Li Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
| | - Yuan Wang
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Qingxiang Sun
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Daniel D. Billadeau
- Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN55905
| | - Zhaoming Su
- Department of Geriatrics and National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University610044Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu610041, China
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12
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Abstract
Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
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Affiliation(s)
- Lindsey N Young
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
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13
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B.R. R, Shah N, Joshi P, Madhusudan MS, Balasubramanian N. Kinetics of Arf1 inactivation regulates Golgi organisation and function in non-adherent fibroblasts. Biol Open 2023; 12:bio059669. [PMID: 36946871 PMCID: PMC10187640 DOI: 10.1242/bio.059669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/13/2023] [Indexed: 03/23/2023] Open
Abstract
Arf1 belongs to the Arf family of small GTPases that localise at the Golgi and plasma membrane. Active Arf1 plays a crucial role in regulating Golgi organisation and function. In mouse fibroblasts, loss of adhesion triggers a consistent drop (∼50%) in Arf1 activation that causes the Golgi to disorganise but not fragment. In suspended cells, the trans-Golgi (GalTase) disperses more prominently than cis-Golgi (Man II), accompanied by increased active Arf1 (detected using GFP-ABD: ARHGAP10 Arf1 binding domain) associated with the cis-Golgi compartment. Re-adhesion restores Arf1 activation at the trans-Golgi as it reorganises. Arf1 activation at the Golgi is regulated by Arf1 Guanine nucleotide exchange factors (GEFs), GBF1, and BIG1/2. In non-adherent fibroblasts, the cis-medial Golgi provides a unique setting to test and understand the role GEF-mediated Arf1 activation has in regulating Golgi organisation. Labelled with Man II-GFP, non-adherent fibroblasts treated with increasing concentrations of Brefeldin-A (BFA) (which inhibits BIG1/2 and GBF1) or Golgicide A (GCA) (which inhibits GBF1 only) comparably decrease active Arf1 levels. They, however, cause a concentration-dependent increase in cis-medial Golgi fragmentation and fusion with the endoplasmic reticulum (ER). Using selected BFA and GCA concentrations, we find a change in the kinetics of Arf1 inactivation could mediate this by regulating cis-medial Golgi localisation of GBF1. On loss of adhesion, a ∼50% drop in Arf1 activation over 120 min causes the Golgi to disorganise. The kinetics of this drop, when altered by BFA or GCA treatment causes a similar decline in Arf1 activation but over 10 min. This causes the Golgi to now fragment which affects cell surface glycosylation and re-adherent cell spreading. Using non-adherent fibroblasts this study reveals the kinetics of Arf1 inactivation, with active Arf1 levels, to be vital for Golgi organisation and function.
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Affiliation(s)
- Rajeshwari B.R.
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Nikita Shah
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Prachi Joshi
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - M. S. Madhusudan
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
| | - Nagaraj Balasubramanian
- Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pashan, Pune, Maharashtra 411008, India
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14
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Xie B, Guillem C, Date SS, Cohen CI, Jung C, Kendall AK, Best JT, Graham TR, Jackson LP. An interaction between β'-COP and the ArfGAP, Glo3, maintains post-Golgi cargo recycling. J Cell Biol 2023; 222:e202008061. [PMID: 36811888 PMCID: PMC9960064 DOI: 10.1083/jcb.202008061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 07/14/2022] [Accepted: 01/24/2023] [Indexed: 02/24/2023] Open
Abstract
The essential COPI coat mediates retrieval of transmembrane proteins at the Golgi and endosomes following recruitment by the small GTPase, Arf1. ArfGAP proteins regulate COPI coats, but molecular details for COPI recognition by ArfGAPs remain elusive. Biochemical and biophysical data reveal how β'-COP propeller domains directly engage the yeast ArfGAP, Glo3, with a low micromolar binding affinity. Calorimetry data demonstrate that both β'-COP propeller domains are required to bind Glo3. An acidic patch on β'-COP (D437/D450) interacts with Glo3 lysine residues located within the BoCCS (binding of coatomer, cargo, and SNAREs) region. Targeted point mutations in either Glo3 BoCCS or β'-COP abrogate the interaction in vitro, and loss of the β'-COP/Glo3 interaction drives Ste2 missorting to the vacuole and aberrant Golgi morphology in budding yeast. These data suggest that cells require the β'-COP/Glo3 interaction for cargo recycling via endosomes and the TGN, where β'-COP serves as a molecular platform to coordinate binding to multiple proteins, including Glo3, Arf1, and the COPI F-subcomplex.
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Affiliation(s)
- Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Clara Guillem
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Swapneeta S. Date
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Cameron I. Cohen
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Christian Jung
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jordan T. Best
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R. Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
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15
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Taylor RJ, Tagiltsev G, Briggs JAG. The structure of COPI vesicles and regulation of vesicle turnover. FEBS Lett 2023; 597:819-835. [PMID: 36513395 DOI: 10.1002/1873-3468.14560] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022]
Abstract
COPI-coated vesicles mediate transport between Golgi stacks and retrograde transport from the Golgi to the endoplasmic reticulum. The COPI coat exists as a stable heptameric complex in the cytosol termed coatomer and is recruited en bloc to the membrane for vesicle formation. Recruitment of COPI onto membranes is mediated by the Arf family of small GTPases, which, in their GTP-bound state, bind both membrane and coatomer. Arf GTPases also influence cargo selection, vesicle scission and vesicle uncoating. Guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) regulate nucleotide binding by Arf GTPases. To understand the mechanism of COPI-coated vesicle trafficking, it is necessary to characterize the interplay between coatomer and Arf GTPases and their effectors. It is also necessary to understand interactions between coatomer and cargo, cargo adaptors/receptors and tethers facilitating binding to the target membrane. Here, we summarize current knowledge of COPI coat protein structure; we describe how structural and biochemical studies contributed to this knowledge; we review mechanistic insights into COPI vesicle biogenesis and disassembly; and we discuss the potential to answer open questions in the field.
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Affiliation(s)
- Rebecca J Taylor
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Grigory Tagiltsev
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - John A G Briggs
- Department of Cell and Virus Structure, Max Planck Institute of Biochemistry, Martinsried, Germany
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16
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Nawrotek A, Dubois P, Zeghouf M, Cherfils J. Molecular principles of bidirectional signalling between membranes and small GTPases. FEBS Lett 2023; 597:778-793. [PMID: 36700390 DOI: 10.1002/1873-3468.14585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/23/2022] [Accepted: 12/30/2022] [Indexed: 01/27/2023]
Abstract
Most small GTPases actuate their functions on subcellular membranes, which are increasingly seen as integral components of small GTPase signalling. In this review, we used the highly studied regulation of Arf GTPases by their GEFs to categorize the molecular principles of membrane contributions to small GTPase signalling, which have been highlighted by integrated structural biology combining in vitro reconstitutions in artificial membranes and high-resolution structures. As an illustration of how this framework can be harnessed to better understand the cooperation between small GTPases, their regulators and membranes, we applied it to the activation of the small GTPase Rac1 by DOCK-ELMO, identifying novel contributions of membranes to Rac1 activation. We propose that these structure-based principles should be considered when interrogating the mechanisms whereby small GTPase systems ensure spatial and temporal control of cellular signalling on membranes.
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Affiliation(s)
- Agata Nawrotek
- CNRS, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pavlina Dubois
- CNRS, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mahel Zeghouf
- CNRS, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jacqueline Cherfils
- CNRS, Ecole Normale Supérieure Paris-Saclay and Université Paris-Saclay, Gif-sur-Yvette, France
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17
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Kozlov MM, Taraska JW. Generation of nanoscopic membrane curvature for membrane trafficking. Nat Rev Mol Cell Biol 2023; 24:63-78. [PMID: 35918535 DOI: 10.1038/s41580-022-00511-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2022] [Indexed: 11/09/2022]
Abstract
Curved membranes are key features of intracellular organelles, and their generation involves dynamic protein complexes. Here we describe the fundamental mechanisms such as the hydrophobic insertion, scaffolding and crowding mechanisms these proteins use to produce membrane curvatures and complex shapes required to form intracellular organelles and vesicular structures involved in endocytosis and secretion. For each mechanism, we discuss its cellular functions as well as the underlying physical principles and the specific membrane properties required for the mechanism to be feasible. We propose that the integration of individual mechanisms into a highly controlled, robust process of curvature generation often relies on the assembly of proteins into coats. How cells unify and organize the curvature-generating factors at the nanoscale is presented for three ubiquitous coats central for membrane trafficking in eukaryotes: clathrin-coated pits, caveolae, and COPI and COPII coats. The emerging theme is that these coats arrange and coordinate curvature-generating factors in time and space to dynamically shape membranes to accomplish membrane trafficking within cells.
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Affiliation(s)
- Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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18
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Wang C, Wojtynek M, Medalia O. Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography. Adv Biol Regul 2023; 87:100923. [PMID: 36280452 DOI: 10.1016/j.jbior.2022.100923] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
Cryo-electron tomography (cryo-ET) combines a close-to-life preservation of the cell with high-resolution three-dimensional (3D) imaging. This allows to study the molecular architecture of the cellular landscape and provides unprecedented views on biological processes and structures. In this review we mainly focus on the application of cryo-ET to visualize and structurally characterize eukaryotic cells - from the periphery to the cellular interior. We discuss strategies that can be employed to investigate the structure of challenging targets in their cellular environment as well as the application of complimentary approaches in conjunction with cryo-ET.
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Affiliation(s)
- Chunyang Wang
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Wojtynek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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19
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Hesketh SJ, Mukhopadhyay AG, Nakamura D, Toropova K, Roberts AJ. IFT-A structure reveals carriages for membrane protein transport into cilia. Cell 2022; 185:4971-4985.e16. [PMID: 36462505 DOI: 10.1016/j.cell.2022.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022]
Abstract
Intraflagellar transport (IFT) trains are massive molecular machines that traffic proteins between cilia and the cell body. Each IFT train is a dynamic polymer of two large complexes (IFT-A and -B) and motor proteins, posing a formidable challenge to mechanistic understanding. Here, we reconstituted the complete human IFT-A complex and obtained its structure using cryo-EM. Combined with AlphaFold prediction and genome-editing studies, our results illuminate how IFT-A polymerizes, interacts with IFT-B, and uses an array of β-propeller and TPR domains to create "carriages" of the IFT train that engage TULP adaptor proteins. We show that IFT-A⋅TULP carriages are essential for cilia localization of diverse membrane proteins, as well as ICK-the key kinase regulating IFT train turnaround. These data establish a structural link between IFT-A's distinct functions, provide a blueprint for IFT-A in the train, and shed light on how IFT evolved from a proto-coatomer ancestor.
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Affiliation(s)
- Sophie J Hesketh
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Aakash G Mukhopadhyay
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Dai Nakamura
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK
| | - Katerina Toropova
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK.
| | - Anthony J Roberts
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck University of London, London, WC1E 7HX, UK.
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20
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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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21
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Zabeo D, Davies KM. Studying membrane modulation mechanisms by electron cryo-tomography. Curr Opin Struct Biol 2022; 77:102464. [PMID: 36174286 DOI: 10.1016/j.sbi.2022.102464] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022]
Abstract
Membrane modulation is a key part of cellular life. Critical to processes like energy production, cell division, trafficking, migration and even pathogen entry, defects in membrane modulation are often associated with diseases. Studying the molecular mechanisms of membrane modulation is challenging due to the highly dynamic nature of the oligomeric assemblies involved, which adopt multiple conformations depending on the precise event they are participating in. With the development of electron cryo-tomography and subtomogram averaging, many of these challenges are being resolved as it is now possible to observe complex macromolecular assemblies inside a cell at nanometre to sub-nanometre resolutions. Here, we review the different ways electron cryo-tomography is being used to help uncover the molecular mechanisms used by cells to shape their membranes.
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Affiliation(s)
- Davide Zabeo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Karen M Davies
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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22
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Hooy RM, Iwamoto Y, Tudorica DA, Ren X, Hurley JH. Self-assembly and structure of a clathrin-independent AP-1:Arf1 tubular membrane coat. SCIENCE ADVANCES 2022; 8:eadd3914. [PMID: 36269825 PMCID: PMC9586487 DOI: 10.1126/sciadv.add3914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/01/2022] [Indexed: 05/28/2023]
Abstract
The adaptor protein (AP) complexes not only form the inner layer of clathrin coats but also have clathrin-independent roles in membrane traffic whose mechanisms are unknown. HIV-1 Nef hijacks AP-1 to sequester major histocompatibility complex class I (MHC-I), evading immune detection. We found that AP-1:Arf1:Nef:MHC-I forms a coat on tubulated membranes without clathrin and determined its structure. The coat assembles via Arf1 dimer interfaces. AP-1-positive tubules are enriched in cells upon clathrin knockdown. Nef localizes preferentially to AP-1 tubules in cells, explaining how Nef sequesters MHC-I. Coat contact residues are conserved across Arf isoforms and the Arf-dependent AP complexes AP-1, AP-3, and AP-4. Thus, AP complexes can self-assemble with Arf1 into tubular coats without clathrin or other scaffolding factors. The AP-1:Arf1 coat defines the structural basis of a broader class of tubulovesicular membrane coats as an intermediate in clathrin vesicle formation from internal membranes and as an MHC-I sequestration mechanism in HIV-1 infection.
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Affiliation(s)
- Richard M. Hooy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yuichiro Iwamoto
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dan A. Tudorica
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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23
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Cui L, Li H, Xi Y, Hu Q, Liu H, Fan J, Xiang Y, Zhang X, Shui W, Lai Y. Vesicle trafficking and vesicle fusion: mechanisms, biological functions, and their implications for potential disease therapy. MOLECULAR BIOMEDICINE 2022; 3:29. [PMID: 36129576 PMCID: PMC9492833 DOI: 10.1186/s43556-022-00090-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Intracellular vesicle trafficking is the fundamental process to maintain the homeostasis of membrane-enclosed organelles in eukaryotic cells. These organelles transport cargo from the donor membrane to the target membrane through the cargo containing vesicles. Vesicle trafficking pathway includes vesicle formation from the donor membrane, vesicle transport, and vesicle fusion with the target membrane. Coat protein mediated vesicle formation is a delicate membrane budding process for cargo molecules selection and package into vesicle carriers. Vesicle transport is a dynamic and specific process for the cargo containing vesicles translocation from the donor membrane to the target membrane. This process requires a group of conserved proteins such as Rab GTPases, motor adaptors, and motor proteins to ensure vesicle transport along cytoskeletal track. Soluble N-ethyl-maleimide-sensitive factor (NSF) attachment protein receptors (SNARE)-mediated vesicle fusion is the final process for vesicle unloading the cargo molecules at the target membrane. To ensure vesicle fusion occurring at a defined position and time pattern in eukaryotic cell, multiple fusogenic proteins, such as synaptotagmin (Syt), complexin (Cpx), Munc13, Munc18 and other tethering factors, cooperate together to precisely regulate the process of vesicle fusion. Dysfunctions of the fusogenic proteins in SNARE-mediated vesicle fusion are closely related to many diseases. Recent studies have suggested that stimulated membrane fusion can be manipulated pharmacologically via disruption the interface between the SNARE complex and Ca2+ sensor protein. Here, we summarize recent insights into the molecular mechanisms of vesicle trafficking, and implications for the development of new therapeutics based on the manipulation of vesicle fusion.
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24
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Langousis G, Cavadini S, Boegholm N, Lorentzen E, Kempf G, Matthias P. Structure of the ciliogenesis-associated CPLANE complex. SCIENCE ADVANCES 2022; 8:eabn0832. [PMID: 35427153 PMCID: PMC9012472 DOI: 10.1126/sciadv.abn0832] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Dysfunctional cilia cause pleiotropic human diseases termed ciliopathies. These hereditary maladies are often caused by defects in cilia assembly, a complex event that is regulated by the ciliogenesis and planar polarity effector (CPLANE) proteins Wdpcp, Inturned, and Fuzzy. CPLANE proteins are essential for building the cilium and are mutated in multiple ciliopathies, yet their structure and molecular functions remain elusive. Here, we show that mammalian CPLANE proteins comprise a bona fide complex and report the near-atomic resolution structures of the human Wdpcp-Inturned-Fuzzy complex and of the mouse Wdpcp-Inturned-Fuzzy complex bound to the small guanosine triphosphatase Rsg1. Notably, the crescent-shaped CPLANE complex binds phospholipids such as phosphatidylinositol 3-phosphate via multiple modules and a CPLANE ciliopathy mutant exhibits aberrant lipid binding. Our study provides critical structural and functional insights into an enigmatic ciliogenesis-associated complex as well as unexpected molecular rationales for ciliopathies.
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Affiliation(s)
- Gerasimos Langousis
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Niels Boegholm
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
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25
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Mehrani A, Stagg SM. Probing intracellular vesicle trafficking and membrane remodelling by cryo-EM. J Struct Biol 2022; 214:107836. [PMID: 35101600 PMCID: PMC8923612 DOI: 10.1016/j.jsb.2022.107836] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/07/2022] [Accepted: 01/24/2022] [Indexed: 11/25/2022]
Abstract
Protein transport between the membranous compartments of the eukaryotic cells is mediated by the constant fission and fusion of the membrane-bounded vesicles from a donor to an acceptor membrane. While there are many membrane remodelling complexes in eukaryotes, COPII, COPI, and clathrin-coated vesicles are the three principal classes of coat protein complexes that participate in vesicle trafficking in the endocytic and secretory pathways. These vesicle-coat proteins perform two key functions: deforming lipid bilayers into vesicles and encasing selective cargoes. The three trafficking complexes share some commonalities in their structural features but differ in their coat structures, mechanisms of cargo sorting, vesicle formation, and scission. While the structures of many of the proteins involved in vesicle formation have been determined in isolation by X-ray crystallography, elucidating the proteins' structures together with the membrane is better suited for cryogenic electron microscopy (cryo-EM). In recent years, advances in cryo-EM have led to solving the structures and mechanisms of several vesicle trafficking complexes and associated proteins.
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Affiliation(s)
- Atousa Mehrani
- Department of Chemistry and Biochemistry, Florida State University
| | - Scott M. Stagg
- Department of Biological Sciences, Florida State University,Institute of Molecular Biophysics, Florida State University
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26
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Foster HE, Ventura Santos C, Carter AP. A cryo-ET survey of microtubules and intracellular compartments in mammalian axons. J Cell Biol 2022; 221:e202103154. [PMID: 34878519 PMCID: PMC7612188 DOI: 10.1083/jcb.202103154] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022] Open
Abstract
The neuronal axon is packed with cytoskeletal filaments, membranes, and organelles, many of which move between the cell body and axon tip. Here, we used cryo-electron tomography to survey the internal components of mammalian sensory axons. We determined the polarity of the axonal microtubules (MTs) by combining subtomogram classification and visual inspection, finding MT plus and minus ends are structurally similar. Subtomogram averaging of globular densities in the MT lumen suggests they have a defined structure, which is surprising given they likely contain the disordered protein MAP6. We found the endoplasmic reticulum in axons is tethered to MTs through multiple short linkers. We surveyed membrane-bound cargos and describe unexpected internal features such as granules and broken membranes. In addition, we detected proteinaceous compartments, including numerous virus-like capsid particles. Our observations outline novel features of axonal cargos and MTs, providing a platform for identification of their constituents.
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27
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ARF1 with Sec7 domain-dependent GBF1 activates coatomer protein I to support classical swine fever virus entry. J Virol 2022; 96:e0219321. [PMID: 35044210 PMCID: PMC8941923 DOI: 10.1128/jvi.02193-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Classical swine fever virus (CSFV), a positive-sense, enveloped RNA virus that belongs to the Flaviviridae family, hijacks cell host proteins for its own replication. We previously demonstrated that Golgi-specific brefeldin A-resistance factor 1 (GBF1), a regulator of intracellular transport, mediates CSFV infection. However, the molecular mechanism by which this protein regulates CSFV proliferation remains unelucidated. In this study, we constructed a series of plasmids expressing GBF1 truncation mutants to investigate their behavior during CSFV infection and found that GBF1 truncation mutants containing the Sec7 domain could rescue CSFV replication in BFA (brefeldin A)- and GCA (Golgicide A)-treated swine umbilical vein endothelial cells (SUVECs), demonstrating that the effect of GBF1 on CSFV infection depended on the activity of guanine nucleotide exchange factor (GEF). Additionally, it was found that ADP ribosylation factors (ARFs), which are known to be activated by the Sec7 domain of GBF1, also regulated CSFV proliferation. Furthermore, we demonstrated that ARF1 is more important for CSFV infection than other ARF members with Sec7 domain dependence. Subsequent experiments established the function of coatomer protein I (COP I), a downstream effector of ARF1, which is also required for CSFV infection by mediating CSFV invasion. Mechanistically, inhibition of COP I function impaired CSFV invasion by inhibiting cholesterol transport to the plasma membrane, and regulating virion transport from early to late endosomes. Collectively, our results suggest that ARF1, with domain-dependent GBF1 Sec7, activates COP I to facilitate CSFV entry into SUVECs. Importance Classical swine fever (CSF), a highly contact infectious disease, caused by the classical swine fever virus (CSFV) infecting domestic pigs or wild boars, has caused huge economic losses to the pig industry. Our previous studies have revealed that GBF1 and class I and II ARFs are required for CSFV proliferation. However, a direct functional link between GBF1, ARF1, and COP I, and the mechanism of the GBF1-ARF1-COP I complex in CSFV infection is still poorly understood. Here, our data support a model in which COP I supports CSFV entry into SUVECs in two different ways, depending on the GBF1-ARF1 function. On the one hand, the GBF1-ARF1-COP I complex mediates cholesterol trafficking to the plasma membrane to support CSFV entry. On the other hand, the GBF1-ARF1-COP I complex mediates CSFV transport from early to late endosomes during the entry steps.
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28
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Pöge M, Mahamid J, Imanishi SS, Plitzko JM, Palczewski K, Baumeister W. Determinants shaping the nanoscale architecture of the mouse rod outer segment. eLife 2021; 10:e72817. [PMID: 34931611 PMCID: PMC8758146 DOI: 10.7554/elife.72817] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022] Open
Abstract
The unique membrane organization of the rod outer segment (ROS), the specialized sensory cilium of rod photoreceptor cells, provides the foundation for phototransduction, the initial step in vision. ROS architecture is characterized by a stack of identically shaped and tightly packed membrane disks loaded with the visual receptor rhodopsin. A wide range of genetic aberrations have been reported to compromise ROS ultrastructure, impairing photoreceptor viability and function. Yet, the structural basis giving rise to the remarkably precise arrangement of ROS membrane stacks and the molecular mechanisms underlying genetically inherited diseases remain elusive. Here, cryo-electron tomography (cryo-ET) performed on native ROS at molecular resolution provides insights into key structural determinants of ROS membrane architecture. Our data confirm the existence of two previously observed molecular connectors/spacers which likely contribute to the nanometer-scale precise stacking of the ROS disks. We further provide evidence that the extreme radius of curvature at the disk rims is enforced by a continuous supramolecular assembly composed of peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) oligomers. We suggest that together these molecular assemblies constitute the structural basis of the highly specialized ROS functional architecture. Our Cryo-ET data provide novel quantitative and structural information on the molecular architecture in ROS and substantiate previous results on proposed mechanisms underlying pathologies of certain PRPH2 mutations leading to blindness.
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Affiliation(s)
- Matthias Pöge
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Julia Mahamid
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Sanae S Imanishi
- Eugene and Marilyn Glick Eye Institute and the Department of Ophthalmology, Indiana University School of MedicineyIndianapolisUnited States
| | - Jürgen M Plitzko
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, Center for Translational Vision Research, Department of Physiology & Biophysics, Department of Chemistry, Department of Molecular Biology and BiochemistryIrvineUnited States
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
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29
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Determining structures in a native environment using single-particle cryoelectron microscopy images. ACTA ACUST UNITED AC 2021; 2:100166. [PMID: 34632438 PMCID: PMC8488058 DOI: 10.1016/j.xinn.2021.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/21/2021] [Indexed: 12/05/2022]
Abstract
Cryo-electron tomography is a powerful tool for structure determination in the native environment. However, this method requires the acquisition of tilt series, which is time-consuming and severely slows structure determination. By treating the densities of non-target protein as non-Gaussian noise, we developed a new target function that greatly improves the efficiency of recognizing the target protein in a single cryo-electron microscopy image. Moreover, we developed a sorting function that effectively eliminates the model dependence and improved the resolution during the subsequent structure refinement procedure. By eliminating model bias, our method allows using homolog proteins as models to recognize the target proteins in a complex context. Together, we developed an in situ single-particle analysis method. Our method was successfully applied to solve structures of glycoproteins on the surface of a non-icosahedral virus and Rubisco inside the carboxysome. Both data were collected within 24 h, thus allowing fast and simple structural determination. Structures could be achieved when proteins are overlapped with surroundings free of tilt series The particle detection efficiency is significantly improved Allowing the usage of homolog proteins as templates The throughput of structure determination is remarkably enhanced
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30
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Quidwai T, Wang J, Hall EA, Petriman NA, Leng W, Kiesel P, Wells JN, Murphy LC, Keighren MA, Marsh JA, Lorentzen E, Pigino G, Mill P. A WDR35-dependent coat protein complex transports ciliary membrane cargo vesicles to cilia. eLife 2021; 10:e69786. [PMID: 34734804 PMCID: PMC8754431 DOI: 10.7554/elife.69786] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. In Wdr35 mouse mutants, the non-core IFT-A components are degraded and core components accumulate at the ciliary base. We reveal deep sequence homology of WDR35 and other IFT-A subunits to α and ß' COPI coatomer subunits and demonstrate an accumulation of 'coat-less' vesicles that fail to fuse with Wdr35 mutant cilia. We determine that recombinant non-core IFT-As can bind directly to lipids and provide the first in situ evidence of a novel coat function for WDR35, likely with other IFT-A proteins, in delivering ciliary membrane cargo necessary for cilia elongation.
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Affiliation(s)
- Tooba Quidwai
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Jiaolong Wang
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Emma A Hall
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Narcis A Petriman
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Weihua Leng
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Petra Kiesel
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Laura C Murphy
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Margaret A Keighren
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
| | - Gaia Pigino
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
- Human TechnopoleMilanItaly
| | - Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of EdinburghEdinburghUnited Kingdom
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31
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Welch LG, Peak-Chew SY, Begum F, Stevens TJ, Munro S. GOLPH3 and GOLPH3L are broad-spectrum COPI adaptors for sorting into intra-Golgi transport vesicles. J Cell Biol 2021; 220:e202106115. [PMID: 34473204 PMCID: PMC8421267 DOI: 10.1083/jcb.202106115] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
The fidelity of Golgi glycosylation is, in part, ensured by compartmentalization of enzymes within the stack. The COPI adaptor GOLPH3 has been shown to interact with the cytoplasmic tails of a subset of Golgi enzymes and direct their retention. However, other mechanisms of retention, and other roles for GOLPH3, have been proposed, and a comprehensive characterization of the clientele of GOLPH3 and its paralogue GOLPH3L is lacking. GOLPH3's role is of particular interest as it is frequently amplified in several solid tumor types. Here, we apply two orthogonal proteomic methods to identify GOLPH3+3L clients and find that they act in diverse glycosylation pathways or have other roles in the Golgi. Binding studies, bioinformatics, and a Golgi retention assay show that GOLPH3+3L bind the cytoplasmic tails of their clients through membrane-proximal positively charged residues. Furthermore, deletion of GOLPH3+3L causes multiple defects in glycosylation. Thus, GOLPH3+3L are major COPI adaptors that impinge on most, if not all, of the glycosylation pathways of the Golgi.
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Affiliation(s)
| | | | | | | | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
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32
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Jalal ASB, Tran NT, Wu LJ, Ramakrishnan K, Rejzek M, Gobbato G, Stevenson CEM, Lawson DM, Errington J, Le TBK. CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc. Mol Cell 2021; 81:3623-3636.e6. [PMID: 34270916 DOI: 10.1101/2021.02.11.430593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/25/2021] [Accepted: 06/18/2021] [Indexed: 05/25/2023]
Abstract
ATP- and GTP-dependent molecular switches are extensively used to control functions of proteins in a wide range of biological processes. However, CTP switches are rarely reported. Here, we report that a nucleoid occlusion protein Noc is a CTPase enzyme whose membrane-binding activity is directly regulated by a CTP switch. In Bacillus subtilis, Noc nucleates on 16 bp NBS sites before associating with neighboring non-specific DNA to form large membrane-associated nucleoprotein complexes to physically occlude assembly of the cell division machinery. By in vitro reconstitution, we show that (1) CTP is required for Noc to form the NBS-dependent nucleoprotein complex, and (2) CTP binding, but not hydrolysis, switches Noc to a membrane-active state. Overall, we suggest that CTP couples membrane-binding activity of Noc to nucleoprotein complex formation to ensure productive recruitment of DNA to the bacterial cell membrane for nucleoid occlusion activity.
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Affiliation(s)
- Adam S B Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | | | - Martin Rejzek
- Chemistry Platform, John Innes Centre, Norwich, NR4 7UH, UK
| | - Giulia Gobbato
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
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33
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Elmasri Z, Nasal BL, Jose J. Alphavirus-Induced Membrane Rearrangements during Replication, Assembly, and Budding. Pathogens 2021; 10:984. [PMID: 34451448 PMCID: PMC8399458 DOI: 10.3390/pathogens10080984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 01/01/2023] Open
Abstract
Alphaviruses are arthropod-borne viruses mainly transmitted by hematophagous insects that cause moderate to fatal disease in humans and other animals. Currently, there are no approved vaccines or antivirals to mitigate alphavirus infections. In this review, we summarize the current knowledge of alphavirus-induced structures and their functions in infected cells. Throughout their lifecycle, alphaviruses induce several structural modifications, including replication spherules, type I and type II cytopathic vacuoles, and filopodial extensions. Type I cytopathic vacuoles are replication-induced structures containing replication spherules that are sites of RNA replication on the endosomal and lysosomal limiting membrane. Type II cytopathic vacuoles are assembly induced structures that originate from the Golgi apparatus. Filopodial extensions are induced at the plasma membrane and are involved in budding and cell-to-cell transport of virions. This review provides an overview of the viral and host factors involved in the biogenesis and function of these virus-induced structures. Understanding virus-host interactions in infected cells will lead to the identification of new targets for antiviral discovery.
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Affiliation(s)
- Zeinab Elmasri
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Department of Biochemistry & Molecular Biology, Eberly College of Science, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Benjamin L. Nasal
- Department of Biochemistry & Molecular Biology, Eberly College of Science, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Joyce Jose
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Department of Biochemistry & Molecular Biology, Eberly College of Science, The Pennsylvania State University, University Park, PA 16802, USA;
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34
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Jalal ASB, Tran NT, Wu LJ, Ramakrishnan K, Rejzek M, Gobbato G, Stevenson CEM, Lawson DM, Errington J, Le TBK. CTP regulates membrane-binding activity of the nucleoid occlusion protein Noc. Mol Cell 2021; 81:3623-3636.e6. [PMID: 34270916 PMCID: PMC8429893 DOI: 10.1016/j.molcel.2021.06.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/25/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023]
Abstract
ATP- and GTP-dependent molecular switches are extensively used to control functions of proteins in a wide range of biological processes. However, CTP switches are rarely reported. Here, we report that a nucleoid occlusion protein Noc is a CTPase enzyme whose membrane-binding activity is directly regulated by a CTP switch. In Bacillus subtilis, Noc nucleates on 16 bp NBS sites before associating with neighboring non-specific DNA to form large membrane-associated nucleoprotein complexes to physically occlude assembly of the cell division machinery. By in vitro reconstitution, we show that (1) CTP is required for Noc to form the NBS-dependent nucleoprotein complex, and (2) CTP binding, but not hydrolysis, switches Noc to a membrane-active state. Overall, we suggest that CTP couples membrane-binding activity of Noc to nucleoprotein complex formation to ensure productive recruitment of DNA to the bacterial cell membrane for nucleoid occlusion activity. CTP is required for Noc to form a higher-order nucleoprotein complex on DNA CTP binding switches DNA-entrapped Noc to a membrane-active state CTP hydrolysis likely reverses the association between Noc-DNA and the membrane The membrane-targeting helix adopts an autoinhibitory conformation in apo-Noc
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Affiliation(s)
- Adam S B Jalal
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ngat T Tran
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | | | - Martin Rejzek
- Chemistry Platform, John Innes Centre, Norwich, NR4 7UH, UK
| | - Giulia Gobbato
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Tung B K Le
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
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35
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Pyle E, Zanetti G. Current data processing strategies for cryo-electron tomography and subtomogram averaging. Biochem J 2021; 478:1827-1845. [PMID: 34003255 PMCID: PMC8133831 DOI: 10.1042/bcj20200715] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 12/25/2022]
Abstract
Cryo-electron tomography (cryo-ET) can be used to reconstruct three-dimensional (3D) volumes, or tomograms, from a series of tilted two-dimensional images of biological objects in their near-native states in situ or in vitro. 3D subvolumes, or subtomograms, containing particles of interest can be extracted from tomograms, aligned, and averaged in a process called subtomogram averaging (STA). STA overcomes the low signal to noise ratio within the individual subtomograms to generate structures of the particle(s) of interest. In recent years, cryo-ET with STA has increasingly been capable of reaching subnanometer resolution due to improvements in microscope hardware and data processing strategies. There has also been an increase in the number and quality of software packages available to process cryo-ET data with STA. In this review, we describe and assess the data processing strategies available for cryo-ET data and highlight the recent software developments which have enabled the extraction of high-resolution information from cryo-ET datasets.
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Affiliation(s)
- Euan Pyle
- Institute of Structural and Molecular Biology, Birkbeck College, Malet St., London WC1E 7HX, U.K
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College, Malet St., London WC1E 7HX, U.K
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36
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Feng H, Cheng H, Hsiao T, Lin T, Hsu J, Huang L, Yu C. ArfGAP1 acts as a GTPase‐activating protein for human ADP‐ribosylation factor‐like 1 protein. FASEB J 2021; 35:e21337. [DOI: 10.1096/fj.202000818rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/13/2020] [Accepted: 12/17/2020] [Indexed: 01/08/2023]
Affiliation(s)
- Hsiang‐Pu Feng
- Graduate Institute of Biomedical Sciences, College of Medicine Chang Gung University Taoyuan Taiwan
| | - Hsiao‐Yun Cheng
- Department of Cell and Molecular Biology, College of Medicine Chang Gung University Taoyuan Taiwan
| | - Ting‐Feng Hsiao
- Graduate Institute of Biomedical Sciences, College of Medicine Chang Gung University Taoyuan Taiwan
| | - Tai‐Wei Lin
- Graduate Institute of Biomedical Sciences, College of Medicine Chang Gung University Taoyuan Taiwan
| | - Jia‐Wei Hsu
- Institute of Molecular Medicine, College of Medicine National Taiwan University Taipei Taiwan
- Institute of Biochemical Sciences, College of Life Science National Taiwan University Taipei Taiwan
| | - Lien‐Hung Huang
- Graduate Institute of Biomedical Sciences, College of Medicine Chang Gung University Taoyuan Taiwan
- Department of Neurosurgery Kaohsiung Chang Gung Memorial Hospital Kaohsiung Taiwan
| | - Chia‐Jung Yu
- Graduate Institute of Biomedical Sciences, College of Medicine Chang Gung University Taoyuan Taiwan
- Department of Cell and Molecular Biology, College of Medicine Chang Gung University Taoyuan Taiwan
- Department of Thoracic Medicine Chang Gung Memorial Hospital Taoyuan Taiwan
- Molecular Medicine Research Center Chang Gung University Taoyuan Taiwan
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37
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Tremel S, Ohashi Y, Morado DR, Bertram J, Perisic O, Brandt LTL, von Wrisberg MK, Chen ZA, Maslen SL, Kovtun O, Skehel M, Rappsilber J, Lang K, Munro S, Briggs JAG, Williams RL. Structural basis for VPS34 kinase activation by Rab1 and Rab5 on membranes. Nat Commun 2021; 12:1564. [PMID: 33692360 PMCID: PMC7946940 DOI: 10.1038/s41467-021-21695-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/01/2021] [Indexed: 02/07/2023] Open
Abstract
The lipid phosphatidylinositol-3-phosphate (PI3P) is a regulator of two fundamental but distinct cellular processes, endocytosis and autophagy, so its generation needs to be under precise temporal and spatial control. PI3P is generated by two complexes that both contain the lipid kinase VPS34: complex II on endosomes (VPS34/VPS15/Beclin 1/UVRAG), and complex I on autophagosomes (VPS34/VPS15/Beclin 1/ATG14L). The endosomal GTPase Rab5 binds complex II, but the mechanism of VPS34 activation by Rab5 has remained elusive, and no GTPase is known to bind complex I. Here we show that Rab5a–GTP recruits endocytic complex II to membranes and activates it by binding between the VPS34 C2 and VPS15 WD40 domains. Electron cryotomography of complex II on Rab5a-decorated vesicles shows that the VPS34 kinase domain is released from inhibition by VPS15 and hovers over the lipid bilayer, poised for catalysis. We also show that the GTPase Rab1a, which is known to be involved in autophagy, recruits and activates the autophagy-specific complex I, but not complex II. Both Rabs bind to the same VPS34 interface but in a manner unique for each. These findings reveal how VPS34 complexes are activated on membranes by specific Rab GTPases and how they are recruited to unique cellular locations. The phosphatidylinositol-3-phosphate (PI3P) is generated by the lipid kinase VPS34, in the context of VPS34 complex I on autophagosomes or complex II on endosomes. Biochemical and structural analyses provide insights into the mechanism of both VPS34 complexes recruitment to and activation on membranes by specific Rab GTPases.
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Affiliation(s)
| | - Yohei Ohashi
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Dustin R Morado
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | | | - Olga Perisic
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Marie-Kristin von Wrisberg
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Garching, Germany
| | - Zhuo A Chen
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | | | | | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kathrin Lang
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Lab for Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, TUM-IAS, Garching, Germany
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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Find your coat: Using correlative light and electron microscopy to study intracellular protein coats. Curr Opin Cell Biol 2021; 71:21-28. [PMID: 33684808 DOI: 10.1016/j.ceb.2021.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/14/2022]
Abstract
Protein coats, important for vesicular trafficking in eukaryotic cells, help shape membranes and package cargo. But their dynamic construction cannot be fully understood until the distinct steps of their assembly in their native intracellular context at molecular resolution can be visualized. For this, correlative light and electron microscopy (CLEM) is an essential tool. Here, we discuss how emerging CLEM techniques have been used to study the assembly of protein coats inside cells. We review how current and developing CLEM technologies are poised to answer fundamental questions of protein coat architecture at the nanoscale.
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Macken WL, Godwin A, Wheway G, Stals K, Nazlamova L, Ellard S, Alfares A, Aloraini T, AlSubaie L, Alfadhel M, Alajaji S, Wai HA, Self J, Douglas AGL, Kao AP, Guille M, Baralle D. Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly. Genome Med 2021; 13:34. [PMID: 33632302 PMCID: PMC7908744 DOI: 10.1186/s13073-021-00850-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as "coatopathies". METHODS Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1's splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2's missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2's mutation. RESULTS We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β'-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. CONCLUSIONS This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.
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Affiliation(s)
- William L Macken
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK
| | - Annie Godwin
- European Xenopus Resource Centre, University of Portsmouth School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Level 3 RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Liliya Nazlamova
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Level 3 RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- University of Exeter Medical School, RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Ahmed Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Lamia AlSubaie
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Sulaiman Alajaji
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Division of Allergy and Clinical Immunology, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Htoo A Wai
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Jay Self
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Alexander P Kao
- Zeiss Global Centre, School of Mechanical and Design Engineering, University of Portsmouth, Portsmouth, PO1 3DJ, UK
| | - Matthew Guille
- European Xenopus Resource Centre, University of Portsmouth School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK.
| | - Diana Baralle
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK.
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK.
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Yperman K, Wang J, Eeckhout D, Winkler J, Vu LD, Vandorpe M, Grones P, Mylle E, Kraus M, Merceron R, Nolf J, Mor E, De Bruyn P, Loris R, Potocký M, Savvides SN, De Rybel B, De Jaeger G, Van Damme D, Pleskot R. Molecular architecture of the endocytic TPLATE complex. SCIENCE ADVANCES 2021; 7:eabe7999. [PMID: 33637534 PMCID: PMC7909872 DOI: 10.1126/sciadv.abe7999] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/15/2021] [Indexed: 05/03/2023]
Abstract
Eukaryotic cells rely on endocytosis to regulate their plasma membrane proteome and lipidome. Most eukaryotic groups, except fungi and animals, have retained the evolutionary ancient TSET complex as an endocytic regulator. Unlike other coatomer complexes, structural insight into TSET is lacking. Here, we reveal the molecular architecture of plant TSET [TPLATE complex (TPC)] using an integrative structural approach. We identify crucial roles for specific TSET subunits in complex assembly and membrane interaction. Our data therefore generate fresh insight into the differences between the hexameric TSET in Dictyostelium and the octameric TPC in plants. Structural elucidation of this ancient adaptor complex represents the missing piece in the coatomer puzzle and vastly advances our functional as well as evolutionary insight into the process of endocytosis.
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Affiliation(s)
- Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Joanna Winkler
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Michael Vandorpe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Peter Grones
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Michael Kraus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Romain Merceron
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
- VIB Center for Inflammation Research, 9052 Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Eliana Mor
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Pieter De Bruyn
- Vrije Universiteit Brussel, Structural Biology Brussels, Department of Biotechnology, 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, Structural Biology Research Center, Molecular Recognition Unit, 1050 Brussels, Belgium
| | - Remy Loris
- VIB-VUB Center for Structural Biology, Structural Biology Research Center, Molecular Recognition Unit, 1050 Brussels, Belgium
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 16502 Prague 6, Czech Republic
| | - Martin Potocký
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 16502 Prague 6, Czech Republic
| | - Savvas N Savvides
- Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
- VIB Center for Inflammation Research, 9052 Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Roman Pleskot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 263, 16502 Prague 6, Czech Republic
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Xie B, Jung C, Chandra M, Engel A, Kendall AK, Jackson LP. The Glo3 GAP crystal structure supports the molecular niche model for ArfGAPs in COPI coats. Adv Biol Regul 2021; 79:100781. [PMID: 33436318 PMCID: PMC7920988 DOI: 10.1016/j.jbior.2020.100781] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 11/27/2022]
Abstract
Arf GTPase activating (ArfGAP) proteins are critical regulatory and effector proteins in membrane trafficking pathways. Budding yeast contain two ArfGAP proteins (Gcs1 and Glo3) implicated in COPI coat function at the Golgi, and yeast require Glo3 catalytic function for viability. A new X-ray crystal structure of the Glo3 GAP domain was determined at 2.1 Å resolution using molecular replacement methods. The structure reveals a Cys4-family zinc finger motif with an invariant residue (R59) positioned to act as an "arginine finger" during catalysis. Comparisons among eukaryotic GAP domains show a key difference between ArfGAP1 and ArfGAP2/3 family members in the final helix located within the domain. Conservation at both the sequence and structural levels suggest the Glo3 GAP domain interacts with yeast Arf1 switch I and II regions to promote catalysis. Together, the structural data presented here provide additional evidence for placing Glo3 near Arf1 triads within membrane-assembled COPI coats and further support the molecular niche model for COPI coat regulation by ArfGAPs.
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Affiliation(s)
- Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Christian Jung
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Andrew Engel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Amy K Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
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42
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Lepelley A, Martin-Niclós MJ, Le Bihan M, Marsh JA, Uggenti C, Rice GI, Bondet V, Duffy D, Hertzog J, Rehwinkel J, Amselem S, Boulisfane-El Khalifi S, Brennan M, Carter E, Chatenoud L, Chhun S, Coulomb l’Hermine A, Depp M, Legendre M, Mackenzie KJ, Marey J, McDougall C, McKenzie KJ, Molina TJ, Neven B, Seabra L, Thumerelle C, Wislez M, Nathan N, Manel N, Crow YJ, Frémond ML. Mutations in COPA lead to abnormal trafficking of STING to the Golgi and interferon signaling. J Exp Med 2020; 217:e20200600. [PMID: 32725128 PMCID: PMC7596811 DOI: 10.1084/jem.20200600] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/04/2020] [Accepted: 07/06/2020] [Indexed: 01/01/2023] Open
Abstract
Heterozygous missense mutations in coatomer protein subunit α, COPA, cause a syndrome overlapping clinically with type I IFN-mediated disease due to gain-of-function in STING, a key adaptor of IFN signaling. Recently, increased levels of IFN-stimulated genes (ISGs) were described in COPA syndrome. However, the link between COPA mutations and IFN signaling is unknown. We observed elevated levels of ISGs and IFN-α in blood of symptomatic COPA patients. In vitro, both overexpression of mutant COPA and silencing of COPA induced STING-dependent IFN signaling. We detected an interaction between COPA and STING, and mutant COPA was associated with an accumulation of ER-resident STING at the Golgi. Given the known role of the coatomer protein complex I, we speculate that loss of COPA function leads to enhanced type I IFN signaling due to a failure of Golgi-to-ER STING retrieval. These data highlight the importance of the ER-Golgi axis in the control of autoinflammation and inform therapeutic strategies in COPA syndrome.
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Affiliation(s)
- Alice Lepelley
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, Paris, France
| | | | - Melvin Le Bihan
- Immunity and Cancer Department, Institut Curie, Paris-Sciences-et-Lettres Research University, Institut National de la Santé et de la Recherche Médicale U932, Paris, France
| | - Joseph A. Marsh
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Carolina Uggenti
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Gillian I. Rice
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Vincent Bondet
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Institut National de la Santé et de la Recherche Médicale U1223, Paris, France
| | - Darragh Duffy
- Immunobiology of Dendritic Cells, Institut Pasteur, Paris, France
- Institut National de la Santé et de la Recherche Médicale U1223, Paris, France
| | - Jonny Hertzog
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Serge Amselem
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale/UMRS_933, Trousseau University Hospital, Paris, France
- Genetics Department, Trousseau University Hospital, Assistance Publique–Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Siham Boulisfane-El Khalifi
- Emergency, Infectious Disease and Pediatric Rheumatology Department, Centre Hospitalier Régional Universitaire Lille, University of Lille, Lille, France
| | - Mary Brennan
- Department of Paediatric Rheumatology, Royal Hospital for Sick Children, Edinburgh, UK
| | - Edwin Carter
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Lucienne Chatenoud
- Paris Descartes University, Université de Paris, Sorbonne-Paris-Cité, Paris, France
- Laboratory of Immunology, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
- Institut Necker-Enfants Malades, Centre National de la Recherche Scientifique UMR8253, Institut National de la Santé et de la Recherche Médicale UMR1151, Team Immunoregulation and Immunopathology, Paris, France
| | - Stéphanie Chhun
- Paris Descartes University, Université de Paris, Sorbonne-Paris-Cité, Paris, France
- Laboratory of Immunology, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
- Institut Necker-Enfants Malades, Centre National de la Recherche Scientifique UMR8253, Institut National de la Santé et de la Recherche Médicale UMR1151, Team Immunoregulation and Immunopathology, Paris, France
| | - Aurore Coulomb l’Hermine
- Pathology Department, Trousseau University Hospital, Assistance Publique–Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Marine Depp
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Marie Legendre
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale/UMRS_933, Trousseau University Hospital, Paris, France
- Genetics Department, Trousseau University Hospital, Assistance Publique–Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Karen J. Mackenzie
- Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Jonathan Marey
- Pneumology Department, Cochin Hospital, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
| | - Catherine McDougall
- Department of Paediatric Respiratory Medicine, Royal Hospital for Sick Children, Edinburgh, UK
| | - Kathryn J. McKenzie
- Paediatric Pathology Department, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Thierry Jo Molina
- Paris Descartes University, Université de Paris, Sorbonne-Paris-Cité, Paris, France
- Pathology Department, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
| | - Bénédicte Neven
- Paris Descartes University, Université de Paris, Sorbonne-Paris-Cité, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Department, Hôpital Necker-Enfants Malades, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
- Institut National de la Santé et de la Recherche Médicale UMR 1163, Laboratory of Immunogenetics of Paediatric Autoimmunity, Imagine Institute, Paris, France
| | - Luis Seabra
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, Paris, France
| | - Caroline Thumerelle
- Pediatric Pneumology Department, Hôpital Jeanne de Flandre, Centre Hospitalier Régional Universitaire Lille, Lille, France
| | - Marie Wislez
- Pneumology Department, Cochin Hospital, Assistance Publique–Hôpitaux de Paris, Centre-Université de Paris, Paris, France
- Cordeliers Research Center, Université Paris Descartes, Université de Paris, UMRS1138 Inflammation, Complement and Cancer Team, Paris, France
| | - Nadia Nathan
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale/UMRS_933, Trousseau University Hospital, Paris, France
- Pediatric Pulmonology Department and Reference Center for Rare Lung Disease RespiRare, Trousseau University Hospital, Assistance Publique–Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Nicolas Manel
- Immunity and Cancer Department, Institut Curie, Paris-Sciences-et-Lettres Research University, Institut National de la Santé et de la Recherche Médicale U932, Paris, France
| | - Yanick J. Crow
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, Paris, France
- Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Marie-Louise Frémond
- Laboratory of Neurogenetics and Neuroinflammation, Imagine Institute, Paris, France
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Turk M, Baumeister W. The promise and the challenges of cryo-electron tomography. FEBS Lett 2020; 594:3243-3261. [PMID: 33020915 DOI: 10.1002/1873-3468.13948] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 01/11/2023]
Abstract
Structural biologists have traditionally approached cellular complexity in a reductionist manner in which the cellular molecular components are fractionated and purified before being studied individually. This 'divide and conquer' approach has been highly successful. However, awareness has grown in recent years that biological functions can rarely be attributed to individual macromolecules. Most cellular functions arise from their concerted action, and there is thus a need for methods enabling structural studies performed in situ, ideally in unperturbed cellular environments. Cryo-electron tomography (Cryo-ET) combines the power of 3D molecular-level imaging with the best structural preservation that is physically possible to achieve. Thus, it has a unique potential to reveal the supramolecular architecture or 'molecular sociology' of cells and to discover the unexpected. Here, we review state-of-the-art Cryo-ET workflows, provide examples of biological applications, and discuss what is needed to realize the full potential of Cryo-ET.
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Affiliation(s)
- Martin Turk
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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44
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Schoppe J, Mari M, Yavavli E, Auffarth K, Cabrera M, Walter S, Fröhlich F, Ungermann C. AP-3 vesicle uncoating occurs after HOPS-dependent vacuole tethering. EMBO J 2020; 39:e105117. [PMID: 32840906 PMCID: PMC7560216 DOI: 10.15252/embj.2020105117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 11/09/2022] Open
Abstract
Heterotetrameric adapter (AP) complexes cooperate with the small GTPase Arf1 or lipids in cargo selection, vesicle formation, and budding at endomembranes in eukaryotic cells. While most AP complexes also require clathrin as the outer vesicle shell, formation of AP-3-coated vesicles involved in Golgi-to-vacuole transport in yeast has been postulated to depend on Vps41, a subunit of the vacuolar HOPS tethering complex. HOPS has also been identified as the tether of AP-3 vesicles on vacuoles. To unravel this conundrum of a dual Vps41 function, we anchored Vps41 stably to the mitochondrial outer membrane. By monitoring AP-3 recruitment, we now show that Vps41 can tether AP-3 vesicles to mitochondria, yet AP-3 vesicles can form in the absence of Vps41 or clathrin. By proximity labeling and mass spectrometry, we identify the Arf1 GTPase-activating protein (GAP) Age2 at the AP-3 coat and show that tethering, but not fusion at the vacuole can occur without complete uncoating. We conclude that AP-3 vesicles retain their coat after budding and that their complete uncoating occurs only after tethering at the vacuole.
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Affiliation(s)
- Jannis Schoppe
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Muriel Mari
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Erdal Yavavli
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Kathrin Auffarth
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany
| | - Margarita Cabrera
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Farba, Barcelona, Spain
| | - Stefan Walter
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany.,Department of Biology/Chemistry, Molecular Membrane Biology Section, University of Osnabrück, Osnabrück, Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytic Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
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Kovtun O, Dickson VK, Kelly BT, Owen DJ, Briggs JAG. Architecture of the AP2/clathrin coat on the membranes of clathrin-coated vesicles. SCIENCE ADVANCES 2020; 6:eaba8381. [PMID: 32743075 PMCID: PMC7375805 DOI: 10.1126/sciadv.aba8381] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/17/2020] [Indexed: 05/19/2023]
Abstract
Clathrin-mediated endocytosis (CME) is crucial for modulating the protein composition of a cell's plasma membrane. Clathrin forms a cage-like, polyhedral outer scaffold around a vesicle, to which cargo-selecting clathrin adaptors are attached. Adaptor protein complex (AP2) is the key adaptor in CME. Crystallography has shown AP2 to adopt a range of conformations. Here, we used cryo-electron microscopy, tomography, and subtomogram averaging to determine structures, interactions, and arrangements of clathrin and AP2 at the key steps of coat assembly, from AP2 in solution to membrane-assembled clathrin-coated vesicles (CCVs). AP2 binds cargo and PtdIns(4,5)P 2 (phosphatidylinositol 4,5-bisphosphate)-containing membranes via multiple interfaces, undergoing conformational rearrangement from its cytosolic state. The binding mode of AP2 β2 appendage into the clathrin lattice in CCVs and buds implies how the adaptor structurally modulates coat curvature and coat disassembly.
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Affiliation(s)
- Oleksiy Kovtun
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg , Germany
| | - Veronica Kane Dickson
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Bernard T. Kelly
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Corresponding author. (B.T.K.); (D.J.O.); (J.A.G.B.)
| | - David J. Owen
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Corresponding author. (B.T.K.); (D.J.O.); (J.A.G.B.)
| | - John A. G. Briggs
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg , Germany
- Corresponding author. (B.T.K.); (D.J.O.); (J.A.G.B.)
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Yang S, Bahl K, Chou HT, Woodsmith J, Stelzl U, Walz T, Nachury MV. Near-atomic structures of the BBSome reveal the basis for BBSome activation and binding to GPCR cargoes. eLife 2020; 9:55954. [PMID: 32510327 PMCID: PMC7311171 DOI: 10.7554/elife.55954] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Dynamic trafficking of G protein-coupled receptors (GPCRs) out of cilia is mediated by the BBSome. In concert with its membrane recruitment factor, the small GTPase ARL6/BBS3, the BBSome ferries GPCRs across the transition zone, a diffusion barrier at the base of cilia. Here, we present the near-atomic structures of the BBSome by itself and in complex with ARL6GTP, and we describe the changes in BBSome conformation induced by ARL6GTP binding. Modeling the interactions of the BBSome with membranes and the GPCR Smoothened (SMO) reveals that SMO, and likely also other GPCR cargoes, must release their amphipathic helix 8 from the membrane to be recognized by the BBSome.
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Affiliation(s)
- Shuang Yang
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Kriti Bahl
- Department of Ophthalmology, University of California San Francisco, San Francisco, United States
| | - Hui-Ting Chou
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Jonathan Woodsmith
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, Graz, Austria
| | - Ulrich Stelzl
- Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, Graz, Austria
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, United States
| | - Maxence V Nachury
- Department of Ophthalmology, University of California San Francisco, San Francisco, United States
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Wagner FR, Watanabe R, Schampers R, Singh D, Persoon H, Schaffer M, Fruhstorfer P, Plitzko J, Villa E. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nat Protoc 2020; 15:2041-2070. [PMID: 32405053 PMCID: PMC8053421 DOI: 10.1038/s41596-020-0320-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/06/2020] [Indexed: 12/31/2022]
Abstract
Recent advances have made cryogenic (cryo) electron microscopy a key technique to achieve near-atomic-resolution structures of biochemically isolated macromolecular complexes. Cryo-electron tomography (cryo-ET) can give unprecedented insight into these complexes in the context of their natural environment. However, the application of cryo-ET is limited to samples that are thinner than most cells, thereby considerably reducing its applicability. Cryo-focused-ion-beam (cryo-FIB) milling has been used to carve (micromachining) out 100-250-nm-thin regions (called lamella) in the intact frozen cells. This procedure opens a window into the cells for high-resolution cryo-ET and structure determination of biomolecules in their native environment. Further combination with fluorescence microscopy allows users to determine cells or regions of interest for the targeted fabrication of lamellae and cryo-ET imaging. Here, we describe how to prepare lamellae using a microscope equipped with both FIB and scanning electron microscopy modalities. Such microscopes (Aquilos Cryo-FIB/Scios/Helios or CrossBeam) are routinely referred to as dual-beam microscopes, and they are equipped with a cryo-stage for all operations in cryogenic conditions. The basic principle of the described methodologies is also applicable for other types of dual-beam microscopes equipped with a cryo-stage. We also briefly describe how to integrate fluorescence microscopy data for targeted milling and critical considerations for cryo-ET data acquisition of the lamellae. Users familiar with cryo-electron microscopy who get basic training in dual-beam microscopy can complete the protocol within 2-3 d, allowing for several pause points during the procedure.
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Affiliation(s)
- Felix R Wagner
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reika Watanabe
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Digvijay Singh
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hans Persoon
- Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter Fruhstorfer
- Thermo Fisher Scientific, Eindhoven, the Netherlands
- Eppendorf AG, Hamburg, Germany
| | - Jürgen Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elizabeth Villa
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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48
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Diestelkoetter-Bachert P, Beck R, Reckmann I, Hellwig A, Garcia-Saez A, Zelman-Hopf M, Hanke A, Nunes Alves A, Wade RC, Mayer MP, Wieland F. Structural characterization of an Arf dimer interface: molecular mechanism of Arf-dependent membrane scission. FEBS Lett 2020; 594:2240-2253. [PMID: 32394429 DOI: 10.1002/1873-3468.13808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022]
Abstract
Dimerization of the small GTPase Arf is prerequisite for the scission of COPI-coated transport vesicles. Here, we quantify the monomer/dimer equilibrium of Arf within the membrane and show that after membrane scission, Arf dimers are restricted to donor membranes. By hydrogen exchange mass spectrometry, we define the interface of activated dimeric Arf within its switch II region. Single amino acid exchanges in this region reduce the propensity of Arf to dimerize. We suggest a mechanism of membrane scission by which the dimeric form of Arf is segregated to the donor membrane. Our data are consistent with the previously reported absence of dimerized Arf in COPI vesicles and could explain the presence of one single scar-like noncoated region in each COPI vesicle.
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Affiliation(s)
| | - Rainer Beck
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Germany
| | - Inge Reckmann
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Germany
| | - Andrea Hellwig
- Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Germany
| | - Ana Garcia-Saez
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Germany.,CECAD Research Center, CECAD Cologne, Germany
| | | | - Anton Hanke
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Germany
| | - Ariane Nunes Alves
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Germany
| | - Matthias P Mayer
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Germany
| | - Felix Wieland
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Germany
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Zhukovsky MA, Filograna A, Luini A, Corda D, Valente C. Protein Amphipathic Helix Insertion: A Mechanism to Induce Membrane Fission. Front Cell Dev Biol 2019; 7:291. [PMID: 31921835 PMCID: PMC6914677 DOI: 10.3389/fcell.2019.00291] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/06/2019] [Indexed: 12/19/2022] Open
Abstract
One of the fundamental features of biomembranes is the ability to fuse or to separate. These processes called respectively membrane fusion and fission are central in the homeostasis of events such as those related to intracellular membrane traffic. Proteins that contain amphipathic helices (AHs) were suggested to mediate membrane fission via shallow insertion of these helices into the lipid bilayer. Here we analyze the AH-containing proteins that have been identified as essential for membrane fission and categorize them in few subfamilies, including small GTPases, Atg proteins, and proteins containing either the ENTH/ANTH- or the BAR-domain. AH-containing fission-inducing proteins may require cofactors such as additional proteins (e.g., lipid-modifying enzymes), or lipids (e.g., phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2], phosphatidic acid [PA], or cardiolipin). Both PA and cardiolipin possess a cone shape and a negative charge (-2) that favor the recruitment of the AHs of fission-inducing proteins. Instead, PtdIns(4,5)P2 is characterized by an high negative charge able to recruit basic residues of the AHs of fission-inducing proteins. Here we propose that the AHs of fission-inducing proteins contain sequence motifs that bind lipid cofactors; accordingly (K/R/H)(K/R/H)xx(K/R/H) is a PtdIns(4,5)P2-binding motif, (K/R)x6(F/Y) is a cardiolipin-binding motif, whereas KxK is a PA-binding motif. Following our analysis, we show that the AHs of many fission-inducing proteins possess five properties: (a) at least three basic residues on the hydrophilic side, (b) ability to oligomerize, (c) optimal (shallow) depth of insertion into the membrane, (d) positive cooperativity in membrane curvature generation, and (e) specific interaction with one of the lipids mentioned above. These lipid cofactors favor correct conformation, oligomeric state and optimal insertion depth. The most abundant lipid in a given organelle possessing high negative charge (more negative than -1) is usually the lipid cofactor in the fission event. Interestingly, naturally occurring mutations have been reported in AH-containing fission-inducing proteins and related to diseases such as centronuclear myopathy (amphiphysin 2), Charcot-Marie-Tooth disease (GDAP1), Parkinson's disease (α-synuclein). These findings add to the interest of the membrane fission process whose complete understanding will be instrumental for the elucidation of the pathogenesis of diseases involving mutations in the protein AHs.
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Affiliation(s)
- Mikhail A. Zhukovsky
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
| | | | | | - Daniela Corda
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
| | - Carmen Valente
- Institute of Biochemistry and Cell Biology, National Research Council, Naples, Italy
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50
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Travis SM, Kokona B, Fairman R, Hughson FM. Roles of singleton tryptophan motifs in COPI coat stability and vesicle tethering. Proc Natl Acad Sci U S A 2019; 116:24031-24040. [PMID: 31712447 PMCID: PMC6883825 DOI: 10.1073/pnas.1909697116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coat protein I (COPI)-coated vesicles mediate retrograde transport from the Golgi to the endoplasmic reticulum (ER), as well as transport within the Golgi. Major progress has been made in defining the structure of COPI coats, in vitro and in vivo, at resolutions as high as 9 Å. Nevertheless, important questions remain unanswered, including what specific interactions stabilize COPI coats, how COPI vesicles recognize their target membranes, and how coat disassembly is coordinated with vesicle fusion and cargo delivery. Here, we use X-ray crystallography to identify a conserved site on the COPI subunit α-COP that binds to flexible, acidic sequences containing a single tryptophan residue. One such sequence, found within α-COP itself, mediates α-COP homo-oligomerization. Another such sequence is contained within the lasso of the ER-resident Dsl1 complex, where it helps mediate the tethering of Golgi-derived COPI vesicles at the ER membrane. Together, our findings suggest that α-COP homo-oligomerization plays a key role in COPI coat stability, with potential implications for the coordination of vesicle tethering, uncoating, and fusion.
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Affiliation(s)
- Sophie M Travis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, PA 19041
- Department of Chemistry, Haverford College, Haverford, PA 19041
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, PA 19041
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