1
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Van Veen D, Galaz-Montoya JG, Shen L, Baldwin P, Chaudhari AS, Lyumkis D, Schmid MF, Chiu W, Pauly J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. Int J Mol Sci 2024; 25:5473. [PMID: 38791508 PMCID: PMC11121946 DOI: 10.3390/ijms25105473] [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: 04/10/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3-20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.
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Affiliation(s)
- Dave Van Veen
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA;
| | - Jesús G. Galaz-Montoya
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; (J.G.G.-M.); (W.C.)
| | - Liyue Shen
- Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Philip Baldwin
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA 92037, USA;
| | | | - Dmitry Lyumkis
- Department of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA 92037, USA;
- Graduate School of Biological Sciences, University of California San Diego, La Jolla, CA 92037, USA
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; (J.G.G.-M.); (W.C.)
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Pauly
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA;
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2
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Patil H, Yi H, Cho KI, Ferreira PA. Proteostatic Remodeling of Small Heat Shock Chaperones─Crystallins by Ran-Binding Protein 2─and the Peptidyl-Prolyl cis-trans Isomerase and Chaperone Activities of Its Cyclophilin Domain. ACS Chem Neurosci 2024; 15:1967-1989. [PMID: 38657106 DOI: 10.1021/acschemneuro.3c00792] [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] [Indexed: 04/26/2024] Open
Abstract
Disturbances in protein phase transitions promote protein aggregation─a neurodegeneration hallmark. The modular Ran-binding protein 2 (Ranbp2) is a cytosolic molecular hub for rate-limiting steps of phase transitions of Ran-GTP-bound protein ensembles exiting nuclear pores. Chaperones also regulate phase transitions and proteostasis by suppressing protein aggregation. Ranbp2 haploinsufficiency promotes the age-dependent neuroprotection of the chorioretina against phototoxicity by proteostatic regulations of neuroprotective substrates of Ranbp2 and by suppressing the buildup of polyubiquitylated substrates. Losses of peptidyl-prolyl cis-trans isomerase (PPIase) and chaperone activities of the cyclophilin domain (CY) of Ranbp2 recapitulate molecular effects of Ranbp2 haploinsufficiency. These CY impairments also stimulate deubiquitylation activities and phase transitions of 19S cap subunits of the 26S proteasome that associates with Ranbp2. However, links between CY moonlighting activity, substrate ubiquitylation, and proteostasis remain incomplete. Here, we reveal the Ranbp2 regulation of small heat shock chaperones─crystallins in the chorioretina by proteomics of mice with total or selective modular deficits of Ranbp2. Specifically, loss of CY PPIase of Ranbp2 upregulates αA-Crystallin, which is repressed in adult nonlenticular tissues. Conversely, impairment of CY's chaperone activity opposite to the PPIase pocket downregulates a subset of αA-Crystallin's substrates, γ-crystallins. These CY-dependent effects cause age-dependent and chorioretinal-selective declines of ubiquitylated substrates without affecting the chorioretinal morphology. A model emerges whereby inhibition of Ranbp2's CY PPIase remodels crystallins' expressions, subdues molecular aging, and preordains the chorioretina to neuroprotection by augmenting the chaperone capacity and the degradation of polyubiquitylated substrates against proteostatic impairments. Further, the druggable Ranbp2 CY holds pan-therapeutic potential against proteotoxicity and neurodegeneration.
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Affiliation(s)
- Hemangi Patil
- Department of Ophthalmology Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Haiqing Yi
- Department of Ophthalmology Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Kyoung-In Cho
- Department of Ophthalmology Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Paulo A Ferreira
- Department of Ophthalmology Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Pathology Duke University Medical Center, Durham, North Carolina 27710, United States
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3
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Van Veen D, Galaz-Montoya JG, Shen L, Baldwin P, Chaudhari AS, Lyumkis D, Schmid MF, Chiu W, Pauly J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589090. [PMID: 38712113 PMCID: PMC11071277 DOI: 10.1101/2024.04.12.589090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3 - 20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.
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Affiliation(s)
- Dave Van Veen
- Dept. of Electrical Engineering, Stanford University
| | | | - Liyue Shen
- Dept. of Electrical and Computer Engineering, University of Michigan
| | - Philip Baldwin
- Dept. of Biochemistry and Molecular Pharmacology, Baylor College of Medicine
- Dept. of Genetics, The Salk Institute for Biological Sciences
| | | | - Dmitry Lyumkis
- Dept. of Genetics, The Salk Institute for Biological Sciences
- Graduate School of Biological Sciences, University of California San Diego
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory
| | - Wah Chiu
- Dept. of Bioengineering, Stanford University
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory
- Dept. of Microbiology and Immunology, Stanford University
| | - John Pauly
- Dept. of Electrical Engineering, Stanford University
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4
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Sun C. Single-Molecule-Resolution Approaches in Synaptic Biology. J Phys Chem B 2024; 128:3061-3068. [PMID: 38513216 DOI: 10.1021/acs.jpcb.3c08026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Synapses between neurons are the primary loci for information transfer and storage in the brain. An individual neuron, alone, can make over 10000 synaptic contacts. It is, however, not easy to investigate what goes on locally within a synapse because many synaptic compartments are only a few hundred nanometers wide in size─close to the diffraction limit of light. To observe the biomolecular machinery and processes within synapses, in situ single-molecule techniques are emerging as powerful tools. Guided by important biological questions, this Perspective will highlight recent advances in using these techniques to obtain in situ measurements of synaptic molecules in three aspects: the cell-biological machinery within synapses, the synaptic architecture, and the synaptic neurotransmitter receptors. These advances showcase the increasing importance of single-molecule-resolution techniques for accessing subcellular biophysical and biomolecular information related to the brain.
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Affiliation(s)
- Chao Sun
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark
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5
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Kim J, Byun I, Kim DY, Joh H, Kim HJ, Lee MJ. Targeted protein degradation directly engaging lysosomes or proteasomes. Chem Soc Rev 2024; 53:3253-3272. [PMID: 38369971 DOI: 10.1039/d3cs00344b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Targeted protein degradation (TPD) has been established as a viable alternative to attenuate the function of a specific protein of interest in both biological and clinical contexts. The unique TPD mode-of-action has allowed previously undruggable proteins to become feasible targets, expanding the landscape of "druggable" properties and "privileged" target proteins. As TPD continues to evolve, a range of innovative strategies, which do not depend on recruiting E3 ubiquitin ligases as in proteolysis-targeting chimeras (PROTACs), have emerged. Here, we present an overview of direct lysosome- and proteasome-engaging modalities and discuss their perspectives, advantages, and limitations. We outline the chemical composition, biochemical activity, and pharmaceutical characteristics of each degrader. These alternative TPD approaches not only complement the first generation of PROTACs for intracellular protein degradation but also offer unique strategies for targeting pathologic proteins located on the cell membrane and in the extracellular space.
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Affiliation(s)
- Jiseong Kim
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Do Young Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hyunhi Joh
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hak Joong Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Min Jae Lee
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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6
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VerPlank JJ, Gawron JM, Silvestri NJ, Wrabetz L, Feltri ML. Knockout of PA200 improves proteasomal degradation and myelination in a proteotoxic neuropathy. Life Sci Alliance 2024; 7:e202302349. [PMID: 38320810 PMCID: PMC10847332 DOI: 10.26508/lsa.202302349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
The cellular response to a decrease in protein degradation by 26S proteasomes in chronic diseases is poorly understood. Pharmacological inhibition of proteasomes increases the expression of proteasome subunits and Proteasome Activator 200 (PA200), an alternative proteasome activator. In the S63del mouse model of the peripheral neuropathy Charcot Marie Tooth 1B (CMT1B), proteasomal protein degradation is decreased and proteasome gene expression is increased. Here, we show an increase in PA200 and PA200-bound proteasomes in the peripheral nerves of S63del mice. To test genetically whether the upregulation of PA200 was compensatory, we generated S63del//PA200-/- mice. Unexpectedly, in the sciatic nerves of these mice, there was greater proteasomal protein degradation than in S63del, less polyubiquitinated proteins and markers of the unfolded protein response, and a greater amount of assembled, active 26S proteasomes. These changes were not seen in PA200-/- controls and were therefore specific to the neuropathy. Furthermore, in S63del//PA200-/- mice, myelin thickness and nerve conduction were restored to WT levels. Thus, the upregulation of PA200 is maladaptive in S63del mice and its genetic ablation prevented neuropathy.
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Affiliation(s)
- Jordan Js VerPlank
- https://ror.org/01y64my43 Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Joseph M Gawron
- https://ror.org/01y64my43 Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Nicholas J Silvestri
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Lawrence Wrabetz
- https://ror.org/01y64my43 Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Maria Laura Feltri
- https://ror.org/01y64my43 Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- IRCCS Neurological Institute "Carlo Besta," Milano, Italy
- Department of Medical Biotechnology and Translational Medicine, Universita' degli Studi di Milano, Milano, Italy
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7
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Nesterov SV, Plokhikh KS, Chesnokov YM, Mustafin DA, Goleva TN, Rogov AG, Vasilov RG, Yaguzhinsky LS. Safari with an Electron Gun: Visualization of Protein and Membrane Interactions in Mitochondria in Natural Environment. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:257-268. [PMID: 38622094 DOI: 10.1134/s0006297924020068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 04/17/2024]
Abstract
This paper presents new structural data about mitochondria using correlative light and electron microscopy (CLEM) and cryo-electron tomography. These state-of-the-art structural biology methods allow studying biological objects at nanometer scales under natural conditions. Non-invasiveness of these methods makes them comparable to observing animals in their natural environment on a safari. The paper highlights two areas of research that can only be accomplished using these methods. The study visualized location of the Aβ42 amyloid aggregates in relation to mitochondria to test a hypothesis of development of mitochondrial dysfunction in Alzheimer's disease. The results showed that the Aβ42 aggregates do not interact with mitochondria, although some of them are closely located. Therefore, the study demonstrated that mitochondrial dysfunction is not directly associated with the effects of aggregates on mitochondrial structure. Other processes should be considered as sources of mitochondrial dysfunction. Second unique area presented in this work is high-resolution visualization of the mitochondrial membranes and proteins in them. Analysis of the cryo-ET data reveals toroidal holes in the lamellar structures of cardiac mitochondrial cristae, where ATP synthases are located. The study proposes a new mechanism for sorting and clustering protein complexes in the membrane based on topology. According to this suggestion, position of the OXPHOS system proteins in the membrane is determined by its curvature. High-resolution tomography expands and complements existing ideas about the structural and functional organization of mitochondria. This makes it possible to study the previously inaccessible structural interactions of proteins with each other and with membranes in vivo.
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Affiliation(s)
- Semen V Nesterov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | | | - Yuriy M Chesnokov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Denis A Mustafin
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Tatyana N Goleva
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Anton G Rogov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Raif G Vasilov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Lev S Yaguzhinsky
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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8
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Beck M, Covino R, Hänelt I, Müller-McNicoll M. Understanding the cell: Future views of structural biology. Cell 2024; 187:545-562. [PMID: 38306981 DOI: 10.1016/j.cell.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 02/04/2024]
Abstract
Determining the structure and mechanisms of all individual functional modules of cells at high molecular detail has often been seen as equal to understanding how cells work. Recent technical advances have led to a flush of high-resolution structures of various macromolecular machines, but despite this wealth of detailed information, our understanding of cellular function remains incomplete. Here, we discuss present-day limitations of structural biology and highlight novel technologies that may enable us to analyze molecular functions directly inside cells. We predict that the progression toward structural cell biology will involve a shift toward conceptualizing a 4D virtual reality of cells using digital twins. These will capture cellular segments in a highly enriched molecular detail, include dynamic changes, and facilitate simulations of molecular processes, leading to novel and experimentally testable predictions. Transferring biological questions into algorithms that learn from the existing wealth of data and explore novel solutions may ultimately unveil how cells work.
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Affiliation(s)
- Martin Beck
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany; Goethe University Frankfurt, Frankfurt, Germany.
| | - Roberto Covino
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
| | - Inga Hänelt
- Goethe University Frankfurt, Frankfurt, Germany.
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9
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Carrascosa JL. Characterization of Complexes and Supramolecular Structures by Electron Microscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:191-205. [PMID: 38507208 DOI: 10.1007/978-3-031-52193-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Recent advancements in cryo-electron microscopy (cryo-TEM) have enabled the determination of structures of macromolecular complexes at near-atomic resolution, establishing it as a pivotal tool in Structural Biology. This high resolution allows for the detection of ligands and substrates under physiological conditions. Enhancements in detectors and imaging devices, like phase plates, improve signal quality, facilitating the reconstruction of even smaller macromolecular complexes. The 100-kDa barrier has been surpassed, presenting new opportunities for pharmacological research and expanding the scope of crystallographic analyses in the pharmaceutical industry. Cryo-TEM produces vast data sets from minimal samples, and refined classification methods can identify different conformational states of macromolecular complexes, offering deeper insights into the functional characteristics of macromolecular systems. Additionally, cryo-TEM is paving the way for time-resolved microscopy, with rapid freezing techniques capturing snapshots of vital structural changes in biological complexes. Finally, in Structural Cell Biology, advanced cryo-TEM, through tomographic procedures, is revealing conformational changes related to the specific subcellular localization of macromolecular systems and their interactions within cells.
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Affiliation(s)
- José L Carrascosa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB, CSIC), Madrid, Spain.
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10
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Ochner H, Bharat TAM. Charting the molecular landscape of the cell. Structure 2023; 31:1297-1305. [PMID: 37699393 PMCID: PMC7615466 DOI: 10.1016/j.str.2023.08.015] [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: 06/07/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
Biological function of macromolecules is closely tied to their cellular location, as well as to interactions with other molecules within the native environment of the cell. Therefore, to obtain detailed mechanistic insights into macromolecular functionality, one of the outstanding targets for structural biology is to produce an atomic-level understanding of the cell. One structural biology technique that has already been used to directly derive atomic models of macromolecules from cells, without any additional external information, is electron cryotomography (cryoET). In this perspective article, we discuss possible routes to chart the molecular landscape of the cell by advancing cryoET imaging as well as by embedding cryoET into correlative imaging workflows.
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Affiliation(s)
- Hannah Ochner
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK.
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11
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Chaillet ML, van der Schot G, Gubins I, Roet S, Veltkamp RC, Förster F. Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms. Int J Mol Sci 2023; 24:13375. [PMID: 37686180 PMCID: PMC10487639 DOI: 10.3390/ijms241713375] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Cryo-electron tomography provides 3D images of macromolecules in their cellular context. To detect macromolecules in tomograms, template matching (TM) is often used, which uses 3D models that are often reliable for substantial parts of the macromolecules. However, the extent of rotational searches in particle detection has not been investigated due to computational limitations. Here, we provide a GPU implementation of TM as part of the PyTOM software package, which drastically speeds up the orientational search and allows for sampling beyond the Crowther criterion within a feasible timeframe. We quantify the improvements in sensitivity and false-discovery rate for the examples of ribosome identification and detection. Sampling at the Crowther criterion, which was effectively impossible with CPU implementations due to the extensive computation times, allows for automated extraction with high sensitivity. Consequently, we also show that an extensive angular sample renders 3D TM sensitive to the local alignment of tilt series and damage induced by focused ion beam milling. With this new release of PyTOM, we focused on integration with other software packages that support more refined subtomogram-averaging workflows. The automated classification of ribosomes by TM with appropriate angular sampling on locally corrected tomograms has a sufficiently low false-discovery rate, allowing for it to be directly used for high-resolution averaging and adequate sensitivity to reveal polysome organization.
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Affiliation(s)
- Marten L. Chaillet
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Gijs van der Schot
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Ilja Gubins
- Department of Information and Computing Sciences, Utrecht University, 3584 CC Utrecht, The Netherlands; (I.G.); (R.C.V.)
| | - Sander Roet
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Remco C. Veltkamp
- Department of Information and Computing Sciences, Utrecht University, 3584 CC Utrecht, The Netherlands; (I.G.); (R.C.V.)
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
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12
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Choi WH, Yun Y, Byun I, Kim S, Lee S, Sim J, Levi S, Park SH, Jun J, Kleifeld O, Kim KP, Han D, Chiba T, Seok C, Kwon YT, Glickman MH, Lee MJ. ECPAS/Ecm29-mediated 26S proteasome disassembly is an adaptive response to glucose starvation. Cell Rep 2023; 42:112701. [PMID: 37384533 DOI: 10.1016/j.celrep.2023.112701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 05/07/2023] [Accepted: 06/09/2023] [Indexed: 07/01/2023] Open
Abstract
The 26S proteasome comprises 20S catalytic and 19S regulatory complexes. Approximately half of the proteasomes in cells exist as free 20S complexes; however, our mechanistic understanding of what determines the ratio of 26S to 20S species remains incomplete. Here, we show that glucose starvation uncouples 26S holoenzymes into 20S and 19S subcomplexes. Subcomplex affinity purification and quantitative mass spectrometry reveal that Ecm29 proteasome adaptor and scaffold (ECPAS) mediates this structural remodeling. The loss of ECPAS abrogates 26S dissociation, reducing degradation of 20S proteasome substrates, including puromycylated polypeptides. In silico modeling suggests that ECPAS conformational changes commence the disassembly process. ECPAS is also essential for endoplasmic reticulum stress response and cell survival during glucose starvation. In vivo xenograft model analysis reveals elevated 20S proteasome levels in glucose-deprived tumors. Our results demonstrate that the 20S-19S disassembly is a mechanism adapting global proteolysis to physiological needs and countering proteotoxic stress.
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Affiliation(s)
- Won Hoon Choi
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yejin Yun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Sumin Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Seho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jiho Sim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Shahar Levi
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Seo Hyeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Jeongmoo Jun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Oded Kleifeld
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin 17104, Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea
| | - Tomoki Chiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8577, Japan
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yong Tae Kwon
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea; Ischemic/Hypoxic Disease Institute, Convergence Research Center for Dementia, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea; Ischemic/Hypoxic Disease Institute, Convergence Research Center for Dementia, Seoul National University College of Medicine, Seoul 03080, Korea.
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13
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Sun C, Desch K, Nassim-Assir B, Giandomenico SL, Nemcova P, Langer JD, Schuman EM. An abundance of free regulatory (19 S) proteasome particles regulates neuronal synapses. Science 2023; 380:eadf2018. [PMID: 37228199 DOI: 10.1126/science.adf2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/04/2023] [Indexed: 05/27/2023]
Abstract
The proteasome, the major protein-degradation machine in cells, regulates neuronal synapses and long-term information storage. Here, using super-resolution microscopy, we found that the two essential subcomplexes of the proteasome, the regulatory (19S) and catalytic (20S) particles, are differentially distributed within individual rat cortical neurons. We discovered an unexpected abundance of free 19S particles near synapses. The free neuronal 19S particles bind and deubiquitylate lysine 63-ubiquitin (Lys63-ub), a non-proteasome-targeting ubiquitin linkage. Pull-down assays revealed a significant overrepresentation of synaptic molecules as Lys63-ub interactors. Inhibition of the 19S deubiquitylase activity significantly altered excitatory synaptic transmission and reduced the synaptic availability of AMPA receptors at multiple trafficking points in a proteasome-independent manner. Together, these results reveal a moonlighting function of the regulatory proteasomal subcomplex near synapses.
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Affiliation(s)
- Chao Sun
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | - Kristina Desch
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | | | | | - Paulina Nemcova
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
| | - Julian D Langer
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
- Max Planck Institute for Biophysics, 60438 Frankfurt am Main, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt am Main, Germany
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14
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Lee D, Zhu Y, Colson L, Wang X, Chen S, Tkacik E, Huang L, Ouyang Q, Goldberg AL, Lu Y. Molecular mechanisms for activation of the 26S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540094. [PMID: 37214989 PMCID: PMC10197607 DOI: 10.1101/2023.05.09.540094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Various hormones, kinases, and stressors (fasting, heat shock) stimulate 26S proteasome activity. To understand how its capacity to degrade ubiquitylated protein can increase, we studied ZFAND5, which promotes protein degradation during muscle atrophy. Cryo-electron microscopy showed that ZFAND5 induces large conformational changes in the 19S regulatory particle. ZFAND5's AN1 Zn finger interacts with the Rpt5 ATPase and its C-terminus with Rpt1 ATPase and Rpn1, a ubiquitin-binding subunit. Surprisingly, these C-terminal interactions are sufficient to activate proteolysis. With ZFAND5 bound, entry into the proteasome's protein translocation channel is wider, and ZFAND5 dissociation causes opening of the 20S gate for substrate entry. Using single-molecular microscopy, we showed that ZFAND5 binds ubiquitylated substrates, prolongs their association with proteasomes, and increases the likelihood that bound substrates undergo degradation, even though ZFAND5 dissociates before substrate deubiquitylation. These changes in proteasome conformation and reaction cycle can explain the accelerated degradation and suggest how other proteasome activators may stimulate proteolysis.
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15
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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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16
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Are extraordinary nucleosome structures more ordinary than we thought? Chromosoma 2023:10.1007/s00412-023-00791-w. [PMID: 36917245 DOI: 10.1007/s00412-023-00791-w] [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: 01/23/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/16/2023]
Abstract
The nucleosome is a DNA-protein assembly that is the basic unit of chromatin. A nucleosome can adopt various structures. In the canonical nucleosome structure, 145-147 bp of DNA is wrapped around a histone heterooctamer. The strong histone-DNA interactions cause the DNA to be inaccessible for nuclear processes such as transcription. Therefore, the canonical nucleosome structure has to be altered into different, non-canonical structures to increase DNA accessibility. While it is recognised that non-canonical structures do exist, these structures are not well understood. In this review, we discuss both the evidence for various non-canonical nucleosome structures in the nucleus and the factors that are believed to induce these structures. The wide range of non-canonical structures is likely to regulate the amount of accessible DNA, and thus have important nuclear functions.
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17
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Buneeva OA, Kopylov AT, Medvedev AE. Proteasome Interactome and Its Role in the Mechanisms of Brain Plasticity. BIOCHEMISTRY (MOSCOW) 2023; 88:319-336. [PMID: 37076280 DOI: 10.1134/s0006297923030033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
Abstract
Proteasomes are highly conserved multienzyme complexes responsible for proteolytic degradation of the short-lived, regulatory, misfolded, and damaged proteins. They play an important role in the processes of brain plasticity, and decrease in their function is accompanied by the development of neurodegenerative pathology. Studies performed in different laboratories both on cultured mammalian and human cells and on preparations of the rat and rabbit brain cortex revealed a large number of proteasome-associated proteins. Since the identified proteins belong to certain metabolic pathways, multiple enrichment of the proteasome fraction with these proteins indicates their important role in proteasome functioning. Extrapolation of the experimental data, obtained on various biological objects, to the human brain suggests that the proteasome-associated proteins account for at least 28% of the human brain proteome. The proteasome interactome of the brain contains a large number of proteins involved in the assembly of these supramolecular complexes, regulation of their functioning, and intracellular localization, which could be changed under different conditions (for example, during oxidative stress) or in different phases of the cell cycle. In the context of molecular functions of the Gene Ontology (GO) Pathways, the proteins of the proteasome interactome mediate cross-talk between components of more than 30 metabolic pathways annotated in terms of GO. The main result of these interactions is binding of adenine and guanine nucleotides, crucial for realization of the nucleotide-dependent functions of the 26S and 20S proteasomes. Since the development of neurodegenerative pathology is often associated with regioselective decrease in the functional activity of proteasomes, a positive therapeutic effect would be obviously provided by the factors increasing proteasomal activity. In any case, pharmacological regulation of the brain proteasomes seems to be realized through the changes in composition and/or activity of the proteins associated with proteasomes (deubiquitinase, PKA, CaMKIIα, etc.).
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Affiliation(s)
- Olga A Buneeva
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
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18
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Yu P, Hua Z. To Kill or to Be Killed: How Does the Battle between the UPS and Autophagy Maintain the Intracellular Homeostasis in Eukaryotes? Int J Mol Sci 2023; 24:ijms24032221. [PMID: 36768543 PMCID: PMC9917186 DOI: 10.3390/ijms24032221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
The ubiquitin-26S proteasome system and autophagy are two major protein degradation machineries encoded in all eukaryotic organisms. While the UPS is responsible for the turnover of short-lived and/or soluble misfolded proteins under normal growth conditions, the autophagy-lysosomal/vacuolar protein degradation machinery is activated under stress conditions to remove long-lived proteins in the forms of aggregates, either soluble or insoluble, in the cytoplasm and damaged organelles. Recent discoveries suggested an integrative function of these two seemly independent systems for maintaining the proteome homeostasis. One such integration is represented by their reciprocal degradation, in which the small 76-amino acid peptide, ubiquitin, plays an important role as the central signaling hub. In this review, we summarized the current knowledge about the activity control of proteasome and autophagosome at their structural organization, biophysical states, and turnover levels from yeast and mammals to plants. Through comprehensive literature studies, we presented puzzling questions that are awaiting to be solved and proposed exciting new research directions that may shed light on the molecular mechanisms underlying the biological function of protein degradation.
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Affiliation(s)
- Peifeng Yu
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
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19
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Jonsson E, Htet ZM, Bard JA, Dong KC, Martin A. Ubiquitin modulates 26 S proteasome conformational dynamics and promotes substrate degradation. SCIENCE ADVANCES 2022; 8:eadd9520. [PMID: 36563145 PMCID: PMC9788759 DOI: 10.1126/sciadv.add9520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
The 26S proteasome recognizes thousands of appropriate protein substrates in eukaryotic cells through attached ubiquitin chains and uses its adenosine triphosphatase (ATPase) motor for mechanical unfolding and translocation into a proteolytic chamber. Here, we used single-molecule Förster resonance energy transfer measurements to monitor the conformational dynamics of the proteasome, observe individual substrates during their progression toward degradation, and elucidate how these processes are regulated by ubiquitin chains. Rapid transitions between engagement- and processing-competent proteasome conformations control substrate access to the ATPase motor. Ubiquitin chain binding functions as an allosteric regulator to slow these transitions, stabilize the engagement-competent state, and aid substrate capture to accelerate degradation initiation. Upon substrate engagement, the proteasome remains in processing-competent states for translocation and unfolding, except for apparent motor slips when encountering stably folded domains. Our studies revealed how ubiquitin chains allosterically regulate degradation initiation, which ensures substrate selectivity in a crowded cellular environment.
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Affiliation(s)
- Erik Jonsson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | | | - Ken C. Dong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
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20
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Sbardella D, Tundo GR, Mecchia A, Palumbo C, Atzori MG, Levati L, Boccaccini A, Caccuri AM, Cascio P, Lacal PM, Graziani G, Varano M, Coletta M, Parravano M. A novel and atypical NF-KB pro-inflammatory program regulated by a CamKII-proteasome axis is involved in the early activation of Muller glia by high glucose. Cell Biosci 2022; 12:108. [PMID: 35842713 PMCID: PMC9287993 DOI: 10.1186/s13578-022-00839-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
Background Diabetic retinopathy (DR) is a microvascular complication of diabetes with a heavy impact on the quality of life of subjects and with a dramatic burden for health and economic systems on a global scale. Although the pathogenesis of DR is largely unknown, several preclinical data have pointed out to a main role of Muller glia (MG), a cell type which spans across the retina layers providing nourishment and support for Retina Ganglion Cells (RGCs), in sensing hyper-glycemia and in acquiring a pro-inflammatory polarization in response to this insult. Results By using a validated experimental model of DR in vitro, rMC1 cells challenged with high glucose, we uncovered the induction of an early (within minutes) and atypical Nuclear Factor-kB (NF-kB) signalling pathway regulated by a calcium-dependent calmodulin kinase II (CamKII)-proteasome axis. Phosphorylation of proteasome subunit Rpt6 (at Serine 120) by CamKII stimulated the accelerated turnover of IkBα (i.e., the natural inhibitor of p65-50 transcription factor), regardless of the phosphorylation at Serine 32 which labels canonical NF-kB signalling. This event allowed the p65-p50 heterodimer to migrate into the nucleus and to induce transcription of IL-8, Il-1β and MCP-1. Pharmacological inhibition of CamKII as well as proteasome inhibition stopped this pro-inflammatory program, whereas introduction of a Rpt6 phospho-dead mutant (Rpt6-S120A) stimulated a paradoxical effect on NF-kB probably through the activation of a compensatory mechanism which may involve phosphorylation of 20S α4 subunit. Conclusions This study introduces a novel pathway of MG activation by high glucose and casts some light on the biological relevance of proteasome post-translational modifications in modulating pathways regulated through targeted proteolysis. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00839-x. High glucose quickly induces an atypical NF-kB pro-inflammatory program. CamKII phosphorylation of Rpt6 subunit of the proteasome stimulates IkBα turnover and p65-p50 release. Inhibition of either CamkII or proteasome blocks this pathway.
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21
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Lovatt M, Leistner C, Frank RAW. Bridging length scales from molecules to the whole organism by cryoCLEM and cryoET. Faraday Discuss 2022; 240:114-126. [PMID: 35959706 PMCID: PMC9642002 DOI: 10.1039/d2fd00081d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 01/09/2023]
Abstract
Resolving atomic structures of isolated proteins has uncovered mechanisms and fundamental processes in biology. However, many functions can only be tested in the context of intact cells and tissues that are many orders of magnitude larger than the macromolecules on which they depend. Therefore, methods that interrogate macromolecular structure in situ provide a means of directly relating structure to function across length scales. Here, we developed several workflows using cryogenic correlated light and electron microscopy (cryoCLEM) and electron tomography (cryoET) that can bridge this gap to reveal the molecular infrastructure that underlies higher order functions within cells and tissues. We also describe experimental design considerations, including cryoCLEM labelling, sample preparation, and quality control, for determining the in situ molecular architectures within native, hydrated cells and tissues.
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Affiliation(s)
- Megan Lovatt
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
| | - Conny Leistner
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
| | - René A W Frank
- Astbury Centre of Structural Molecular Biology, School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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22
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Osei-Amponsa V, Walters KJ. Proteasome substrate receptors and their therapeutic potential. Trends Biochem Sci 2022; 47:950-964. [PMID: 35817651 PMCID: PMC9588529 DOI: 10.1016/j.tibs.2022.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 11/22/2022]
Abstract
The ubiquitin-proteasome system (UPS) is critical for protein quality control and regulating protein lifespans. Following ubiquitination, UPS substrates bind multidomain receptors that, in addition to ubiquitin-binding sites, contain functional domains that bind to deubiquitinating enzymes (DUBs) or the E3 ligase E6AP/UBE3A. We provide an overview of the proteasome, focusing on its receptors and DUBs. We highlight the key role of dynamics and importance of the substrate receptors having domains for both binding and processing ubiquitin chains. The UPS is rich with therapeutic opportunities, with proteasome inhibitors used clinically and ongoing development of small molecule proteolysis targeting chimeras (PROTACs) for the degradation of disease-associated proteins. We discuss the therapeutic potential of proteasome receptors, including hRpn13, for which PROTACs have been developed.
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Affiliation(s)
- Vasty Osei-Amponsa
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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23
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Esfahanian N, Nelson M, Autenried R, Pattison JS, Callegari E, Rezvani K. Comprehensive Analysis of Proteasomal Complexes in Mouse Brain Regions Detects ENO2 as a Potential Partner of the Proteasome in the Striatum. Cell Mol Neurobiol 2022; 42:2305-2319. [PMID: 34037901 PMCID: PMC8617079 DOI: 10.1007/s10571-021-01106-2] [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: 02/11/2021] [Accepted: 05/19/2021] [Indexed: 11/28/2022]
Abstract
Defects in the activity of the proteasome or its regulators are linked to several pathologies, including neurodegenerative diseases. We hypothesize that proteasome heterogeneity and its selective partners vary across brain regions and have a significant impact on proteasomal catalytic activities. Using neuronal cell cultures and brain tissues obtained from mice, we compared proteasomal activities from two distinct brain regions affected in neurodegenerative diseases, the striatum and the hippocampus. The results indicated that proteasome activities and their responses to proteasome inhibitors are determined by their subcellular localizations and their brain regions. Using an iodixanol gradient fractionation method, proteasome complexes were isolated, followed by proteomic analysis for proteasomal interaction partners. Proteomic results revealed brain region-specific non-proteasomal partners, including gamma-enolase (ENO2). ENO2 showed more association to proteasome complexes purified from the striatum than to those from the hippocampus. These results highlight a potential key role for non-proteasomal partners of proteasomes regarding the diverse activities of the proteasome complex recorded in several brain regions.
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Affiliation(s)
- Niki Esfahanian
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Morgan Nelson
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Rebecca Autenried
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - J Scott Pattison
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Eduardo Callegari
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA
| | - Khosrow Rezvani
- Division of Basic Biomedical Sciences, Sanford School of Medicine,, University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, 57069, USA.
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24
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Isolation, cryo-laser scanning confocal microscope imaging and cryo-FIB milling of mouse glutamatergic synaptosomes. PLoS One 2022; 17:e0271799. [PMID: 35960737 PMCID: PMC9374259 DOI: 10.1371/journal.pone.0271799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/07/2022] [Indexed: 11/19/2022] Open
Abstract
Ionotropic glutamate receptors (iGluRs) at postsynaptic terminals mediate the majority of fast excitatory neurotransmission in response to release of glutamate from the presynaptic terminal. Obtaining structural information on the molecular organization of iGluRs in their native environment, along with other signaling and scaffolding proteins in the postsynaptic density (PSD), and associated proteins on the presynaptic terminal, would enhance understanding of the molecular basis for excitatory synaptic transmission in normal and in disease states. Cryo-electron tomography (ET) studies of synaptosomes is one attractive vehicle by which to study iGluR-containing excitatory synapses. Here we describe a workflow for the preparation of glutamatergic synaptosomes for cryo-ET studies. We describe the utilization of fluorescent markers for the facile detection of the pre and postsynaptic terminals of glutamatergic synaptosomes using cryo-laser scanning confocal microscope (cryo-LSM). We further provide the details for preparation of lamellae, between ~100 to 200 nm thick, of glutamatergic synaptosomes using cryo-focused ion-beam (FIB) milling. We monitor the lamella preparation using a scanning electron microscope (SEM) and following lamella production, we identify regions for subsequent cryo-ET studies by confocal fluorescent imaging, exploiting the pre and postsynaptic fluorophores.
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25
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26S proteasomes become stably activated upon heat shock when ubiquitination and protein degradation increase. Proc Natl Acad Sci U S A 2022; 119:e2122482119. [PMID: 35704754 PMCID: PMC9231471 DOI: 10.1073/pnas.2122482119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heat shock (HS) promotes protein unfolding, and cells respond by stimulating HS gene expression, ubiquitination of cell proteins, and proteolysis by the proteasome. Exposing HeLa and other cells to 43 °C for 2 h caused a twofold increase in the 26S proteasomes' peptidase activity assayed at 37 °C. This increase in activity occurred without any change in proteasome amount and did not require new protein synthesis. After affinity-purification from HS cells, 26S proteasomes still hydrolyzed peptides, adenosine 5'-triphosphate, and ubiquitinated substrates more rapidly without any evident change in subunit composition, postsynthetic modification, or association with reported proteasome-activating proteins. After returning HS cells to 37 °C, ubiquitin conjugates and proteolysis fell rapidly, but proteasome activity remained high for at least 16 h. Exposure to arsenite, which also causes proteotoxic stress in the cytosol, but not tunicamycin, which causes endoplasmic reticulum stress, also increased ubiquitin conjugate levels and 26S proteasome activity. Although the molecular basis for the enhanced proteasomal activity remains elusive, we studied possible signaling mechanisms. Proteasome activation upon proteotoxic stress required the accumulation of ubiquitinated proteins since blocking ubiquitination by E1 inhibition during HS or arsenite exposure prevented the stimulation of 26S activity. Furthermore, increasing cellular content of ubiquitin conjugates at 37 °C by inhibiting deubiquitinating enzymes with RA190 or b-AP15 also caused proteasome activation. Thus, cells respond to proteotoxic stresses, apparently in response to the accumulation of ubiquitinated proteins, by activating 26S proteasomes, which should help promote the clearance of damaged cell proteins.
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26
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Riemenschneider H, Guo Q, Bader J, Frottin F, Farny D, Kleinberger G, Haass C, Mann M, Hartl FU, Baumeister W, Hipp MS, Meissner F, Fernández‐Busnadiego R, Edbauer D. Gel-like inclusions of C-terminal fragments of TDP-43 sequester stalled proteasomes in neurons. EMBO Rep 2022; 23:e53890. [PMID: 35438230 PMCID: PMC9171420 DOI: 10.15252/embr.202153890] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 12/11/2022] Open
Abstract
Aggregation of the multifunctional RNA-binding protein TDP-43 defines large subgroups of amyotrophic lateral sclerosis and frontotemporal dementia and correlates with neurodegeneration in both diseases. In disease, characteristic C-terminal fragments of ~25 kDa ("TDP-25") accumulate in cytoplasmic inclusions. Here, we analyze gain-of-function mechanisms of TDP-25 combining cryo-electron tomography, proteomics, and functional assays. In neurons, cytoplasmic TDP-25 inclusions are amorphous, and photobleaching experiments reveal gel-like biophysical properties that are less dynamic than nuclear TDP-43. Compared with full-length TDP-43, the TDP-25 interactome is depleted of low-complexity domain proteins. TDP-25 inclusions are enriched in 26S proteasomes adopting exclusively substrate-processing conformations, suggesting that inclusions sequester proteasomes, which are largely stalled and no longer undergo the cyclic conformational changes required for proteolytic activity. Reporter assays confirm that TDP-25 impairs proteostasis, and this inhibitory function is enhanced by ALS-causing TDP-43 mutations. These findings support a patho-physiological relevance of proteasome dysfunction in ALS/FTD.
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Affiliation(s)
| | - Qiang Guo
- Department of Molecular Structural BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life Sciences and Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Jakob Bader
- Department of Proteomics and Signal TransductionMax Planck Institute for BiochemistryMartinsriedGermany
| | - Frédéric Frottin
- Department of Cellular BiochemistryMax Planck Institute for BiochemistryMartinsriedGermany
- Institute for Integrative Biology of the Cell (I2BC)Université Paris‐SaclayCEACNRSGif‐sur‐YvetteFrance
| | - Daniel Farny
- German Center for Neurodegenerative Diseases (DZNE), MunichMunichGermany
| | - Gernot Kleinberger
- German Center for Neurodegenerative Diseases (DZNE), MunichMunichGermany
| | - Christian Haass
- German Center for Neurodegenerative Diseases (DZNE), MunichMunichGermany
- Chair of Metabolic BiochemistryFaculty of MedicineBiomedical Center (BMC)Ludwig‐Maximilians‐Universität MunichMunichGermany
- Munich Cluster of Systems Neurology (SyNergy)MunichGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute for BiochemistryMartinsriedGermany
| | - F. Ulrich Hartl
- Department of Cellular BiochemistryMax Planck Institute for BiochemistryMartinsriedGermany
- Munich Cluster of Systems Neurology (SyNergy)MunichGermany
| | - Wolfgang Baumeister
- Department of Molecular Structural BiologyMax Planck Institute of BiochemistryMartinsriedGermany
| | - Mark S Hipp
- Department of Cellular BiochemistryMax Planck Institute for BiochemistryMartinsriedGermany
- Department of Biomedical Sciences of Cells and SystemsUniversity Medical Center GroningenUniversity of GroningenGroningenThe Netherlands
- School of Medicine and Health SciencesCarl von Ossietzky University OldenburgOldenburgGermany
| | - Felix Meissner
- Department of Proteomics and Signal TransductionMax Planck Institute for BiochemistryMartinsriedGermany
- Department of Systems Immunology and ProteomicsMedical FacultyInstitute of Innate ImmunityUniversity of BonnGermany
| | - Rubén Fernández‐Busnadiego
- Department of Molecular Structural BiologyMax Planck Institute of BiochemistryMartinsriedGermany
- Institute of NeuropathologyUniversity Medical Center GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGöttingenGermany
| | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), MunichMunichGermany
- Munich Cluster of Systems Neurology (SyNergy)MunichGermany
- Graduate School of Systemic Neurosciences (GSN)Ludwig‐Maximilians‐University MunichMunichGermany
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Allostery Modulates Interactions between Proteasome Core Particles and Regulatory Particles. Biomolecules 2022; 12:biom12060764. [PMID: 35740889 PMCID: PMC9221237 DOI: 10.3390/biom12060764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 01/27/2023] Open
Abstract
Allostery-regulation at distant sites is a key concept in biology. The proteasome exhibits multiple forms of allosteric regulation. This regulatory communication can span a distance exceeding 100 Ångstroms and can modulate interactions between the two major proteasome modules: its core particle and regulatory complexes. Allostery can further influence the assembly of the core particle with regulatory particles. In this focused review, known and postulated interactions between these proteasome modules are described. Allostery may explain how cells build and maintain diverse populations of proteasome assemblies and can provide opportunities for therapeutic interventions.
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28
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Abstract
The mechanistic target of rapamycin (mTOR) regulates numerous extracellular and intracellular signals involved in the maintenan-ce of cellular homeostasis and cell growth. mTOR also functions as an endogenous inhibitor of autophagy. Under nutrient-rich conditions, mTOR complex 1 (mTORC1) phosphorylates the ULK1 complex, preventing its activation and subsequent autophagosome formation, while inhibition of mTORC1 using either rapamycin or nutrient deprivation induces autophagy. Autophagy and proteasomal proteolysis provide amino acids necessary for protein translation. Although the connection between mTORC1 and autophagy is well characterized, the association of mTORC1 inhibition with proteasome biogenesis and activity has not been fully elucidated yet. Proteasomes are long-lived cellular organelles. Their spatiotemporal rather than homeostatic regulation could be another adaptive cellular mechanism to respond to starvation. Here, we reviewed several published reports and the latest research from our group to examine the connection between mTORC1 and proteasome. We have also investigated and described the effect of mTORC1 inhibition on proteasome activity using purified proteasomes. Since mTORC1 inhibitors are currently evaluated as treatments for several human diseases, a better understanding of the link between mTORC1 activity and proteasome function is of utmost importance.
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Affiliation(s)
- Seo Hyeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Won Hoon Choi
- BK21 FOUR Biomedical Science Program, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
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29
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VerPlank JJS, Gawron J, Silvestri NJ, Feltri ML, Wrabetz L, Goldberg AL. Raising cGMP restores proteasome function and myelination in mice with a proteotoxic neuropathy. Brain 2022; 145:168-178. [PMID: 34382059 PMCID: PMC9126006 DOI: 10.1093/brain/awab249] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/12/2021] [Accepted: 06/16/2021] [Indexed: 11/14/2022] Open
Abstract
Agents that raise cyclic guanosine monophosphate (cGMP) by activating protein kinase G increase 26S proteasome activities, protein ubiquitination and degradation of misfolded proteins. Therefore, they may be useful in treating neurodegenerative and other diseases caused by an accumulation of misfolded proteins. Mutations in myelin protein zero (MPZ) cause the peripheral neuropathy Charcot-Marie-Tooth type 1B (CMT1B). In peripheral nerves of a mouse model of CMT1B, where the mutant MPZS63del is expressed, proteasome activities are reduced, mutant MPZS63del and polyubiquitinated proteins accumulate and the unfolded protein response (p-eif2α) is induced. In HEK293 cells, raising cGMP stimulated ubiquitination and degradation of MPZS63del, but not of wild-type MPZ. Treating S63del mice with the phosphodiesterase 5 inhibitor, sildenafil-to raise cGMP-increased proteasome activity in sciatic nerves and reduced the levels of polyubiquitinated proteins, the proteasome reporter ubG76V-GFP and p-elF2α. Furthermore, sildenafil treatment reduced the number of amyelinated axons, and increased myelin thickness and nerve conduction velocity in sciatic nerves. Thus, agents that raise cGMP, including those widely used in medicine, may be useful therapies for CMT1B and other proteotoxic diseases.
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Affiliation(s)
- Jordan J S VerPlank
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Joseph Gawron
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Nicholas J Silvestri
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - M Laura Feltri
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Lawrence Wrabetz
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Alfred L Goldberg
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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30
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Vargas G, Cortés O, Arias-Muñoz E, Hernández S, Cerda-Troncoso C, Hernández L, González AE, Tatham MH, Bustamante HA, Retamal C, Cancino J, Varas-Godoy M, Hay RT, Rojas-Fernández A, Cavieres VA, Burgos PV. Negative Modulation of Macroautophagy by Stabilized HERPUD1 is Counteracted by an Increased ER-Lysosomal Network With Impact in Drug-Induced Stress Cell Survival. Front Cell Dev Biol 2022; 10:743287. [PMID: 35309917 PMCID: PMC8924303 DOI: 10.3389/fcell.2022.743287] [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: 07/18/2021] [Accepted: 01/27/2022] [Indexed: 11/25/2022] Open
Abstract
Macroautophagy and the ubiquitin proteasome system work as an interconnected network in the maintenance of cellular homeostasis. Indeed, efficient activation of macroautophagy upon nutritional deprivation is sustained by degradation of preexisting proteins by the proteasome. However, the specific substrates that are degraded by the proteasome in order to activate macroautophagy are currently unknown. By quantitative proteomic analysis we identified several proteins downregulated in response to starvation independently of ATG5 expression. Among them, the most significant was HERPUD1, an ER membrane protein with low expression and known to be degraded by the proteasome under normal conditions. Contrary, under ER stress, levels of HERPUD1 increased rapidly due to a blockage in its proteasomal degradation. Thus, we explored whether HERPUD1 stability could work as a negative regulator of autophagy. In this work, we expressed a version of HERPUD1 with its ubiquitin-like domain (UBL) deleted, which is known to be crucial for its proteasome degradation. In comparison to HERPUD1-WT, we found the UBL-deleted version caused a negative role on basal and induced macroautophagy. Unexpectedly, we found stabilized HERPUD1 promotes ER remodeling independent of unfolded protein response activation observing an increase in stacked-tubular structures resembling previously described tubular ER rearrangements. Importantly, a phosphomimetic S59D mutation within the UBL mimics the phenotype observed with the UBL-deleted version including an increase in HERPUD1 stability and ER remodeling together with a negative role on autophagy. Moreover, we found UBL-deleted version and HERPUD1-S59D trigger an increase in cellular size, whereas HERPUD1-S59D also causes an increased in nuclear size. Interestingly, ER remodeling by the deletion of the UBL and the phosphomimetic S59D version led to an increase in the number and function of lysosomes. In addition, the UBL-deleted version and phosphomimetic S59D version established a tight ER-lysosomal network with the presence of extended patches of ER-lysosomal membrane-contact sites condition that reveals an increase of cell survival under stress conditions. Altogether, we propose stabilized HERPUD1 downregulates macroautophagy favoring instead a closed interplay between the ER and lysosomes with consequences in drug-cell stress survival.
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Affiliation(s)
- Gabriela Vargas
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Omar Cortés
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Eloisa Arias-Muñoz
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Sergio Hernández
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Cristobal Cerda-Troncoso
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Laura Hernández
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Alexis E González
- Facultad de Medicina, Instituto de Fisiología, Universidad Austral de Chile, Valdivia, Chile
| | - Michael H Tatham
- Center for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hianara A Bustamante
- Facultad de Medicina, Instituto de Microbiología Clínica, Universidad Austral de Chile, Valdivia, Chile
| | - Claudio Retamal
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Jorge Cancino
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Manuel Varas-Godoy
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ronald T Hay
- Center for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Alejandro Rojas-Fernández
- Center for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom.,Instituto de Medicina & Centro Interdisciplinario de Estudios del Sistema Nervioso (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Viviana A Cavieres
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile
| | - Patricia V Burgos
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Centro de Envejecimiento y Regeneración (CARE-UC), Facultad de Ciencias Biológicas, Pontificia Universidad Católica, Santiago, Chile.,Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
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31
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Förster F. Subtomogram analysis: The sum of a tomogram's particles reveals molecular structure in situ. J Struct Biol X 2022; 6:100063. [PMID: 36684812 PMCID: PMC9846452 DOI: 10.1016/j.yjsbx.2022.100063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 01/25/2023] Open
Abstract
Cryo-electron tomography is uniquely suited to provide insights into the molecular architecture of cells and tissue in the native state. While frozen hydrated specimens tolerate sufficient electron doses to distinguish different types of particles in a tomogram, the accumulating beam damage does not allow resolving their detailed molecular structure individually. Statistical methods for subtomogram averaging and classification that coherently enhance the signal of particles corresponding to copies of the same type of macromolecular allow obtaining much higher resolution insights into macromolecules. Here, I review the developments in subtomogram analysis at Wolfgang Baumeister's laboratory that make the dream of structural biology in the native cell become reality.
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Affiliation(s)
- Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Uni-versiteitsweg 99, 3584 CG Utrecht, the Netherlands
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32
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Guo X. Localized Proteasomal Degradation: From the Nucleus to Cell Periphery. Biomolecules 2022; 12:biom12020229. [PMID: 35204730 PMCID: PMC8961600 DOI: 10.3390/biom12020229] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/31/2022] Open
Abstract
The proteasome is responsible for selective degradation of most cellular proteins. Abundantly present in the cell, proteasomes not only diffuse in the cytoplasm and the nucleus but also associate with the chromatin, cytoskeleton, various membranes and membraneless organelles/condensates. How and why the proteasome gets to these specific subcellular compartments remains poorly understood, although increasing evidence supports the hypothesis that intracellular localization may have profound impacts on the activity, substrate accessibility and stability/integrity of the proteasome. In this short review, I summarize recent advances on the functions, regulations and targeting mechanisms of proteasomes, especially those localized to the nuclear condensates and membrane structures of the cell, and I discuss the biological significance thereof in mediating compartmentalized protein degradation.
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Affiliation(s)
- Xing Guo
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China;
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Hangzhou 310058, China
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33
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OUP accepted manuscript. Microscopy (Oxf) 2022; 71:i60-i65. [DOI: 10.1093/jmicro/dfab059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/19/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
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34
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Zuber B, Lučić V. Neurons as a model system for cryo-electron tomography. J Struct Biol X 2022; 6:100067. [PMID: 35310407 PMCID: PMC8924422 DOI: 10.1016/j.yjsbx.2022.100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Cryo-ET imaging of neurons is a versatile system for cell biology in situ. Structural and spatial localization analysis yields new insights into synaptic transmission. The synapse provides a rich environment for the development of image processing tools.
Cryo-electron tomography (Cryo-ET) provides unique opportunities to image cellular components at high resolution in their native state and environment. While many different cell types were investigated by cryo-ET, here we review application to neurons. We show that neurons are a versatile system that can be used to investigate general cellular components such as the cytoskeleton and membrane-bound organelles, in addition to neuron-specific processes such as synaptic transmission. Furthermore, the synapse provides a rich environment for the development of cryo-ET image processing tools suitable to elucidate the functional and spatial organization of compositionally and morphologically heterogeneous macromolecular complexes involved in biochemical signaling cascades, within their native, crowded cellular environments.
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35
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Kim S, Park SH, Choi WH, Lee MJ. Evaluation of Immunoproteasome-Specific Proteolytic Activity Using Fluorogenic Peptide Substrates. Immune Netw 2022; 22:e28. [PMID: 35799704 PMCID: PMC9250865 DOI: 10.4110/in.2022.22.e28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 12/01/2022] Open
Abstract
The 26S proteasome irreversibly hydrolyzes polyubiquitylated substrates to maintain protein homeostasis; it also regulates immune responses by generating antigenic peptides. An alternative form of the 26S proteasome is the immunoproteasome, which contains substituted catalytic subunits (β1i/PSMB9, β2i/PSMB10, and β5i/PSMB8) instead of constitutively expressed counterparts (β1/PSMB6, β2/PSMB7, and β5/PSMB5). The immunoproteasome expands the peptide repertoire presented on MHC class I molecules. However, how its activity changes in this context is largely elusive, possibly due to the lack of a standardized methodology to evaluate its specific activity. Here, we describe an assay protocol that measures the immunoproteasome activity of whole-cell lysates using commercially available fluorogenic peptide substrates. Our results showed that the most accurate assessment of immunoproteasome activity could be achieved by combining β5i-targeting substrate Ac-ANW-AMC and immunoproteasome inhibitor ONX-0914. This simple and reliable protocol may contribute to future studies of immunoproteasomes and their pathophysiological roles during viral infection, inflammation, and tumorigenesis.
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Affiliation(s)
- Sumin Kim
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- BK21 FOUR Biomedical Science Program, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Seo Hyeong Park
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- BK21 FOUR Biomedical Science Program, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Won Hoon Choi
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- BK21 FOUR Biomedical Science Program, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Min Jae Lee
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
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36
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Croxford M, Elbaum M, Arigovindan M, Kam Z, Agard D, Villa E, Sedat J. Entropy-regularized deconvolution of cellular cryotransmission electron tomograms. Proc Natl Acad Sci U S A 2021; 118:e2108738118. [PMID: 34876518 PMCID: PMC8685678 DOI: 10.1073/pnas.2108738118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/01/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) allows for the high-resolution visualization of biological macromolecules. However, the technique is limited by a low signal-to-noise ratio (SNR) and variance in contrast at different frequencies, as well as reduced Z resolution. Here, we applied entropy-regularized deconvolution (ER-DC) to cryo-ET data generated from transmission electron microscopy (TEM) and reconstructed using weighted back projection (WBP). We applied deconvolution to several in situ cryo-ET datasets and assessed the results by Fourier analysis and subtomogram analysis (STA).
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Affiliation(s)
- Matthew Croxford
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Michael Elbaum
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 760001, Israel
| | - Muthuvel Arigovindan
- Department of Electrical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Zvi Kam
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 760001, Israel
| | - David Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Elizabeth Villa
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093;
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - John Sedat
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158;
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37
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Zeng X, Howe G, Xu M. End-to-end robust joint unsupervised image alignment and clustering. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION 2021; 2021:3834-3846. [PMID: 35392630 PMCID: PMC8986091 DOI: 10.1109/iccv48922.2021.00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Computing dense pixel-to-pixel image correspondences is a fundamental task of computer vision. Often, the objective is to align image pairs from the same semantic category for manipulation or segmentation purposes. Despite achieving superior performance, existing deep learning alignment methods cannot cluster images; consequently, clustering and pairing images needed to be a separate laborious and expensive step. Given a dataset with diverse semantic categories, we propose a multi-task model, Jim-Net, that can directly learn to cluster and align images without any pixel-level or image-level annotations. We design a pair-matching alignment unsupervised training algorithm that selectively matches and aligns image pairs from the clustering branch. Our unsupervised Jim-Net achieves comparable accuracy with state-of-the-art supervised methods on benchmark 2D image alignment dataset PF-PASCAL. Specifically, we apply Jim-Net to cryo-electron tomography, a revolutionary 3D microscopy imaging technique of native subcellular structures. After extensive evaluation on seven datasets, we demonstrate that Jim-Net enables systematic discovery and recovery of representative macromolecular structures in situ, which is essential for revealing molecular mechanisms underlying cellular functions. To our knowledge, Jim-Net is the first end-to-end model that can simultaneously align and cluster images, which significantly improves the performance as compared to performing each task alone.
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Affiliation(s)
- Xiangrui Zeng
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Gregory Howe
- Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Min Xu
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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38
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Lee J, Le LTHL, Kim E, Lee MJ. Formation of Non-Nucleoplasmic Proteasome Foci during the Late Stage of Hyperosmotic Stress. Cells 2021; 10:cells10092493. [PMID: 34572142 PMCID: PMC8467775 DOI: 10.3390/cells10092493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
Cellular stress induces the formation of membraneless protein condensates in both the nucleus and cytoplasm. The nucleocytoplasmic transport of proteins mainly occurs through nuclear pore complexes (NPCs), whose efficiency is affected by various stress conditions. Here, we report that hyperosmotic stress compartmentalizes nuclear 26S proteasomes into dense nuclear foci, independent of signaling cascades. Most of the proteasome foci were detected between the condensed chromatin mass and inner nuclear membrane. The proteasome-positive puncta were not colocalized with other types of nuclear bodies and were reversibly dispersed when cells were returned to the isotonic medium. The structural integrity of 26S proteasomes in the nucleus was slightly affected under the hyperosmotic condition. We also found that these insulator-body-like proteasome foci were possibly formed through disrupted nucleus-to-cytosol transport, which was mediated by the sequestration of NPC components into osmostress-responding stress granules. These data suggest that phase separation in both the nucleus and cytosol may be a major cell survival mechanism during hyperosmotic stress conditions.
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Affiliation(s)
- Jeeyoung Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Ly Thi Huong Luu Le
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Eunkyoung Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Correspondence:
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39
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Giandomenico SL, Alvarez-Castelao B, Schuman EM. Proteostatic regulation in neuronal compartments. Trends Neurosci 2021; 45:41-52. [PMID: 34489114 DOI: 10.1016/j.tins.2021.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/16/2021] [Accepted: 08/05/2021] [Indexed: 12/16/2022]
Abstract
Neurons continuously adapt to external cues and challenges, including stimulation, plasticity-inducing signals and aging. These adaptations are critical for neuronal physiology and extended survival. Proteostasis is the process by which cells adjust their protein content to achieve the specific protein repertoire necessary for cellular function. Due to their complex morphology and polarized nature, neurons possess unique proteostatic requirements. Proteostatic control in axons and dendrites must be implemented through regulation of protein synthesis and degradation in a decentralized fashion, but at the same time, it requires integration, at least in part, in the soma. Here, we discuss current understanding of neuronal proteostasis, as well as open questions and future directions requiring further exploration.
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Affiliation(s)
| | - Beatriz Alvarez-Castelao
- Department of Biochemistry and Molecular Biology, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.
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40
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Chen X, Htet ZM, López-Alfonzo E, Martin A, Walters KJ. Proteasome interaction with ubiquitinated substrates: from mechanisms to therapies. FEBS J 2021; 288:5231-5251. [PMID: 33211406 PMCID: PMC8131406 DOI: 10.1111/febs.15638] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022]
Abstract
The 26S proteasome is responsible for regulated proteolysis in eukaryotic cells. Its substrates are diverse in structure, function, sequence length, and amino acid composition, and are targeted to the proteasome by post-translational modification with ubiquitin. Ubiquitination occurs through a complex enzymatic cascade and can also signal for other cellular events, unrelated to proteasome-catalyzed degradation. Like other post-translational protein modifications, ubiquitination is reversible, with ubiquitin chain hydrolysis catalyzed by the action of deubiquitinating enzymes (DUBs), ~ 90 of which exist in humans and allow for temporal events and dynamic ubiquitin-chain remodeling. DUBs have been known for decades to be an integral part of the proteasome, as deubiquitination is coupled to substrate unfolding and translocation into the internal degradation chamber. Moreover, the proteasome also binds several ubiquitinating enzymes and shuttle factors that recruit ubiquitinated substrates. The role of this intricate machinery and how ubiquitinated substrates interact with proteasomes remains an area of active investigation. Here, we review what has been learned about the mechanisms used by the proteasome to bind ubiquitinated substrates, substrate shuttle factors, ubiquitination machinery, and DUBs. We also discuss many open questions that require further study or the development of innovative approaches to be answered. Finally, we address the promise of expanded therapeutic targeting that could benefit from such new discoveries.
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Affiliation(s)
- Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Zaw Min Htet
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
| | - Erika López-Alfonzo
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California at Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California at Berkeley, CA, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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Perez JD, Fusco CM, Schuman EM. A Functional Dissection of the mRNA and Locally Synthesized Protein Population in Neuronal Dendrites and Axons. Annu Rev Genet 2021; 55:183-207. [PMID: 34460296 DOI: 10.1146/annurev-genet-030321-054851] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neurons are characterized by a complex morphology that enables the generation of subcellular compartments with unique biochemical and biophysical properties, such as dendrites, axons, and synapses. To sustain these different compartments and carry a wide array of elaborate operations, neurons express a diverse repertoire of gene products. Extensive regulation at both the messenger RNA (mRNA) and protein levels allows for the differentiation of subcellular compartments as well as numerous forms of plasticity in response to variable stimuli. Among the multiple mechanisms that control cellular functions, mRNA translation is manipulated by neurons to regulate where and when a protein emerges. Interestingly, transcriptomic and translatomic profiles of both dendrites and axons have revealed that the mRNA population only partially predicts the local protein population and that this relation significantly varies between different gene groups. Here, we describe the space that local translation occupies within the large molecular and regulatory complexity of neurons, in contrast to other modes of regulation. We then discuss the specialized organization of mRNAs within different neuronal compartments, as revealed by profiles of the local transcriptome. Finally, we discuss the features and functional implications of both locally correlated-and anticorrelated-mRNA-protein relations both under baseline conditions and during synaptic plasticity. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Julio D Perez
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
| | - Claudia M Fusco
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
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Reboud-Ravaux M. [The proteasome - structural aspects and inhibitors: a second life for a validated drug target]. Biol Aujourdhui 2021; 215:1-23. [PMID: 34397372 DOI: 10.1051/jbio/2021005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 02/06/2023]
Abstract
The proteasome is the central component of the adaptable ubiquitin proteasome system (UPS) discovered in the 1980's. It sustains protein homeostasis (proteostasis) under a large variety of physiological and pathological conditions. Its dysregulation has been often associated to various human diseases. Its potential regulation by modulators has emerged as promising avenue to develop treatments of various pathologies. The FDA approval in 2003 of the proteasome inhibitor bortezomib to treat multiple myeloma, then mantle lymphoma in 2006, has considerably increased the clinical interest of proteasome inhibition. Second-generation proteasome inhibitors (carfilzomib and ixazomib) have been approved to overcome bortezomib resistance and improved toxicity profile and route of administration. Selective inhibition of immunoproteasome is a promising approach towards the development of immunomodulatory drugs. The design of these drugs relies greatly on the elucidation of high-resolution structures of the targeted proteasomes. The ATPase-dependent 26S proteasome (2.4 MDa) consists of a 20S proteolytic core and one or two 19S regulatory particles. The 20S core contains three types of catalytic sites. In recent years, due to technical advances especially in atomic cryo-electron microscopy, significant progress has been made in the understanding of 26S proteasome structure and its dynamics. Stepwise conformational changes of the 19S particle induced by ATP hydrolysis lead to substrate translocation, 20S pore opening and processive protein degradation by the 20S proteolytic subunits (2β1, 2β2 and 2β5). A large variety of structurally different inhibitors, both natural products or synthetic compounds targeting immuno- and constitutive proteasomes, has been discovered. The latest advances in this drug discovery are presented. Knowledge about structures, inhibition mechanism and detailed biological regulations of proteasomes can guide strategies for the development of next-generation inhibitors to treat human diseases, especially cancers, immune disorders and pathogen infections. Proteasome activators are also potentially applicable to the reduction of proteotoxic stresses in neurodegeneration and aging.
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Affiliation(s)
- Michèle Reboud-Ravaux
- Sorbonne Université, Institut de Biologie Paris Seine (IBPS), CNRS UMR 8256, Inserm ERL U1164, 7 quai Saint Bernard, 75252 Paris Cedex 05, France
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Bäuerlein FJB, Baumeister W. Towards Visual Proteomics at High Resolution. J Mol Biol 2021; 433:167187. [PMID: 34384780 DOI: 10.1016/j.jmb.2021.167187] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations.
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Affiliation(s)
- Felix J B Bäuerlein
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany; Georg-August-University, Institute for Neuropathology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.
| | - Wolfgang Baumeister
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany.
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Creekmore BC, Chang YW, Lee EB. The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Proteostasis Factors. J Neuropathol Exp Neurol 2021; 80:494-513. [PMID: 33860329 PMCID: PMC8177850 DOI: 10.1093/jnen/nlab029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neurodegenerative diseases are characterized by the accumulation of misfolded proteins. This protein aggregation suggests that abnormal proteostasis contributes to aging-related neurodegeneration. A better fundamental understanding of proteins that regulate proteostasis may provide insight into the pathophysiology of neurodegenerative disease and may perhaps reveal novel therapeutic opportunities. The 26S proteasome is the key effector of the ubiquitin-proteasome system responsible for degrading polyubiquitinated proteins. However, additional factors, such as valosin-containing protein (VCP/p97/Cdc48) and C9orf72, play a role in regulation and trafficking of substrates through the normal proteostasis systems of a cell. Nonhuman AAA+ ATPases, such as the disaggregase Hsp104, also provide insights into the biochemical processes that regulate protein aggregation. X-ray crystallography and cryo-electron microscopy (cryo-EM) structures not bound to substrate have provided meaningful information about the 26S proteasome, VCP, and Hsp104. However, recent cryo-EM structures bound to substrate have provided new information about the function and mechanism of these proteostasis factors. Cryo-EM and cryo-electron tomography data combined with biochemical data have also increased the understanding of C9orf72 and its role in maintaining proteostasis. These structural insights provide a foundation for understanding proteostasis mechanisms with near-atomic resolution upon which insights can be gleaned regarding the pathophysiology of neurodegenerative diseases.
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Affiliation(s)
- Benjamin C Creekmore
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Graduate Program in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yi-Wei Chang
- From the Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Translational Neuropathology Research Laboratory, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
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An overview of the recent advances in cryo-electron microscopy for life sciences. Emerg Top Life Sci 2021; 5:151-168. [PMID: 33760078 DOI: 10.1042/etls20200295] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Cryo-electron microscopy (CryoEM) has superseded X-ray crystallography and NMR to emerge as a popular and effective tool for structure determination in recent times. It has become indispensable for the characterization of large macromolecular assemblies, membrane proteins, or samples that are limited, conformationally heterogeneous, and recalcitrant to crystallization. Besides, it is the only tool capable of elucidating high-resolution structures of macromolecules and biological assemblies in situ. A state-of-the-art electron microscope operable at cryo-temperature helps preserve high-resolution details of the biological sample. The structures can be determined, either in isolation via single-particle analysis (SPA) or helical reconstruction, electron diffraction (ED) or within the cellular environment via cryo-electron tomography (cryoET). All the three streams of SPA, ED, and cryoET (along with subtomogram averaging) have undergone significant advancements in recent times. This has resulted in breaking the boundaries with respect to both the size of the macromolecules/assemblies whose structures could be determined along with the visualization of atomic details at resolutions unprecedented for cryoEM. In addition, the collection of larger datasets combined with the ability to sort and process multiple conformational states from the same sample are providing the much-needed link between the protein structures and their functions. In overview, these developments are helping scientists decipher the molecular mechanism of critical cellular processes, solve structures of macromolecules that were challenging targets for structure determination until now, propelling forward the fields of biology and biomedicine. Here, we summarize recent advances and key contributions of the three cryo-electron microscopy streams of SPA, ED, and cryoET.
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Davis C, Spaller BL, Matouschek A. Mechanisms of substrate recognition by the 26S proteasome. Curr Opin Struct Biol 2021; 67:161-169. [PMID: 33296738 PMCID: PMC8096638 DOI: 10.1016/j.sbi.2020.10.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/12/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
The majority of regulated protein degradation in eukaryotes is accomplished by the 26S proteasome, the large proteolytic complex responsible for removing regulatory proteins and damaged proteins. Proteins are targeted to the proteasome by ubiquitination, and degradation is initiated at a disordered region within the protein. The ability of the proteasome to precisely select which proteins to break down is necessary for cellular functioning. Recent studies reveal the subtle mechanisms of substrate recognition by the proteasome - diverse ubiquitin chains can act as potent proteasome targeting signals, ubiquitin receptors function uniquely and cooperatively, and modification of initiation regions modulate degradation. Here, we summarize recent findings illuminating the nature of substrate recognition by the proteasome.
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Affiliation(s)
- Caroline Davis
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Brian Logan Spaller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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Molecular and cellular dynamics of the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140583. [PMID: 33321258 DOI: 10.1016/j.bbapap.2020.140583] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/16/2023]
Abstract
In eukaryotic cells, the ubiquitin-proteasome system serves to remove proteins that are either dysfunctional or no longer needed. The 26S proteasome is a 2.5 MDa multisubunit complex comprising the 20S core particle, where degradation is executed, and one or two regulatory particles which prepare substrates for degradation. Whereas the 20S core particles of several species had been studied extensively by X-ray crystallography, the 26S holocomplex structure had remained elusive for a long time. Recent advances in single-particle cryo-electron microscopy have changed the situation and provided atomic resolution models of this intriguing molecular machine and its dynamics. Besides, cryo-electron tomography enables structural studies in situ, providing molecular resolution images of macromolecules inside pristinely preserved cellular environments. This has greatly contributed to our understanding of proteasome dynamics in the context of cells.
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Zhang X, Mahamid J. Addressing the challenge of in situ structural studies of RNP granules in light of emerging opportunities. Curr Opin Struct Biol 2020; 65:149-158. [DOI: 10.1016/j.sbi.2020.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/01/2020] [Accepted: 06/16/2020] [Indexed: 01/23/2023]
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50
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In Situ Studies of Mitochondrial Translation by Cryo-Electron Tomography. Methods Mol Biol 2020. [PMID: 33230778 DOI: 10.1007/978-1-0716-0834-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Cryo-electron tomography (cryo-ET) enables the three-dimensional (3D) visualization of macromolecular complexes in their native environment (in situ). The ability to visualize macromolecules in situ is in particular advantageous for complex, membrane-associated processes, such as mitochondrial translation. Mitochondrial translation occurs almost exclusively associated with the inner mitochondrial membrane, giving rise to the mitochondrial DNA-encoded subunits of oxidative phosphorylation machinery. In cryo-ET, the 3D volume is reconstructed from a set of 2D projections of a frozen-hydrated specimen, which is sequentially tilted and imaged at different angles in a transmission electron microscope. In combination with subtomogram analysis, cryo-ET enables the structure determination of macromolecular complexes and their 3D organization. In this chapter, we summarize all steps required for structural characterization of mitochondrial ribosomes in situ, ranging from data acquisition to tomogram reconstruction and subtomogram analysis.
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