1
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Al Rawi S, Simpson L, Agnarsdóttir G, McDonald NQ, Chernuha V, Elpeleg O, Zeviani M, Barker RA, Spiegel R, Laman H. Study of an FBXO7 patient mutation reveals Fbxo7 and PI31 co-regulate proteasomes and mitochondria. FEBS J 2024; 291:2565-2589. [PMID: 38466799 DOI: 10.1111/febs.17114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/18/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Mutations in FBXO7 have been discovered to be associated with an atypical parkinsonism. We report here a new homozygous missense mutation in a paediatric patient that causes an L250P substitution in the dimerisation domain of Fbxo7. This alteration selectively ablates the Fbxo7-PI31 interaction and causes a significant reduction in Fbxo7 and PI31 levels in patient cells. Consistent with their association with proteasomes, patient fibroblasts have reduced proteasome activity and proteasome subunits. We also show PI31 interacts with the MiD49/51 fission adaptor proteins, and unexpectedly, PI31 acts to facilitate SCFFbxo7-mediated ubiquitination of MiD49. The L250P mutation reduces the SCFFbxo7 ligase-mediated ubiquitination of a subset of its known substrates. Although MiD49/51 expression was reduced in patient cells, there was no effect on the mitochondrial network. However, patient cells show reduced levels of mitochondrial function and mitophagy, higher levels of ROS and are less viable under stress. Our study demonstrates that Fbxo7 and PI31 regulate proteasomes and mitochondria and reveals a new function for PI31 in enhancing the SCFFbxo7 E3 ubiquitin ligase activity.
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Affiliation(s)
- Sara Al Rawi
- Department of Pathology, University of Cambridge, UK
| | - Lorna Simpson
- Department of Pathology, University of Cambridge, UK
| | | | - Neil Q McDonald
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Biological Sciences, Institute of Structural and Molecular Biology, London, UK
| | - Veronika Chernuha
- Pediatric Neurology Institute, Dana-Dwek Children's Hospital, Tel Aviv Medical Centre and Sackler Faculty of Medicine, Israel
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Massimo Zeviani
- Mitochondrial Biology Unit, The MRC and University of Cambridge, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, UK
| | - Ronen Spiegel
- Pediatric Department, Emek Medical Center, Afula, Israel
| | - Heike Laman
- Department of Pathology, University of Cambridge, UK
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2
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Helena-Bueno K, Chan LI, Melnikov SV. Rippling life on a dormant planet: hibernation of ribosomes, RNA polymerases, and other essential enzymes. Front Microbiol 2024; 15:1386179. [PMID: 38770025 PMCID: PMC11102965 DOI: 10.3389/fmicb.2024.1386179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/21/2024] [Indexed: 05/22/2024] Open
Abstract
Throughout the tree of life, cells and organisms enter states of dormancy or hibernation as a key feature of their biology: from a bacterium arresting its growth in response to starvation, to a plant seed anticipating placement in fertile ground, to a human oocyte poised for fertilization to create a new life. Recent research shows that when cells hibernate, many of their essential enzymes hibernate too: they disengage from their substrates and associate with a specialized group of proteins known as hibernation factors. Here, we summarize how hibernation factors protect essential cellular enzymes from undesired activity or irreparable damage in hibernating cells. We show how molecular hibernation, once viewed as rare and exclusive to certain molecules like ribosomes, is in fact a widespread property of biological molecules that is required for the sustained persistence of life on Earth.
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Affiliation(s)
| | | | - Sergey V. Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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3
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Wang J, Kjellgren A, DeMartino GN. Differential Interactions of the Proteasome Inhibitor PI31 with Constitutive and Immuno-20S Proteasomes. Biochemistry 2024; 63:1000-1015. [PMID: 38577872 DOI: 10.1021/acs.biochem.3c00707] [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] [Indexed: 04/06/2024]
Abstract
PI31 (Proteasome Inhibitor of 31,000 Da) is a 20S proteasome binding protein originally identified as an in vitro inhibitor of 20S proteasome proteolytic activity. Recently reported cryo-electron microscopy structures of 20S-PI31 complexes have revealed that the natively disordered proline-rich C-terminus of PI31 enters the central chamber in the interior of the 20S proteasome and interacts directly with the proteasome's multiple catalytic threonine residues in a manner predicted to inhibit their enzymatic function while evading its own proteolysis. Higher eukaryotes express an alternative form of the 20S proteasome (termed "immuno-proteasome") that features genetically and functionally distinct catalytic subunits. The effect of PI31 on immuno-proteasome function is unknown. We examine the relative inhibitory effects of PI31 on purified constitutive (20Sc) and immuno-(20Si) 20S proteasomes in vitro and show that PI31 inhibits 20Si hydrolytic activity to a significantly lesser degree than that of 20Sc. Unlike 20Sc, 20Si hydrolyzes the carboxyl-terminus of PI31 and this effect contributes to the reduced inhibitory activity of PI31 toward 20Si. Conversely, loss of 20Sc inhibition by PI31 point mutants leads to PI31 degradation by 20Sc. These results demonstrate unexpected differential interactions of PI31 with 20Sc and 20Si and document their functional consequences.
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Affiliation(s)
- Jason Wang
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
| | - Abbey Kjellgren
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
| | - George N DeMartino
- Department of Physiology, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9040, United States
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4
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Parrella P, Elikan AB, Snow JW. Pathogen- and host-directed pharmacologic strategies for control of Vairimorpha (Nosema) spp. infection in honey bees. J Eukaryot Microbiol 2024:e13026. [PMID: 38572630 DOI: 10.1111/jeu.13026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Microsporidia are obligate intracellular parasites of the Fungal Kingdom that cause widespread infections in nature, with important effects on invertebrates involved in food production systems. The two microsporidian species Vairimorpha (Nosema) ceranae (and the less common Vairimorpha (Nosema) apis) can cause individual disease in honey bees and contribute to colony collapse. The efficacy, safety, and availability of fumagillin, the only drug currently approved to treat microsporidia infection in bees, is uncertain. In this review, we will discuss some of the most promising alternative strategies for the mitigation of Vairimorpha spp. with an emphasis on infection by V. ceranae, now the dominant species infecting bees. We will focus on pharmacologic interventions where the mechanism of action is known and examine both pathogen-directed and host-directed approaches. As limiting toxicity to host cells has been especially emphasized in treating bees that are already facing numerous stressors, strategies that disrupt pathogen-specific targets may be especially advantageous. Therefore, efforts to increase the knowledge and tools for facilitating the discovery of such targets and pharmacologic agents directed against them should be prioritized.
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Affiliation(s)
- Parker Parrella
- Department of Biology, Barnard College, New York, New York, USA
| | | | - Jonathan W Snow
- Department of Biology, Barnard College, New York, New York, USA
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5
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Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Baslé A, Schneider C, Connolly JPR, Blaza JN, Csörgő B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV. A new family of bacterial ribosome hibernation factors. Nature 2024; 626:1125-1132. [PMID: 38355796 PMCID: PMC10901736 DOI: 10.1038/s41586-024-07041-8] [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: 02/17/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage1,2. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery3-6. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.
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Affiliation(s)
| | - Mariia Yu Rybak
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Rudi Sullivan
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Charlotte R Brown
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Arnaud Baslé
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Claudia Schneider
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - James N Blaza
- Department of Chemistry, University of York, York, UK
- York Structural Biology Laboratory, University of York, York, UK
- York Biomedical Research Institute, University of York, York, UK
| | - Bálint Csörgő
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
| | | | - Matthieu G Gagnon
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections & Immunity, University of Texas Medical Branch, Galveston, TX, USA.
| | - Chris H Hill
- York Structural Biology Laboratory, University of York, York, UK.
- York Biomedical Research Institute, University of York, York, UK.
- Department of Biology, University of York, York, UK.
| | - Sergey V Melnikov
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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6
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Sharma H, Jespersen N, Ehrenbolger K, Carlson LA, Barandun J. Ultrastructural insights into the microsporidian infection apparatus reveal the kinetics and morphological transitions of polar tube and cargo during host cell invasion. PLoS Biol 2024; 22:e3002533. [PMID: 38422169 DOI: 10.1371/journal.pbio.3002533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 03/12/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
During host cell invasion, microsporidian spores translocate their entire cytoplasmic content through a thin, hollow superstructure known as the polar tube. To achieve this, the polar tube transitions from a compact spring-like state inside the environmental spore to a long needle-like tube capable of long-range sporoplasm delivery. The unique mechanical properties of the building blocks of the polar tube allow for an explosive transition from compact to extended state and support the rapid cargo translocation process. The molecular and structural factors enabling this ultrafast process and the structural changes during cargo delivery are unknown. Here, we employ light microscopy and in situ cryo-electron tomography to visualize multiple ultrastructural states of the Vairimorpha necatrix polar tube, allowing us to evaluate the kinetics of its germination and characterize the underlying morphological transitions. We describe a cargo-filled state with a unique ordered arrangement of microsporidian ribosomes, which cluster along the thin tube wall, and an empty post-translocation state with a reduced diameter but a thicker wall. Together with a proteomic analysis of endogenously affinity-purified polar tubes, our work provides comprehensive data on the infection apparatus of microsporidia and uncovers new aspects of ribosome regulation and transport.
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Affiliation(s)
- Himanshu Sharma
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Wallenberg Centre for Molecular Medicine, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Nathan Jespersen
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Kai Ehrenbolger
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Biophysics, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Wallenberg Centre for Molecular Medicine, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Wallenberg Centre for Molecular Medicine, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Science for Life Laboratory, Umeå University, Umeå, Sweden
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7
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Svedberg D, Winiger RR, Berg A, Sharma H, Tellgren-Roth C, Debrunner-Vossbrinck BA, Vossbrinck CR, Barandun J. Functional annotation of a divergent genome using sequence and structure-based similarity. BMC Genomics 2024; 25:6. [PMID: 38166563 PMCID: PMC10759460 DOI: 10.1186/s12864-023-09924-y] [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: 08/27/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes. RESULTS In this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes. CONCLUSION We provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.
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Affiliation(s)
- Dennis Svedberg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Rahel R Winiger
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Himanshu Sharma
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Charles R Vossbrinck
- Department of Environmental Science, Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden.
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8
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Velez B, Razi A, Hubbard RD, Walsh R, Rawson S, Tian G, Finley D, Hanna J. Rational design of proteasome inhibitors based on the structure of the endogenous inhibitor PI31/Fub1. Proc Natl Acad Sci U S A 2023; 120:e2308417120. [PMID: 38091293 PMCID: PMC10743371 DOI: 10.1073/pnas.2308417120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Proteasome inhibitors are widely used anticancer drugs. The three clinically approved agents are modified small peptides that preferentially target one of the proteasome's three active sites (β5) at physiologic concentrations. In addition to these drugs, there is also an endogenous proteasome inhibitor, PI31/Fub1, that enters the proteasome's interior to simultaneously yet specifically inhibit all three active sites. Here, we have used PI31's evolutionarily optimized inhibitory mechanisms to develop a suite of potent and specific β2 inhibitors. The lead compound strongly inhibited growth of multiple myeloma cells as a standalone agent, indicating the compound's cell permeability and establishing β2 as a potential therapeutic target in multiple myeloma. The lead compound also showed strong synergy with the existing β5 inhibitor bortezomib; such combination therapies might help with existing challenges of resistance and severe side effects. These results represent an effective method for rational structure-guided development of proteasome inhibitors.
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Affiliation(s)
- Benjamin Velez
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
| | - Aida Razi
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
| | | | - Richard Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology,Harvard Medical School,Boston, MA02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Shaun Rawson
- Harvard Cryo-Electron Microscopy Center for Structural Biology,Harvard Medical School,Boston, MA02115
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
| | - Geng Tian
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - John Hanna
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA02115
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9
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Nemec AA, Tomko RJ. An unstructured proteasome inhibitor comes into focus. J Biol Chem 2023; 299:105145. [PMID: 37562568 PMCID: PMC10463253 DOI: 10.1016/j.jbc.2023.105145] [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] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
The inhibitory mechanism of an intrinsically disordered proteasome inhibitor identified over 30 years ago has finally been revealed by cryo-electron microscopy by Hsu et al. in a recent report in the Journal of Biological Chemistry. The structure, coupled with biochemical and cell-based experiments, resolves lingering questions about how the inhibitor achieves multisite inhibition of proteasomal protease activity, while raising several exciting new questions on the nature of proteasome subpopulations in the process.
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Affiliation(s)
- Antonia A Nemec
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA.
| | - Robert J Tomko
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, Florida, USA.
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10
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Hsu HC, Wang J, Kjellgren A, Li H, DeMartino GN. Ηigh-resolution structure of mammalian PI31-20S proteasome complex reveals mechanism of proteasome inhibition. J Biol Chem 2023:104862. [PMID: 37236357 PMCID: PMC10319324 DOI: 10.1016/j.jbc.2023.104862] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/08/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Proteasome-catalyzed protein degradation mediates and regulates critical aspects of many cellular functions and is an important element of proteostasis in health and disease. Proteasome function is determined in part by the types of proteasome holoenzymes formed between the 20S core particle that catalyzes peptide bond hydrolysis and any of multiple regulatory proteins to which it binds. One of these regulators, PI31, was previously identified as an in vitro 20S proteasome inhibitor, but neither the molecular mechanism nor the possible physiologic significance of PI31-mediated proteasome inhibition has been clear. Here we report a high-resolution cryo-EM structure of the mammalian 20S proteasome in complex with PI31. The structure shows that two copies of the intrinsically-disordered carboxyl-terminus of PI31 are present in the central cavity of the closed-gate conformation of the proteasome and interact with proteasome catalytic sites in a manner that blocks proteolysis of substrates but resists their own degradation. The two inhibitory polypeptide chains appear to originate from PI31 monomers that enter the catalytic chamber from opposite ends of the 20S cylinder. We present evidence that PI31 can inhibit proteasome activity in mammalian cells and may serve regulatory functions for the control of cellular proteostasis.
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Affiliation(s)
- Hao-Chi Hsu
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503
| | - Jason Wang
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Abbey Kjellgren
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503.
| | - George N DeMartino
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390.
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11
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Hsu HC, Wang J, Kjellgren A, Li H, DeMartino GN. High-resolution structure of mammalian PI31â€"20S proteasome complex reveals mechanism of proteasome inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535455. [PMID: 37066326 PMCID: PMC10103979 DOI: 10.1101/2023.04.03.535455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proteasome-catalyzed protein degradation mediates and regulates critical aspects of many cellular functions and is an important element of proteostasis in health and disease. Proteasome function is determined in part by the types of proteasome holoenzymes formed between the 20S core particle that catalyzes peptide bond hydrolysis and any of multiple regulatory proteins to which it binds. One of these regulators, PI31, was previously identified as an in vitro 20S proteasome inhibitor, but neither the molecular mechanism nor the possible physiologic significance of PI31-mediated proteasome inhibition has been clear. Here we report a high- resolution cryo-EM structure of the mammalian 20S proteasome in complex with PI31. The structure shows that two copies of the intrinsically-disordered carboxyl-terminus of PI31 are present in the central cavity of the closed-gate conformation of the proteasome and interact with proteasome catalytic sites in a manner that blocks proteolysis of substrates but resists their own degradation. The two inhibitory polypeptide chains appear to originate from PI31 monomers that enter the catalytic chamber from opposite ends of the 20S cylinder. We present evidence that PI31 can inhibit proteasome activity in mammalian cells and may serve regulatory functions for the control of cellular proteostasis.
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