51
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CYRI/FAM49B negatively regulates RAC1-driven cytoskeletal remodelling and protects against bacterial infection. Nat Microbiol 2019; 4:1516-1531. [PMID: 31285585 DOI: 10.1038/s41564-019-0484-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 05/08/2019] [Indexed: 12/20/2022]
Abstract
Salmonella presents a global public health concern. Central to Salmonella pathogenicity is an ability to subvert host defences through strategically targeting host proteins implicated in restricting infection. Therefore, to gain insight into the host-pathogen interactions governing Salmonella infection, we performed an in vivo genome-wide mutagenesis screen to uncover key host defence proteins. This revealed an uncharacterized role of CYRI (FAM49B) in conferring host resistance to Salmonella infection. We show that CYRI binds to the small GTPase RAC1 through a conserved domain present in CYFIP proteins, which are known RAC1 effectors that stimulate actin polymerization. However, unlike CYFIP proteins, CYRI negatively regulates RAC1 signalling, thereby attenuating processes such as macropinocytosis, phagocytosis and cell migration. This enables CYRI to counteract Salmonella at various stages of infection, including bacterial entry into non-phagocytic and phagocytic cells as well as phagocyte-mediated bacterial dissemination. Intriguingly, to dampen its effects, the bacterial effector SopE, a RAC1 activator, selectively targets CYRI following infection. Together, this outlines an intricate host-pathogen signalling interplay that is crucial for determining bacterial fate. Notably, our study also outlines a role for CYRI in restricting infection mediated by Mycobacterium tuberculosis and Listeria monocytogenes. This provides evidence implicating CYRI cellular functions in host defence beyond Salmonella infection.
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52
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Ludwicki MB, Li J, Stephens EA, Roberts RW, Koide S, Hammond PT, DeLisa MP. Broad-Spectrum Proteome Editing with an Engineered Bacterial Ubiquitin Ligase Mimic. ACS CENTRAL SCIENCE 2019; 5:852-866. [PMID: 31139721 PMCID: PMC6535771 DOI: 10.1021/acscentsci.9b00127] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Indexed: 05/03/2023]
Abstract
Manipulation of the ubiquitin-proteasome pathway to achieve targeted silencing of cellular proteins has emerged as a reliable and customizable strategy for remodeling the mammalian proteome. One such approach involves engineering bifunctional proteins called ubiquibodies that are comprised of a synthetic binding protein fused to an E3 ubiquitin ligase, thus enabling post-translational ubiquitination and degradation of a target protein independent of its function. Here, we have designed a panel of new ubiquibodies based on E3 ubiquitin ligase mimics from bacterial pathogens that are capable of effectively interfacing with the mammalian proteasomal degradation machinery for selective removal of proteins of interest. One of these, the Shigella flexneri effector protein IpaH9.8 fused to a fibronectin type III (FN3) monobody that specifically recognizes green fluorescent protein (GFP), was observed to potently eliminate GFP and its spectral derivatives as well as 15 different FP-tagged mammalian proteins that varied in size (27-179 kDa) and subcellular localization (cytoplasm, nucleus, membrane-associated, and transmembrane). To demonstrate therapeutically relevant delivery of ubiquibodies, we leveraged a bioinspired molecular assembly method whereby synthetic mRNA encoding the GFP-specific ubiquibody was coassembled with poly A binding proteins and packaged into nanosized complexes using biocompatible, structurally defined polypolypeptides bearing cationic amine side groups. The resulting nanoplexes delivered ubiquibody mRNA in a manner that caused efficient target depletion in cultured mammalian cells stably expressing GFP as well as in transgenic mice expressing GFP ubiquitously. Overall, our results suggest that IpaH9.8-based ubiquibodies are a highly modular proteome editing technology with the potential for pharmacologically modulating disease-causing proteins.
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Affiliation(s)
- Morgan B. Ludwicki
- Robert F. Smith
School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New
York 14853, United
States
| | - Jiahe Li
- Department of Chemical Engineering and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Erin A. Stephens
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Richard W. Roberts
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University
Langone Medical Center, New York, New York 10016, United States
- Department of Biochemistry and Molecular
Pharmacology, New York University School
of Medicine, New York, New York 10016, United States
| | - Paula T. Hammond
- Department of Chemical Engineering and Koch Institute for
Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Matthew P. DeLisa
- Robert F. Smith
School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New
York 14853, United
States
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
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53
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Qiu J, Luo ZQ. Methods for NAD-Dependent Ubiquitination Catalyzed by Legionella pneumophila Effector Proteins. Methods Mol Biol 2019; 1844:33-38. [PMID: 30242701 DOI: 10.1007/978-1-4939-8706-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ubiquitination is one of the most important posttranslational modifications in eukaryotic cells where it regulates the activity, cellular localization, and half-life of proteins. Ubiquitination thus affects many essential cellular processes, including vesicle trafficking, cell cycle, DNA repair, immune response, and protein homeostasis. The ubiquitin system is exclusive to eukaryotes; however, pathogenic bacteria have developed effective strategies to influence the host ubiquitin system for their own benefit. Legionella pneumophila is the causative agent of Legionnaires' disease, a severe form of pneumonia. This bacterium utilizes a type IV secretion system to translocate more than 300 effector proteins into host cells. These virulence factors modulate a wide spectrum of host processes to support its intracellular survival and replication. Hijacking of host ubiquitin system is an important theme in Legionella virulence, and a number of L. pneumophila effector proteins have been shown to possess ubiquitin ligase or deubiquitinase activity. Among these, members of the SidE family effector proteins (SidEs) catalyze ubiquitination of several ER-associated Rab small GTPases by a mechanism that bypasses the requirement of ATP and the E1, E2 enzymes. Here, we summarize the experimental details of Rab small GTPases ubiquitination catalyzed by SdeA, a member of the SidE family.
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Affiliation(s)
- Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, USA.
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54
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Zhang W, Sidhu SS. Generating Intracellular Modulators of E3 Ligases and Deubiquitinases from Phage-Displayed Ubiquitin Variant Libraries. Methods Mol Biol 2019; 1844:101-119. [PMID: 30242706 DOI: 10.1007/978-1-4939-8706-1_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ubiquitination is a posttranslational protein modification pathway regulating diverse cellular processes that are implicated in numerous human diseases. However, targeting the enzymes in the ubiquitination cascade potently and selectively remains a major challenge. Recently we devised a methodology to generate ubiquitin-based modulators for E3 ligases and deubiquitinases, enzymes that control the specificity of protein ubiquitination and deubiquitination, respectively. Here, we describe methods to generate libraries of ubiquitin variants and perform phage display selections to isolate high-affinity binders for target proteins. Importantly, the strategy introduced here can be applied to other small protein domains mediating protein-protein interactions to engineer tools for target validation and potential therapeutic development.
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Affiliation(s)
- Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada. .,Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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55
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Ubiquitination-Mediated Inflammasome Activation during Bacterial Infection. Int J Mol Sci 2019; 20:ijms20092110. [PMID: 31035661 PMCID: PMC6539186 DOI: 10.3390/ijms20092110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammasome activation is essential for host immune responses during pathogenic infection and sterile signals insult, whereas excessive activation is injurious. Thus, inflammasome activation is tightly regulated at multiple layers. Ubiquitination is an important post-translational modification for orchestrating inflammatory immune responses during pathogenic infection, and a major target hijacked by pathogenic bacteria for promoting their survival and proliferation. This review summarizes recent insights into distinct mechanisms of the inflammasome activation and ubiquitination process triggered by bacterial infection. We discuss the complex regulatory of inflammasome activation mediated by ubiquitination machinery during bacterial infection, and provide therapeutic approaches for specifically targeting aberrant inflammasome activation.
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56
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Song L, Luo ZQ. Post-translational regulation of ubiquitin signaling. J Cell Biol 2019; 218:1776-1786. [PMID: 31000580 PMCID: PMC6548142 DOI: 10.1083/jcb.201902074] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 12/22/2022] Open
Abstract
Song and Luo review the roles of post-translational modifications in ubiquitin signaling. Ubiquitination regulates many essential cellular processes in eukaryotes. This post-translational modification (PTM) is typically achieved by E1, E2, and E3 enzymes that sequentially catalyze activation, conjugation, and ligation reactions, respectively, leading to covalent attachment of ubiquitin, usually to lysine residues of substrate proteins. Ubiquitin can also be successively linked to one of the seven lysine residues on ubiquitin to form distinctive forms of polyubiquitin chains, which, depending upon the lysine used and the length of the chains, dictate the fate of substrate proteins. Recent discoveries revealed that this ubiquitin code is further expanded by PTMs such as phosphorylation, acetylation, deamidation, and ADP-ribosylation, on ubiquitin, components of the ubiquitination machinery, or both. These PTMs provide additional regulatory nodes to integrate development or insulting signals with cellular homeostasis. Understanding the precise roles of these PTMs in the regulation of ubiquitin signaling will provide new insights into the mechanisms and treatment of various human diseases linked to ubiquitination, including neurodegenerative diseases, cancer, infection, and immune disorders.
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Affiliation(s)
- Lei Song
- Department of Respiratory Medicine and Center of Infection and Immunity, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Department of Respiratory Medicine and Center of Infection and Immunity, The First Hospital of Jilin University, Changchun, China .,Purdue Institute for Inflammation, Immunology and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN
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57
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Sandstrom A, Mitchell PS, Goers L, Mu EW, Lesser CF, Vance RE. Functional degradation: A mechanism of NLRP1 inflammasome activation by diverse pathogen enzymes. Science 2019; 364:science.aau1330. [PMID: 30872533 PMCID: PMC6532986 DOI: 10.1126/science.aau1330] [Citation(s) in RCA: 254] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/05/2018] [Accepted: 03/05/2019] [Indexed: 12/14/2022]
Abstract
Inflammasomes are multiprotein platforms that initiate innate immunity by recruitment and activation of caspase-1. The NLRP1B inflammasome is activated upon direct cleavage by the anthrax lethal toxin protease. However, the mechanism by which cleavage results in NLRP1B activation is unknown. In this study, we find that cleavage results in proteasome-mediated degradation of the amino-terminal domains of NLRP1B, liberating a carboxyl-terminal fragment that is a potent caspase-1 activator. Proteasome-mediated degradation of NLRP1B is both necessary and sufficient for NLRP1B activation. Consistent with our functional degradation model, we identify IpaH7.8, a Shigella flexneri ubiquitin ligase secreted effector, as an enzyme that induces NLRP1B degradation and activation. Our results provide a unified mechanism for NLRP1B activation by diverse pathogen-encoded enzymatic activities.
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Affiliation(s)
- Andrew Sandstrom
- Division of Immunology and Pathogenesis, Department of Molecular & Cell Biology, and Cancer Research Laboratory, University of California, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Patrick S Mitchell
- Division of Immunology and Pathogenesis, Department of Molecular & Cell Biology, and Cancer Research Laboratory, University of California, Berkeley, CA, USA
| | - Lisa Goers
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Edward W Mu
- Division of Immunology and Pathogenesis, Department of Molecular & Cell Biology, and Cancer Research Laboratory, University of California, Berkeley, CA, USA
| | - Cammie F Lesser
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Russell E Vance
- Division of Immunology and Pathogenesis, Department of Molecular & Cell Biology, and Cancer Research Laboratory, University of California, Berkeley, CA, USA. .,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
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58
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Qiu J, Luo ZQ. Methods to study phosphoribosylated ubiquitin ligation and removal. Methods Enzymol 2019; 618:149-166. [PMID: 30850050 DOI: 10.1016/bs.mie.2019.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ubiquitination is a prevalent protein modification catalyzed by E1, E2, and E3 enzymes that activate, conjugate, and ligate, respectively, the ubiquitin protein to substrate protein. In order to establish a mutualistic or parasitic relationship with their eukaryotic hosts, many microorganisms hijack different aspects of the ubiquitination machinery using bacterial proteins that function as E3 ligases or as enzymes that modify E2s or ubiquitin. Recently, the SidE family of effector proteins (SidEs) from the intracellular bacterial pathogen Legionella pneumophila was found to catalyze ubiquitination by a mechanism unrelated to the classical three-enzyme cascade. Instead of utilizing ATP, SidEs-catalyzed ubiquitination reactions are energized by nicotinamide adenine dinucleotide (NAD). Ubiquitin is first activated by ADP-ribosylation at residue Arg42 to form ADP-ribosylated ubiquitin (ADPR-Ub). ADPR-Ub is then cleaved by an activity conferred by a phosphodiesterase (PDE)-related domain also embedded in the SidE family proteins. ADPR-Ub cleavage is coupled to covalent attachment of phosphoribosylated ubiquitin to serine residues of target proteins and the release of AMP. Furthermore, SidE-induced ubiquitination can be reversed by SidJ, another virulence factor from L. pneumophila. Here, we describe the experimental details for SdeA-induced ubiquitination of the small GTPase Rab33b and its reversal by SidJ.
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Affiliation(s)
- Jiazhang Qiu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, United States.
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59
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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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60
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Li P, Liu C, Deng WH, Yao DM, Pan LL, Li YQ, Liu YQ, Liang Y, Zhou XP, Wang XW. Plant begomoviruses subvert ubiquitination to suppress plant defenses against insect vectors. PLoS Pathog 2019; 15:e1007607. [PMID: 30789967 PMCID: PMC6400417 DOI: 10.1371/journal.ppat.1007607] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 03/05/2019] [Accepted: 01/30/2019] [Indexed: 11/18/2022] Open
Abstract
Most plant viruses are vectored by insects and the interactions of virus-plant-vector have important ecological and evolutionary implications. Insect vectors often perform better on virus-infected plants. This indirect mutualism between plant viruses and insect vectors promotes the spread of virus and has significant agronomical effects. However, few studies have investigated how plant viruses manipulate plant defenses and promote vector performance. Begomoviruses are a prominent group of plant viruses in tropical and sub-tropical agro-ecosystems and are transmitted by whiteflies. Working with the whitefly Bemisia tabaci, begomoviruses and tobacco, we revealed that C2 protein of begomoviruses lacking DNA satellites was responsible for the suppression of plant defenses against whitefly vectors. We found that infection of plants by tomato yellow leaf curl virus (TYLCV), one of the most devastating begomoviruses worldwide, promoted the survival and reproduction of whitefly vectors. TYLCV C2 protein suppressed plant defenses by interacting with plant ubiquitin. This interaction compromised the degradation of JAZ1 protein, thus inhibiting jasmonic acid defense and the expression of MYC2-regulated terpene synthase genes. We further demonstrated that function of C2 protein among begomoviruses not associated with satellites is well conserved and ubiquitination is an evolutionarily conserved target of begomoviruses for the suppression of plant resistance to whitefly vectors. Taken together, these results demonstrate that ubiquitination inhibition by begomovirus C2 protein might be a general mechanism in begomovirus, whitefly and plant interactions.
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Affiliation(s)
- Ping Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Chao Liu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Wen-Hao Deng
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Dan-Mei Yao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Li-Long Pan
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yun-Qin Li
- Center of Analysis and Measurement, Zhejiang University, Hangzhou, China
| | - Yin-Quan Liu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yan Liang
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xue-Ping Zhou
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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61
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Legionella pneumophila inhibits immune signalling via MavC-mediated transglutaminase-induced ubiquitination of UBE2N. Nat Microbiol 2018; 4:134-143. [PMID: 30420781 PMCID: PMC6294664 DOI: 10.1038/s41564-018-0282-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 10/03/2018] [Indexed: 01/16/2023]
Abstract
The bacterial pathogen Legionella pneumophila modulates host immunity using effectors translocated by its Dot/Icm transporter to facilitate its intracellular replication. A number of these effectors employ diverse mechanisms to interfere with protein ubiquitination, a posttranslational modification essential for immunity. Here we found that L. pneumophila induces monoubiquitination of the E2 enzyme UBE2N by its Dot/Icm substrate MavC(Lpg2147). We demonstrate that MavC is a transglutaminase that catalyzes covalent linkage of ubiquitin to Lys92 and Lys94 of UBE2N via Gln40. Similar to canonical transglutaminases, MavC possess deamidase activity that targets ubiquitin at Gln40. We identified Cys74 as the catalytic residue for both ubiquitination and deamidation activities. Furthermore, ubiquitination of UBE2N by MavC abolishes its activity in the formation of K63-type polyubiquitin chains, which dampens NFκB signaling in the initial phase of bacterial infection. Our results reveal an unprecedented mechanism of modulating host immunity by modifying a key ubiquitination enzyme by ubiquitin transglutamination.
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62
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Qi W, Cascarano MC, Schlapbach R, Katharios P, Vaughan L, Seth-Smith HMB. Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity. Genome Biol Evol 2018; 10:1363-1374. [PMID: 29726925 PMCID: PMC6007542 DOI: 10.1093/gbe/evy092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2018] [Indexed: 02/06/2023] Open
Abstract
Endozoicomonas bacteria are generally beneficial symbionts of diverse marine invertebrates including reef-building corals, sponges, sea squirts, sea slugs, molluscs, and Bryozoans. In contrast, the recently reported Ca. Endozoicomonas cretensis was identified as a vertebrate pathogen, causing epitheliocystis in fish larvae resulting in massive mortality. Here, we described the Ca. E. cretensis draft genome, currently undergoing genome decay as evidenced by massive insertion sequence (IS element) expansion and pseudogene formation. Many of the insertion sequences are also predicted to carry outward-directed promoters, implying that they may be able to modulate the expression of neighbouring coding sequences (CDSs). Comparative genomic analysis has revealed many Ca. E. cretensis-specific CDSs, phage integration and novel gene families. Potential virulence related CDSs and machineries were identified in the genome, including secretion systems and related effector proteins, and systems related to biofilm formation and directed cell movement. Mucin degradation would be of importance to a fish pathogen, and many candidate CDSs associated with this pathway have been identified. The genome may reflect a bacterium in the process of changing niche from symbiont to pathogen, through expansion of virulence genes and some loss of metabolic capacity.
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Affiliation(s)
- Weihong Qi
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Maria Chiara Cascarano
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich, Switzerland
| | - Pantelis Katharios
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Lloyd Vaughan
- Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland.,Pathovet AG, Tagelswangen, Switzerland
| | - Helena M B Seth-Smith
- Functional Genomics Center Zurich, University of Zurich, Switzerland.,Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
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63
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Ubiquitin, SUMO, and NEDD8: Key Targets of Bacterial Pathogens. Trends Cell Biol 2018; 28:926-940. [PMID: 30107971 DOI: 10.1016/j.tcb.2018.07.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 01/09/2023]
Abstract
Manipulation of host protein post-translational modifications (PTMs) is used by various pathogens to interfere with host cell functions. Among these modifications, ubiquitin (UBI) and ubiquitin-like proteins (UBLs) constitute key targets because they are regulators of pathways essential for the host cell. In particular, these PTM modifiers control pathways that have been described as crucial for infection such as pathogen entry, replication, propagation, or detection by the host. Although bacterial pathogens lack eucaryotic-like UBI or UBL systems, many of them produce proteins that specifically interfere with these host PTMs during infection. In this review we discuss the different mechanisms used by bacteria to interfere with host UBI and the two UBLs, SUMO and NEDD8.
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64
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Foote PK, Statsyuk AV. Monitoring PARKIN RBR Ubiquitin Ligase Activation States with UbFluor. ACTA ACUST UNITED AC 2018; 10:e45. [PMID: 30063295 DOI: 10.1002/cpch.45] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PARKIN is a RING-Between-RING (RBR) E3 ligase, which ubiquitinates mitochondrial proteins in response to mitochondrial damage. Ser65 of PARKIN is phosphorylated by kinase PINK1 (pPARKIN), which causes partial PARKIN activation. PINK1 also phosphorylates Ser65 of ubiquitin (pUb), which further activates pPARKIN. Due to the lack of precise and quantitative assays to quantify the activity of PARKIN, there were many conflicting reports on the role of pUb as a PARKIN activator, whether S65E PARKIN is a true phosphomimetic of pPARKIN, and the effect of substrate of PARKIN turnover was also not known. This protocol provides a step-by-step guide on the use of the UbFluor probe to precisely quantitate changes in the activity of PARKIN in response to phosphorylation, allosteric activation by pUb, protein substrates, and activating structural mutations. These results pave the way to discover PARKIN activators and to precisely quantify the activity of other RBR E3s. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Peter K Foote
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
| | - Alexander V Statsyuk
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois.,The Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas
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65
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Kim L, Kwon DH, Kim BH, Kim J, Park MR, Park ZY, Song HK. Structural and Biochemical Study of the Mono-ADP-Ribosyltransferase Domain of SdeA, a Ubiquitylating/Deubiquitylating Enzyme from Legionella pneumophila. J Mol Biol 2018; 430:2843-2856. [PMID: 29870726 DOI: 10.1016/j.jmb.2018.05.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/24/2018] [Accepted: 05/27/2018] [Indexed: 11/18/2022]
Abstract
Conventional ubiquitylation occurs through an ATP-dependent three-enzyme cascade (E1, E2, and E3) that mediates the covalent conjugation of the C-terminus of ubiquitin to a lysine on the substrate. SdeA, which belongs to the SidE effector family of Legionella pneumophila, can transfer ubiquitin to endoplasmic reticulum-associated Rab-family GTPases in a manner independent of E1 and E2 enzymes. The novel ubiquitin-modifying enzyme SdeA utilizes NAD+ as a cofactor to attach ubiquitin to a serine residue of the substrate. Here, to elucidate the coupled enzymatic reaction of NAD+ hydrolysis and ADP-ribosylation of ubiquitin in SdeA, we characterized the mono-ADP-ribosyltransferase domain of SdeA and show that it consists of two sub-domains termed mART-N and mART-C. The crystal structure of the mART-C domain of SdeA was also determined in free form and in complex with NAD+ at high resolution. Furthermore, the spatial orientations of the N-terminal deubiquitylase, phosphodiesterase, mono-ADP-ribosyltransferase, and C-terminal coiled-coil domains within the 180-kDa full-length SdeA were determined. These results provide insight into the unusual ubiquitylation mechanism of SdeA and expand our knowledge on the structure-function of mono-ADP-ribosyltransferases.
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Affiliation(s)
- Leehyeon Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Do Hoon Kwon
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Bong Heon Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Jiyeon Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Mi Rae Park
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Korea.
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66
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Immunomodulatory Role of Vitamin D: A Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1108:13-23. [PMID: 30143987 DOI: 10.1007/5584_2018_246] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Vitamin D is well known for its classical hormonal action related to the maintenance of mineral and skeletal homeostasis. However, the discovery that vitamin D receptor (VDR) is expressed in most non-skeletal tissues points to its broad role in the human organism. Current literature emphasizes a multidirectional role of vitamin D, with a special focus on its immunomodulatory properties. As VDR and the enzyme 1-α-hydroxylase are expressed in most immune cells, vitamin D modulates the phagocytic activity of macrophages and natural killer cells. In addition, it induces the microbicidal activity of phagocytes. In contrast, vitamin D suppresses differentiation and maturation of antigen-presenting dendritic cells and B lymphocytes, and it inhibits proliferation of Th1 and Th17 cells. In this review we aimed to describe the current scientific discoveries on the role of vitamin D as immunomodulator.
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67
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Qiu J, Luo ZQ. Hijacking of the Host Ubiquitin Network by Legionella pneumophila. Front Cell Infect Microbiol 2017; 7:487. [PMID: 29376029 PMCID: PMC5770618 DOI: 10.3389/fcimb.2017.00487] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 11/13/2017] [Indexed: 12/26/2022] Open
Abstract
Protein ubiquitination is critical for regulation of numerous eukaryotic cellular processes such as protein homeostasis, cell cycle progression, immune response, DNA repair, and vesicular trafficking. Ubiquitination often leads to the alteration of protein stability, subcellular localization, or interaction with other proteins. Given the importance of ubiquitination in the regulation of host immunity, it is not surprising that many infectious agents have evolved strategies to interfere with the ubiquitination network with sophisticated mechanisms such as functional mimicry. The facultative intracellular pathogen Legionella pneumophila is the causative agent of Legionnaires' disease. L. pneumophila is phagocytosed by macrophages and is able to replicate within a niche called Legionella-containing vacuole (LCV). The biogenesis of LCV is dependent upon the Dot/Icm type IV secretion system which delivers more than 330 effector proteins into host cytosol. The optimal intracellular replication of L. pneumophila requires the host ubiquitin-proteasome system. Furthermore, membranes of the bacterial phagosome are enriched with ubiquitinated proteins in a way that requires its Dot/Icm type IV secretion system, suggesting the involvement of effectors in the manipulation of the host ubiquitination machinery. Here we summarize recent advances in our understanding of mechanisms exploited by L. pneumophila effector proteins to hijack the host ubiquitination pathway.
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Affiliation(s)
- Jiazhang Qiu
- Center of Infection and Immunity, First Hospital, Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Center of Infection and Immunity, First Hospital, Jilin University, Changchun, China.,Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China.,Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN, United States
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68
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Comparative Profiling of Ubiquitin Proteasome System Interplay with Influenza A Virus PB2 Polymerase Protein Recapitulating Virus Evolution in Humans. mSphere 2017; 2:mSphere00330-17. [PMID: 29202037 PMCID: PMC5700371 DOI: 10.1128/msphere.00330-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023] Open
Abstract
Influenza A viruses (IAVs) are responsible for mild-to-severe seasonal respiratory illness of public health concern worldwide, and the risk of avian strain outbreaks in humans is a constant threat. Elucidating the requisites of IAV adaptation to humans is thus of prime importance. In this study, we explored how PB2 replication proteins of IAV strains with different levels of virulence in humans hijack a major protein modification pathway of the human host cell, the ubiquitin proteasome system (UPS). We found that the PB2 protein engages in an extended interplay with the UPS that evolved along with the virus’s adaptation to humans. This suggests that UPS hijacking underlies the efficient infection of humans and can be used as an indicator for evaluation of the potential of avian IAVs to infect humans. Several UPS factors were found to be necessary for infection with circulating IAV strains, pointing to potential targets for therapeutic approaches. The optimized exploitation of cell resources is one cornerstone of a successful infection. Differential mapping of host-pathogen protein-protein interactions (PPIs) on the basis of comparative interactomics of multiple strains is an effective strategy to highlight correlations between host proteome hijacking and biological or pathogenic traits. Here, we developed an interactomic pipeline to deliver high-confidence comparative maps of PPIs between a given pathogen and the human ubiquitin proteasome system (UPS). This subarray of the human proteome represents a range of essential cellular functions and promiscuous targets for many viruses. The screening pipeline was applied to the influenza A virus (IAV) PB2 polymerase proteins of five strains representing different levels of virulence in humans. An extensive PB2-UPS interplay has been detected that recapitulates the evolution of IAVs in humans. Functional validation with several IAV strains, including the seasonal H1N1pdm09 and H3N2 viruses, confirmed the biological relevance of most identified UPS factors and revealed strain-independent and strain-specific effects of UPS factor invalidation on IAV infection. This strategy is applicable to proteins from any other virus or pathogen, providing a valuable resource with which to explore the UPS-pathogen interplay and its relationship with pathogenicity. IMPORTANCE Influenza A viruses (IAVs) are responsible for mild-to-severe seasonal respiratory illness of public health concern worldwide, and the risk of avian strain outbreaks in humans is a constant threat. Elucidating the requisites of IAV adaptation to humans is thus of prime importance. In this study, we explored how PB2 replication proteins of IAV strains with different levels of virulence in humans hijack a major protein modification pathway of the human host cell, the ubiquitin proteasome system (UPS). We found that the PB2 protein engages in an extended interplay with the UPS that evolved along with the virus’s adaptation to humans. This suggests that UPS hijacking underlies the efficient infection of humans and can be used as an indicator for evaluation of the potential of avian IAVs to infect humans. Several UPS factors were found to be necessary for infection with circulating IAV strains, pointing to potential targets for therapeutic approaches.
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69
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Lamberto I, Liu X, Seo HS, Schauer NJ, Iacob RE, Hu W, Das D, Mikhailova T, Weisberg EL, Engen JR, Anderson KC, Chauhan D, Dhe-Paganon S, Buhrlage SJ. Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7. Cell Chem Biol 2017; 24:1490-1500.e11. [PMID: 29056421 DOI: 10.1016/j.chembiol.2017.09.003] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/09/2017] [Accepted: 09/05/2017] [Indexed: 01/30/2023]
Abstract
Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5-10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially proteins that are challenging to directly target but which are stabilized by DUB family members. Highly optimized and well-characterized DUB inhibitors have thus become highly sought after tools. Most reported DUB inhibitors, however, are polypharmacological agents possessing weak (micromolar) potency toward their primary target, limiting their utility in target validation and mechanism studies. Due to a lack of high-resolution DUB⋅small-molecule ligand complex structures, no structure-guided optimization efforts have been reported for a mammalian DUB. Here, we report a small-molecule⋅ubiquitin-specific protease (USP) family DUB co-structure and rapid design of potent and selective inhibitors of USP7 guided by the structure. Interestingly, the compounds are non-covalent active-site inhibitors.
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Affiliation(s)
- Ilaria Lamberto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xiaoxi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan J Schauer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Wanyi Hu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepika Das
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tatiana Mikhailova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dharminder Chauhan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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70
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Bacterial effector NleL promotes enterohemorrhagic E. coli-induced attaching and effacing lesions by ubiquitylating and inactivating JNK. PLoS Pathog 2017; 13:e1006534. [PMID: 28753655 PMCID: PMC5549993 DOI: 10.1371/journal.ppat.1006534] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 08/09/2017] [Accepted: 07/15/2017] [Indexed: 11/25/2022] Open
Abstract
As a major diarrheagenic human pathogen, enterohemorrhagic Escherichia coli (EHEC) produce attaching and effacing (A/E) lesions, characterized by the formation of actin pedestals, on mammalian cells. A bacterial T3SS effector NleL from EHEC O157:H7 was recently shown to be a HECT-like E3 ligase in vitro, but its biological functions and host targets remain elusive. Here, we report that NleL is required to effectively promote EHEC-induced A/E lesions and bacterial infection. Furthermore, human c-Jun NH2-terminal kinases (JNKs) were identified as primary substrates of NleL. NleL-induced JNK ubiquitylation, particularly mono-ubiquitylation at the Lys 68 residue of JNK, impairs JNK’s interaction with an upstream kinase MKK7, thus disrupting JNK phosphorylation and activation. This subsequently suppresses the transcriptional activity of activator protein-1 (AP-1), which modulates the formation of the EHEC-induced actin pedestals. Moreover, JNK knockdown or inhibition in host cells complements NleL deficiency in EHEC infection. Thus, we demonstrate that the effector protein NleL enhances the ability of EHEC to infect host cells by targeting host JNK, and elucidate an inhibitory role of ubiquitylation in regulating JNK phosphorylation. Enterohemorrhagic Escherichia coli (EHEC) can cause attaching and effacing (A/E) lesions to form in the colons of animals and humans, contributing to severe bacterial infection. NleL, an E3 ubiquitin ligase from EHEC O157:H7 is one of the bacterial type III secretion effectors that may be involved in the regulation of A/E lesions. However, NleL’s exact host targets and the detailed mechanistic actions are still unclear. Here, we report that the effector protein NleL effectively promotes EHEC-induced A/E lesions and bacterial infection by targeting the host JNK protein. Specifically, we find that NleL-mediated JNK ubiquitylation abolishes phosphorylation and activation of host JNK, subsequently suppressing the host JNK/AP-1 signaling pathway to favor the formation of EHEC-mediated actin pedestals on the surface of mammalian cells. Collectively, our work has not only discovered the A/E lesion-promoting function of NleL during EHEC infection, but also revealed a novel regulatory mechanism of host JNK protein.
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72
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Abstract
This brief disquisition about the early history of studies on regulated protein degradation introduces several detailed reviews about the ubiquitin system and autophagy.
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Affiliation(s)
- Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125;
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73
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Marei H, Malliri A. Rac1 in human diseases: The therapeutic potential of targeting Rac1 signaling regulatory mechanisms. Small GTPases 2017; 8:139-163. [PMID: 27442895 PMCID: PMC5584733 DOI: 10.1080/21541248.2016.1211398] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 12/11/2022] Open
Abstract
Abnormal Rac1 signaling is linked to a number of debilitating human diseases, including cancer, cardiovascular diseases and neurodegenerative disorders. As such, Rac1 represents an attractive therapeutic target, yet the search for effective Rac1 inhibitors is still underway. Given the adverse effects associated with Rac1 signaling perturbation, cells have evolved several mechanisms to ensure the tight regulation of Rac1 signaling. Thus, characterizing these mechanisms can provide invaluable information regarding major cellular events that lead to aberrant Rac1 signaling. Importantly, this information can be utilized to further facilitate the development of effective pharmacological modulators that can restore normal Rac1 signaling. In this review, we focus on the pathological role of Rac1 signaling, highlighting the benefits and potential drawbacks of targeting Rac1 in a clinical setting. Additionally, we provide an overview of available compounds that target key Rac1 regulatory mechanisms and discuss future therapeutic avenues arising from our understanding of these mechanisms.
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Affiliation(s)
- Hadir Marei
- Cell Signaling Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
| | - Angeliki Malliri
- Cell Signaling Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
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74
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Nakano M, Oda K, Mukaihara T. Ralstonia solanacearum novel E3 ubiquitin ligase (NEL) effectors RipAW and RipAR suppress pattern-triggered immunity in plants. MICROBIOLOGY (READING, ENGLAND) 2017; 163:992-1002. [PMID: 28708051 DOI: 10.1099/mic.0.000495] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Ralstonia solanacearum is the causal agent of bacterial wilt in solanaceous crops. This pathogen injects more than 70 effector proteins into host plant cells via the Hrp type III secretion system to cause a successful infection. However, the function of these effectors in plant cells, especially in the suppression of plant immunity, remains largely unknown. In this study, we characterized two Ralstonia solanacearum effectors, RipAW and RipAR, which share homology with the IpaH family of effectors from animal and plant pathogenic bacteria, that have a novel E3 ubiquitin ligase (NEL) domain. Recombinant RipAW and RipAR show E3 ubiquitin ligase activity in vitro. RipAW and RipAR localized to the cytoplasm of plant cells and significantly suppressed pattern-triggered immunity (PTI) responses such as the production of reactive oxygen species and the expression of defence-related genes when expressed in leaves of Nicotiana benthamiana. Mutation in the conserved cysteine residue in the NEL domain of RipAW completely abolished the E3 ubiquitin ligase activity in vitro and the ability to suppress PTI responses in plant leaves. These results indicate that RipAW suppresses plant PTI responses through the E3 ubiquitin ligase activity. Unlike other members of the IpaH family of effectors, RipAW and RipAR had no leucine-rich repeat motifs in their amino acid sequences. A conserved C-terminal region of RipAW is indispensable for PTI suppression. Transgenic Arabidopsis plants expressing RipAW and RipAR showed increased disease susceptibility, suggesting that RipAW and RipAR contribute to bacterial virulence in plants.
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Affiliation(s)
- Masahito Nakano
- Research Institute for Biological Sciences, Okayama (RIBS), 7549-1 Yoshikawa, Kibichuo-cho, Okayama 716-1241, Japan
| | - Kenji Oda
- Research Institute for Biological Sciences, Okayama (RIBS), 7549-1 Yoshikawa, Kibichuo-cho, Okayama 716-1241, Japan
| | - Takafumi Mukaihara
- Research Institute for Biological Sciences, Okayama (RIBS), 7549-1 Yoshikawa, Kibichuo-cho, Okayama 716-1241, Japan
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75
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The DUB blade goes snicker-snack: Novel ubiquitin cleavage by a Legionella effector protein. Cell Res 2017; 27:845-846. [PMID: 28574056 DOI: 10.1038/cr.2017.80] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recently, a Legionella pneumophila effector protein was shown to have an unprecedented ATP-independent ubiquitin ligase activity that couples phosphoribosylated ubiquitin (PR-Ub) to serine residues of host proteins. A new study published in Cell Research by Qiu et al. reveals that another Legionella effector protein, SidJ, catalyzes deubiquitination of PR-Ub by cleavage of the substrate-linked phosphodiester bond.
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76
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Rao S, Schieber AMP, O'Connor CP, Leblanc M, Michel D, Ayres JS. Pathogen-Mediated Inhibition of Anorexia Promotes Host Survival and Transmission. Cell 2017; 168:503-516.e12. [PMID: 28129542 DOI: 10.1016/j.cell.2017.01.006] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/21/2016] [Accepted: 01/06/2017] [Indexed: 01/06/2023]
Abstract
Sickness-induced anorexia is a conserved behavior induced during infections. Here, we report that an intestinal pathogen, Salmonella Typhimurium, inhibits anorexia by manipulating the gut-brain axis. Inhibition of inflammasome activation by the S. Typhimurium effector, SlrP, prevented anorexia caused by IL-1β-mediated signaling to the hypothalamus via the vagus nerve. Rather than compromising host defenses, pathogen-mediated inhibition of anorexia increased host survival. SlrP-mediated inhibition of anorexia prevented invasion and systemic infection by wild-type S. Typhimurium, reducing virulence while increasing transmission to new hosts, suggesting that there are trade-offs between transmission and virulence. These results clarify the complex and contextual role of anorexia in host-pathogen interactions and suggest that microbes have evolved mechanisms to modulate sickness-induced behaviors to promote health of their host and their transmission at the expense of virulence.
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Affiliation(s)
- Sheila Rao
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Alexandria M Palaferri Schieber
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Carolyn P O'Connor
- Flow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Mathias Leblanc
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Daniela Michel
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Janelle S Ayres
- Nomis Center for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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77
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Qiu J, Yu K, Fei X, Liu Y, Nakayasu ES, Piehowski PD, Shaw JB, Puvar K, Das C, Liu X, Luo ZQ. A unique deubiquitinase that deconjugates phosphoribosyl-linked protein ubiquitination. Cell Res 2017; 27:865-881. [PMID: 28497808 PMCID: PMC5518988 DOI: 10.1038/cr.2017.66] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/05/2017] [Accepted: 04/11/2017] [Indexed: 12/22/2022] Open
Abstract
Ubiquitination regulates many aspects of host immunity and thus is a common target for infectious agents. Recent studies have revealed that members of the SidE effector family of the bacterial pathogen Legionella pneumophila attack several small GTPases associated with the endoplasmic reticulum by a novel ubiquitination mechanism that does not require the E1 and E2 enzymes of the host ubiquitination machinery. In this case, ubiquitin is first activated by ADP-ribosylation at Arg42 by a mono-ADP-ribosyltransferase activity; the intermediate is then cleaved by a phosphodiesterase activity also residing within SdeA, concomitant with the attachment of ubiquitin to serine residues of substrate proteins via a phosphoribosyl linker. Here we demonstrate that the effect of SidEs is antagonized by SidJ, an effector encoded by a gene situated in the locus coding for three members of the SidE family (SdeC, SdeB and SdeA). SidJ reverses ubiquitination of SidEs-modified substrates by cleaving the phosphodiester bond that links phosphoribosylated ubiquitin to protein substrates. SidJ also displays classical deubiquitinase activity but does not require catalytic cysteine residues. Further, these deubiquitinase activities of SidJ are essential for its role in L. pneumophila infection. Finally, the activity of SidJ is required for efficiently reducing the abundance of ubiquitinated Rab33b in infected cells within a few hours after bacterial uptake. Our results establish SidJ as a ubiquitin-deconjugating enzyme that functions to impose temporal regulation on the activity of SidE effectors. SidJ may be important in future studies of signaling cascades mediated by this unique ubiquitination, one that also potentially regulates cellular processes in eukaryotic cells.
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Affiliation(s)
- Jiazhang Qiu
- Center of Infection and Immunity, The First Hospital, Jilin University, Changchun, Jilin 130001, China.,Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Kaiwen Yu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaowen Fei
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.,Department of Biochemistry and Molecular Biology, Hainan Medical College, Haikou, Hainan 571101, China
| | - Yao Liu
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jared B Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Kedar Puvar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Xiaoyun Liu
- Institute of Analytical Chemistry and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhao-Qing Luo
- Center of Infection and Immunity, The First Hospital, Jilin University, Changchun, Jilin 130001, China.,Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
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78
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Bhogaraju S, Kalayil S, Liu Y, Bonn F, Colby T, Matic I, Dikic I. Phosphoribosylation of Ubiquitin Promotes Serine Ubiquitination and Impairs Conventional Ubiquitination. Cell 2017; 167:1636-1649.e13. [PMID: 27912065 DOI: 10.1016/j.cell.2016.11.019] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 10/28/2016] [Accepted: 11/10/2016] [Indexed: 01/13/2023]
Abstract
Conventional ubiquitination involves the ATP-dependent formation of amide bonds between the ubiquitin C terminus and primary amines in substrate proteins. Recently, SdeA, an effector protein of pathogenic Legionella pneumophila, was shown to mediate NAD-dependent and ATP-independent ubiquitin transfer to host proteins. Here, we identify a phosphodiesterase domain in SdeA that efficiently catalyzes phosphoribosylation of ubiquitin on a specific arginine via an ADP-ribose-ubiquitin intermediate. SdeA also catalyzes a chemically and structurally distinct type of substrate ubiquitination by conjugating phosphoribosylated ubiquitin to serine residues of protein substrates via a phosphodiester bond. Furthermore, phosphoribosylation of ubiquitin prevents activation of E1 and E2 enzymes of the conventional ubiquitination cascade, thereby impairing numerous cellular processes including mitophagy, TNF signaling, and proteasomal degradation. We propose that phosphoribosylation of ubiquitin potently modulates ubiquitin functions in mammalian cells.
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Affiliation(s)
- Sagar Bhogaraju
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Sissy Kalayil
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Yaobin Liu
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Thomas Colby
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Ivan Matic
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, School of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; Department of Immunology and Medical Genetics, University of Split, School of Medicine, Soltanska 2, 21000 Split, Croatia.
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79
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O'Connor HF, Huibregtse JM. Enzyme-substrate relationships in the ubiquitin system: approaches for identifying substrates of ubiquitin ligases. Cell Mol Life Sci 2017; 74:3363-3375. [PMID: 28455558 DOI: 10.1007/s00018-017-2529-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/05/2017] [Accepted: 04/18/2017] [Indexed: 02/06/2023]
Abstract
Protein ubiquitylation is an important post-translational modification, regulating aspects of virtually every biochemical pathway in eukaryotic cells. Hundreds of enzymes participate in the conjugation and deconjugation of ubiquitin, as well as the recognition, signaling functions, and degradation of ubiquitylated proteins. Regulation of ubiquitylation is most commonly at the level of recognition of substrates by E3 ubiquitin ligases. Characterization of the network of E3-substrate relationships is a major goal and challenge in the field, as this expected to yield fundamental biological insights and opportunities for drug development. There has been remarkable success in identifying substrates for some E3 ligases, in many instances using the standard protein-protein interaction techniques (e.g., two-hybrid screens and co-immunoprecipitations paired with mass spectrometry). However, some E3s have remained refractory to characterization, while others have simply not yet been studied due to the sheer number and diversity of E3s. This review will discuss the range of tools and techniques that can be used for substrate profiling of E3 ligases.
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Affiliation(s)
- Hazel F O'Connor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jon M Huibregtse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
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80
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Structural basis for the recognition and degradation of host TRIM proteins by Salmonella effector SopA. Nat Commun 2017; 8:14004. [PMID: 28084320 PMCID: PMC5241803 DOI: 10.1038/ncomms14004] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/21/2016] [Indexed: 12/25/2022] Open
Abstract
The hallmark of Salmonella Typhimurium infection is an acute intestinal inflammatory response, which is mediated through the action of secreted bacterial effector proteins. The pro-inflammatory Salmonella effector SopA is a HECT-like E3 ligase, which was previously proposed to activate host RING ligases TRIM56 and TRIM65. Here we elucidate an inhibitory mechanism of TRIM56 and TRIM65 targeting by SopA. We present the crystal structure of SopA in complex with the RING domain of human TRIM56, revealing the atomic details of their interaction and the basis for SopA selectivity towards TRIM56 and TRIM65. Structure-guided biochemical analysis shows that SopA inhibits TRIM56 E3 ligase activity by occluding the E2-interacting surface of TRIM56. We further demonstrate that SopA ubiquitinates TRIM56 and TRIM65, resulting in their proteasomal degradation during infection. Our results provide the basis for how a bacterial HECT ligase blocks host RING ligases and exemplifies the multivalent power of bacterial effectors during infection.
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Candido-Ferreira IL, Kronenberger T, Sayegh RSR, Batista IDFC, da Silva Junior PI. Evidence of an Antimicrobial Peptide Signature Encrypted in HECT E3 Ubiquitin Ligases. Front Immunol 2017; 7:664. [PMID: 28119686 PMCID: PMC5220581 DOI: 10.3389/fimmu.2016.00664] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin-proteasome pathway (UPP) is a hallmark of the eukaryotic cell. In jawed vertebrates, it has been co-opted by the adaptive immune system, where proteasomal degradation produces endogenous peptides for major histocompatibility complex class I antigen presentation. However, proteolytic products are also necessary for the phylogenetically widespread innate immune system, as they often play a role as host defense peptides (HDPs), pivotal effectors against pathogens. Here, we report the identification of the arachnid HDP oligoventin, which shares homology to a core member of the UPP, E3 ubiquitin ligases. Oligoventin has broad antimicrobial activity and shows strong synergy with lysozymes. Using computational and phylogenetic approaches, we show high conservation of the oligoventin signature in HECT E3s. In silico simulation of HECT E3s self-proteolysis provides evidence that HDPs can be generated by fine-tuned 26S proteasomal degradation, and therefore are consistent with the hypothesis that oligoventin is a cryptic peptide released by the proteolytic processing of an Nedd4 E3 precursor protein. Finally, we compare the production of HDPs and endogenous antigens from orthologous HECT E3s by proteasomal degradation as a means of analyzing the UPP coupling to metazoan immunity. Our results highlight the functional plasticity of the UPP in innate and adaptive immune systems as a possibly recurrent mechanism to generate functionally diverse peptides.
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Affiliation(s)
- Ivan Lavander Candido-Ferreira
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, Brazil; Biosciences Institute, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Thales Kronenberger
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo , São Paulo, São Paulo , Brazil
| | - Raphael Santa Rosa Sayegh
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, São Paulo, Brazil; Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Pedro Ismael da Silva Junior
- Special Laboratory for Applied Toxinology (LETA), Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Butantan Institute , São Paulo, São Paulo , Brazil
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Torraca V, Mostowy S. Septins and Bacterial Infection. Front Cell Dev Biol 2016; 4:127. [PMID: 27891501 PMCID: PMC5104955 DOI: 10.3389/fcell.2016.00127] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/26/2016] [Indexed: 12/04/2022] Open
Abstract
Septins, a unique cytoskeletal component associated with cellular membranes, are increasingly recognized as having important roles in host defense against bacterial infection. A role for septins during invasion of Listeria monocytogenes into host cells was first proposed in 2002. Since then, work has shown that septins assemble in response to a wide variety of invasive bacterial pathogens, and septin assemblies can have different roles during the bacterial infection process. Here we review the interplay between septins and bacterial pathogens, highlighting septins as a structural determinant of host defense. We also discuss how investigation of septin assembly in response to bacterial infection can yield insight into basic cellular processes including phagocytosis, autophagy, and mitochondrial dynamics.
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Affiliation(s)
- Vincenzo Torraca
- Department of Medicine, MRC Centre of Molecular Bacteriology and Infection, Imperial College London London, UK
| | - Serge Mostowy
- Department of Medicine, MRC Centre of Molecular Bacteriology and Infection, Imperial College London London, UK
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Zhao Y, Zhang T, Huo H, Ye Y, Liu Y. Lunapark Is a Component of a Ubiquitin Ligase Complex Localized to the Endoplasmic Reticulum Three-way Junctions. J Biol Chem 2016; 291:18252-62. [PMID: 27387505 DOI: 10.1074/jbc.m116.737783] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 11/06/2022] Open
Abstract
The endoplasmic reticulum (ER) network comprises sheets and tubules that are connected by dynamic three-way junctions. Lunapark (Lnp) localizes to and stabilizes ER three-way junctions by antagonizing the small GTPase Atlastin, but how Lnp shapes the ER network is unclear. Here, we used an affinity purification approach and mass spectrometry to identify Lnp as an interacting partner of the ER protein quality control ubiquitin ligase gp78. Accordingly, Lnp purified from mammalian cells has a ubiquitin ligase activity in vitro Intriguingly, biochemical analyses show that this activity can be attributed not only to associated ubiquitin ligase, but also to an intrinsic ubiquitin ligase activity borne by Lnp itself. This activity is contained in the N-terminal 45 amino acids of Lnp although this segment does not share homology to any known ubiquitin ligase motifs. Despite its interaction with gp78, Lnp does not seem to have a broad function in degradation of misfolded ER proteins. On the other hand, the N-terminal ubiquitin ligase-bearing motif is required for the ER three-way junction localization of Lnp. Our study identifies a new type of ubiquitin ligase and reveals a potential link between ubiquitin and ER morphology regulation.
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Affiliation(s)
- Yupeng Zhao
- From the School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Shanghai 201210, China and
| | - Ting Zhang
- the Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Huanhuan Huo
- From the School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Shanghai 201210, China and
| | - Yihong Ye
- the Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Yanfen Liu
- From the School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Shanghai 201210, China and
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Abstract
Qiu et al. (2016) show that a mono-ADP-ribosyltransferase, SdeA, from Legionella pneumophila catalyzes ADP-ribosylation of ubiquitin, allowing SdeA to modify substrate with ubiquitin in the absence of E1 and E2 enzymes.
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Affiliation(s)
- Mark A Nakasone
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.
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