1
|
Gürkan B, Poelman H, Pereverzeva L, Kruijswijk D, de Vos AF, Groenen AG, Nollet EE, Wichapong K, Lutgens E, van der Poll T, Du J, Wiersinga WJ, Nicolaes GAF, van ‘t Veer C. The IRAK-M death domain: a tale of three surfaces. Front Mol Biosci 2024; 10:1265455. [PMID: 38268724 PMCID: PMC10806146 DOI: 10.3389/fmolb.2023.1265455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 12/29/2023] [Indexed: 01/26/2024] Open
Abstract
The anti-inflammatory interleukin-1 receptor associated kinase-M (IRAK-M) is a negative regulator of MyD88/IRAK-4/IRAK-1 signaling. However, IRAK-M has also been reported to activate NF-κB through the MyD88/IRAK-4/IRAK-M myddosome in a MEKK-3 dependent manner. Here we provide support that IRAK-M uses three surfaces of its Death Domain (DD) to activate NF-κB downstream of MyD88/IRAK-4/IRAK-M. Surface 1, with central residue Trp74, binds to MyD88/IRAK-4. Surface 2, with central Lys60, associates with other IRAK-M DDs to form an IRAK-M homotetramer under the MyD88/IRAK-4 scaffold. Surface 3; with central residue Arg97 is located on the opposite side of Trp74 in the IRAK-M DD tetramer, lacks any interaction points with the MyD88/IRAK-4 complex. Although the IRAK-M DD residue Arg97 is not directly involved in the association with MyD88/IRAK-4, Arg97 was responsible for 50% of the NF-κB activation though the MyD88/IRAK-4/IRAK-M myddosome. Arg97 was also found to be pivotal for IRAK-M's interaction with IRAK-1, and important for IRAK-M's interaction with TRAF6. Residue Arg97 was responsible for 50% of the NF-κB generated by MyD88/IRAK-4/IRAK-M myddosome in IRAK-1/MEKK3 double knockout cells. By structural modeling we found that the IRAK-M tetramer surface around Arg97 has excellent properties that allow formation of an IRAK-M homo-octamer. This model explains why mutation of Arg97 results in an IRAK-M molecule with increased inhibitory properties: it still binds to myddosome, competing with myddosome IRAK-1 binding, while resulting in less NF-κB formation. The findings further identify the structure-function properties of IRAK-M, which is a potential therapeutic target in inflammatory disease.
Collapse
Affiliation(s)
- Berke Gürkan
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Hessel Poelman
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
- Medical Biochemistry, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Liza Pereverzeva
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Danielle Kruijswijk
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Alex F. de Vos
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Anouk G. Groenen
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Edgar E. Nollet
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Esther Lutgens
- Medical Biochemistry, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Jiangfeng Du
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - W. Joost Wiersinga
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Gerry A. F. Nicolaes
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
- Medical Biochemistry, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| | - Cornelis van ‘t Veer
- Center of Experimental and Molecular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Infection and Immunity Institute, Amsterdam UMC Location University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
2
|
Yagi S, Yasuno S, Ansai O, Hayashi R, Shimomura Y. Different degree of loss-of-function among four missense mutations in the EDAR gene responsible for autosomal recessive hypohidrotic ectodermal dysplasia may be associated with the phenotypic severity. J Dermatol 2023; 50:349-356. [PMID: 36258277 DOI: 10.1111/1346-8138.16610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022]
Abstract
Hypohidrotic ectodermal dysplasia is a rare condition characterized by hypohidrosis, hypodontia, and hypotrichosis. The disease can show X-linked recessive, autosomal dominant or autosomal recessive inheritance trait. Of these, the autosomal forms are caused by mutations in either EDAR or EDARADD. To date, the underlying pathomechanisms or genotype-phenotype correlations for autosomal forms have not completely been disclosed. In this study, we performed a series of in vitro studies for four missense mutations in the death domain of EDAR protein: p.R358Q, p.G382S, p.I388T, and p.T403M. The results revealed that p.R358Q- and p.T403M-mutant EDAR showed different expression patterns from wild-type EDAR in both western blots and immunostainings. NF-κB reporter assays demonstrated that all the mutant EDAR showed reduced activation of NF-κB, but the reduction by p.G382S- and p.I388T-mutant EDAR was moderate. Co-immunoprecipitation assays showed that p.R358Q- and p.T403M-mutant EDAR did not bind with EDARADD at all, whereas p.G382S- and p.I388T-mutant EDAR maintained the affinity to some extent. Furthermore, we demonstrated that all the mutant EDAR proteins analyzed aberrantly bound with TRAF6. Sum of the data suggest that the degree of loss-of-function is different among the mutant EDAR proteins, which may be associated with the severity of the disease.
Collapse
Affiliation(s)
- Sasagu Yagi
- Department of Dermatology, Yamaguchi University Graduate School of Medicine, Ube, Japan.,Department of Plastic Surgery, Yamaguchi University Hospital, Ube, Japan
| | - Shuichiro Yasuno
- Department of Dermatology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Osamu Ansai
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryota Hayashi
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yutaka Shimomura
- Department of Dermatology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| |
Collapse
|
3
|
Xia S, Chen Z, Shen C, Fu TM. Higher-order assemblies in immune signaling: supramolecular complexes and phase separation. Protein Cell 2021; 12:680-694. [PMID: 33835418 PMCID: PMC8403095 DOI: 10.1007/s13238-021-00839-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/01/2021] [Indexed: 12/31/2022] Open
Abstract
Signaling pathways in innate and adaptive immunity play vital roles in pathogen recognition and the functions of immune cells. Higher-order assemblies have recently emerged as a central principle that governs immune signaling and, by extension, cellular communication in general. There are mainly two types of higher-order assemblies: 1) ordered, solid-like large supramolecular complexes formed by stable and rigid protein-protein interactions, and 2) liquid-like phase-separated condensates formed by weaker and more dynamic intermolecular interactions. This review covers key examples of both types of higher-order assemblies in major immune pathways. By placing emphasis on the molecular structures of the examples provided, we discuss how their structural organization enables elegant mechanisms of signaling regulation.
Collapse
MESH Headings
- Adaptive Immunity
- Animals
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- DEAD Box Protein 58/metabolism
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/immunology
- DEAD-box RNA Helicases/metabolism
- Gene Expression Regulation
- Humans
- Immunity, Innate
- Inflammasomes/genetics
- Inflammasomes/immunology
- Inflammasomes/ultrastructure
- Models, Molecular
- Multiprotein Complexes/genetics
- Multiprotein Complexes/immunology
- Multiprotein Complexes/metabolism
- Protein Conformation
- Protein Interaction Mapping
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Receptors, Immunologic/metabolism
- Receptors, Tumor Necrosis Factor, Type I/genetics
- Receptors, Tumor Necrosis Factor, Type I/immunology
- Receptors, Tumor Necrosis Factor, Type I/metabolism
- Signal Transduction/immunology
- Toll-Like Receptors/genetics
- Toll-Like Receptors/immunology
- Toll-Like Receptors/metabolism
Collapse
Affiliation(s)
- Shiyu Xia
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Zhenhang Chen
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Chen Shen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA.
| |
Collapse
|
4
|
Zhang N, Kisiswa L, Ramanujan A, Li Z, Sim EW, Tian X, Yuan W, Ibáñez CF, Lin Z. Structural basis of NF-κB signaling by the p75 neurotrophin receptor interaction with adaptor protein TRADD through their respective death domains. J Biol Chem 2021; 297:100916. [PMID: 34175311 PMCID: PMC8318917 DOI: 10.1016/j.jbc.2021.100916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
The p75 neurotrophin receptor (p75NTR) is a critical mediator of neuronal death and tissue remodeling and has been implicated in various neurodegenerative diseases and cancers. The death domain (DD) of p75NTR is an intracellular signaling hub and has been shown to interact with diverse adaptor proteins. In breast cancer cells, binding of the adaptor protein TRADD to p75NTR depends on nerve growth factor and promotes cell survival. However, the structural mechanism and functional significance of TRADD recruitment in neuronal p75NTR signaling remain poorly understood. Here we report an NMR structure of the p75NTR-DD and TRADD-DD complex and reveal the mechanism of specific recognition of the TRADD-DD by the p75NTR-DD mainly through electrostatic interactions. Furthermore, we identified spatiotemporal overlap of p75NTR and TRADD expression in developing cerebellar granule neurons (CGNs) at early postnatal stages and discover the physiological relevance of the interaction between TRADD and p75NTR in the regulation of canonical NF-κB signaling and cell survival in CGNs. Our results provide a new structural framework for understanding how the recruitment of TRADD to p75NTR through DD interactions creates a membrane-proximal platform, which can be efficiently regulated by various neurotrophic factors through extracellular domains of p75NTR, to propagate downstream signaling in developing neurons.
Collapse
Affiliation(s)
- Ning Zhang
- School of Life Sciences, Tianjin University, Tianjin, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, PR China
| | - Lilian Kisiswa
- Department of Physiology, National University of Singapore, Singapore; Life Sciences Institute, National University of Singapore, Singapore; Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ajeena Ramanujan
- Department of Physiology, National University of Singapore, Singapore; Life Sciences Institute, National University of Singapore, Singapore
| | - Zhen Li
- School of Life Sciences, Tianjin University, Tianjin, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, PR China
| | - Eunice Weiling Sim
- Department of Physiology, National University of Singapore, Singapore; Life Sciences Institute, National University of Singapore, Singapore
| | - Xianbin Tian
- School of Life Sciences, Tianjin University, Tianjin, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, PR China
| | - Wensu Yuan
- School of Life Sciences, Tianjin University, Tianjin, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, PR China
| | - Carlos F Ibáñez
- Department of Physiology, National University of Singapore, Singapore; Life Sciences Institute, National University of Singapore, Singapore; Department of Neuroscience, Karolinska Institute, Stockholm, Sweden; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University School of Life Sciences and Chinese Institute for Brain Research, Beijing, China
| | - Zhi Lin
- School of Life Sciences, Tianjin University, Tianjin, PR China; Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, PR China; Department of Physiology, National University of Singapore, Singapore; Life Sciences Institute, National University of Singapore, Singapore.
| |
Collapse
|
5
|
Valenti M, Molina M, Cid VJ. Heterologous Expression and Auto-Activation of Human Pro-Inflammatory Caspase-1 in Saccharomyces cerevisiae and Comparison to Caspase-8. Front Immunol 2021; 12:668602. [PMID: 34335569 PMCID: PMC8317575 DOI: 10.3389/fimmu.2021.668602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/28/2021] [Indexed: 01/15/2023] Open
Abstract
Caspases are a family of cysteine proteases that play an essential role in inflammation, apoptosis, cell death, and development. Here we delve into the effects caused by heterologous expression of human caspase-1 in the yeast Saccharomyces cerevisiae and compare them to those of caspase-8. Overexpression of both caspases in the heterologous model led to their activation and caused mitochondrial hyperpolarization, damage to different organelles, and cell death. All these effects were dependent on their protease activity, and caspase-8 was more aggressive than caspase-1. Growth arrest could be at least partially explained by dysfunction of the actin cytoskeleton as a consequence of the processing of the yeast Bni1 formin, which we identify here as a likely direct substrate of both caspases. Through the modulation of the GAL1 promoter by using different galactose:glucose ratios in the culture medium, we have established a scenario in which caspase-1 is sufficiently expressed to become activated while yeast growth is not impaired. Finally, we used the yeast model to explore the role of death-fold domains (DD) of both caspases in their activity. Peculiarly, the DDs of either caspase showed an opposite involvement in its intrinsic activity, as the deletion of the caspase activation and recruitment domain (CARD) of caspase-1 enhanced its activity, whereas the deletion of the death effector domain (DED) of caspase-8 diminished it. We show that caspase-1 is able to efficiently process its target gasdermin D (GSDMD) when co-expressed in yeast. In sum, we propose that S. cerevisiae provides a manageable tool to explore caspase-1 activity and structure–function relationships.
Collapse
Affiliation(s)
- Marta Valenti
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Universidad Complutense de Madrid, Madrid, Spain
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Universidad Complutense de Madrid, Madrid, Spain
| | - Víctor J Cid
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
6
|
Asano N, Yasuno S, Hayashi R, Shimomura Y. Characterization of EDARADD gene mutations responsible for hypohidrotic ectodermal dysplasia. J Dermatol 2021; 48:1533-1541. [PMID: 34219261 DOI: 10.1111/1346-8138.16044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/08/2021] [Indexed: 11/27/2022]
Abstract
Hypohidrotic ectodermal dysplasia (HED) is a genetic disorder characterized by hypohidrosis, hypodontia, and hypotrichosis. Autosomal forms of the disease are caused by mutations in either EDAR or EDARADD. To date, the underlying pathomechanisms for HED resulting from EDARADD mutations have not fully been disclosed. In this study, we performed detailed in vitro analyses in order to characterize three dominantly inherited missense mutations, p.D120Y, p.L122R, and p.D123N, and one recessively inherited missense mutation, p.E152K, in the EDARADD gene. Nuclear factor (NF)-κB reporter assays demonstrated that all the mutant EDARADD showed reduction in activation of NF-κB. Importantly, p.D120Y-, p.L122R-, and p.D123N-mutant EDARADD slightly reduced the NF-κB activity induced by wild-type EDARADD in a dominant negative manner. Co-immunoprecipitation assays showed that all of the mutant EDARADD were capable of binding to EDAR and wild-type EDARADD. Additional co-immunoprecipitation assays revealed that p.D120Y-, p.L122R-, and p.D123N-mutant EDARADD markedly prevented the interaction between EDAR and wild-type EDARADD, which further indicated a dominant negative effect by these mutations. Finally, we found that p.D120Y-, p.L122R-, and p.D123N-mutant EDARADD completely lost the ability to bind with TRAF6, while p.E152K-mutant EDARADD showed a mild reduction in the affinity. Our findings will provide crucial information toward unraveling the molecular mechanisms how EDARADD gene mutations cause the disease.
Collapse
Affiliation(s)
- Nobuyuki Asano
- Department of Dermatology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Shuichiro Yasuno
- Department of Dermatology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Ryota Hayashi
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yutaka Shimomura
- Department of Dermatology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| |
Collapse
|
7
|
Abstract
Signaling activation is a tightly regulated process involving myriad posttranslational modifications such as phosphorylation/dephosphorylation, ubiquitylation/deubiquitylation, proteolytical cleavage events as well as translocation of proteins to new compartments within the cell. In addition to each of these events potentially regulating individual proteins, the assembly of very large supramolecular complexes has emerged as a common theme in signal transduction and is now known to regulate many signaling events. This is particularly evident in pathways regulating both inflammation and cell death/survival. Regulation of the assembly and silencing of these complexes plays important roles in immune signaling and inflammation and the fate of cells to either die or survive. Here we will give a summary of some of the better studied supramolecular complexes involved in inflammation and cell death, particularly with a focus on diseases caused by their autoactivation and the role autophagy either plays or may be playing in their regulation.
Collapse
Affiliation(s)
- Ian E Gentle
- Faculty of Medicine, Institute of Medical Microbiology and Hygiene, Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| |
Collapse
|
8
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
9
|
Ding J, Pan X, Du L, Yao Q, Xue J, Yao H, Wang DC, Li S, Shao F. Structural and Functional Insights into Host Death Domains Inactivation by the Bacterial Arginine GlcNAcyltransferase Effector. Mol Cell 2019; 74:922-935.e6. [PMID: 30979585 DOI: 10.1016/j.molcel.2019.03.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/27/2018] [Accepted: 03/22/2019] [Indexed: 01/10/2023]
Abstract
Enteropathogenic E. coli NleB and related type III effectors catalyze arginine GlcNAcylation of death domain (DD) proteins to block host defense, but the underlying mechanism is unknown. Here we solve crystal structures of NleB alone and in complex with FADD-DD, UDP, and Mn2+ as well as NleB-GlcNAcylated DDs of TRADD and RIPK1. NleB adopts a GT-A fold with a unique helix-pair insertion to hold FADD-DD; the interface contacts explain the selectivity of NleB for certain DDs. The acceptor arginine is fixed into a cleft, in which Glu253 serves as a base to activate the guanidinium. Analyses of the enzyme-substrate complex and the product structures reveal an inverting sugar-transfer reaction and a detailed catalytic mechanism. These structural insights are validated by mutagenesis analyses of NleB-mediated GlcNAcylation in vitro and its function in mouse infection. Our study builds a structural framework for understanding of NleB-catalyzed arginine GlcNAcylation of host death domain.
Collapse
Affiliation(s)
- Jingjin Ding
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; National Institute of Biological Sciences, Beijing 102206, China.
| | - Xing Pan
- Bio-Medical Center, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Lijie Du
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Qing Yao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Hongwei Yao
- College of Chemistry and Chemical Engineering, High-Field Nuclear Magnetic Resonance Center, Xiamen University, Xiamen, Fujian 361005, China
| | - Da-Cheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shan Li
- Bio-Medical Center, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, China.
| | - Feng Shao
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
| |
Collapse
|
10
|
Yuan W, Ibáñez CF, Lin Z. Death domain of p75 neurotrophin receptor: a structural perspective on an intracellular signalling hub. Biol Rev Camb Philos Soc 2019; 94:1282-1293. [PMID: 30762293 DOI: 10.1111/brv.12502] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 12/19/2022]
Abstract
The death domain (DD) is a globular protein motif with a signature feature of an all-helical Greek-key motif. It is a primary mediator of a variety of biological activities, including apoptosis, cell survival and cytoskeletal changes, which are related to many neurodegenerative diseases, neurotrauma, and cancers. DDs exist in a wide range of signalling proteins including p75 neurotrophin receptor (p75NTR ), a member of the tumour necrosis factor receptor superfamily. The specific signalling mediated by p75NTR in a given cell depends on the type of ligand engaging the extracellular domain and the recruitment of cytosolic interactors to the intracellular domain, especially the DD, of the receptor. In solution, the p75NTR -DDs mainly form a symmetric non-covalent homodimer. In response to extracellular signals, conformational changes in the p75NTR extracellular domain (ECD) propagate to the p75NTR -DD through the disulfide-bonded transmembrane domain (TMD) and destabilize the p75NTR -DD homodimer, leading to protomer separation and exposure of binding sites on the DD surface. In this review, we focus on recent advances in the study of the structural mechanism of p75NTR -DD signalling through recruitment of diverse intracellular interactors for the regulation and control of diverse functional outputs.
Collapse
Affiliation(s)
- Wensu Yuan
- School of Life Sciences, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Carlos F Ibáñez
- Department of Physiology, National University of Singapore, 117456, Singapore.,Life Sciences Institute, National University of Singapore, 117456, Singapore.,Department of Cell & Molecular Biology, Karolinska Institute, 17165, Stockholm, Sweden
| | - Zhi Lin
- School of Life Sciences, Tianjin University, Tianjin, 300072, People's Republic of China.,Department of Physiology, National University of Singapore, 117456, Singapore.,Life Sciences Institute, National University of Singapore, 117456, Singapore
| |
Collapse
|
11
|
Meng H, Liu Z, Li X, Wang H, Jin T, Wu G, Shan B, Christofferson DE, Qi C, Yu Q, Li Y, Yuan J. Death-domain dimerization-mediated activation of RIPK1 controls necroptosis and RIPK1-dependent apoptosis. Proc Natl Acad Sci U S A 2018; 115:E2001-9. [PMID: 29440439 DOI: 10.1073/pnas.1722013115] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
RIPK1 is a critical mediator of cell death and inflammation downstream of TNFR1 upon stimulation by TNFα, a potent proinflammatory cytokine involved in a multitude of human inflammatory and degenerative diseases. RIPK1 contains an N-terminal kinase domain, an intermediate domain, and a C-terminal death domain (DD). The kinase activity of RIPK1 promotes cell death and inflammation. Here, we investigated the involvement of RIPK1-DD in the regulation of RIPK1 kinase activity. We show that a charge-conserved mutation of a lysine located on the surface of DD (K599R in human RIPK1 or K584R in murine RIPK1) blocks RIPK1 activation in necroptosis and RIPK1-dependent apoptosis and the formation of complex II. Ripk1K584R/K584R knockin mutant cells are resistant to RIPK1 kinase-dependent apoptosis and necroptosis. The resistance of K584R cells, however, can be overcome by forced dimerization of RIPK1. Finally, we show that the K584R RIPK1 knockin mutation protects mice against TNFα-induced systematic inflammatory response syndrome. Our study demonstrates the role of RIPK1-DD in mediating RIPK1 dimerization and activation of its kinase activity during necroptosis and RIPK1-dependent apoptosis.
Collapse
|
12
|
Hashiramoto A, Konishi Y, Murayama K, Kawasaki H, Yoshida K, Tsumiyama K, Tanaka K, Mizuhara M, Shiotsuki T, Kitamura H, Komai K, Kimura T, Yagita H, Shiozawa K, Shiozawa S. A variant of death-receptor 3 associated with rheumatoid arthritis interferes with apoptosis-induction of T cell. J Biol Chem 2017; 293:1933-1943. [PMID: 29180447 PMCID: PMC5808757 DOI: 10.1074/jbc.m117.798884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/14/2017] [Indexed: 12/12/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic polyarthritis of unknown etiology. To unravel the molecular mechanisms in RA, we performed targeted DNA sequencing analysis of patients with RA. This analysis identified a variant of the death receptor 3 (DR3) gene, a member of the family of apoptosis-inducing Fas genes, which contains four single-nucleotide polymorphisms (SNPs) and a 14-nucleotide deletion within exon 5 and intron 5. We found that the deletion causes the binding of splicing regulatory proteins to DR3 pre-mRNA intron 5, resulting in a portion of intron 5 becoming part of the coding sequence, thereby generating a premature stop codon. We also found that this truncated DR3 protein product lacks the death domain and forms a heterotrimer complex with wildtype DR3 that dominant-negatively inhibits ligand-induced apoptosis in lymphocytes. Myelocytes from transgenic mice expressing the human DR3 variant produced soluble truncated DR3, forming a complex with TNF-like ligand 1A (TL1A), which inhibited apoptosis induction. In summary, our results reveal that a DR3 splice variant that interferes with ligand-induced T cell responses and apoptosis may contribute to RA pathogenesis.
Collapse
Affiliation(s)
- Akira Hashiramoto
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Yoshitake Konishi
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Koichi Murayama
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Hiroki Kawasaki
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Kohsuke Yoshida
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Ken Tsumiyama
- the Department of Medicine, Rheumatic Diseases Unit, Kyushu University Beppu Hospital, Beppu 874-0838
| | - Kimie Tanaka
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Masaru Mizuhara
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Toshio Shiotsuki
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Hitomi Kitamura
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Koichiro Komai
- From the Department of Biophysics, Kobe University Graduate School of Health Science, Kobe 654-0142
| | - Tomoatsu Kimura
- the Department of Orthopedic Surgery, Faculty of Medicine, University of Toyama, 3190 Gofuku, 930-0194 Toyama
| | - Hideo Yagita
- the Department of Immunology, Juntendo University School of Medicine, Tokyo 113-8431, and
| | - Kazuko Shiozawa
- the Department of Rheumatology, Hyogo Prefectural Kakogawa Medical Center, Kakogawa 675-8555, Japan
| | - Shunichi Shiozawa
- the Department of Medicine, Rheumatic Diseases Unit, Kyushu University Beppu Hospital, Beppu 874-0838,
| |
Collapse
|
13
|
Fu TM, Li Y, Lu A, Li Z, Vajjhala PR, Cruz AC, Srivastava DB, DiMaio F, Penczek PA, Siegel RM, Stacey KJ, Egelman EH, Wu H. Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex. Mol Cell 2016; 64:236-250. [PMID: 27746017 PMCID: PMC5089849 DOI: 10.1016/j.molcel.2016.09.009] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/10/2016] [Accepted: 09/07/2016] [Indexed: 12/20/2022]
Abstract
Caspase-8 activation can be triggered by death receptor-mediated formation of the death-inducing signaling complex (DISC) and by the inflammasome adaptor ASC. Caspase-8 assembles with FADD at the DISC and with ASC at the inflammasome through its tandem death effector domain (tDED), which is regulated by the tDED-containing cellular inhibitor cFLIP and the viral inhibitor MC159. Here we present the caspase-8 tDED filament structure determined by cryoelectron microscopy. Extensive assembly interfaces not predicted by the previously proposed linear DED chain model were uncovered, and were further confirmed by structure-based mutagenesis in filament formation in vitro and Fas-induced apoptosis and ASC-mediated caspase-8 recruitment in cells. Structurally, the two DEDs in caspase-8 use quasi-equivalent contacts to enable assembly. Using the tDED filament structure as a template, structural analyses reveal the interaction surfaces between FADD and caspase-8 and the distinct mechanisms of regulation by cFLIP and MC159 through comingling and capping, respectively.
Collapse
Affiliation(s)
- Tian-Min Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yang Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alvin Lu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Zongli Li
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Parimala R Vajjhala
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Anthony C Cruz
- Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Devendra B Srivastava
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Pawel A Penczek
- Department of Biochemistry and Molecular Biology, University of Texas-Houston Medical School, Houston, TX 77030, USA
| | - Richard M Siegel
- Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Katryn J Stacey
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| |
Collapse
|
14
|
Fancy RM, Wang L, Zeng Q, Wang H, Zhou T, Buchsbaum DJ, Song Y. Characterization of the Interactions between Calmodulin and Death Receptor 5 in Triple-negative and Estrogen Receptor-positive Breast Cancer Cells: AN INTEGRATED EXPERIMENTAL AND COMPUTATIONAL STUDY. J Biol Chem 2016; 291:12862-12870. [PMID: 27129269 DOI: 10.1074/jbc.m116.727727] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 01/26/2023] Open
Abstract
Activation of death receptor-5 (DR5) leads to the formation of death inducing signaling complex (DISC) for apoptotic signaling. Targeting DR5 to induce breast cancer apoptosis is a promising strategy to circumvent drug resistance and present a target for breast cancer treatment. Calmodulin (CaM) has been shown to regulate DR5-mediated apoptotic signaling, however, its mechanism remains unknown. In this study, we characterized CaM and DR5 interactions in breast cancer cells with integrated experimental and computational approaches. Results show that CaM directly binds to DR5 in a calcium dependent manner in breast cancer cells. The direct interaction of CaM with DR5 is localized at DR5 death domain. We have predicted and verified the CaM-binding site in DR5 being (354)WEPLMRKLGL(363) that is located at the α2 helix and the loop between α2 helix and α3 helix of DR5 DD. The residues of Trp-354, Arg-359, Glu-355, Leu-363, and Glu-367 in DR5 death domain that are important for DR5 recruitment of FADD and caspase-8 for DISC formation to signal apoptosis also play an important role for CaM-DR5 binding. The changed electrostatic potential distribution in the CaM-binding site in DR5 DD by the point mutations of W354A, E355K, R359A, L363N, or E367K in DR5 DD could directly contribute to the experimentally observed decreased CaM-DR5 binding by the point mutations of the key residues in DR5 DD. Results from this study provide a key step for the further investigation of the role of CaM-DR5 binding in DR5-mediated DISC formation for apoptosis in breast cancer cells.
Collapse
Affiliation(s)
| | | | | | | | | | - Donald J Buchsbaum
- Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Yuhua Song
- From the Departments of Biomedical Engineering,.
| |
Collapse
|
15
|
Baratchian M, Davis CA, Shimizu A, Escors D, Bagnéris C, Barrett T, Collins MK. Distinct Activation Mechanisms of NF-κB Regulator Inhibitor of NF-κB Kinase (IKK) by Isoforms of the Cell Death Regulator Cellular FLICE-like Inhibitory Protein (cFLIP). J Biol Chem 2016; 291:7608-20. [PMID: 26865630 PMCID: PMC4817188 DOI: 10.1074/jbc.m116.718122] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 11/06/2022] Open
Abstract
The viral FLICE-like inhibitory protein (FLIP) protein from Kaposi sarcoma-associated herpesvirus activates the NF-κB pathway by forming a stable complex with a central region (amino acids 150-272) of the inhibitor of NF-κB kinase (IKK) γ subunits, thereby activating IKK. Cellular FLIP (cFLIP) forms are also known to activate the NF-κB pathway via IKK activation. Here we demonstrate that cFLIPL, cFLIPS, and their proteolytic product p22-FLIP all require the C-terminal region of NEMO/IKKγ (amino acids 272-419) and its ubiquitin binding function for activation of the IKK kinase (or kinase complex), but none form a stable complex with IKKγ. Our results further reveal that cFLIPLrequires the linear ubiquitin chain assembly complex and the kinase TAK1 for activation of the IKK kinase. Similarly, cFLIPSand p22-FLIP also require TAK1 but do not require LUBAC. In contrast, these isoforms are both components of complexes that incorporate Fas-associated death domain and RIP1, which appear essential for kinase activation. This conservation of IKK activation among the cFLIP family using different mechanisms suggests that the mechanism plays a critical role in their function.
Collapse
Affiliation(s)
- Mehdi Baratchian
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom, Division of Advanced Therapies, National Institute of Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3QG, United Kingdom, and
| | - Christopher A Davis
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Akira Shimizu
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - David Escors
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Claire Bagnéris
- Institute of Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - Tracey Barrett
- Institute of Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - Mary K Collins
- From the Medical Research Council Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom, Division of Advanced Therapies, National Institute of Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3QG, United Kingdom, and
| |
Collapse
|
16
|
Abstract
Cell death appears to be a basic biological phenomenon which is maintained by the human body. The term apoptosis, also known as programmed cell death, is characterized by several unique morphological and biochemical features. Apoptosis and its different forms are essential for tissue homeostasis. Alteration in molecular mechanisms involved in apoptotic signaling contributes to a vast range of oral diseases. An understanding of the regulation of apoptosis has led to the development of many therapeutic approaches and better management of oral diseases. The review updates us the correlation between apoptosis in normal oral tissues and oral diseases.
Collapse
Affiliation(s)
- Akansha Misra
- Department of Oral Pathology, Institute of Dental Studies and Technologies, Modinagar, Uttar Pradesh, India
| | - Shalu Rai
- Department of Oral Medicine and Radiology, Institute of Dental Studies and Technologies, Modinagar, Uttar Pradesh, India
| | - Deepankar Misra
- Department of Oral Medicine and Radiology, Institute of Dental Studies and Technologies, Modinagar, Uttar Pradesh, India
| |
Collapse
|
17
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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,
| |
Collapse
|
18
|
Kemplen KR, De Sancho D, Clarke J. The response of Greek key proteins to changes in connectivity depends on the nature of their secondary structure. J Mol Biol 2015; 427:2159-65. [PMID: 25861761 PMCID: PMC4451459 DOI: 10.1016/j.jmb.2015.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/09/2015] [Accepted: 03/30/2015] [Indexed: 11/15/2022]
Abstract
What governs the balance between connectivity and topology in regulating the mechanism of protein folding? We use circular permutation to vary the order of the helices in the all-α Greek key protein FADD (Fas-associated death domain) to investigate this question. Unlike all-β Greek key proteins, where changes in the order of secondary structure cause a shift in the folding nucleus, the position of the nucleus in FADD is unchanged, even when permutation reduces the complexity significantly. We suggest that this is because local helical contacts are so dominant that permutation has little effect on the entropic cost of forming the folding nucleus whereas, in all-β Greek key proteins, all interactions in the nucleus are long range. Thus, the type of secondary structure modulates the sensitivity of proteins to changes in connectivity.
Collapse
Affiliation(s)
- Katherine R Kemplen
- University of Cambridge Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - David De Sancho
- University of Cambridge Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jane Clarke
- University of Cambridge Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK.
| |
Collapse
|
19
|
Abstract
Infections with enteropathogenic Escherichia coli (EPEC) are remarkably devoid of gut inflammation and necrotic damage compared to infections caused by invasive pathogens such as Salmonella and Shigella. Recently, we observed that EPEC blocks cell death using the type III secretion system (T3SS) effector NleB. NleB mediated post-translational modification of death domain containing adaptor proteins by the covalent attachment of N-acetylglucosamine (GlcNAc) to a conserved arginine in the death domain. N-linked glycosylation of arginine has not previously been reported in mammalian cell biology and the precise biochemistry of this modification is not yet defined. Although the addition of a single GlcNAc to arginine is a seemingly slight alteration, the impact of NleB is considerable as arginine in this location is critical for death domain interactions and death receptor induced apoptosis. Hence, by blocking cell death, NleB promotes enterocyte survival and thereby prolongs EPEC attachment to the gut epithelium.
Collapse
Affiliation(s)
- Jaclyn S Pearson
- Department of Microbiology and Immunology; University of Melbourne at the Peter Doherty Institute for Infection and Immunity; Melbourne, Australia
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology; University of Melbourne at the Peter Doherty Institute for Infection and Immunity; Melbourne, Australia,Correspondence to: Elizabeth L Hartland;
| |
Collapse
|
20
|
Nematollahi LA, Garza-Garcia A, Bechara C, Esposito D, Morgner N, Robinson CV, Driscoll PC. Flexible stoichiometry and asymmetry of the PIDDosome core complex by heteronuclear NMR spectroscopy and mass spectrometry. J Mol Biol 2014; 427:737-752. [PMID: 25528640 PMCID: PMC4332690 DOI: 10.1016/j.jmb.2014.11.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/14/2014] [Accepted: 11/22/2014] [Indexed: 11/24/2022]
Abstract
Homotypic death domain (DD)–DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing five PIDD-DDs in one layer, five RAIDD-DDs in a second layer and an additional two RAIDD-DDs. We addressed complex formation between PIDD-DD and RAIDD-DD in solution using heteronuclear nuclear magnetic resonance (NMR) spectroscopy, nanoflow electrospray ionization mass spectrometry and size-exclusion chromatography with multi-angle light scattering. The DDs assemble into complexes displaying molecular masses in the range 130–158 kDa and RAIDD-DD:PIDD-DD stoichiometries of 5:5, 6:5 and 7:5. These data suggest that the crystal structure is representative of only the heaviest species in solution and that two RAIDD-DDs are loosely attached to the 5:5 core. Two-dimensional 1H,15N-NMR experiments exhibited signal loss upon complexation consistent with the formation of high-molecular-weight species. 13C-Methyl-transverse relaxation optimized spectroscopy measurements of the PIDDosome core exhibit signs of differential line broadening, cross-peak splitting and chemical shift heterogeneity that reflect the presence of non-equivalent sites at interfaces within an asymmetric complex. Experiments using a mutant RAIDD-DD that forms a monodisperse 5:5 complex with PIDD-DD show that the spectroscopic signature derives from the quasi- but non-exact equivalent environments of each DD. Since this characteristic was previously demonstrated for the complex between the DDs of CD95 and FADD, the NMR data for this system are consistent with the formation of a structure homologous to the PIDDosome core. The PIDDosome core particle that has been crystallized as a 7:5 complex displays heterogeneous stoichiometry in solution. Methyl-transverse relaxation optimized spectroscopy NMR spectra for the complex suggest that individual PIDD-DDs and RAIDD-DDs experience non-equivalent environments in the PIDDosome core. A mutant PIDDosome core particle that is monodisperse displays similar NMR features, suggesting that the complexity of the spectra is a reflection of the absence of formal symmetry consistent with the crystal structure. The NMR characteristics are reminiscent of those reported for the complex formed between the DDs of CD95 and FADD, suggesting that this latter complex has similar architecture to the PIDDosome core.
Collapse
Affiliation(s)
- Lily A Nematollahi
- Division of Molecular Structure, Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Acely Garza-Garcia
- Division of Molecular Structure, Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Chérine Bechara
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Diego Esposito
- Division of Molecular Structure, Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Nina Morgner
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Paul C Driscoll
- Division of Molecular Structure, Medical Research Council, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
| |
Collapse
|
21
|
Brietzke A, Goldammer T, Rebl H, Korytář T, Köllner B, Yang W, Rebl A, Seyfert HM. Characterization of the interleukin 1 receptor-associated kinase 4 (IRAK4)-encoding gene in salmonid fish: the functional copy is rearranged in Oncorhynchus mykiss and that factor can impair TLR signaling in mammalian cells. Fish Shellfish Immunol 2014; 36:206-214. [PMID: 24239597 DOI: 10.1016/j.fsi.2013.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/28/2013] [Accepted: 11/04/2013] [Indexed: 06/02/2023]
Abstract
The interleukin 1 receptor-associated kinase 4 (IRAK4) is an essential factor for TLR-mediated activation of the host's immune functions subsequent to pathogen contact. We have characterized the respective cDNA and gene sequences from three salmonid species, salmon, rainbow trout and maraena whitefish. The gene from salmon is structured into eleven exons, as is the mammalian homologue, while exons have been fused in the genes from the two other salmonid species. Rainbow trout expresses also a pseudogene at low levels. Its basic structure resembles more closely the primordial gene than the functional copy does. The N-terminal death domain and the C-terminal protein kinase domain of the factors are better conserved throughout evolution than the linker domain. The deduced amino acid sequences of the factors from all three species group together in an evolutionary tree of IRAK4 factors. Scrutinizing expression and function of IRAK4 from rainbow trout, we found its highest expression in head kidney and spleen and lowest expression in muscle tissue. Infecting fish with Aeromonas salmonicida did not modulate its expression during 72 h of observation. Expression of a GFP-tagged trout IRAK4 revealed, expectedly, its cytoplasmic localization in human HEK-293 cells. However, this factor significantly quenched in a dose-dependent fashion not only the pathogen-induced stimulation of NF-κB factors in the HEK-293 reconstitution system of TLR2 signaling, but also the basal NF-κB levels in unstimulated control cells. Our data unexpectedly imply that IRAK4 is involved in establishing threshold levels of active NF-κB in resting cells.
Collapse
Affiliation(s)
- Andreas Brietzke
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Tom Goldammer
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Henrike Rebl
- Rostock University Medical Center, Department of Cell Biology, Schillingallee 69, 18057 Rostock, Germany
| | - Tomáš Korytář
- Friedrich-Loeffler-Institute (FLI), Federal Research Institute for Animal Health, Institute of Immunology, Südufer 10, 17493 Greifswald, Insel Riems, Germany
| | - Bernd Köllner
- Friedrich-Loeffler-Institute (FLI), Federal Research Institute for Animal Health, Institute of Immunology, Südufer 10, 17493 Greifswald, Insel Riems, Germany
| | - Wei Yang
- Department of Anesthesiology, Duke University Medical Center, PO Box 3094, Durham, NC 27710, USA
| | - Alexander Rebl
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
| | - Hans-Martin Seyfert
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| |
Collapse
|
22
|
Hu R, Du Q, Yin X, Li J, Wang T, Zhang L. Agonist antibody activates death receptor 6 downstream signaling involving TRADD recruitment. FEBS Lett 2013; 588:401-7. [PMID: 24374337 DOI: 10.1016/j.febslet.2013.12.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/05/2013] [Accepted: 12/07/2013] [Indexed: 11/30/2022]
Abstract
Death receptor 6 (DR6) is a member of the death domain-containing receptors that belong to the TNFR superfamily. To date, the ligand for DR6 is still not clearly defined. Here, we developed a functional agonist monoclonal antibody (DQM3) against DR6, which bound to the first cysteine-rich domain. Importantly, DR6 signaling could be clearly activated by DQM3, which was dependent on its intracellular death domain. In addition, we demonstrated that the association between DR6 and TRADD was enhanced upon DQM3 stimulation and TRADD was involved in DR6-induced signaling activation. Taken together, our findings provide new insight into a novel mechanism by which DR6 induces downstream signaling in response to an agonist antibody.
Collapse
Affiliation(s)
- Rui Hu
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiumei Du
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangyun Yin
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyun Li
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Wang
- Department of Neurology, General Hospital of PLA Shenyang Military Area Command, Shenyang 110015, China
| | - Liguo Zhang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
23
|
Yamamoto T, Tsutsumi N, Tochio H, Ohnishi H, Kubota K, Kato Z, Shirakawa M, Kondo N. Functional assessment of the mutational effects of human IRAK4 and MyD88 genes. Mol Immunol 2014; 58:66-76. [PMID: 24316379 DOI: 10.1016/j.molimm.2013.11.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/08/2013] [Accepted: 11/09/2013] [Indexed: 01/08/2023]
Abstract
Human interleukin-1 receptor-associated kinase 4 (IRAK4) deficiency and myeloid differentiating factor 88 (MyD88) deficiency syndromes are two primary immune-deficiency disorders with innate immune defects. Although new genetic variations of IRAK4 and MyD88 have recently been deposited in the single nucleotide polymorphism (SNP) database, the clinical significance of these variants has not yet been established. Therefore, it is important to establish methods for assessing the association of each gene variation with human diseases. Because cell-based assays, western blotting and an NF-κB reporter gene assay, showed no difference in protein expression and NF-κB activity between R12C and wild-type IRAK4, we examined protein-protein interactions of purified recombinant IRAK4 and MyD88 proteins by analytical gel filtration and NMR titration. We found that the variant of IRAK4, R12C, as well as R20W, located in the death domain of IRAK4 and regarded as a SNP, caused a loss of interaction with MyD88. Our studies suggest that not only the loss of protein expression but also the defect of Myddosome formation could cause IRAK4 and MyD88 deficiency syndromes. Moreover a combination of in vitro functional assays is effective for confirming the pathogenicity of mutants found in IRAK4 and MyD88-deficiency patients.
Collapse
|
24
|
Pearson JS, Giogha C, Ong SY, Kennedy CL, Kelly M, Robinson KS, Wong T, Mansell A, Riedmaier P, Oates CVL, Zaid A, Mühlen S, Crepin VF, Marches O, Ang CS, Williamson NA, O’Reilly LA, Bankovacki A, Nachbur U, Infusini G, Webb AI, Silke J, Strasser A, Frankel G, Hartland EL. A type III effector antagonizes death receptor signalling during bacterial gut infection. Nature 2013; 501:247-51. [PMID: 24025841 PMCID: PMC3836246 DOI: 10.1038/nature12524] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/02/2013] [Indexed: 02/07/2023]
Abstract
Successful infection by enteric bacterial pathogens depends on the ability of the bacteria to colonize the gut, replicate in host tissues and disseminate to other hosts. Pathogens such as Salmonella, Shigella and enteropathogenic and enterohaemorrhagic (EPEC and EHEC, respectively) Escherichia coli use a type III secretion system (T3SS) to deliver virulence effector proteins into host cells during infection that promote colonization and interfere with antimicrobial host responses. Here we report that the T3SS effector NleB1 from EPEC binds to host cell death-domain-containing proteins and thereby inhibits death receptor signalling. Protein interaction studies identified FADD, TRADD and RIPK1 as binding partners of NleB1. NleB1 expressed ectopically or injected by the bacterial T3SS prevented Fas ligand or TNF-induced formation of the canonical death-inducing signalling complex (DISC) and proteolytic activation of caspase-8, an essential step in death-receptor-induced apoptosis. This inhibition depended on the N-acetylglucosamine transferase activity of NleB1, which specifically modified Arg 117 in the death domain of FADD. The importance of the death receptor apoptotic pathway to host defence was demonstrated using mice deficient in the FAS signalling pathway, which showed delayed clearance of the EPEC-like mouse pathogen Citrobacter rodentium and reversion to virulence of an nleB mutant. The activity of NleB suggests that EPEC and other attaching and effacing pathogens antagonize death-receptor-induced apoptosis of infected cells, thereby blocking a major antimicrobial host response.
Collapse
Affiliation(s)
- Jaclyn S Pearson
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Cristina Giogha
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Sze Ying Ong
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Catherine L Kennedy
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Michelle Kelly
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Keith S Robinson
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Tania Wong
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Ashley Mansell
- Centre for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Victoria 3010, Australia
| | - Patrice Riedmaier
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Clare VL Oates
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Ali Zaid
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Sabrina Mühlen
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
| | - Valerie F Crepin
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Olivier Marches
- Centre for Immunology and Infectious Disease, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Lorraine A O’Reilly
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Aleksandra Bankovacki
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Ueli Nachbur
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Giuseppe Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - John Silke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Victoria 3010, Australia
| | - Gad Frankel
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne, Victoria 3010, Australia
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| |
Collapse
|
25
|
Dall E, Brandstetter H. Mechanistic and structural studies on legumain explain its zymogenicity, distinct activation pathways, and regulation. Proc Natl Acad Sci U S A 2013; 110:10940-5. [PMID: 23776206 DOI: 10.1073/pnas.1300686110] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The cysteine protease legumain plays important functions in immunity and cancer at different cellular locations, some of which appeared conflicting with its proteolytic activity and stability. Here, we report crystal structures of legumain in the zymogenic and fully activated form in complex with different substrate analogs. We show that the eponymous asparagine-specific endopeptidase activity is electrostatically generated by pH shift. Completely unexpectedly, the structure points toward a hidden carboxypeptidase activity that develops upon proteolytic activation with the release of an activation peptide. These activation routes reconcile the enigmatic pH stability of legumain, e.g., lysosomal, nuclear, and extracellular activities with relevance in immunology and cancer. Substrate access and turnover is controlled by selective protonation of the S1 pocket (KM) and the catalytic nucleophile (kcat), respectively. The multibranched and context-dependent activation process of legumain illustrates how proteases can act not only as signal transducers but as decision makers.
Collapse
|
26
|
Shirley S, Morizot A, Micheau O. Regulating TRAIL receptor-induced cell death at the membrane : a deadly discussion. Recent Pat Anticancer Drug Discov 2011; 6:311-23. [PMID: 21756247 PMCID: PMC3204462 DOI: 10.2174/157489211796957757] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 02/20/2011] [Accepted: 02/20/2011] [Indexed: 12/20/2022]
Abstract
The use of TRAIL/APO2L and monoclonal antibodies targeting TRAIL receptors for cancer therapy holds great promise, due to their ability to restore cancer cell sensitivity to apoptosis in association with conventional chemotherapeutic drugs in a large variety of tumors. TRAIL-induced cell death is tightly regulated right from the membrane and at the DISC (Death-Inducing Signaling Complex) level. The following patent and literature review aims to present and highlight recent findings of the deadly discussion that determines tumor cell fate upon TRAIL engagement.
Collapse
Affiliation(s)
- Sarah Shirley
- INSERM, U866, Dijon, F-21079 France; Faculty of Medicine and Pharmacy, University of Bourgogne, Dijon, F-21079 France.
| | | | | |
Collapse
|
27
|
Toivonen HT, Meinander A, Asaoka T, Westerlund M, Pettersson F, Mikhailov A, Eriksson JE, Saxén H. Modeling reveals that dynamic regulation of c-FLIP levels determines cell-to-cell distribution of CD95-mediated apoptosis. J Biol Chem 2011; 286:18375-82. [PMID: 21324892 PMCID: PMC3099654 DOI: 10.1074/jbc.m110.177097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 02/11/2011] [Indexed: 12/22/2022] Open
Abstract
The expression levels of caspase-8 inhibitory c-FLIP proteins play an important role in regulating death receptor-mediated apoptosis, as their concentration at the moment when the death-inducing signaling complex (DISC) is formed determines the outcome of the DISC signal. Experimental studies have shown that c-FLIP proteins are subject to dynamic turnover and that their stability and expression levels can be rapidly altered. Even though the influence of c-FLIP on the apoptotic behavior of a single cell has been captured in mathematical simulation studies, the effect of c-FLIP turnover and stability has not been investigated. In this study, a mathematical model of apoptosis was developed to analyze how the dynamic turnover and stability of the c-FLIP isoforms regulate apoptotic signaling for both individual cells and cell populations. Intercellular parameter and concentration distributions were used to describe the behavior of cell populations. Monte-Carlo simulations of cell populations showed that c-FLIP turnover is a key determinant of death receptor responses. The fact that the developed model simulates the state of whole cell populations makes it possible to validate it by comparison with empirical data. The proposed modeling approach can be used to further determine limiting factors in the DISC signaling process.
Collapse
Affiliation(s)
| | | | - Tomoko Asaoka
- Biosciences and
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku, FI-20520 Turku, Finland
| | | | - Frank Pettersson
- Chemical Engineering, Åbo Akademi University, FI-20500 Turku, Finland and
| | | | - John E. Eriksson
- Biosciences and
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku, FI-20520 Turku, Finland
| | - Henrik Saxén
- Chemical Engineering, Åbo Akademi University, FI-20500 Turku, Finland and
| |
Collapse
|
28
|
Sung B, Park B, Yadav VR, Aggarwal BB. Celastrol, a triterpene, enhances TRAIL-induced apoptosis through the down-regulation of cell survival proteins and up-regulation of death receptors. J Biol Chem 2010; 285:11498-507. [PMID: 20154087 PMCID: PMC2857028 DOI: 10.1074/jbc.m109.090209] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Whether celastrol, a triterpene from traditional Chinese medicine, can modulate the anticancer effects of TRAIL, the cytokine that is currently in clinical trial, was investigated. As indicated by assays that measure plasma membrane integrity, phosphatidylserine exposure, mitochondrial activity, and activation of caspase-8, caspase-9, and caspase-3, celastrol potentiated the TRAIL-induced apoptosis in human breast cancer cells, and converted TRAIL-resistant cells to TRAIL-sensitive cells. When examined for its mechanism, we found that the triterpene down-regulated the expression of cell survival proteins including cFLIP, IAP-1, Bcl-2, Bcl-xL, survivin, and XIAP and up-regulated Bax expression. In addition, we found that celastrol induced the cell surface expression of both the TRAIL receptors DR4 and DR5. This increase in receptors was noted in a wide variety of cancer cells including breast, lung, colorectal, prostate, esophageal, and pancreatic cancer cells, and myeloid and leukemia cells. Gene silencing of the death receptor abolished the effect of celastrol on TRAIL-induced apoptosis. Induction of the death receptor by the triterpenoid was found to be p53-independent but required the induction of CAAT/enhancer-binding protein homologous protein (CHOP), inasmuch as gene silencing of CHOP abolished the induction of DR5 expression by celastrol and associated enhancement of TRAIL-induced apoptosis. We found that celastrol also induced reactive oxygen species (ROS) generation, and ROS sequestration inhibited celastrol-induced expression of CHOP and DR5, and consequent sensitization to TRAIL. Overall, our results demonstrate that celastrol can potentiate the apoptotic effects of TRAIL through down-regulation of cell survival proteins and up-regulation of death receptors via the ROS-mediated up-regulation of CHOP pathway.
Collapse
Affiliation(s)
- Bokyung Sung
- From the Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Byoungduck Park
- From the Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Vivek R. Yadav
- From the Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030
| | - Bharat B. Aggarwal
- From the Cytokine Research Laboratory, Department of Experimental Therapeutics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, The Ransom Horne, Jr., Professor of Cancer Research. To whom correspondence should be addressed: 1515 Holcombe Blvd., Box 143, Houston, TX 77030. Tel.: 713-794-1817; Fax: 713-745-6339; E-mail:
| |
Collapse
|
29
|
Park HH, Wu H. Crystallization and preliminary X-ray crystallographic studies of the oligomeric death-domain complex between PIDD and RAIDD. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:229-32. [PMID: 17329820 PMCID: PMC2330181 DOI: 10.1107/s1744309107007889] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 02/16/2007] [Indexed: 05/14/2023]
Abstract
Three large macromolecular complexes known as the death-inducing signaling complex (DISC), the apoptosome and the PIDDosome mediate caspase activation in apoptosis signaling pathways. The PIDDosome, which activates caspase-2, is composed of three protein components: PIDD, RAIDD and caspase-2. Within the PIDDosome, the interaction between PIDD and RAIDD is mediated by a homotypic interaction between their death domains (DDs). PIDD DD and RAIDD DD were overexpressed in Escherichia coli with engineered C-terminal His tags. The proteins were purified and mixed to allow complex formation. Gel-filtration and multi-angle light scattering (MALS) analyses showed that the complex is around 150 kDa in solution. The purified PIDD DD-RAIDD DD complex was crystallized at 293 K. X-ray diffraction data were collected to resolutions of 3.2 and 4.0 A from a native and a Hg-derivative crystal, respectively. The crystals belong to space group P6(5), with unit-cell parameters a = b = 138.4, c = 207.6 A.
Collapse
Affiliation(s)
- Hyun Ho Park
- Department of Biochemistry, Weill Medical College and Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Hao Wu
- Department of Biochemistry, Weill Medical College and Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
- Correspondence e-mail:
| |
Collapse
|
30
|
Lasker MV, Kuruvilla SM, Gajjar MM, Kapoor A, Nair SK. Metal ion-mediated reduction in surface entropy improves diffraction quality of crystals of the IRAK-4 death domain. J Biomol Tech 2006; 17:114-21. [PMID: 16741238 PMCID: PMC2291770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Interleukin-1 receptor-associated kinase-4 (IRAK-4) is an essential component of innate immunity in mice and humans. IRAK-4 is a bipartite protein composed of a death domain (DD) that mediates molecular recognition, and a catalytic kinase domain. Structure determination of the proteolytically stable, soluble IRAK-4 DD was hampered by poor diffraction quality. Addition of manganese (II) chloride to the crystallization solution produced significant improvements in diffraction, and the structure has been determined to 1.7-Angstrom resolution. Examination of the IRAK-4 DD crystal structure reveals a single manganese ion coordinated to surface residues lysine-21 and aspartate-24. Coordination of the manganese ion resulted in a reduction in the surface entropy at this region of the molecule, by generating a contact-forming and conformationally homogenous surface patch. Prior studies have shown that surface entropy reduction by mutation of surface residues with large flexible side chains (i.e., Lys and Glu) to smaller side chains results in the production of diffraction-quality crystals. The intrinsic high surface entropy of Lys residues can also be decreased by reductive methylation. Our results suggest that screening of manganese ions as a crystallization additive may also facilitate ordered crystallization by reduction of surface entropy. Given the quick and inexpensive nature of screening, this technique is likely to be amenable to high-throughput methods such as those employed by Protein Structure Initiatives.
Collapse
Affiliation(s)
- Michael V Lasker
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.
| | | | | | | | | |
Collapse
|
31
|
Abstract
PYRIN domains were identified recently as putative protein-protein interaction domains at the N-termini of several proteins thought to function in apoptotic and inflammatory signaling pathways. The approximately 95 residue PYRIN domains have no statistically significant sequence homology to proteins with known three-dimensional structure. Using secondary structure prediction and potential-based fold recognition methods, however, the PYRIN domain is predicted to be a member of the six-helix bundle death domain-fold superfamily that includes death domains (DDs), death effector domains (DEDs), and caspase recruitment domains (CARDs). Members of the death domain-fold superfamily are well established mediators of protein-protein interactions found in many proteins involved in apoptosis and inflammation, indicating further that the PYRIN domains serve a similar function. An homology model of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1, a member of the Apaf-1/Ced-4 family of proteins, was constructed using the three-dimensional structures of the FADD and p75 neurotrophin receptor DDs, and of the Apaf-1 and caspase-9 CARDs, as templates. Validation of the model using a variety of computational techniques indicates that the fold prediction is consistent with the sequence. Comparison of a circular dichroism spectrum of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1 with spectra of several proteins known to adopt the death domain-fold provides experimental support for the structure prediction.
Collapse
Affiliation(s)
- W J Fairbrother
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.
| | | | | | | | | | | | | |
Collapse
|
32
|
Khursigara G, Bertin J, Yano H, Moffett H, DiStefano PS, Chao MV. A prosurvival function for the p75 receptor death domain mediated via the caspase recruitment domain receptor-interacting protein 2. J Neurosci 2001; 21:5854-63. [PMID: 11487608 PMCID: PMC6763175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2000] [Revised: 05/08/2001] [Accepted: 05/18/2001] [Indexed: 02/21/2023] Open
Abstract
In addition to promoting cell survival, neurotrophins also can elicit apoptosis in restricted cell types. Recent results indicate that nerve growth factor (NGF) can induce Schwann cell death via engagement of the p75 neurotrophin receptor. Here we describe a novel interaction between the p75 receptor and receptor-interacting protein 2, RIP2 (RICK/CARDIAK), that accounts for the ability of neurotrophins to choose between a survival-versus-death pathway. RIP2, an adaptor protein with a serine threonine kinase and a caspase recruitment domain (CARD), is highly expressed in dissociated Schwann cells and displays an endogenous association with p75. RIP2 binds to the death domain of p75 via its CARD domain in an NGF-dependent manner. The introduction of RIP2 into Schwann cells deficient in RIP2 conferred NGF-dependent nuclear transcription factor-kappaB (NF-kappaB) activity and decreased the cell death induced by NGF. Conversely, the expression of a dominant-negative version of RIP2 protein resulted in a loss of NGF-induced NF-kappaB induction and increased NGF-mediated cell death. These results indicate that adaptor proteins like RIP2 can provide a bifunctional switch for cell survival or cell death decisions mediated by the p75 neurotrophin receptor.
Collapse
Affiliation(s)
- G Khursigara
- Weill Medical College of Cornell University, New York, New York 10021, USA
| | | | | | | | | | | |
Collapse
|
33
|
Cohen O, Inbal B, Kissil JL, Raveh T, Berissi H, Spivak-Kroizaman T, Feinstein E, Kimchi A. DAP-kinase participates in TNF-alpha- and Fas-induced apoptosis and its function requires the death domain. J Cell Biol 1999; 146:141-8. [PMID: 10402466 PMCID: PMC2199731 DOI: 10.1083/jcb.146.1.141] [Citation(s) in RCA: 109] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Death-associated protein (DAP)-kinase is a calcium/calmodulin regulated serine/threonine kinase that carries ankyrin repeats, a death domain, and is localized to the cytoskeleton. Here, we report that this kinase is involved in tumor necrosis factor (TNF)-alpha and Fas-induced apoptosis. Expression of DAP-kinase antisense RNA protected cells from killing by anti-Fas/APO-1 agonistic antibodies. Deletion of the death domain abrogated the apoptotic functions of the kinase, thus, documenting for the first time the importance of this protein domain. Overexpression of a fragment encompassing the death domain of DAP-kinase acted as a specific dominant negative mutant that protected cells from TNF-alpha, Fas, and FADD/MORT1-induced cell death. DAP-kinase apoptotic function was blocked by bcl-2 as well as by crmA and p35 inhibitors of caspases, but not by the dominant negative mutants of FADD/MORT1 or of caspase 8. Thus, it functions downstream to the receptor complex and upstream to other caspases. The multidomain structure of this serine/threonine kinase, combined with its involvement in cell death induced by several different triggers, place DAP-kinase at one of the central molecular pathways leading to apoptosis.
Collapse
Affiliation(s)
- Ofer Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Boaz Inbal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joseph L. Kissil
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tal Raveh
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hanna Berissi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Taly Spivak-Kroizaman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elena Feinstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adi Kimchi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
34
|
Maeda T, Yamada Y, Moriuchi R, Sugahara K, Tsuruda K, Joh T, Atogami S, Tsukasaki K, Tomonaga M, Kamihira S. Fas gene mutation in the progression of adult T cell leukemia. J Exp Med 1999; 189:1063-71. [PMID: 10190897 PMCID: PMC2193006 DOI: 10.1084/jem.189.7.1063] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Fas antigen (Apo-1/CD95) is an apoptosis-signaling cell surface receptor belonging to the tumor necrosis factor receptor superfamily. Adult T cell leukemia (ATL) cells express Fas antigen and show apoptosis after treatment with an anti-Fas monoclonal antibody. We established the ATL cell line KOB, which showed resistance to Fas-mediated apoptosis, and found that KOB expressed two forms of Fas mRNA, the normal form and a truncated form. The truncated transcript lacked 20 base pairs at exon 9, resulting in a frame shift and the generation of a premature stop codon at amino acid 239. The same mutation was detected in primary ascitic cells and peripheral blood cells. The mutation was not detected in lymph node cells, however, although all of the primary ATL cells were of the same clonal origin. A retroviral-mediated gene transfer of the truncated Fas to Jurkat cells rendered the cells resistant to Fas-mediated apoptosis, suggesting a dominant negative interference mechanism. These results indicate that an ATL subclone acquires a Fas mutation in the lymph nodes, enabling the subclone to escape from apoptosis mediated by the Fas/Fas ligand system and proliferate in the body. Mutation of the Fas gene may be one of the mechanisms underlying the progression of ATL.
Collapse
Affiliation(s)
- T Maeda
- Department of Hematology and Molecular Medicine Unit, Atomic Bomb Disease Institute, Aichi 464-0221, Japan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Abstract
Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known. Comparison with established databases showed that 25% of our domain set could not be deduced from SwissProt and 41% could not be annotated by Pfam. SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homologous domains in focal adhesion kinases; (ii) previously unknown domain families, including a citron-homology domain; (iii) putative functions of domain families after identification of additional family members, for example, a ubiquitin-binding role for ubiquitin-associated domains (UBA); (iv) cellular roles for proteins, such predicted DEATH domains in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY domains in both marenostrin/pyrin and Midline 1; (vi) domains in unexpected phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exemplified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.
Collapse
Affiliation(s)
- J Schultz
- European Molecular Biology Laboratory, Meyerhofstr.1, 69012 Heidelberg, Germany
| | | | | | | |
Collapse
|