1
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Pruneda JN, Nguyen JV, Nagai H, Kubori T. Bacterial usurpation of the OTU deubiquitinase fold. FEBS J 2024; 291:3303-3316. [PMID: 36636866 PMCID: PMC10338644 DOI: 10.1111/febs.16725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/10/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023]
Abstract
The extensive cellular signalling events controlled by posttranslational ubiquitination are tightly regulated through the action of specialized proteases termed deubiquitinases. Among them, the OTU family of deubiquitinases can play very specialized roles in the regulation of discrete subtypes of ubiquitin signals that control specific cellular functions. To exert control over host cellular functions, some pathogenic bacteria have usurped the OTU deubiquitinase fold as a secreted virulence factor that interferes with ubiquitination inside infected cells. Herein, we provide a review of the function of bacterial OTU deubiquitinases during infection, the structural basis for their deubiquitinase activities and the bioinformatic approaches leading to their identification. Understanding bacterial OTU deubiquitinases holds the potential for discoveries not only in bacterial pathogenesis but in eukaryotic biology as well.
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Affiliation(s)
- Jonathan N. Pruneda
- 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
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu, Gifu 501-1194, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
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2
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Kubori T, Arasaki K, Oide H, Kitao T, Nagai H. Multi-tiered actions of Legionella effectors to modulate host Rab10 dynamics. eLife 2024; 12:RP89002. [PMID: 38771316 PMCID: PMC11108646 DOI: 10.7554/elife.89002] [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] [Indexed: 05/22/2024] Open
Abstract
Rab GTPases are representative targets of manipulation by intracellular bacterial pathogens for hijacking membrane trafficking. Legionella pneumophila recruits many Rab GTPases to its vacuole and exploits their activities. Here, we found that infection-associated regulation of Rab10 dynamics involves ubiquitin signaling cascades mediated by the SidE and SidC families of Legionella ubiquitin ligases. Phosphoribosyl-ubiquitination of Rab10 catalyzed by the SidE ligases is crucial for its recruitment to the bacterial vacuole. SdcB, the previously uncharacterized SidC-family effector, resides on the vacuole and contributes to retention of Rab10 at the late stages of infection. We further identified MavC as a negative regulator of SdcB. By the transglutaminase activity, MavC crosslinks ubiquitin to SdcB and suppresses its function, resulting in elimination of Rab10 from the vacuole. These results demonstrate that the orchestrated actions of many L. pneumophila effectors fine-tune the dynamics of Rab10 during infection.
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Affiliation(s)
- Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life SciencesHachiojiJapan
| | - Hiromu Oide
- School of Life Sciences, Tokyo University of Pharmacy and Life SciencesHachiojiJapan
| | - Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu UniversityGifuJapan
- Center for One Medicine Innovative Translational Research (COMIT), Gifu UniversityGifuJapan
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3
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Spano D, Catara G. Targeting the Ubiquitin-Proteasome System and Recent Advances in Cancer Therapy. Cells 2023; 13:29. [PMID: 38201233 PMCID: PMC10778545 DOI: 10.3390/cells13010029] [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: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Ubiquitination is a reversible post-translational modification based on the chemical addition of ubiquitin to proteins with regulatory effects on various signaling pathways. Ubiquitination can alter the molecular functions of tagged substrates with respect to protein turnover, biological activity, subcellular localization or protein-protein interaction. As a result, a wide variety of cellular processes are under ubiquitination-mediated control, contributing to the maintenance of cellular homeostasis. It follows that the dysregulation of ubiquitination reactions plays a relevant role in the pathogenic states of human diseases such as neurodegenerative diseases, immune-related pathologies and cancer. In recent decades, the enzymes of the ubiquitin-proteasome system (UPS), including E3 ubiquitin ligases and deubiquitinases (DUBs), have attracted attention as novel druggable targets for the development of new anticancer therapeutic approaches. This perspective article summarizes the peculiarities shared by the enzymes involved in the ubiquitination reaction which, when deregulated, can lead to tumorigenesis. Accordingly, an overview of the main pharmacological interventions based on targeting the UPS that are in clinical use or still in clinical trials is provided, also highlighting the limitations of the therapeutic efficacy of these approaches. Therefore, various attempts to circumvent drug resistance and side effects as well as UPS-related emerging technologies in anticancer therapeutics are discussed.
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Affiliation(s)
- Daniela Spano
- Institute for Endocrinology and Experimental Oncology “G. Salvatore”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
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4
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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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5
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Yang Y, Mei L, Chen J, Chen X, Wang Z, Liu L, Yang A. Legionella pneumophila-mediated host posttranslational modifications. J Mol Cell Biol 2023; 15:mjad032. [PMID: 37156500 PMCID: PMC10720952 DOI: 10.1093/jmcb/mjad032] [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: 09/16/2022] [Revised: 01/17/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023] Open
Abstract
Legionella pneumophila is a Gram-negative bacterium ubiquitously present in freshwater environments and causes a serious type of pneumonia called Legionnaires' disease. During infections, L. pneumophila releases over 300 effector proteins into host cells through an Icm/Dot type IV secretion system to manipulate the host defense system for survival within the host. Notably, certain effector proteins mediate posttranslational modifications (PTMs), serving as useful approaches exploited by L. pneumophila to modify host proteins. Some effectors catalyze the addition of host protein PTMs, while others mediate the removal of PTMs from host proteins. In this review, we summarize L. pneumophila effector-mediated PTMs of host proteins, including phosphorylation, ubiquitination, glycosylation, AMPylation, phosphocholination, methylation, and ADP-ribosylation, as well as dephosphorylation, deubiquitination, deAMPylation, deADP-ribosylation, dephosphocholination, and delipidation. We describe their molecular mechanisms and biological functions in the regulation of bacterial growth and Legionella-containing vacuole biosynthesis and in the disruption of host immune and defense machinery.
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Affiliation(s)
- Yi Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
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6
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Wehrmann M, Vilchez D. The emerging role and therapeutic implications of bacterial and parasitic deubiquitinating enzymes. Front Immunol 2023; 14:1303072. [PMID: 38077335 PMCID: PMC10703165 DOI: 10.3389/fimmu.2023.1303072] [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: 09/27/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) are emerging as key factors for the infection of human cells by pathogens such as bacteria and parasites. In this review, we discuss the most recent studies on the role of deubiquitinase activity in exploiting and manipulating ubiquitin (Ub)-dependent host processes during infection. The studies discussed here highlight the importance of DUB host-pathogen research and underscore the therapeutic potential of inhibiting pathogen-specific DUB activity to prevent infectious diseases.
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Affiliation(s)
- Markus Wehrmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
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7
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Boll V, Hermanns T, Uthoff M, Erven I, Hörner EM, Kozjak-Pavlovic V, Baumann U, Hofmann K. Functional and structural diversity in deubiquitinases of the Chlamydia-like bacterium Simkania negevensis. Nat Commun 2023; 14:7335. [PMID: 37957213 PMCID: PMC10643670 DOI: 10.1038/s41467-023-43144-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Besides the regulation of many cellular pathways, ubiquitination is important for defense against invading pathogens. Some intracellular bacteria have evolved deubiquitinase (DUB) effector proteins, which interfere with the host ubiquitin system and help the pathogen to evade xenophagy and lysosomal degradation. Most intracellular bacteria encode one or two DUBs, which are often linkage-promiscuous or preferentially cleave K63-linked chains attached to bacteria or bacteria-containing vacuoles. By contrast, the respiratory pathogen Legionella pneumophila possesses a much larger number of DUB effectors, including a K6-specific enzyme belonging to the OTU family and an M1-specific DUB uniquely found in this bacterium. Here, we report that the opportunistic pathogen Simkania negevensis, which is unrelated to Legionella but has a similar lifestyle, encodes a similarly large number of DUBs, including M1- and K6-specific enzymes. Simkania DUBs are highly diverse and include DUB classes never before seen in bacteria. Interestingly, the M1- and K6-specific DUBs of Legionella and Simkania are unrelated, suggesting that their acquisition occurred independently. We characterize the DUB activity of eight Simkania-encoded enzymes belonging to five different DUB classes. We also provide a structural basis for the M1-specificity of a Simkania DUB, which most likely evolved from a eukaryotic otubain-like precursor.
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Affiliation(s)
- Vanessa Boll
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Thomas Hermanns
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Matthias Uthoff
- Institute of Biochemistry, University of Cologne, Cologne, Germany
- Bayer AG, Research & Development, Pharmaceuticals, Biologics Research, Wuppertal, Germany
| | - Ilka Erven
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Eva-Maria Hörner
- Chair of Microbiology, Biocenter, Julius Maximilian University, Würzburg, Würzburg, Germany
| | - Vera Kozjak-Pavlovic
- Chair of Microbiology, Biocenter, Julius Maximilian University, Würzburg, Würzburg, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany.
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8
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Harumoto T. Self-stabilization mechanism encoded by a bacterial toxin facilitates reproductive parasitism. Curr Biol 2023; 33:4021-4029.e6. [PMID: 37673069 DOI: 10.1016/j.cub.2023.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/30/2023] [Accepted: 08/10/2023] [Indexed: 09/08/2023]
Abstract
A wide variety of maternally transmitted endosymbionts in insects are associated with reproductive parasitism, whereby they interfere with host reproduction to increase the ratio of infected females and spread within populations.1,2 Recent successes in identifying bacterial factors responsible for reproductive parasitism3,4,5,6,7 as well as further omics approaches8,9,10,11,12 have highlighted the common appearance of deubiquitinase domains, although their biological roles-in particular, how they link to distinct manipulative phenotypes-remain poorly defined. Spiroplasma poulsonii is a helical and motile bacterial endosymbiont of Drosophila,13,14 which selectively kills male progeny with a male-killing toxin Spaid (S. poulsonii androcidin), which encodes an ovarian tumor (OTU) deubiquitinase domain.6 Artificial expression of Spaid in flies reproduces male-killing-associated pathologies that include abnormal apoptosis and neural defects during embryogenesis6,15,16,17,18,19; moreover, it highly accumulates on the dosage-compensated male X chromosome,20 congruent with cellular defects such as the DNA damage/chromatin bridge breakage specifically induced upon that chromosome.6,21,22,23 Here, I show that without the function of OTU, Spaid is polyubiquitinated and degraded through the host ubiquitin-proteasome pathway, leading to the attenuation of male-killing activity as shown previously.6 Furthermore, I find that Spaid utilizes its OTU domain to deubiquitinate itself in an intermolecular manner. Collectively, the deubiquitinase domain of Spaid serves as a self-stabilization mechanism to facilitate male killing in flies, optimizing a molecular strategy of endosymbionts that enables the efficient manipulation of the host at a low energetic cost.
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Affiliation(s)
- Toshiyuki Harumoto
- Hakubi Center for Advanced Research, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan; Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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9
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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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10
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Kang S, Kim G, Choi M, Jeong M, van der Heden van Noort GJ, Roh SH, Shin D. Structural insights into ubiquitin chain cleavage by Legionella ovarian tumor deubiquitinases. Life Sci Alliance 2023; 6:e202201876. [PMID: 37100438 PMCID: PMC10133868 DOI: 10.26508/lsa.202201876] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Although ubiquitin is found only in eukaryotes, several pathogenic bacteria and viruses possess proteins that hinder the host ubiquitin system. Legionella, a gram-negative intracellular bacterium, possesses an ovarian tumor (OTU) family of deubiquitinases (Lot DUBs). Herein, we describe the molecular characteristics of Lot DUBs. We elucidated the structure of the LotA OTU1 domain and revealed that entire Lot DUBs possess a characteristic extended helical lobe that is not found in other OTU-DUBs. The structural topology of an extended helical lobe is the same throughout the Lot family, and it provides an S1' ubiquitin-binding site. Moreover, the catalytic triads of Lot DUBs resemble those of the A20-type OTU-DUBs. Furthermore, we revealed a unique mechanism by which LotA OTU domains cooperate together to distinguish the length of the chain and preferentially cleave longer K48-linked polyubiquitin chains. The LotA OTU1 domain itself cleaves K6-linked ubiquitin chains, whereas it is also essential for assisting the cleavage of longer K48-linked polyubiquitin chains by the OTU2 domain. Thus, this study provides novel insights into the structure and mechanism of action of Lot DUBs.
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Affiliation(s)
- Sangwoo Kang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Gyuhee Kim
- School of Biological Science, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Minhyeong Choi
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Minwoo Jeong
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | | | - Soung-Hun Roh
- School of Biological Science, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Donghyuk Shin
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
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11
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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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12
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Zhang Z, Das C. Pathogen-defending deubiquitinase possesses distinct specificity towards K6-polyubiquitination. Trends Microbiol 2023; 31:423-425. [PMID: 36890008 DOI: 10.1016/j.tim.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023]
Abstract
The bacterial pathogen Legionella pneumophila encodes numerous effectors to manipulate host ubiquitin signaling. Recently, Warren et al. revealed the structural basis of K6-polyubiquitination recognition by Legionella deubiquitinase LotA, while validating its potential as an enzymatic tool to study linkage-specific ubiquitination. During Legionella infection, LotA counteracts valosin-containing protein (VCP) recruitment to the Legionella-containing vacuole.
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Affiliation(s)
- Zhengrui Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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13
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Shi Y, Liu H, Ma K, Luo ZQ, Qiu J. Legionella longbeachae Regulates the Association of Polyubiquitinated Proteins on Bacterial Phagosome with Multiple Deubiquitinases. Microbiol Spectr 2023; 11:e0417922. [PMID: 36790208 PMCID: PMC10100730 DOI: 10.1128/spectrum.04179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/16/2023] [Indexed: 02/16/2023] Open
Abstract
Legionella spp. are the causative agents of a severe pneumonia known as Legionnaires' disease. Upon being engulfed by host cells, these environmental bacteria replicate intracellularly in a plasma membrane-derived niche termed Legionella-containing vacuole (LCV) in a way that requires the defective in organelle trafficking/intracellular multiplication (Dot/Icm) protein transporter. Our understanding of interactions between Legionella and its hosts was mostly based on studies of Legionella pneumophila. In this study, we found that the LCVs created by virulent Legionella longbeachae are similarly decorated by polyubiquitinated proteins to those formed by L. pneumophila and that the ubiquitin-proteasome system (UPS) is required for optimal intracellular growth of L. longbeachae. Furthermore, we utilized bioinformatics methods and the ubiquitin-vinylmethyl ester probe to obtain potential deubiquitinases (DUBs) encoded by L. longbeachae. These efforts led to the identification of 9 L. longbeachae DUBs that displayed distinct specificity toward ubiquitin chain types. Among these, LLO_1014 and LLO_2238 are associated with the LCVs and impact the accumulation of polyubiquitinated species on the bacterial phagosome. Moreover, LLO_1014 and LLO_2238 could fully restore the phenotypes associated with Δceg23 (lotB) and Δlem27 (lotC) mutants of L. pneumophila, indicating that these DUBs have similar functions. Together, these results reveal that L. longbeachae uses multiple DUBs to construct an intracellular niche for its replication. IMPORTANCE Legionella spp. are opportunistic intracellular bacterial pathogens that cause Legionnaires' disease. Legionella utilizes the Dot/Icm type IV secretion system to deliver effector protein into host cells to modulate various cellular functions. At least 26 L. pneumophila effectors are known to hijack the host ubiquitin system via diverse mechanisms. L. longbeachae is the second leading cause of Legionnaires' disease worldwide. However, our knowledge about the interactions between L. longbeachae and its hosts is very limited. Here, we found that, similar to L. pneumophila infection, the host ubiquitin proteasome system is also important for the intracellular replication of L. longbeachae. In addition, the bacterial phagosomes harboring L. longbeachae are enriched with polyubiquitinated proteins in a Dot/Icm system-dependent manner. We further identified 9 L. longbeachae proteins that function as DUBs with distinct ubiquitin chain specificity. Of note, several of the phagosome-associated L. longbeachae DUBs regulate the recruitment of polyubiquitinated proteins to the LCV.
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Affiliation(s)
- Yunjia Shi
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Hongtao Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Kelong Ma
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Jiazhang Qiu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
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14
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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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15
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Erven I, Abraham E, Hermanns T, Baumann U, Hofmann K. A widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins. Nat Commun 2022; 13:7643. [PMID: 36496440 PMCID: PMC9741609 DOI: 10.1038/s41467-022-35244-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Distinct families of eukaryotic deubiquitinases (DUBs) are regulators of ubiquitin signaling. Here, we report on the presence of an additional DUB class broadly distributed in eukaryotes and several bacteria. The only described members of this family are the large tegument proteins of herpesviruses, which are attached to the outside of the viral capsid. By using a bioinformatics screen, we have identified distant homologs of this VTD (Viral tegument-like DUB) family in vertebrate transposons, fungi, insects, nematodes, cnidaria, protists and bacteria. While some VTD activities resemble viral tegument DUBs in that they favor K48-linked ubiquitin chains, other members are highly specific for K6- or K63-linked ubiquitin chains. The crystal structures of K48- and K6-specific members reveal considerable differences in ubiquitin recognition. The VTD family likely evolved from non-DUB proteases and spread through transposons, many of which became 'domesticated', giving rise to the Drosophila male sterile (3)76Ca gene and several nematode genes with male-specific expression.
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Affiliation(s)
- Ilka Erven
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Elena Abraham
- grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, D-50674 Cologne, Germany
| | - Thomas Hermanns
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
| | - Ulrich Baumann
- grid.6190.e0000 0000 8580 3777Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, D-50674 Cologne, Germany
| | - Kay Hofmann
- grid.6190.e0000 0000 8580 3777Institute for Genetics, University of Cologne, Zülpicher Straße 47a, D-50674 Cologne, Germany
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16
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Tomaskovic I, Gonzalez A, Dikic I. Ubiquitin and Legionella: From bench to bedside. Semin Cell Dev Biol 2022; 132:230-241. [PMID: 35177348 DOI: 10.1016/j.semcdb.2022.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022]
Abstract
Legionella pneumophila, a Gram-negative intracellular bacterium, is one of the major causes of Legionnaires' disease, a specific type of atypical pneumonia. Despite intensive research efforts that elucidated many relevant structural, molecular and medical insights into Legionella's pathogenicity, Legionnaires' disease continues to present an ongoing public health concern. Legionella's virulence is based on its ability to simultaneously hijack multiple molecular pathways of the host cell to ensure its fast replication and dissemination. Legionella usurps the host ubiquitin system through multiple effector proteins, using the advantage of both conventional and unconventional (phosphoribosyl-linked) ubiquitination, thus providing optimal conditions for its replication. In this review, we summarize the current understanding of L. pneumophila from medical, biochemical and molecular perspectives. We describe the clinical disease presentation, its diagnostics and treatment, as well as host-pathogen interactions, with the emphasis on the ability of Legionella to target the host ubiquitin system upon infection. Furthermore, the interdisciplinary use of innovative technologies enables better insights into the pathogenesis of Legionnaires' disease and provides new opportunities for its treatment and prevention.
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Affiliation(s)
- Ines Tomaskovic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alexis Gonzalez
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany.
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17
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Vogel K, Bläske T, Nagel MK, Globisch C, Maguire S, Mattes L, Gude C, Kovermann M, Hauser K, Peter C, Isono E. Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking. Nat Commun 2022; 13:6897. [PMID: 36371501 PMCID: PMC9653390 DOI: 10.1038/s41467-022-34637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
The abundance of plasma membrane-resident receptors and transporters has to be tightly regulated by ubiquitin-mediated endosomal degradation for the proper coordination of environmental stimuli and intracellular signaling. Arabidopsis OVARIAN TUMOR PROTEASE (OTU) 11 and OTU12 are plasma membrane-localized deubiquitylating enzymes (DUBs) that bind to phospholipids through a polybasic motif in the OTU domain. Here we show that the DUB activity of OTU11 and OTU12 towards K63-linked ubiquitin is stimulated by binding to lipid membranes containing anionic lipids. In addition, we show that the DUB activity of OTU11 against K6- and K11-linkages is also stimulated by anionic lipids, and that OTU11 and OTU12 can modulate the endosomal degradation of a model cargo and the auxin efflux transporter PIN2-GFP in vivo. Our results suggest that the catalytic activity of OTU11 and OTU12 is tightly connected to their ability to bind membranes and that OTU11 and OTU12 are involved in the fine-tuning of plasma membrane proteins in Arabidopsis.
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Affiliation(s)
- Karin Vogel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Tobias Bläske
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Marie-Kristin Nagel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Christoph Globisch
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Shane Maguire
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Lorenz Mattes
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christian Gude
- grid.6936.a0000000123222966School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Kovermann
- grid.9811.10000 0001 0658 7699NMR, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Karin Hauser
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christine Peter
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Erika Isono
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
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18
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Luo J, Ruan X, Huang Z, Li Z, Ye L, Wu Y, Zhen X, Ouyang S. Structural basis for the dual catalytic activity of the Legionella pneumophila ovarian-tumor (OTU) domain deubiquitinase LotA. J Biol Chem 2022; 298:102414. [PMID: 36007613 PMCID: PMC9486567 DOI: 10.1016/j.jbc.2022.102414] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022] Open
Abstract
Legionella pneumophila, a bacterial pathogen that causes a severe pneumonia known as Legionnaires’ disease, extensively exploits the ubiquitin (Ub) pathway in the infected host cells through certain virulence effectors excreted by the Dot/Icm system. To date, several Dot/Icm effectors have been found to act as Ub ligases, and four effectors, including LotA, LotB, LotC, and Ceg7, have been identified as deubiquitinases (DUBs) from the ovarian tumor (OTU) domain family. LotA is unique among other OTU DUBs because it possesses two distinct DUB domains and exclusively exhibits catalytic activity against K6-linked diUb and polyUb chains. However, the structure of LotA and the molecular mechanism for the dual DUB activity remains elusive. In this study, we solved the structure of LotA in complex with proximally bound Ub and distal covalently bound Ub. Both Ub molecules are bound to the DUB1 domain and mimic a K6-linked diUb. Structural analysis reveals that the DUB1 domain utilizes a distinct mechanism for recognition of the K6-linked diUb within a large S1′ binding site that is uncommon to OTU DUBs. Structural fold of the LotA DUB2 domain closely resembles LotB and LotC, similarly containing an extra α-helix lobe that has been demonstrated to play an important role in Ub binding. Collectively, our study uncovers the structural basis for the dual catalytic activity of the unique OTU family DUB LotA.
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Affiliation(s)
- Jiwei Luo
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xinglin Ruan
- Department of Neurology, Fujian Medical University Union Hospital, 29 Xinquan Road Gulou District, Fuzhou 350001, China
| | - Zhijie Huang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Zekai Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Le Ye
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Yongyu Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Xiangkai Zhen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
| | - Songying Ouyang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
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19
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Reversible modification of mitochondrial ADP/ATP translocases by paired Legionella effector proteins. Proc Natl Acad Sci U S A 2022; 119:e2122872119. [PMID: 35653564 DOI: 10.1073/pnas.2122872119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceMitochondria are organelles of the central metabolism that produce ATP and play fundamental roles in eukaryotic cell function and thereby become targets for pathogenic bacteria to manipulate. We found that the intracellular bacterial pathogen, Legionella pneumophila, targets mitochondrial ADP/ATP translocases (ANTs), the function of which is linked to the mitochondrial ATP synthesis. This is achieved by a pair of effector proteins, Lpg0080 and Lpg0081, which have opposing enzymatic activities as an ADP ribosyltransferase (ART) and an ADP ribosylhydrolase (ARH), respectively, coordinately regulating the chemical modification of ANTs upon infection. Our structural analyses indicate that Lpg0081 is an ARH with a noncanonical macrodomain, whose folding topology is distinct from that of the canonical macrodomain of known eukaryotic, archaeal, and bacterial proteins.
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20
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Lockwood DC, Amin H, Costa TRD, Schroeder GN. The Legionella pneumophila Dot/Icm type IV secretion system and its effectors. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35639581 DOI: 10.1099/mic.0.001187] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To prevail in the interaction with eukaryotic hosts, many bacterial pathogens use protein secretion systems to release virulence factors at the host–pathogen interface and/or deliver them directly into host cells. An outstanding example of the complexity and sophistication of secretion systems and the diversity of their protein substrates, effectors, is the Defective in organelle trafficking/Intracellular multiplication (Dot/Icm) Type IVB secretion system (T4BSS) of
Legionella pneumophila
and related species.
Legionella
species are facultative intracellular pathogens of environmental protozoa and opportunistic human respiratory pathogens. The Dot/Icm T4BSS translocates an exceptionally large number of effectors, more than 300 per
L. pneumophila
strain, and is essential for evasion of phagolysosomal degradation and exploitation of protozoa and human macrophages as replicative niches. Recent technological advancements in the imaging of large protein complexes have provided new insight into the architecture of the T4BSS and allowed us to propose models for the transport mechanism. At the same time, significant progress has been made in assigning functions to about a third of
L. pneumophila
effectors, discovering unprecedented new enzymatic activities and concepts of host subversion. In this review, we describe the current knowledge of the workings of the Dot/Icm T4BSS machinery and provide an overview of the activities and functions of the to-date characterized effectors in the interaction of
L. pneumophila
with host cells.
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Affiliation(s)
- Daniel C Lockwood
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
| | - Himani Amin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Tiago R D Costa
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Gunnar N Schroeder
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland, UK
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21
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Luo J, Wang L, Song L, Luo ZQ. Exploitation of the Host Ubiquitin System: Means by Legionella pneumophila. Front Microbiol 2022; 12:790442. [PMID: 35003021 PMCID: PMC8727461 DOI: 10.3389/fmicb.2021.790442] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/30/2021] [Indexed: 01/12/2023] Open
Abstract
Ubiquitination is a commonly used post-translational modification (PTM) in eukaryotic cells, which regulates a wide variety of cellular processes, such as differentiation, apoptosis, cell cycle, and immunity. Because of its essential role in immunity, the ubiquitin network is a common target of infectious agents, which have evolved various effective strategies to hijack and co-opt ubiquitin signaling for their benefit. The intracellular pathogen Legionella pneumophila represents one such example; it utilizes a large cohort of virulence factors called effectors to modulate diverse cellular processes, resulting in the formation a compartment called the Legionella-containing vacuole (LCV) that supports its replication. Many of these effectors function to re-orchestrate ubiquitin signaling with distinct biochemical activities. In this review, we highlight recent progress in the mechanism of action of L. pneumophila effectors involved in ubiquitination and discuss their roles in bacterial virulence and host cell biology.
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Affiliation(s)
- Jingjing Luo
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lidong Wang
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lei Song
- Department of Respiratory Medicine, Center for Pathogen Biology and Infectious Diseases, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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22
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Lammers M. Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective. Front Microbiol 2021; 12:757179. [PMID: 34721364 PMCID: PMC8556138 DOI: 10.3389/fmicb.2021.757179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/21/2022] Open
Abstract
Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.
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Affiliation(s)
- Michael Lammers
- Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Greifswald, Germany
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23
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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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24
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Kitao T, Taguchi K, Seto S, Arasaki K, Ando H, Nagai H, Kubori T. Legionella Manipulates Non-canonical SNARE Pairing Using a Bacterial Deubiquitinase. Cell Rep 2021; 32:108107. [PMID: 32905772 DOI: 10.1016/j.celrep.2020.108107] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 05/30/2020] [Accepted: 08/12/2020] [Indexed: 10/23/2022] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila uses many effector proteins delivered by the bacterial type IV secretion system (T4SS) to hijack the early secretory pathway to establish its replicative niche, known as the Legionella-containing vacuole (LCV). On LCV biogenesis, the endoplasmic reticulum (ER) vesicular soluble N-ethylmaleimide-sensitive factor attachment protein receptors (v-SNARE) Sec22b is recruited to the bacterial phagosome and forms non-canonical pairings with target membrane SNAREs (t-SNAREs) from the plasma membrane. Here, we identify a Legionella deubiquitinase (DUB), LotB, that can modulate the early secretory pathway by interacting with coatomer protein complex I (COPI) vesicles when ectopically expressed. We show that Sec22b is ubiquitinated upon L. pneumophila infection in a T4SS-dependent manner and that, subsequently, LotB deconjugates K63-linked ubiquitins from Sec22b. The DUB activity of LotB stimulates dissociation of the t-SNARE syntaxin 3 (Stx3) from Sec22b, which resides on the LCV. Our study highlights a bacterial strategy manipulating the dynamics of infection-induced SNARE pairing using a bacterial DUB.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Kyoichiro Taguchi
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan; Laboratory of Veterinary Microbiology, Faculty of Applied Biological Science, Gifu University, Gifu, Gifu 501-1193, Japan
| | - Shintaro Seto
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Tokyo 204-8533, Japan
| | - Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Hiroki Ando
- G-CHAIN, Gifu University, Gifu, Gifu 501-1194, Japan; Laboratory of Phage Biologics, Graduate School of Medicine, 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.
| | - 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.
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25
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Ong SY, Schuelein R, Wibawa RR, Thomas DW, Handoko Y, Freytag S, Bahlo M, Simpson KJ, Hartland EL. Genome-wide genetic screen identifies host ubiquitination as important for Legionella pneumophila Dot/Icm effector translocation. Cell Microbiol 2021; 23:e13368. [PMID: 34041837 DOI: 10.1111/cmi.13368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 11/30/2022]
Abstract
The Dot/Icm system of Legionella pneumophila is essential for virulence and delivers a large repertoire of effectors into infected host cells to create the Legionella containing vacuole. Since the secretion of effectors via the Dot/Icm system does not occur in the absence of host cells, we hypothesised that host factors actively participate in Dot/Icm effector translocation. Here we employed a high-throughput, genome-wide siRNA screen to systematically test the effect of silencing 18,120 human genes on translocation of the Dot/Icm effector, RalF, into HeLa cells. For the primary screen, we found that silencing of 119 genes led to increased translocation of RalF, while silencing of 321 genes resulted in decreased translocation. Following secondary screening, 70 genes were successfully validated as 'high confidence' targets. Gene set enrichment analysis of siRNAs leading to decreased RalF translocation, showed that ubiquitination was the most highly overrepresented category in the pathway analysis. We further showed that two host factors, the E2 ubiquitin-conjugating enzyme, UBE2E1, and the E3 ubiquitin ligase, CUL7, were important for supporting Dot/Icm translocation and L. pneumophila intracellular replication. In summary, we identified host ubiquitin pathways as important for the efficiency of Dot/Icm effector translocation by L. pneumophila, suggesting that host-derived ubiquitin-conjugating enzymes and ubiquitin ligases participate in the translocation of Legionella effector proteins and influence intracellular persistence and survival.
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Affiliation(s)
- Sze Ying Ong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Ralf Schuelein
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Rachelia R Wibawa
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Daniel W Thomas
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yanny Handoko
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Saskia Freytag
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Melanie Bahlo
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Elizabeth L Hartland
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
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26
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Schlüter D, Schulze-Niemand E, Stein M, Naumann M. Ovarian tumor domain proteases in pathogen infection. Trends Microbiol 2021; 30:22-33. [PMID: 34016513 DOI: 10.1016/j.tim.2021.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 01/06/2023]
Abstract
With the aim of overcoming host immune responses, and to permit persistence, numerous bacterial and viral pathogens have evolved effective strategies to control the activity of ovarian tumor domain proteases (OTUs), a group of deubiquitinylases crucial for regulating ubiquitin-modified proteins. Due to the important role of eukaryotic OTUs in cellular physiology, it is not surprising that pathogens have evolutionarily developed effector proteins which mimic host OTUs. Here, we focus on recent findings that illustrate how pathogen-encoded OTUs modulate eukaryotic host proteins and how they are implicated in cellular dysregulation. Further, we discuss the biological effects of OTUs in the context of structural features and pharmacological targeting. We point out the potentiality of selective OTU inhibitors, which shield ubiquitin-binding sites, as pharmacologic targets to treat harmful infections.
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Affiliation(s)
- Dirk Schlüter
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Eric Schulze-Niemand
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany; Molecular Simulations and Design Group, Max Planck Institute of Dynamic of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute of Dynamic of Complex Technical Systems, 39106 Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany.
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27
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Vozandychova V, Stojkova P, Hercik K, Rehulka P, Stulik J. The Ubiquitination System within Bacterial Host-Pathogen Interactions. Microorganisms 2021; 9:638. [PMID: 33808578 PMCID: PMC8003559 DOI: 10.3390/microorganisms9030638] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022] Open
Abstract
Ubiquitination of proteins, like phosphorylation and acetylation, is an important regulatory aspect influencing numerous and various cell processes, such as immune response signaling and autophagy. The study of ubiquitination has become essential to learning about host-pathogen interactions, and a better understanding of the detailed mechanisms through which pathogens affect ubiquitination processes in host cell will contribute to vaccine development and effective treatment of diseases. Pathogenic bacteria (e.g., Salmonella enterica, Legionella pneumophila and Shigella flexneri) encode many effector proteins, such as deubiquitinating enzymes (DUBs), targeting the host ubiquitin machinery and thus disrupting pertinent ubiquitin-dependent anti-bacterial response. We focus here upon the host ubiquitination system as an integral unit, its interconnection with the regulation of inflammation and autophagy, and primarily while examining pathogens manipulating the host ubiquitination system. Many bacterial effector proteins have already been described as being translocated into the host cell, where they directly regulate host defense processes. Due to their importance in pathogenic bacteria progression within the host, they are regarded as virulence factors essential for bacterial evasion. However, in some cases (e.g., Francisella tularensis) the host ubiquitination system is influenced by bacterial infection, although the responsible bacterial effectors are still unknown.
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Affiliation(s)
- Vera Vozandychova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
| | - Pavla Stojkova
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
| | - Kamil Hercik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 542/2, 16000 Prague, Czech Republic
| | - Pavel Rehulka
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
| | - Jiri Stulik
- Department of Molecular Pathology and Biology, Faculty of Military Health Sciences, University of Defence, Trebesska 1575, 50001 Hradec Kralove, Czech Republic; (V.V.); (P.S.); (K.H.); (P.R.)
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28
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Affiliation(s)
- Tyler G. Franklin
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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29
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Grishin A, Voth K, Gagarinova A, Cygler M. Structural biology of the invasion arsenal of Gram-negative bacterial pathogens. FEBS J 2021; 289:1385-1427. [PMID: 33650300 DOI: 10.1111/febs.15794] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/11/2021] [Accepted: 02/26/2021] [Indexed: 12/20/2022]
Abstract
In the last several years, there has been a tremendous progress in the understanding of host-pathogen interactions and the mechanisms by which bacterial pathogens modulate behavior of the host cell. Pathogens use secretion systems to inject a set of proteins, called effectors, into the cytosol of the host cell. These effectors are secreted in a highly regulated, temporal manner and interact with host proteins to modify a multitude of cellular processes. The number of effectors varies between pathogens from ~ 30 to as many as ~ 350. The functional redundancy of effectors encoded by each pathogen makes it difficult to determine the cellular effects or function of individual effectors, since their individual knockouts frequently produce no easily detectable phenotypes. Structural biology of effector proteins and their interactions with host proteins, in conjunction with cell biology approaches, has provided invaluable information about the cellular function of effectors and underlying molecular mechanisms of their modes of action. Many bacterial effectors are functionally equivalent to host proteins while being structurally divergent from them. Other effector proteins display new, previously unobserved functionalities. Here, we summarize the contribution of the structural characterization of effectors and effector-host protein complexes to our understanding of host subversion mechanisms used by the most commonly investigated Gram-negative bacterial pathogens. We describe in some detail the enzymatic activities discovered among effector proteins and how they affect various cellular processes.
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Affiliation(s)
- Andrey Grishin
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Kevin Voth
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Alla Gagarinova
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology, & Immunology, University of Saskatchewan, Saskatoon, Canada
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30
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Price CT, Abu Kwaik Y. Evolution and Adaptation of Legionella pneumophila to Manipulate the Ubiquitination Machinery of Its Amoebae and Mammalian Hosts. Biomolecules 2021; 11:biom11010112. [PMID: 33467718 PMCID: PMC7830128 DOI: 10.3390/biom11010112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin pathway is highly conserved across the eukaryotic domain of life and plays an essential role in a plethora of cellular processes. It is not surprising that many intracellular bacterial pathogens often target the essential host ubiquitin pathway. The intracellular bacterial pathogen Legionella pneumophila injects into the host cell cytosol multiple classes of classical and novel ubiquitin-modifying enzymes that modulate diverse ubiquitin-related processes in the host cell. Most of these pathogen-injected proteins, designated as effectors, mimic known E3-ubiquitin ligases through harboring F-box or U-box domains. The classical F-box effector, AnkB targets host proteins for K48-linked polyubiquitination, which leads to excessive proteasomal degradation that is required to generate adequate supplies of amino acids for metabolism of the pathogen. In contrast, the SidC and SdcA effectors share no structural similarity to known eukaryotic ligases despite having E3-ubiquitin ligase activity, suggesting that the number of E3-ligases in eukaryotes is under-represented. L. pneumophila also injects into the host many novel ubiquitin-modifying enzymes, which are the SidE family of effectors that catalyze phosphoribosyl-ubiquitination of serine residue of target proteins, independently of the canonical E1-2-3 enzymatic cascade. Interestingly, the environmental bacterium, L. pneumophila, has evolved within a diverse range of amoebal species, which serve as the natural hosts, while accidental transmission through contaminated aerosols can cause pneumonia in humans. Therefore, it is likely that the novel ubiquitin-modifying enzymes of L. pneumophila were acquired by the pathogen through interkingdom gene transfer from the diverse natural amoebal hosts. Furthermore, conservation of the ubiquitin pathway across eukaryotes has enabled these novel ubiquitin-modifying enzymes to function similarly in mammalian cells. Studies on the biological functions of these effectors are likely to reveal further novel ubiquitin biology and shed further lights on the evolution of ubiquitin.
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Affiliation(s)
- Christopher T.D. Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA;
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA;
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, KY 40202, USA
- Correspondence:
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31
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Shin D, Bhattacharya A, Cheng YL, Alonso MC, Mehdipour AR, van der Heden van Noort GJ, Ovaa H, Hummer G, Dikic I. Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 2020; 9:58277. [PMID: 33185526 PMCID: PMC7690952 DOI: 10.7554/elife.58277] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 11/12/2020] [Indexed: 12/16/2022] Open
Abstract
Legionella pneumophila causes a severe pneumonia known as Legionnaires' disease. During the infection, Legionella injects more than 300 effector proteins into host cells. Among them are enzymes involved in altering the host-ubiquitination system. Here, we identified two LegionellaOTU (ovarian tumor)-like deubiquitinases (LOT-DUBs; LotB [Lpg1621/Ceg23] and LotC [Lpg2529]). The crystal structure of the LotC catalytic core (LotC14-310) was determined at 2.4 Å. Unlike the classical OTU-family, the LOT-family shows an extended helical lobe between the Cys-loop and the variable loop, which defines them as a unique class of OTU-DUBs. LotB has an additional ubiquitin-binding site (S1'), which enables the specific cleavage of Lys63-linked polyubiquitin chains. By contrast, LotC only contains the S1 site and cleaves different species of ubiquitin chains. MS analysis of LotB and LotC identified different categories of host-interacting proteins and substrates. Together, our results provide new structural insights into bacterial OTU-DUBs and indicate distinct roles in host-pathogen interactions.
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Affiliation(s)
- Donghyuk Shin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany.,Department of Nano-Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Anshu Bhattacharya
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Yi-Lin Cheng
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Marta Campos Alonso
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | | | | | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, Netherlands
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany.,Max Planck Institute of Biophysics, Frankfurt, Germany
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32
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Liu S, Luo J, Zhen X, Qiu J, Ouyang S, Luo ZQ. Interplay between bacterial deubiquitinase and ubiquitin E3 ligase regulates ubiquitin dynamics on Legionella phagosomes. eLife 2020; 9:58114. [PMID: 33136002 PMCID: PMC7669269 DOI: 10.7554/elife.58114] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/01/2020] [Indexed: 12/12/2022] Open
Abstract
Legionella pneumophila extensively modulates the host ubiquitin network to create the Legionella-containing vacuole (LCV) for its replication. Many of its virulence factors function as ubiquitin ligases or deubiquitinases (DUBs). Here, we identify Lem27 as a DUB that displays a preference for diubiquitin formed by K6, K11, or K48. Lem27 is associated with the LCV where it regulates Rab10 ubiquitination in concert with SidC and SdcA, two bacterial E3 ubiquitin ligases. Structural analysis of the complex formed by an active fragment of Lem27 and the substrate-based suicide inhibitor ubiquitin-propargylamide (PA) reveals that it harbors a fold resembling those in the OTU1 DUB subfamily with a Cys-His catalytic dyad and that it recognizes ubiquitin via extensive hydrogen bonding at six contact sites. Our results establish Lem27 as a DUB that functions to regulate protein ubiquitination on L. pneumophila phagosomes by counteracting the activity of bacterial ubiquitin E3 ligases.
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Affiliation(s)
- Shuxin Liu
- Department of Respiratory Medicine and Center of Infection and Immunity, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital, Jilin University, Changchun, China
| | - Jiwei Luo
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xiangkai Zhen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Zhao-Qing Luo
- Department of Respiratory Medicine and Center of Infection and Immunity, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital, Jilin University, Changchun, China.,Department of Biological Sciences, Purdue University, West Lafayette, United States
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33
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Abstract
Through coevolution with host cells, microorganisms have acquired mechanisms to avoid the detection by the host surveillance system and to use the cell's supplies to establish themselves. Indeed, certain pathogens have evolved proteins that imitate specific eukaryotic cell proteins, allowing them to manipulate host pathways, a phenomenon termed molecular mimicry. Bacterial "eukaryotic-like proteins" are a remarkable example of molecular mimicry. They are defined as proteins that strongly resemble eukaryotic proteins or that carry domains that are predominantly present in eukaryotes and that are generally absent from prokaryotes. The widest diversity of eukaryotic-like proteins known to date can be found in members of the bacterial genus Legionella, some of which cause a severe pneumonia in humans. The characterization of a number of these proteins shed light on their importance during infection. The subsequent identification of eukaryotic-like genes in the genomes of other amoeba-associated bacteria and bacterial symbionts suggested that eukaryotic-like proteins are a common means of bacterial evasion and communication, shaped by the continuous interactions between bacteria and their protozoan hosts. In this review, we discuss the concept of molecular mimicry using Legionella as an example and show that eukaryotic-like proteins effectively manipulate host cell pathways. The study of the function and evolution of such proteins is an exciting field of research that is leading us toward a better understanding of the complex world of bacterium-host interactions. Ultimately, this knowledge will teach us how host pathways are manipulated and how infections may possibly be tackled.
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34
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Kitao T, Nagai H, Kubori T. Divergence of Legionella Effectors Reversing Conventional and Unconventional Ubiquitination. Front Cell Infect Microbiol 2020; 10:448. [PMID: 32974222 PMCID: PMC7472693 DOI: 10.3389/fcimb.2020.00448] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/21/2020] [Indexed: 02/05/2023] Open
Abstract
The intracellular bacterial pathogen Legionella pneumophila employs bacteria-derived effector proteins in a variety of functions to exploit host cellular systems. The ubiquitination machinery constitutes a crucial eukaryotic system for the regulation of numerous cellular processes, and is a representative target for effector-mediated bacterial manipulation. L. pneumophila transports over 300 effector proteins into host cells through its Dot/Icm type IV secretion system. Among these, several effector proteins have been found to function as ubiquitin ligases, including unprecedented enzymes that catalyze ubiquitination through unconventional mechanisms. Recent studies have identified many L. pneumophila effector proteins that can interfere with ubiquitination. These effectors include proteins that are distantly related to the ovarian tumor protein superfamily described as deubiquitinases (DUBs), which regulate important signaling cascades in human cells. Intriguingly, L. pneumophila DUBs are not limited to enzymes that exhibit canonical DUB activity. Some L. pneumophila DUBs can catalyze the cleavage of the unconventional linkage between ubiquitin and substrates. Furthermore, novel mechanisms have been found that adversely affect the function of specific ubiquitin ligases; for instance, effector-mediated posttranslational modifications of ubiquitin ligases result in the inhibition of their activity. In the context of L. pneumophila infection, the existence of enzymes that reverse ubiquitination primarily relates to a fine tuning of biogenesis and remodeling of the Legionella-containing vacuole as a replicative niche. The complexity of the effector arrays reflects sophisticated strategies that bacteria have adopted to adapt their host environment and enable their survival in host cells. This review summarizes the current state of knowledge on the divergent mechanisms of the L. pneumophila effectors that can reverse ubiquitination, which is mediated by other effectors as well as the host ubiquitin machinery.
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Affiliation(s)
- Tomoe Kitao
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Hiroki Nagai
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
| | - Tomoko Kubori
- Department of Microbiology, Graduate School of Medicine, Gifu University, Gifu, Japan
- G-CHAIN, Gifu University, Gifu, Japan
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35
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Schubert AF, Nguyen JV, Franklin TG, Geurink PP, Roberts CG, Sanderson DJ, Miller LN, Ovaa H, Hofmann K, Pruneda JN, Komander D. Identification and characterization of diverse OTU deubiquitinases in bacteria. EMBO J 2020; 39:e105127. [PMID: 32567101 PMCID: PMC7396840 DOI: 10.15252/embj.2020105127] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
Manipulation of host ubiquitin signaling is becoming an increasingly apparent evolutionary strategy among bacterial and viral pathogens. By removing host ubiquitin signals, for example, invading pathogens can inactivate immune response pathways and evade detection. The ovarian tumor (OTU) family of deubiquitinases regulates diverse ubiquitin signals in humans. Viral pathogens have also extensively co-opted the OTU fold to subvert host signaling, but the extent to which bacteria utilize the OTU fold was unknown. We have predicted and validated a set of OTU deubiquitinases encoded by several classes of pathogenic bacteria. Biochemical assays highlight the ubiquitin and polyubiquitin linkage specificities of these bacterial deubiquitinases. By determining the ubiquitin-bound structures of two examples, we demonstrate the novel strategies that have evolved to both thread an OTU fold and recognize a ubiquitin substrate. With these new examples, we perform the first cross-kingdom structural analysis of the OTU fold that highlights commonalities among distantly related OTU deubiquitinases.
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Affiliation(s)
- Alexander F Schubert
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of Structural BiologyGenentech Inc.South San FranciscoCAUSA
| | - Justine V Nguyen
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Tyler G Franklin
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Paul P Geurink
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Cameron G Roberts
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Daniel J Sanderson
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Lauren N Miller
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - Huib Ovaa
- Oncode Institute & Department of Cell and Chemical BiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Kay Hofmann
- Institute for GeneticsUniversity of CologneCologneGermany
| | - Jonathan N Pruneda
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
- Department of Molecular Microbiology & ImmunologyOregon Health & Science UniversityPortlandORUSA
| | - David Komander
- Medical Research Council Laboratory of Molecular BiologyCambridgeUK
- Ubiquitin Signalling DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Medical BiologyThe University of MelbourneMelbourneVICAustralia
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36
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Hermanns T, Woiwode I, Guerreiro RF, Vogt R, Lammers M, Hofmann K. An evolutionary approach to systematic discovery of novel deubiquitinases, applied to Legionella. Life Sci Alliance 2020; 3:3/9/e202000838. [PMID: 32719160 PMCID: PMC7391069 DOI: 10.26508/lsa.202000838] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/19/2022] Open
Abstract
The analysis of the relationships between different deubiquitinase classes leads to the definition of an aromatic “gatekeeper” motif that distinguishes DUBs from other cysteine proteases and helps to predict new bacterial DUBs. Deubiquitinating enzymes (DUBs) are important regulators of the posttranslational protein ubiquitination system. Mammalian genomes encode about 100 different DUBs, which can be grouped into seven different classes. Members of other DUB classes are found in pathogenic bacteria, which use them to target the host defense. By combining bioinformatical and experimental approaches, we address the question if the known DUB families have a common evolutionary ancestry and share conserved features that set them apart from other proteases. By systematically comparing family-specific hidden Markov models, we uncovered distant relationships between established DUBs and other cysteine protease families. Most DUB families share a conserved aromatic residue linked to the active site, which restricts the cleavage of substrates with side chains at the S2 position, corresponding to Gly-75 in ubiquitin. By applying these criteria to Legionella pneumophila ORFs, we identified lpg1621 and lpg1148 as deubiquitinases, characterized their cleavage specificities, and confirmed the importance of the aromatic gatekeeper motif for substrate selection.
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Affiliation(s)
- Thomas Hermanns
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Ilka Woiwode
- Institute for Genetics, University of Cologne, Cologne, Germany
| | | | - Robert Vogt
- Institute of Biochemistry, Synthetic and Structural Biochemistry, University of Greifswald, Greifswald, Germany
| | - Michael Lammers
- Institute of Biochemistry, Synthetic and Structural Biochemistry, University of Greifswald, Greifswald, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
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Berglund J, Gjondrekaj R, Verney E, Maupin-Furlow JA, Edelmann MJ. Modification of the host ubiquitome by bacterial enzymes. Microbiol Res 2020; 235:126429. [PMID: 32109687 PMCID: PMC7369425 DOI: 10.1016/j.micres.2020.126429] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/03/2020] [Accepted: 02/09/2020] [Indexed: 12/14/2022]
Abstract
Attachment of ubiquitin molecules to protein substrates is a reversible post-translational modification (PTM), which occurs ubiquitously in eukaryotic cells and controls most cellular processes. As a consequence, ubiquitination is an attractive target of pathogen-encoded virulence factors. Pathogenic bacteria have evolved multiple mechanisms to hijack the host's ubiquitin system to their advantage. In this review, we discuss the bacteria-encoded E3 ligases and deubiquitinases translocated to the host for an addition or removal of eukaryotic ubiquitin modification, effectively hijacking the host's ubiquitination processes. We review bacterial enzymes homologous to host proteins in sequence and functions, as well as enzymes with novel mechanisms in ubiquitination, which have significant structural differences in comparison to the mammalian E3 ligases. Finally, we will also discuss examples of molecular "counter-weapons" - eukaryotic proteins, which counteract pathogen-encoded E3 ligases. The many examples of the pathogen effector molecules that catalyze eukaryotic ubiquitin modification bring to light the intricate pathways involved in the pathogenesis of some of the most virulent bacterial infections with human pathogens. The role of these effector molecules remains an essential determinant of bacterial virulence in terms of infection, invasion, and replication. A comprehensive understanding of the mechanisms dictating the mimicry employed by bacterial pathogens is of vital importance in developing new strategies for therapeutic approaches.
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Affiliation(s)
- Jennifer Berglund
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Rafaela Gjondrekaj
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Ellen Verney
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA
| | - Mariola J Edelmann
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 1355 Museum Drive, Gainesville, 32611-0700, FL USA.
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38
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Bacterial DUBs: deubiquitination beyond the seven classes. Biochem Soc Trans 2020; 47:1857-1866. [PMID: 31845741 DOI: 10.1042/bst20190526] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022]
Abstract
Protein ubiquitination is a posttranslational modification that regulates many aspects of cellular life, including proteostasis, vesicular trafficking, DNA repair and NF-κB activation. By directly targeting intracellular bacteria or bacteria-containing vacuoles to the lysosome, ubiquitination is also an important component of cell-autonomous immunity. Not surprisingly, several pathogenic bacteria encode deubiquitinases (DUBs) and use them as secreted effectors that prevent ubiquitination of bacterial components. A systematic overview of known bacterial DUBs, including their cleavage specificities and biological roles, suggests multiple independent acquisition events from host-encoded DUBs and other proteases. The widely used classification of DUBs into seven well-defined families should only be applied to eukaryotic DUBs, since several bacterial DUBs do not follow this classification.
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Gan N, Guan H, Huang Y, Yu T, Fu J, Nakayasu ES, Puvar K, Das C, Wang D, Ouyang S, Luo Z. Legionella pneumophila regulates the activity of UBE2N by deamidase-mediated deubiquitination. EMBO J 2020; 39:e102806. [PMID: 31825121 PMCID: PMC7024838 DOI: 10.15252/embj.2019102806] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 12/21/2022] Open
Abstract
The Legionella pneumophila effector MavC induces ubiquitination of the E2 ubiquitin-conjugating enzyme UBE2N by transglutamination, thereby abolishing its function in the synthesis of K63 -type polyubiquitin chains. The inhibition of UBE2N activity creates a conundrum because this E2 enzyme is important in multiple signaling pathways, including some that are important for intracellular L. pneumophila replication. Here, we show that prolonged inhibition of UBE2N activity by MavC restricts intracellular bacterial replication and that the activity of UBE2N is restored by MvcA, an ortholog of MavC (50% identity) with ubiquitin deamidase activity. MvcA functions to deubiquitinate UBE2N-Ub using the same catalytic triad required for its deamidase activity. Structural analysis of the MvcA-UBE2N-Ub complex reveals a crucial role of the insertion domain in MvcA in substrate recognition. Our study establishes a deubiquitination mechanism catalyzed by a deamidase, which, together with MavC, imposes temporal regulation of the activity of UBE2N during L. pneumophila infection.
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Affiliation(s)
- Ninghai Gan
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Hongxin Guan
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Yini Huang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Ting Yu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Jiaqi Fu
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Ernesto S Nakayasu
- Biological Science DivisionPacific Northwest National LaboratoryRichlandWAUSA
| | - Kedar Puvar
- Department of ChemistryPurdue UniversityWest LafayetteINUSA
| | | | - Dongmei Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Songying Ouyang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic RegulationThe Key Laboratory of Innate Immune Biology of Fujian ProvinceBiomedical Research Center of South ChinaKey Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of EducationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Laboratory for Marine Biology and BiotechnologyPilot National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Zhao‐Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
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Ma K, Zhen X, Zhou B, Gan N, Cao Y, Fan C, Ouyang S, Luo ZQ, Qiu J. The bacterial deubiquitinase Ceg23 regulates the association of Lys-63-linked polyubiquitin molecules on the Legionella phagosome. J Biol Chem 2020; 295:1646-1657. [PMID: 31907282 PMCID: PMC7008378 DOI: 10.1074/jbc.ra119.011758] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/19/2019] [Indexed: 01/07/2023] Open
Abstract
Legionella pneumophila is the causative agent of the lung malady Legionnaires' disease, it modulates host function to create a niche termed the Legionella-containing vacuole (LCV) that permits intracellular L. pneumophila replication. One important aspect of such modulation is the co-option of the host ubiquitin network with a panel of effector proteins. Here, using recombinantly expressed and purified proteins, analytic ultracentrifugation, structural analysis, and computational modeling, along with deubiquitinase (DUB), and bacterial infection assays, we found that the bacterial defective in organelle trafficking/intracellular multiplication effector Ceg23 is a member of the ovarian tumor (OTU) DUB family. We found that Ceg23 displays high specificity toward Lys-63-linked polyubiquitin chains and is localized on the LCV, where it removes ubiquitin moieties from proteins ubiquitinated by the Lys-63-chain type. Analysis of the crystal structure of a Ceg23 variant lacking two putative transmembrane domains at 2.80 Å resolution revealed that despite very limited homology to established members of the OTU family at the primary sequence level, Ceg23 harbors a catalytic motif resembling those associated with typical OTU-type DUBs. ceg23 deletion increased the association of Lys-63-linked polyubiquitin with the bacterial phagosome, indicating that Ceg23 regulates Lys-63-linked ubiquitin signaling on the LCV. In summary, our findings indicate that Ceg23 contributes to the regulation of the association of Lys-63 type polyubiquitin with the Legionella phagosome. Future identification of host substrates targeted by Ceg23 could clarify the roles of these polyubiquitin chains in the intracellular life cycle of L. pneumophila and Ceg23's role in bacterial virulence.
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Affiliation(s)
- Kelong Ma
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiangkai Zhen
- Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Biao Zhou
- Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Ninghai Gan
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Chengpeng Fan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Songying Ouyang
- Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907.
| | - Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.
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Mondino S, Schmidt S, Rolando M, Escoll P, Gomez-Valero L, Buchrieser C. Legionnaires’ Disease: State of the Art Knowledge of Pathogenesis Mechanisms of Legionella. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:439-466. [DOI: 10.1146/annurev-pathmechdis-012419-032742] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Legionella species are environmental gram-negative bacteria able to cause a severe form of pneumonia in humans known as Legionnaires’ disease. Since the identification of Legionella pneumophila in 1977, four decades of research on Legionella biology and Legionnaires’ disease have brought important insights into the biology of the bacteria and the molecular mechanisms that these intracellular pathogens use to cause disease in humans. Nowadays, Legionella species constitute a remarkable model of bacterial adaptation, with a genus genome shaped by their close coevolution with amoebae and an ability to exploit many hosts and signaling pathways through the secretion of a myriad of effector proteins, many of which have a eukaryotic origin. This review aims to discuss current knowledge of Legionella infection mechanisms and future research directions to be taken that might answer the many remaining open questions. This research will without a doubt be a terrific scientific journey worth taking.
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Affiliation(s)
- Sonia Mondino
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Silke Schmidt
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
- Sorbonne Université, Collège doctoral, 75005 Paris, France
| | - Monica Rolando
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Pedro Escoll
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, CNRS UMR 3525, 75015 Paris, France;, , , , ,
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42
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Study of Legionella Effector Domains Revealed Novel and Prevalent Phosphatidylinositol 3-Phosphate Binding Domains. Infect Immun 2019; 87:IAI.00153-19. [PMID: 30962397 DOI: 10.1128/iai.00153-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/27/2019] [Indexed: 12/31/2022] Open
Abstract
Legionella pneumophila and other Legionella species replicate intracellularly using the Icm/Dot type IV secretion system. In L. pneumophila this system translocates >300 effectors into host cells and in the Legionella genus thousands of effectors were identified, the function of most of which is unknown. Fourteen L. pneumophila effectors were previously shown to specifically bind phosphoinositides (PIs) using dedicated domains. We found that PI-binding domains of effectors are usually not homologous to one another; they are relatively small and located at the effectors' C termini. We used the previously identified Legionella effector domains (LEDs) with unknown function and the above characteristics of effector PI-binding domains to discover novel PI-binding LEDs. We identified three predicted PI-binding LEDs that are present in 14 L. pneumophila effectors and in >200 effectors in the Legionella genus. Using an in vitro protein-lipid overlay assay, we found that 11 of these L. pneumophila effectors specifically bind phosphatidylinositol 3-phosphate (PI3P), almost doubling the number of L. pneumophila effectors known to bind PIs. Further, we identified in each of these newly discovered PI3P-binding LEDs conserved, mainly positively charged, amino acids that are essential for PI3P binding. Our results indicate that Legionella effectors harbor unique domains, shared by many effectors, which directly mediate PI3P binding.
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43
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Pike CM, Boyer-Andersen R, Kinch LN, Caplan JL, Neunuebel MR. The Legionella effector RavD binds phosphatidylinositol-3-phosphate and helps suppress endolysosomal maturation of the Legionella-containing vacuole. J Biol Chem 2019; 294:6405-6415. [PMID: 30733336 PMCID: PMC6484141 DOI: 10.1074/jbc.ra118.007086] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Indexed: 12/25/2022] Open
Abstract
Upon phagocytosis into macrophages, the intracellular bacterial pathogen Legionella pneumophila secretes effector proteins that manipulate host cell components, enabling it to evade lysosomal degradation. However, the bacterial proteins involved in this evasion are incompletely characterized. Here we show that the L. pneumophila effector protein RavD targets host membrane compartments and contributes to the molecular mechanism the pathogen uses to prevent encounters with lysosomes. Protein-lipid binding assays revealed that RavD selectively binds phosphatidylinositol-3-phosphate (PI(3)P) in vitro We further determined that a C-terminal RavD region mediates the interaction with PI(3)P and that this interaction requires Arg-292. In transiently transfected mammalian cells, mCherry-RavD colocalized with the early endosome marker EGFP-Rab5 as well as the PI(3)P biosensor EGFP-2×FYVE. However, treatment with the phosphoinositide 3-kinase inhibitor wortmannin did not disrupt localization of mCherry-RavD to endosomal compartments, suggesting that RavD's interaction with PI(3)P is not necessary to anchor RavD to endosomal membranes. Using superresolution and immunogold transmission EM, we observed that, upon translocation into macrophages, RavD was retained onto the Legionella-containing vacuole and was also present on small vesicles adjacent to the vacuole. We also report that despite no detectable effects on intracellular growth of L. pneumophila within macrophages or amebae, the lack of RavD significantly increased the number of vacuoles that accumulate the late endosome/lysosome marker LAMP-1 during macrophage infection. Together, our findings suggest that, although not required for intracellular replication of L. pneumophila, RavD is a part of the molecular mechanism that steers the Legionella-containing vacuole away from endolysosomal maturation pathways.
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Affiliation(s)
| | | | - Lisa N Kinch
- the Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Jeffrey L Caplan
- From the Delaware Biotechnology Institute and
- Departments of Biological Sciences and
- Plant and Soil Sciences, University of Delaware, Newark, Delaware 19716 and
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44
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Emerging insights into bacterial deubiquitinases. Curr Opin Microbiol 2019; 47:14-19. [DOI: 10.1016/j.mib.2018.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 02/01/2023]
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