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Simon2019 - NIK-dependent p100 processing into p52 and IkBd degradation, Michaelis-Menten, SBML 2v4

ABSTRACT: This model represents NIK-dependent p100 processing into p52 and NIK-dependent IkBd degradation with Michaelis-Menten kinetics. Compare this Michaelis-Menten representation to the mass action model in which the dose-response to increasing p100 mRNA is no longer monotonic due to substrate complex competition.

SUBMITTER: Simon Mitchell

PROVIDER: BIOMD0000000869 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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			Action	DRS
	BIOMD0000000869?filename=MM-p52-IkBd.xml	Xml
	BIOMD0000000869?filename=Simon2019_model3.cps	Other
	BIOMD0000000869?filename=Simon2019_model3.sedml	Other
	BIOMD0000000869?filename=Simon2019_model3.xml	Xml

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Publications

Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB.

Mitchell Simon S Hoffmann Alexander A

Proceedings of the National Academy of Sciences of the United States of America 20190502 21

Signaling pathways often share molecular components, tying the activity of one pathway to the functioning of another. In the NFκB signaling system, distinct kinases mediate inflammatory and developmental signaling via RelA and RelB, respectively. Although the substrates of the developmental, so-called noncanonical, pathway are induced by inflammatory/canonical signaling, crosstalk is limited. Through dynamical systems modeling, we identified the underlying regulatory mechanism. We found that as ...[more]

PMID: 31048505

Similar Datasets

Simon2019 - NIK-dependent p100 processing into p52 and IkBd degradation, mass action, SBML 2v4

Project description:This model represents NIK-dependent p100 processing into p52 and NIK-dependent IkBd degradation with mass action kinetics. Compare this mass action representation to the Michaelis-Menten model. In this model the dose-response to increasing p100 mRNA is not monotonic due to substrate complex competition.

2024-09-02 | BIOMD0000000870 | BioModels

Simon2019 - NIK-dependent p100 processing into p52, Mass Action, SBML 2v4

Project description:This model represents NIK-dependent p100 processing into p52 with mass action kinetics. While this model shows identical dose-response to the Michaelis-Menten representation, when IkBd degradation is included the dose-response is no longer monotonic in mass action models due to substrate complex competition.

2024-09-02 | BIOMD0000000868 | BioModels

Simon2019 - NIK-dependent p100 processing into p52, Michaelis-Menten, SBML 2v4

Project description:This model represents NIK-dependent p100 processing into p52 with Michaelis-Menten kinetics. While this model shows identical dose-response to the mass action representation, when IkBd degradation is included the dose-response is no-longer monotonic in mass action models due to substrate complex competition.

2024-09-02 | BIOMD0000000866 | BioModels

NIK-dependent p100 processing into p52 with RelB binding and IkBd degradation, mass action, SBML 2v4

Project description:This model represents NIK-dependent p100 processing into p52 followed by binding to RelB and NIK-dependent IkBd degradation. This model assesses the impact of substrate complex competition on RelB-p52.

2024-09-02 | BIOMD0000000871 | BioModels

NIK expression stimulated G6PD phosphorylation

Project description:Our findings establish NIK as a pivotal regulator of T cell metabolism in anti-tumor immunity and highlight a posttranslational mechanism of metabolic regulation involving the G6PD-NADPH redox system. CoIP assays revealed a strong physical interaction between NIK and G6PD in both T cells and transiently transfected 293 cells, suggesting G6PD to be a direct target of NIK. Using a phosphoprotein gel analysis approach, we demonstrated that NIK expression stimulated G6PD phosphorylation. To further study the mechanism, we performed mass spectrometry identify phosphorylation sites of G6PD stimulated by NIK

2020-10-05 | PXD020943 | Pride

p100 deficiency alone is insufficient for full activation of the alternative NF-?B pathway: TNF signaling cooperates with p52-RelB activation in the transcriptional regulation of the enpp2/autotaxin promoter

Project description:Background: Constitutive activation of the alternative NF-?B pathway leads to marginal zone B cell expansion and disorganized spleen microarchitecture. Furthermore, uncontrolled alternative NF-?B signaling results in the development and progression of cancer. We aimed here to learn about the mechanisms how does the constitutively active alternative NF-?B pathway exert its effects in these malignant processes. Methodology/Principal Findings: To explore the consequences of constitutive alternative NF-?B activation on genome-wide transcription, we compared gene expression profiles of wild-type and NF-kB2/p100-deficient (p100-/-) primary mouse embryonic fibroblasts (MEFs) and spleens. Microarray experiments revealed 73 differentially regulated genes in p100-/- vs. wild-type MEFs. Chromatin immunoprecipitation (ChIP) assays showed in p100-/- MEFs direct binding of RelB and p52 to the promoter of the enpp2 gene encoding Enpp2/Autotaxin, a protein with an important role in lymphocyte homing and cell migration. Gene ontology analysis revealed upregulation of genes with anti-apoptotic/proliferative activity (enpp2, serpina3g, traf1, rrad), chemotactic/locomotory activity (enpp2, ccl8), and lymphocyte homing activity (enpp2, cd34). Most importantly, biochemical analyses of MEFs and gene expression analyses of mice indicated a crosstalk between classical and alternative NF-?B pathways. Conclusions/Significance: The present results show that uncontrolled alternative NF-?B signaling is further enhanced by classical NF-?B activation, indicating that p100 deficiency alone is insufficient for full induction of a subset of genes by the alternative NF-?B pathway. cell type comparison (wt vs p100-/-) after genetic modification

2012-12-21 | E-GEOD-30317 | biostudies-arrayexpress

TRIM55 promotes noncanonical NF-kB signaling and B-cell-mediated immune responses by coordinating p100 ubiquitination and processing

Project description:The ubiquitination-dependent processing of NF-B2 (also known as p100) is a critical step in the activation of the noncanonical NF-B pathway. We investigated the molecular mechanisms regulating this process and showed that TRIM55 was the ubiquitin E3 ligase that mediated the ubiquitination of p100 and coordinated its processing. TRIM55 deficiency impaired noncanonical NF-B activation and B-cell function. Mice with a B cell-specific Trim55 deficiency exhibited reduced germinal center formation and antibody production. In addition, our data indicated a critical role of TRIM55 in the pathogenesis of lupus-like autoimmunological disorders, suggesting B-cell intrinsic functions of TRIM55 in humoral immune responses and autoimmunity. Mechanistically, the ubiquitination of p100 mediated by TRIM55 was crucial for p100 processing by VCP, an ATPase that mediates ubiquitin-dependent protein degradation by the proteasome. Furthermore, we found that TRIM55 facilitated the interaction between TRIM21 and VCP as well as TRIM21-mediated K63-ubiquitination of VCP, both of which were indispensable for the formation of the VCP-UFD1-NPL4 complex and p100 processing. Collectively, our results revealed a mechanism by which TRIM55 fine-tunes p100 processing and regulates B-cell-dependent immune responses in vivo, highlighting TRIM55 as a potential therapeutic target for lupus-like disease.

2023-08-28 | PXD044895 |

Proteus vulgaris P100

Project description:Draft genome of Proteus vulgaris P100

| PRJEB9439 | ENA

p100 deficiency alone is insufficient for full activation of the alternative NF-κB pathway: TNF signaling cooperates with p52-RelB activation in the transcriptional regulation of the enpp2/autotaxin promoter

Project description:Background: Constitutive activation of the alternative NF-κB pathway leads to marginal zone B cell expansion and disorganized spleen microarchitecture. Furthermore, uncontrolled alternative NF-κB signaling results in the development and progression of cancer. We aimed here to learn about the mechanisms how does the constitutively active alternative NF-κB pathway exert its effects in these malignant processes. Methodology/Principal Findings: To explore the consequences of constitutive alternative NF-κB activation on genome-wide transcription, we compared gene expression profiles of wild-type and NF-kB2/p100-deficient (p100-/-) primary mouse embryonic fibroblasts (MEFs) and spleens. Microarray experiments revealed 73 differentially regulated genes in p100-/- vs. wild-type MEFs. Chromatin immunoprecipitation (ChIP) assays showed in p100-/- MEFs direct binding of RelB and p52 to the promoter of the enpp2 gene encoding Enpp2/Autotaxin, a protein with an important role in lymphocyte homing and cell migration. Gene ontology analysis revealed upregulation of genes with anti-apoptotic/proliferative activity (enpp2, serpina3g, traf1, rrad), chemotactic/locomotory activity (enpp2, ccl8), and lymphocyte homing activity (enpp2, cd34). Most importantly, biochemical analyses of MEFs and gene expression analyses of mice indicated a crosstalk between classical and alternative NF-κB pathways. Conclusions/Significance: The present results show that uncontrolled alternative NF-κB signaling is further enhanced by classical NF-κB activation, indicating that p100 deficiency alone is insufficient for full induction of a subset of genes by the alternative NF-κB pathway.

2012-12-21 | GSE30317 | GEO

Comparasion between MCF7-NIK overexpressing cells, MCF7-control cells and MCF7-NIK depleted cells

Project description:Analysis of differentially expressed genes in MCF7 cancer cells transfected with an expression vector containing the ORF of NIK, a shRNA of NIK and a control shRNA. Transient transfections were performed in triplicates . We use micorarrays to elucidate the machanisms by which NIK regulates stem cells biology

2015-11-30 | GSE63382 | GEO

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