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Anglès F, Gupta V, Wang C, Balch WE. COPII cage assembly factor Sec13 integrates information flow regulating endomembrane function in response to human variation. Sci Rep 2024; 14:10160. [PMID: 38698045 PMCID: PMC11065896 DOI: 10.1038/s41598-024-60687-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
How information flow is coordinated for managing transit of 1/3 of the genome through endomembrane pathways by the coat complex II (COPII) system in response to human variation remains an enigma. By examining the interactome of the COPII cage-assembly component Sec13, we show that it is simultaneously associated with multiple protein complexes that facilitate different features of a continuous program of chromatin organization, transcription, translation, trafficking, and degradation steps that are differentially sensitive to Sec13 levels. For the trafficking step, and unlike other COPII components, reduction of Sec13 expression decreased the ubiquitination and degradation of wild-type (WT) and F508del variant cargo protein cystic fibrosis transmembrane conductance regulator (CFTR) leading to a striking increase in fold stability suggesting that the events differentiating export from degradation are critically dependent on COPII cage assembly at the ER Golgi intermediate compartment (ERGIC) associated recycling and degradation step linked to COPI exchange. Given Sec13's multiple roles in protein complex assemblies that change in response to its expression, we suggest that Sec13 serves as an unanticipated master regulator coordinating information flow from the genome to the proteome to facilitate spatial covariant features initiating and maintaining design and function of membrane architecture in response to human variation.
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Affiliation(s)
- Frédéric Anglès
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Vijay Gupta
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - William E Balch
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA.
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Wang B, Pareek G, Kundu M. ULK/Atg1: phasing in and out of autophagy. Trends Biochem Sci 2024:S0968-0004(24)00065-3. [PMID: 38565496 DOI: 10.1016/j.tibs.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/28/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Autophagy - a highly regulated intracellular degradation process - is pivotal in maintaining cellular homeostasis. Liquid-liquid phase separation (LLPS) is a fundamental mechanism regulating the formation and function of membrane-less compartments. Recent research has unveiled connections between LLPS and autophagy, suggesting that phase separation events may orchestrate the spatiotemporal organization of autophagic machinery and cargo sequestration. The Unc-51-like kinase (ULK)/autophagy-related 1 (Atg1) family of proteins is best known for its regulatory role in initiating autophagy, but there is growing evidence that the functional spectrum of ULK/Atg1 extends beyond autophagy regulation. In this review, we explore the spatial and temporal regulation of the ULK/Atg1 family of kinases, focusing on their recruitment to LLPS-driven compartments, and highlighting their multifaceted functions beyond their traditional role.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; Shenzhen Research Institute of Xiamen University, Shenzhen, 518057, China
| | - Gautam Pareek
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mondira Kundu
- Department of Cell and Molecular Biology, St Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Robinson CM, Duggan A, Forrester A. ER exit in physiology and disease. Front Mol Biosci 2024; 11:1352970. [PMID: 38314136 PMCID: PMC10835805 DOI: 10.3389/fmolb.2024.1352970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
The biosynthetic secretory pathway is comprised of multiple steps, modifications and interactions that form a highly precise pathway of protein trafficking and secretion, that is essential for eukaryotic life. The general outline of this pathway is understood, however the specific mechanisms are still unclear. In the last 15 years there have been vast advancements in technology that enable us to advance our understanding of this complex and subtle pathway. Therefore, based on the strong foundation of work performed over the last 40 years, we can now build another level of understanding, using the new technologies available. The biosynthetic secretory pathway is a high precision process, that involves a number of tightly regulated steps: Protein folding and quality control, cargo selection for Endoplasmic Reticulum (ER) exit, Golgi trafficking, sorting and secretion. When deregulated it causes severe diseases that here we categorise into three main groups of aberrant secretion: decreased, excess and altered secretion. Each of these categories disrupts organ homeostasis differently, effecting extracellular matrix composition, changing signalling events, or damaging the secretory cells due to aberrant intracellular accumulation of secretory proteins. Diseases of aberrant secretion are very common, but despite this, there are few effective therapies. Here we describe ER exit sites (ERES) as key hubs for regulation of the secretory pathway, protein quality control and an integratory hub for signalling within the cell. This review also describes the challenges that will be faced in developing effective therapies, due to the specificity required of potential drug candidates and the crucial need to respect the fine equilibrium of the pathway. The development of novel tools is moving forward, and we can also use these tools to build our understanding of the acute regulation of ERES and protein trafficking. Here we review ERES regulation in context as a therapeutic strategy.
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Affiliation(s)
- Claire M Robinson
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Aislinn Duggan
- School of Medicine, Health Sciences Centre, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Alison Forrester
- Research Unit of Cell Biology (URBC), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Namur, Belgium
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Wilfling F, Kaksonen M, Stachowiak J. Protein condensates as flexible platforms for membrane traffic. Curr Opin Cell Biol 2023; 85:102258. [PMID: 37832166 DOI: 10.1016/j.ceb.2023.102258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023]
Abstract
With an essential role in nearly every physiological process and disease state, trafficking vesicles are fundamental to cell biology. Canonical understanding of membrane traffic has been driven by key achievements in structural biology. Nonetheless, discoveries over the past few years progressively point to the critical role of intrinsically disordered domains and proteins, which lack a well-defined secondary structure. From the initiation of endocytosis and the sequestration of synaptic vesicles to the stabilization of endoplasmic reticulum exit sites and the extension of the autophagic cup, flexible protein condensates, rich in intrinsic disorder, are increasingly implicated. While important debates about the physical nature and mechanistic interpretation of these findings remain, the significance of transient, multivalent protein assemblies in membrane traffic is increasingly clear.
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Affiliation(s)
- Florian Wilfling
- Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, Frankfurt a. M., Germany.
| | - Marko Kaksonen
- University of Geneva, Department of Biochemistry, Geneva, Switzerland.
| | - Jeanne Stachowiak
- University of Texas at Austin, Department of Biomedical Engineering, USA; University of Texas at Austin, Department of Chemical Engineering, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hutchings J, Stancheva VG, Brown NR, Cheung ACM, Miller EA, Zanetti G. Structure of the complete, membrane-assembled COPII coat reveals a complex interaction network. Nat Commun 2021; 12:2034. [PMID: 33795673 DOI: 10.1038/s41467-021-22110-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/12/2021] [Indexed: 01/02/2023] Open
Abstract
COPII mediates Endoplasmic Reticulum to Golgi trafficking of thousands of cargoes. Five essential proteins assemble into a two-layer architecture, with the inner layer thought to regulate coat assembly and cargo recruitment, and the outer coat forming cages assumed to scaffold membrane curvature. Here we visualise the complete, membrane-assembled COPII coat by cryo-electron tomography and subtomogram averaging, revealing the full network of interactions within and between coat layers. We demonstrate the physiological importance of these interactions using genetic and biochemical approaches. Mutagenesis reveals that the inner coat alone can provide membrane remodelling function, with organisational input from the outer coat. These functional roles for the inner and outer coats significantly move away from the current paradigm, which posits membrane curvature derives primarily from the outer coat. We suggest these interactions collectively contribute to coat organisation and membrane curvature, providing a structural framework to understand regulatory mechanisms of COPII trafficking and secretion. Cytosolic coat proteins capture secretory cargo and sculpt membrane carriers for intracellular transport, such as COPII which mediates Endoplasmic Reticulum to Golgi trafficking of thousands of cargoes. Here authors visualise the complete, membrane-assembled COPII coat by cryo-electron tomography and subtomogram averaging, revealing the full network of interactions within and between coat layers.
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Abstract
Intracellular trafficking requires extensive changes in membrane morphology. Cells use several distinct molecular factors and physical cues to remodel membranes. Here, we highlight recent advances in identifying the biophysical mechanisms of membrane curvature generation. In particular, we focus on the cooperation of molecular and physical drivers of membrane bending during three stages of vesiculation: budding, cargo selection, and scission. Taken together, the studies reviewed here emphasize that, rather than a single dominant mechanism, several mechanisms typically work in parallel during each step of membrane remodeling. Important challenges for the future of this field are to understand how multiple mechanisms work together synergistically and how a series of stochastic events can be combined to achieve a deterministic result-assembly of the trafficking vesicle.
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Affiliation(s)
- Kasey J Day
- Department of Biomedical Engineering, 107 W. Dean Keeton St., C0800, Austin, TX, 78712, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, 107 W. Dean Keeton St., C0800, Austin, TX, 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Norman Hackerman Building, 100 East 24th St., NHB 4500, Austin, TX, 78712, USA.
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Peotter J, Kasberg W, Pustova I, Audhya A. COPII-mediated trafficking at the ER/ERGIC interface. Traffic 2019; 20:491-503. [PMID: 31059169 DOI: 10.1111/tra.12654] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/25/2019] [Accepted: 05/02/2019] [Indexed: 12/16/2022]
Abstract
Coat proteins play multiple roles in the life cycle of a membrane-bound transport intermediate, functioning in lipid bilayer remodeling, cargo selection and targeting to an acceptor compartment. The Coat Protein complex II (COPII) coat is known to act in each of these capacities, but recent work highlights the necessity for numerous accessory factors at all stages of transport carrier existence. Here, we review recent findings that highlight the roles of COPII and its regulators in the biogenesis of tubular COPII-coated carriers in mammalian cells that enable cargo transport between the endoplasmic reticulum and ER-Golgi intermediate compartments, the first step in a series of trafficking events that ultimately allows for the distribution of biosynthetic secretory cargoes throughout the entire endomembrane system.
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Affiliation(s)
- Jennifer Peotter
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin
| | - William Kasberg
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin
| | - Iryna Pustova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin
| | - Anjon Audhya
- Department of Biomolecular Chemistry, University of Wisconsin-Madison School of Medicine and Public Health, Madison, Wisconsin
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Abstract
The name “eukaryote” is derived from Greek, meaning “true kernel”, and describes the domain of organisms whose cells have a nucleus. The nucleus is thus the defining feature of eukaryotes and distinguishes them from prokaryotes (Archaea and Bacteria), whose cells lack nuclei. Despite this, we discuss the intriguing possibility that organisms on the path from the first eukaryotic common ancestor to the last common ancestor of all eukaryotes did not possess a nucleus at all—at least not in a form we would recognize today—and that the nucleus in fact arrived relatively late in the evolution of eukaryotes. The clues to this alternative evolutionary path lie, most of all, in recent discoveries concerning the structure of the nuclear pore complex. We discuss the evidence for such a possibility and how this impacts our views of eukaryote origins and how eukaryotes have diversified subsequent to their last common ancestor.
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Affiliation(s)
- Mark C Field
- School of Life Sciences, University of Dundee, Dundee, UK.,Biology Centre, Institute of Parasitology, Faculty of Sciences, University of South Bohemia, Ceske Budejovice, Czech Republic
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