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Dai Y, Zhou J, Shi C. Inflammasome: structure, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e391. [PMID: 37817895 PMCID: PMC10560975 DOI: 10.1002/mco2.391] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 10/12/2023] Open
Abstract
Inflammasomes are a group of protein complex located in cytoplasm and assemble in response to a wide variety of pathogen-associated molecule patterns, damage-associated molecule patterns, and cellular stress. Generally, the activation of inflammasomes will lead to maturation of proinflammatory cytokines and pyroptotic cell death, both associated with inflammatory cascade amplification. A sensor protein, an adaptor, and a procaspase protein interact through their functional domains and compose one subunit of inflammasome complex. Under physiological conditions, inflammasome functions against pathogen infection and endogenous dangers including mtROS, mtDNA, and so on, while dysregulation of its activation can lead to unwanted results. In recent years, advances have been made to clarify the mechanisms of inflammasome activation, the structural details of them and their functions (negative/positive) in multiple disease models in both animal models and human. The wide range of the stimuli makes the function of inflammasome diverse and complex. Here, we review the structure, biological functions, and therapeutic targets of inflammasomes, while highlight NLRP3, NLRC4, and AIM2 inflammasomes, which are the most well studied. In conclusion, this review focuses on the activation process, biological functions, and structure of the most well-studied inflammasomes, summarizing and predicting approaches for disease treatment and prevention with inflammasome as a target. We aim to provide fresh insight into new solutions to the challenges in this field.
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Affiliation(s)
- Yali Dai
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
| | - Jing Zhou
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
- Institute of ImmunologyArmy Medical UniversityChongqingChina
| | - Chunmeng Shi
- Institute of Rocket Force MedicineState Key Laboratory of Trauma and Chemical PoisoningArmy Medical UniversityChongqingChina
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2
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Xiong H, Cui M, Kong N, Jing J, Xu Y, Liu X, Yang F, Xu Z, Yan Y, Zhao D, Zou Z, Xia M, Cen J, Tan G, Huai C, Fu Q, Guo Q, Chen K. Cytotoxic CD161 -CD8 + T EMRA cells contribute to the pathogenesis of systemic lupus erythematosus. EBioMedicine 2023; 90:104507. [PMID: 36893588 PMCID: PMC10011749 DOI: 10.1016/j.ebiom.2023.104507] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease affecting multiple organs and tissues with high cellular heterogeneity. CD8+ T cell activity is involved in the SLE pathogenesis. However, the cellular heterogeneity and the underlying mechanisms of CD8+ T cells in SLE remain to be identified. METHODS Single-cell RNA sequencing (scRNA-seq) of PBMCs from a SLE family pedigree (including 3 HCs and 2 SLE patients) was performed to identify the SLE-associated CD8+ T cell subsets. Flow cytometry analysis of a SLE cohort (including 23 HCs and 33 SLE patients), qPCR analysis of another SLE cohort (including 30 HCs and 25 SLE patients) and public scRNA-seq datasets of autoimmune diseases were employed to validate the finding. Whole-exome sequencing (WES) of this SLE family pedigree was used to investigate the genetic basis in dysregulation of CD8+ T cell subsets identified in this study. Co-culture experiments were performed to analyze the activity of CD8+ T cells. FINDINGS We elucidated the cellular heterogeneity of SLE and identified a new highly cytotoxic CD8+ T cell subset, CD161-CD8+ TEMRA cell subpopulation, which was remarkably increased in SLE patients. Meanwhile, we discovered a close correlation between mutation of DTHD1 and the abnormal accumulation of CD161-CD8+ TEMRA cells in SLE. DTHD1 interacted with MYD88 to suppress its activity in T cells and DTHD1 mutation promoted MYD88-dependent pathway and subsequently increased the proliferation and cytotoxicity of CD161-CD8+ TEMRA cells. Furthermore, the differentially expressed genes in CD161-CD8+ TEMRA cells displayed a strong out-of-sample prediction for case-control status of SLE. INTERPRETATION This study identified DTHD1-associated expansion of CD161-CD8+ TEMRA cell subpopulation is critical for SLE. Our study highlights genetic association and cellular heterogeneity of SLE pathogenesis and provides a mechanistical insight into the diagnosis and treatment of SLE. FUNDINGS Stated in the Acknowledgements section of the manuscript.
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Affiliation(s)
- Hui Xiong
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China
| | - Mintian Cui
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200127, China
| | - Ni Kong
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200127, China
| | - Jiongjie Jing
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200127, China
| | - Ying Xu
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China
| | - Xiuting Liu
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China
| | - Fan Yang
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200127, China
| | - Zhen Xu
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200127, China
| | - Yu Yan
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200127, China
| | - Dongyang Zhao
- Department of Internal Emergency Medicine and Critical Care, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Ziqi Zou
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Meng Xia
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Junjie Cen
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China
| | - Guozhen Tan
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qiong Fu
- Department of Rheumatology, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200127, China
| | - Qing Guo
- Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China.
| | - Kun Chen
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200127, China; Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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3
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Novel NLRP14 Mutations Induce Azoospermia. Andrologia 2023. [DOI: 10.1155/2023/9295049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Background. LR family pyrin domain-containing 14 (NLRP14 or NALP14) is one of the important members of the NLR family and was mainly expressed in testis. It is reported that deficiency in the NALP14 gene in mice can cause spermatogenic failure, and several NALP14 mutations have been found in oligospermia and infertile men. Case Presentation. This study reported two novel NALP14 mutations (c.2076delC: p.L697X and c.T2963C: p.F988S) in our patients with azoospermia. The exonic deletion mutation (c.2076delC) and one missense mutation (c.T2963C) were firstly screened out by whole-exome sequencing (WES) and further verified by amplifying and sequencing the specific exons 5 and 10. Histological analysis of testicular biopsy revealed that NALP14 expression was detected strongly in spermatogonia and weakly in early spermatocytes. Additionally, mutations in this gene caused meiotic arrest, and no postmeiotic round spermatids and mature spermatozoa were observed in the seminiferous tubules. Conclusions. This study and previous literatures showed that NLRP14 mutations are closely related to male infertility; we discovered two novel NALP14 mutations and summarized the kinds of literatures on NLRP14 mutations and male infertility. This is the first report that deletion mutation (c.2076delC) and one missense mutation (c.T2963C) in NALP14 all lead to azoospermia, which is still significant to the clinical auxiliary diagnosis of male infertility.
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Li K, Zheng J, Wirawan M, Trinh NM, Fedorova O, Griffin PR, Pyle AM, Luo D. Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3). Nucleic Acids Res 2021; 49:9978-9991. [PMID: 34403472 PMCID: PMC8464030 DOI: 10.1093/nar/gkab712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
DRH-3 is critically involved in germline development and RNA interference (RNAi) facilitated chromosome segregation via the 22G-siRNA pathway in Caenorhabditis elegans. DRH-3 has similar domain architecture to RIG-I-like receptors (RLRs) and belongs to the RIG-I-like RNA helicase family. The molecular understanding of DRH-3 and its function in endogenous RNAi pathways remains elusive. In this study, we solved the crystal structures of the DRH-3 N-terminal domain (NTD) and the C-terminal domains (CTDs) in complex with 5'-triphosphorylated RNAs. The NTD of DRH-3 adopts a distinct fold of tandem caspase activation and recruitment domains (CARDs) structurally similar to the CARDs of RIG-I and MDA5, suggesting a signaling function in the endogenous RNAi biogenesis. The CTD preferentially recognizes 5'-triphosphorylated double-stranded RNAs bearing the typical features of secondary siRNA transcripts. The full-length DRH-3 displays unique structural dynamics upon binding to RNA duplexes that differ from RIG-I or MDA5. These features of DRH-3 showcase the evolutionary divergence of the Dicer and RLR family of helicases.
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Affiliation(s)
- Kuohan Li
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Jie Zheng
- The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Melissa Wirawan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Nguyen Mai Trinh
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
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Mahdizadeh SJ, Thomas M, Eriksson LA. Reconstruction of the Fas-Based Death-Inducing Signaling Complex (DISC) Using a Protein-Protein Docking Meta-Approach. J Chem Inf Model 2021; 61:3543-3558. [PMID: 34196179 PMCID: PMC8389534 DOI: 10.1021/acs.jcim.1c00301] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The death-inducing signaling complex (DISC) is a fundamental multiprotein complex, which triggers the extrinsic apoptosis pathway through stimulation by death ligands. DISC consists of different death domain (DD) and death effector domain (DED) containing proteins such as the death receptor Fas (CD95) in complex with FADD, procaspase-8, and cFLIP. Despite many experimental and theoretical studies in this area, there is no global agreement neither on the DISC architecture nor on the mechanism of action of the involved species. In the current work, we have tried to reconstruct the DISC structure by identifying key protein interactions using a new protein-protein docking meta-approach. We combined the benefits of five of the most employed protein-protein docking engines, HADDOCK, ClusPro, HDOCK, GRAMM-X, and ZDOCK, in order to improve the accuracy of the predicted docking complexes. Free energy of binding and hot spot interacting residues were calculated and determined for each protein-protein interaction using molecular mechanics generalized Born surface area and alanine scanning techniques, respectively. In addition, a series of in-cellulo protein-fragment complementation assays were conducted to validate the protein-protein docking procedure. The results show that the DISC formation initiates by dimerization of adjacent FasDD trimers followed by recruitment of FADD through homotypic DD interactions with the oligomerized death receptor. Furthermore, the in-silico outcomes indicate that cFLIP cannot bind directly to FADD; instead, cFLIP recruitment to the DISC is a hierarchical and cooperative process where FADD initially recruits procaspase-8, which in turn recruits and heterodimerizes with cFLIP. Finally, a possible structure of the entire DISC is proposed based on the docking results.
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Affiliation(s)
- Sayyed Jalil Mahdizadeh
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Melissa Thomas
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Göteborg, Sweden
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6
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Great balls of fire: activation and signalling of inflammatory caspases. Biochem Soc Trans 2021; 49:1311-1324. [PMID: 34060593 PMCID: PMC8286819 DOI: 10.1042/bst20200986] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/17/2022]
Abstract
Innate immune responses are tightly regulated by various pathways to control infections and maintain homeostasis. One of these pathways, the inflammasome pathway, activates a family of cysteine proteases called inflammatory caspases. They orchestrate an immune response by cleaving specific cellular substrates. Canonical inflammasomes activate caspase-1, whereas non-canonical inflammasomes activate caspase-4 and -5 in humans and caspase-11 in mice. Caspases are highly specific enzymes that select their substrates through diverse mechanisms. During inflammation, caspase activity is responsible for the secretion of inflammatory cytokines and the execution of a form of lytic and inflammatory cell death called pyroptosis. This review aims to bring together our current knowledge of the biochemical processes behind inflammatory caspase activation, substrate specificity, and substrate signalling.
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7
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Giamogante F, Poggio E, Barazzuol L, Covallero A, Calì T. Apoptotic signals at the endoplasmic reticulum-mitochondria interface. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 126:307-343. [PMID: 34090618 DOI: 10.1016/bs.apcsb.2021.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The maintenance of cellular homeostasis involves the participation of multiple organelles, such as the endoplasmic reticulum (ER) and mitochondria. Specifically, ER plays a key role in calcium (Ca2+) storage, lipid synthesis, protein folding, and assembly, while mitochondria are the "energy factories" and provide energy to drive intracellular processes. Hence, alteration in ER or mitochondrial homeostasis has detrimental effects on cell survival, being linked to the triggering of apoptosis, a programmed form of cell death. Besides, ER stress conditions affect mitochondria functionality and vice-versa, as ER and mitochondria communicate via mitochondria-associated ER membranes (MAMs) to carry out a number of fundamental cellular functions. It is not surprising, thus, that also MAMs perturbations are involved in the regulation of apoptosis. This chapter intends to accurately discuss the involvement of MAMs in apoptosis, highlighting their crucial role in controlling this delicate cellular process.
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Affiliation(s)
- Flavia Giamogante
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Elena Poggio
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Alberto Covallero
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
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8
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Devi S, Stehlik C, Dorfleutner A. An Update on CARD Only Proteins (COPs) and PYD Only Proteins (POPs) as Inflammasome Regulators. Int J Mol Sci 2020; 21:E6901. [PMID: 32962268 PMCID: PMC7555848 DOI: 10.3390/ijms21186901] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/17/2020] [Accepted: 09/17/2020] [Indexed: 12/18/2022] Open
Abstract
Inflammasomes are protein scaffolds required for the activation of caspase-1 and the subsequent release of interleukin (IL)-1β, IL-18, and danger signals, as well as the induction of pyroptotic cell death to restore homeostasis following infection and sterile tissue damage. However, excessive inflammasome activation also causes detrimental inflammatory disease. Therefore, extensive control mechanisms are necessary to prevent improper inflammasome responses and inflammatory disease. Inflammasomes are assembled by sequential nucleated polymerization of Pyrin domain (PYD) and caspase recruitment domain (CARD)-containing inflammasome components. Once polymerization is nucleated, this process proceeds in a self-perpetuating manner and represents a point of no return. Therefore, regulation of this key step is crucial for a controlled inflammasome response. Here, we provide an update on two single domain protein families containing either a PYD or a CARD, the PYD-only proteins (POPs) and CARD-only proteins (COPs), respectively. Their structure allows them to occupy and block access to key protein-protein interaction domains necessary for inflammasome assembly, thereby regulating the threshold of these nucleated polymerization events, and consequently, the inflammatory host response.
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Affiliation(s)
- Savita Devi
- Department of Pathology and Laboratory Medicine, Cedars Sinai, Los Angeles, CA 90048, USA;
| | - Christian Stehlik
- Department of Pathology and Laboratory Medicine, Cedars Sinai, Los Angeles, CA 90048, USA;
- Department of Biomedical Sciences, and Samuel Oschin Comprehensive Cancer Institute, Cedars Sinai, Los Angeles, CA 90048, USA
| | - Andrea Dorfleutner
- Department of Pathology and Laboratory Medicine, Cedars Sinai, Los Angeles, CA 90048, USA;
- Department of Biomedical Sciences, Cedars Sinai, Los Angeles, CA 90048, USA
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The Evolutionary Origins of Programmed Cell Death Signaling. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036442. [PMID: 31818855 DOI: 10.1101/cshperspect.a036442] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Programmed cell death (PCD) pathways are found in many phyla, ranging from developmentally programmed apoptosis in animals to cell-autonomous programmed necrosis pathways that limit the spread of biotrophic pathogens in multicellular assemblies. Prominent examples for the latter include animal necroptosis and pyroptosis, plant hypersensitive response (HR), and fungal heterokaryon incompatibility (HI) pathways. PCD pathways in the different kingdoms show fundamental differences in execution mechanism, morphology of the dying cells, and in the biological sequelae. Nevertheless, recent studies have revealed remarkable evolutionary parallels, including a striking sequence relationship between the "HeLo" domains found in the pore-forming components of necroptosis and some types of plant HR and fungal HI pathways. Other PCD execution components show cross-kingdom conservation as well, or are derived from prokaryotic ancestors. The currently available data suggest a model, wherein the primordial eukaryotic PCD pathway used proteins similar to present-day plant R-proteins and caused necrotic cell death by direct action of Toll and IL-1 receptor (TIR) and HeLo-like domains.
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Wang B, Bhattacharya M, Roy S, Tian Y, Yin Q. Immunobiology and structural biology of AIM2 inflammasome. Mol Aspects Med 2020; 76:100869. [PMID: 32660715 DOI: 10.1016/j.mam.2020.100869] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/15/2022]
Abstract
Absent in melanoma 2 (AIM2) is a cytoplasmic sensor that upon recognizing double-stranded DNA assembles with apoptosis-associated speck-like protein containing a CARD (ASC) and procaspase-1 to form the multi-protein complex AIM2 inflammasome. Double-stranded DNA from bacterial, viral, or host cellular origins triggers AIM2 inflammasome assembly and activation, ultimately resulting in secretion of proinflammatory cytokines and pyroptotic cell death in order to eliminate microbial infection. Many pathogens therefore evade or suppress AIM2 inflammasome to establish infection. On the other hand, AIM2 activation is tightly controlled by multiple cellular factors to prevent autoinflammation. Extensive structural studies have captured the molecular details of multiple steps in AIM2 inflammasome assembly. The structures collectively revealed a nucleated polymerization mechanism that not only pervades each step of AIM2 inflammasome assembly, but also underlies assembly of other inflammasomes and complexes in immune signaling. In this article, we briefly review the identification of AIM2 as a cytoplasmic DNA sensor, summarize the importance of AIM2 inflammasome in infections and diseases, and discuss the molecular mechanisms of AIM2 assembly, activation, and regulation using recent cellular, biochemical, and structural results.
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Affiliation(s)
- Bing Wang
- Department of Biological Science, Florida State University, Tallahassee, FL, 32301, USA
| | - Madhurima Bhattacharya
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32301, USA
| | - Sayantan Roy
- Department of Biological Science, Florida State University, Tallahassee, FL, 32301, USA
| | - Yuan Tian
- Department of Biological Science, Florida State University, Tallahassee, FL, 32301, USA
| | - Qian Yin
- Department of Biological Science, Florida State University, Tallahassee, FL, 32301, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32301, USA.
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11
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Assembly of platforms for signal transduction in the new era: dimerization, helical filament assembly, and beyond. Exp Mol Med 2020; 52:356-366. [PMID: 32139779 PMCID: PMC7156525 DOI: 10.1038/s12276-020-0391-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/31/2020] [Indexed: 11/08/2022] Open
Abstract
Supramolecular organizing center (SMOC)-mediated signal transduction is an emerging concept in the field of signal transduction that is ushering in a new era. The formation of location-specific, higher-order SMOCs is particularly important for cell death and innate immune signaling processes. Several protein interaction domains, including the death domain (DD) superfamily and the CIDE domain, are representative mediators of SMOC assembly in cell death and innate immune signaling pathways. DD superfamily- and CIDE domain-containing proteins form SMOCs that activate various caspases and provide signaling scaffold platforms. These assemblies can lead to signal transduction and amplification during signaling events. In this review, we summarize recent findings on the molecular basis of DD superfamily- and CIDE domain-mediated SMOC formation. Improved understanding of large molecular signaling complexes that form during innate (nonspecific) immune responses could help develop treatments for multiple diseases including cancer. Correct cell signaling requires precise protein interactions and binding, which are mediated by specific sites on the surface of the protein molecules involved. Innate immune responses and cell death mechanisms rely on such protein interactions, and defects can cause signaling abnormalities and trigger disease. Hyun Ho Park and co-workers at Chung-Ang University in Seoul, South Korea, reviewed recent insights into the presence of supramolecular organizing centers (SMOCs), localized complexes of signaling proteins that form during immune responses. The researchers highlight existing understanding of SMOC assembly processes. A better understanding of SMOCs will help to explain enzyme activation, signal amplification and cell signaling control mechanisms.
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12
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Agrawal I, Jha S. Comprehensive review of ASC structure and function in immune homeostasis and disease. Mol Biol Rep 2020; 47:3077-3096. [PMID: 32124174 DOI: 10.1007/s11033-020-05345-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/22/2020] [Indexed: 12/17/2022]
Abstract
Apoptosis associated speck like protein containing CARD (ASC) is widely researched and recognized as an adaptor protein participating in inflammasome assembly and pyroptosis. It contains a bipartite structure comprising of a pyrin and a caspase recruitment domain (CARD) domain. These two domains help ASC function as an adaptor molecule. ASC is encoded by the gene PYCARD. ASC plays pivotal role in various diseases as well as different homeostatic processes. ASC plays a regulatory role in different cancers showing differential regulation with respect to tissue and stage of disease. Besides cancer, ASC also plays a central role in sensing, regulation, and/or disease progression in bacterial infections, viral infections and in varied inflammatory diseases. ASC is expressed in different types of immune and non-immune cells. Its localization pattern also varies with different kinds of stimuli encountered by cell. This review will summarize the literature on the structure cellular and tissue expression, localization and disease association of ASC.
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Affiliation(s)
- Ishan Agrawal
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 65, Nagaur Road, Karwad, Jodhpur, Rajasthan, 342037, India
| | - Sushmita Jha
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 65, Nagaur Road, Karwad, Jodhpur, Rajasthan, 342037, India.
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13
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Dimos BA, Butler CC, Ricci CA, MacKnight NJ, Mydlarz LD. Responding to Threats Both Foreign and Domestic: NOD-Like Receptors in Corals. Integr Comp Biol 2020; 59:819-829. [PMID: 31236558 DOI: 10.1093/icb/icz111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Historically mechanisms with which basal animals such as reef-building corals use to respond to changing and increasingly stressful environments have remained elusive. However, the increasing availability of genomic and transcriptomic data from these organisms has provided fundamental insights into the biology of these critically important ecosystem engineers. Notably, insights into cnidarians gained in the post-genomics age have revealed a surprisingly complex immune system which bears a surprising level of similarity with the vertebrate innate immune system. This system has been critically linked to how corals respond to the two most prominent threats on a global scale, emerging coral diseases and increasing water temperature, which are recognized cellularly as either foreign or domestic threats, respectively. These threats can arise from pathogenic microbes or internal cellular dysfunction, underscoring the need to further understand mechanisms corals use to sense and respond to threats to their cellular integrity. In this investigation and meta-analysis, we utilize resources only recently available in the post-genomic era to identify and characterize members of an underexplored class of molecules known as NOD-like receptors in the endangered Caribbean coral Orbicella faveolata. We then leverage these data to identify pathways possibly mediated by NLRs in both O. faveolata and the ecologically important branching coral Acropora digitifera. Overall, we find support that this class of proteins may provide a mechanistic link to how reef-building corals respond to threats both foreign and domestic.
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Affiliation(s)
- Bradford A Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Caleb C Butler
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Contessa A Ricci
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Nicholas J MacKnight
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Laura D Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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14
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Zhang P, Wang J, Zhang X, Wang X, Jiang L, Gu X. Identification of AIDS-Associated Kaposi Sarcoma: A Functional Genomics Approach. Front Genet 2020; 10:1376. [PMID: 32038721 PMCID: PMC6992650 DOI: 10.3389/fgene.2019.01376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Kaposi sarcoma-associated herpes virus (KSHV) is one of the most common causal agents of Kaposi Sarcoma (KS) in individuals with HIV-infections. The virus has gained attention over the past few decades due to its remarkable pathogenic mechanisms. A group of genes, ORF71, ORF72, and ORF73, are expressed as polycistronic mRNAs and the functions of ORF71 and ORF72 in KSHV are already reported in the literature. However, the function of ORF73 has remained a mystery. The aim of this study is to conduct comprehensive exploratory experiments to clarify the role of ORF73 in KSHV pathology and discover markers of AIDS-associated KSHV-induced KS by bioinformatic approaches. METHODS AND RESULTS We searched for homologues of ORF-73 and attempted to predict protein-protein interactions (PPI) based on GeneCards and UniProtKB, utilizing Position-Specific Iterated BLAST (PSI-BLAST). We applied Gene Ontology (GO) and KEGG pathway analyses to identify highly conserved regions between ORF-73 and p53to help us identify potential markers with predominant hits and interactions in the KEGG pathway associated with host apoptosis and cell arrest. The protein p53 is selected because it is an important tumor suppressor antigen. To identify the potential roles of the candidate markers at the molecular level, we used PSIPRED keeping the conserved domains as the major parameters to predict secondary structures. We based the FUGE interpretation consolidations of the sequence-structure comparisons on distance homology, where the score for the amino acids matching the insertion/deletion (indels) detected were based on structures compared to the FUGE database of structural profiles. We also calculated the compatibility scores of sequence alignments accordingly. Based on the PSI-BLAST homologues, we checked the disordered structures predicted using PSI-Pred and DISO-Pred for developing a hidden Markov model (HMM). We further applied these HMMs models based on the alignment of constructed 3D models between the known structure and the HMM of our sequence. Moreover, stable homology and structurally conserved domains confirmed that ORF-73 maybe an important prognostic marker for AIDS-associated KS. CONCLUSION Collectively, similar variants of ORF-73 markers involved in the immune response may interact with targeted host proteins as predicted by our computational analysis. This work also suggests the existence of potential conformational changes that need to be further explored to help elucidate the role of immune signaling during KS towards the development of therapeutic applications.
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Affiliation(s)
- Peng Zhang
- School of Clinical Medicine, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Public Health, Shanghai General Practice Medical Education and Research Center, Shanghai, China
| | - Jiafeng Wang
- Stem Cell Research and Cellular Therapy Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhang
- Department of Implant Dentistry, Ninth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaolan Wang
- College of Nursing and Health Management, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Liying Jiang
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xuefeng Gu
- Shanghai Key Laboratory of Molecular Imaging, Collaborative Research Center, Shanghai University of Medicine & Health Sciences, Shanghai, China
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15
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Del Re DP, Amgalan D, Linkermann A, Liu Q, Kitsis RN. Fundamental Mechanisms of Regulated Cell Death and Implications for Heart Disease. Physiol Rev 2019; 99:1765-1817. [PMID: 31364924 DOI: 10.1152/physrev.00022.2018] [Citation(s) in RCA: 520] [Impact Index Per Article: 104.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Twelve regulated cell death programs have been described. We review in detail the basic biology of nine including death receptor-mediated apoptosis, death receptor-mediated necrosis (necroptosis), mitochondrial-mediated apoptosis, mitochondrial-mediated necrosis, autophagy-dependent cell death, ferroptosis, pyroptosis, parthanatos, and immunogenic cell death. This is followed by a dissection of the roles of these cell death programs in the major cardiac syndromes: myocardial infarction and heart failure. The most important conclusion relevant to heart disease is that regulated forms of cardiomyocyte death play important roles in both myocardial infarction with reperfusion (ischemia/reperfusion) and heart failure. While a role for apoptosis in ischemia/reperfusion cannot be excluded, regulated forms of necrosis, through both death receptor and mitochondrial pathways, are critical. Ferroptosis and parthanatos are also likely important in ischemia/reperfusion, although it is unclear if these entities are functioning as independent death programs or as amplification mechanisms for necrotic cell death. Pyroptosis may also contribute to ischemia/reperfusion injury, but potentially through effects in non-cardiomyocytes. Cardiomyocyte loss through apoptosis and necrosis is also an important component in the pathogenesis of heart failure and is mediated by both death receptor and mitochondrial signaling. Roles for immunogenic cell death in cardiac disease remain to be defined but merit study in this era of immune checkpoint cancer therapy. Biology-based approaches to inhibit cell death in the various cardiac syndromes are also discussed.
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Affiliation(s)
- Dominic P Del Re
- Departments of Medicine and Cell Biology, Wilf Family Cardiovascular Research Institute, Albert Einstein Cancer Center, and Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York; Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey; Department of Internal Medicine 3, Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; and Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Dulguun Amgalan
- Departments of Medicine and Cell Biology, Wilf Family Cardiovascular Research Institute, Albert Einstein Cancer Center, and Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York; Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey; Department of Internal Medicine 3, Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; and Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Andreas Linkermann
- Departments of Medicine and Cell Biology, Wilf Family Cardiovascular Research Institute, Albert Einstein Cancer Center, and Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York; Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey; Department of Internal Medicine 3, Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; and Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Qinghang Liu
- Departments of Medicine and Cell Biology, Wilf Family Cardiovascular Research Institute, Albert Einstein Cancer Center, and Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York; Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey; Department of Internal Medicine 3, Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; and Department of Physiology and Biophysics, University of Washington, Seattle, Washington
| | - Richard N Kitsis
- Departments of Medicine and Cell Biology, Wilf Family Cardiovascular Research Institute, Albert Einstein Cancer Center, and Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York; Department of Cell Biology and Molecular Medicine, Cardiovascular Research Institute, Rutgers New Jersey Medical School, Newark, New Jersey; Department of Internal Medicine 3, Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany; and Department of Physiology and Biophysics, University of Washington, Seattle, Washington
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16
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Park HH. Domain swapping of death domain superfamily: Alternative strategy for dimerization. Int J Biol Macromol 2019; 138:565-572. [DOI: 10.1016/j.ijbiomac.2019.07.139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/20/2023]
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17
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de Alba E. Structure, interactions and self-assembly of ASC-dependent inflammasomes. Arch Biochem Biophys 2019; 670:15-31. [PMID: 31152698 PMCID: PMC8455077 DOI: 10.1016/j.abb.2019.05.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
The inflammasome is a multi-protein platform that assembles upon the presence of cues derived from infection or tissue damage, and triggers the inflammatory response. Inflammasome components include sensor proteins that detect danger signals, procaspase 1 and the adapter ASC (apoptosis-associated speck-like protein containing a CARD) tethering these molecules together. Upon inflammasome assembly, procaspase 1 self-activates and renders functional cytokines to arbitrate in the defense mechanism. This assembly is mediated by self-association and protein interactions via Death Domains. The inflammasome plays a critical role in innate immunity and its dysregulation is the culprit of many autoimmune disorders. An in-depth understanding of the factors involved in inflammasome assembly could help fight these conditions. This review describes our current knowledge on the biophysical aspects of inflammasome formation from the perspective of ASC. The specific characteristics of the three-dimensional solution structure and interdomain dynamics of ASC are explained in relation to its function in inflammasome assembly. Additionally, the review elaborates on the identification of ASC interacting surfaces at the amino acid level using NMR techniques. Finally, the macrostructures formed by full-length ASC and its two Death Domains studied with Transmission Electron Microscopy are compared in the context of a directional model for inflammasome assembly.
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Affiliation(s)
- Eva de Alba
- Department of Bioengineering. School of Engineering. University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA.
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18
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Regulation of the expression of nine antimicrobial peptide genes by TmIMD confers resistance against Gram-negative bacteria. Sci Rep 2019; 9:10138. [PMID: 31300668 PMCID: PMC6626034 DOI: 10.1038/s41598-019-46222-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/31/2019] [Indexed: 12/23/2022] Open
Abstract
Immune deficiency (IMD) is a death domain-containing protein that is essential for the IMD/NF-κB humoral and epithelial immune responses to Gram-negative bacteria and viruses in insects. In the immune signaling cascade, IMD is recruited together with FADD and the caspase DREDD after the mobilization of PGRP receptors. Activated IMD regulates the expression of effector antimicrobial peptides (AMP) that protect against invading microorganisms. To date, most studies of the IMD pathway, and the IMD gene in particular, have been restricted to Drosophila; few similar studies have been conducted in other model insects. Herein, we cloned and functionally characterized an IMD homolog from the mealworm beetle Tenebrio molitor (TmIMD) and studied its role in host survival in the context of pathogenic infections. Phylogenetic analysis revealed the conserved caspase cleavage site and inhibitor of apoptosis (IAP)-binding motif (IBM). TmIMD expression was high in the hemocytes and Malpighian tubules of Tenebrio late-instar larvae and adults. At 3 and 6 hours’ post-infection with Escherichia coli, Staphylococcus aureus, or Candida albicans, TmIMD expression significantly increased compared with mock-infected controls. Knockdown of the TmIMD transcript by RNAi significantly reduced host resistance to the Gram-negative bacterium E. coli and fungus C. albicans in a survival assay. Strikingly, the expression of nine T. molitor AMPs (TmTenecin1, TmTenecin2, TmTenecin4, TmDefensin2, TmColeoptericin1, TmColeoptericin2, TmAttacin1a, TmAttacin1b, and TmAttacin2) showed significant downregulation in TmIMD knockdown larvae challenged with E. coli. These results suggest that TmIMD is required to confer humoral immunity against the Gram-negative bacteria, E. coli by inducing the expression of critical transcripts that encode AMPs.
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19
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Abstract
The inflammasome is a multi-molecular platform crucial to the induction of an inflammatory response to cellular danger. Recognition in the cytoplasm of endogenously and exogenously derived ligands initiates conformational change in sensor proteins, such as NLRP3, that permits the subsequent rapid recruitment of adaptor proteins, like ASC, and the resulting assembly of a large-scale inflammatory signalling platform. The assembly process is driven by sensor-sensor interactions as well as sensor-adaptor and adaptor-adaptor interactions. The resulting complex, which can reach diameters of around 1 micron, has a variable composition and stoichiometry. The inflammasome complex functions as a platform for the proximity induced activation of effector caspases, such as caspase-1 and caspase-8. This ultimately leads to the processing of the inflammatory cytokines pro-IL1β and pro-IL18 into their active forms, along with the cleavage of Gasdermin D, a key activator of cell death via pyroptosis.
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20
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Yin X, Li W, Ma H, Zeng W, Peng C, Li Y, Liu M, Chen Q, Zhou R, Jin T. Crystal structure and activation mechanism of DR3 death domain. FEBS J 2019; 286:2593-2610. [PMID: 30941855 DOI: 10.1111/febs.14834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/01/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022]
Abstract
Death receptor 3 (DR3) (a.k.a. tumor necrosis factor receptor superfamily 25) plays a key role in the immune system by activating nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway. Here we present the crystal structures of human and mouse DR3 intracellular death domain (DD) at 2.7 and 2.5 Å resolutions, respectively. The mouse DR3 DD adopts a classical six-helix bundle structure while human DR3 DD displays an extended fold. Though there is one-amino-acid difference in the linker between maltose-binding protein (MBP) tag and DR3 DD, according to our self-interaction analysis, the hydrophobic interface discovered in MBP-hDR3 DD crystal structure is responsible for both hDR3 DD and mDR3 DD homotypic interaction. Furthermore, our biochemical analysis indicates that the sequence variation between human and mouse DR3 DD does not affect its structure and function. Small-angle X-ray scattering analysis shows the averaged solution structures of both human and mouse MBP-DR3 DD are the combination of different conformations with different proportion. Through switching to the open conformation, DR3 DD could improve the interaction with downstream element TNFR-associated death domain (TRADD). Here we propose an activation-dependent structural rearrangement model: the DD region is folded as the six-helix bundles in the resting state, while upon extracellular ligand engagement, it switches to the open conformation, which facilitates its self-association and the recruitment of TRADD. Our results provide detailed insights into the architecture of DR3 DD and the molecular mechanism of activation. DATABASES: All refined structure coordinates as well as the corresponding structure factors have been deposited in the PDB under the accession codes 5YGS, 5YEV, 5YGP, 5ZNY, 5ZNZ.
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Affiliation(s)
- Xueying Yin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Wenqian Li
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Huan Ma
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Weihong Zeng
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Chao Peng
- Zhangjiang Lab, National Facility for Protein Science in Shanghai, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yajuan Li
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Muziying Liu
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Quan Chen
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongbin Zhou
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai, China
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai, China
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21
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Nambayan RJT, Sandin SI, Quint DA, Satyadi DM, de Alba E. The inflammasome adapter ASC assembles into filaments with integral participation of its two Death Domains, PYD and CARD. J Biol Chem 2019; 294:439-452. [PMID: 30459235 PMCID: PMC6333874 DOI: 10.1074/jbc.ra118.004407] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 11/17/2018] [Indexed: 11/06/2022] Open
Abstract
The inflammasome is a multiprotein complex necessary for the onset of inflammation. The adapter protein ASC assembles inflammasome components by acting as a molecular glue between danger-signal sensors and procaspase-1. The assembly is mediated by ASC self-association and protein interactions via its two Death Domains, PYD and CARD. Truncated versions of ASC have been shown to form filaments, but information on the filaments formed by full-length ASC is needed to construct a meaningful model of inflammasome assembly. To gain insights into this system, we used a combination of transmission EM, NMR, and computational analysis to investigate intact ASC structures. We show that ASC forms ∼6-7-nm-wide filaments that stack laterally to form bundles. The structural characteristics and dimensions of the bundles indicate that both PYD and CARD are integral parts of the filament. A truncated version of ASC with only the CARD domain (ASCCARD) forms different filaments (∼3-4-nm width), providing further evidence that both domains work in concert in filament assembly. Ring-shaped protein particles bound to pre-existing filaments match the size of ASC dimer structures generated by NMR-based protein docking, suggesting that the ASC dimer could be a basic building block for filament formation. Solution NMR binding studies identified the protein surfaces involved in the ASCCARD-ASCCARD interaction. These data provide new insights into the structural underpinnings of the inflammasome and should inform future efforts to interrogate this important biological system.
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Affiliation(s)
| | - Suzanne I Sandin
- From the Department of Bioengineering
- Chemistry and Chemical Biology Graduate Program
| | - David A Quint
- NSF-CREST Center for Cellular and Biomolecular Machines, and
- Department of Physics, University of California, Merced, California 95343
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22
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Post-translational modification of the death receptor complex as a potential therapeutic target in cancer. Arch Pharm Res 2019; 42:76-87. [PMID: 30610617 DOI: 10.1007/s12272-018-01107-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/27/2018] [Indexed: 12/26/2022]
Abstract
Programmed cell death is critical to the physiological function of multi-cellular organisms, controlling development, immunity, inflammation, and cancer progression. Death receptor (DR)-mediated regulation of a protease functions as a second messenger to initiate a death signal cascade to induce apoptosis or necroptosis. Recently, it has become clear that post-translational modifications (PTMs) of signaling components in the DR complex are highly complex, temporally controlled, and tightly regulated, and play an important role in cell death signaling. This review focuses on the molecular mechanisms and pathophysiological consequences of PTMs on the formation of the DR signaling complex, especially with respect to tumor necrosis factor receptor 1 (TNFR1). Furthermore, characterization of the role of PTMs in spatially different TNFR1 complexes (complexes I and II), especially with respect to the role of ubiquitination and phosphorylation of receptor interacting protein 1 (RIP1) in programmed cell death in cancer cells, will be reviewed. By integrating recently gained insight of the functional importance of PTMs in complex I or II, this review discusses how the concerted action of PTMs results in life or death upon DR ligation. Finally, the emerging concept of a sequential cell death checkpoint by the PTMs of RIP1, which may reveal novel therapeutic opportunities for the treatment of some cancers, will be discussed.
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23
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Diaz-Parga P, de Alba E. Protein interactions of the inflammasome adapter ASC by solution NMR. Methods Enzymol 2019; 625:223-252. [PMID: 31455529 PMCID: PMC8455076 DOI: 10.1016/bs.mie.2019.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ASC (apoptosis-associated speck-like protein containing a CARD) is a modular protein that functions as an adapter of the inflammasome, a multi-protein complex that triggers the inflammatory response in the presence of infection or cell damage. ASC bridges the inflammasome components (PYD-containing sensors and procaspase 1) via homotypic interactions mediated by its two death domains, PYD and CARD. The self-assembly and oligomerization of multiple copies of these three proteins result in the activation of procaspase 1, in turn rendering different cytokines functional. An in-depth understanding of ASC binding capabilities is crucial to decipher the molecular mechanisms of its role in inflammasome formation. In this chapter, we discuss the use of solution NMR to identify specific interacting surfaces of the inflammasome adapter ASC, and describe detailed protocols to perform NMR titrations with Death Domains to obtain apparent dissociation constants of the resulting complexes. The incorporation of NMR restraints in molecular docking to obtain models of these protein assemblies is presented.
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Affiliation(s)
- Pedro Diaz-Parga
- Department of Bioengineering, School of Engineering, University of California, Merced, CA, United States,Quantitative Systems Biology Graduate Program, University of California, Merced, CA, United States
| | - Eva de Alba
- Department of Bioengineering, School of Engineering, University of California, Merced, CA, United States,Corresponding author:
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24
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Shen C, Pei J, Guo X, Zhou L, Li Q, Quan J. Structural basis for dimerization of the death effector domain of the F122A mutant of Caspase-8. Sci Rep 2018; 8:16723. [PMID: 30425291 PMCID: PMC6233201 DOI: 10.1038/s41598-018-35153-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/19/2018] [Indexed: 11/09/2022] Open
Abstract
Caspase-8 is an apoptotic protease that is activated by a proximity-induced dimerization mechanism within the death-inducing signaling complex (DISC). The death effector domain (DED) of caspase-8 is involved in protein-protein interactions and is essential for the activation. Here, we report two crystal structures of the dimeric DEDs of the F122A mutant of caspase-8, both of which illustrate a novel domain-swapped dimerization, while differ in the relative orientation of the two subunits and the solvent exposure of the conserved hydrophobic patch Phe122/Leu123. We demonstrate that mutations disrupting the dimerization of the DEDs abrogate the formation of cellular death effector filaments (DEFs) and the induced apoptosis by overexpressed DEDs. Furthermore, such dimerization-disrupting mutations also impair the activation of the full-length caspase-8 and the downstream apoptosis cascade. The structures provide new insights into understanding the mechanism underlying the activation of procaspase-8 within the DISC and DEFs.
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Affiliation(s)
- Chen Shen
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Jianwen Pei
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xiaomin Guo
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Lu Zhou
- School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qinkai Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Junmin Quan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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25
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Ha HJ, Park HH. RAIDD mutations underlie the pathogenesis of thin lissencephaly (TLIS). PLoS One 2018; 13:e0205042. [PMID: 30281648 PMCID: PMC6169973 DOI: 10.1371/journal.pone.0205042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/18/2018] [Indexed: 11/18/2022] Open
Abstract
Abnormal regulation of caspase-2-mediated neuronal cell death causes neurodegenerative diseases and defective brain development. PIDDosome is caspase-2 activating complex composed of PIDD, RAIDD, and caspase-2. Recent whole-exome sequencing study showed that the RAIDD mutations in the death domain (DD), including G128R, F164C, R170C, and R170H mutations, cause thin lissencephaly (TLIS) by reducing caspase-2-mediated neuronal apoptosis. Given that the molecular structure of the RAIDD DD:PIDD DD complex is available, in this study, we analyzed the molecular mechanisms underlying TLIS caused by the RAIDD TLIS variants by performing mutagenesis and biochemical assays.
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Affiliation(s)
- Hyun Ji Ha
- College of Pharmacy, Chung-Ang University, Seoul, South Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Seoul, South Korea
- * E-mail:
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26
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Wallach D. The Tumor Necrosis Factor Family: Family Conventions and Private Idiosyncrasies. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028431. [PMID: 28847899 DOI: 10.1101/cshperspect.a028431] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The tumor necrosis factor (TNF) cytokine family and the TNF/nerve growth factor (NGF) family of their cognate receptors together control numerous immune functions, as well as tissue-homeostatic and embryonic-development processes. These diverse functions are dictated by both shared and distinct features of family members, and by interactions of some members with nonfamily ligands and coreceptors. The spectra of their activities are further expanded by the occurrence of the ligands and receptors in both membrane-anchored and soluble forms, by "re-anchoring" of soluble forms to extracellular matrix components, and by signaling initiation via intracellular domains (IDs) of both receptors and ligands. Much has been learned about shared features of the receptors as well as of the ligands; however, we still have only limited knowledge of the mechanistic basis for their functional heterogeneity and for the differences between their functions and those of similarly acting cytokines of other families.
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Affiliation(s)
- David Wallach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
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27
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Molecular basis of dimerization of initiator caspase was revealed by crystal structure of caspase-8 pro-domain. Cell Death Differ 2018; 26:1213-1220. [PMID: 30206319 DOI: 10.1038/s41418-018-0200-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/28/2018] [Indexed: 11/08/2022] Open
Abstract
The assembly of death-inducing signaling complex (DISC) for activation of initiator caspase is a key step for the receptor-mediated apoptosis signaling. Many death effector domain (DED)-containing proteins are involved in DISC assembly and controlling. One of the main DISC component, caspase-8, contains DED and DED-mediated dimerization and oligomerization in the DISC is critical for the activation of this initiator caspase. There have been intensive studies to understand DED-mediated dimerization and oligomerization for the DISC assembly but no clear answer has been provided and there are many controversial arguments. Here, we suggested novel dimerization process of tandem DED of caspase-8 with crystallographic study.
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28
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Yang D, Zheng X, Chen S, Wang Z, Xu W, Tan J, Hu T, Hou M, Wang W, Gu Z, Wang Q, Zhang R, Zhang Y, Liu Q. Sensing of cytosolic LPS through caspy2 pyrin domain mediates noncanonical inflammasome activation in zebrafish. Nat Commun 2018; 9:3052. [PMID: 30076291 PMCID: PMC6076302 DOI: 10.1038/s41467-018-04984-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 04/17/2018] [Indexed: 12/26/2022] Open
Abstract
The noncanonical inflammasome is critical for cytosolic sensing of Gram-negative pathogens. Here, we show that bacterial infection induces caspy2 activation in zebrafish fibroblasts, which mediates pyroptosis via a caspase-5-like activity. Zebrafish caspy2 binds directly to lipopolysaccharide via the N-terminal pyrin death domain, resulting in caspy2 oligomerization, which is critical for pyroptosis. Furthermore, we show that caspy2 is highly expressed in the zebrafish gut and is activated during infection. Knockdown of caspy2 expression impairs the ability of zebrafish to restrict bacterial invasion in vivo, and protects larvae from lethal sepsis. Collectively, our results identify a crucial event in the evolution of pattern recognition into the death domain superfamily-mediated intracellular lipopolysaccharide-sensing pathway in innate immunity. In humans, caspase-5 is an LPS sensor that can induce gasdermin D cleavage and pyroptosis. Here, the authors show that zebrafish caspy2 is a functional homolog as it also senses cytosolic LPS to activate the noncanonical inflammasome and to protect against bacterial infection, but it does so via pyrin death domain interactions.
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Affiliation(s)
- Dahai Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xin Zheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Shouwen Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhuang Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wenting Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jinchao Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Tianjian Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Mingyu Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Wenhui Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhaoyan Gu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.,Shanghai Engineering Research Center of Marine Cultured Animal Vaccines, Shanghai, 200237, China.,Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, China
| | - Ruilin Zhang
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.,Shanghai Engineering Research Center of Marine Cultured Animal Vaccines, Shanghai, 200237, China.,Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China. .,Shanghai Engineering Research Center of Marine Cultured Animal Vaccines, Shanghai, 200237, China. .,Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, China.
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Jin T, Huang M, Jiang J, Smith P, Xiao TS. Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction. PLoS One 2018; 13:e0190547. [PMID: 29293680 PMCID: PMC5749810 DOI: 10.1371/journal.pone.0190547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/15/2017] [Indexed: 11/23/2022] Open
Abstract
NLRP12 is a NOD-like receptor that plays multiple roles in both inflammation and tumorigenesis. Despite the importance, little is known about its mechanism of action at the molecular level. Here, we report the crystal structure of NLRP12 PYD domain at 1.70 Å fused with an maltose-binding protein (MBP) tag. Interestingly, the PYD domain forms a dimeric configuration through a disulfide bond in the crystal. The possible biological significance is discussed in the context of ROS induced NF-κB activation.
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Affiliation(s)
- Tengchuan Jin
- Laboratory of structural immunology, CAS Key Laboratory of innate immunity and chronic diseases, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, Anhui, PRC
- Structural Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (TJ); (TSX)
| | - Mo Huang
- Structural Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jiansheng Jiang
- Structural Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Patrick Smith
- Structural Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tsan Sam Xiao
- Structural Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Pathology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (TJ); (TSX)
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Abstract
All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks. Here we propose a role for KaiC family ATPases, known to be key components of the circadian clock in cyanobacteria, in archaeal signal transduction. The KaiC family is notably expanded in most archaeal genomes, and although most of these ATPases remain poorly characterized, members of the KaiC family have been shown to control archaellum assembly and have been found to be a stable component of the gas vesicle system in Halobacteria Computational analyses described here suggest that KaiC-like ATPases and their homologues with inactivated ATPase domains are involved in many other archaeal signal transduction pathways and comprise major hubs of complex regulatory networks. We predict numerous input and output domains that are linked to KaiC-like proteins, including putative homologues of eukaryotic DEATH domains that could function as adapters in archaeal signaling networks. We further address the relationships of the archaeal family of KaiC homologues to the bona fide KaiC of cyanobacteria and implications for the existence of a KaiC-based circadian clock apparatus in archaea.IMPORTANCE Little is currently known about signal transduction pathways in Archaea Recent studies indicate that KaiC-like ATPases, known as key components of the circadian clock apparatus in cyanobacteria, are involved in the regulation of archaellum assembly and, likely, type IV pili and the gas vesicle system in Archaea We performed comprehensive comparative genomic analyses of the KaiC family. A vast protein interaction network was revealed, with KaiC family proteins as hubs for numerous input and output components, many of which are shared with two-component signal transduction systems. Putative KaiC-based signal transduction systems are predicted to regulate the activities of membrane-associated complexes and individual proteins, such as signal recognition particle and membrane transporters, and also could be important for oxidative stress response regulation. KaiC-centered signal transduction networks are predicted to play major roles in archaeal physiology, and this work is expected to stimulate their experimental characterization.
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31
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Indramohan M, Stehlik C, Dorfleutner A. COPs and POPs Patrol Inflammasome Activation. J Mol Biol 2017; 430:153-173. [PMID: 29024695 DOI: 10.1016/j.jmb.2017.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/28/2017] [Accepted: 10/04/2017] [Indexed: 01/07/2023]
Abstract
Sensing and responding to pathogens and tissue damage is a core mechanism of innate immune host defense, and inflammasomes represent a central cytosolic pattern recognition receptor pathway leading to the generation of the pro-inflammatory cytokines interleukin-1β and interleukin-18 and pyroptotic cell death that causes the subsequent release of danger signals to propagate and perpetuate inflammatory responses. While inflammasome activation is essential for host defense, deregulated inflammasome responses and excessive release of inflammatory cytokines and danger signals are linked to an increasing spectrum of inflammatory diseases. In this review, we will discuss recent developments in elucidating the role of PYRIN domain-only proteins (POPs) and the related CARD-only proteins (COPs) in regulating inflammasome responses and their impact on inflammatory disease.
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Affiliation(s)
- Mohanalaxmi Indramohan
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Christian Stehlik
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Interdepartmental Immunobiology Center and Skin Disease Research Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
| | - Andrea Dorfleutner
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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32
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Vajjhala PR, Ve T, Bentham A, Stacey KJ, Kobe B. The molecular mechanisms of signaling by cooperative assembly formation in innate immunity pathways. Mol Immunol 2017; 86:23-37. [PMID: 28249680 DOI: 10.1016/j.molimm.2017.02.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/16/2017] [Accepted: 02/19/2017] [Indexed: 12/25/2022]
Abstract
The innate immune system is the first line of defense against infection and responses are initiated by pattern recognition receptors (PRRs) that detect pathogen-associated molecular patterns (PAMPs). PRRs also detect endogenous danger-associated molecular patterns (DAMPs) that are released by damaged or dying cells. The major PRRs include the Toll-like receptor (TLR) family members, the nucleotide binding and oligomerization domain, leucine-rich repeat containing (NLR) family, the PYHIN (ALR) family, the RIG-1-like receptors (RLRs), C-type lectin receptors (CLRs) and the oligoadenylate synthase (OAS)-like receptors and the related protein cyclic GMP-AMP synthase (cGAS). The different PRRs activate specific signaling pathways to collectively elicit responses including the induction of cytokine expression, processing of pro-inflammatory cytokines and cell-death responses. These responses control a pathogenic infection, initiate tissue repair and stimulate the adaptive immune system. A central theme of many innate immune signaling pathways is the clustering of activated PRRs followed by sequential recruitment and oligomerization of adaptors and downstream effector enzymes, to form higher-order arrangements that amplify the response and provide a scaffold for proximity-induced activation of the effector enzymes. Underlying the formation of these complexes are co-operative assembly mechanisms, whereby association of preceding components increases the affinity for downstream components. This ensures a rapid immune response to a low-level stimulus. Structural and biochemical studies have given key insights into the assembly of these complexes. Here we review the current understanding of assembly of immune signaling complexes, including inflammasomes initiated by NLR and PYHIN receptors, the myddosomes initiated by TLRs, and the MAVS CARD filament initiated by RIG-1. We highlight the co-operative assembly mechanisms during assembly of each of these complexes.
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Affiliation(s)
- Parimala R Vajjhala
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Ve
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; Institute for Glycomics, Griffith University, Southport, QLD 4222, Australia
| | - Adam Bentham
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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33
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Maharana J, Vats A, Gautam S, Nayak BP, Kumar S, Sendha J, De S. POP1 might be recruiting its type-Ia interface for NLRP3-mediated PYD-PYD interaction: Insights from MD simulation. J Mol Recognit 2017; 30. [PMID: 28370480 DOI: 10.1002/jmr.2632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 02/14/2017] [Accepted: 02/23/2017] [Indexed: 11/12/2022]
Abstract
Inflammasomes are multiprotein caspase-activating complexes that enhance the maturation and release of proinflammatory cytokines (IL-1β and IL-18) in response to the invading pathogen and/or host-derived cellular stress. These are assembled by the sensory proteins (viz NLRC4, NLRP1, NLRP3, and AIM-2), adaptor protein (ASC), and effector molecule procaspase-1. In NLRP3-mediated inflammasome activation, ASC acts as a mediator between NLRP3 and procaspase-1 for the transmission of signals. A series of homotypic protein-protein interactions (NLRP3PYD :ASCPYD and ASCCARD :CASP1CARD ) propagates the downstream signaling for the production of proinflammatory cytokines. Pyrin-only protein 1 (POP1) is known to act as the regulator of inflammasome. It modulates the ASC-mediated inflammasome assembly by interacting with pyrin domain (PYD) of ASC. However, despite similar electrostatic surface potential, the interaction of POP1 with NLRP3PYD is obscured till date. Herein, to explore the possible PYD-PYD interactions between NLRP3PYD and POP1, a combined approach of protein-protein docking and molecular dynamics simulation was adapted. The current study revealed that POP1's type-Ia interface and type-Ib interface of NLRP3PYD might be crucial for 1:1 PYD-PYD interaction. In addition to type-I mode of interaction, we also observed type-II and type-III interaction modes in two different dynamically stable heterotrimeric complexes (POP1-NLRP3-NLRP3 and POP1-NLRP3-POP1). The inter-residual/atomic distance calculation exposed several critical residues that possibly govern the said interaction, which need further investigation. Overall, the findings of this study will shed new light on hitherto concealed molecular mechanisms underlying NLRP3-mediated inflammasome, which will have strong future therapeutic implications.
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Affiliation(s)
- Jitendra Maharana
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Ashutosh Vats
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
| | - Santwana Gautam
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Bibhu Prasad Nayak
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Sushil Kumar
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
| | - Jasobanta Sendha
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, -751003, Odisha, India
| | - Sachinandan De
- Animal Genomics Lab, Animal Biotechnology Centre, ICAR-National Dairy Research Institute, Karnal, 751003, Haryana, India
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34
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Jin T, Chuenchor W, Jiang J, Cheng J, Li Y, Fang K, Huang M, Smith P, Xiao TS. Design of an expression system to enhance MBP-mediated crystallization. Sci Rep 2017; 7:40991. [PMID: 28112203 PMCID: PMC5256280 DOI: 10.1038/srep40991] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/13/2016] [Indexed: 11/09/2022] Open
Abstract
Crystallization chaperones have been used to facilitate the crystallization of challenging proteins. Even though the maltose-binding protein (MBP) is one of the most commonly used crystallization chaperones, the design of optimal expression constructs for crystallization of MBP fusion proteins remains a challenge. To increase the success rate of MBP-facilitated crystallization, a series of expression vectors have been designed with either a short flexible linker or a set of rigid helical linkers. Seven death domain superfamily members were tested for crystallization with this set of vectors, six of which had never been crystallized before. All of the seven targets were crystallized, and their structures were determined using at least one of the vectors. Our successful crystallization of all of the targets demonstrates the validity of our approach and expands the arsenal of the crystallization chaperone toolkit, which may be applicable to crystallization of other difficult protein targets, as well as to other crystallization chaperones.
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Affiliation(s)
- Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China.,Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Watchalee Chuenchor
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jiansheng Jiang
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jinbo Cheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China
| | - Yajuan Li
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China
| | - Kang Fang
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Diseases, CAS Center for Excellence in Molecular Cell Sciences, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei 230027 China
| | - Mo Huang
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Patrick Smith
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Tsan Sam Xiao
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106 USA
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35
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Park YH, Jeong MS, Jang SB. Structural insights of homotypic interaction domains in the ligand-receptor signal transduction of tumor necrosis factor (TNF). BMB Rep 2017; 49:159-66. [PMID: 26615973 PMCID: PMC4915230 DOI: 10.5483/bmbrep.2016.49.3.205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Indexed: 11/21/2022] Open
Abstract
Several members of tumor necrosis factor receptor (TNFR) superfamily that these
members activate caspase-8 from death-inducing signaling complex (DISC) in TNF
ligand-receptor signal transduction have been identified. In the extrinsic
pathway, apoptotic signal transduction is induced in death domain (DD)
superfamily; it consists of a hexahelical bundle that contains 80 amino acids.
The DD superfamily includes about 100 members that belong to four subfamilies:
death domain (DD), caspase recruitment domain (CARD), pyrin domain (PYD), and
death effector domain (DED). This superfamily contains key building blocks: with
these blocks, multimeric complexes are formed through homotypic interactions.
Furthermore, each DD-binding event occurs exclusively. The DD superfamily
regulates the balance between death and survival of cells. In this study, the
structures, functions, and unique features of DD superfamily members are
compared with their complexes. By elucidating structural insights of DD
superfamily members, we investigate the interaction mechanisms of DD domains;
these domains are involved in TNF ligand-receptor signaling. These DD
superfamily members play a pivotal role in the development of more specific
treatments of cancer. [BMB Reports 2016; 49(3): 159-166]
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Affiliation(s)
- Young-Hoon Park
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Mi Suk Jeong
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan 46241, Korea
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University; Genetic Engineering Institute, Pusan National University, Busan 46241, Korea
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36
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Vilar M. Structural Characterization of the p75 Neurotrophin Receptor: A Stranger in the TNFR Superfamily. VITAMINS AND HORMONES 2016; 104:57-87. [PMID: 28215307 DOI: 10.1016/bs.vh.2016.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Although p75 neurotrophin receptor (p75NTR) was the founding member of the tumor necrosis factor (TNF) receptor superfamily (TNFRSF), it is an atypical TNFRSF protein. p75NTR like TNF-R1 and Fas-R contain an extracellular domain with four cysteine-rich domains (CRD) and a death domain (DD) in the intracellular region. While TNFRSF proteins are activated by trimeric TNFSF ligands, p75NTR forms dimers activated by dimeric neurotrophins that are structurally unrelated to TNFSF proteins. In addition, although p75NTR shares with other members the interaction with the TNF receptor-associated factors to activate the NF-κB and cell death pathways, p75NTR does not interact with the DD-containing proteins FADD, TRADD, or MyD88. By contrast, the DD of p75NTR is able to recruit several protein interactors via a full catalog of DD interactions not described before in the TNFRSF. p75-DD forms homotypic symmetrical DD-DD complexes with itself and with the related p45-DD; forms heterotypic DD-CARD interactions with the RIP2-CARD domain, and forms a new interaction between a DD and RhoGDI. All these features, in addition to its promiscuous interactions with several ligands and coreceptors, its processing by α- and γ-secretases, the dimeric nature of its transmembrane domain and its "special" juxtamembrane region, make p75NTR a truly stranger in the TNFR superfamily. In this chapter, I will summarize the known structural aspects of p75NTR and I will analyze from a structural point of view, the similitudes and differences between p75NTR and the other members of the TNFRSF.
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Affiliation(s)
- M Vilar
- Molecular Basis of Neurodegeneration Unit, Institute of Biomedicine of Valencia (IBV-CSIC), València, Spain.
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37
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Oroz J, Barrera-Vilarmau S, Alfonso C, Rivas G, de Alba E. ASC Pyrin Domain Self-associates and Binds NLRP3 Protein Using Equivalent Binding Interfaces. J Biol Chem 2016; 291:19487-501. [PMID: 27432880 PMCID: PMC5016686 DOI: 10.1074/jbc.m116.741082] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/08/2016] [Indexed: 11/06/2022] Open
Abstract
Death domain superfamily members typically act as adaptors mediating in the assembly of supramolecular complexes with critical apoptosis and inflammation functions. These modular proteins consist of death domains, death effector domains, caspase recruitment domains, and pyrin domains (PYD). Despite the high structural similarity among them, only homotypic interactions participate in complex formation, suggesting that subtle factors differentiate each interaction type. It is thus critical to identify these factors as an essential step toward the understanding of the molecular basis of apoptosis and inflammation. The proteins apoptosis-associated speck-like protein containing a CARD (ASC) and NLRP3 play key roles in the regulation of apoptosis and inflammation through self-association and protein-protein interactions mediated by their PYDs. To better understand the molecular basis of their function, we have characterized ASC and NLRP3 PYD self-association and their intermolecular interaction by solution NMR spectroscopy and analytical ultracentrifugation. We found that ASC self-associates and binds NLRP3 PYD through equivalent protein regions, with higher binding affinity for the latter. These regions are located at opposite sides of the protein allowing multimeric complex formation previously shown in ASC PYD fibril assemblies. We show that NLRP3 PYD coexists in solution as a monomer and highly populated large-order oligomerized species. Despite this, we determined its monomeric three-dimensional solution structure by NMR and characterized its binding to ASC PYD. Using our novel structural data, we propose molecular models of ASC·ASC and ASC·NLRP3 PYD early supramolecular complexes, providing new insights into the molecular mechanisms of inflammasome and apoptosis signaling.
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Affiliation(s)
- Javier Oroz
- From the Centro de Investigaciones Biológicas, Departments of Chemical and Physical Biology and the German Center for Neurodegenerative Diseases (DZNE), ℅Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen-37077, Germany, and
| | - Susana Barrera-Vilarmau
- From the Centro de Investigaciones Biológicas, Departments of Chemical and Physical Biology and
| | | | | | - Eva de Alba
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9 Madrid-28040, Spain, the Health Sciences Research Institute, University of California at Merced, Merced, California 95343
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38
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Dondelinger Y, Hulpiau P, Saeys Y, Bertrand MJM, Vandenabeele P. An evolutionary perspective on the necroptotic pathway. Trends Cell Biol 2016; 26:721-732. [PMID: 27368376 DOI: 10.1016/j.tcb.2016.06.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 02/08/2023]
Abstract
Throughout the animal kingdom, innate immune receptors protect the organism from microbial intruders by activating pathways that mediate inflammation and pathogen clearance. Necroptosis contributes to the innate immune response by killing pathogen-infected cells and by alerting the immune system through the release of danger signals. Components of the necroptotic signaling axis - TIR-domain-containing adapter-inducing interferon-β (TRIF), Z-DNA sensor DAI, receptor-interacting kinase (RIPK)1, RIPK3 and mixed-lineage kinase domain-like protein (MLKL) - are therefore expected to be found in all animals. However, a phylogenetic analysis reveals that the necroptotic axis, except for RIPK1, is poorly conserved in the animal kingdom, suggesting that alternative mechanisms regulate necroptosis in these species or that necroptosis would apparently be absent. These findings question the universal role of necroptosis during innate immunity in the animal kingdom.
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Affiliation(s)
- Yves Dondelinger
- VIB Inflammation Research Center, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium
| | - Paco Hulpiau
- VIB Inflammation Research Center, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium
| | - Yvan Saeys
- VIB Inflammation Research Center, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Mathieu J M Bertrand
- VIB Inflammation Research Center, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium
| | - Peter Vandenabeele
- VIB Inflammation Research Center, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Technologiepark 927, Zwijnaarde-Ghent, 9052, Belgium.
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39
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Abstract
Inflammasomes are protein complexes that promote the maturation and release of pro-inflammatory cytokines and danger signals as well as pyroptosis in response to infections and cellular stress. Inflammasomes consist of a sensor, an adapter, and the effector caspase-1, which interact through homotypic interactions of caspase recruitment domains (CARDs) or PYRIN domains (PYDs). Hence, decoy proteins encoding only a CARD or PYD, COPs and POPs, respectively, are assumed to inhibit inflammasome assembly. Sensors encoding a PYD belong to the families of NOD-like receptors containing a PYD (NLRPs) or AIM2-like receptors (ALRs), which interact with the PYD- and CARD-containing adapter ASC through homotypic PYD interactions. Subsequently, ASC undergoes PYD-dependent oligomerization, which promotes CARD-mediated interactions between ASC and caspase-1, resulting in caspase-1 activation. POPs are suggested to interfere with the interaction between NLRPs/ALRs and ASC to prevent nucleation of ASC and therefore prevent an oligomeric platform for caspase-1 activation. Similarly, COPs are suggested to bind to the CARD of caspase-1 to prevent its recruitment to the oligomeric ASC platform and its activation. Alternatively, the adapter ASC may regulate inflammasome activity by expressing different isoforms, which are either capable or incapable of assembling an oligomeric ASC platform. The molecular mechanism of inflammasome assembly has only recently been elucidated, but the effects of most COPs and POPs on inflammasome assembly have not been investigated. Here, we discuss our model of COP- and POP-mediated inflammasome regulation.
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Affiliation(s)
- Andrea Dorfleutner
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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40
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Abstract
As a front line of defense against pathogenic microbes, our body employs a primitive, yet highly sophisticated and potent innate immune response pathway collectively referred to as the inflammasome. Innate immune cells, epithelial cells, and many other cell types are capable of detecting infection or tissue injury and mounting a coordinated molecular defense. For example, Gram-negative bacteria are specifically detected via a surveillance mechanism that involves activation of extracellular receptors such as Toll-like receptors (TLRs) followed by intracellular recognition and activation of pathways such as caspase-11 (caspase-4/5 in humans). Importantly, lipopolysaccharide (LPS), the major component of the outer membrane of Gram-negative bacteria, is a strong trigger of these pathways. Extracellular LPS primarily stimulates TLR4, which can serve as a priming signal for expression of inflammasome components. Intracellular LPS can then trigger caspase-11-dependent inflammasome activation in the cytoplasm. Here, we briefly review the burgeoning caspase-11-dependent non-canonical inflammasome field, focusing mainly on the innate sensing of LPS.
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Affiliation(s)
- Irma Stowe
- Department of Physiological Chemistry, Genentech Inc., South San Francisco, CA, USA
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41
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Abstract
The role of caspase proteases in regulated processes such as apoptosis and inflammation has been studied for more than two decades, and the activation cascades are known in detail. Apoptotic caspases also are utilized in critical developmental processes, although it is not known how cells maintain the exquisite control over caspase activity in order to retain subthreshold levels required for a particular adaptive response while preventing entry into apoptosis. In addition to active site-directed inhibitors, caspase activity is modulated by post-translational modifications or metal binding to allosteric sites on the enzyme, which stabilize inactive states in the conformational ensemble. This review provides a comprehensive global view of the complex conformational landscape of caspases and mechanisms used to select states in the ensemble. The caspase structural database provides considerable detail on the active and inactive conformations in the ensemble, which provide the cell multiple opportunities to fine tune caspase activity. In contrast, the current database on caspase modifications is largely incomplete and thus provides only a low-resolution picture of global allosteric communications and their effects on the conformational landscape. In recent years, allosteric control has been utilized in the design of small drug compounds or other allosteric effectors to modulate caspase activity.
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Affiliation(s)
- A Clay Clark
- Department of Biology, University of Texas at Arlington , Arlington, Texas 76019, United States
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42
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Abstract
In multicellular organisms, cell death is a critical and active process that maintains tissue homeostasis and eliminates potentially harmful cells. There are three major types of morphologically distinct cell death: apoptosis (type I cell death), autophagic cell death (type II), and necrosis (type III). All three can be executed through distinct, and sometimes overlapping, signaling pathways that are engaged in response to specific stimuli. Apoptosis is triggered when cell-surface death receptors such as Fas are bound by their ligands (the extrinsic pathway) or when Bcl2-family proapoptotic proteins cause the permeabilization of the mitochondrial outer membrane (the intrinsic pathway). Both pathways converge on the activation of the caspase protease family, which is ultimately responsible for the dismantling of the cell. Autophagy defines a catabolic process in which parts of the cytosol and specific organelles are engulfed by a double-membrane structure, known as the autophagosome, and eventually degraded. Autophagy is mostly a survival mechanism; nevertheless, there are a few examples of autophagic cell death in which components of the autophagic signaling pathway actively promote cell death. Necrotic cell death is characterized by the rapid loss of plasma membrane integrity. This form of cell death can result from active signaling pathways, the best characterized of which is dependent on the activity of the protein kinase RIP3.
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Affiliation(s)
- Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Fabien Llambi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
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43
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Vajjhala PR, Lu A, Brown DL, Pang SW, Sagulenko V, Sester DP, Cridland SO, Hill JM, Schroder K, Stow JL, Wu H, Stacey KJ. The Inflammasome Adaptor ASC Induces Procaspase-8 Death Effector Domain Filaments. J Biol Chem 2015; 290:29217-30. [PMID: 26468282 DOI: 10.1074/jbc.m115.687731] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 01/19/2023] Open
Abstract
Inflammasomes mediate inflammatory and cell death responses to pathogens and cellular stress signals via activation of procaspases-1 and -8. During inflammasome assembly, activated receptors of the NLR or PYHIN family recruit the adaptor protein ASC and initiate polymerization of its pyrin domain (PYD) into filaments. We show that ASC filaments in turn nucleate procaspase-8 death effector domain (DED) filaments in vitro and in vivo. Interaction between ASC PYD and procaspase-8 tandem DEDs optimally required both DEDs and represents an unusual heterotypic interaction between domains of the death fold superfamily. Analysis of ASC PYD mutants showed that interaction surfaces that mediate procaspase-8 interaction overlap with those required for ASC self-association and interaction with the PYDs of inflammasome initiators. Our data indicate that multiple types of death fold domain filaments form at inflammasomes and that PYD/DED and homotypic PYD interaction modes are similar. Interestingly, we observed condensation of procaspase-8 filaments containing the catalytic domain, suggesting that procaspase-8 interactions within and/or between filaments may be involved in caspase-8 activation. Procaspase-8 filaments may also be relevant to apoptosis induced by death receptors.
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Affiliation(s)
| | - Alvin Lu
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, and the Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Darren L Brown
- the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Siew Wai Pang
- From the School of Chemistry and Molecular Biosciences and
| | | | - David P Sester
- From the School of Chemistry and Molecular Biosciences and
| | | | - Justine M Hill
- From the School of Chemistry and Molecular Biosciences and
| | - Kate Schroder
- the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jennifer L Stow
- the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hao Wu
- the Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, and the Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Katryn J Stacey
- From the School of Chemistry and Molecular Biosciences and the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia,
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44
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Bryant CE, Orr S, Ferguson B, Symmons MF, Boyle JP, Monie TP. International Union of Basic and Clinical Pharmacology. XCVI. Pattern recognition receptors in health and disease. Pharmacol Rev 2015; 67:462-504. [PMID: 25829385 DOI: 10.1124/pr.114.009928] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Since the discovery of Toll, in the fruit fly Drosophila melanogaster, as the first described pattern recognition receptor (PRR) in 1996, many families of these receptors have been discovered and characterized. PRRs play critically important roles in pathogen recognition to initiate innate immune responses that ultimately link to the generation of adaptive immunity. Activation of PRRs leads to the induction of immune and inflammatory genes, including proinflammatory cytokines and chemokines. It is increasingly clear that many PRRs are linked to a range of inflammatory, infectious, immune, and chronic degenerative diseases. Several drugs to modulate PRR activity are already in clinical trials and many more are likely to appear in the near future. Here, we review the different families of mammalian PRRs, the ligands they recognize, the mechanisms of activation, their role in disease, and the potential of targeting these proteins to develop the anti-inflammatory therapeutics of the future.
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Affiliation(s)
- Clare E Bryant
- Departments of Veterinary Medicine (C.E.B., J.P.B., T.P.M.), Pathology (B.F.), and Biochemistry (M.F.S., J.P.B.), University of Cambridge, Cambridge, United Kingdom; and Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom (S.O.)
| | - Selinda Orr
- Departments of Veterinary Medicine (C.E.B., J.P.B., T.P.M.), Pathology (B.F.), and Biochemistry (M.F.S., J.P.B.), University of Cambridge, Cambridge, United Kingdom; and Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom (S.O.)
| | - Brian Ferguson
- Departments of Veterinary Medicine (C.E.B., J.P.B., T.P.M.), Pathology (B.F.), and Biochemistry (M.F.S., J.P.B.), University of Cambridge, Cambridge, United Kingdom; and Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom (S.O.)
| | - Martyn F Symmons
- Departments of Veterinary Medicine (C.E.B., J.P.B., T.P.M.), Pathology (B.F.), and Biochemistry (M.F.S., J.P.B.), University of Cambridge, Cambridge, United Kingdom; and Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom (S.O.)
| | - Joseph P Boyle
- Departments of Veterinary Medicine (C.E.B., J.P.B., T.P.M.), Pathology (B.F.), and Biochemistry (M.F.S., J.P.B.), University of Cambridge, Cambridge, United Kingdom; and Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom (S.O.)
| | - Tom P Monie
- Departments of Veterinary Medicine (C.E.B., J.P.B., T.P.M.), Pathology (B.F.), and Biochemistry (M.F.S., J.P.B.), University of Cambridge, Cambridge, United Kingdom; and Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom (S.O.)
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45
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Structure and function of legumain in health and disease. Biochimie 2015; 122:126-50. [PMID: 26403494 DOI: 10.1016/j.biochi.2015.09.022] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/18/2015] [Indexed: 12/27/2022]
Abstract
The last years have seen a steady increase in our understanding of legumain biology that is driven from two largely uncoupled research arenas, the mammalian and the plant legumain field. Research on legumain, which is also referred to as asparaginyl endopeptidase (AEP) or vacuolar processing enzyme (VPE), is slivered, however. Here we summarise recent important findings and put them into a common perspective. Legumain is usually associated with its cysteine endopeptidase activity in lysosomes where it contributes to antigen processing for class II MHC presentation. However, newly recognized functions disperse previously assumed boundaries with respect to their cellular compartmentalisation and enzymatic activities. Legumain is also found extracellularly and even translocates to the cytosol and the nucleus, with seemingly incompatible pH and redox potential. These different milieus translate into changes of legumain's molecular properties, including its (auto-)activation, conformational stability and enzymatic functions. Contrasting its endopeptidase activity, legumain can develop a carboxypeptidase activity which remains stable at neutral pH. Moreover, legumain features a peptide ligase activity, with intriguing mechanistic peculiarities in plant and human isoforms. In pathological settings, such as cancer or Alzheimer's disease, the proper association of legumain activities with the corresponding cellular compartments is breached. Legumain's increasingly recognized physiological and pathological roles also indicate future research opportunities in this vibrant field.
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46
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Singh N, Hassan A, Bose K. Molecular basis of death effector domain chain assembly and its role in caspase-8 activation. FASEB J 2015; 30:186-200. [PMID: 26370846 DOI: 10.1096/fj.15-272997] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/31/2015] [Indexed: 12/20/2022]
Abstract
Assembly of a death-inducing signaling complex is a key event in the extrinsic apoptotic pathway, enabling activation of the caspase cascade and subsequent cell death. However, the molecular events governing DISC assembly have remained largely elusive because of the lack of information on mechanism and specificity regulating the death effector domain (DED)-DED interaction network. Using molecular modeling, mutagenesis, and biochemical and ex vivo experiments, we identified the precise binding interface and hot spots crucial for intermolecular DED chain assembly. Mutation of key interface residues (Leu42/Phe45) in procaspase-8 DED-A completely abrogated DED chain formation in HEK293 cells and prevented its association with FADD. A significant 2.6-3.6-fold reduction in procaspase-8 activation was observed in functional cell-death assays after substitution of the interfacial residues. Based on our results we propose a new model for DISC formation that refines the current understanding of the activation mechanism. Upon stimulation, FADD self-associates weakly via reciprocal interaction between helices α1/α4 and α2/α3 of the DED to form an oligomeric signaling platform that provides a stage for the initial recruitment of procaspase-8 through direct interaction with α1/α4 of DED-A, followed by sequential interaction mediated by helices α2/α5 of DED-B, to form the procaspase-8 DED chain that is crucial for its activation and subsequent cell death.
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Affiliation(s)
- Nitu Singh
- Integrated Biophysics and Structural Biology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, India
| | - Ali Hassan
- Integrated Biophysics and Structural Biology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, India
| | - Kakoli Bose
- Integrated Biophysics and Structural Biology Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Navi Mumbai, India
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47
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Abstract
The PYRIN domain (PYD) is a protein-protein interaction domain, which belongs to the death domain fold (DDF) superfamily. It is best known for its signaling function in innate immune responses and particularly in the assembly of inflammasomes, which are large protein complexes that allow the induced proximity-mediated activation of caspase-1 and subsequently the release of pro-inflammatory cytokines. The molecular mechanism of inflammasome assembly was only recently elucidated and specifically requires PYD oligomerization. Here we discuss the recent advances in our understanding of PYD signaling and its regulation by PYD-only proteins.
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48
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Kao WP, Yang CY, Su TW, Wang YT, Lo YC, Lin SC. The versatile roles of CARDs in regulating apoptosis, inflammation, and NF-κB signaling. Apoptosis 2015; 20:174-95. [PMID: 25420757 DOI: 10.1007/s10495-014-1062-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CARD subfamily is the second largest subfamily in the DD superfamily that plays important roles in regulating various signaling pathways, including but not limited to NF-kB activation signaling, apoptosis signaling and inflammatory signaling. The CARD subfamily contains 33 human CARD-containing proteins, regulating the assembly of many signaling complexes, including apoptosome, inflammsome, nodosome, the CBM complex, PIDDosome, the TRAF2 complex, and the MAVS signalosome, by homotypic CARD-CARD interactions. The mechanism of how CARDs find the right binding partner to form a specific complex remains unclear. This review uses different classification schemes to update the classification of CARD-containing proteins. Combining the classification based on domain structures, functions, associated signaling complexes, and roles would help better understand the structural and function diversity of CARD-containing proteins. This review also summarizes recent structural studies on CARDs. Especially, the CARD-containing complexes can be divided into the homodimeric, heterodimeric, oligomeric, filamentous CARD complexes and the CARD-ubiquitin complex. This review will give an overview of the versatile roles of CARDs in regulating signaling transduction, as well as the therapeutic drugs targeting CARD-containing proteins.
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Affiliation(s)
- Wen-Pin Kao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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49
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Sahillioğlu AC, Özören N. Artificial Loading of ASC Specks with Cytosolic Antigens. PLoS One 2015; 10:e0134912. [PMID: 26258904 PMCID: PMC4530869 DOI: 10.1371/journal.pone.0134912] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/15/2015] [Indexed: 12/14/2022] Open
Abstract
Inflammasome complexes form upon interaction of Nod Like Receptor (NLR) proteins with pathogen associated molecular patterns (PAPMS) inside the cytosol. Stimulation of a subset of inflammasome receptors including NLRP3, NLRC4 and AIM2 triggers formation of the micrometer-sized spherical supramolecular complex called the ASC speck. The ASC speck is thought to be the platform of inflammasome activity, but the reason why a supramolecular complex is preferred against oligomeric platforms remains elusive. We observed that a set of cytosolic proteins, including the model antigen ovalbumin, tend to co-aggregate on the ASC speck. We suggest that co-aggregation of antigenic proteins on the ASC speck during intracellular infection might be instrumental in antigen presentation.
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Affiliation(s)
- Ali Can Sahillioğlu
- Apoptosis and Cancer Immunology Laboratory (AKiL), Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Nesrin Özören
- Apoptosis and Cancer Immunology Laboratory (AKiL), Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
- Life Sciences and Technologies Research Center, Bogazici University, Istanbul, Turkey
- * E-mail:
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50
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Choi JY, Kim CM, Seo EK, Bhat EA, Jang TH, Lee JH, Park HH. Crystal structure of human POP1 and its distinct structural feature for PYD domain. Biochem Biophys Res Commun 2015; 460:957-63. [PMID: 25839653 DOI: 10.1016/j.bbrc.2015.03.134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/24/2015] [Indexed: 01/20/2023]
Abstract
Inflammatory caspases, such as caspase-1, which is critical for the innate immune response, are activated upon the formation of a molecular complex called the inflammasome. The inflammasome is composed of three proteins, the Nod-like receptor (NLRP, NLRC or AIM2), apoptosis associated speck-loke protein containing a caspase-recruitment domain (ASC), and caspase-1. ASC is an adaptor molecule that contains an N-terminal PYD domain and a C-terminal CARD domain for interaction with other proteins. Upon activation, the N-terminal PYD of ASC homotypically interacts with the PYD domain of the Nod-like receptor, while its C-terminal CARD homotypically interacts with the CARD domain of caspase-1. PYD only protein 1 (POP1) negatively regulates inflammatory response by blocking the formation of the inflammasome. POP1 directly binds to ASC via a PYD:PYD interaction, thereby preventing ASC recruitment to Nod-like receptor NLRPs. POP1-mediated regulation of inflammation is of great biological importance. Here, we report the crystal structure of human POP1 and speculate about the inhibitory mechanism of POP1-mediated inflammasome formation based on the current structure.
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Affiliation(s)
- Jae Young Choi
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan 712-749, South Korea
| | - Chang Min Kim
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan 712-749, South Korea
| | - Eun Kyung Seo
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan 712-749, South Korea
| | - Eijaz Ahmed Bhat
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan 712-749, South Korea
| | - Tae-Ho Jang
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan 712-749, South Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea; Department of Polar Sciences, Korea University of Science and Technology, Incheon 406-840, Republic of Korea
| | - Hyun Ho Park
- School of Biotechnology and Graduate School of Biochemistry at Yeungnam University, Gyeongsan 712-749, South Korea.
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