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Hermanns T, Uthoff M, Baumann U, Hofmann K. The structural basis for deubiquitination by the fingerless USP-type effector TssM. Life Sci Alliance 2024; 7:e202302422. [PMID: 38170641 PMCID: PMC10719079 DOI: 10.26508/lsa.202302422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Intracellular bacteria are threatened by ubiquitin-mediated autophagy, whenever the bacterial surface or enclosing membrane structures become targets of host ubiquitin ligases. As a countermeasure, many intracellular pathogens encode deubiquitinase (DUB) effectors to keep their surfaces free of ubiquitin. Most bacterial DUBs belong to the OTU or CE-clan families. The betaproteobacteria Burkholderia pseudomallei and Burkholderia mallei, causative agents of melioidosis and glanders, respectively, encode the TssM effector, the only known bacterial DUB belonging to the USP class. TssM is much shorter than typical eukaryotic USP enzymes and lacks the canonical ubiquitin-recognition region. By solving the crystal structures of isolated TssM and its complex with ubiquitin, we found that TssM lacks the entire "Fingers" subdomain of the USP fold. Instead, the TssM family has evolved the functionally analog "Littlefinger" loop, which is located towards the end of the USP domain and recognizes different ubiquitin interfaces than those used by USPs. The structures revealed the presence of an N-terminal immunoglobulin-fold domain, which is able to form a strand-exchange dimer and might mediate TssM localization to the bacterial surface.
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Affiliation(s)
- Thomas Hermanns
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
| | - Matthias Uthoff
- https://ror.org/00rcxh774 Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Ulrich Baumann
- https://ror.org/00rcxh774 Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Kay Hofmann
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
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2
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Franklin TG, Brzovic PS, Pruneda JN. Bacterial ligases reveal fundamental principles of polyubiquitin specificity. Mol Cell 2023; 83:4538-4554.e4. [PMID: 38091999 PMCID: PMC10872931 DOI: 10.1016/j.molcel.2023.11.017] [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: 06/29/2023] [Revised: 09/28/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023]
Abstract
Homologous to E6AP C terminus (HECT) E3 ubiquitin (Ub) ligases direct substrates toward distinct cellular fates dictated by the specific form of monomeric or polymeric Ub (polyUb) signal attached. How polyUb specificity is achieved has been a long-standing mystery, despite extensive study in various hosts, ranging from yeast to human. The bacterial pathogens enterohemorrhagic Escherichia coli and Salmonella Typhimurium encode outlying examples of "HECT-like" (bHECT) E3 ligases, but commonalities to eukaryotic HECT (eHECT) mechanism and specificity had not been explored. We expanded the bHECT family with examples in human and plant pathogens. Three bHECT structures in primed, Ub-loaded states resolved key details of the entire Ub ligation process. One structure provided a rare glimpse into the act of ligating polyUb, yielding a means to rewire polyUb specificity of both bHECT and eHECT ligases. Studying this evolutionarily distinct bHECT family has revealed insight into the function of key bacterial virulence factors as well as fundamental principles underlying HECT-type Ub ligation.
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Affiliation(s)
- Tyler G Franklin
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA.
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3
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Bialek W, Collawn JF, Bartoszewski R. Ubiquitin-Dependent and Independent Proteasomal Degradation in Host-Pathogen Interactions. Molecules 2023; 28:6740. [PMID: 37764516 PMCID: PMC10536765 DOI: 10.3390/molecules28186740] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Ubiquitin, a small protein, is well known for tagging target proteins through a cascade of enzymatic reactions that lead to protein degradation. The ubiquitin tag, apart from its signaling role, is paramount in destabilizing the modified protein. Here, we explore the complex role of ubiquitin-mediated protein destabilization in the intricate proteolysis process by the 26S proteasome. In addition, the significance of the so-called ubiquitin-independent pathway and the role of the 20S proteasome are considered. Next, we discuss the ubiquitin-proteasome system's interplay with pathogenic microorganisms and how the microorganisms manipulate this system to establish infection by a range of elaborate pathways to evade or counteract host responses. Finally, we focus on the mechanisms that rely either on (i) hijacking the host and on delivering pathogenic E3 ligases and deubiquitinases that promote the degradation of host proteins, or (ii) counteracting host responses through the stabilization of pathogenic effector proteins.
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Affiliation(s)
- Wojciech Bialek
- Department of Biophysics, Faculty of Biotechnology, University of Wrocław, 50-383 Wrocław, Poland
| | - James F. Collawn
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
| | - Rafal Bartoszewski
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
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4
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Roberts CG, Franklin TG, Pruneda JN. Ubiquitin-targeted bacterial effectors: rule breakers of the ubiquitin system. EMBO J 2023; 42:e114318. [PMID: 37555693 PMCID: PMC10505922 DOI: 10.15252/embj.2023114318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
Regulation through post-translational ubiquitin signaling underlies a large portion of eukaryotic biology. This has not gone unnoticed by invading pathogens, many of which have evolved mechanisms to manipulate or subvert the host ubiquitin system. Bacteria are particularly adept at this and rely heavily upon ubiquitin-targeted virulence factors for invasion and replication. Despite lacking a conventional ubiquitin system of their own, many bacterial ubiquitin regulators loosely follow the structural and mechanistic rules established by eukaryotic ubiquitin machinery. Others completely break these rules and have evolved novel structural folds, exhibit distinct mechanisms of regulation, or catalyze foreign ubiquitin modifications. Studying these interactions can not only reveal important aspects of bacterial pathogenesis but also shed light on unexplored areas of ubiquitin signaling and regulation. In this review, we discuss the methods by which bacteria manipulate host ubiquitin and highlight aspects that follow or break the rules of ubiquitination.
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Affiliation(s)
- Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
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5
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Patel R, Negrón Terón K, Zhou M, Nakayasu E, Drown B, Das C. Genetically Encoded Crosslinking Enables Identification of Multivalent Ubiquitin-Deubiquitylating Enzyme Interactions. Chembiochem 2023; 24:e202300305. [PMID: 37262077 PMCID: PMC11088939 DOI: 10.1002/cbic.202300305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/30/2023] [Accepted: 05/30/2023] [Indexed: 06/03/2023]
Abstract
Ubiquitin (Ub) proteoforms control nearly every aspect of eukaryotic cell biology through their diversity. Inspired by the widely used Ub C-terminal electrophiles (Ub-E), here we report the identification of multivalent binding of Ub with deubiquitylating enzymes (Dubs) using genetic code expansion (GCE) and crosslinking mass spectrometry. While the Ub-Es only gather structural information with the S1 Dub sites, we demonstrate that GCE of Ub with p-benzoyl-L-phenylalanine enables identification of interaction modes beyond the S1 site with a panel of Dubs of both eukaryotic and prokaryotic origin. Collectively, this represents the next generation of Ub-based affinity probes with a unique ability to unravel Ub interaction landscapes beyond what is afforded by cysteine-based chemistries.
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Affiliation(s)
- Rishi Patel
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Kristos Negrón Terón
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Mowei Zhou
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA
| | - Ernesto Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA
| | - Bryon Drown
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
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6
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Franklin TG, Brzovic PS, Pruneda JN. Bacterial mimicry of eukaryotic HECT ubiquitin ligation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543783. [PMID: 37333152 PMCID: PMC10274628 DOI: 10.1101/2023.06.05.543783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
HECT E3 ubiquitin (Ub) ligases direct their modified substrates toward a range of cellular fates dictated by the specific form of monomeric or polymeric Ub (polyUb) signal that is attached. How polyUb specificity is achieved has been a longstanding mystery, despite extensive study ranging from yeast to human. Two outlying examples of bacterial "HECT-like" (bHECT) E3 ligases have been reported in the human pathogens Enterohemorrhagic Escherichia coli and Salmonella Typhimurium, but what parallels can be drawn to eukaryotic HECT (eHECT) mechanism and specificity had not been explored. Here, we expanded the bHECT family and identified catalytically active, bona fide examples in both human and plant pathogens. By determining structures for three bHECT complexes in their primed, Ub-loaded states, we resolved key details of the full bHECT Ub ligation mechanism. One structure provided the first glimpse of a HECT E3 ligase in the act of ligating polyUb, yielding a means to rewire the polyUb specificity of both bHECT and eHECT ligases. Through studying this evolutionarily distinct bHECT family, we have not only gained insight into the function of key bacterial virulence factors but also revealed fundamental principles underlying HECT-type Ub ligation.
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Affiliation(s)
- Tyler G. Franklin
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Peter S. Brzovic
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
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7
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Warren GD, Kitao T, Franklin TG, Nguyen JV, Geurink PP, Kubori T, Nagai H, Pruneda JN. Mechanism of Lys6 poly-ubiquitin specificity by the L. pneumophila deubiquitinase LotA. Mol Cell 2023; 83:105-120.e5. [PMID: 36538933 PMCID: PMC9825671 DOI: 10.1016/j.molcel.2022.11.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/13/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022]
Abstract
The versatility of ubiquitination to control vast domains of eukaryotic biology is due, in part, to diversification through differently linked poly-ubiquitin chains. Deciphering signaling roles for some chain types, including those linked via K6, has been stymied by a lack of specificity among the implicated regulatory proteins. Forged through strong evolutionary pressures, pathogenic bacteria have evolved intricate mechanisms to regulate host ubiquitin during infection. Herein, we identify and characterize a deubiquitinase domain of the secreted effector LotA from Legionella pneumophila that specifically regulates K6-linked poly-ubiquitin. We demonstrate the utility of LotA for studying K6 poly-ubiquitin signals. We identify the structural basis of LotA activation and poly-ubiquitin specificity and describe an essential "adaptive" ubiquitin-binding domain. Without LotA activity during infection, the Legionella-containing vacuole becomes decorated with K6 poly-ubiquitin as well as the AAA ATPase VCP/p97/Cdc48. We propose that LotA's deubiquitinase activity guards Legionella-containing vacuole components from ubiquitin-dependent extraction.
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Affiliation(s)
- Gus D Warren
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Tyler G Franklin
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Justine V Nguyen
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul P Geurink
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA.
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Bullones-Bolaños A, Bernal-Bayard J, Ramos-Morales F. The NEL Family of Bacterial E3 Ubiquitin Ligases. Int J Mol Sci 2022; 23:7725. [PMID: 35887072 PMCID: PMC9320238 DOI: 10.3390/ijms23147725] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 12/16/2022] Open
Abstract
Some pathogenic or symbiotic Gram-negative bacteria can manipulate the ubiquitination system of the eukaryotic host cell using a variety of strategies. Members of the genera Salmonella, Shigella, Sinorhizobium, and Ralstonia, among others, express E3 ubiquitin ligases that belong to the NEL family. These bacteria use type III secretion systems to translocate these proteins into host cells, where they will find their targets. In this review, we first introduce type III secretion systems and the ubiquitination process and consider the various ways bacteria use to alter the ubiquitin ligation machinery. We then focus on the members of the NEL family, their expression, translocation, and subcellular localization in the host cell, and we review what is known about the structure of these proteins, their function in virulence or symbiosis, and their specific targets.
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Affiliation(s)
| | | | - Francisco Ramos-Morales
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Sevilla, Spain; (A.B.-B.); (J.B.-B.)
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9
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Schulze-Niemand E, Naumann M, Stein M. Substrate-assisted activation and selectivity of the bacterial RavD effector deubiquitinylase. Proteins 2021; 90:947-958. [PMID: 34825414 DOI: 10.1002/prot.26286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/02/2021] [Accepted: 11/22/2021] [Indexed: 11/12/2022]
Abstract
Deubiquitinylases (DUBs) catalyze the peptide bond cleavage of specific ubiquitin linkages at distinct protein substrates. Pathogens from viruses and bacteria independently developed effector proteins with DUB activity to mimic host DUB functions and circumvent immune responses. The effector protein RavD from Legionella pneumophila cleaves linear ubiquitin chains with an exclusive methionine-1 selectivity. It thus performs as a functional analogue of the human DUB OTULIN, which achieves its selectivity only via a specialized proximal ubiquitin S1' binding site as well as a substrate-assisted activation of the catalytic triad. An analysis of the crystal structures of bacterial RavD in its free and di-ubiquitin-bound forms, in order to rationalize the structural basis for its selectivity and activation mechanism, is not fully conclusive. As these ambiguities might arise from the introduced double mutation of the di-ubiquitin substrate in the RavD-di-ubiquitin complex crystal structure, biomolecular modeling, and molecular dynamics sampling (1-2 μs for each system of RavD and OTULIN) were employed to reconstitute the physiological RavD-di-ubiquitin complex. The simulations show that the distal S1 ubiquitin binding sites of RavD and OTULIN are similar in terms of interface area, composition, and ubiquitin binding affinity. The proximal S1' site of RavD, in contrast, is significantly smaller and ubiquitin binding is weaker and more flexible than in OTULIN. Upon substrate access, the residues of the catalytic triad of RavD show a reduction of flexibility and a conformational transition toward a catalytically active state. Thus, the enzymatic activation of RavD is presumably also substrate-assisted and a clear rationale for the common M1-substrate selectivity.
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Affiliation(s)
- Eric Schulze-Niemand
- Institute for Experimental Internal Medicine, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany.,Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Michael Naumann
- Institute for Experimental Internal Medicine, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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10
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Structural basis of ubiquitin recognition by a bacterial OTU deubiquitinase LotA. J Bacteriol 2021; 204:e0037621. [PMID: 34633867 DOI: 10.1128/jb.00376-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogenic bacteria have acquired a vast array of eukaryotic-like proteins via intimate interaction with host cells. Bacterial effector proteins that function as ubiquitin ligases and deubiquitinases (DUBs) are remarkable examples of such molecular mimicry. LotA, a Legionella pneumophila effector, belongs to the ovarian tumor (OTU) superfamily, which regulates diverse ubiquitin signals by their DUB activities. LotA harbors two OTU domains that have distinct reactivities; the first one is responsible for the cleavage of the K6-linked ubiquitin chain, and the second one shows an uncommon preference for long chains of ubiquitin. Here, we report the crystal structure of a middle domain of LotA (LotAM), which contains the second OTU domain. LotAM consists of two distinct subdomains, a catalytic domain having high structural similarity with human OTU DUBs and an extended helical lobe (EHL) domain, which is characteristically conserved only in Legionella OTU DUBs. The docking simulation of LotAM with ubiquitin suggested that hydrophobic and electrostatic interactions between the EHL of LotAM and the C-terminal region of ubiquitin are crucial for the binding of ubiquitin to LotAM. The structure-based mutagenesis demonstrated that the acidic residue in the characteristic short helical segment termed the 'helical arm' is essential for the enzymatic activity of LotAM. The EHL domain of the three Legionella OTU DUBs, LotA, LotB, and LotC, share the 'helical arm' structure, suggesting that the EHL domain defines the Lot-OTUs as a unique class of DUBs. Importance To successfully colonize, some pathogenic bacteria hijack the host ubiquitin system. Legionella OTU-like-DUBs (Lot-DUBs) are novel bacterial deubiquitinases found in effector proteins of L. pneumophila. LotA is a member of Lot-DUBs and has two OTU domains (OTU1 and OTU2). We determined the structure of a middle fragment of LotA (LotAM), which includes OTU2. LotAM consists of the conserved catalytic domain and the Legionella OTUs-specific EHL domain. The docking simulation with ubiquitin and the mutational analysis suggested that the acidic surface in the EHL is essential for enzymatic activity. The structure of the EHL differs from those of other Lot-DUBs, suggesting that the variation of the EHL is related to the variable cleaving specificity of each DUB.
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