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Nakamura T, Ohyama C, Sakamoto M, Toma T, Tateishi H, Matsuo M, Chirifu M, Ikemizu S, Morioka H, Fujita M, Inoue JI, Yamagata Y. TIFAB regulates the TIFA-TRAF6 signaling pathway involved in innate immunity by forming a heterodimer complex with TIFA. Proc Natl Acad Sci U S A 2024; 121:e2318794121. [PMID: 38442163 PMCID: PMC10945758 DOI: 10.1073/pnas.2318794121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Nuclear factor κB (NF-κB) is activated by various inflammatory and infectious molecules and is involved in immune responses. It has been elucidated that ADP-β-D-manno-heptose (ADP-Hep), a metabolite in gram-negative bacteria, activates NF-κB through alpha-kinase 1 (ALPK1)-TIFA-TRAF6 signaling. ADP-Hep stimulates the kinase activity of ALPK1 for TIFA phosphorylation. Complex formation between phosphorylation-dependent TIFA oligomer and TRAF6 promotes the polyubiquitination of TRAF6 for NF-κB activation. TIFAB, a TIFA homolog lacking a phosphorylation site and a TRAF6 binding motif, is a negative regulator of TIFA-TRAF6 signaling and is implicated in myeloid diseases. TIFAB is indicated to regulate TIFA-TRAF6 signaling through interactions with TIFA and TRAF6; however, little is known about its biological function. We demonstrated that TIFAB forms a complex not with the TIFA dimer, an intrinsic form of TIFA involved in NF-κB activation, but with monomeric TIFA. The structural analysis of the TIFA/TIFAB complex and the biochemical and cell-based analyses showed that TIFAB forms a stable heterodimer with TIFA, inhibits TIFA dimer formation, and suppresses TIFA-TRAF6 signaling. The resultant TIFA/TIFAB complex is a "pseudo-TIFA dimer" lacking the phosphorylation site and TRAF6 binding motif in TIFAB and cannot form the orderly structure as proposed for the phosphorylated TIFA oligomer involved in NF-κB activation. This study elucidated the molecular and structural basis for the regulation of TIFA-TRAF6 signaling by TIFAB.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Chiaki Ohyama
- School of Pharmacy, Kumamoto University, Kumamoto862-0973, Japan
| | - Madoka Sakamoto
- School of Pharmacy, Kumamoto University, Kumamoto862-0973, Japan
| | - Tsugumasa Toma
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Hiroshi Tateishi
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mihoko Matsuo
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Hiroshi Morioka
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Mikako Fujita
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
| | - Jun-ichiro Inoue
- The University of Tokyo Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), 4-6-1 Shirokanedai, Minato-ku, Tokyo108-0071, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto862-0973, Japan
- Shokei University and Shokei University Junior College, Kumamoto862-8678, Japan
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Li L, Wang J, Zhong X, Jiang Y, Pei G, Yang X, Zhang K, Shen S, Jin X, Sun G, Su C, Chen S, Yin H. ADP-Hep-Induced Liquid Phase Condensation of TIFA-TRAF6 Activates ALPK1/TIFA-Dependent Innate Immune Responses. RESEARCH (WASHINGTON, D.C.) 2024; 7:0315. [PMID: 38357697 PMCID: PMC10865109 DOI: 10.34133/research.0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
The ALPK1 (alpha-kinase 1)-TIFA (TRAF-interacting protein with fork head-associated domain)-TRAF6 signaling pathway plays a pivotal role in regulating inflammatory processes, with TIFA and TRAF6 serving as key molecules in this cascade. Despite its significance, the functional mechanism of TIFA-TRAF6 remains incompletely understood. In this study, we unveil that TIFA undergoes liquid-liquid phase separation (LLPS) induced by ALPK1 in response to adenosine diphosphate (ADP)-β-D-manno-heptose (ADP-Hep) recognition. The phase separation of TIFA is primarily driven by ALPK1, the pT9-FHA domain, and the intrinsically disordered region segment. Simultaneously, TRAF6 exhibits phase separation during ADP-Hep-induced inflammation, a phenomenon observed consistently across various inflammatory signal pathways. Moreover, TRAF6 is recruited within the TIFA condensates, facilitating lysine (K) 63-linked polyubiquitin chain synthesis. The subsequent recruitment, enrichment, and activation of downstream effectors within these condensates contribute to robust inflammatory signal transduction. Utilizing a novel chemical probe (compound 22), our analysis demonstrates that the activation of the ALPK1-TIFA-TRAF6 signaling pathway in response to small molecules necessitates the phase separation of TIFA. In summary, our findings reveal TIFA as a sensor for upstream signals, initiating the LLPS of itself and downstream proteins. This process results in the formation of membraneless condensates within the ALPK1-TIFA-TRAF6 pathway, suggesting potential applications in therapeutic biotechnology development.
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Affiliation(s)
- Liping Li
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- Department of Cancer Research, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, College of Future Technology,
Peking University, Beijing, China
| | - Xincheng Zhong
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yaoyao Jiang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
- School of Life Sciences,
Tsinghua University, Beijing, 100084, China
| | - Xikang Yang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Kaixiang Zhang
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Siqi Shen
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Xue Jin
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Gaoge Sun
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Chaofei Su
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Shuzhen Chen
- Department of Cancer Research, Institute of Medicinal Biotechnology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hang Yin
- State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Institute for Precision Medicine, Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorous chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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Liu S, Zhuang Z, Liu F, Yuan X, Zhang Z, Liang X, Li X, Chen Y. Identification of potential biomarkers and infiltrating immune cells from scalp psoriasis. Gene 2024; 893:147918. [PMID: 37871808 DOI: 10.1016/j.gene.2023.147918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/16/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Scalp psoriasis seriously affects the appearance and psychological status of patients. The aim of this study was to investigate the effect and potential mechanism of RPL9 and TIFA in scalp psoriasis, so as to provide a precise and effective way for the clinical treatment of scalp psoriasis. METHODS The Gene Expression Omnibus (GEO) database was employed to download the GSE75343 dataset to search for differentially expressed genes (DEGs) in scalp psoriasis through Sangerbox. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) enrichment analysis, functional enrichment analysis, immune cell infiltration analysis, immune responses and correlation analysis with 12 hub genes were performed. Then, STRING was used to develop a protein-protein interaction (PPI) network, used Cytoscape to locate hub genes, and SVM-RFE and random forest were utilized to identified RPL9 as the targeted gene. TIFA-RPL9 interaction predictions were made viathe Open Targets Platform and Uniprot. Further, the RPL9 and TIFA expression, molecular mechanism, and function were assessed in scalp psoriasis. RESULTS Immunohistochemistry, qPCR, and western blotting verified that RPL9 and TIFA were highly expressed in lesional tissues of scalp psoriasis and IL17A-stimulated HaCaT cells. RPL9 knockdown effectively suppressed the proliferative capacity of IL17A-stimulated HaCaT cells in the CCK8 assay. The co-immunoprecipitation results revealed that RPL9 could interact with TIFA in IL17A-stimulated HaCaT cells. In qPCR and western blotting, RPL9 knockdown significantly inhibited TIFA at the mRNA and protein levels in IL17A-stimulated HaCaT cells. In ELISA, the secretion of TNF-α was markedly inhibited after downregulating RPL9 in IL17A-stimulated HaCaT cells. CONCLUSION To our knowledge, we have elucidated the expression and role of RPL9 and TIFA in scalp psoriatic skin and keratinocytes, and our findings confirm that RPL9 might act as a candidate therapeutic target for scalp psoriasis.
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Affiliation(s)
- Shougang Liu
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Zhe Zhuang
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, China; Department of Dermatology, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Fanghua Liu
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, China; Department of Dermatology, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Xiuqing Yuan
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Zeqiao Zhang
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoqian Liang
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Xinhui Li
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Yongfeng Chen
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Guangzhou, Guangdong, China.
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Sokolova O, Maubach G, Naumann M. Helicobacter pylori regulates TIFA turnover in gastric epithelial cells. Eur J Cell Biol 2023; 102:151307. [PMID: 36965415 DOI: 10.1016/j.ejcb.2023.151307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/01/2023] [Accepted: 03/11/2023] [Indexed: 03/19/2023] Open
Abstract
The human pathogen Helicobacter pylori induces a strong inflammatory response in gastric mucosa manifested by the recruitment of neutrophils and macrophages to the places of infection, and by changes in epithelial integrity and function. At the molecular level, this innate immune response is essentially dependent on the activation of NF-κB transcription factors regulating the expression of chemotactic factors, e.g., IL-8. Recently, it has been demonstrated that the NF-κB signaling pathway is triggered by the bacterial heptose metabolites, which activate the host ALPK1-TIFA axis. TIFA has been suggested to promote oligomerization and activity of the E3 ubiquitin ligase TRAF6, which further stimulates TAK1-IKK signaling. Here, we demonstrate that ALPK1-dependent TIFA activation in H. pylori-infected gastric epithelial cells is followed in time by a decline in TIFA levels, and that this process is impeded by inhibitors of the proteasomal and lysosomal degradation. According to our data, TRAF2, TRAF6, TAK1 or NEMO are not required for TIFA degradation. Additionally, H. pylori promotes the interaction of TIFA with free polyubiquitin as well as with optineurin, TAX1BP1 and LAMP1, which are known protein adaptors involved in intracellular trafficking to lysosomes.
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Affiliation(s)
- Olga Sokolova
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany.
| | - Gunter Maubach
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Michael Naumann
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
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5
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Mohamed Farhan H, Nassar M, Hassan Ahmed M, Abougabal K, Abd Elazim Taha N. An association between the sarcolemmal membrane-associated protein gene and microvascular endothelial diabetic retinopathy in patients with type 2 diabetes mellitus: A preliminary case control study. Diabetes Metab Syndr 2022; 16:102653. [PMID: 36308782 DOI: 10.1016/j.dsx.2022.102653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND AND AIMS Diabetic retinopathy (DR) is one of the most common microvascular diabetic complications. Sarcolemmal membrane-associated protein (SLMAP) has been implicated in playing a role in microvascular endothelial dysfunction. This study aimed to assess the significance of SLMAP rs17058639C > T gene polymorphism among patients with type 2 diabetes mellitus (T2DM) and its relevance to microvascular endothelial diabetic retinopathy. METHODS We conducted this case-control study on 100 individuals divided into 60 participants with T2DM and 40 healthy controls. Patients with T2D were stratified into two groups: 40 patients with DR and 20 patients with diabetic non-retinopathy (DNR). Patients with T2DM were compared with age- and sex-matched healthy controls. Fundus examinations were conducted to detect microvascular endothelial changes. The polymorphism of SLMAP rs17058639C > T gene was identified by real-time polymerase chain reaction (RT-PCR) TaqMan allelic discrimination. RESULTS Patients with DR have significantly increased glycated hemoglobin (HbA1c) compared to patients with DNR (P < 0.001). There was no statistically significant difference found between diabetic and control groups regarding the frequency of SLMAP rs17058639C > T genotypes. The homozygous CC genotype was the most common variant among patients with DR; however, the results did not reach statistical significance. CONCLUSIONS Diabetic retinopathy is correlated with poor glycemic control, and SLMAP rs17058639C > T polymorphism was associated with microvascular endothelial DR in patients with T2DM, although further studies with a large sample size are needed to confirm our findings.
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Affiliation(s)
- Hanan Mohamed Farhan
- Clinical & Chemical Pathology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt.
| | - Mahmoud Nassar
- Medicine Department, Icahn School of Medicine at Mount Sinai / NYC Health + Hospital / Queens, New York, USA.
| | - Mansour Hassan Ahmed
- Ophthalmology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt.
| | - Khadiga Abougabal
- Clinical & Chemical Pathology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt.
| | - Niveen Abd Elazim Taha
- Clinical & Chemical Pathology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt.
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Shen W, Du W, Li Y, Huang Y, Jiang X, Yang C, Tang J, Liu H, Luo N, Zhang X, Zhang Z. TIFA promotes CRC cell proliferation via RSK- and PRAS40- dependent manner. Cancer Sci 2022; 113:3018-3031. [PMID: 35635239 PMCID: PMC9459298 DOI: 10.1111/cas.15432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/02/2022] [Accepted: 05/15/2022] [Indexed: 11/26/2022] Open
Abstract
Previous studies have reported that TIFA plays different roles in various tumor types. However, the function of TIFA in colorectal cancer (CRC) remains unclear. Here, we showed that the expression of TIFA was markedly increased in CRC versus normal tissue, and positively correlated with CRC TNM stages. In agreement, we found that the CRC cell lines show increased TIFA expression levels versus normal control. The knockdown of TIFA inhibited cell proliferation but had no effect on cell apoptosis in vitro or in vivo. Moreover, the ectopic expression of TIFA enhanced cell proliferation ability in vitro and in vivo. In contrast, the expression of mutant TIFA (T9A, oligomerization site mutation; D6, TRAF6 binding site deletion) abolished TIFA‐mediated cell proliferation enhancement. Exploration of the underlying mechanism revealed that the protein synthesis‐associated kinase RSK and PRAS40 activation were responsible for TIFA‐mediated CRC progression. In summary, these findings suggest that TIFA plays a role in mediating CRC progression. This could provide a promising target for CRC therapy.
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Affiliation(s)
- Wenzhi Shen
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining 272067, Shandong, China
| | - Wenfei Du
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining 272067, Shandong, China
| | - Yanping Li
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining 272067, Shandong, China
| | - Yongming Huang
- Department of General Surgery, Affiliated Hospital of, Jining Medical University, Jining Medical University, Jining, 272067, China
| | - Xinyu Jiang
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining 272067, Shandong, China
| | - Chenglong Yang
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining 272067, Shandong, China
| | - Jiaping Tang
- Department of Anatomy and Histology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Huan Liu
- Surgery Teaching and Research Section, Clinical Medical School, Jining Medical University, Jining, 272067, China
| | - Na Luo
- Department of Anatomy and Histology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Xiaoyuan Zhang
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining 272067, Shandong, China
| | - Zhixin Zhang
- Key Laboratory of Precision Oncology in Universities of Shandong, Institute of Precision Medicine, Jining Medical University, Jining 272067, Shandong, China.,Department of Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining 272029, China
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Kliche J, Ivarsson Y. Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. Biochem J 2022; 479:1-22. [PMID: 34989786 PMCID: PMC8786283 DOI: 10.1042/bcj20200714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is based on protein-protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the interactions. In addition, motif-based interactions are involved in targeting serine/threonine kinases and phosphatases to their substrate and contribute to the specificity of the enzymatic actions regulating which sites are phosphorylated. Here, we review how SLiM-based interactions assist in determining the specificity of serine/threonine kinases and phosphatases, and how phosphorylation, in turn, affects motif-based interactions. We provide examples of SLiM-based interactions that are turned on/off, or are tuned by serine/threonine phosphorylation and exemplify how this affects SLiM-based protein complex formation.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, Box 576 751 23 Uppsala, Sweden
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García-Weber D, Arrieumerlou C. ADP-heptose: a bacterial PAMP detected by the host sensor ALPK1. Cell Mol Life Sci 2021; 78:17-29. [PMID: 32591860 PMCID: PMC11072087 DOI: 10.1007/s00018-020-03577-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 01/16/2023]
Abstract
The innate immune response constitutes the first line of defense against pathogens. It involves the recognition of pathogen-associated molecular patterns (PAMPs) by pathogen recognition receptors (PRRs), the production of inflammatory cytokines and the recruitment of immune cells to infection sites. Recently, ADP-heptose, a soluble intermediate of the lipopolysaccharide biosynthetic pathway in Gram-negative bacteria, has been identified by several research groups as a PAMP. Here, we recapitulate the evidence that led to this identification and discuss the controversy over the immunogenic properties of heptose 1,7-bisphosphate (HBP), another bacterial heptose previously defined as an activator of innate immunity. Then, we describe the mechanism of ADP-heptose sensing by alpha-protein kinase 1 (ALPK1) and its downstream signaling pathway that involves the proteins TIFA and TRAF6 and induces the activation of NF-κB and the secretion of inflammatory cytokines. Finally, we discuss possible delivery mechanisms of ADP-heptose in cells during infection, and propose new lines of thinking to further explore the roles of the ADP-heptose/ALPK1/TIFA axis in infections and its potential implication in the control of intestinal homeostasis.
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Affiliation(s)
- Diego García-Weber
- INSERM, U1016, Institut Cochin, CNRS, UMR8104, Université de Paris, 22 rue Méchain, 75014, Paris, France
| | - Cécile Arrieumerlou
- INSERM, U1016, Institut Cochin, CNRS, UMR8104, Université de Paris, 22 rue Méchain, 75014, Paris, France.
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Niederkorn M, Agarwal P, Starczynowski DT. TIFA and TIFAB: FHA-domain proteins involved in inflammation, hematopoiesis, and disease. Exp Hematol 2020; 90:18-29. [PMID: 32910997 DOI: 10.1016/j.exphem.2020.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/19/2022]
Abstract
Forkhead-associated (FHA) domain-containing proteins are widely expressed across eubacteria and in eukaryotes. FHA domains contain phosphopeptide recognition motifs, which operate in a variety of phosphorylation-dependent and -independent biological processes, including the DNA damage response, signal transduction, and regulation of the cell cycle. More recently, two FHA domain-containing proteins were discovered in mammalian cells as tumor necrosis factor receptor-associated factor (TRAF)-interacting proteins: TIFA and TIFAB. TIFA and TIFAB are important modifiers of the innate immune signaling through their regulation of TRAF proteins. Recent studies have also revealed distinct roles for TIFA and TIFAB in the context of immune cell function, chronic inflammation, hematopoiesis, and hematologic disorders. Collectively, these studies indicate the important role of TIFA- and TIFAB-dependent signaling in hematopoietic cells and their dysregulation in several human diseases. In this review, we summarize the molecular mechanisms and biological role of these FHA-domain homologues, placing them into the context of human disease.
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Affiliation(s)
- Madeline Niederkorn
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Cancer Biology, University of Cincinnati, Cincinnati, OH
| | - Puneet Agarwal
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Cancer Biology, University of Cincinnati, Cincinnati, OH; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.
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Nakamura T, Hashikawa C, Okabe K, Yokote Y, Chirifu M, Toma-Fukai S, Nakamura N, Matsuo M, Kamikariya M, Okamoto Y, Gohda J, Akiyama T, Semba K, Ikemizu S, Otsuka M, Inoue JI, Yamagata Y. Structural analysis of TIFA: Insight into TIFA-dependent signal transduction in innate immunity. Sci Rep 2020; 10:5152. [PMID: 32198460 PMCID: PMC7083832 DOI: 10.1038/s41598-020-61972-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/03/2020] [Indexed: 11/28/2022] Open
Abstract
TRAF-interacting protein with a forkhead-associated (FHA) domain (TIFA), originally identified as an adaptor protein of TRAF6, has recently been shown to be involved in innate immunity, induced by a pathogen-associated molecular pattern (PAMP). ADP-β-D-manno-heptose, a newly identified PAMP, binds to alpha-kinase 1 (ALPK1) and activates its kinase activity to phosphorylate TIFA. Phosphorylation triggers TIFA oligomerisation and formation of a subsequent TIFA-TRAF6 oligomeric complex for ubiquitination of TRAF6, eventually leading to NF-κB activation. However, the structural basis of TIFA-dependent TRAF6 signalling, especially oligomer formation of the TIFA-TRAF6 complex remains unknown. In the present study, we determined the crystal structures of mouse TIFA and two TIFA mutants-Thr9 mutated to either Asp or Glu to mimic the phosphorylation state-to obtain the structural information for oligomer formation of the TIFA-TRAF6 complex. Crystal structures show the dimer formation of mouse TIFA to be similar to that of human TIFA, which was previously reported. This dimeric structure is consistent with the solution structure obtained from small angle X-ray scattering analysis. In addition to the structural analysis, we examined the molecular assembly of TIFA and the TIFA-TRAF6 complex by size-exclusion chromatography, and suggested a model for the TIFA-TRAF6 signalling complex.
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Affiliation(s)
- Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan.
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan.
| | - Chie Hashikawa
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kohtaro Okabe
- School of Pharmacy, Kumamoto University, Kumamoto, Japan
| | - Yuya Yokote
- School of Pharmacy, Kumamoto University, Kumamoto, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Sachiko Toma-Fukai
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | | | - Mihoko Matsuo
- Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan
| | | | - Yoshinari Okamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kentaro Semba
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Shinji Ikemizu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Masami Otsuka
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun-Ichiro Inoue
- Research Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Cellular and Molecular Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuriko Yamagata
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
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EspM Is a Conserved Transcription Factor That Regulates Gene Expression in Response to the ESX-1 System. mBio 2020; 11:mBio.02807-19. [PMID: 32019792 PMCID: PMC7002343 DOI: 10.1128/mbio.02807-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Pathogenic mycobacteria encounter multiple environments during macrophage infection. Temporally, the bacteria are engulfed into the phagosome, lyse the phagosomal membrane, and interact with the cytosol before spreading to another cell. Virulence factors secreted by the mycobacterial ESX-1 (ESAT-6-system-1) secretion system mediate the essential transition from the phagosome to the cytosol. It was recently discovered that the ESX-1 system also regulates mycobacterial gene expression in Mycobacterium marinum (R. E. Bosserman, T. T. Nguyen, K. G. Sanchez, A. E. Chirakos, et al., Proc Natl Acad Sci U S A 114:E10772-E10781, 2017, https://doi.org/10.1073/pnas.1710167114), a nontuberculous mycobacterial pathogen, and in the human-pathogenic species M. tuberculosis (A. M. Abdallah, E. M. Weerdenburg, Q. Guan, R. Ummels, et al., PLoS One 14:e0211003, 2019, https://doi.org/10.1371/journal.pone.0211003). It is not known how the ESX-1 system regulates gene expression. Here, we identify the first transcription factor required for the ESX-1-dependent transcriptional response in pathogenic mycobacteria. We demonstrate that the gene divergently transcribed from the whiB6 gene and adjacent to the ESX-1 locus in mycobacterial pathogens encodes a conserved transcription factor (MMAR_5438, Rv3863, now espM). We prove that EspM from both M. marinum and M. tuberculosis directly and specifically binds the whiB6-espM intergenic region. We show that EspM is required for ESX-1-dependent repression of whiB6 expression and for the regulation of ESX-1-associated gene expression. Finally, we demonstrate that EspM functions to fine-tune ESX-1 activity in M. marinum Taking the data together, this report extends the esx-1 locus, defines a conserved regulator of the ESX-1 virulence pathway, and begins to elucidate how the ESX-1 system regulates gene expression.IMPORTANCE Mycobacterial pathogens use the ESX-1 system to transport protein substrates that mediate essential interactions with the host during infection. We previously demonstrated that in addition to transporting proteins, the ESX-1 secretion system regulates gene expression. Here, we identify a conserved transcription factor that regulates gene expression in response to the ESX-1 system. We demonstrate that this transcription factor is functionally conserved in M. marinum, a pathogen of ectothermic animals; M. tuberculosis, the human-pathogenic species that causes tuberculosis; and M. smegmatis, a nonpathogenic mycobacterial species. These findings provide the first mechanistic insight into how the ESX-1 system elicits a transcriptional response, a function of this protein transport system that was previously unknown.
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Meek RW, Cadby IT, Moynihan PJ, Lovering AL. Structural basis for activation of a diguanylate cyclase required for bacterial predation in Bdellovibrio. Nat Commun 2019; 10:4086. [PMID: 31501441 PMCID: PMC6733907 DOI: 10.1038/s41467-019-12051-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 08/13/2019] [Indexed: 11/28/2022] Open
Abstract
The bacterial second messenger cyclic-di-GMP is a widespread, prominent effector of lifestyle change. An example of this occurs in the predatory bacterium Bdellovibrio bacteriovorus, which cycles between free-living and intraperiplasmic phases after entering (and killing) another bacterium. The initiation of prey invasion is governed by DgcB (GGDEF enzyme) that produces cyclic-di-GMP in response to an unknown stimulus. Here, we report the structure of DgcB, and demonstrate that the GGDEF and sensory forkhead-associated (FHA) domains form an asymmetric dimer. Our structures indicate that the FHA domain is a consensus phosphopeptide sensor, and that the ligand for activation is surprisingly derived from the N-terminal region of DgcB itself. We confirm this hypothesis by determining the structure of a FHA:phosphopeptide complex, from which we design a constitutively-active mutant (confirmed via enzyme assays). Our results provide an understanding of the stimulus driving DgcB-mediated prey invasion and detail a unique mechanism of GGDEF enzyme regulation. The initiation of prey invasion by the predatory bacterium Bdellovibrio bacteriovorus is governed by the activity of the diguanlylate cyclase DgcB. Here the authors show that the stimulus regulating DgcB activity is a phosphopeptide derived from DgcB itself and present the crystal structures of full-length DgcB and of its empty and peptide-bound sensor domain.
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Affiliation(s)
- Richard W Meek
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ian T Cadby
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Patrick J Moynihan
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Andrew L Lovering
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
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13
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The potential probiotic Lactobacillus rhamnosus CNCM I-3690 strain protects the intestinal barrier by stimulating both mucus production and cytoprotective response. Sci Rep 2019; 9:5398. [PMID: 30931953 PMCID: PMC6443702 DOI: 10.1038/s41598-019-41738-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/11/2019] [Indexed: 12/14/2022] Open
Abstract
The gut barrier plays an important role in human health. When barrier function is impaired, altered permeability and barrier dysfunction can occur, leading to inflammatory bowel diseases, irritable bowel syndrome or obesity. Several bacteria, including pathogens and commensals, have been found to directly or indirectly modulate intestinal barrier function. The use of probiotic strains could be an important landmark in the management of gut dysfunction with a clear impact on the general population. Previously, we found that Lactobacillus rhamnosus CNCM I-3690 can protect intestinal barrier functions in mice inflammation model. Here, we investigated its mechanism of action. Our results show that CNCM I-3690 can (i) physically maintain modulated goblet cells and the mucus layer and (ii) counteract changes in local and systemic lymphocytes. Furthermore, mice colonic transcriptome analysis revealed that CNCM I-3690 enhances the expression of genes related to healthy gut permeability: motility and absorption, cell proliferation; and protective functions by inhibiting endogenous proteases. Finally, SpaFED pili are clearly important effectors since an L. rhamnosus ΔspaF mutant failed to provide the same benefits as the wild type strain. Taken together, our data suggest that CNCM I-3690 restores impaired intestinal barrier functions via anti-inflammatory and cytoprotective responses.
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14
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Huang WC, Liao JH, Hsiao TC, Wei TYW, Maestre-Reyna M, Bessho Y, Tsai MD. Binding and Enhanced Binding between Key Immunity Proteins TRAF6 and TIFA. Chembiochem 2018; 20:140-146. [PMID: 30378729 DOI: 10.1002/cbic.201800436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/30/2018] [Indexed: 01/01/2023]
Abstract
Human tumor necrosis factor receptor associated factor (TRAF)-interacting protein, with a forkhead-associated domain (TIFA), is a key regulator of NF-κB activation. It also plays a key role in the activation of innate immunity in response to bacterial infection, through heptose 1,7-bisphosphate (HBP); a metabolite of lipopolysaccharide (LPS). However, the mechanism of TIFA function is largely unexplored, except for the suggestion of interaction with TRAF6. Herein, we provide evidence for direct binding, albeit weak, between TIFA and the TRAF domain of TRAF6, and it is shown that the binding is enhanced for a rationally designed double mutant, TIFA S174Q/M179D. Enhanced binding was also demonstrated for endogenous full-length TRAF6. Furthermore, the structures of the TRAF domain complexes with the consensus TRAF-binding peptides from the C terminus of wild-type and S174Q/M179D mutant TIFA, showing salt-bridge formation between residues 177-181 of TIFA and the binding pocket residues of the TRAF domain, were solved. Taken together, the results provide direct evidence and a structural basis for the TIFA-TRAF6 interaction, and show how this important biological function can be modulated.
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Affiliation(s)
- Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Tzu-Chun Hsiao
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Tong-You Wade Wei
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115, Taiwan.,Institute of Biochemical Sciences, National (Taiwan) University, 1, Roosevelt Road Sec. 4, Taipei, 106, Taiwan
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15
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Generating a recombinant phosphothreonine-binding domain for a phosphopeptide of the human transcription factor, c-Myc. N Biotechnol 2018; 45:36-44. [PMID: 29763736 DOI: 10.1016/j.nbt.2018.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/28/2018] [Accepted: 05/02/2018] [Indexed: 11/21/2022]
Abstract
Transcription factor c-Myc is an oncoprotein that is regulated at the post-translational level through phosphorylation of two conserved residues, Serine 62 (Ser62) and Threonine 58 (Thr58). A highly specific tool capable of recognizing Myc via pThr58 is needed to monitor activation and localization. Through phage display, we have isolated 10 engineered Forkhead-associated (FHA) domains that selectively bind to a phosphothreonine (pThr)-containing peptide (53-FELLPpTPPLSPS-64) segment of human c-Myc. One domain variant was observed to bind to the Myc-pThr58 peptide with a KD value of 800 nM and had >1000-fold discrimination between the phosphorylated and non-phosphorylated peptide. The crystal structure of the engineered FHA Myc-pThr-binding domain (Myc-pTBD) was solved in complex with its cognate ligand. The Myc-pTBD was observed to be structurally similar to the yeast Rad9 FHA1 domain, except that its β4-β5 and β10-β11 loops form a hydrophobic pocket to facilitate the interaction between the domain and the peptide ligand. The Myc-pTBD's specificity for its cognate ligand was demonstrated to be on a par with 3 commercial polyclonal antibodies, suggesting that this recombinant reagent is a viable alternative to antibodies for monitoring Myc regulation.
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16
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Xie C, He C, Jiang Y, Yu H, Cheng L, Nshogoza G, Ala MS, Tian C, Wu J, Shi Y, Li F. Structural insights into the recognition of phosphorylated Hop1 by Mek1. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1027-1038. [PMID: 30289413 DOI: 10.1107/s2059798318011993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/24/2018] [Indexed: 11/10/2022]
Abstract
The FHA domain-containing protein Mek1 is a meiosis-specific kinase that is involved in the regulation of interhomolog recombination in meiosis in Saccharomyces cerevisiae. The recruitment and activation of Mek1 require the phosphorylation of the chromosome axis protein Hop1 at Thr318 (pT318), which is necessary for recognition by the Mek1 FHA domain. Here, crystal structures of the Mek1 FHA domain in the apo state and in complex with the Hop1 pT318 peptide are presented, demonstrating that the hydrophobic residues Phe320 and Val321 at the pT+2 and pT+3 positions in the ligand contribute to the preferential recognition. It was further found that in Schizosaccharomyces pombe Mek1 FHA binds both pT15 in its N-terminal SQ/TQ cluster domain (SCD) and pT270 in the Hop1 SCD. The results revealed the structural basis for the preferential recognition of phosphorylated Hop1 by Mek1 in S. cerevisiae and facilitate the understanding of the interaction between the S. pombe Mek1 FHA domain and its binding targets.
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Affiliation(s)
- Changlin Xie
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Chao He
- Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Yiyang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Hailong Yu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Lin Cheng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Gilbert Nshogoza
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Moududee Sayed Ala
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Changlin Tian
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
| | - Yunyu Shi
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 50 Shushanhu Road, Hefei, Anhui 230031, People's Republic of China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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17
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Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747. Structure 2018; 26:972-986.e6. [PMID: 29861345 DOI: 10.1016/j.str.2018.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/13/2018] [Accepted: 04/27/2018] [Indexed: 11/23/2022]
Abstract
The Mycobacterium tuberculosis ATP-binding cassette transporter Rv1747 is a putative exporter of cell wall biosynthesis intermediates. Rv1747 has a cytoplasmic regulatory module consisting of two pThr-interacting Forkhead-associated (FHA) domains connected by a conformationally disordered linker with two phospho-acceptor threonines (pThr). The structures of FHA-1 and FHA-2 were determined by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, respectively. Relative to the canonical 11-strand β-sandwich FHA domain fold of FHA-1, FHA-2 is circularly permuted and lacking one β-strand. Nevertheless, the two share a conserved pThr-binding cleft. FHA-2 is less stable and more dynamic than FHA-1, yet binds model pThr peptides with moderately higher affinity (∼50 μM versus 500 μM equilibrium dissociation constants). Based on NMR relaxation and chemical shift perturbation measurements, when joined within a polypeptide chain, either FHA domain can bind either linker pThr to form intra- and intermolecular complexes. We hypothesize that this enables tunable phosphorylation-dependent multimerization to regulate Rv1747 transporter activity.
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18
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Fu J, Huang D, Yuan F, Xie N, Li Q, Sun X, Zhou X, Li G, Tong T, Zhang Y. TRAF-interacting protein with forkhead-associated domain (TIFA) transduces DNA damage-induced activation of NF-κB. J Biol Chem 2018; 293:7268-7280. [PMID: 29581234 DOI: 10.1074/jbc.ra117.001684] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/23/2018] [Indexed: 02/03/2023] Open
Abstract
DNA damage-induced NF-κB activation and the secretion of inflammatory cytokines play crucial roles in carcinogenesis and cellular senescence. However, the underlying mechanisms, especially the initial sensors and transducers connecting the nuclear DNA damage signal with cytoplasmic NF-κB activation remain incompletely understood. Here, we report that TRAF-interacting protein with forkhead-associated domain (TIFA), an established NF-κB activator in the cytosol, unexpectedly exhibited nuclear translocation and accumulation on damaged chromatin following genotoxic stress. Accordingly, we also found that DNA damage-induced transcriptional activation and the resulting secretion of classic NF-κB targets, including interleukin (IL)-6 and IL-8, was greatly enhanced in TIFA-overexpressing cells compared with control cells. Mechanistically, DNA damage-induced TIFA phosphorylation at threonine 9 (pThr-9), and this phosphorylation event, involving the pThr-binding forkhead-associated domain, was crucial for its enrichment on damaged chromatin and subsequent NF-κB activation. Moreover, in conjunction with its partner protein, the E3 ligase TNF receptor-associated factor 2 (TRAF2), TIFA relayed the DNA damage signals by stimulating ubiquitination of NF-κB essential modulator (NEMO), whose sumoylation, phosphorylation, and ubiquitination were critical for NF-κB's response to DNA damage. Consistently, TRAF2 knockdown suppressed TIFA overexpression-enhanced NEMO ubiquitination under genotoxic stress, and a unphosphorylatable Thr-9-mutated TIFA variant had only minor effects on NEMO poly-ubiquitination. Finally, in agreement with the model of DNA damage-associated secretory senescence barrier against carcinogenesis, ectopic TIFA expression limited proliferation of multiple myeloma cancer cells. In conclusion our results indicate that TIFA functions as a key transducer in DNA damage-induced NF-κB activation.
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Affiliation(s)
- Jingxuan Fu
- Peking University Research Center on Aging, Beijing 100191; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191
| | - Daoyuan Huang
- Peking University Research Center on Aging, Beijing 100191; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191
| | - Fuwen Yuan
- Peking University Research Center on Aging, Beijing 100191; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191
| | - Nan Xie
- Peking University Research Center on Aging, Beijing 100191; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191
| | - Qian Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing 100081, People's Republic of China
| | - Xinpei Sun
- Peking University Research Center on Aging, Beijing 100191; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191
| | - Xuehong Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191
| | - Guodong Li
- Peking University Research Center on Aging, Beijing 100191; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191
| | - Tanjun Tong
- Peking University Research Center on Aging, Beijing 100191; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191.
| | - Yu Zhang
- Peking University Research Center on Aging, Beijing 100191; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191.
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19
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Pachathundikandi K, Backert S. Heptose 1,7-Bisphosphate Directed TIFA Oligomerization: A Novel PAMP-Recognizing Signaling Platform in the Control of Bacterial Infections. Gastroenterology 2018; 154:778-783. [PMID: 29337150 DOI: 10.1053/j.gastro.2018.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | - Steffen Backert
- Friedrich Alexander University Erlangen/Nuremberg, Erlangen, Germany
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20
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Gaudet RG, Guo CX, Molinaro R, Kottwitz H, Rohde JR, Dangeard AS, Arrieumerlou C, Girardin SE, Gray-Owen SD. Innate Recognition of Intracellular Bacterial Growth Is Driven by the TIFA-Dependent Cytosolic Surveillance Pathway. Cell Rep 2018; 19:1418-1430. [PMID: 28514661 DOI: 10.1016/j.celrep.2017.04.063] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 02/12/2017] [Accepted: 04/21/2017] [Indexed: 12/21/2022] Open
Abstract
Intestinal epithelial cells (IECs) act as sentinels for incoming pathogens. Cytosol-invasive bacteria, such as Shigella flexneri, trigger a robust pro-inflammatory nuclear factor κB (NF-κB) response from IECs that is believed to depend entirely on the peptidoglycan sensor NOD1. We found that, during Shigella infection, the TRAF-interacting forkhead-associated protein A (TIFA)-dependent cytosolic surveillance pathway, which senses the bacterial metabolite heptose-1,7-bisphosphate (HBP), functions after NOD1 to detect bacteria replicating free in the host cytosol. Whereas NOD1 mediated a transient burst of NF-κB activation during bacterial entry, TIFA sensed HBP released during bacterial replication, assembling into large signaling complexes to drive a dynamic inflammatory response that reflected the rate of intracellular bacterial proliferation. Strikingly, IECs lacking TIFA were unable to discriminate between proliferating and stagnant intracellular bacteria, despite the NOD1/2 pathways being intact. Our results define TIFA as a rheostat for intracellular bacterial replication, escalating the immune response to invasive Gram-negative bacteria that exploit the host cytosol for growth.
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Affiliation(s)
- Ryan G Gaudet
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Cynthia X Guo
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Raphael Molinaro
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Haila Kottwitz
- Departments of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - John R Rohde
- Departments of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Anne-Sophie Dangeard
- INSERM, U1016, Institut Cochin, CNRS, UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Cécile Arrieumerlou
- INSERM, U1016, Institut Cochin, CNRS, UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris 75014, France
| | - Stephen E Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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21
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Almawi AW, Matthews LA, Guarné A. FHA domains: Phosphopeptide binding and beyond. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:105-110. [DOI: 10.1016/j.pbiomolbio.2016.12.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/06/2016] [Indexed: 01/18/2023]
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22
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Helicobacter pylori modulates host cell responses by CagT4SS-dependent translocation of an intermediate metabolite of LPS inner core heptose biosynthesis. PLoS Pathog 2017; 13:e1006514. [PMID: 28715499 PMCID: PMC5531669 DOI: 10.1371/journal.ppat.1006514] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/27/2017] [Accepted: 07/05/2017] [Indexed: 12/15/2022] Open
Abstract
Highly virulent Helicobacter pylori cause proinflammatory signaling inducing the transcriptional activation and secretion of cytokines such as IL-8 in epithelial cells. Responsible in part for this signaling is the cag pathogenicity island (cagPAI) that codetermines the risk for pathological sequelae of an H. pylori infection such as gastric cancer. The Cag type IV secretion system (CagT4SS), encoded on the cagPAI, can translocate various molecules into cells, the effector protein CagA, peptidoglycan metabolites and DNA. Although these transported molecules are known to contribute to cellular responses to some extent, a major part of the cagPAI-induced signaling leading to IL-8 secretion remains unexplained. We report here that biosynthesis of heptose-1,7-bisphosphate (HBP), an important intermediate metabolite of LPS inner heptose core, contributes in a major way to the H. pylori cagPAI-dependent induction of proinflammatory signaling and IL-8 secretion in human epithelial cells. Mutants defective in the genes required for synthesis of HBP exhibited a more than 95% reduction of IL-8 induction and impaired CagT4SS-dependent cellular signaling. The loss of HBP biosynthesis did not abolish the ability to translocate CagA. The human cellular adaptor TIFA, which was described before to mediate HBP-dependent activity in other Gram-negative bacteria, was crucial in the cagPAI- and HBP pathway-induced responses by H. pylori in different cell types. The active metabolite was present in H. pylori lysates but not enriched in bacterial supernatants. These novel results advance our mechanistic understanding of H. pylori cagPAI-dependent signaling mediated by intracellular pattern recognition receptors. They will also allow to better dissect immunomodulatory activities by H. pylori and to improve the possibilities of intervention in cagPAI- and inflammation-driven cancerogenesis. The Cag Type IV secretion system, which contributes to inflammation and cancerogenesis during chronic infection, is one of the major virulence and fitness factors of the bacterial gastric pathogen Helicobacter pylori. Up to now, the mechanisms leading to cagPAI-dependent signal transduction and cytokine secretion were not completely understood. We report here that HBP, an intermediate metabolite in LPS core heptose biosynthesis, is translocated into host cells dependent on the CagT4SS, and is a major factor leading to the activation of cellular responses. This response is connected to the human cellular adaptor protein TIFA. The knowledge of this specific response pathway is a major advance in understanding CagT4SS-dependent signaling and will enable us to understand better how H. pylori modulates the immune response repertoire in its human host.
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23
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Abstract
Toll-like receptor-mediated NF-κB activation is a major innate immune reaction of vascular endothelial cells (ECs) in response to prooxidative and proinflammatory stimuli. We identified that TNF-α receptor-associated factor-interacting protein with a forkhead-associated domain (TIFA) is a regulator of priming (signal 1) and activating (signal 2) signals of nucleotide oligomerization domain-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome in ECs. Oxidative and inflammatory stresses such as atheroprone flow and hyperlipidemia induce and activate TIFA in vitro and in vivo. For the priming of signal 1, sterol regulatory element-binding protein 2 transactivates TIFA, which in turn induces NF-κB activation and augments the transcription of NLRP3 inflammasome components. For the activation of signal 2, Akt is involved in TIFA Thr9 phosphorylation, which is essential for TIFA-TIFA homophilic oligomerization. Thr9 phosphorylation-dependent TIFA oligomerization facilitates the higher-order assembly of NLRP3 inflammasome, as indicated by the interaction between TIFA and caspase-1 in the activated ECs. Our results suggest that TIFA is a crucial mediator in the endothelial innate immune response by potentiating and amplifying NLRP3 inflammasome via augmenting signals 1 and 2.
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Almawi AW, Matthews LA, Larasati, Myrox P, Boulton S, Lai C, Moraes T, Melacini G, Ghirlando R, Duncker BP, Guarné A. 'AND' logic gates at work: Crystal structure of Rad53 bound to Dbf4 and Cdc7. Sci Rep 2016; 6:34237. [PMID: 27681475 PMCID: PMC5041073 DOI: 10.1038/srep34237] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023] Open
Abstract
Forkhead-associated (FHA) domains are phosphopeptide recognition modules found in many signaling proteins. The Saccharomyces cerevisiae protein kinase Rad53 is a key regulator of the DNA damage checkpoint and uses its two FHA domains to interact with multiple binding partners during the checkpoint response. One of these binding partners is the Dbf4-dependent kinase (DDK), a heterodimer composed of the Cdc7 kinase and its regulatory subunit Dbf4. Binding of Rad53 to DDK, through its N-terminal FHA (FHA1) domain, ultimately inhibits DDK kinase activity, thereby preventing firing of late origins. We have previously found that the FHA1 domain of Rad53 binds simultaneously to Dbf4 and a phosphoepitope, suggesting that this domain functions as an 'AND' logic gate. Here, we present the crystal structures of the FHA1 domain of Rad53 bound to Dbf4, in the presence and absence of a Cdc7 phosphorylated peptide. Our results reveal how the FHA1 uses a canonical binding interface to recognize the Cdc7 phosphopeptide and a non-canonical interface to bind Dbf4. Based on these data we propose a mechanism to explain how Rad53 enhances the specificity of FHA1-mediated transient interactions.
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Affiliation(s)
- Ahmad W. Almawi
- Department of Biochemistry and Biomedical Sciences, ON, Canada
| | | | - Larasati
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Polina Myrox
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Stephen Boulton
- Department of Chemistry and Chemical Biology, McMaster University, ON, Canada
| | - Christine Lai
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Trevor Moraes
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, ON, Canada
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Alba Guarné
- Department of Biochemistry and Biomedical Sciences, ON, Canada,
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26
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Shen W, Du R, Li J, Luo X, Zhao S, Chang A, Zhou W, Gao R, Luo D, Wang J, Hao N, Liu Y, Chen Y, Luo Y, Sun P, Yang S, Luo N, Xiang R. TIFA suppresses hepatocellular carcinoma progression via MALT1-dependent and -independent signaling pathways. Signal Transduct Target Ther 2016; 1:16013. [PMID: 29263897 PMCID: PMC5661659 DOI: 10.1038/sigtrans.2016.13] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/23/2016] [Accepted: 07/04/2016] [Indexed: 02/05/2023] Open
Abstract
TIFA, also called T2BP, was first identified using yeast two-hybrid screening. Our previous work showed that TIFA suppresses hepatocellular carcinoma (HCC) progression via apoptosis and cell cycle arrest. However, the mechanism by which this TIFA suppression occurs remains unclear. Here we demonstrated that TIFA-induced apoptosis demonstrates two distinct time patterns (i.e., at 48 h and >7 days) when TIFA reconstitution occurs. Moreover, we found that MALT1 (a competitor of TIFA) plays a crucial role in short-duration TIFA reconstitution. In this regard, MALT1 silencing with shRNA markedly enhances TIFA-induced apoptosis in vitro and in vivo. In addition, TIFA overexpression triggers JNK and p38 activation in long-duration TIFA reconstitution through TRAF6 binding. In particular, JNK activation leads to TIFA-induced apoptosis while p38 activation governs TIFA-induced cell cycle arrest by p53-p21 signaling in vitro and in vivo. Our data suggest a novel mechanism by which TIFA suppresses HCC progression via both MALT1-dependent and MALT1-independent signaling pathways. This may provide insights into a novel targets where HCC progression may be vulnerable to clinical treatment.
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Affiliation(s)
- Wenzhi Shen
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Renle Du
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Jun Li
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Xiaohe Luo
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Shuangtao Zhao
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Antao Chang
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Wei Zhou
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Ruifang Gao
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Dehong Luo
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Juan Wang
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Na Hao
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Yanhua Liu
- International Joint Center for Biomedical Research of the Ministry of Education, Tianjin, China
| | - Yanan Chen
- International Joint Center for Biomedical Research of the Ministry of Education, Tianjin, China
| | - Yunping Luo
- Department of Immunology, Institute of Basic Medical Science, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Peiqing Sun
- Department of Cancer Biology and Comprehensive Cancer Center, Wake Forest University Medical Center, Winston-Salem, North Carolina, USA
| | - Shengyong Yang
- West China Hospital, Molecular Medicine Research Centre, State Key Lab Biotherapy, Sichuan University, Chengdu, China
| | - Na Luo
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China
| | - Rong Xiang
- Department of Immunology, School of Medicine, Nankai University, Tianjin, China.,International Joint Center for Biomedical Research of the Ministry of Education, Tianjin, China
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