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Polewko-Klim A, Lesiński W, Golińska AK, Mnich K, Siwek M, Rudnicki WR. Sensitivity analysis based on the random forest machine learning algorithm identifies candidate genes for regulation of innate and adaptive immune response of chicken. Poult Sci 2020; 99:6341-6354. [PMID: 33248550 PMCID: PMC7704721 DOI: 10.1016/j.psj.2020.08.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 07/14/2020] [Accepted: 08/11/2020] [Indexed: 11/25/2022] Open
Abstract
Two categories of immune responses—innate and adaptive immunity—have both polygenic backgrounds and a significant environmental component. The goal of the reported study was to define candidate genes and mutations for the immune traits of interest in chickens using machine learning–based sensitivity analysis for single-nucleotide polymorphisms (SNPs) located in candidate genes defined in quantitative trait loci regions. Here the adaptive immunity is represented by the specific antibody response toward keyhole limpet hemocyanin (KLH), whereas the innate immunity was represented by natural antibodies toward lipopolysaccharide (LPS) and lipoteichoic acid (LTA). The analysis consisted of 3 basic steps: an identification of candidate SNPs via feature selection, an optimisation of the feature set using recursive feature elimination, and finally a gene-level sensitivity analysis for final selection of models. The predictive model based on 5 genes (MAPK8IP3 CRLF3, UNC13D, ILR9, and PRCKB) explains 14.9% of variance for KLH adaptive response. The models obtained for LTA and LPS use more genes and have lower predictive power, explaining respectively 7.8 and 4.5% of total variance. In comparison, the linear models built on genes identified by a standard statistical analysis explain 1.5, 0.5, and 0.3% of variance for KLH, LTA, and LPS response, respectively. The present study shows that machine learning methods applied to systems with a complex interaction network can discover phenotype-genotype associations with much higher sensitivity than traditional statistical models. It adds contribution to evidence suggesting a role of MAPK8IP3 in the adaptive immune response. It also indicates that CRLF3 is involved in this process as well. Both findings need additional verification.
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Affiliation(s)
- Aneta Polewko-Klim
- Institute of Computer Science, University of Bialystok, Białystok, Poland.
| | - Wojciech Lesiński
- Institute of Computer Science, University of Bialystok, Białystok, Poland
| | | | - Krzysztof Mnich
- Computational Centre, University of Bialystok, Białystok, Poland
| | - Maria Siwek
- Animal Biotechnology and Genetics Department, University of Technology and Life Sciences, Bydgoszcz, Poland
| | - Witold R Rudnicki
- Institute of Computer Science, University of Bialystok, Białystok, Poland; Computational Centre, University of Bialystok, Białystok, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
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2
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Park EJ, Zahari NEM, Kang MS, Lee SJ, Lee K, Lee BS, Yoon C, Cho MH, Kim Y, Kim JH. Toxic response of HIPCO single-walled carbon nanotubes in mice and RAW264.7 macrophage cells. Toxicol Lett 2014; 229:167-77. [PMID: 24929217 DOI: 10.1016/j.toxlet.2014.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/06/2014] [Accepted: 06/07/2014] [Indexed: 01/08/2023]
Abstract
In this study, we identified the toxic response of pristine single-walled carbon nanotubes (P-SWCNTs) synthesized by HIPCO method in mice and RAW264.7 cells, a murine peritoneal macrophage cell line. P-SWCNT contained a large amount of Fe ion (36 wt%). In the lungs of mice 24 h after intratracheal administration, P-SWCNTs increased the secretion of IL-6 and MCP-1, and the number of total cells, the portion of neutrophils, lymphocytes, and eosinophils, also significantly increased at a 100 μg/mL of concentration. In RAW264.7 cells, cell viability and ATP production decreased in a dose-dependent manner at 24 h after exposure, whereas the generations of ROS and NO were enhanced at all concentrations together with the activation of the MAP kinase pathway. Moreover, the levels of both apoptosis- and autophagy-related proteins and ER stress-related proteins clearly increased, and the concentrations of Fe, Cu, and Zn ions, but not of Mn ions, increased in a dose-dependent manner. TEM images also revealed that P-SWCNTs induced the formation of autophagosome-like vacuoles, the dilatation of the ER, the generation of mitochondrial flocculent densities, and the separation of organelle by disappearance of the cell membrane. Taken together, we suggest that P-SWCNTs cause acute inflammatory response in the lungs of mice, and induce autophagy accompanied with apoptosis through mitochondrial dysfunction and ER stress in RAW264.7 cells. Furthermore, further study is required to elucidate how the physicochemical properties of SWCNTs determine the cell death pathway and an immune response.
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Affiliation(s)
- Eun-Jung Park
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Republic of Korea.
| | - Nur Elida M Zahari
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Republic of Korea
| | - Min-Sung Kang
- Inhalation Toxicology Center, Korea Institute of Toxicology, Jeongeup 580-185, Republic of Korea
| | - Sang jin Lee
- Inhalation Toxicology Center, Korea Institute of Toxicology, Jeongeup 580-185, Republic of Korea
| | - Kyuhong Lee
- Inhalation Toxicology Center, Korea Institute of Toxicology, Jeongeup 580-185, Republic of Korea
| | - Byoung-Seok Lee
- Toxicologic Pathology Center, Korea Institute of Toxicology, Daejeon, Republic of Korea
| | - Cheolho Yoon
- Seoul Center, Korea Basic Science Institute, Seoul 126-16, Republic of Korea
| | - Myung-Haing Cho
- College of Veterinary Medicine, Seoul National University, Seoul 151-742, Republic of Korea
| | - Younghun Kim
- Department of Chemical Engineering, Kwangwoon University, Seoul 139-701, Republic of Korea
| | - Jae-Ho Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Republic of Korea.
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Pan CQ, Sudol M, Sheetz M, Low BC. Modularity and functional plasticity of scaffold proteins as p(l)acemakers in cell signaling. Cell Signal 2012; 24:2143-65. [PMID: 22743133 DOI: 10.1016/j.cellsig.2012.06.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 05/22/2012] [Accepted: 06/16/2012] [Indexed: 01/14/2023]
Abstract
Cells coordinate and integrate various functional modules that control their dynamics, intracellular trafficking, metabolism and gene expression. Such capacity is mediated by specific scaffold proteins that tether multiple components of signaling pathways at plasma membrane, Golgi apparatus, mitochondria, endoplasmic reticulum, nucleus and in more specialized subcellular structures such as focal adhesions, cell-cell junctions, endosomes, vesicles and synapses. Scaffold proteins act as "pacemakers" as well as "placemakers" that regulate the temporal, spatial and kinetic aspects of protein complex assembly by modulating the local concentrations, proximity, subcellular dispositions and biochemical properties of the target proteins through the intricate use of their modular protein domains. These regulatory mechanisms allow them to gate the specificity, integration and crosstalk of different signaling modules. In addition to acting as physical platforms for protein assembly, many professional scaffold proteins can also directly modify the properties of their targets while they themselves can be regulated by post-translational modifications and/or mechanical forces. Furthermore, multiple scaffold proteins can form alliances of higher-order regulatory networks. Here, we highlight the emerging themes of scaffold proteins by analyzing their common and distinctive mechanisms of action and regulation, which underlie their functional plasticity in cell signaling. Understanding these mechanisms in the context of space, time and force should have ramifications for human physiology and for developing new therapeutic approaches to control pathological states and diseases.
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Affiliation(s)
- Catherine Qiurong Pan
- Cell Signaling and Developmental Biology Laboratory, Department of Biological Sciences, National University of Singapore, Republic of Singapore.
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4
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Sato T, Enkhbat A, Yoshioka K. Role of plasma membrane localization of the scaffold protein JSAP1 during differentiation of cerebellar granule cell precursors. Genes Cells 2010; 16:58-68. [PMID: 21156008 DOI: 10.1111/j.1365-2443.2010.01465.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We previously reported that the scaffold protein c-Jun NH₂-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1 (JSAP1) functions in cerebellar granule cell precursors (GCPs) to promote their cell-cycle exit and differentiation. In this study, we used immunocytochemistry to examine the subcellular distribution of JSAP1 in proliferating cultured GCPs. We found that when stimulated with fibroblast growth factor-2 (FGF-2), a factor that promotes GCP differentiation through JNK and extracellular signal-regulated kinase (ERK) signaling, JSAP1 translocated to the plasma membrane and colocalized with activated JNK and ERK. In transfected cells expressing a constitutively activated FGF receptor (FGFR), JSAP1 and the activated FGFR colocalized at the plasma membrane with not only activated but also unphosphorylated and inactive JNK and ERK. These colocalizations did not occur when a mutant JSAP1 lacking the JNK-binding domain was substituted for wild-type JSAP1. Biochemical analyses of transfected cells showed that activated FGFR increased JSAP1's affinity for JNK and ERK and that JSAP1 enhanced FGFR-induced JNK and ERK activation. Collectively, these results suggest that when stimulated by FGFR, JSAP1 translocates to the plasma membrane, where it recruits JNK and ERK and facilitates their activation, leading to the differentiation of cerebellar GCPs.
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Affiliation(s)
- Tokiharu Sato
- Division of Molecular Cell Signaling, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
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5
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Abstract
This paper summarises how scaffold proteins affects and regulate the JNK signalling pathway. We believe that some of these scaffold proteins, by virtue of their anchoring and catalytic properties contribute to a high degree of specificity of intra cellular signalling pathways that regulate the progression through the cell cycle.
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Affiliation(s)
- W Engström
- Department of Zoology, University of Oxford, Oxford, UK.
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Ha HY, Kim JB, Cho IH, Joo HJ, Kim KS, Lee KW, Sunwoo H, Im JY, Lee JK, Hong JH, Han PL. Morphogenetic lung defects of JSAP1-deficient embryos proceeds via the disruptions of the normal expressions of cytoskeletal and chaperone proteins. Proteomics 2008; 8:1071-80. [PMID: 18324732 DOI: 10.1002/pmic.200700815] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Recent studies have shown that JNK/stress-activated protein kinase-associated protein 1 (JSAP1)-deficient mice die from respiratory failure shortly after birth. To understand the underlying mechanism, we investigated the histological appearances and cell type changes in developing jsap1(-/-) lungs between E12.5 and E18.5. At the light microscopic level, no overt abnormality was detected in jsap1(-/-) until E16.5. However, alveoli and airway formations that normally occur after E16.5 were poorly advanced in jsap1(-/-). Despite these morphological defects, surfactant secreting cells labeled by anti-SP-B or anti-SP-C were present in normal ranges in jsap1(-/-) lungs. Smooth muscle alpha-actin expressing cells were also developed in jsap1(-/-) lungs, although actin expression was decreased. The expressions of transcriptional factors, such as, nuclear factor Ib (Nfib), N-myc, and octamer transcriptional factor 1 (Oct-1), which play a critical role in lung morphogenesis, were found to be down-regulated, whereas signal transducer and activator of transcription 3 (Stat3), sonic hedgehog (Shh), and smoothened (Smo) were up-regulated, in jsap1(-/-) lungs at E17.5-E18.5 compared with those in jsap1(+/+) lungs. Proteomics analysis of E17.5 lung identified 39 proteins with altered expressions, which included actin, tropomyosin, myosin light chain, vimentin, heat shock protein (Hsp27), and Hsp84. These results suggest that JSAP1 is required for the normal expressions of cytoskeletal and chaperone proteins in the developing lung, and that impaired expressions of these proteins might cause morphogenetic defects observed in jsap1(-/-) lungs.
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Affiliation(s)
- Hye-Yeong Ha
- Division of Nano Sciences and Brain Disease Research Institute, Ewha Womans University, Seoul, Republic of Korea
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Abstract
Mitogen-activated protein kinases (MAPKs) regulate critical signaling pathways involved in cell proliferation, differentiation and apoptosis. Recent studies have shown that a novel class of scaffold proteins mediates the structural and functional organization of the three-tier MAPK module. By linking the MAP3K, MAP2K and MAPK into a multienzyme complex, these MAPK-specific scaffold proteins provide an insulated physical conduit through which signals from the respective MAPK can be transmitted to the appropriate spatiotemporal cellular loci. Scaffold proteins play a determinant role in modulating the signaling strength of their cognate MAPK module by regulating the signal amplitude and duration. The scaffold proteins themselves are finely regulated resulting in dynamic intra- and inter-molecular interactions that can modulate the signaling outputs of MAPK modules. This review focuses on defining the diverse mechanisms by which these scaffold proteins interact with their respective MAPK modules and the role of such interactions in the spatiotemporal organization as well as context-specific signaling of the different MAPK modules.
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Affiliation(s)
- D N Dhanasekaran
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA
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8
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Chae HJ, Ha HY, Im JY, Song JY, Park S, Han PL. JSAP1 is required for the cell adhesion and spreading of mouse embryonic fibroblasts. Biochem Biophys Res Commun 2006; 345:809-16. [PMID: 16707108 DOI: 10.1016/j.bbrc.2006.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 05/01/2006] [Indexed: 12/18/2022]
Abstract
The roles of JSAP1 and JIP1 in cell adhesion and spreading were examined using mouse embryonic fibroblasts (MEFs) deficient in JIP1 (JIP1-KO), JSAP1 (JSAP1-KO), and in both JIP1 and JSAP1 (double-KO), and by using their wild type. After being plated on fibronectin-coated culture plates, wild type MEFs rapidly adhered and differentiated to typical longitudinal fibroblasts in 4 h. JSAP1-KO MEFs showed a similar sequence of adhesion and cell spreading, but their adhesion was weak, and cell spreading sequence proceeded in a delayed manner compared with the wild type. In spreading JSAP1-KO MEFs, adhesion-triggered actin cytoskeleton reorganization and FAK activation proceeded at a slower pace than in wild type MEFs. The cellular properties of double-KO MEFs and JIP1-KO MEFs were similar to those of JSAP1-KO MEFs and wild type MEFs, respectively. These results suggest that JSAP1 plays a role in adhesion and cell spreading by regulating the rapid reorganization of the actin cytoskeleton.
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Affiliation(s)
- Hee-Jung Chae
- Division of Nano Sciences and Ewha Institute of Neuroscience, Ewha Womans University, Seoul 120-750, Republic of Korea
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9
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Sato T, Hidaka K, Iwanaga A, Ito M, Asano M, Nakabeppu Y, Morisaki T, Yoshioka K. Impairment of cardiomyogenesis in embryonic stem cells lacking scaffold protein JSAP1. Biochem Biophys Res Commun 2005; 338:1152-7. [PMID: 16253209 DOI: 10.1016/j.bbrc.2005.10.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Accepted: 10/12/2005] [Indexed: 10/25/2022]
Abstract
We previously reported that c-Jun NH(2)-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1 (JSAP1), a scaffold protein for JNK signaling, is important in embryonic stem (ES) cells during neurogenesis. In that study, we also observed the altered expression of mesodermal marker genes, which indicated that JSAP1 is involved in the differentiation of mesodermal lineages. Here, we investigated the function of JSAP1 in cardiomyocyte development using JSAP1-null ES cells, and found that cardiomyogenesis was impaired in the JSAP1-null mutant. The JSAP1 deficiency resulted in lower gene expression of the cardiac transcription factor Nkx2.5 and contractile proteins. In contrast, the mutant showed a significantly higher expression of mesoderm-related markers other than those of the cardiomyocyte lineage. Together, these results suggest that JSAP1 may be important for the differentiation of the mesodermal lineages, functioning as a positive factor for cardiomyocyte differentiation, and as an inhibitory factor for differentiation into other lineages.
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Affiliation(s)
- Tokiharu Sato
- Division of Cell Cycle Regulation, Cancer Research Institute, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-0934, Japan
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10
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Takino T, Nakada M, Miyamori H, Watanabe Y, Sato T, Gantulga D, Yoshioka K, Yamada KM, Sato H. JSAP1/JIP3 cooperates with focal adhesion kinase to regulate c-Jun N-terminal kinase and cell migration. J Biol Chem 2005; 280:37772-81. [PMID: 16141199 DOI: 10.1074/jbc.m505241200] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
c-Jun N-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1 (JSAP1) (also termed JNK-interacting protein 3; JIP3) is a member of a family of scaffold factors for the mitogen-activated protein kinase (MAPK) cascades, and it also forms a complex with focal adhesion kinase (FAK). Here we demonstrate that JSAP1 serves as a cooperative scaffold for activation of JNK and regulation of cell migration in response to fibronectin (FN) stimulation. JSAP1 mediated an association between FAK and JNK, which was induced by either co-expression of Src or attachment of cells to FN. Complex formation of FAK with JSAP1 and p130 Crk-associated substrate (p130(Cas)) resulted in augmentation of FAK activity and phosphorylation of both JSAP1 and p130(Cas), which required p130(Cas) hyperphosphorylation and was abolished by inhibition of Src. JNK activation by FN was enhanced by JSAP1, which was suppressed by disrupting the FAK/p130(Cas) pathway by expression of a dominant-negative form of p130(Cas) or by inhibiting Src. We also documented the co-localization of JSAP1 with JNK and phosphorylated FAK at the leading edge and stimulation of cell migration by JSAP1 expression, which depended on its JNK binding domain and was suppressed by inhibition of JNK. The level of JSAP1 mRNA correlated with advanced malignancy in brain tumors, unlike other JIPs. We propose that the JSAP1.FAK complex functions cooperatively as a scaffold for the JNK signaling pathway and regulator of cell migration on FN, and we suggest that JSAP1 is also associated with malignancy in brain tumors.
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Affiliation(s)
- Takahisa Takino
- Department of Molecular Virology, Cancer Research Institute, Division of Neuroscience, Graduate School of Medical Science, Kanazawa University, Japan
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Dong Z, Zhou L, Del Villar K, Ghanevati M, Tashjian V, Miller CA. JIP1 regulates neuronal apoptosis in response to stress. ACTA ACUST UNITED AC 2005; 134:282-93. [PMID: 15836924 DOI: 10.1016/j.molbrainres.2004.10.039] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2004] [Revised: 10/21/2004] [Accepted: 10/27/2004] [Indexed: 12/13/2022]
Abstract
We examined if the relative expression of JNK-interacting protein 1 (JIP1) and phosphorylated c-Jun N-terminal kinase (JNK) regulates cell signaling and contributes to selective neuronal vulnerability in response to environmental stress. In clonal neuroblastoma cultures, stresses such as hypoxia, ischemia, Abeta peptides, and UV irradiation rapidly reduced JIP1 expression. JIP1 mRNA expression was also down-regulated by UV stress and was accompanied by increased JNK and c-Jun activation and cell death. JIP1 protein reduction was partially reversed both by inhibitors predominantly of caspase 3 and of the JNK pathway and resulted in significantly increased cell survival. Conversely, overexpression of JIP1 decreased both nuclear translocation of activated-JNK, and c-Jun phosphorylation induced by either UV irradiation, or the JNK upstream activators, MKK7 or MEKK1. Cell death was reduced about 50% compared to GFP-transfected controls. JIP1 overexpression did not facilitate either JNK expression or activation. In the normal, non-stressed human hippocampus and rat hippocampal organotypic cultures, JIP1 and JNK3 were inversely expressed with more JIP1 in CA2 and CA3 and less in CA1 neurons. In the human hippocampus, transient hypoxia/ischemia selectively spares neurons in CA2 and CA3 and induces death of neurons in the hippocampal CA1 subregion. In the cultures, ischemia reduced JIP1 expression and activated JNK, c-Jun, and caspase 3. Inhibitors of the JNK pathway, JNK activation directly and of caspase 3 activation each partially reversed these effects. Thus, under certain stress conditions, down-regulation of JIP1 expression makes neurons more susceptible to apoptosis, suggesting JIP may serve as an anti-apoptosis factor.
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Affiliation(s)
- Zhaohui Dong
- Department of Pathology, Keck School of Medicine, USC, MCA-341A, 2011 Zonal Avenue, Los Angeles, CA 90033, USA
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Yoshimura SI, Yoshioka K, Barr FA, Lowe M, Nakayama K, Ohkuma S, Nakamura N. Convergence of Cell Cycle Regulation and Growth Factor Signals on GRASP65. J Biol Chem 2005; 280:23048-56. [PMID: 15834132 DOI: 10.1074/jbc.m502442200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Together with other Golgi matrix components, GRASP65 contributes to the stacking of Golgi cisternae in interphase cells. During mitosis, GRASP65 is heavily phosphorylated, and in turn, cisternal stacking is inhibited leading to the breakdown of the Golgi apparatus. Here we show that GRASP65 is phosphorylated on serine 277 in interphase cells, and this is strongly enhanced in response to the addition of serum or epidermal growth factor. This is directly mediated by ERK suggesting that GRASP65 has some role in growth factor signal transduction. Phosphorylation of Ser-277 is also dramatically increased during mitosis, however this is mediated by Cdk1 and not by ERK. The microinjection of recombinant GRASP65 without N-terminal myristoylation or a peptide fragment containing Ser-277 into the cytosol of normal rat kidney cells inhibits passage through mitosis. This effect is abolished when Ser-277 is replaced with alanine suggesting the phosphorylation of Ser-277 plays an important role in cell cycle regulation. The convergence of cell cycle regulation and growth factor signals on GRASP65 Ser-277 suggests that GRASP65 may function as a signal integrator controlling the cell growth.
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Affiliation(s)
- Shin-ichiro Yoshimura
- Division of Life Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Japan
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Pelisch F, Blaustein M, Kornblihtt AR, Srebrow A. Cross-talk between signaling pathways regulates alternative splicing: a novel role for JNK. J Biol Chem 2005; 280:25461-9. [PMID: 15886203 DOI: 10.1074/jbc.m412007200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The regulation of alternative splicing by extracellular signals represents a key event in the control of gene expression. There is increasing evidence showing that many extracellular cues regulate alternative splicing. Nevertheless, the broad picture regarding the role of different signaling pathways and their interaction remains incomplete. Using the fibronectin gene as a model, we show that a laminin-rich basement membrane regulates the alternative splicing of two out of three regions of the transcript (extra domain I and type III connecting segment) in mammary epithelial cells, through a non-stress c-Jun N-terminal kinase (JNK) signaling pathway. We propose that dephosphorylation of the extracellular signal-regulated kinase is involved in this regulatory process. Furthermore, the laminin-rich basement membrane blocks the effect of a mammary mesenchymal cell-conditioned medium, which stimulates the inclusion of extra domain I and type III connecting segment through a phosphatidylinositol3-kinase-dependent cascade, indicating that JNK signaling can inhibit the phosphatidylinositol 3-kinase-mediated splicing regulation. These results implicate JNK in the regulation of alternative splicing and provide new evidence on how extracellular stimuli are converted into changes in splicing patterns, strengthening the view that the control of alternative splicing is as complex and relevant as transcriptional control, together accounting for the spatiotemporal requirements of gene expression.
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Affiliation(s)
- Federico Pelisch
- Biología Molecular y Neurociencias-Consejo Nacional de Investigaciones Científicas y Técnicas, Departamento de Fisiología, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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Ha HY, Cho IH, Lee KW, Lee KW, Song JY, Kim KS, Yu YM, Lee JK, Song JS, Yang SD, Shin HS, Han PL. The axon guidance defect of the telencephalic commissures of the JSAP1-deficient brain was partially rescued by the transgenic expression of JIP1. Dev Biol 2005; 277:184-99. [PMID: 15572149 DOI: 10.1016/j.ydbio.2004.09.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 09/12/2004] [Accepted: 09/13/2004] [Indexed: 11/17/2022]
Abstract
The JNK interacting protein, JSAP1, has been identified as a scaffold protein for mitogen-activated protein kinase (MAPK) signaling pathways and as a linker protein for the cargo transport along the axons. To investigate the physiological function of JSAP1 in vivo, we generated mice lacking JSAP1. The JSAP1 null mutation produced various developmental deficits in the brain, including an axon guidance defect of the corpus callosum, in which phospho-FAK and phospho-JNK were distributed at reduced levels. The axon guidance defect of the corpus callosum in the jsap1-/- brain was correlated with the misplacement of glial sling cells, which reverted to their normal position after the transgenic expression of JNK interacting protein 1(JIP1). The transgenic JIP1 partially rescued the axon guidance defect of the corpus callosum and the anterior commissure of the jsap1-/- brain. The JSAP1 null mutation impaired the normal distribution of the Ca+2 regulating protein, calretinin, but not the synaptic vesicle marker, SNAP-25, along the axons of the thalamocortical tract. These results suggest that JSAP1 is required for the axon guidance of the telencephalic commissures and the distribution of cellular protein(s) along axons in vivo, and that the signaling network organized commonly by JIP1 and JSAP1 regulates the axon guidance in the developing brain.
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Affiliation(s)
- Hye-Yeong Ha
- Department of Neuroscience, Neuroscience Research Center and Medical Research Institute, Ewha Womans University School of Medicine, Seoul 110-783, Korea
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Sato S, Ito M, Ito T, Yoshioka K. Scaffold protein JSAP1 is transported to growth cones of neurites independent of JNK signaling pathways in PC12h cells. Gene 2004; 329:51-60. [PMID: 15033528 DOI: 10.1016/j.gene.2003.12.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Revised: 12/05/2003] [Accepted: 12/30/2003] [Indexed: 11/27/2022]
Abstract
The c-Jun NH(2)-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1 [JSAP1; also known as JNK-interacting protein 3 (JIP3)] has been identified as a scaffold protein for JNK mitogen-activated protein kinase signal transduction pathways and as a cargo adapter in the conventional kinesin-mediated transport system. Furthermore, a functional relationship between UNC-16, the C. elegans ortholog of JSAP1, and JNK signaling has been established genetically. In this study, we first demonstrated that the kinesin light chain is required for the targeting and localization of JSAP1 to the tips of neurites in PC12h cells. Furthermore, to understand whether JNK signaling is involved in kinesin-mediated JSAP1 trafficking, we established stable PC12h cell lines that expressed wild-type JSAP1 or its mutant lacking the JNK-binding domain (JBD). Immunocytochemical studies of the cell lines indicated that the mutant JSAP1 was localized to the growth cones of differentiating PC12h cells in a similar manner to wild-type JSAP1. Taken together, these results suggest that the proper subcellular localization of JSAP1 along microtubules probably does not require JNK signaling.
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Affiliation(s)
- Shinji Sato
- Department of Biosciences, School of Science, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
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Takino T, Miyamori H, Watanabe Y, Yoshioka K, Seiki M, Sato H. Membrane Type 1 Matrix Metalloproteinase Regulates Collagen-Dependent Mitogen-Activated Protein/Extracellular Signal-Related Kinase Activation and Cell Migration. Cancer Res 2004; 64:1044-9. [PMID: 14871836 DOI: 10.1158/0008-5472.can-03-1843] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mitogen-activated protein kinase-extracellular signal-related kinase (ERK) kinase 1 (MEK1)/ERK signaling has been implicated in the regulation of tumor cell invasion and metastasis. Migration of HT1080 cells on type I collagen was suppressed by the matrix metalloproteinase (MMP) inhibitors BB94 and tissue inhibitor of metalloproteinase (TIMP)-2 but not by TIMP-1. TIMP-2-specific inhibition suggests that membrane type 1 MMP (MT1-MMP) is likely involved in this process. Activation of ERK was induced in HT1080 cells adhered on dishes coated with type I collagen, and this was inhibited by BB94. MMP-2 processing in HT1080 cells, which also was stimulated by cultivation on type I collagen, was inhibited by MEK inhibitor PD98059. Expression of a constitutively active form of MEK1 promoted MMP-2 processing concomitant with the increase of MT1-MMP levels, suggesting that MT1-MMP is regulated by MEK/ERK signaling. In addition, expression of the hemopexin-like domain of MT1-MMP in HT1080 cells interfered with MMP-2 processing, ERK activation, and cell migration, implying that the enzymatic activity of MT1-MMP is involved in collagen-induced ERK activation, which results in enhanced cell migration. Thus, adhesion of HT1080 cells to type I collagen induces MT1-MMP-dependent ERK activation, which in turn causes an increase in MT1-MMP levels and subsequent cell migration.
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Affiliation(s)
- Takahisa Takino
- Department of Molecular Virology and Oncology and Cell Cycle Regulation, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
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17
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Xu P, Yoshioka K, Yoshimura D, Tominaga Y, Nishioka T, Ito M, Nakabeppu Y. In vitro development of mouse embryonic stem cells lacking JNK/stress-activated protein kinase-associated protein 1 (JSAP1) scaffold protein revealed its requirement during early embryonic neurogenesis. J Biol Chem 2003; 278:48422-33. [PMID: 12968026 DOI: 10.1074/jbc.m307888200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Jsap1 gene encodes a scaffold protein for c-Jun N-terminal kinase cascades. We established c-Jun N-terminal kinase (JNK)/stress-activated protein kinase-associated protein 1 (JSAP1)-null mouse embryonic stem cell lines by homologous recombination. The JSAP1-null embryonic stem cells were viable, however, exhibited hyperplasia of the ectoderm during embryoid body formation, and spontaneously differentiated into neurons more efficiently than did wild type. The expression of components of c-Jun N-terminal kinase cascades and a subset of marker mRNAs during early embryogenesis was altered in the JSAP1-null mutants. Retinoic acid dramatically increased the expression of JSAP1 and JNK3, which were co-precipitated with anti-JNK3 in the neuroectoderm of wild type but not JSAP1-null embryoid bodies. In the neurons differentiated from the wild type embryoid bodies, JSAP1 was localized in the soma, neurites, and growth cone-like structure of the neurites, and neurite outgrowth from the JSAP1-null embryoid bodies was apparently less efficient than from wild type. JSAP1 and c-Jun N-terminal kinase 3 were coexpressed in the embryonic ectoderm of E7.5 mouse embryo, whereas Wnt1 and Pax2 were coexpressed with JSAP1 at the midbrain-hindbrain junction in E12.5 mouse embryo, thus suggesting that JSAP1 is required for early embryonic neurogenesis.
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Affiliation(s)
- Ping Xu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University and CREST, Japan Science and Technology Corp., Fukuoka 812-8582, Japan
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18
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Yang J, Yu Y, Duerksen-Hughes PJ. Protein kinases and their involvement in the cellular responses to genotoxic stress. Mutat Res 2003; 543:31-58. [PMID: 12510016 DOI: 10.1016/s1383-5742(02)00069-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cells are constantly subjected to genotoxic stress, and much has been learned regarding their response to this type of stress during the past year. In general, the cellular genotoxic response can be thought to occur in three stages: (1) damage sensing; (2) activation of signal transduction pathways; (3) biological consequences and attenuation of the response. The biological consequences, in particular, include cell cycle arrest and cell death. Although our understanding of the molecular mechanisms underlying cellular genotoxic stress responses remains incomplete, many cellular components have been identified over the years, including a group of protein kinases that appears to play a major role. Various DNA-damaging agents can activate these protein kinases, triggering a protein phosphorylation cascade that leads to the activation of transcription factors, and altering gene expression. In this review, the involvement of protein kinases, particularly the mitogen-activated protein kinases (MAPKs), at different stages of the genotoxic response is discussed.
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Affiliation(s)
- Jun Yang
- Department of Pathophysiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310031, China
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19
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Matsuura H, Nishitoh H, Takeda K, Matsuzawa A, Amagasa T, Ito M, Yoshioka K, Ichijo H. Phosphorylation-dependent scaffolding role of JSAP1/JIP3 in the ASK1-JNK signaling pathway. A new mode of regulation of the MAP kinase cascade. J Biol Chem 2002; 277:40703-9. [PMID: 12189133 DOI: 10.1074/jbc.m202004200] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
JSAP1 (also termed JIP3) is a scaffold protein that interacts with specific components of the JNK signaling pathway. Apoptosis signal-regulating kinase (ASK) 1 is a MAP kinase kinase kinase that activates the JNK and p38 mitogen-activated protein (MAP) kinase cascades in response to environmental stresses such as reactive oxygen species. Here we show that JSAP1 bound ASK1 and enhanced ASK1- and H(2)O(2)-induced JNK activity. ASK1 phosphorylated JSAP1 in vitro and in vivo, and the phosphorylation facilitated interactions of JSAP1 with SEK1/MKK4, MKK7 and JNK3. Furthermore, ASK1-dependent phosphorylation was required for JSAP1 to recruit and thereby activate JNK in response to H(2)O(2). We thus conclude that JSAP1 functions not only as a simple scaffold, but it dynamically participates in signal transduction by forming a phosphorylation-dependent signaling complex in the ASK1-JNK signaling module.
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Affiliation(s)
- Hiroshi Matsuura
- Laboratory of Cell Signaling, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8549, Japan
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20
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Takino T, Yoshioka K, Miyamori H, Yamada KM, Sato H. A scaffold protein in the c-Jun N-terminal kinase signaling pathway is associated with focal adhesion kinase and tyrosine-phosphorylated. Oncogene 2002; 21:6488-97. [PMID: 12226752 DOI: 10.1038/sj.onc.1205840] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2002] [Revised: 06/12/2002] [Accepted: 06/23/2002] [Indexed: 12/25/2022]
Abstract
Focal adhesion kinase (FAK) becomes activated and tyrosine-phosphorylated in response to cell adhesion to extracellular matrix proteins in a variety of cell types, and associates with a number of signaling molecules, structural proteins, and beta integrin cytoplasmic domains. Here we demonstrated that c-Jun N-terminal kinase (JNK)/stress activated protein kinase-associated protein 1 (JSAP1), a scaffold factor in the mitogen-activated protein kinase (MAPK) cascades, forms a complex with the N-terminus of FAK. The complex formation was further stimulated by c-Src, in which JSAP1 was tyrosine-phosphorylated and other FAK/Src signaling molecules were recruited. Fibronectin (FN) stimulation of cells expressing JSAP1 induced its tyrosine phosphorylation concomitant with association with FAK. Expression of JSAP1 in Hela cells facilitated formation of well-organized focal contacts and actin stress fibers, and promoted cell spreading onto FN. Taken together, these results suggest that JSAP1 is involved an integrin-mediated signaling pathway through FAK/Src by recruiting other signaling molecules, resulting in promotion of cell spreading onto FN.
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Affiliation(s)
- Takahisa Takino
- Division of Molecular Virology and Oncology, Cancer Research Institute, Kanazawa University, 13-1 Takara-machi, Kanazawa 920-0934, Japan.
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21
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Abstract
In this review we describe an emerging understanding of the roles of the Extracellular-signal regulated kinase/mitogen-activated protein kinase (ERK/MAPK) cascade in learning and memory. We begin by describing several behavioral memory paradigms and review data implicating ERK as an essential component of the signal transduction mechanisms subserving these processes. We then describe evidence implicating ERK as a critical player in synaptic and neuronal plasticity-a cellular role likely to underlie ERK's behavioral role in the animal. We then proceed to parsing the complexities of biochemical regulation of ERK in neurons and to a description of a few likely cellular targets of ERK. This is in order to begin discussing the possible molecular basis of ERK-mediated behavioral change. We close our review with speculations concerning how the complexities and idiosyncrasies of ERK regulation may allow for sophisticated information processing at the biochemical level in neurons-attributes that may make the ERK cascade well-suited for triggering complex and long-lasting behavioral change. Our goal in this review is not so much to portray ERK as unique regarding its role as a signal transducter in memory, but rather to use ERK as one specific example of recent studies beginning to address the molecules and signal transduction pathways subserving cognition.
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Affiliation(s)
- J Paige Adams
- Division of Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA.
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22
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Sudlow A. Suppression of ERK cascade by scaffold protein JSAP1. Arthritis Res Ther 2001. [DOI: 10.1186/ar-2001-68053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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Villalonga P, López-Alcalá C, Bosch M, Chiloeches A, Rocamora N, Gil J, Marais R, Marshall CJ, Bachs O, Agell N. Calmodulin binds to K-Ras, but not to H- or N-Ras, and modulates its downstream signaling. Mol Cell Biol 2001; 21:7345-54. [PMID: 11585916 PMCID: PMC99908 DOI: 10.1128/mcb.21.21.7345-7354.2001] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Activation of Ras induces a variety of cellular responses depending on the specific effector activated and the intensity and amplitude of this activation. We have previously shown that calmodulin is an essential molecule in the down-regulation of the Ras/Raf/MEK/extracellularly regulated kinase (ERK) pathway in cultured fibroblasts and that this is due at least in part to an inhibitory effect of calmodulin on Ras activation. Here we show that inhibition of calmodulin synergizes with diverse stimuli (epidermal growth factor, platelet-derived growth factor, bombesin, or fetal bovine serum) to induce ERK activation. Moreover, even in the absence of any added stimuli, activation of Ras by calmodulin inhibition was observed. To identify the calmodulin-binding protein involved in this process, calmodulin affinity chromatography was performed. We show that Ras and Raf from cellular lysates were able to bind to calmodulin. Furthermore, Ras binding to calmodulin was favored in lysates with large amounts of GTP-bound Ras, and it was Raf independent. Interestingly, only one of the Ras isoforms, K-RasB, was able to bind to calmodulin. Furthermore, calmodulin inhibition preferentially activated K-Ras. Interaction between calmodulin and K-RasB is direct and is inhibited by the calmodulin kinase II calmodulin-binding domain. Thus, GTP-bound K-RasB is a calmodulin-binding protein, and we suggest that this binding may be a key element in the modulation of Ras signaling.
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Affiliation(s)
- P Villalonga
- Departament de Biologia Cellular i Anatomia Patològica, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Facultat de Medicina, Universitat de Barcelona, 08036 Barcelona, Spain
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24
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Denis GV. Bromodomain motifs and "scaffolding"? FRONTIERS IN BIOSCIENCE : A JOURNAL AND VIRTUAL LIBRARY 2001; 6:D1065-8. [PMID: 11532602 PMCID: PMC3042883 DOI: 10.2741/a668] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bromodomain-containing multiprotein complexes share some of the properties of signal transduction scaffolds. Insights from MAP kinase signaling scaffolds, for example, may provide useful perspectives for future studies of bromodomain proteins. The regulatory processes of modification (phosphorylation, acetylation, ubiquitination), turnover, nuclear compartmentalization, feedback regulation and signaling pathway specificity are all likely to contribute to the mechanisms by which bromodomain-containing multiprotein complexes control transcription.
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Affiliation(s)
- G V Denis
- Cancer Research Center, Boston University School of Medicine, Room L910, 80 East Concord Street, Boston, MA, USA 02118, USA.
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25
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Rustgi AK. Paclitaxel induces prolonged activation of the Ras/MEK/ERK pathway independently of activating the programmed cell death machinery. J Biol Chem 2001; 276:19555-64. [PMID: 11278851 DOI: 10.1074/jbc.m011164200] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Paclitaxel is a widely used chemotherapeutic agent and is known to induce programmed cell death (apoptosis) in a variety of cell types, but the precise underlying mechanisms are poorly understood. To elucidate these mechanisms, we challenged human esophageal squamous cancer cell lines with paclitaxel and investigated its effects upon signal transduction pathways. Physiologically relevant concentrations of paclitaxel (1-1,000 nm) induced apoptosis. All three mitogen-activated protein kinase (MAPK) family members, c-Jun N-terminal kinase (JNK), p38 MAPK, and extracellular signal-regulated kinase (ERK) were activated upon paclitaxel treatment. Interestingly, JNK activation and p38 MAPK activation were delayed and peaked at 48 h, whereas ERK activity was sustained over 72 h. In addition, Ras activation and MAPK/ERK kinase (MEK) phosphorylation were observed in concordance with ERK activation. While ERK activation was completely ablated by MEK inhibitors, immunoprecipitation and Western blot analysis revealed that neither MEK-1 nor MEK-2 was involved, but instead another member of the MEK family may potentially participate. Although pretreatment with a general caspase inhibitor, benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone rescued the cell death, it did not prevent Ras or ERK activation. Furthermore, inhibition of JNK, p38 MAPK, or MEK did not alter PARP cleavage and the cell death induced by paclitaxel. These results in aggregate suggest that the delayed activation of JNK, p38 MAPK, and ERK was not linked to activation of the cell death machinery.
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26
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Herdegen T, Waetzig V. AP-1 proteins in the adult brain: facts and fiction about effectors of neuroprotection and neurodegeneration. Oncogene 2001; 20:2424-37. [PMID: 11402338 DOI: 10.1038/sj.onc.1204387] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Jun and Fos proteins are induced and activated following most physiological and pathophysiological stimuli in the brain. Only few data allow conclusions about distinct functions of AP-1 proteins in neurodegeneration and neuroregeneration, and these functions mainly refer to c-Jun and its activation by JNKs. Apoptotic functions of activated c-Jun affect hippocampal, nigral and primary cultured neurons following excitotoxic stimulation and destruction of the neuron-target-axis including withdrawal of trophic molecules. The inhibition of JNKs might exert neuroprotection by subsequent omission of c-Jun activation. Besides endogenous neuronal functions, the c-Jun/AP-1 proteins can damage the nervous system by upregulation of harmful programs in non-neuronal cells (e.g. microglia) with release of neurodegenerative molecules. In contrast, the differentiation with neurite extension and maturation of neural cells in vitro indicate physiological and potentially neuroprotective functions of c-Jun and JNKs including sensoring for alterations in the cytoskeleton. This review summarizes the multiple molecular interfunctions which are involved in the shift from the physiological role to degenerative effects of the Jun/JNK-axis such as cell type-specific expression and intracellular localization of scaffold proteins and upstream activators, antagonistic phosphatases, interaction with other kinase systems, or the activation of transcription factors competing for binding to JNK proteins and AP-1 DNA elements.
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Affiliation(s)
- T Herdegen
- Institute of Pharmacology, Hospitalstrasse 4, 24105 Kiel, Germany
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