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Szczesna M, Huang Y, Lacoursiere RE, Bonini F, Pol V, Koc F, Ward B, Geurink PP, Pruneda JN, Thurston TLM. Bacterial esterases reverse lipopolysaccharide ubiquitylation to block host immunity. Cell Host Microbe 2024; 32:913-924.e7. [PMID: 38870903 DOI: 10.1016/j.chom.2024.04.012] [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: 02/14/2024] [Revised: 03/15/2024] [Accepted: 04/11/2024] [Indexed: 06/15/2024]
Abstract
Aspects of how Burkholderia escape the host's intrinsic immune response to replicate in the cell cytosol remain enigmatic. Here, we show that Burkholderia has evolved two mechanisms to block the activity of Ring finger protein 213 (RNF213)-mediated non-canonical ubiquitylation of bacterial lipopolysaccharide (LPS), thereby preventing the initiation of antibacterial autophagy. First, Burkholderia's polysaccharide capsule blocks RNF213 association with bacteria and second, the Burkholderia deubiquitylase (DUB), TssM, directly reverses the activity of RNF213 through a previously unrecognized esterase activity. Structural analysis provides insight into the molecular basis of TssM esterase activity, allowing it to be uncoupled from its isopeptidase function. Furthermore, a putative TssM homolog also displays esterase activity and removes ubiquitin from LPS, establishing this as a virulence mechanism. Of note, we also find that additional immune-evasion mechanisms exist, revealing that overcoming this arm of the host's immune response is critical to the pathogen.
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Affiliation(s)
- Magdalena Szczesna
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Yizhou Huang
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Rachel E Lacoursiere
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Francesca Bonini
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Vito Pol
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Fulya Koc
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Beatrice Ward
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Paul P Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Jonathan N Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA.
| | - Teresa L M Thurston
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
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2
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Morito D. Molecular structure and function of mysterin/RNF213. J Biochem 2024; 175:495-505. [PMID: 38378744 DOI: 10.1093/jb/mvae020] [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: 12/05/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/22/2024] Open
Abstract
Mysterin is a large intracellular protein harboring a RING finger ubiquitin ligase domain and is also referred to as RING finger protein 213 (RNF213). The author performed the first molecular cloning of the mysterin gene as the final step in genetic exploration of cerebrovascular moyamoya disease (MMD) and initiated the next round of exploration to understand its molecular and cellular functions. Although much remains unknown, accumulating findings suggest that mysterin functions in cells by targeting massive intracellular structures, such as lipid droplets (LDs) and various invasive pathogens. In the latter case, mysterin appears to directly surround and ubiquitylate the surface of pathogens and stimulate cell-autonomous antimicrobial reactions, such as xenophagy and inflammatory response. To date, multiple mutations causing MMD have been identified within and near the RING finger domain of mysterin; however, their functional relevance remains largely unknown. Besides the RING finger, mysterin harbors a dynein-like ATPase core and an RZ finger, another ubiquitin ligase domain unique to mysterin, while functional exploration of these domains has also just commenced. In this review, the author attempts to summarize the core findings regarding the molecular structure and function of the mysterin protein, with an emphasis on the perspective of MMD research.
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Affiliation(s)
- Daisuke Morito
- Department of Biochemistry, Showa University School of Medicine, Hatanodai 1-5-8, Shinagawa, Tokyo 142-0064, Japan
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3
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Lee KW, Ryu KJ, Kim M, Lim S, Kim J, Kim JY, Hwangbo C, Yoo J, Cho YY, Kim KD. RCHY1 and OPTN are required for melanophagy, selective autophagy of melanosomes. Proc Natl Acad Sci U S A 2024; 121:e2318039121. [PMID: 38536750 PMCID: PMC10998605 DOI: 10.1073/pnas.2318039121] [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: 10/24/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024] Open
Abstract
Melanosomes are specific organelles dedicated to melanin synthesis and accumulation in melanocytes. Autophagy is suggestively involved in melanosome degradation, although the potential underlying molecular mechanisms remain elusive. In selective autophagy, autophagy receptors and E3-ligases are the key factors conferring cargo selectivity. In B16F10 cells, β-mangostin efficiently induced melanosome degradation without affecting other organelles such as mitochondria, peroxisomes, and the endoplasmic reticulum. Among various autophagy receptors, optineurin (OPTN) contributes TANK-binding kinase 1 (TBK1)-dependently to melanosome degradation and its knockdown inhibited β-mangostin-mediated melanosome degradation. OPTN translocation to melanosomes was dependent on its ubiquitin-binding domain. Moreover, OPTN-mediated TBK1 activation and subsequent TBK1-mediated S187 OPTN phosphorylation were essential for melanosome degradation. β-mangostin increased K63-linked melanosome ubiquitination. Finally, the E3-ligase RCHY1 knockdown inhibited the melanosome ubiquitination required for OPTN- and TBK1-phosphorylation as well as melanosome degradation. This study suggests that melanophagy, melanosome-selective autophagy, contributes to melanosome degradation, and OPTN and RCHY1 are an essential autophagy receptor and a E3-ligase, respectively, conferring cargo selectivity in melanophagy.
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Affiliation(s)
- Ki Won Lee
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju52828, South Korea
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
| | - Ki-jun Ryu
- Research Institute of Life Sciences, Gyeongsang National University, Jinju52828, South Korea
| | - Minju Kim
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
| | - Seyeon Lim
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
| | - Jisu Kim
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
| | - Jeong Yoon Kim
- Department of Pharmaceutical Engineering, Gyeongsang National University, Jinju52725, South Korea
| | - Cheol Hwangbo
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
- Division of Life Science, Gyeongsang National University, Jinju52828, South Korea
| | - Jiyun Yoo
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
- Division of Life Science, Gyeongsang National University, Jinju52828, South Korea
| | - Yong-Yeon Cho
- College of Pharmacy, The Catholic University of Korea, Wonmi-Gu, Bucheon-si, Gyeonggi-Do14662, South Korea
| | - Kwang Dong Kim
- Anti-aging Bio Cell factory Regional Leading Research Center, Gyeongsang National University, Jinju52828, South Korea
- Division of Applied Life Science (Brain Korea 21 Four), Gyeongsang National University, Jinju 52828, South Korea
- Division of Life Science, Gyeongsang National University, Jinju52828, South Korea
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju52828, South Korea
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4
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Wang Y, Hollingsworth LR, Sangaré LO, Paredes-Santos TC, Krishnamurthy S, Penn BH, Wu H, Saeij JPJ. Host E3 ubiquitin ligase ITCH mediates Toxoplasma gondii effector GRA35-triggered NLRP1 inflammasome activation and cell-autonomous immunity. mBio 2024; 15:e0330223. [PMID: 38376248 PMCID: PMC10936166 DOI: 10.1128/mbio.03302-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Toxoplasma gondii is an intracellular parasite that can activate the NLRP1 inflammasome leading to macrophage pyroptosis in Lewis rats, but the underlying mechanism is not well understood. In this study, we performed a genome-wide CRISPR screen and identified the dense granule proteins GRA35, GRA42, and GRA43 as the Toxoplasma effectors mediating cell death in Lewis rat macrophages. GRA35 localizes on the parasitophorous vacuole membrane, where it interacts with the host E3 ubiquitin ligase ITCH. Inhibition of proteasome activity or ITCH knockout prevented pyroptosis in Toxoplasma-infected Lewis rat macrophages, consistent with the "NLRP1 functional degradation model." However, there was no evidence that ITCH directly ubiquitinates or interacts with rat NLRP1. We also found that GRA35-ITCH interaction affected Toxoplasma fitness in IFNγ-activated human fibroblasts, likely due to ITCH's role in recruiting ubiquitin and the parasite-restriction factor RNF213 to the parasitophorous vacuole membrane. These findings identify a new role of host E3 ubiquitin ligase ITCH in mediating effector-triggered immunity, a critical concept that involves recognizing intracellular pathogens and initiating host innate immune responses.IMPORTANCEEffector-triggered immunity represents an innate immune defense mechanism that plays a crucial role in sensing and controlling intracellular pathogen infection. The NLRP1 inflammasome in the Lewis rats can detect Toxoplasma infection, which triggers proptosis in infected macrophages and eliminates the parasite's replication niche. The work reported here revealed that host E3 ubiquitin ligase ITCH is able to recognize and interact with Toxoplasma effector protein GRA35 localized on the parasite-host interface, leading to NLRP1 inflammasome activation in Lewis rat macrophages. Furthermore, ITCH-GRA35 interaction contributes to the restriction of Toxoplasma in human fibroblasts stimulated by IFNγ. Thus, this research provides valuable insights into understanding pathogen recognition and restriction mediated by host E3 ubiquitin ligase.
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Affiliation(s)
- Yifan Wang
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - L. Robert Hollingsworth
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Lamba Omar Sangaré
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Tatiana C. Paredes-Santos
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Shruthi Krishnamurthy
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Bennett H. Penn
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis Health, Sacramento, California, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Jeroen P. J. Saeij
- Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, California, USA
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5
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Lüder CGK. IFNs in host defence and parasite immune evasion during Toxoplasma gondii infections. Front Immunol 2024; 15:1356216. [PMID: 38384452 PMCID: PMC10879624 DOI: 10.3389/fimmu.2024.1356216] [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: 12/15/2023] [Accepted: 01/23/2024] [Indexed: 02/23/2024] Open
Abstract
Interferons (IFNs) are a family of cytokines with diverse functions in host resistance to pathogens and in immune regulation. Type II IFN, i.e. IFN-γ, is widely recognized as a major mediator of resistance to intracellular pathogens, including the protozoan Toxoplasma gondii. More recently, IFN-α/β, i.e. type I IFNs, and IFN-λ (type III IFN) have been identified to also play important roles during T. gondii infections. This parasite is a widespread pathogen of humans and animals, and it is a model organism to study cell-mediated immune responses to intracellular infection. Its success depends, among other factors, on the ability to counteract the IFN system, both at the level of IFN-mediated gene expression and at the level of IFN-regulated effector molecules. Here, I review recent advances in our understanding of the molecular mechanisms underlying IFN-mediated host resistance and immune regulation during T. gondii infections. I also discuss those mechanisms that T. gondii has evolved to efficiently evade IFN-mediated immunity. Knowledge of these fascinating host-parasite interactions and their underlying signalling machineries is crucial for a deeper understanding of the pathogenesis of toxoplasmosis, and it might also identify potential targets of parasite-directed or host-directed supportive therapies to combat the parasite more effectively.
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Affiliation(s)
- Carsten G. K. Lüder
- Institute for Medical Microbiology and Virology, University Medical Center Göttingen, Göttingen, Germany
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6
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Matta SK, Kohio HP, Chandra P, Brown A, Doench JG, Philips JA, Ding S, Sibley LD. Genome-wide and targeted CRISPR screens identify RNF213 as a mediator of interferon gamma-dependent pathogen restriction in human cells. Proc Natl Acad Sci U S A 2024; 121:e2315865120. [PMID: 38147552 PMCID: PMC10769850 DOI: 10.1073/pnas.2315865120] [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: 09/14/2023] [Accepted: 11/15/2023] [Indexed: 12/28/2023] Open
Abstract
To define cellular immunity to the intracellular pathogen Toxoplasma gondii, we performed a genome-wide CRISPR loss-of-function screen to identify genes important for (interferon gamma) IFN-γ-dependent growth restriction. We revealed a role for the tumor suppressor NF2/Merlin for maximum induction of Interferon Stimulated Genes (ISG), which are positively regulated by the transcription factor IRF-1. We then performed an ISG-targeted CRISPR screen that identified the host E3 ubiquitin ligase RNF213 as necessary for IFN-γ-mediated control of T. gondii in multiple human cell types. RNF213 was also important for control of bacterial (Mycobacterium tuberculosis) and viral (Vesicular Stomatitis Virus) pathogens in human cells. RNF213-mediated ubiquitination of the parasitophorous vacuole membrane (PVM) led to growth restriction of T. gondii in response to IFN-γ. Moreover, overexpression of RNF213 in naive cells also impaired growth of T. gondii. Surprisingly, growth inhibition did not require the autophagy protein ATG5, indicating that RNF213 initiates restriction independent of a previously described noncanonical autophagy pathway. Mutational analysis revealed that the ATPase domain of RNF213 was required for its recruitment to the PVM, while loss of a critical histidine in the RZ finger domain resulted in partial reduction of recruitment to the PVM and complete loss of ubiquitination. Both RNF213 mutants lost the ability to restrict growth of T. gondii, indicating that both recruitment and ubiquitination are required. Collectively, our findings establish RNF213 as a critical component of cell-autonomous immunity that is both necessary and sufficient for control of intracellular pathogens in human cells.
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Affiliation(s)
- Sumit K. Matta
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St Louis, MO63130
| | - Hinissan P. Kohio
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St Louis, MO63130
| | - Pallavi Chandra
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Washington University in St. Louis, St Louis, MO63130
| | - Adam Brown
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA02142
| | - John G. Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA02142
| | - Jennifer A. Philips
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St Louis, MO63130
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Washington University in St. Louis, St Louis, MO63130
| | - Siyuan Ding
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St Louis, MO63130
| | - L. David Sibley
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St Louis, MO63130
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7
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Clough B, Fisch D, Mize TH, Encheva V, Snijders A, Frickel EM. p97/VCP targets Toxoplasma gondii vacuoles for parasite restriction in interferon-stimulated human cells. mSphere 2023; 8:e0051123. [PMID: 37975677 PMCID: PMC10732073 DOI: 10.1128/msphere.00511-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Toxoplasma gondii (Tg) is a ubiquitous parasitic pathogen, infecting about one-third of the global population. Tg is controlled in immunocompetent people by mechanisms that are not fully understood. Tg infection drives the production of the inflammatory cytokine interferon gamma (IFNγ), which upregulates intracellular anti-pathogen defense pathways. In this study, we describe host proteins p97/VCP, UBXD1, and ANKRD13A that control Tg at the parasitophorous vacuole (PV) in IFNγ-stimulated endothelial cells. p97/VCP is an ATPase that interacts with a network of cofactors and is active in a wide range of ubiquitin-dependent cellular processes. We demonstrate that PV ubiquitination is a pre-requisite for recruitment of these host defense proteins, and their deposition directs Tg PVs to acidification in endothelial cells. We show that p97/VCP universally targets PVs in human cells and restricts Tg in different human cell types. Overall, these findings reveal new players of intracellular host defense of a vacuolated pathogen.
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Affiliation(s)
- Barbara Clough
- Institute for Microbiology and Infection, School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Daniel Fisch
- Institute for Microbiology and Infection, School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Todd H. Mize
- Advanced Mass Spectrometry Facility, School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
| | - Vesela Encheva
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Ambrosius Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Eva-Maria Frickel
- Institute for Microbiology and Infection, School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, London, United Kingdom
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8
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Gao L, Zhang W, Shi XH, Chang X, Han Y, Liu C, Jiang Z, Yang X. The mechanism of linear ubiquitination in regulating cell death and correlative diseases. Cell Death Dis 2023; 14:659. [PMID: 37813853 PMCID: PMC10562472 DOI: 10.1038/s41419-023-06183-3] [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: 06/23/2023] [Revised: 09/13/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Linear ubiquitination is a specific post-translational modification in which ubiquitin is linked through M1 residue to form multiple types of polyubiquitin chains on substrates in order to regulate cellular processes. LUBAC comprised by HOIP, HOIL-1L, and SHARPIN as a sole E3 ligase catalyzes the generation of linear ubiquitin chains, and it is simultaneously adjusted by deubiquitinases such as OTULIN and CYLD. Several studies have shown that gene mutation of linear ubiquitination in mice accompanied by different modalities of cell death would develop relative diseases. Cell death is a fundamental physiological process and responsible for embryonic development, organ maintenance, and immunity response. Therefore, it is worth speculating that linear ubiquitin mediated signaling pathway would participate in different diseases. The relative literature search was done from core collection of electronic databases such as Web of Science, PubMed, and Google Scholar using keywords about main regulators of linear ubiquitination pathway. Here, we summarize the regulatory mechanism of linear ubiquitination on cellular signaling pathway in cells with apoptosis, necroptosis, autophagy, pyroptosis, and ferroptosis. Intervening generation of linear ubiquitin chains in relative signaling pathway to regulate cell death might provide novel therapeutic insights for various human diseases.
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Affiliation(s)
- Liyuan Gao
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Wei Zhang
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Xiao Hui Shi
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Xiaoyan Chang
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Yi Han
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Chundi Liu
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China
| | - Zhitao Jiang
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China.
| | - Xiang Yang
- Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou, China.
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9
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Rivera-Cuevas Y, Clough B, Frickel EM. Human guanylate-binding proteins in intracellular pathogen detection, destruction, and host cell death induction. Curr Opin Immunol 2023; 84:102373. [PMID: 37536111 DOI: 10.1016/j.coi.2023.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/05/2023]
Abstract
Cell-intrinsic defense is an essential part of the immune response against intracellular pathogens regulated by cytokine-induced proteins and pathways. One of the most upregulated families of proteins in this defense system are the guanylate-binding proteins (GBPs), large GTPases of the dynamin family, induced in response to interferon gamma. Human GBPs (hGBPs) exert their antimicrobial activity through detection of pathogen-associated molecular patterns and/or damage-associated molecular patterns to execute control mechanisms directed at the pathogen itself as well as the vacuolar compartments in which it resides. Consequently, hGBPs are also inducers of canonical and noncanonical inflammasome responses leading to host cell death. The mechanisms are both cell-type and pathogen-dependent with hGBP1 acting as a pioneer sensor for intracellular invaders. This review focuses on the most recent functional roles of hGBPs in pathways of pathogen detection, destruction, and host cell death induction.
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Affiliation(s)
- Yolanda Rivera-Cuevas
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Barbara Clough
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom
| | - Eva-Maria Frickel
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston B15 2TT, United Kingdom.
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10
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Zhang Y, Yuan Y, Jiang L, Liu Y, Zhang L. The emerging role of E3 ubiquitin ligase RNF213 as an antimicrobial host determinant. Front Cell Infect Microbiol 2023; 13:1205355. [PMID: 37655297 PMCID: PMC10465799 DOI: 10.3389/fcimb.2023.1205355] [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: 04/13/2023] [Accepted: 07/24/2023] [Indexed: 09/02/2023] Open
Abstract
Ring finger protein 213 (RNF213) is a large E3 ubiquitin ligase with a molecular weight of 591 kDa that is associated with moyamoya disease, a rare cerebrovascular disease. It is located in the cytosol and perinuclear space. Missense mutations in this gene have been found to be more prevalent in patients with moyamoya disease compared with that in healthy individuals. Understanding the molecular function of RNF213 could provide insights into moyamoya disease. RNF213 contains a C3HC4-type RING finger domain with an E3 ubiquitin ligase domain and six AAA+ adenosine triphosphatase (ATPase) domains. It is the only known protein with both AAA+ ATPase and ubiquitin ligase activities. Recent studies have highlighted the role of RNF213 in fighting against microbial infections, including viruses, parasites, bacteria, and chlamydiae. This review aims to summarize the recent research progress on the mechanisms of RNF213 in pathogenic infections, which will aid researchers in understanding the antimicrobial role of RNF213.
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Affiliation(s)
- Yulu Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yupei Yuan
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Lu Jiang
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yihan Liu
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Leiliang Zhang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, China
- Department of Pathogen Biology, School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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11
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Szczesna M, Huang Y, Lacoursiere RE, Bonini F, Pol V, Koc F, Ward B, Geurink PP, Pruneda JN, Thurston TL. Dedicated bacterial esterases reverse lipopolysaccharide ubiquitylation to block immune sensing. RESEARCH SQUARE 2023:rs.3.rs-2986327. [PMID: 37503018 PMCID: PMC10371091 DOI: 10.21203/rs.3.rs-2986327/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Pathogenic bacteria have evolved diverse mechanisms to counteract cell-autonomous immunity, which otherwise guards both immune and non-immune cells from the onset of an infection1,2. The versatile immunity protein Ring finger protein 213 (RNF213)3-6 mediates the non-canonical ester-linked ubiquitylation of lipopolysaccharide (LPS), marking bacteria that sporadically enter the cytosol for destruction by antibacterial autophagy4. However, whether cytosol-adapted pathogens are ubiquitylated on their LPS and whether they escape RNF213-mediated immunity, remains unknown. Here we show that Burkholderia deubiquitylase (DUB), TssM7-9, is a potent esterase that directly reverses the ubiquitylation of LPS. Without TssM, cytosolic Burkholderia became coated in polyubiquitin and autophagy receptors in an RNF213-dependent fashion. Whereas the expression of TssM was sufficient to enable the replication of the non-cytosol adapted pathogen Salmonella, we demonstrate that Burkholderia has evolved a multi-layered defence system to proliferate in the host cell cytosol, including a block in antibacterial autophagy10-12. Structural analysis provided insight into the molecular basis of TssM esterase activity, allowing it to be uncoupled from isopeptidase function. TssM homologs conserved in another Gram-negative pathogen also reversed non-canonical LPS ubiquitylation, establishing esterase activity as a bacterial virulence mechanism to subvert host cell-autonomous immunity.
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Affiliation(s)
- Magdalena Szczesna
- Department of Infectious Disease, Centre for Bacteriology Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - Yizhou Huang
- Department of Infectious Disease, Centre for Bacteriology Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - Rachel E. Lacoursiere
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Francesca Bonini
- Department of Infectious Disease, Centre for Bacteriology Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - Vito Pol
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Fulya Koc
- Department of Infectious Disease, Centre for Bacteriology Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - Beatrice Ward
- Department of Infectious Disease, Centre for Bacteriology Resistance Biology, Imperial College London, London, SW7 2AZ, UK
| | - Paul P. Geurink
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Teresa L.M. Thurston
- Department of Infectious Disease, Centre for Bacteriology Resistance Biology, Imperial College London, London, SW7 2AZ, UK
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12
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Lockyer EJ, Torelli F, Butterworth S, Song OR, Howell S, Weston A, East P, Treeck M. A heterotrimeric complex of Toxoplasma proteins promotes parasite survival in interferon gamma-stimulated human cells. PLoS Biol 2023; 21:e3002202. [PMID: 37459303 PMCID: PMC10373997 DOI: 10.1371/journal.pbio.3002202] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 07/27/2023] [Accepted: 06/16/2023] [Indexed: 07/28/2023] Open
Abstract
Toxoplasma gondii secretes protein effectors to subvert the human immune system sufficiently to establish a chronic infection. Relative to murine infections, little is known about which parasite effectors disarm human immune responses. Here, we used targeted CRISPR screening to identify secreted protein effectors required for parasite survival in IFNγ-activated human cells. Independent screens were carried out using 2 Toxoplasma strains that differ in virulence in mice, leading to the identification of effectors required for survival in IFNγ-activated human cells. We identify the secreted protein GRA57 and 2 other proteins, GRA70 and GRA71, that together form a complex which enhances the ability of parasites to persist in IFNγ-activated human foreskin fibroblasts (HFFs). Components of the protein machinery required for export of Toxoplasma proteins into the host cell were also found to be important for parasite resistance to IFNγ in human cells, but these export components function independently of the identified protein complex. Host-mediated ubiquitination of the parasite vacuole has previously been associated with increased parasite clearance from human cells, but we find that vacuoles from GRA57, GRA70, and GRA71 knockout strains are surprisingly less ubiquitinated by the host cell. We hypothesise that this is likely a secondary consequence of deletion of the complex, unlinked to the IFNγ resistance mediated by these effectors.
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Affiliation(s)
- Eloise J Lockyer
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Francesca Torelli
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Simon Butterworth
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ok-Ryul Song
- High-Throughput Screening Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Steven Howell
- Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Anne Weston
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Philip East
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
- Cell Biology of Host-Pathogen Interaction Laboratory, Instituto Gulbenkian Ciência, Oeiras, Portugal
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13
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Apte S, Bhutda S, Ghosh S, Sharma K, Barton TE, Dibyachintan S, Sahay O, Roy S, Sinha AR, Adicherla H, Rakshit J, Tang S, Datey A, Santra S, Joseph J, Sasidharan S, Hammerschmidt S, Chakravortty D, Oggioni MR, Santra MK, Neill DR, Banerjee A. An innate pathogen sensing strategy involving ubiquitination of bacterial surface proteins. SCIENCE ADVANCES 2023; 9:eade1851. [PMID: 36947610 PMCID: PMC10032600 DOI: 10.1126/sciadv.ade1851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Sensing of pathogens by ubiquitination is a critical arm of cellular immunity. However, universal ubiquitination targets on microbes remain unidentified. Here, using in vitro, ex vivo, and in vivo studies, we identify the first protein-based ubiquitination substrates on phylogenetically diverse bacteria by unveiling a strategy that uses recognition of degron-like motifs. Such motifs form a new class of intra-cytosolic pathogen-associated molecular patterns (PAMPs). Their incorporation enabled recognition of nonubiquitin targets by host ubiquitin ligases. We find that SCFFBW7 E3 ligase, supported by the regulatory kinase, glycogen synthase kinase 3β, is crucial for effective pathogen detection and clearance. This provides a mechanistic explanation for enhanced risk of infections in patients with chronic lymphocytic leukemia bearing mutations in F-box and WD repeat domain containing 7 protein. We conclude that exploitation of this generic pathogen sensing strategy allows conservation of host resources and boosts antimicrobial immunity.
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Affiliation(s)
- Shruti Apte
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Smita Bhutda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Sourav Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Kuldeep Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Thomas E. Barton
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, L69 7BE Liverpool, UK
| | - Soham Dibyachintan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Osheen Sahay
- Cancer Biology and Epigenetics Laboratory, National Centre for Cell Science, Ganeshkhind Road, Pune 411007, Maharashtra, India
| | - Suvapriya Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Akash Raj Sinha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Harikrishna Adicherla
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Habsiguda, Hyderabad 500007 Telangana, India
| | - Jyotirmoy Rakshit
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Shiying Tang
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Akshay Datey
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Shweta Santra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Jincy Joseph
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Sreeja Sasidharan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute of Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, D-17487 Greifswald, Germany
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Marco R. Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Manas Kumar Santra
- Cancer Biology and Epigenetics Laboratory, National Centre for Cell Science, Ganeshkhind Road, Pune 411007, Maharashtra, India
| | - Daniel R. Neill
- Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, L69 7BE Liverpool, UK
| | - Anirban Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
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14
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CRISPR Screens Identify Toxoplasma Genes That Determine Parasite Fitness in Interferon Gamma-Stimulated Human Cells. mBio 2023; 14:e0006023. [PMID: 36916910 PMCID: PMC10128063 DOI: 10.1128/mbio.00060-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Toxoplasma virulence depends on its ability to evade or survive the toxoplasmacidal mechanisms induced by interferon gamma (IFNγ). While many Toxoplasma genes involved in the evasion of the murine IFNγ response have been identified, genes required to survive the human IFNγ response are largely unknown. In this study, we used a genome-wide loss-of-function screen to identify Toxoplasma genes important for parasite fitness in IFNγ-stimulated primary human fibroblasts. We generated gene knockouts for the top six hits from the screen and confirmed their importance for parasite growth in IFNγ-stimulated human fibroblasts. Of these six genes, three have homology to GRA32, localize to dense granules, and coimmunoprecipitate with each other and GRA32, suggesting they might form a complex. Deletion of individual members of this complex leads to early parasite egress in IFNγ-stimulated cells. Thus, prevention of early egress is an important Toxoplasma fitness determinant in IFNγ-stimulated human cells. IMPORTANCE Toxoplasma infection causes serious complications in immunocompromised individuals and in the developing fetus. During infection, certain immune cells release a protein called interferon gamma that activates cells to destroy the parasite or inhibit its growth. While most Toxoplasma parasites are cleared by this immune response, some can survive by blocking or evading the IFNγ-induced restrictive environment. Many Toxoplasma genes that determine parasite survival in IFNγ-activated murine cells are known but parasite genes conferring fitness in IFNγ-activated human cells are largely unknown. Using a Toxoplasma adapted genome-wide loss-of-function screen, we identified many Toxoplasma genes that determine parasite fitness in IFNγ-activated human cells. The gene products of four top hits play a role in preventing early parasite egress in IFNγ-stimulated human cells. Understanding how IFNγ-stimulated human cells inhibit Toxoplasma growth and how Toxoplasma counteracts this, could lead to the development of novel therapeutics.
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15
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Gilliland HN, Olive AJ. GarD-ing the pathogen-containing vacuole from destruction. Cell Host Microbe 2022; 30:1655-1657. [PMID: 36521440 DOI: 10.1016/j.chom.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human pathogen Chlamydia trachomatis evades killing by IFNγ-activated mechanisms, yet how this occurs remains unclear. In this issue of Cell Host & Microbe, Walsh et al. identify an IFNγ-dependent antimicrobial mechanism mediated by the host ubiquitin ligase RNF213 that is evaded by the Chlamydia effector GarD.
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Affiliation(s)
- Haleigh N Gilliland
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Andrew J Olive
- Department of Microbiology and Molecular Genetics, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA.
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