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Wu Q, Cui D, Chao X, Chen P, Liu J, Wang Y, Su T, Li M, Xu R, Zhu Y, Zhang Y. Transcriptome Analysis Identifies Strategies Targeting Immune Response-Related Pathways to Control Enterotoxigenic Escherichia coli Infection in Porcine Intestinal Epithelial Cells. Front Vet Sci 2021; 8:677897. [PMID: 34447800 PMCID: PMC8383179 DOI: 10.3389/fvets.2021.677897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is an important cause of post-weaning diarrhea (PWD) worldwide, resulting in huge economic losses to the swine industry worldwide. In this study, to understand the pathogenesis, the transcriptomic analysis was performed to explore the biological processes (BP) in porcine intestinal epithelial J2 cells infected with an emerging ETEC strain isolated from weaned pigs with diarrhea. Under the criteria of |fold change| (FC) ≥ 2 and P < 0.05 with false discovery rate < 0.05, a total of 131 referenced and 19 novel differentially expressed genes (DEGs) were identified after ETEC infection, including 96 upregulated DEGs and 54 downregulated DEGs. The Gene Ontology (GO) analysis of DEGs showed that ETEC evoked BP specifically involved in response to lipopolysaccharide (LPS) and negative regulation of intracellular signal transduction. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that immune response-related pathways were mainly enriched in J2 cells after ETEC infection, in which tumor necrosis factor (TNF), interleukin 17, and mitogen-activated protein kinase (MAPK) signaling pathways possessed the highest rich factor, followed by nucleotide-binding and oligomerization domain-like receptor (NLRs), C-type lectin receptor (CLR), cytokine–cytokine receptor interaction, and Toll-like receptor (TLR), and nuclear factor kappa-B (NF-κB) signaling pathways. Furthermore, 30 of 131 referenced DEGs, especially the nuclear transcription factor AP-1 and NF-κB, participate in the immune response to infection through an integral signal cascade and can be target molecules for prevention and control of enteric ETEC infection by probiotic Lactobacillus reuteri. Our data provide a comprehensive insight into the immune response of porcine intestinal epithelial cells (IECs) to ETEC infection and advance the identification of targets for prevention and control of ETEC-related PWD.
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Affiliation(s)
- Qiong Wu
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China.,Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, China
| | - Defeng Cui
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China.,Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, China
| | - Xinyu Chao
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Peng Chen
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Jiaxuan Liu
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yiding Wang
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Tongjian Su
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Meng Li
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ruyu Xu
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yaohong Zhu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yonghong Zhang
- Department of Animal Medicine, College of Animal Science and Technology, Beijing University of Agriculture, Beijing, China.,Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Beijing, China
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Sun XH, Xiao HM, Zhang M, Lin ZY, Yang Y, Chen R, Liu PQ, Huang KP, Huang HQ. USP9X deubiquitinates connexin43 to prevent high glucose-induced epithelial-to-mesenchymal transition in NRK-52E cells. Biochem Pharmacol 2021; 188:114562. [PMID: 33857489 DOI: 10.1016/j.bcp.2021.114562] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 01/24/2023]
Abstract
Epithelial-to-mesenchymal transition (EMT) plays an important role in diabetic nephropathy (DN). Ubiquitin-specific protease 9X (USP9X/FAM) is closely linked to TGF-β and fibrosis signaling pathway. However, it remains unknown whether USP9X is involved in the process of EMT in DN. Our previous study has shown that connexin 43 (Cx43) activation attenuated the development of diabetic renal tubulointerstitial fibrosis (RIF). Here, we showed that USP9X is a novel negative regulator of EMT and the potential mechanism is related to the deubiquitination and degradation of Cx43. To explore the potential regulatory mechanism of USP9X, the expression and activity of USP9X were studied by CRISPR/Cas9-based synergistic activation mediator (SAM) system, short hairpin RNAs, and selective inhibitor. The following findings were observed: (1) Expression of USP9X was down-regulated in the kidney tissue of db/db diabetic mice; (2) overexpression of USP9X suppressed high glucose (HG)-induced expressions of EMT markers and extra cellular matrix (ECM) in NRK-52E cells; (3) depletion of USP9X further aggravated EMT process and ECM production in NRK-52E cells; (4) USP9X deubiquitinated Cx43 and suppressed its degradation to regulate EMT process; (5) USP9X deubiquitinated Cx43 by directly binding to the C-terminal Tyr286 of Cx43. The current study determined the protective role of USP9X in the process of EMT and the molecular mechanism clarified that the protective effects of USP9X on DN were associated with the deubiquitination of Cx43.
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Affiliation(s)
- Xiao-Hong Sun
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hai-Ming Xiao
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Meng Zhang
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ze-Yuan Lin
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yan Yang
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Rui Chen
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Pei-Qing Liu
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Kai-Peng Huang
- Phase I Clinical Trial Center, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510060, China.
| | - He-Qing Huang
- Laboratory of Pharmacology & Toxicology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China.
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Yeh SJ, Yeh CC, Lan CY, Chen BS. Investigating Common Pathogenic Mechanisms between Homo sapiens and Different Strains of Candida albicans for Drug Design: Systems Biology Approach via Two-Sided NGS Data Identification. Toxins (Basel) 2019; 11:toxins11020119. [PMID: 30769958 PMCID: PMC6409619 DOI: 10.3390/toxins11020119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 01/15/2023] Open
Abstract
Candida albicans (C. albicans) is the most prevalent fungal species. Although it is a healthy microbiota, genetic and epigenetic alterations in host and pathogen, and microenvironment changes would lead to thrush, vaginal yeast infection, and even hematogenously disseminated infection. Despite the fact that cytotoxicity is well-characterized, few studies discuss the genome-wide genetic and epigenetic molecular mechanisms between host and C. albicans. The aim of this study is to identify drug targets and design a multiple-molecule drug to prevent the infection from C. albicans. To investigate the common and specific pathogenic mechanisms in human oral epithelial OKF6/TERT-2 cells during the C. albicans infection in different strains, systems modeling and big databases mining were used to construct candidate host–pathogen genetic and epigenetic interspecies network (GEIN). System identification and system order detection are applied on two-sided next generation sequencing (NGS) data to build real host–pathogen cross-talk GEINs. Core host–pathogen cross-talk networks (HPCNs) are extracted by principal network projection (PNP) method. By comparing with core HPCNs in different strains of C. albicans, common pathogenic mechanisms were investigated and several drug targets were suggested as follows: orf19.5034 (YBP1) with the ability of anti-ROS; orf19.939 (NAM7), orf19.2087 (SAS2), orf19.1093 (FLO8) and orf19.1854 (HHF22) with high correlation to the hyphae growth and pathogen protein interaction; orf19.5585 (SAP5), orf19.5542 (SAP6) and orf19.4519 (SUV3) with the cause of biofilm formation. Eventually, five corresponding compounds—Tunicamycin, Terbinafine, Cerulenin, Tetracycline and Tetrandrine—with three known drugs could be considered as a potential multiple-molecule drug for therapeutic treatment of C. albicans.
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Affiliation(s)
- Shan-Ju Yeh
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Chun-Chieh Yeh
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Chung-Yu Lan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.
- Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
- Department of Electrical Engineering, Yuan Ze University, Chungli 32003, Taiwan.
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Transcriptome Analysis of Phycocyanin-Mediated Inhibitory Functions on Non-Small Cell Lung Cancer A549 Cell Growth. Mar Drugs 2018; 16:md16120511. [PMID: 30558318 PMCID: PMC6316159 DOI: 10.3390/md16120511] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 01/11/2023] Open
Abstract
Phycocyanin (PC), derived from cyanobacteria and Spirulina cells, is a type of natural antineoplastic marine protein. It has been reported that phycocyanin exerts an antitumor function in non-small cell lung cancer (NSCLC) cells, but the underlying mechanism has not been elucidated. In this research, a transcriptome study was performed to investigate the regulatory mechanisms of phycocyanin on human NSCLC A549 cells. The survival rate and proliferation ability of A549 cells were markedly reduced by phycocyanin, along with abnormal morphologic changes. The transcriptome analysis showed that 2970 genes were differentially expressed after phycocyanin treatment in A549 cells, including 1431 down-regulated and 1539 up-regulated genes. Gene ontology and KEGG analysis suggested that some classical pathways, such as Wnt, NF-κB, and PI3K-AKT signaling, were significantly enriched. Strikingly, protein–protein interaction (PPI) analysis showed that ubiquitin-C (UBC) occupied the highest degree (the highest number of interactions) in differential genes, indicating that it might play a key role in the phycocyanin-mediated regulatory process in A549 cells. Moreover, qRT-PCR results showed consistent expression trends of differential genes with transcriptome analysis. Consequently, this study has provided a theoretical basis for regulation of phycocyanin in A549 cells, which lays a foundation for the treatment of NSCLC.
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Kharman-Biz A, Gao H, Ghiasvand R, Haldosen LA, Zendehdel K. Expression of the three components of linear ubiquitin assembly complex in breast cancer. PLoS One 2018; 13:e0197183. [PMID: 29763465 PMCID: PMC5953448 DOI: 10.1371/journal.pone.0197183] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/27/2018] [Indexed: 11/19/2022] Open
Abstract
Proteins belonging to the linear ubiquitin assembly complex (LUBAC) are believed to be important in tumorigenesis. LUBAC has been demonstrated to be composed of RBCK1, RNF31 and SHARPIN. The aim of this study was to explore all members of the LUBAC complex as novel biomarkers in breast cancer. We have already reported that RNF31 mRNA levels are higher in breast cancer samples compared to adjacent non-tumor tissue. In this study we extend these findings by demonstrating that the mRNA levels of RBCK1 and SHARPIN are also higher in tumors compared to adjacent non-tumor tissue in the same cross sectional study of samples (p < 0.001). In addition, up-regulated mRNA expression of all three members of the LUBAC complex displayed high predictive value in distinguishing tumor tissues from adjacent non-tumor tissue as determined by ROC curve analysis. Furthermore, we investigated whether there is an association between the mRNA and protein expression levels of RBCK1, RNF31 and SHARPIN and clinicopathological parameters including estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor (HER2) status and found that RNF31 protein is significantly higher in ERalpha-negative tumors than ERalpha-positive tumors (p = 0.034). Collectively, our findings indicate that up-regulated mRNA expression of RNF31, RBCK1 and SHARPIN could potentially be diagnostic biomarkers of breast cancer and RNF31 might be a drug target for ERalpha-negative breast cancers.
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Affiliation(s)
- Amirhossein Kharman-Biz
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Hui Gao
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Reza Ghiasvand
- Oslo Centre for Biostatistics and Epidemiology, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Lars-Arne Haldosen
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kazem Zendehdel
- Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
- * E-mail:
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Miraghazadeh B, Cook MC. Nuclear Factor-kappaB in Autoimmunity: Man and Mouse. Front Immunol 2018; 9:613. [PMID: 29686669 PMCID: PMC5900062 DOI: 10.3389/fimmu.2018.00613] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
NF-κB (nuclear factor-kappa B) is a transcription complex crucial for host defense mediated by innate and adaptive immunity, where canonical NF-κB signaling, mediated by nuclear translocation of RelA, c-Rel, and p50, is important for immune cell activation, differentiation, and survival. Non-canonical signaling mediated by nuclear translocation of p52 and RelB contributes to lymphocyte maturation and survival and is also crucial for lymphoid organogenesis. We outline NF-κB signaling and regulation, then summarize important molecular contributions of NF-κB to mechanisms of self-tolerance. We relate these mechanisms to autoimmune phenotypes described in what is now a substantial catalog of immune defects conferred by mutations in NF-κB pathways in mouse models. Finally, we describe Mendelian autoimmune syndromes arising from human NF-κB mutations, and speculate on implications for understanding sporadic autoimmune disease.
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Affiliation(s)
- Bahar Miraghazadeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, ACT, Australia
- Translational Research Unit, Canberra Hospital, Acton, ACT, Australia
| | - Matthew C. Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, ACT, Australia
- Translational Research Unit, Canberra Hospital, Acton, ACT, Australia
- Department of Immunology, Canberra Hospital, Acton, ACT, Australia
- *Correspondence: Matthew C. Cook,
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Elton L, Carpentier I, Staal J, Driege Y, Haegman M, Beyaert R. MALT1 cleaves the E3 ubiquitin ligase HOIL-1 in activated T cells, generating a dominant negative inhibitor of LUBAC-induced NF-κB signaling. FEBS J 2015; 283:403-12. [DOI: 10.1111/febs.13597] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 11/10/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Lynn Elton
- Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Department of Biomedical Molecular Biology; Ghent University; Belgium
| | - Isabelle Carpentier
- Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Department of Biomedical Molecular Biology; Ghent University; Belgium
| | - Jens Staal
- Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Department of Biomedical Molecular Biology; Ghent University; Belgium
| | - Yasmine Driege
- Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Department of Biomedical Molecular Biology; Ghent University; Belgium
| | - Mira Haegman
- Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Department of Biomedical Molecular Biology; Ghent University; Belgium
| | - Rudi Beyaert
- Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Department of Biomedical Molecular Biology; Ghent University; Belgium
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HSCARG downregulates NF-κB signaling by interacting with USP7 and inhibiting NEMO ubiquitination. Cell Death Dis 2014; 5:e1229. [PMID: 24832601 PMCID: PMC4047896 DOI: 10.1038/cddis.2014.197] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 04/01/2014] [Accepted: 04/04/2014] [Indexed: 12/22/2022]
Abstract
Nuclear factor κB (NF-κB) signaling is a central pathway that participates in a variety of key processes, including immunity, inflammation, cell growth and differentiation. The activity of NF-κB is strictly regulated by a cluster of proteins, and modifications of these proteins either promote or suppress signal transduction at various steps. Here we demonstrated that HSCARG suppresses TNFα-stimulated NF-κB signaling under physiological conditions. We elucidated the detailed mechanism through which HSCARG inhibits NF-κB activation. HSCARG interacts with NEMO and suppresses polyubiquitination of NEMO by interacting with the deubiquitinase USP7. HSACRG attenuates its inhibitory effect on NEMO ubiquitination in USP7 knockdown cells, and inhibition of NEMO polyubiquitination by USP7 is impaired in HSCARG−/− cells as well. Moreover, we demonstrated that USP7 is a negative regulator of TNFα-stimulated NF-κB activity. Altogether, our data indicate that HSCARG and USP7 function in concert in inhibiting polyubiquination of NEMO, thus inhibiting NF-κB activity.
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Yick CY, Zwinderman AH, Kunst PW, Grünberg K, Mauad T, Fluiter K, Bel EH, Lutter R, Baas F, Sterk PJ. Glucocorticoid-induced changes in gene expression of airway smooth muscle in patients with asthma. Am J Respir Crit Care Med 2013; 187:1076-84. [PMID: 23491407 DOI: 10.1164/rccm.201210-1886oc] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
RATIONALE Glucocorticoids are the mainstay of asthma therapy. However, it is unclear whether the benefits of glucocorticoids in asthma are merely based on antiinflammatory properties. Glucocorticoids may also alter gene expression of airway smooth muscle (ASM). We hypothesized that the gene expression profile of the ASM layer in endobronchial biopsies of patients with asthma is altered by oral glucocorticoid therapy as compared with placebo. OBJECTIVES First, we investigated the change in ASM transcriptomic profile in endobronchial biopsies after 14 days of oral glucocorticoid therapy. Second, we investigated the association between changes in ASM transcriptomic profile and lung function. METHODS Twelve steroid-free patients with atopic asthma were included in this double-blind intervention study. Endobronchial biopsies were taken before and after 14 days of oral prednisolone (n = 6) or placebo (n = 6). RNA of laser-dissected ASM was sequenced (RNA-Seq) using GS FLX+ (454/Roche). Gene networks were identified by Ingenuity Pathway Analysis. RNA-Seq reads were assumed to follow a negative binomial distribution. At the current sample size the estimated false discovery rate was approximately 3%. MEASUREMENTS AND MAIN RESULTS Fifteen genes were significantly changed by 14 days of oral prednisolone. Two of these genes (FAM129A, SYNPO2) were associated with airway hyperresponsiveness (provocative concentration of methacholine causing a 20% drop in FEV1: r = -0.740, P < 0.01; r = -0.746, P < 0.01). Pathway analysis revealed three gene networks that were associated with cellular functions including cellular growth, proliferation, and development. CONCLUSIONS Oral prednisolone changes the transcriptomic profile of the ASM layer in asthma. This indicates that in parallel to antiinflammatory properties, glucocorticoids also exert effects on gene expression of ASM, which is correlated with improved airway function.
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Affiliation(s)
- Ching Yong Yick
- Department of Respiratory Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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A20 inhibits LUBAC-mediated NF-κB activation by binding linear polyubiquitin chains via its zinc finger 7. EMBO J 2012; 31:3845-55. [PMID: 23032186 DOI: 10.1038/emboj.2012.240] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Accepted: 08/03/2012] [Indexed: 12/20/2022] Open
Abstract
Linear polyubiquitination of proteins has recently been implicated in NF-κB signalling and is mediated by the linear ubiquitin chain assembly complex (LUBAC), consisting of HOIL-1, HOIP and Sharpin. However, the mechanisms that regulate linear ubiquitination are still unknown. Here, we show that A20 is rapidly recruited to NEMO and LUBAC upon TNF stimulation and that A20 inhibits LUBAC-induced NF-κB activation via its C-terminal zinc-finger 7 (ZF7) domain. Expression of a polypeptide corresponding to only ZF7 was sufficient to inhibit TNF-induced NF-κB activation. Both A20 and ZF7 can form a complex with NEMO and LUBAC, and are able to prevent the TNF-induced binding of NEMO to LUBAC. Finally, we show that ZF7 preferentially binds linear polyubiquitin chains in vitro, indicating A20-ZF7 as a novel linear ubiquitin-binding domain (LUBID). We thus propose a model in which A20 inhibits TNF- and LUBAC-induced NF-κB signalling by binding to linear polyubiquitin chains via its seventh zinc finger, which prevents the TNF-induced interaction between LUBAC and NEMO.
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van Wijk SJL, Fiskin E, Putyrski M, Pampaloni F, Hou J, Wild P, Kensche T, Grecco HE, Bastiaens P, Dikic I. Fluorescence-based sensors to monitor localization and functions of linear and K63-linked ubiquitin chains in cells. Mol Cell 2012; 47:797-809. [PMID: 22819327 DOI: 10.1016/j.molcel.2012.06.017] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/02/2012] [Accepted: 06/12/2012] [Indexed: 10/28/2022]
Abstract
Ubiquitin chains modify a major subset of the proteome, but detection of ubiquitin signaling dynamics and localization is limited due to a lack of appropriate tools. Here, we employ ubiquitin-binding domain (UBD)-based fluorescent sensors to monitor linear and K63-linked chains in vitro and in vivo. We utilize the UBD in NEMO and ABIN (UBAN) for detection of linear chains, and RAP80 ubiquitin-interacting motif (UIM) and TAB2 Npl4 zinc finger (NZF) domains to detect K63 chains. Linear and K63 sensors decorated the ubiquitin coat surrounding cytosolic Salmonella during bacterial autophagy, whereas K63 sensors selectively monitored Parkin-induced mitophagy and DNA damage responses in fixed and living cells. In addition, linear and K63 sensors could be used to monitor endogenous signaling pathways, as demonstrated by their ability to differentially interfere with TNF- and IL-1-induced NF-κB pathway. We propose that UBD-based biosensors could serve as prototypes to track and trace other chain types and ubiquitin-like signals in vivo.
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Affiliation(s)
- Sjoerd J L van Wijk
- Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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12
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Hayden MS, Ghosh S. NF-κB, the first quarter-century: remarkable progress and outstanding questions. Genes Dev 2012; 26:203-34. [PMID: 22302935 DOI: 10.1101/gad.183434.111] [Citation(s) in RCA: 1284] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to sense and adjust to the environment is crucial to life. For multicellular organisms, the ability to respond to external changes is essential not only for survival but also for normal development and physiology. Although signaling events can directly modify cellular function, typically signaling acts to alter transcriptional responses to generate both transient and sustained changes. Rapid, but transient, changes in gene expression are mediated by inducible transcription factors such as NF-κB. For the past 25 years, NF-κB has served as a paradigm for inducible transcription factors and has provided numerous insights into how signaling events influence gene expression and physiology. Since its discovery as a regulator of expression of the κ light chain gene in B cells, research on NF-κB continues to yield new insights into fundamental cellular processes. Advances in understanding the mechanisms that regulate NF-κB have been accompanied by progress in elucidating the biological significance of this transcription factor in various physiological processes. NF-κB likely plays the most prominent role in the development and function of the immune system and, not surprisingly, when dysregulated, contributes to the pathophysiology of inflammatory disease. As our appreciation of the fundamental role of inflammation in disease pathogenesis has increased, so too has the importance of NF-κB as a key regulatory molecule gained progressively greater significance. However, despite the tremendous progress that has been made in understanding the regulation of NF-κB, there is much that remains to be understood. In this review, we highlight both the progress that has been made and the fundamental questions that remain unanswered after 25 years of study.
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Affiliation(s)
- Matthew S Hayden
- Department of Microbiology and Immunology, College of Physicians and Surgeons, New York, New York 10032, USA
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Maelfait J, Beyaert R. Emerging role of ubiquitination in antiviral RIG-I signaling. Microbiol Mol Biol Rev 2012; 76:33-45. [PMID: 22390971 PMCID: PMC3294425 DOI: 10.1128/mmbr.05012-11] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Detection of viruses by the innate immune system involves the action of specialized pattern recognition receptors. Intracellular RIG-I receptors sense the presence of viral nucleic acids in infected cells and trigger signaling pathways that lead to the production of proinflammatory and antiviral proteins. Over the past few years, posttranslational modification of RIG-I and downstream signaling proteins by different types of ubiquitination has been found to be a key event in the regulation of RIG-I-induced NF-κB and interferon regulatory factor 3 (IRF3) activation. Multiple ubiquitin ligases, deubiquitinases, and ubiquitin binding scaffold proteins contribute to both positive and negative regulation of the RIG-I-induced antiviral immune response. A better understanding of the function and activity of these proteins might eventually lead to the development of novel therapeutic approaches for management of viral diseases.
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Affiliation(s)
- Jonathan Maelfait
- Unit of Molecular Signal Transduction in Inflammation, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rudi Beyaert
- Unit of Molecular Signal Transduction in Inflammation, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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14
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Schmukle AC, Walczak H. No one can whistle a symphony alone – how different ubiquitin linkages cooperate to orchestrate NF-κB activity. J Cell Sci 2012; 125:549-59. [DOI: 10.1242/jcs.091793] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although it has been known for a long time that ubiquitylation has a major role in the activation and regulation of the nuclear factor kappa B (NF-κB) pathway, recent studies have revealed that the picture is a lot more complex than originally thought. NF-κB and ubiquitylation initially became linked when it was recognised that lysine (K)48-linked ubiquitin chains are involved in the processing of NF-κB precursors and the degradation of inhibitor of kappa B (IκB) proteins. Soon thereafter, it was reported that K63-linked chains were involved in the assembly of IκB kinase (IKK)-activating complexes and required for activation of the NF-κB signalling pathway. Recently, the discovery that atypical ubiquitin linkages, including linear and K11 linkages, are also involved in the activation of NF-κB has led to the need to re-evaluate existing models of how activation of this transcription factor is initiated and regulated. It is now becoming apparent that not only the canonical types of ubiquitin chains but possibly all linkage types have to be investigated in order to fully comprehend NF-κB activation. This can be considered a turning point in our view of the regulation of one of the most important pathways of gene induction. Hence, in this Commentary, we summarise the information that is currently available and incorporate it into a new model of NF-κB activation, thereby highlighting the emerging new challenges in understanding the role of ubiquitylation in NF-κB activation.
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Affiliation(s)
- Anna C. Schmukle
- Tumour Immunology Unit, Division of Immunology and Inflammation, Department of Medicine, Imperial College London, 10th floor, Commonwealth Building, Du Cane Road, London W12 0NN, UK
| | - Henning Walczak
- Tumour Immunology Unit, Division of Immunology and Inflammation, Department of Medicine, Imperial College London, 10th floor, Commonwealth Building, Du Cane Road, London W12 0NN, UK
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Fushman D, Wilkinson KD. Structure and recognition of polyubiquitin chains of different lengths and linkage. F1000 BIOLOGY REPORTS 2011; 3:26. [PMID: 22162729 PMCID: PMC3229271 DOI: 10.3410/b3-26] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The polyubiquitin signal is post-translationally attached to a large number of proteins, often directing formation of macromolecular complexes resulting in the translocation, assembly or degradation of the attached protein. Recent structural and functional studies reveal general mechanisms by which different architectures and length of the signal are distinguished.
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Affiliation(s)
- David Fushman
- Department of Chemistry and Biochemistry, University of MarylandCollege Park, MD 20742USA
| | - Keith D. Wilkinson
- Department of Biochemistry, Emory University School of MedicineAtlanta, GA 30322USA
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Verhelst K, Carpentier I, Beyaert R. Regulation of TNF-induced NF-κB activation by different cytoplasmic ubiquitination events. Cytokine Growth Factor Rev 2011; 22:277-86. [DOI: 10.1016/j.cytogfr.2011.11.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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