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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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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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3
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Xu W, Gao W, Bu Q, Li Y. Degradation Mechanism of AAA+ Proteases and Regulation of Streptomyces Metabolism. Biomolecules 2022; 12:biom12121848. [PMID: 36551276 PMCID: PMC9775585 DOI: 10.3390/biom12121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Hundreds of proteins work together in microorganisms to coordinate and control normal activity in cells. Their degradation is not only the last step in the cell's lifespan but also the starting point for its recycling. In recent years, protein degradation has been extensively studied in both eukaryotic and prokaryotic organisms. Understanding the degradation process is essential for revealing the complex regulatory network in microorganisms, as well as further artificial reconstructions and applications. This review will discuss several studies on protein quality-control family members Lon, FtsH, ClpP, the proteasome in Streptomyces, and a few classical model organisms, mainly focusing on their structure, recognition mechanisms, and metabolic influences.
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Affiliation(s)
- Weifeng Xu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Wenli Gao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qingting Bu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
- Correspondence:
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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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5
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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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6
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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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7
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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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8
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Zhang H, Hsu HC, Kahne SC, Hara R, Zhan W, Jiang X, Burns-Huang K, Ouellette T, Imaeda T, Okamoto R, Kawasaki M, Michino M, Wong TT, Toita A, Yukawa T, Moraca F, Vendome J, Saha P, Sato K, Aso K, Ginn J, Meinke PT, Foley M, Nathan CF, Darwin KH, Li H, Lin G. Macrocyclic Peptides that Selectively Inhibit the Mycobacterium tuberculosis Proteasome. J Med Chem 2021; 64:6262-6272. [PMID: 33949190 PMCID: PMC8194371 DOI: 10.1021/acs.jmedchem.1c00296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Treatment of tuberculosis (TB) currently takes at least 6 months. Latent Mycobacterium tuberculosis (Mtb) is phenotypically tolerant to most anti-TB drugs. A key hypothesis is that drugs that kill nonreplicating (NR) Mtb may shorten treatment when used in combination with conventional drugs. The Mtb proteasome (Mtb20S) could be such a target because its pharmacological inhibition kills NR Mtb and its genetic deletion renders Mtb unable to persist in mice. Here, we report a series of macrocyclic peptides that potently and selectively target the Mtb20S over human proteasomes, including macrocycle 6. The cocrystal structure of macrocycle 6 with Mtb20S revealed structural bases for the species selectivity. Inhibition of 20S within Mtb by 6 dose dependently led to the accumulation of Pup-tagged GFP that is degradable but resistant to depupylation and death of nonreplicating Mtb under nitrosative stress. These results suggest that compounds of this class have the potential to develop as anti-TB therapeutics.
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Affiliation(s)
- Hao Zhang
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065
| | - Hao-Chi Hsu
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI 49503
| | - Shoshanna C. Kahne
- Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016
| | - Ryoma Hara
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Wenhu Zhan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065
| | - Xiuju Jiang
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065
| | - Kristin Burns-Huang
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065
| | - Tierra Ouellette
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065
| | - Toshihiro Imaeda
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Rei Okamoto
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Masanori Kawasaki
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Tzu-Tshin Wong
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Akinori Toita
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Takafumi Yukawa
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | | | | | - Priya Saha
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065
| | - Kenjiro Sato
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Kazuyoshi Aso
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - John Ginn
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Peter T. Meinke
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Michael Foley
- Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th St, New York, NY 10065
| | - Carl F Nathan
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065
| | - K. Heran Darwin
- Department of Microbiology, New York University School of Medicine, 430 E. 29th Street, New York, NY 10016
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, 333 Bostwick Ave. NE, Grand Rapids, MI 49503
| | - Gang Lin
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Ave., New York, NY 10065
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9
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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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10
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Molecular and cellular dynamics of the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140583. [PMID: 33321258 DOI: 10.1016/j.bbapap.2020.140583] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/16/2023]
Abstract
In eukaryotic cells, the ubiquitin-proteasome system serves to remove proteins that are either dysfunctional or no longer needed. The 26S proteasome is a 2.5 MDa multisubunit complex comprising the 20S core particle, where degradation is executed, and one or two regulatory particles which prepare substrates for degradation. Whereas the 20S core particles of several species had been studied extensively by X-ray crystallography, the 26S holocomplex structure had remained elusive for a long time. Recent advances in single-particle cryo-electron microscopy have changed the situation and provided atomic resolution models of this intriguing molecular machine and its dynamics. Besides, cryo-electron tomography enables structural studies in situ, providing molecular resolution images of macromolecules inside pristinely preserved cellular environments. This has greatly contributed to our understanding of proteasome dynamics in the context of cells.
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11
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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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12
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Abstract
Over the past decade the number and variety of protein post-translational modifications that have been detected and characterized in bacteria have rapidly increased. Most post-translational protein modifications occur in a relatively low number of bacterial proteins in comparison with eukaryotic proteins, and most of the modified proteins carry low, substoichiometric levels of modification; therefore, their structural and functional analysis is particularly challenging. The number of modifying enzymes differs greatly among bacterial species, and the extent of the modified proteome strongly depends on environmental conditions. Nevertheless, evidence is rapidly accumulating that protein post-translational modifications have vital roles in various cellular processes such as protein synthesis and turnover, nitrogen metabolism, the cell cycle, dormancy, sporulation, spore germination, persistence and virulence. Further research of protein post-translational modifications will fill current gaps in the understanding of bacterial physiology and open new avenues for treatment of infectious diseases.
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13
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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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14
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Müller AU, Weber-Ban E. The Bacterial Proteasome at the Core of Diverse Degradation Pathways. Front Mol Biosci 2019; 6:23. [PMID: 31024929 PMCID: PMC6466877 DOI: 10.3389/fmolb.2019.00023] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/18/2019] [Indexed: 12/02/2022] Open
Abstract
Proteasomal protein degradation exists in mycobacteria and other actinobacteria, and expands their repertoire of compartmentalizing protein degradation pathways beyond the usual bacterial types. A product of horizontal gene transfer, bacterial proteasomes have evolved to support the organism's survival under challenging environmental conditions like nutrient starvation and physical or chemical stresses. Like the eukaryotic 20S proteasome, the bacterial core particle is gated and must associate with a regulator complex to form a fully active protease capable of recruiting and internalizing substrate proteins. By association with diverse regulator complexes that employ different recruitment strategies, the bacterial 20S core particle is able to act in different cellular degradation pathways. In association with the mycobacterial proteasomal ATPase Mpa, the proteasome degrades substrates post-translationally modified with prokaryotic, ubiquitin-like protein Pup in a process called pupylation. Upon interaction with the ATP-independent bacterial proteasome activator Bpa, poorly structured substrates are recruited for proteasomal degradation. A potential third degradation route might employ a Cdc48-like protein of actinobacteria (Cpa), for which interaction with the 20S core was recently demonstrated but no degradation substrates have been identified yet. The alternative interaction partners and wide range of substrate proteins suggest that the bacterial proteasome is a modular, functionally flexible and conditionally regulated degradation machine in bacteria that encounter rapidly changing and challenging conditions.
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Affiliation(s)
- Andreas U Müller
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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15
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Sciolino N, Burz DS, Shekhtman A. In-Cell NMR Spectroscopy of Intrinsically Disordered Proteins. Proteomics 2019; 19:e1800055. [PMID: 30489014 DOI: 10.1002/pmic.201800055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/29/2018] [Indexed: 01/14/2023]
Abstract
This review summarizes the results of in-cell Nuclear Magnetic Resonance, NMR, spectroscopic investigations of the eukaryotic and prokaryotic intrinsically disordered proteins, IDPs: α-synuclein, prokaryotic ubiquitin-like protein, Pup, tubulin-related neuronal protein, Tau, phenylalanyl-glycyl-repeat-rich nucleoporins, FG Nups, and the negative regulator of flagellin synthesis, FlgM. The results show that the cellular behavior of IDPs may differ significantly from that observed in the test tube.
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Affiliation(s)
- Nicholas Sciolino
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
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16
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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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17
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Jiang HW, Czajkowsky DM, Wang T, Wang XD, Wang JB, Zhang HN, Liu CX, Wu FL, He X, Xu ZW, Chen H, Guo SJ, Li Y, Bi LJ, Deng JY, Xie J, Pei JF, Zhang XE, Tao SC. Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis. EBioMedicine 2018; 30:225-236. [PMID: 29622495 PMCID: PMC5952411 DOI: 10.1016/j.ebiom.2018.03.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 12/26/2022] Open
Abstract
Owing to the spread of multidrug resistance (MDR) and extensive drug resistance (XDR), there is a pressing need to identify potential targets for the development of more-effective anti-M. tuberculosis (Mtb) drugs. PafA, as the sole Prokaryotic Ubiquitin-like Protein ligase in the Pup-proteasome System (PPS) of Mtb, is an attractive drug target. Here, we show that the activity of purified Mtb PafA is significantly inhibited upon the association of AEBSF (4-(2-aminoethyl) benzenesulfonyl fluoride) to PafA residue Serine 119 (S119). Mutation of S119 to amino acids that resemble AEBSF has similar inhibitory effects on the activity of purified Mtb PafA. Structural analysis reveals that although S119 is distant from the PafA catalytic site, it is located at a critical position in the groove where PafA binds the C-terminal region of Pup. Phenotypic studies demonstrate that S119 plays critical roles in the function of Mtb PafA when tested in M. smegmatis. Our study suggests that targeting S119 is a promising direction for developing an inhibitor of M. tuberculosis PafA. The pupylation activity of purified M. tuberculosis PafA is almost completely inhibited upon the association of AEBSF. The AEBSF binding site, Ser 119 plays critical roles in both the pupylation and depupylation activity of purified M. tuberculosis PafA. Disruption of purified M. tuberculosis PafA Ser 119 causes a dramatic reduction in Pup binding.
Drug-resistant tuberculosis is a major challenge worldwide, there is an urgent need to identify potential drug targets for developing more effective anti-tubercular drugs. M. tuberculosis ubiquitin-like protein ligase PafA is an attractive drug target, however, effective PafA inhibitors have not yet been identified. Here, we show that interruption of a single amino acid, S119, causes dramatic loss of PafA activity. S119 could thus serve as a promising precise target for developing M. tuberculosis PafA inhibitors.
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Affiliation(s)
- He-Wei Jiang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai 200240, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China; SZCDC-SUSTech Joint Key Laboratory for Tropical Diseases, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
| | - Xu-De Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jia-Bin Wang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Nan Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng-Xi Liu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan-Lin Wu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiang He
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhao-Wei Xu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Chen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shu-Juan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li-Jun Bi
- National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; TB Healthcare Biotechnology Co., Ltd., Foshan, Guangdong 528000, China; School of Stomatology and Medicine, Foshan University, Foshan 528000, Guangdong Province, China
| | - Jiao-Yu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jin Xie
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jian-Feng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China; School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China.
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18
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Krupovic M, Koonin EV. Cellular origin of the viral capsid-like bacterial microcompartments. Biol Direct 2017; 12:25. [PMID: 29132422 PMCID: PMC5683377 DOI: 10.1186/s13062-017-0197-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/06/2017] [Indexed: 11/10/2022] Open
Abstract
ᅟ: Bacterial microcompartments (BMC) are proteinaceous organelles that structurally resemble viral capsids, but encapsulate enzymes that perform various specialized biochemical reactions in the cell cytoplasm. The BMC are constructed from two major shell proteins, BMC-H and BMC-P, which form the facets and vertices of the icosahedral assembly, and are functionally equivalent to the major and minor capsid proteins of viruses, respectively. This equivalence notwithstanding, neither of the BMC proteins displays structural similarity to known capsid proteins, rendering the origins of the BMC enigmatic. Here, using structural and sequence comparisons, we show that both BMC-H and BMC-P, most likely, were exapted from bona fide cellular proteins, namely, PII signaling protein and OB-fold domain-containing protein, respectively. This finding is in line with the hypothesis that many major viral structural proteins have been recruited from cellular proteomes. REVIEWERS This article was reviewed by Igor Zhulin, Jeremy Selengut and Narayanaswamy Srinivasan. For complete reviews, see the Reviewers' reports section.
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Affiliation(s)
- Mart Krupovic
- Department of Microbiology, Institut Pasteur, 25 rue du Dr. Roux, 75015, Paris, France.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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19
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Jamaati H, Mortaz E, Pajouhi Z, Folkerts G, Movassaghi M, Moloudizargari M, Adcock IM, Garssen J. Nitric Oxide in the Pathogenesis and Treatment of Tuberculosis. Front Microbiol 2017; 8:2008. [PMID: 29085351 PMCID: PMC5649180 DOI: 10.3389/fmicb.2017.02008] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/29/2017] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is globally known as one of the most important human pathogens. Mtb is estimated to infect nearly one third of the world's population with many subjects having a latent infection. Thus, from an estimated 2 billion people infected with Mtb, less than 10% may develop symptomatic TB. This indicates that the host immune system may constrain pathogen replication in most infected individuals. On entering the lungs of the host, Mtb initially encounters resident alveolar macrophages which can engulf and subsequently eliminate intracellular microbes via a plethora of bactericidal mechanisms including the generation of free radicals such as reactive oxygen and nitrogen species. Nitric oxide (NO), a key anti-mycobacterial molecule, is detected in the exhaled breath of patients infected with Mtb. Recent knowledge regarding the regulatory role of NO in airway function and Mtb proliferation paves the way of exploiting the beneficial effects of this molecule for the treatment of airway diseases. Here, we discuss the importance of NO in the pathogenesis of TB, the diagnostic use of exhaled and urinary NO in Mtb infection and the potential of NO-based treatments.
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Affiliation(s)
- Hamidreza Jamaati
- Chronic Respiratory Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Esmaeil Mortaz
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Zeinab Pajouhi
- Chronic Respiratory Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Gert Folkerts
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Mehrnaz Movassaghi
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Milad Moloudizargari
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ian M Adcock
- Cell and Molecular Biology Group, Airways Disease Section, Faculty of Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Priority Research Centre for Asthma and Respiratory Disease, Hunter Medical Research Institute, University of Newcastle, Newcastle, NSW, Australia
| | - Johan Garssen
- Division of Pharmacology, Faculty of Science, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands.,Nutricia Research Centre for Specialized Nutrition, Utrecht, Netherlands
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20
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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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21
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Wu Y, Hu K, Li D, Bai L, Yang S, Jastrab JB, Xiao S, Hu Y, Zhang S, Darwin KH, Wang T, Li H. Mycobacterium tuberculosis proteasomal ATPase Mpa has a β-grasp domain that hinders docking with the proteasome core protease. Mol Microbiol 2017; 105:227-241. [PMID: 28419599 DOI: 10.1111/mmi.13695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2017] [Indexed: 12/21/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has a proteasome system that is essential for its ability to cause lethal infections in mice. A key component of the system is the proteasomal adenosine triphosphatase (ATPase) Mpa, which captures, unfolds, and translocates protein substrates into the Mtb proteasome core particle for degradation. Here, we report the crystal structures of near full-length hexameric Mtb Mpa in apo and ADP-bound forms. Surprisingly, the structures revealed a ubiquitin-like β-grasp domain that precedes the proteasome-activating carboxyl terminus. This domain, which was only found in bacterial proteasomal ATPases, buries the carboxyl terminus of each protomer in the central channel of the hexamer and hinders the interaction of Mpa with the proteasome core protease. Thus, our work reveals the structure of a bacterial proteasomal ATPase in the hexameric form, and the structure finally explains why Mpa is unable to stimulate robust protein degradation in vitro in the absence of other, yet-to-be-identified co-factors.
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Affiliation(s)
- Yujie Wu
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Kuan Hu
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Defeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Lin Bai
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Shaoqing Yang
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Jordan B Jastrab
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - Shuhao Xiao
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Yonglin Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Susan Zhang
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China.,SZCDC-SUSTech Joint Key Laboratory for Tropical Diseases, Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
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22
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Delley CL, Müller AU, Ziemski M, Weber-Ban E. Prokaryotic Ubiquitin-Like Protein and Its Ligase/Deligase Enyzmes. J Mol Biol 2017; 429:3486-3499. [PMID: 28478282 DOI: 10.1016/j.jmb.2017.04.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/11/2017] [Accepted: 04/28/2017] [Indexed: 11/30/2022]
Abstract
Prokaryotic ubiquitin-like protein (Pup) and the modification enzymes involved in attaching Pup to or removing it from target proteins present a fascinating example of convergent evolution with respect to eukaryotic ubiquitination. Like ubiquitin (Ub), Pup is a small protein that can be covalently attached to lysine side chains of cellular proteins, and like Ub, it can serve to recruit tagged proteins for proteasomal degradation. However, unlike Ub, Pup is conformationally highly dynamic, exhibits a different linkage connectivity to its target lysines, and its ligase belongs to a different class of enzymes than the E1/E2/E3 cascade of ubiquitination. A specific feature of actinobacteria (aside from sporadic cases in a few other lineages), pupylation appears to have evolved to provide an advantage to the bacteria under certain environmental stresses rather than act as a constitutive modification. For Mycobacterium tuberculosis, pupylation and the recruitment of pupylated substrates to the proteasome support persistence inside host macrophages during pathogenesis, rendering the Pup-proteasome system an attractive drug target. In this review, we consider the dynamic nature of Pup in relation to its function, discuss the reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, and put them in context of the evolutionary history of this post-translational modification.
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Affiliation(s)
- Cyrille L Delley
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Andreas U Müller
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Michal Ziemski
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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23
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Structural Analysis of Mycobacterium tuberculosis Homologues of the Eukaryotic Proteasome Assembly Chaperone 2 (PAC2). J Bacteriol 2017; 199:JB.00846-16. [PMID: 28193903 DOI: 10.1128/jb.00846-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022] Open
Abstract
A previous bioinformatics analysis identified the Mycobacterium tuberculosis proteins Rv2125 and Rv2714 as orthologs of the eukaryotic proteasome assembly chaperone 2 (PAC2). We set out to investigate whether Rv2125 or Rv2714 can function in proteasome assembly. We solved the crystal structure of Rv2125 at a resolution of 3.0 Å, which showed an overall fold similar to that of the PAC2 family proteins that include the archaeal PbaB and the yeast Pba1. However, Rv2125 and Rv2714 formed trimers, whereas PbaB forms tetramers and Pba1 dimerizes with Pba2. We also found that purified Rv2125 and Rv2714 could not bind to M. tuberculosis 20S core particles. Finally, proteomic analysis showed that the levels of known proteasome components and substrate proteins were not affected by disruption of Rv2125 in M. tuberculosis Our work suggests that Rv2125 does not participate in bacterial proteasome assembly or function.IMPORTANCE Although many bacteria do not encode proteasomes, M. tuberculosis not only uses proteasomes but also has evolved a posttranslational modification system called pupylation to deliver proteins to the proteasome. Proteasomes are essential for M. tuberculosis to cause lethal infections in animals; thus, determining how proteasomes are assembled may help identify new ways to combat tuberculosis. We solved the structure of a predicted proteasome assembly factor, Rv2125, and isolated a genetic Rv2125 mutant of M. tuberculosis Our structural, biochemical, and genetic studies indicate that Rv2125 and Rv2714 do not function as proteasome assembly chaperones and are unlikely to have roles in proteasome biology in mycobacteria.
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24
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Bacterial Proteasomes: Mechanistic and Functional Insights. Microbiol Mol Biol Rev 2016; 81:81/1/e00036-16. [PMID: 27974513 DOI: 10.1128/mmbr.00036-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Regulated proteolysis is essential for the normal physiology of all organisms. While all eukaryotes and archaea use proteasomes for protein degradation, only certain orders of bacteria have proteasomes, whose functions are likely as diverse as the species that use them. In this review, we discuss the most recent developments in the understanding of how proteins are targeted to proteasomes for degradation, including ATP-dependent and -independent mechanisms, and the roles of proteasome-dependent degradation in protein quality control and the regulation of cellular physiology. Furthermore, we explore newly established functions of proteasome system accessory factors that function independently of proteolysis.
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25
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Bolten M, Delley CL, Leibundgut M, Boehringer D, Ban N, Weber-Ban E. Structural Analysis of the Bacterial Proteasome Activator Bpa in Complex with the 20S Proteasome. Structure 2016; 24:2138-2151. [PMID: 27839949 DOI: 10.1016/j.str.2016.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/04/2016] [Accepted: 10/12/2016] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial proteasome activator) was shown to support an alternate proteasomal degradation pathway. Here, we present the cryo-electron microscopy (cryo-EM) structure of Bpa in complex with the 20S core particle (CP). For docking into the cryo-EM density, we solved the X-ray structure of Bpa, showing that it forms tight four-helix bundles arranged into a 12-membered ring with a 40 Å wide central pore and the C-terminal helix of each protomer protruding from the ring. The Bpa model was fitted into the cryo-EM map of the Bpa-CP complex, revealing its architecture and striking symmetry mismatch. The Bpa-CP interface was resolved to 3.5 Å, showing the interactions between the C-terminal GQYL motif of Bpa and the proteasome α-rings. This docking mode is related to the one observed for eukaryotic activators with features specific to the bacterial complex.
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Affiliation(s)
- Marcel Bolten
- ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Cyrille L Delley
- ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Marc Leibundgut
- ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Daniel Boehringer
- ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Nenad Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, 8093 Zurich, Switzerland.
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26
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Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study. Proc Natl Acad Sci U S A 2016; 113:E4190-9. [PMID: 27402735 DOI: 10.1073/pnas.1603980113] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded.
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27
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Abstract
Interest in bacterial proteasomes was sparked by the discovery that proteasomal degradation is required for the pathogenesis of Mycobacterium tuberculosis, one of the world's deadliest pathogens. Although bacterial proteasomes are structurally similar to their eukaryotic and archaeal homologs, there are key differences in their mechanisms of assembly, activation, and substrate targeting for degradation. In this article, we compare and contrast bacterial proteasomes with their archaeal and eukaryotic counterparts, and we discuss recent advances in our understanding of how bacterial proteasomes function to influence microbial physiology.
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Affiliation(s)
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, New York, NY 10016;
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28
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Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2016; 113:E1983-92. [PMID: 27001842 DOI: 10.1073/pnas.1512094113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis (Mtb) requires a proteasome system to cause lethal infections in mice. We recently found that proteasome accessory factor E (PafE, Rv3780) activates proteolysis by the Mtb proteasome independently of adenosine triphosphate (ATP). Moreover, PafE contributes to the heat-shock response and virulence of Mtb Here, we show that PafE subunits formed four-helix bundles similar to those of the eukaryotic ATP-independent proteasome activator subunits of PA26 and PA28. However, unlike any other known proteasome activator, PafE formed dodecamers with 12-fold symmetry, which required a glycine-XXX-glycine-XXX-glycine motif that is not found in previously described activators. Intriguingly, the truncation of the PafE carboxyl-terminus resulted in the robust binding of PafE rings to native proteasome core particles and substantially increased proteasomal activity, suggesting that the extended carboxyl-terminus of this cofactor confers suboptimal binding to the proteasome core particle. Collectively, our data show that proteasomal activation is not limited to hexameric ATPases in bacteria.
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29
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Abstract
Proteasomes are ATP-dependent, barrel-shaped proteases found in all three domains of life. In eukaryotes, proteins are typically targeted for degradation by posttranslational modification with the small protein ubiquitin. In 2008, the first bacterial protein modifier, Pup (prokaryotic ubiquitin-like protein), was identified in Mycobacterium tuberculosis. Functionally analogous to ubiquitin, conjugation with Pup serves as a signal for degradation by the mycobacterial proteasome. Proteolysis-dependent and -independent functions of the M. tuberculosis proteasome are essential for virulence of this successful pathogen. In this article we describe the discovery of the proteasome as a key player in tuberculosis pathogenesis and the biology and biochemistry of the Pup-proteasome system.
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30
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Jastrab JB, Wang T, Murphy JP, Bai L, Hu K, Merkx R, Huang J, Chatterjee C, Ovaa H, Gygi SP, Li H, Darwin KH. An adenosine triphosphate-independent proteasome activator contributes to the virulence of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2015; 112:E1763-72. [PMID: 25831519 PMCID: PMC4394314 DOI: 10.1073/pnas.1423319112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis encodes a proteasome that is highly similar to eukaryotic proteasomes and is required to cause lethal infections in animals. The only pathway known to target proteins for proteasomal degradation in bacteria is pupylation, which is functionally analogous to eukaryotic ubiquitylation. However, evidence suggests that the M. tuberculosis proteasome contributes to pupylation-independent pathways as well. To identify new proteasome cofactors that might contribute to such pathways, we isolated proteins that bound to proteasomes overproduced in M. tuberculosis and found a previously uncharacterized protein, Rv3780, which formed rings and capped M. tuberculosis proteasome core particles. Rv3780 enhanced peptide and protein degradation by proteasomes in an adenosine triphosphate (ATP)-independent manner. We identified putative Rv3780-dependent proteasome substrates and found that Rv3780 promoted robust degradation of the heat shock protein repressor, HspR. Importantly, an M. tuberculosis Rv3780 mutant had a general growth defect, was sensitive to heat stress, and was attenuated for growth in mice. Collectively, these data demonstrate that ATP-independent proteasome activators are not confined to eukaryotes and can contribute to the virulence of one the world's most devastating pathogens.
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Affiliation(s)
- Jordan B Jastrab
- Department of Microbiology, New York University School of Medicine, New York, NY 10016
| | - Tong Wang
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973
| | - J Patrick Murphy
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Lin Bai
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973
| | - Kuan Hu
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - Remco Merkx
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and
| | - Jessica Huang
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | | | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; and
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Huilin Li
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973; Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, New York, NY 10016;
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31
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Bacterial proteasome activator bpa (rv3780) is a novel ring-shaped interactor of the mycobacterial proteasome. PLoS One 2014; 9:e114348. [PMID: 25469515 PMCID: PMC4254994 DOI: 10.1371/journal.pone.0114348] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/06/2014] [Indexed: 12/14/2022] Open
Abstract
The occurrence of the proteasome in bacteria is limited to the phylum of actinobacteria, where it is maintained in parallel to the usual bacterial compartmentalizing proteases. The role it plays in these organisms is still not fully understood, but in the human pathogen Mycobacterium tuberculosis (Mtb) the proteasome supports persistence in the host. In complex with the ring-shaped ATPase Mpa (called ARC in other actinobacteria), the proteasome can degrade proteins that have been post-translationally modified with the prokaryotic ubiquitin-like protein Pup. Unlike for the eukaryotic proteasome core particle, no other bacterial proteasome interactors have been identified to date. Here we describe and characterize a novel bacterial proteasome activator of Mycobacterium tuberculosis we termed Bpa (Rv3780), using a combination of biochemical and biophysical methods. Bpa features a canonical C-terminal proteasome interaction motif referred to as the HbYX motif, and its orthologs are only found in those actinobacteria encoding the proteasomal subunits. Bpa can inhibit degradation of Pup-tagged substrates in vitro by competing with Mpa for association with the proteasome. Using negative-stain electron microscopy, we show that Bpa forms a ring-shaped homooligomer that can bind coaxially to the face of the proteasome cylinder. Interestingly, Bpa can stimulate the proteasomal degradation of the model substrate β-casein, which suggests it could play a role in the removal of non-native or damaged proteins.
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32
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Forer N, Korman M, Elharar Y, Vishkautzan M, Gur E. Bacterial proteasome and PafA, the pup ligase, interact to form a modular protein tagging and degradation machine. Biochemistry 2013; 52:9029-35. [PMID: 24228735 DOI: 10.1021/bi401017b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteasome-containing bacteria possess a tagging system that directs proteins to proteasomal degradation by conjugating them to a prokaryotic ubiquitin-like protein (Pup). A single ligating enzyme, PafA, is responsible for Pup conjugation to lysine side chains of protein substrates. As Pup is recognized by the regulatory subunit of the proteasome, Pup functions as a degradation tag. Pup presents overlapping regions for binding of the proteasome and PafA. It was, therefore, unclear whether Pup binding by the proteasome regulatory subunit, Mpa, and by PafA are mutually exclusive events. The work presented here provides evidence for the simultaneous interaction of Pup with both Mpa and PafA. Surprisingly, we found that PafA and Mpa can form a complex both in vitro and in vivo. Our results thus suggest that PafA and the proteasome can function as a modular machine for the tagging and degradation of cytoplasmic proteins.
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Affiliation(s)
- Nadav Forer
- Department of Life Sciences and ‡The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
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33
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Roberts DM, Personne Y, Ollinger J, Parish T. Proteases in Mycobacterium tuberculosis pathogenesis: potential as drug targets. Future Microbiol 2013; 8:621-31. [PMID: 23642117 DOI: 10.2217/fmb.13.25] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
TB is still a major global health problem causing over 1 million deaths per year. An increasing problem of drug resistance in the causative agent, Mycobacterium tuberculosis, as well as problems with the current lengthy and complex treatment regimens, lends urgency to the need to develop new antitubercular agents. Proteases have been targeted for therapy in other infections, most notably these have been successful as antiviral agents in the treatment of HIV infection. M. tuberculosis has a number of proteases with good potential as novel drug targets and developing drugs against these should result in agents that are effective against drug-resistant and drug-sensitive strains. In this review, the authors summarize the current status of proteases with potential as drug targets in this pathogen, particularly focusing on proteases involved in protein secretion (signal peptidases LepB and LspA), protein degradation and turnover (ClpP and the proteasome) and virulence (mycosins and HtrA).
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Affiliation(s)
- David M Roberts
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
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34
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Maldonado AY, Burz DS, Reverdatto S, Shekhtman A. Fate of pup inside the Mycobacterium proteasome studied by in-cell NMR. PLoS One 2013; 8:e74576. [PMID: 24040288 PMCID: PMC3769308 DOI: 10.1371/journal.pone.0074576] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 08/06/2013] [Indexed: 12/18/2022] Open
Abstract
The Mycobacterium tuberculosis proteasome is required for maximum virulence and to resist killing by the host immune system. The prokaryotic ubiquitin-like protein, Pup-GGE, targets proteins for proteasome-mediated degradation. We demonstrate that Pup-GGQ, a precursor of Pup-GGE, is not a substrate for proteasomal degradation. Using STINT-NMR, an in-cell NMR technique, we studied the interactions between Pup-GGQ, mycobacterial proteasomal ATPase, Mpa, and Mtb proteasome core particle (CP) inside a living cell at amino acid residue resolution. We showed that under in-cell conditions, in the absence of the proteasome CP, Pup-GGQ interacts with Mpa only weakly, primarily through its C-terminal region. When Mpa and non-stoichiometric amounts of proteasome CP are present, both the N-terminal and C-terminal regions of Pup-GGQ bind strongly to Mpa. This suggests a mechanism by which transient binding of Mpa to the proteasome CP controls the fate of Pup.
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Affiliation(s)
- Andres Y. Maldonado
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - David S. Burz
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany, Albany, New York, United States of America
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35
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Humbard MA, Maupin-Furlow JA. Prokaryotic proteasomes: nanocompartments of degradation. J Mol Microbiol Biotechnol 2013; 23:321-34. [PMID: 23920495 DOI: 10.1159/000351348] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Proteasomes are self-compartmentalized energy-dependent proteolytic machines found in Archaea, Actinobacteria species of bacteria and eukaryotes. Proteasomes consist of two separate protein complexes, the core particle that hydrolyzes peptide bonds and an AAA+ ATPase domain responsible for the binding, unfolding and translocation of protein substrates into the core particle for degradation. Similarly to eukaryotes, proteasomes play a central role in protein degradation and can be essential in Archaea. Core particles associate with and utilize a variety of ATPase complexes to carry out protein degradation in Archaea. In actinobacterial species, such as Mycobacterium tuberculosis, proteasome-mediated degradation is associated with pathogenesis and does not appear to be essential. Interestingly, both actinobacterial species and Archaea use small proteins to covalently modify proteins, prokaryotic ubiquitin-like proteins (Pup) in Actinobacteria and ubiquitin-like small archaeal modifier proteins (SAMP) in Archaea. These modifications may play a role in proteasome targeting similar to the ubiquitin-proteasome system in eukaryotes.
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Affiliation(s)
- Matthew A Humbard
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Md., USA
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36
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Striebel F, Imkamp F, Özcelik D, Weber-Ban E. Pupylation as a signal for proteasomal degradation in bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:103-13. [PMID: 23557784 DOI: 10.1016/j.bbamcr.2013.03.022] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/21/2013] [Accepted: 03/12/2013] [Indexed: 12/23/2022]
Abstract
Posttranslational modifications in the form of covalently attached proteins like ubiquitin (Ub), were long considered an exclusive feature of eukaryotic organisms. The discovery of pupylation, the modification of lysine residues with a prokaryotic, ubiquitin-like protein (Pup), demonstrated that certain bacteria use a tagging pathway functionally related to ubiquitination in order to target proteins for proteasomal degradation. However, functional analogies do not translate into structural or mechanistic relatedness. Bacterial Pup, unlike eukaryotic Ub, does not adopt a β-grasp fold, but is intrinsically disordered. Furthermore, isopeptide bond formation in the pupylation process is carried out by enzymes evolutionary descendent from glutamine synthetases. While in eukaryotes, the proteasome is the main energy-dependent protein degradation machine, bacterial proteasomes exist in addition to other architecturally related degradation complexes, and their specific role along with the role of pupylation is still poorly understood. In Mycobacterium tuberculosis (Mtb), the Pup-proteasome system contributes to pathogenicity by supporting the bacterium's persistence within host macrophages. Here, we describe the mechanism and structural framework of pupylation and the targeting of pupylated proteins to the proteasome complex. Particular attention is given to the comparison of the bacterial Pup-proteasome system and the eukaryotic ubiquitin-proteasome system. Furthermore, the involvement of pupylation and proteasomal degradation in Mtb pathogenesis is discussed together with efforts to establish the Pup-proteasome system as a drug target. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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Affiliation(s)
- Frank Striebel
- Max Planck Institute of Biochemistry, Department of Molecular Cell Biology, D-82152 Martinsried, Germany
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37
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Abstract
The proteasome refers to a collection of complexes centered on the 20S proteasome core particle (20S CP), a complex of 28 subunits that houses proteolytic sites in its hollow interior. Proteasomes are found in eukaryotes, archaea, and some eubacteria, and their activity is critical for many cellular pathways. Important recent advances include inhibitor binding studies and the structure of the immunoproteasome, whose specificity is altered by the incorporation of inducible catalytic subunits. The inherent repression of the 20S CP is relieved by the ATP-independent activators 11S and Blm10/PA200, whose structures reveal principles of proteasome mechanism. The structure of the ATP-dependent 19S regulatory particle, which mediates degradation of polyubiquitylated proteins, is being revealed by a combination of crystal or NMR structures of individual subunits and electron microscopy reconstruction of the intact complex. Other recent structural advances inform us about mechanisms of assembly and the role of conformational changes in the functional cycle.
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Affiliation(s)
- Erik Kish-Trier
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112-5650, USA
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38
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Bipartite determinants mediate an evolutionarily conserved interaction between Cdc48 and the 20S peptidase. Proc Natl Acad Sci U S A 2013; 110:3327-32. [PMID: 23401548 DOI: 10.1073/pnas.1300408110] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Proteasomes are essential and ubiquitous ATP-dependent proteases that function in eukarya, archaea, and some bacteria. These destructive but critically important proteolytic machines use a 20S core peptidase and a hexameric ATPase associated with a variety of cellular activities (AAA+) unfolding ring that unfolds and spools substrates into the peptidase chamber. In archaea, 20S can function with the AAA+ Cdc48 or proteasome-activating nucleotidase (PAN) unfoldases. Both interactions are stabilized by C-terminal tripeptides in AAA+ subunits that dock into pockets on the 20S periphery. Here, we provide evidence that archaeal Cdc48 also uses a distinct set of near-axial interactions to bind 20S and propose that similar dual determinants mediate PAN-20S interactions and Rpt(1-6)-20S interactions in the 26S proteasome. Current dogma holds that the Rpt(1-6) unfolding ring of the 19S regulatory particle is the only AAA+ partner of eukaryotic 20S. By contrast, we show that mammalian Cdc48, a key player in cell-cycle regulation, membrane fusion, and endoplasmic-reticulum-associated degradation, activates mammalian 20S and find that a mouse Cdc48 variant supports protein degradation in combination with 20S. Our results suggest that eukaryotic Cdc48 orthologs function directly with 20S to maintain intracellular protein quality control.
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39
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Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway. Nat Commun 2013; 3:1014. [PMID: 22910360 DOI: 10.1038/ncomms2009] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 07/19/2012] [Indexed: 12/30/2022] Open
Abstract
Pupylation is a posttranslational protein modification occurring in mycobacteria and other actinobacteria that is functionally analogous to ubiquitination. Here we report the crystal structures of the modification enzymes involved in this pathway, the prokaryotic ubiquitin-like protein (Pup) ligase PafA and the depupylase/deamidase Dop. Both feature a larger amino-terminal domain consisting of a central β-sheet packed against a cluster of helices, a fold characteristic for carboxylate-amine ligases, and a smaller C-terminal domain unique to PafA/Dop members. The active site is located on the concave surface of the β-sheet with the nucleotide bound in a deep pocket. A conserved groove leading into the active site could have a role in Pup-binding. Nuclear magnetic resonance and biochemical experiments determine the region of Pup that interacts with PafA and Dop. Structural data and mutational studies identify crucial residues for the catalysis of both enzymes.
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40
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Abstract
Proteasomes are ATP-dependent protein degradation machines present in all archaea and eukaryotes, and found in several bacterial species of the order Actinomycetales. Mycobacterium tuberculosis (Mtb), an Actinomycete pathogenic to humans, requires proteasome function to cause disease. In this chapter, we describe what is currently understood about the biochemistry of the Mtb proteasome and its role in virulence. The characterization of the Mtb proteasome has led to the discovery that proteins can be targeted for degradation by a small protein modifier in bacteria as they are in eukaryotes. Furthermore, the understanding of proteasome function in Mtb has helped reveal new insight into how the host battles infections.
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Affiliation(s)
- Marie I Samanovic
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, MSB 236, New York, NY, 10016, USA
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41
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Chim N, Owens CP, Contreras H, Goulding CW. Withdrawn. Infect Disord Drug Targets 2012:CDTID-EPUB-20121116-2. [PMID: 23167715 PMCID: PMC3695056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Withdrawn by the publisher.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Cedric P. Owens
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Heidi Contreras
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine CA 92697, USA
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42
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Burns KE, McAllister FE, Schwerdtfeger C, Mintseris J, Cerda-Maira F, Noens EE, Wilmanns M, Hubbard SR, Melandri F, Ovaa H, Gygi SP, Darwin KH. Mycobacterium tuberculosis prokaryotic ubiquitin-like protein-deconjugating enzyme is an unusual aspartate amidase. J Biol Chem 2012; 287:37522-9. [PMID: 22942282 DOI: 10.1074/jbc.m112.384784] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Deamidase of Pup (Dop), the prokaryotic ubiquitin-like protein (Pup)-deconjugating enzyme, is critical for the full virulence of Mycobacterium tuberculosis and is unique to bacteria, providing an ideal target for the development of selective chemotherapies. We used a combination of genetics and chemical biology to characterize the mechanism of depupylation. We identified an aspartate as a potential nucleophile in the active site of Dop, suggesting a novel protease activity to target for inhibitor development.
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Affiliation(s)
- Kristin E Burns
- Department of Microbiology, New York University, New York, New York 10016, USA
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43
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Gengenbacher M, Kaufmann SHE. Mycobacterium tuberculosis: success through dormancy. FEMS Microbiol Rev 2012; 36:514-32. [PMID: 22320122 PMCID: PMC3319523 DOI: 10.1111/j.1574-6976.2012.00331.x] [Citation(s) in RCA: 464] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 12/22/2011] [Accepted: 01/31/2012] [Indexed: 01/21/2023] Open
Abstract
Tuberculosis (TB) remains a major health threat, killing nearly 2 million individuals around this globe, annually. The only vaccine, developed almost a century ago, provides limited protection only during childhood. After decades without the introduction of new antibiotics, several candidates are currently undergoing clinical investigation. Curing TB requires prolonged combination of chemotherapy with several drugs. Moreover, monitoring the success of therapy is questionable owing to the lack of reliable biomarkers. To substantially improve the situation, a detailed understanding of the cross-talk between human host and the pathogen Mycobacterium tuberculosis (Mtb) is vital. Principally, the enormous success of Mtb is based on three capacities: first, reprogramming of macrophages after primary infection/phagocytosis to prevent its own destruction; second, initiating the formation of well-organized granulomas, comprising different immune cells to create a confined environment for the host-pathogen standoff; third, the capability to shut down its own central metabolism, terminate replication, and thereby transit into a stage of dormancy rendering itself extremely resistant to host defense and drug treatment. Here, we review the molecular mechanisms underlying these processes, draw conclusions in a working model of mycobacterial dormancy, and highlight gaps in our understanding to be addressed in future research.
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Affiliation(s)
- Martin Gengenbacher
- Max Planck Institute for Infection Biology, Department of Immunology Charitéplatz 1, 10117 Berlin, Germany
| | - Stefan H. E. Kaufmann
- Max Planck Institute for Infection Biology, Department of Immunology Charitéplatz 1, 10117 Berlin, Germany
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44
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Delley CL, Striebel F, Heydenreich FM, Özcelik D, Weber-Ban E. Activity of the mycobacterial proteasomal ATPase Mpa is reversibly regulated by pupylation. J Biol Chem 2011; 287:7907-14. [PMID: 22210775 DOI: 10.1074/jbc.m111.331124] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pupylation is a bacterial post-translational modification of target proteins on lysine residues with prokaryotic ubiquitin-like protein Pup. Pup-tagged substrates are recognized by a proteasome-interacting ATPase termed Mpa in Mycobacterium tuberculosis. Mpa unfolds pupylated substrates and threads them into the proteasome core particle for degradation. Interestingly, Mpa itself is also a pupylation target. Here, we show that the Pup ligase PafA predominantly produces monopupylated Mpa modified homogeneously on a single lysine residue within its C-terminal region. We demonstrate that this modification renders Mpa functionally inactive. Pupylated Mpa can no longer support Pup-mediated proteasomal degradation due to its inability to associate with the proteasome core. Mpa is further inactivated by rapid Pup- and ATPase-driven deoligomerization of the hexameric Mpa ring. We show that pupylation of Mpa is chemically and functionally reversible. Mpa regains its enzymatic activity upon depupylation by the depupylase Dop, affording a rapid and reversible activity control over Mpa function.
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Affiliation(s)
- Cyrille L Delley
- Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
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45
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Abstract
Like other energy-dependent proteases, proteasomes, which are found across the three domains of life, are self-compartmentalized and important in the early steps of proteolysis. Proteasomes degrade improperly synthesized, damaged or misfolded proteins and hydrolyse regulatory proteins that must be specifically removed or cleaved for cell signalling. In eukaryotes, proteins are typically targeted for proteasome-mediated destruction through polyubiquitylation, although ubiquitin-independent pathways also exist. Interestingly, actinobacteria and archaea also covalently attach small proteins (prokaryotic ubiquitin-like protein (Pup) and small archaeal modifier proteins (Samps), respectively) to certain proteins, and this may serve to target the modified proteins for degradation by proteasomes.
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Affiliation(s)
- Julie Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA.
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46
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Gur E, Biran D, Ron EZ. Regulated proteolysis in Gram-negative bacteria--how and when? Nat Rev Microbiol 2011; 9:839-48. [PMID: 22020261 DOI: 10.1038/nrmicro2669] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Most bacteria live in a dynamic environment where temperature, availability of nutrients and the presence of various chemicals vary, which requires rapid adaptation. Many of the adaptive changes are determined by changes in the transcription of global regulatory networks, but this response is slow because most bacterial proteins are stable and their concentration remains high even after transcription slows down. To respond rapidly, an additional level of regulation has evolved: the degradation of key proteins. However, as proteolysis is an irreversible process, it is subject to tight regulation of substrate binding and degradation. Here we review the roles of the proteolytic enzymes in Gram-negative bacteria and how these enzymes can be regulated to target only a subset of proteins.
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Affiliation(s)
- Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
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47
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Stadtmueller BM, Hill CP. Proteasome activators. Mol Cell 2011; 41:8-19. [PMID: 21211719 DOI: 10.1016/j.molcel.2010.12.020] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 01/25/2023]
Abstract
Proteasomes degrade a multitude of protein substrates in the cytosol and nucleus, and thereby are essential for many aspects of cellular function. Because the proteolytic sites are sequestered in a closed barrel-shaped structure, activators are required to facilitate substrate access. Structural and biochemical studies of two activator families, 11S and Blm10, have provided insights to proteasome activation mechanisms, although the biological functions of these factors remain obscure. Recent advances have improved our understanding of the third activator family, including the 19S activator, which targets polyubiquitylated proteins for degradation. Here we present a structural perspective on how proteasomes are activated and how substrates are delivered to the proteolytic sites.
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Affiliation(s)
- Beth M Stadtmueller
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA
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Bedford L, Lowe J, Dick LR, Mayer RJ, Brownell JE. Ubiquitin-like protein conjugation and the ubiquitin-proteasome system as drug targets. Nat Rev Drug Discov 2010; 10:29-46. [PMID: 21151032 PMCID: PMC7097807 DOI: 10.1038/nrd3321] [Citation(s) in RCA: 433] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ubiquitin is a highly conserved 76 amino-acid protein that covalently attaches to protein substrates targeted for degradation by the 26S proteasome. The coordinated effort of a series of enzymes, including an activating enzyme (E1), a conjugating enzyme (E2) and a ligase (E3), uses ATP to ultimately form an isopeptide bond between ubiquitin and a substrate. Another class of enzymes called deubiquitylating enzymes (DUBs) deconstruct these linkages and also have an essential role in ubiquitin function. In addition, ubiquitin-like proteins (UBLs), including NEDD8, SUMO and ISG15, share a characteristic three-dimensional fold with ubiquitin but have their own dedicated enzyme cascades and distinct (although sometimes overlapping) biological functions. The ubiquitin–proteasome system (UPS) and UBL conjugation pathways have important roles in various human diseases, including numerous types of cancer, cardiovascular disease, viral diseases and neurodegenerative disorders. The proteasome inhibitor bortezomib (Velcade; Millennium Pharmaceuticals) is the first clinically validated drug to target the UPS and is approved for the treatment of multiple myeloma. This suggests that other diseases may conceivably be targeted by modulating components of the UPS and UBL conjugation pathways using small-molecule inhibitors. A significant hurdle to identifying drug-like inhibitors of enzyme targets within the UPS and UBL conjugation pathways is the limited understanding of the molecular mechanisms and biological consequences of UBL conjugation. Here, we provide an overview of the enzyme classes in the UPS and UBL pathways that are potential therapeutic targets, and highlight considerations that are important for drug discovery. We also discuss the progress in the development of small-molecule inhibitors, and review developments in understanding of the role of the components of the UPS and the UBL pathways in disease and their potential for therapeutic intervention.
The ubiquitin–proteasome system (UPS) and ubiquitin-like protein (UBL) conjugation pathways are integral to cellular protein homeostasis, and their functional importance in various diseases, including cancer, cardiovascular disease and neurodegenerative disorders, is now beginning to emerge. Brownell and colleagues review developments in understanding of the role of the components of the UPS and the UBL pathways in disease and their potential for therapeutic intervention. The ubiquitin–proteasome system (UPS) and ubiquitin-like protein (UBL) conjugation pathways are integral to cellular protein homeostasis. The growing recognition of the fundamental importance of these pathways to normal cell function and in disease has prompted an in-depth search for small-molecule inhibitors that selectively block the function of these pathways. However, our limited understanding of the molecular mechanisms and biological consequences of UBL conjugation is a significant hurdle to identifying drug-like inhibitors of enzyme targets within these pathways. Here, we highlight recent advances in understanding the role of some of these enzymes and how these new insights may be the key to developing novel therapeutics for diseases including immuno-inflammatory disorders, cancer, infectious diseases, cardiovascular disease and neurodegenerative disorders.
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Affiliation(s)
- Lynn Bedford
- School of Biomedical Sciences, University of Nottingham, Nottingham, UK.
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Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation. Nat Struct Mol Biol 2010; 17:1352-7. [PMID: 20953180 PMCID: PMC2988878 DOI: 10.1038/nsmb.1918] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 08/27/2010] [Indexed: 01/17/2023]
Abstract
Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an α-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.
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Imkamp F, Striebel F, Sutter M, Ozcelik D, Zimmermann N, Sander P, Weber-Ban E. Dop functions as a depupylase in the prokaryotic ubiquitin-like modification pathway. EMBO Rep 2010; 11:791-7. [PMID: 20798673 DOI: 10.1038/embor.2010.119] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 07/25/2010] [Accepted: 07/26/2010] [Indexed: 12/21/2022] Open
Abstract
Post-translational modification of proteins with prokaryotic ubiquitin-like protein (Pup) is the bacterial equivalent of ubiquitination in eukaryotes. Mycobacterial pupylation is a two-step process in which the carboxy-terminal glutamine of Pup is first deamidated by Dop (deamidase of Pup) before ligation of the generated γ-carboxylate to substrate lysines by the Pup ligase PafA. In this study, we identify a new feature of the pupylation system by demonstrating that Dop also acts as a depupylase in the Pup proteasome system in vivo and in vitro. Dop removes Pup from substrates by specific cleavage of the isopeptide bond. Depupylation can be enhanced by the unfolding activity of the mycobacterial proteasomal ATPase Mpa.
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Affiliation(s)
- Frank Imkamp
- Department of Biology, Eidgenössische Technische Hochschule Zurich, Institute of Molecular Biology and Biophysics, Schafmattstrasse 20, Zurich CH-8093, Switzerland
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