1
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Turner M, Uday AB, Velyvis A, Rennella E, Zeytuni N, Vahidi S. Structural basis for allosteric modulation of M. tuberculosis proteasome core particle. Nat Commun 2025; 16:3138. [PMID: 40169579 PMCID: PMC11962144 DOI: 10.1038/s41467-025-58430-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Accepted: 03/24/2025] [Indexed: 04/03/2025] Open
Abstract
The Mycobacterium tuberculosis (Mtb) proteasome system selectively degrades damaged or misfolded proteins and is crucial for the pathogen's survival within the host. Targeting the 20S core particle (CP) offers a viable strategy for developing tuberculosis treatments. The activity of Mtb 20S CP, like that of its eukaryotic counterpart, is allosterically regulated, yet the specific conformations involved have not been captured in high-resolution structures to date. Here, we use single-particle electron cryomicroscopy and H/D exchange mass spectrometry to determine the Mtb 20S CP structure in an auto-inhibited state that is distinguished from the canonical resting state by the conformation of switch helices at the α/β interface. The rearrangement of these helices collapses the S1 pocket, effectively inhibiting substrate binding. Biochemical experiments show that the Mtb 20S CP activity can be altered through allosteric sites far from the active site. Our findings underscore the potential of targeting allostery to develop antituberculosis therapeutics.
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Affiliation(s)
- Madison Turner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Adwaith B Uday
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada
| | - Algirdas Velyvis
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Enrico Rennella
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Natalie Zeytuni
- Department of Anatomy and Cell Biology, McGill University, Montréal, QC, Canada.
- Centre de Recherche en Biologie Structurale (CRBS), Montréal, QC, Canada.
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
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2
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von Rosen T, Zdanowicz R, El Hadeg Y, Afanasyev P, Boehringer D, Leitner A, Glockshuber R, Weber-Ban E. Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa. Nat Commun 2025; 16:3042. [PMID: 40155375 PMCID: PMC11953334 DOI: 10.1038/s41467-025-58073-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/12/2025] [Indexed: 04/01/2025] Open
Abstract
Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host macrophages. The core particle of the proteasome (20S CP) associates with ring-shaped activator complexes to degrade protein substrates. One of these is the bacterial proteasome activator Bpa that stimulates the ATP-independent proteasomal degradation of the heat shock repressor HspR. In this study, we determine the cryogenic electron microscopy 3D reconstruction of the complex between Bpa and its natural substrate HspR at 4.1 Å global resolution. The resulting maps allow us to identify regions of Bpa that interact with HspR. Using structure-guided site-directed mutagenesis and in vitro biochemical assays, we confirm the importance of the identified residues for Bpa-mediated substrate recruitment and subsequent proteasomal degradation. Additionally, we show that the dodecameric Bpa ring associates asymmetrically with the heptameric α-rings of the 20S CP, adopting a conformation resembling a hinged lid, while still engaging all seven docking sites on the proteasome.
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Affiliation(s)
- Tatjana von Rosen
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Rafal Zdanowicz
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
- International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Warsaw, Poland
| | - Yasser El Hadeg
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, Zurich, Switzerland
| | | | - Alexander Leitner
- Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Rudi Glockshuber
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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3
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Clausen T. Protein waste turned into antibiotics as a defence strategy of human cells. Nature 2025; 639:872-873. [PMID: 40045121 DOI: 10.1038/d41586-025-00514-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
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4
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Mueller AU, Molina N, Darst SA. Real-time capture of σ N transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.637174. [PMID: 39974980 PMCID: PMC11839083 DOI: 10.1101/2025.02.07.637174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Bacterial σ factors bind RNA polymerase (E) to form holoenzyme (Eσ), conferring promoter specificity to E and playing a key role in transcription bubble formation. σN is unique among σ factors in its structure and functional mechanism, requiring activation by specialized AAA+ ATPases. EσN forms an inactive promoter complex where the N-terminal σN region I (σN-RI) threads through a small DNA bubble. On the opposite side of the DNA, the ATPase engages σN-RI within the pore of its hexameric ring. Here, we perform kinetics-guided structural analysis of de novo formed EσN initiation complexes and engineer a biochemical assay to measure ATPase-mediated σN-RI translocation during promoter melting. We show that the ATPase exerts mechanical action to translocate about 30 residues of σN-RI through the DNA bubble, disrupting inhibitory structures of σN to allow full transcription bubble formation. A local charge switch of σN-RI from positive to negative may help facilitate disengagement of the otherwise processive ATPase, allowing subsequent σN disentanglement from the DNA bubble.
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Affiliation(s)
- Andreas U. Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, 10065 USA
| | - Nina Molina
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, 10065 USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, 10065 USA
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5
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Kahne SC, Yoo JH, Chen J, Nakedi K, Iyer LM, Putzel G, Samhadaneh NM, Pironti A, Aravind L, Ekiert DC, Bhabha G, Rhee KY, Darwin KH. Identification of a depupylation regulator for an essential enzyme in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2024; 121:e2407239121. [PMID: 39585979 PMCID: PMC11626117 DOI: 10.1073/pnas.2407239121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 10/08/2024] [Indexed: 11/27/2024] Open
Abstract
In Mycobacterium tuberculosis (Mtb), proteins that are posttranslationally modified with a prokaryotic ubiquitin-like protein (Pup) can be degraded by bacterial proteasomes. A single Pup-ligase and depupylase shape the pupylome, but the mechanisms regulating their substrate specificity are incompletely understood. Here, we identified a depupylation regulator, a protein called CoaX, through its copurification with the depupylase Dop. CoaX is a pseudopantothenate kinase that showed evidence of binding to pantothenate, an essential nutrient Mtb synthesizes, but not its phosphorylation. In a ∆coaX mutant, pantothenate synthesis enzymes including PanB, a substrate of the Pup-proteasome system (PPS), were more abundant than in the parental strain. In vitro, CoaX specifically accelerated depupylation of Pup~PanB, while addition of pantothenate inhibited this reaction. In culture, media supplementation with pantothenate decreased PanB levels, which required CoaX. Collectively, we propose CoaX regulates PanB abundance in response to pantothenate levels by modulating its vulnerability to proteolysis by Mtb proteasomes.
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Affiliation(s)
- Shoshanna C. Kahne
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY10016
| | - Jin Hee Yoo
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY10016
| | - James Chen
- Department of Cell Biology, New York University School of Medicine, New York, NY10016
| | - Kehilwe Nakedi
- Department of Medicine, Weill Cornell Medicine, New York, NY10021
| | - Lakshminarayan M. Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
| | - Gregory Putzel
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY10016
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY10016
- Microbial Computational Genomic Core Lab, New York University Grossman School of Medicine, New York, NY10016
| | - Nora M. Samhadaneh
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY10016
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY10016
- Microbial Computational Genomic Core Lab, New York University Grossman School of Medicine, New York, NY10016
| | - Alejandro Pironti
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY10016
- Antimicrobial-Resistant Pathogens Program, New York University Grossman School of Medicine, New York, NY10016
- Microbial Computational Genomic Core Lab, New York University Grossman School of Medicine, New York, NY10016
| | - L. Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD20894
| | - Damian C. Ekiert
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY10016
- Department of Cell Biology, New York University School of Medicine, New York, NY10016
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY10016
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
| | - Kyu Y. Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY10021
| | - K. Heran Darwin
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY10016
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6
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Salcedo-Tacuma D, Howells GD, McHose C, Gutierrez-Diaz A, Schupp J, Smith DM. ProEnd: a comprehensive database for identifying HbYX motif-containing proteins across the tree of life. BMC Genomics 2024; 25:951. [PMID: 39396964 PMCID: PMC11475706 DOI: 10.1186/s12864-024-10864-4] [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: 07/29/2024] [Accepted: 10/03/2024] [Indexed: 10/15/2024] Open
Abstract
The proteasome plays a crucial role in cellular homeostasis by degrading misfolded, damaged, or unnecessary proteins. Understanding the regulatory mechanisms of proteasome activity is vital, particularly the interaction with activators containing the hydrophobic-tyrosine-any amino acid (HbYX) motif. Here, we present ProEnd, a comprehensive database designed to identify and catalog HbYX motif-containing proteins across the tree of life. Using a simple bioinformatics pipeline, we analyzed approximately 73 million proteins from 22,000 reference proteomes in the UniProt/SwissProt database. Our findings reveal the widespread presence of HbYX motifs in diverse organisms, highlighting their evolutionary conservation and functional significance. Notably, we observed an interesting prevalence of these motifs in viral proteomes, suggesting strategic interactions with the host proteasome. As validation two novel HbYX proteins found in this database were experimentally tested by pulldowns, confirming that they directly interact with the proteasome, with one of them directly activating it. ProEnd's extensive dataset and user-friendly interface enable researchers to explore the potential proteasomal regulator landscape, generating new hypotheses to advance proteasome biology. This resource is set to facilitate the discovery of novel therapeutic targets, enhancing our approach to treating diseases such as neurodegenerative disorders and cancer.
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Affiliation(s)
- David Salcedo-Tacuma
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Giovanni D Howells
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Coleman McHose
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - Aimer Gutierrez-Diaz
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Jane Schupp
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA
| | - David M Smith
- Department of Biochemistry and Molecular Medicine, West Virginia University School of Medicine, 4 Medical Center Dr, Morgantown, WV, USA.
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, USA.
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7
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Mor-Rashti Z, Levin R, Eichler J, Gur E. The Bacterial Proteasome Inter-domain Is a Selectivity Barrier for Degradation-tag Binding. J Mol Biol 2024; 436:168462. [PMID: 38301806 DOI: 10.1016/j.jmb.2024.168462] [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: 08/25/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Protein degradation, which occurs in all cells, is essential for proper cellular function by regulating many cellular processes, destroying misfolded proteins, and providing protein building blocks under starvation conditions. As proteolysis is a destructive process, it is carried out by tightly regulated enzymes that evolved to interact with their protein substrates in a highly controlled and selective manner. The agents of protein degradation include proteasomes, AAA+ proteolytic machines found in all kingdoms of life. The bacterial proteasome specifically recognizes proteins conjugated to a protein tag termed Pup, with the proteasome regulatory particle, a ring-shaped hexamer termed Mpa in mycobacteria, being responsible for Pup recognition. Once Pup binds Mpa, Pup enters the central pore, where the Mpa AAA+ domain links ATP hydrolysis to the translocation of Pup and its conjugated substrate into a barrel-shaped proteasome core particle, where peptide bond cleavage occurs. As Pup traverses the Mpa pore en route to the AAA+ domain, it passes the inter-domain. Although the inter-domain is conserved in all proteasomes, its role in substrate processing remained unclear. We report here that the Mpa inter-domain promotes Pup binding via electrostatic interactions between conserved charged inter-domain pore loops and charged Pup residues. As such, the inter-domain serves as a gatekeeper that selects for Pup binding, thus facilitating tag interaction with the downstream AAA+ domain. Our findings thus reveal the existence of an additional level of substrate binding regulation in an AAA+ protease.
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Affiliation(s)
- Zohar Mor-Rashti
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Roni Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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8
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Mukai K, Shibayama T, Imai Y, Hosaka T. Phenomenological interpretations of the mechanism for the concentration-dependent positive effect of antibiotic lincomycin on Streptomyces coelicolor A3(2). Appl Environ Microbiol 2023; 89:e0113323. [PMID: 37732750 PMCID: PMC10617593 DOI: 10.1128/aem.01133-23] [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: 07/06/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
The antibiotic lincomycin binds to the 23S ribosomal RNA peptidyl transferase loop region to inhibit protein synthesis. However, lincomycin can also stimulate the growth and secondary metabolism of actinomycetes in a concentration-dependent manner. In Streptomyces coelicolor A3(2), lincomycin stimulates the production of the blue-pigmented antibiotic actinorhodin at concentrations below the minimum inhibitory concentration. To better understand the molecular mechanism underlying these concentration-dependent positive effects, this study investigated how the target molecule, the ribosome, undergoes dynamic changes in the presence of lincomycin and explored the ribosome-related factors involved. Lincomycin, at a concentration that stimulates actinorhodin production of S. coelicolor A3(2), could restore temporarily arrested ribosome function by utilizing ribosome-related proteins and translation factors, presumably under the control of the transcription factor WblC protein that confers intrinsic resistance to multiple translation-inhibiting antibiotics, to eventually produce stable and active ribosomes even during the late growth phase. This qualitatively and quantitatively positive ribosome alteration can be advantageous for producing actinorhodin biosynthetic enzymes. A series of gene expression and biochemical analyses revealed that lincomycin at the concentration that induces ribosomal stabilization in S. coelicolor A3(2) could influence the localization of the 20S proteasome-related proteins, resulting in reduced proteasome activity. These findings suggest that the functional analysis of 20S proteasome represents a potential pivotal challenge for understanding the molecular mechanism of ribosome stabilization induced by lincomycin. Therefore, as lincomycin can dynamically alter its target molecule, the ribosome, we discuss the future issues and prospects for an increased understanding of the concentration-dependent properties of antibiotics. IMPORTANCE Antibiotics were originally defined as chemical compounds produced by a microbe that inhibits the growth of other microbes. However, an unexplained effect of this is that a low concentration of antibiotics, such as those below the minimum inhibitory concentration, can positively affect microbial growth and metabolism. The secondary metabolic activation of streptomycetes in the presence of the translation-inhibiting antibiotic lincomycin illustrates the concentration-dependent positive effect of the antibiotic. The significance of this study is that the phenomenological interpretation of the molecular mechanism of the concentration-dependent positive effect of lincomycin in Streptomyces coelicolor A3(2) has provided novel insight into the possible role of antibiotics in making their target molecules stable and active with the assistance of various related factors that benefit their function. Further exploration of this idea would lead to an essential understanding of antibiotics, including why actinomycetes make them and their role in nature.
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Affiliation(s)
- Keiichiro Mukai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
| | - Tomoko Shibayama
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- Graduate School of Science and Technology, Shinshu University, Nagano, Japan
| | - Yu Imai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
| | - Takeshi Hosaka
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, Nagano, Japan
- Graduate School of Medicine, Science and Technology, Shinshu University, Nagano, Japan
- Graduate School of Science and Technology, Shinshu University, Nagano, Japan
- Renaissance Center for Applied Microbiology, Shinshu University, Nagano, Japan
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9
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von Rosen T, Pepelnjak M, Quast JP, Picotti P, Weber-Ban E. ATP-independent substrate recruitment to proteasomal degradation in mycobacteria. Life Sci Alliance 2023; 6:e202301923. [PMID: 37562848 PMCID: PMC10415612 DOI: 10.26508/lsa.202301923] [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: 01/13/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Mycobacteria and other actinobacteria possess proteasomal degradation pathways in addition to the common bacterial compartmentalizing protease systems. Proteasomal degradation plays a crucial role in the survival of these bacteria in adverse environments. The mycobacterial proteasome interacts with several ring-shaped activators, including the bacterial proteasome activator (Bpa), which enables energy-independent degradation of heat shock repressor HspR. However, the mechanism of substrate selection and processing by the Bpa-proteasome complex remains unclear. In this study, we present evidence that disorder in substrates is required but not sufficient for recruitment to Bpa-mediated proteasomal degradation. We demonstrate that Bpa binds to the folded N-terminal helix-turn-helix domain of HspR, whereas the unstructured C-terminal tail of the substrate acts as a sequence-specific threading handle to promote efficient proteasomal degradation. In addition, we establish that the heat shock chaperone DnaK, which interacts with and co-regulates HspR, stabilizes HspR against Bpa-mediated proteasomal degradation. By phenotypical characterization of Mycobacterium smegmatis parent and bpa deletion mutant strains, we show that Bpa-dependent proteasomal degradation supports the survival of the bacterium under stress conditions by degrading HspR that regulates vital chaperones.
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Affiliation(s)
- Tatjana von Rosen
- ETH Zurich, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
| | - Monika Pepelnjak
- ETH Zurich, Institute of Molecular Systems Biology, Zurich Switzerland
| | - Jan-Philipp Quast
- ETH Zurich, Institute of Molecular Systems Biology, Zurich Switzerland
| | - Paola Picotti
- ETH Zurich, Institute of Molecular Systems Biology, Zurich Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology and Biophysics, Zurich, Switzerland
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10
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Block MF, Delley CL, Keller LML, Stuehlinger TT, Weber-Ban E. Electrostatic interactions guide substrate recognition of the prokaryotic ubiquitin-like protein ligase PafA. Nat Commun 2023; 14:5266. [PMID: 37644028 PMCID: PMC10465538 DOI: 10.1038/s41467-023-40807-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Pupylation, a post-translational modification found in Mycobacterium tuberculosis and other Actinobacteria, involves the covalent attachment of prokaryotic ubiquitin-like protein (Pup) to lysines on target proteins by the ligase PafA (proteasome accessory factor A). Pupylated proteins, like ubiquitinated proteins in eukaryotes, are recruited for proteasomal degradation. Proteomic studies suggest that hundreds of potential pupylation targets are modified by the sole existing ligase PafA. This raises intriguing questions regarding the selectivity of this enzyme towards a diverse range of substrates. Here, we show that the availability of surface lysines alone is not sufficient for interaction between PafA and target proteins. By identifying the interacting residues at the pupylation site, we demonstrate that PafA recognizes authentic substrates via a structural recognition motif centered around exposed lysines. Through a combination of computational analysis, examination of available structures and pupylated proteomes, and biochemical experiments, we elucidate the mechanism by which PafA achieves recognition of a wide array of substrates while retaining selective protein turnover.
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Affiliation(s)
- Matthias F Block
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
| | - Cyrille L Delley
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
- University of California, San Francisco, USA
| | - Lena M L Keller
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
| | - Timo T Stuehlinger
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, Zurich, Switzerland.
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11
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The β-Grasp Domain of Proteasomal ATPase Mpa Makes Critical Contacts with the Mycobacterium tuberculosis 20S Core Particle to Facilitate Degradation. mSphere 2022; 7:e0027422. [PMID: 35993699 PMCID: PMC9599533 DOI: 10.1128/msphere.00274-22] [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] [Indexed: 01/12/2023] Open
Abstract
Mycobacterium tuberculosis possesses a Pup-proteasome system analogous to the eukaryotic ubiquitin-proteasome pathway. We have previously shown that the hexameric mycobacterial proteasome ATPase (Mpa) recruits pupylated protein substrates via interactions between amino-terminal coiled-coils in Mpa monomers and the degradation tag Pup. However, it is unclear how Mpa rings interact with a proteasome due to the presence of a carboxyl-terminal β-grasp domain unique to Mpa homologues that makes the interaction highly unstable. Here, we describe newly identified critical interactions between Mpa and 20S core proteasomes. Interestingly, the Mpa C-terminal GQYL motif binds the 20S core particle activation pocket differently than the same motif of the ATP-independent proteasome accessory factor PafE. We further found that the β-hairpin of the Mpa β-grasp domain interacts variably with the H0 helix on top of the 20S core particle via a series of ionic and hydrogen-bond interactions. Individually mutating several involved residues reduced Mpa-mediated protein degradation both in vitro and in vivo. IMPORTANCE The Pup-proteasome system in Mycobacterium tuberculosis is critical for this species to cause lethal infections in mice. Investigating the molecular mechanism of how the Mpa ATPase recruits and unfolds pupylated substrates to the 20S proteasomal core particle for degradation will be essential to fully understand how degradation is regulated, and the structural information we report may be useful for the development of new tuberculosis chemotherapies.
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12
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AAA+ protease-adaptor structures reveal altered conformations and ring specialization. Nat Struct Mol Biol 2022; 29:1068-1079. [PMID: 36329286 PMCID: PMC9663308 DOI: 10.1038/s41594-022-00850-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022]
Abstract
ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze the protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated, tucked away from the channel and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies show additional structures and functions for key AAA+ elements. Pore-loop tucking may be used broadly by AAA+ unfoldases, for example, during enzyme pausing/unloading.
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