1
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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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2
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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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3
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Kavalchuk M, Jomaa A, Müller AU, Weber-Ban E. Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex. Nat Commun 2022; 13:276. [PMID: 35022401 PMCID: PMC8755798 DOI: 10.1038/s41467-021-27787-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/13/2021] [Indexed: 12/19/2022] Open
Abstract
Proteasomes are present in eukaryotes, archaea and Actinobacteria, including the human pathogen Mycobacterium tuberculosis, where proteasomal degradation supports persistence inside the host. In mycobacteria and other members of Actinobacteria, prokaryotic ubiquitin-like protein (Pup) serves as a degradation tag post-translationally conjugated to target proteins for their recruitment to the mycobacterial proteasome ATPase (Mpa). Here, we use single-particle cryo-electron microscopy to determine the structure of Mpa in complex with the 20S core particle at an early stage of pupylated substrate recruitment, shedding light on the mechanism of substrate translocation. Two conformational states of Mpa show how substrate is translocated stepwise towards the degradation chamber of the proteasome core particle. We also demonstrate, in vitro and in vivo, the importance of a structural feature in Mpa that allows formation of alternating charge-complementary interactions with the proteasome resulting in radial, rail-guided movements during the ATPase conformational cycle. Pup is the bacterial analog of ubiquitin for targeting proteins to the proteasome. Here, the authors use cryoEM to visualize structures of the Mycobacterium tuberculosis proteasome translocating a Pup-tagged substrate.
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Affiliation(s)
- Mikhail Kavalchuk
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland
| | - Ahmad Jomaa
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland.
| | - Andreas U Müller
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, CH-8093, Zurich, Switzerland.
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4
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Abstract
Proteasomes are compartmentalized, ATP-dependent, N-terminal nucleophile hydrolases that play essentials roles in intracellular protein turnover. They are present in all 3 kingdoms. Pharmacological inhibition of proteasomes is detrimental to cell viability. Proteasome inhibitor rugs revolutionize the treatment of multiple myeloma. Proteasomes in pathogenic microbes such as Mycobacterium tuberculosis (Mtb), Plasmodium falciparum (Pf), and other parasites and worms have been validated as therapeutic targets. Starting with Mtb proteasome, efforts in developing inhibitors selective for microbial proteasomes have made great progress lately. In this review, we describe the strategies and pharmacophores that have been used in developing proteasome inhibitors with potency and selectivity that spare human proteasomes and highlight the development of clinical proteasome inhibitor candidates for treatment of leishmaniasis and Chagas disease. Finally, we discuss the future challenges and therapeutical potentials of the microbial proteasome inhibitors.
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Affiliation(s)
- Hao Zhang
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, United States of America
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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5
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Zerbib E, Schlussel S, Hecht N, Bagdadi N, Eichler J, Gur E. The prokaryotic ubiquitin-like protein presents poor cleavage sites for proteasomal degradation. Cell Rep 2021; 36:109428. [PMID: 34320347 DOI: 10.1016/j.celrep.2021.109428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 05/09/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
In an event reminiscent of eukaryotic ubiquitination, the bacterial prokaryotic ubiquitin-like protein (Pup)-proteasome system (PPS) marks target proteins for proteasomal degradation by covalently attaching Pup, the bacterial tagging molecule. Yet, ubiquitin is released from its conjugated target following proteasome binding, whereas Pup enters the proteasome and remains conjugated to the target. Here, we report that although Pup can be degraded by the bacterial proteasome, it lacks favorable 20S core particle (CP) cleavage sites and is thus a very poor 20S CP substrate. Reconstituting the PPS in vitro, we demonstrate that during pupylated protein degradation, Pup can escape unharmed and remain conjugated to a target-derived degradation fragment. Removal of this degradation fragment by Dop, a depupylase, facilitates Pup recycling and re-conjugation to a new target. This study thus offers a mechanistic model for Pup recycling and demonstrates how a lack of protein susceptibility to proteasome-mediated cleavage can play a mechanistic role in a biological system.
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Affiliation(s)
- Erez Zerbib
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shai Schlussel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Noy Bagdadi
- 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; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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6
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Izert MA, Klimecka MM, Górna MW. Applications of Bacterial Degrons and Degraders - Toward Targeted Protein Degradation in Bacteria. Front Mol Biosci 2021; 8:669762. [PMID: 34026843 PMCID: PMC8138137 DOI: 10.3389/fmolb.2021.669762] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
A repertoire of proteolysis-targeting signals known as degrons is a necessary component of protein homeostasis in every living cell. In bacteria, degrons can be used in place of chemical genetics approaches to interrogate and control protein function. Here, we provide a comprehensive review of synthetic applications of degrons in targeted proteolysis in bacteria. We describe recent advances ranging from large screens employing tunable degradation systems and orthogonal degrons, to sophisticated tools and sensors for imaging. Based on the success of proteolysis-targeting chimeras as an emerging paradigm in cancer drug discovery, we discuss perspectives on using bacterial degraders for studying protein function and as novel antimicrobials.
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Affiliation(s)
| | | | - Maria Wiktoria Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
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7
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Yin Y, Kovach A, Hsu HC, Darwin KH, Li H. The mycobacterial proteasomal ATPase Mpa forms a gapped ring to engage the 20S proteasome. J Biol Chem 2021; 296:100713. [PMID: 33930464 PMCID: PMC8142254 DOI: 10.1016/j.jbc.2021.100713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/17/2021] [Accepted: 04/26/2021] [Indexed: 11/25/2022] Open
Abstract
Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. Previous structural analyses of the mycobacterial proteasome ATPase Mpa revealed a general structural conservation with the archaeal proteasome-activating nucleotidase and eukaryotic proteasomal Rpt1–6 ATPases, such as the N-terminal coiled-coil domain, oligosaccharide-/oligonucleotide-binding domain, and ATPase domain. However, Mpa has a unique β-grasp domain that in the ADP-bound crystal structure appears to interfere with the docking to the 20S proteasome core particle (CP). Thus, it is unclear how Mpa binds to proteasome CPs. In this report, we show by cryo-EM that the Mpa hexamer in the presence of a degradation substrate and ATP forms a gapped ring, with two of its six ATPase domains being highly flexible. We found that the linkers between the oligonucleotide-binding and ATPase domains undergo conformational changes that are important for function, revealing a previously unappreciated role of the linker region in ATP hydrolysis–driven protein unfolding. We propose that this gapped ring configuration is an intermediate state that helps rearrange its β-grasp domains and activating C termini to facilitate engagement with proteasome CPs. This work provides new insights into the crucial process of how an ATPase interacts with a bacterial proteasome protease.
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Affiliation(s)
- Yanting Yin
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Amanda Kovach
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Hao-Chi Hsu
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - K Heran Darwin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
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8
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Kahne SC, Darwin KH. Structural determinants of regulated proteolysis in pathogenic bacteria by ClpP and the proteasome. Curr Opin Struct Biol 2021; 67:120-126. [PMID: 33221704 PMCID: PMC8096641 DOI: 10.1016/j.sbi.2020.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 01/05/2023]
Abstract
Bacteria use gated proteolytic machines for routine protein quality control and regulated responses to environmental conditions. This review discusses recent advances in understanding the structure and regulation of ClpP proteases, nanomachines widely distributed across bacteria, and the bacterial proteasome, a protease found in relatively few species. For both machines, activators confer substrate specificity. We highlight new data from organisms encoding two ClpP isoforms and the central role of activators as platforms for integrating regulatory signals. Because proteolytic systems contribute to survival and virulence of many bacterial pathogens, understanding their forms and functions enables new approaches to design targeted therapeutics.
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Affiliation(s)
- Shoshanna C Kahne
- New York University Robert Grossman School of Medicine, Department of Microbiology, 430 E. 29th Street, Room 312, New York, NY 10016, USA
| | - K Heran Darwin
- New York University Robert Grossman School of Medicine, Department of Microbiology, 430 E. 29th Street, Room 312, New York, NY 10016, USA.
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9
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Majumder P, Baumeister W. Proteasomes: unfoldase-assisted protein degradation machines. Biol Chem 2020; 401:183-199. [PMID: 31665105 DOI: 10.1515/hsz-2019-0344] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/02/2019] [Indexed: 01/05/2023]
Abstract
Proteasomes are the principal molecular machines for the regulated degradation of intracellular proteins. These self-compartmentalized macromolecular assemblies selectively degrade misfolded, mistranslated, damaged or otherwise unwanted proteins, and play a pivotal role in the maintenance of cellular proteostasis, in stress response, and numerous other processes of vital importance. Whereas the molecular architecture of the proteasome core particle (CP) is universally conserved, the unfoldase modules vary in overall structure, subunit complexity, and regulatory principles. Proteasomal unfoldases are AAA+ ATPases (ATPases associated with a variety of cellular activities) that unfold protein substrates, and translocate them into the CP for degradation. In this review, we summarize the current state of knowledge about proteasome - unfoldase systems in bacteria, archaea, and eukaryotes, the three domains of life.
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Affiliation(s)
- Parijat Majumder
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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10
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Zhan W, Hsu HC, Morgan T, Ouellette T, Burns-Huang K, Hara R, Wright AG, Imaeda T, Okamoto R, Sato K, Michino M, Ramjee M, Aso K, Meinke PT, Foley M, Nathan CF, Li H, Lin G. Selective Phenylimidazole-Based Inhibitors of the Mycobacterium tuberculosis Proteasome. J Med Chem 2019; 62:9246-9253. [PMID: 31560200 DOI: 10.1021/acs.jmedchem.9b01187] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteasomes of pathogenic microbes have become attractive targets for anti-infectives. Coevolving with its human host, Mycobacterium tuberculosis (Mtb) has developed mechanisms to resist host-imposed nitrosative and oxidative stresses. Genetic deletion or pharmacological inhibition of the Mtb proteasome (Mtb20S) renders nonreplicating Mtb susceptible to reactive nitrogen species in vitro and unable to survive in the lungs of mice, validating the Mtb proteasome as a promising target for anti-Mtb agents. Using a structure-guided and flow chemistry-enabled study of structure-activity relationships, we developed phenylimidazole-based peptidomimetics that are highly potent for Mtb20S. X-ray structures of selected compounds with Mtb20S shed light on their selectivity for mycobacterial over human proteasomes.
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Affiliation(s)
- Wenhu Zhan
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Hao-Chi Hsu
- Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States
| | - Trevor Morgan
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Tierra Ouellette
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Kristin Burns-Huang
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Ryoma Hara
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Adrian G Wright
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Toshihiro Imaeda
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Rei Okamoto
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Kenjiro Sato
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Manoj Ramjee
- Cyclofluidic Limited , Biopark Broadwater Road , Welwyn Garden City AL7 3AX , U.K
| | - Kazuyoshi Aso
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Peter T Meinke
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Michael Foley
- Tri-Institutional Therapeutics Discovery Institute , 413 East 69th Street , New York , New York 10065 , United States
| | - Carl F Nathan
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
| | - Huilin Li
- Structural Biology Program , Van Andel Institute , 333 Bostwick Avenue Northeast , Grand Rapids , Michigan 49503 , United States
| | - Gang Lin
- Department of Microbiology & Immunology , Weill Cornell Medicine , 1300 York Avenue , New York , New York 10065 , United States
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11
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Pupylated proteins are subject to broad proteasomal degradation specificity and differential depupylation. PLoS One 2019; 14:e0215439. [PMID: 31009487 PMCID: PMC6476560 DOI: 10.1371/journal.pone.0215439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 04/02/2019] [Indexed: 11/19/2022] Open
Abstract
In actinobacteria, post-translational modification of proteins with prokaryotic ubiquitin-like protein Pup targets them for degradation by a bacterial proteasome assembly consisting of the 20S core particle (CP) and the mycobacterial proteasomal ATPase (Mpa). Modification of hundreds of cellular proteins with Pup at specific surface lysines is carried out by a single Pup-ligase (PafA, proteasome accessory factor A). Pupylated substrates are recruited to the degradative pathway by binding of Pup to the N-terminal coiled-coil domains of Mpa. Alternatively, pupylation can be reversed by the enzyme Dop (deamidase of Pup). Although pupylated substrates outcompete free Pup in proteasomal degradation, potential discrimination of the degradation complex between the various pupylated substrates has not been investigated. Here we show that Mpa binds stably to an open-gate variant of the proteasome (oCP) and associates with bona fide substrates with highly similar affinities. The proteasomal degradation of substrates differing in size, structure and assembly state was recorded in real-time, showing that the pupylated substrates are processed by the Mpa-oCP complex with comparable kinetic parameters. Furthermore, the members of a complex, pupylated proteome (pupylome) purified from Mycobacterium smegmatis are degraded evenly as followed by western blotting. In contrast, analysis of the depupylation behavior of several pupylome members suggests substrate-specific differences in enzymatic turnover, leading to the conclusion that largely indiscriminate degradation competes with differentiated depupylation to control the ultimate fate of pupylated substrates.
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12
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The Mycobacterium tuberculosis Pup-proteasome system regulates nitrate metabolism through an essential protein quality control pathway. Proc Natl Acad Sci U S A 2019; 116:3202-3210. [PMID: 30723150 DOI: 10.1073/pnas.1819468116] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis encodes a proteasome that carries out regulated degradation of bacterial proteins. It has been proposed that the proteasome contributes to nitrogen metabolism in M. tuberculosis, although this hypothesis had not been tested. Upon assessing M. tuberculosis growth in several nitrogen sources, we found that a mutant strain lacking the Mycobacterium proteasomal activator Mpa was unable to use nitrate as a sole nitrogen source due to a specific failure in the pathway of nitrate reduction to ammonium. We found that the robust activity of the nitrite reductase complex NirBD depended on expression of the groEL/groES chaperonin genes, which are regulated by the repressor HrcA. We identified HrcA as a likely proteasome substrate, and propose that the degradation of HrcA is required for the full expression of chaperonin genes. Furthermore, our data suggest that degradation of HrcA, along with numerous other proteasome substrates, is enhanced during growth in nitrate to facilitate the derepression of the chaperonin genes. Importantly, growth in nitrate is an example of a specific condition that reduces the steady-state levels of numerous proteasome substrates in M. tuberculosis.
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13
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Abstract
Proteasomes are a class of protease that carry out the degradation of a specific set of cellular proteins. While essential for eukaryotic life, proteasomes are found only in a small subset of bacterial species. In this chapter, we present the current knowledge of bacterial proteasomes, detailing the structural features and catalytic activities required to achieve proteasomal proteolysis. We describe the known mechanisms by which substrates are doomed for degradation, and highlight potential non-degradative roles for components of bacterial proteasome systems. Additionally, we highlight several pathways of microbial physiology that rely on proteasome activity. Lastly, we explain the various gaps in our understanding of bacterial proteasome function and emphasize several opportunities for further study.
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Affiliation(s)
- Samuel H Becker
- Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, Room 312, New York, NY, 10016, USA
| | - Huilin Li
- Van Andel Research Institute, Cryo-EM Structural Biology Laboratory, 333 Bostwick Ave, NE, Grand Rapids, MI, 4950, USA
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, Room 312, New York, NY, 10016, USA.
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14
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Lupoli TJ, Vaubourgeix J, Burns-Huang K, Gold B. Targeting the Proteostasis Network for Mycobacterial Drug Discovery. ACS Infect Dis 2018; 4:478-498. [PMID: 29465983 PMCID: PMC5902792 DOI: 10.1021/acsinfecdis.7b00231] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the world's deadliest infectious diseases and urgently requires new antibiotics to treat drug-resistant strains and to decrease the duration of therapy. During infection, Mtb encounters numerous stresses associated with host immunity, including hypoxia, reactive oxygen and nitrogen species, mild acidity, nutrient starvation, and metal sequestration and intoxication. The Mtb proteostasis network, composed of chaperones, proteases, and a eukaryotic-like proteasome, provides protection from stresses and chemistries of host immunity by maintaining the integrity of the mycobacterial proteome. In this Review, we explore the proteostasis network as a noncanonical target for antibacterial drug discovery.
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Affiliation(s)
- Tania J. Lupoli
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Kristin Burns-Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
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15
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Hu K, Jastrab JB, Zhang S, Kovach A, Zhao G, Darwin KH, Li H. Proteasome substrate capture and gate opening by the accessory factor PafE from Mycobacterium tuberculosis. J Biol Chem 2018; 293:4713-4723. [PMID: 29414791 DOI: 10.1074/jbc.ra117.001471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/31/2018] [Indexed: 11/06/2022] Open
Abstract
In all domains of life, proteasomes are gated, chambered proteases that require opening by activators to facilitate protein degradation. Twelve proteasome accessory factor E (PafE) monomers assemble into a single dodecameric ring that promotes proteolysis required for the full virulence of the human bacterial pathogen Mycobacterium tuberculosis Whereas the best characterized proteasome activators use ATP to deliver proteins into a proteasome, PafE does not require ATP. Here, to unravel the mechanism of PafE-mediated protein targeting and proteasome activation, we studied the interactions of PafE with native substrates, including a newly identified proteasome substrate, the ParA-like protein, Rv3213c, and with proteasome core particles. We characterized the function of a highly conserved feature in bacterial proteasome activator proteins: a glycine-glutamine-tyrosine-leucine (GQYL) motif at their C termini that is essential for stimulating proteolysis. Using cryo-electron microscopy (cryo-EM), we found that the GQYL motif of PafE interacts with specific residues in the α subunits of the proteasome core particle to trigger gate opening and degradation. Finally, we also found that PafE rings have 40-Å openings lined with hydrophobic residues that form a chamber for capturing substrates before they are degraded, suggesting PafE has a previously unrecognized chaperone activity. In summary, we have identified the interactions between PafE and the proteasome core particle that cause conformational changes leading to the opening of the proteasome gate and have uncovered a mechanism of PafE-mediated substrate degradation. Collectively, our results provide detailed insights into the mechanism of ATP-independent proteasome degradation in bacteria.
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Affiliation(s)
- Kuan Hu
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Jordan B Jastrab
- Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Susan Zhang
- Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Amanda Kovach
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Gongpu Zhao
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, New York, New York 10016.
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan 49503.
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Gur E, Korman M, Hecht N, Regev O, Schlussel S, Silberberg N, Elharar Y. How to control an intracellular proteolytic system: Coordinated regulatory switches in the mycobacterial Pup-proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2253-2260. [PMID: 28887055 DOI: 10.1016/j.bbamcr.2017.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/26/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
Intracellular proteolysis is critical for the proper functioning of all cells, owing to its involvement in a wide range of processes. Because of the destructive nature of protein degradation, intracellular proteolysis is restricted by control mechanisms at almost every step of the proteolytic process. Understanding the coordination of such mechanisms is a challenging task, especially in systems as complex as the eukaryotic ubiquitin-proteasome system (UPS). In comparison, the bacterial analog of the UPS, the Pup-proteasome system (PPS) is much simpler and, therefore, allows for insight into the control of a proteolytic system. This review integrates available information to present a coherent picture of what is known of PPS regulatory switches and describes how these switches act in concert to enforce regulation at the system level. Finally, open questions regarding PPS regulation are discussed, providing readers with a sense of what lies ahead in the field.
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Affiliation(s)
- Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Maayan Korman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ofir Regev
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shai Schlussel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nimrod Silberberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yifat Elharar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Alhuwaider AAH, Dougan DA. AAA+ Machines of Protein Destruction in Mycobacteria. Front Mol Biosci 2017; 4:49. [PMID: 28770209 PMCID: PMC5515868 DOI: 10.3389/fmolb.2017.00049] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 06/27/2017] [Indexed: 01/05/2023] Open
Abstract
The bacterial cytosol is a complex mixture of macromolecules (proteins, DNA, and RNA), which collectively are responsible for an enormous array of cellular tasks. Proteins are central to most, if not all, of these tasks and as such their maintenance (commonly referred to as protein homeostasis or proteostasis) is vital for cell survival during normal and stressful conditions. The two key aspects of protein homeostasis are, (i) the correct folding and assembly of proteins (coupled with their delivery to the correct cellular location) and (ii) the timely removal of unwanted or damaged proteins from the cell, which are performed by molecular chaperones and proteases, respectively. A major class of proteins that contribute to both of these tasks are the AAA+ (ATPases associated with a variety of cellular activities) protein superfamily. Although much is known about the structure of these machines and how they function in the model Gram-negative bacterium Escherichia coli, we are only just beginning to discover the molecular details of these machines and how they function in mycobacteria. Here we review the different AAA+ machines, that contribute to proteostasis in mycobacteria. Primarily we will focus on the recent advances in the structure and function of AAA+ proteases, the substrates they recognize and the cellular pathways they control. Finally, we will discuss the recent developments related to these machines as novel drug targets.
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Affiliation(s)
- Adnan Ali H Alhuwaider
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe UniversityMelbourne, VIC, Australia
| | - David A Dougan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe UniversityMelbourne, VIC, Australia
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