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ETS domain transcription factor superfamily is highly conserved throughout metazoa and is involved in many aspects of development and tissue morphogenesis, and as such, the deregulation of ETS proteins is quite common in many diseases, including cancer. The PEA3 subfamily in particular has been extensively studied with respect to tumorigenesis and metastasis; however, they are also involved in the development of many tissues with branching morphogenesis, such as lung or kidney development. In this review, we aim to summarize findings from various studies on the role of Pea3 subfamily members in nervous system development in the embryo, as well as their functions in the adult neurons. We further discuss the different signals that were shown to regulate the function of the Pea3 family and indicate how this signal-dependent regulation of Pea3 proteins can generate neuronal circuit specificity through unique gene regulation. Finally, we discuss how these developmental roles of Pea3 proteins relate to their role in tumorigenesis.
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Elk-1 is a member of the ETS domain transcription factor superfamily that is phosphorylated upon mitogen-activated protein kinase (MAPK) pathway activation, which in turn regulated its interaction with partner protein serum response factor (SRF), leading to formation of a ternary complex with DNA. It has previously been reported that Elk-1 interacts with a mitotic kinase Aurora-A, although the mechanisms or the relevance of this interaction was unclear. Elk-1 was also reported to be phosphorylated by CDK5 on Thr417 residue. In this study, we show for the first time that this transcription factor interacts not only with Aurora-A but also with other mitotic kinases Aurora-B, Plk1, and Cdk1, and we define the interaction domain on Elk-1 to the first N-terminal 205 amino acids. We also describe putative phosphorylation sites of these mitotic kinases on Elk-1 and show that Elk-1 peptides containing these residues get phosphorylated by the mitotic kinases in in vitro kinase assays. We also perform bioinformatic analysis of mitotic phosphoproteomes and determine potential interaction partners for Elk-1 in Plk or Aurora phosphoproteomes. We propose that understanding the dynamic phosphorylation of Elk-1 by mitotic kinases is important and that it can present a novel target for anticancer strategies.
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Multiple sclerosis (MS) is a demyelinating disorder that affects multiple regions of the central nervous system such as the brain, spinal cord, and optic nerves. Susceptibility to MS, as well as disease progression rates, displays marked patient-to-patient variability. To date, biomarkers that forecast differences in clinical phenotypes and outcomes have been limited. In this context, cell-type-specific interactome analyses offer important prospects and hope for novel diagnostics and therapeutics. We report here an original study using bioinformatic analysis of MS data sets that revealed interaction profiles as well as specific hub proteins in white matter (WM) and gray matter (GM) that appear critical for disease mechanisms. First, cell-type-specific interactome analyses suggested that while interactions within the WM were focused on oligodendrocytes, interactions within the GM were mostly neuron centric. Second, hub proteins such as APP, EGLN3, PTEN, and LRRK2 were identified to be differentially regulated in MS data sets. Lastly, a comparison of the brain and peripheral blood samples identified biomarker candidates such as NRGN, CRTC1, CDC42, and IFITM3 to be differentially expressed in different types of MS. These findings offer a unique cell-type-specific cell-to-cell interaction network in MS and identify potential biomarkers by comparative analysis of the brain and the blood transcriptomics. From a study design and methodology perspective, we suggest that the cell-type-specific interactome analysis is an important systems science frontier that might offer new insights on other neurodegenerative and brain disorders as well.
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Esclerosis Múltiple , Sustancia Blanca , Biomarcadores/metabolismo , Encéfalo/metabolismo , Sustancia Gris/metabolismo , Humanos , Imagen por Resonancia Magnética , Proteínas de la Membrana/metabolismo , Esclerosis Múltiple/genética , Esclerosis Múltiple/metabolismo , Proteínas de Unión al ARN/metabolismo , Sustancia Blanca/metabolismoRESUMEN
The ETS domain family of transcription factors is involved in a number of biological processes, and is commonly misregulated in various forms of cancer. Using microarray datasets from patients with different grades of glioma, we have analyzed the expression profiles of various ETS genes, and have identified ETV1, ELK3, ETV4, ELF4, and ETV6 as novel biomarkers for the identification of different glioma grades. We have further analyzed the gene regulatory networks of ETS transcription factors and compared them to previous microarray studies, where Elk-1-VP16 or PEA3-VP16 were overexpressed in neuroblastoma cell lines, and we identify unique and common regulatory networks for these ETS proteins.
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Elk-1, a member of the ternary complex factors (TCFs) within the ETS (E26 transformation-specific) domain superfamily, is a transcription factor implicated in neuroprotection, neurodegeneration, and brain tumor proliferation. Except for known targets, c-fos and egr-1, few targets of Elk-1 have been identified. Interestingly, SMN, SOD1, and PSEN1 promoters were shown to be regulated by Elk-1. On the other hand, Elk-1 was shown to regulate the CD133 gene, which is highly expressed in brain-tumor-initiating cells (BTICs) and used as a marker for separating this cancer stem cell population. In this study, we have carried out microarray analysis in SH-SY5Y cells overexpressing Elk-1-VP16, which has revealed a large number of genes significantly regulated by Elk-1 that function in nervous system development, embryonic development, pluripotency, apoptosis, survival, and proliferation. Among these, we have shown that genes related to pluripotency, such as Sox2, Nanog, and Oct4, were indeed regulated by Elk-1, and in the context of brain tumors, we further showed that Elk-1 overexpression in CD133+ BTIC population results in the upregulation of these genes. When Elk-1 expression is silenced, the expression of these stemness genes is decreased. We propose that Elk-1 is a transcription factor upstream of these genes, regulating the self-renewal of CD133+ BTICs.
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PEA3 transcription factor subfamily is present in a variety of tissues with branching morphogenesis, and play a particularly significant role in neural circuit formation and specificity. Many target genes in axon guidance and cell-cell adhesion pathways have been identified for Pea3 transcription factor (but not for Erm or Er81); however it was not so far clear whether all Pea3 subfamily members regulate same target genes, or whether there are unique targets for each subfamily member that help explain the exclusivity and specificity of these proteins in neuronal circuit formation. In this study, using transcriptomics and qPCR analyses in SH-SY5Y neuroblastoma cells, hypothalamic and hippocampal cell line, we have identified cell type-specific and subfamily member-specific targets for PEA3 transcription factor subfamily. While Pea3 upregulates transcription of Sema3D and represses Sema5B, for example, Erm and Er81 upregulate Sema5A and Er81 regulates Unc5C and Sema4G while repressing EFNB3 in SH-SY5Y neuroblastoma cells. We furthermore present a molecular model of how unique sites within the ETS domain of each family member can help recognize specific target motifs. Such cell-context and member-specific combinatorial expression profiles help identify cell-cell and cell-extracellular matrix communication networks and how they establish specific connections.
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Proteínas de Unión al ADN/metabolismo , Regulación del Desarrollo de la Expresión Génica , Proyección Neuronal/genética , Proteínas Proto-Oncogénicas c-ets/metabolismo , Factores de Transcripción/metabolismo , Axones , Línea Celular Tumoral , Movimiento Celular/genética , Efrina-B3/genética , Matriz Extracelular/genética , Matriz Extracelular/metabolismo , Perfilación de la Expresión Génica , Hipocampo/citología , Humanos , Hipotálamo/citología , Simulación de Dinámica Molecular , Proteínas del Tejido Nervioso/genética , Neuronas/citología , Neuronas/metabolismo , Análisis de Secuencia por Matrices de Oligonucleótidos , Dominios Proteicos , Reacción en Cadena en Tiempo Real de la Polimerasa , Semaforinas/genética , Activación TranscripcionalRESUMEN
Pea3 proteins belong to a subfamily of the E-twentysix (ETS) domain superfamily of transcription factors, which play various roles during development. Polyoma Enhancer-Activator 3 (Pea3) proteins Pea3, ERM and Er81 are particularly involved in tissues with branching morphogenesis, including kidney, lung, mammary gland and nervous system development. A recent transcriptomic study on novel targets of Pea3 transcription factor revealed various axon guidance and nervous system development related targets, supporting a role of Pea3 proteins in motor neuron connectivity, as well as novel targets in signaling pathways involved in synaptic plasticity. This study focuses on the expression of Pea3 family members in hippocampal neurons, and regulation of putative Pea3 targets in Pea3-overexpressing cell lines and following induction of long-term potentiation or seizure in vivo. We show that Pea3 proteins are expressed in hippocampus in both neuronal and non-neuronal cells, and that Pea3 represses Elk-1 but activates Prkca and Nrcam expression in hippocampal cell lines. We also show that mRNA and protein levels of Pea3 family members are differentially regulated in the dentate gyrus and CA1 region upon MECS stimulation, but not upon LTP induction.
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Proteínas de Unión al ADN/metabolismo , Hipocampo/metabolismo , Potenciación a Largo Plazo/fisiología , Neuronas/metabolismo , Transactivadores/metabolismo , Factores de Transcripción/metabolismo , Animales , Línea Celular , Proteínas de Unión al ADN/genética , Potenciales Postsinápticos Excitadores/fisiología , Masculino , Ratas , Ratas Sprague-Dawley , Transactivadores/genética , Factores de Transcripción/genética , TranscriptomaRESUMEN
Postgenomics drug development is undergoing major transformation in the age of multi-omics studies and drug repositioning. Rather than applications solely in personalized medicine, omics science thus additionally offers a better understanding of a broader range of drug targets and drug repositioning. Berberine is an isoquinoline alkaloid found in many medicinal plants. We report here a whole genome microarray study in tandem with proteomics techniques for mining the plethora of targets that are putatively involved in the antimicrobial activity of berberine against Escherichia coli. We found DNA replication/repair and transcription to be triggered by berberine, indicating that nucleic acids, in general, are among its targets. Our combined transcriptomics and proteomics multi-omics findings underscore that, in the presence of berberine, cell wall or cell membrane transport and motility-related functions are also specifically regulated. We further report a general decline in metabolism, as seen by repression of genes in carbohydrate and amino acid metabolism, energy production, and conversion. An involvement of multidrug efflux pumps, as well as reduced membrane permeability for developing resistance against berberine in E. coli was noted. Collectively, these findings offer original and significant leads for omics-guided drug discovery and future repositioning approaches in the postgenomics era, using berberine as a multi-omics case study.
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Antibacterianos/farmacología , Berberina/farmacología , Escherichia coli/efectos de los fármacos , Regulación Bacteriana de la Expresión Génica , Genoma Bacteriano , Transcriptoma/efectos de los fármacos , Transporte Biológico/efectos de los fármacos , Permeabilidad de la Membrana Celular , Reparación del ADN/efectos de los fármacos , Replicación del ADN/efectos de los fármacos , Minería de Datos , Farmacorresistencia Bacteriana/efectos de los fármacos , Farmacorresistencia Bacteriana/genética , Metabolismo Energético/efectos de los fármacos , Escherichia coli/genética , Escherichia coli/metabolismo , Genes MDRRESUMEN
The phenotypes of biological systems are to some extent robust to genotypic changes. Such robustness exists on multiple levels of biological organization. We analyzed this robustness for two categories of amino acids in proteins. Specifically, we studied the codons of amino acids that bind or do not bind small molecular ligands. We asked to what extent codon changes caused by mutation or mistranslation may affect physicochemical amino acid properties or protein folding. We found that the codons of ligand-binding amino acids are on average more robust than those of non-binding amino acids. Because mistranslation is usually more frequent than mutation, we speculate that selection for error mitigation at the translational level stands behind this phenomenon. Our observations suggest that natural selection can affect the robustness of very small units of biological organization.
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Aminoácidos/química , Codón/química , Mutación , Proteínas/genética , Selección Genética , Aminoácidos/genética , Sitios de Unión , Genotipo , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Ligandos , Fenotipo , Biosíntesis de Proteínas , Pliegue de ProteínaRESUMEN
Elk-1 is a member of the E-twenty-six (ETS) domain superfamily of transcription factors and has been traditionally associated with mitogen-induced immediate early gene transcription upon phosphorylation by mitogen activated protein kinases (ERK/MAPK). Elk-1 is not only upregulated but also phosphorylated in brain tumour cells. However, in this study, we show for the first time that S383-phosphorylated Elk-1 (P-S383-Elk-1) is associated with mitotic spindle poles from metaphase through telophase and relocates to the spindle midbody during cytokinesis, while Thr417Ala mutation is associated with DNA throughout mitosis. Serine 383 phosphorylation appears to be important for polar localization of Elk-1, since exogenous protein including serine-to-alanine mutation was seen to be distributed throughout the spindle fibres. We further show that Elk-1 interacts with the cell cycle kinase Aurora-A, and when Aurora inhibitors are used, P-S383-Elk-1 fails to localize to the poles and remains associated with DNA. Apart from one transcriptional repressor molecule, Kaiso, this is the first time a transactivator was shown to possess such mitotic localization and interaction. The functional significance and detailed mechanism of this cell cycle-related localization of Elk-1 are yet to be determined.
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Aurora Quinasa A/metabolismo , Serina/genética , Polos del Huso/metabolismo , Proteína Elk-1 con Dominio ets/metabolismo , Aurora Quinasa A/antagonistas & inhibidores , Línea Celular Tumoral , Citocinesis , Humanos , Mitosis , Mutación , Fosforilación , Proteína Elk-1 con Dominio ets/genéticaRESUMEN
Epidermal growth factor (EGF) and its receptor (EGFR) have been shown to play a significant role in the pathogenesis of glioblastoma. In our study, the EGFR was stimulated with EGF in human U138 glioblastoma cells. We show that the activated mitogen-activated protein kinase (MAPK)/extracellular-signal-regulated kinases (ERK) 1/2 pathway phosphorylated the E twenty-six (ETS)-like transcription factor 1 (Elk-1) mainly at serine 383 residue. Mitogen-activated protein kinase kinase (MEK) 1/2 inhibitor, UO126 and ERK inhibitor II, FR180204 blocked the Elk-1 phosphorylation and activation. The phosphatidylinositide-3-OH kinase (PI3K)/Akt pathway was also involved in the Elk-1 activation. Activation of the Elk-1 led to an increased survival and a proliferative response with the EGF stimulation in the U138 glioblastoma cells. Knocking-down the Elk-1 using an RNA interference technique caused a decrease in survival of the unstimulated U138 glioblastoma cells and also decreased the proliferative response to the EGF stimulation. The Elk-1 transcription factor was important for the survival and proliferation of U138 glioblastoma cells upon the stimulation of EGFR with EGF. The MAPK/ERK1/2 and PI3K/Akt pathways regulated this response via activation of the Elk-1 transcription factor. The Elk-1 may be one of the convergence points for pathways located downstream of EGFR in glioblastoma cells. Utilization of the Elk-1 as a therapeutic target may lead to a novel strategy in treatment of glioblastoma.
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Factor de Crecimiento Epidérmico/farmacología , Quinasas MAP Reguladas por Señal Extracelular/metabolismo , Glioblastoma/metabolismo , Fosfatidilinositol 3-Quinasas/metabolismo , Proteínas Proto-Oncogénicas c-akt/metabolismo , Proteína Elk-1 con Dominio ets/metabolismo , Línea Celular Tumoral , Glioblastoma/enzimología , Glioblastoma/genética , Humanos , Sistema de Señalización de MAP Quinasas/efectos de los fármacos , Sistema de Señalización de MAP Quinasas/fisiología , Proteína Quinasa 1 Activada por Mitógenos/metabolismo , Proteína Quinasa 3 Activada por Mitógenos/metabolismo , Transducción de Señal/efectos de los fármacos , Transducción de Señal/fisiología , Factores de Transcripción/metabolismo , Activación TranscripcionalRESUMEN
Elk-1 belongs to the Ternary Complex Factor (TCF) subfamily of the ETS (from E26 viral oncogene) domain superfamily of transcription factors, and has been known as a regulator of mitogen-induced immediate early gene transcription upon Mitogen Activated Protein Kinase (MAPK) activation. Elk-1 has been previously shown to interact with neuronal microtubules, and here we show that P-S383-Elk-1, in addition to co-localizing with motor proteins kinesin, Eg5 and Mitotik Kinesin-Like Protein (MKLP) at the mitotic spindles, it physically interacts with dynein in a serum induction-dependent but Ser383 phosphorylation-independent manner.
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Dineínas/metabolismo , Fosfoserina/metabolismo , Suero/metabolismo , Proteína Elk-1 con Dominio ets/metabolismo , Animales , Línea Celular Tumoral , ADN/metabolismo , Humanos , Fosforilación , Unión Proteica , Transporte de Proteínas , Ratas , Tubulina (Proteína)/metabolismoRESUMEN
Elk-1 belongs to the ternary complex factors (TCFs) subfamily of the ETS domain proteins, and plays a critical role in the expression of immediate-early genes (IEGs) upon mitogen stimulation and activation of the mitogen-activated protein kinase (MAPK) cascade. The association of TCFs with serum response elements (SREs) on IEG promoters has been widely studied and a role for Elk-1 in promoting cell cycle entry has been determined. However, the presence of the ETS domain transcription factor Elk-1 in axons and dendrites of post-mitotic adult brain neurons has implications for an alternative function for Elk-1 in neurons other than controlling proliferation. In this study, possible alternative roles for Elk-1 in neurons were investigated, and it was demonstrated that blocking TCF-mediated transactivation in neuronal cells leads to apoptosis through a caspase-dependent mechanism. Indeed RNAi-mediated depletion of endogenous Elk-1 results in increased caspase activity. Conversely, overexpression of either Elk-1 or Elk-VP16 fusion proteins was shown to rescue PC12 cells from chemically-induced apoptosis, and that higher levels of endogenous Elk-1 correlated with longer survival of DRGs in culture. It was shown that Elk-1 regulated the Mcl-1 gene expression required for survival, and that RNAi-mediated degradation of endogenous Elk-1 resulted in elimination of the mcl-1 message. We have further identified the survival-of-motor neuron-1 (SMN1) gene as a novel target of Elk-1, and show that the ets motifs in the SMN1 promoter are involved in this regulation.
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Neuronas/fisiología , Proteína 1 para la Supervivencia de la Neurona Motora/genética , Proteína Elk-1 con Dominio ets/fisiología , Animales , Apoptosis , Caspasas/fisiología , Supervivencia Celular , Proteína 1 de la Secuencia de Leucemia de Células Mieloides , Neuronas/citología , Células PC12 , Regiones Promotoras Genéticas , Proteínas Proto-Oncogénicas c-bcl-2/genética , RatasRESUMEN
Since the identification of the Standard Coding Table as a "universal" method to translate genetic information into amino acids, exceptions to this rule have been reported, and to date there are nearly 20 alternative genetic coding tables deployed by either nuclear genomes or organelles of organisms. Why are these codes still in use and why are new codon reassignments occurring? This present study aims to provide a new method to address these questions and to analyze whether these alternative codes present any advantages or disadvantages to the organisms or organelles in terms of robustness to error. We show that two of the alternative coding tables, The Ciliate, Dasycladacean and Hexamita Nuclear Code (CDH) and The Flatworm Mitochondrial Code (FMC), exhibit an advantage, while others such as The Yeast Mitochondrial Code (YMC) are at a significant disadvantage. We propose that the Standard Code is likely to have emerged as a "local minimum" and that the "coding landscape" is still being searched for a "global" minimum.
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Código Genético , Secuencia de Aminoácidos , Animales , Codón/genética , Código Genético/genética , Humanos , Datos de Secuencia MolecularRESUMEN
Neurogenesis in the embryo involves many signaling pathways and transcriptional programs and an elaborate orchestration of cell cycle exit in differentiating precursors. However, while the neurons differentiate into a plethora of different subtypes and different identities, they also presume a highly polar structure with a particular morphology of the cytoskeleton, thereby making it almost impossible for any differentiated cell to re-enter the cell cycle. It has been observed that dysregulated or forced cell cycle reentry is closely linked to neurodegeneration and apoptosis in neurons, most likely through changes in the neurocytoskeleton. However, proliferative cells still exist within the nervous system, and adult neural stem cells (NSCs) have been identified in the Central Nervous System (CNS) in the past decade, raising a great stir in the neuroscience community. NSCs present a new therapeutic potential, and much effort has since gone into understanding the molecular mechanisms driving differentiation of specific neuronal lineages, such as dopaminergic neurons, for use in regenerative medicine, either through transplanted NSCs or manipulation of existing ones. Nevertheless, differentiation and proliferation are two sides of the same coin, just like tumorigenesis and degeneration. Tumor formation may be regarded as a de-differentiation of tissues, where cell cycle mechanisms are reactivated in differentiated cell types. It is thus important to understand the molecular mechanisms underlying various brain tumors in this perspective. The recent Cancer Stem Cell (CSC) hypothesis also suggests the presence of Brain Tumor Initiating Cells (BTICs) within a tumor population, although the exact origin of these rare and mostly elusive BTICs are yet to be identified. This review attempts to investigate the correlation of neural stem cells/precursors, mature neurons, BTICs and brain tumors with respect to cell cycle regulation and the impact of cell cycle in neurodegeneration.
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Ciclo Celular/fisiología , Transformación Celular Neoplásica/genética , Sistema Nervioso Central/embriología , Sistema Nervioso Central/fisiología , Degeneración Nerviosa/fisiopatología , Neurogénesis/fisiología , Células Madre/fisiología , Animales , Diferenciación Celular/fisiología , Linaje de la Célula/fisiología , Sistema Nervioso Central/citología , Humanos , Células Madre Neoplásicas/citología , Células Madre Neoplásicas/fisiología , Células Madre/citologíaRESUMEN
ETS domain transcription factor Elk-1 has been primarily studied in the regulation of genes in response to mitogenic stimuli, however the presence of Elk-1 in axonal projections of largely post-mitotic adult hippocampal sections has been reported. This finding has initially led us to a basic question: how is Elk-1 anchored to neuronal projections? To that end, we have investigated the intracellular localization of Elk-1 and its biochemical interactions with neuronal microtubules in model systems. Our results showed co-localization of Elk-1 with microtubules in hippocampal cultures and SH-SY5Y neuroblastoma cell lines, and have further demonstrated that Elk-1 protein can biochemically interact with microtubules in vitro. Analysis of the protein sequence has indicated many putative microtubule binding domains, with the strongest binding prediction in amino acids 314-325, and our results show that Elk-1 can bind to microtubules through most of these regions, but no interaction was observed through the DNA binding domain, where no putative binding motifs were predicted. We further show that upon serum induction, most of the phospho-Elk-1 translocates to the nucleus, which is independent of translation. We propose that Elk-1 is anchored to neuronal microtubules in resting or unstimulated cells, and upon stimulation is phosphorylated, which relocalizes phospho-Elk-1 to the nucleus in neurons.
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Núcleo Celular/metabolismo , Microtúbulos/metabolismo , Neuronas , Proteína Elk-1 con Dominio ets/metabolismo , Secuencia de Aminoácidos , Animales , Células Cultivadas , Hipocampo/citología , Humanos , Datos de Secuencia Molecular , Neuroblastoma , Neuronas/citología , Neuronas/metabolismo , Fosforilación , Ratas , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Proteína Elk-1 con Dominio ets/genéticaRESUMEN
The rules that specify how the information contained in DNA is translated into amino acid "language" during protein synthesis are called "the genetic code", commonly called the "Standard" or "Universal" Genetic Code Table. As a matter of fact, this coding table is not at all "universal": in addition to different genetic code tables used by different organisms, even within the same organism the nuclear and mitochondrial genes may be subject to two different coding tables. Results In an attempt to understand the advantages and disadvantages these coding tables may bring to an organism, we have decided to analyze various coding tables on genes subject to mutations, and have estimated how these genes "survive" over generations. We have used this as indicative of the "evolutionary" success of that particular coding table. We find that the "standard" genetic code is not actually the most robust of all coding tables, and interestingly, Flatworm Mitochondrial Code (FMC) appears to be the highest ranking coding table given our assumptions. Conclusions It is commonly hypothesized that the more robust a genetic code, the better suited it is for maintenance of the genome. Our study shows that, given the assumptions in our model, Standard Genetic Code is quite poor when compared to other alternate code tables in terms of robustness. This brings about the question of why Standard Code has been so widely accepted by a wider variety of organisms instead of FMC, which needs to be addressed for a thorough understanding of genetic code evolution.
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The dependency of the growth and metastasis of tumors on the new blood vessel formation, or angiogenesis, has opened up new potentials to tumor therapy, nevertheless understanding the molecular mechanisms involved in angiogenesis is crucial in the bioengineering of novel anti-angiogenic drugs. The key component in hypoxia sensing in tumor cells is the hypoxia-inducible factor, HIF-1alpha, which is inactivated through proteosome-mediated degradation under normoxic conditions. Two enzymes have been reported to hydroxylate HIF-1alpha, namely prolyl hydroxylase (PH), recruiting the proetasome complex and degrading cytoplasmic HIF-1alpha, and asparaginyl hydroxylase/factor inhibiting HIF-1alpha (FIH-1), downregulating the recruitment of p300 to the promoter, thereby reducing the transcriptional activity of HIF-1alpha. In this study, we have constructed an in silico model of a tumor cell using the GEPASI 3.30 biochemical simulation software (http://www.gepasi.org) and studied the performances of PH and FIH-1 on HIF-1alpha degradation and inactivation, respectively, as monitored by expression of the vascular endothelial growth factor, VEGF, during hypoxia. In our biochemical models, FIH-1 can successfully increase hypoxic transcription of VEGF, however FIH-1 on its own is not sufficient to inactivate HIF-1 completely, leading to background VEGF transcription under normoxic conditions. On the other hand, PH is necessary to increase the hypoxic transcriptional response, and can effectively shut off normoxic transcription. We therefore propose that regulating PH activity can be a primary target for anti-angiogenic bioengineering research.
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Biología Computacional , Regulación Neoplásica de la Expresión Génica , Subunidad alfa del Factor 1 Inducible por Hipoxia/genética , Hipoxia , Simulación por Computador , Subunidad alfa del Factor 1 Inducible por Hipoxia/biosíntesis , Modelos Biológicos , Células Tumorales CultivadasRESUMEN
Cytoplasmic volume undergoes a series of changes during mitosis in eukaryotes; in turn, signaling events such as osmotic stress can regulate the cytoplasmic volume in cells. In some organisms, increase in cytoplasmic-to-nuclear volume ratio was seen to affect the growth potential in cells, however, the mechanistics of such a regulation, if at all present, was unclear. In a computational model, we have constructed a growth factor-induced signaling pathway leading to AP-1 heterodimer formation through transcriptional regulation, and analyzed the effects of increasing the cytoplasmic-to-nuclear ratio on c-jun transcription and AP-1 complex. We have observed that larger cytoplasmic volumes caused both an increase in the final AP-1 product and a delay in the time of AP-1 accumulation.
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Ciclo Celular , Núcleo Celular/fisiología , Citoplasma/fisiología , Transducción de Señal , Factor de Transcripción AP-1/metabolismo , Animales , Tamaño de la Célula , Biología Computacional , Simulación por Computador , Factor de Crecimiento Epidérmico/farmacología , Factor de Crecimiento Epidérmico/fisiología , Quinasas de Proteína Quinasa Activadas por Mitógenos/fisiología , Modelos Biológicos , Proteínas Proto-Oncogénicas c-fos/genética , Proteínas Proto-Oncogénicas c-fos/fisiología , Proteínas Proto-Oncogénicas c-jun/genética , Proteínas Proto-Oncogénicas c-jun/fisiologíaRESUMEN
Members of the ternary complex factor (TCF) subfamily of the ETS-domain transcription factors are activated through phosphorylation by mitogen-activated protein kinases (MAPKs) in response to a variety of mitogenic and stress stimuli. The TCFs bind and activate serum response elements (SREs) in the promoters of target genes in a ternary complex with a second transcription factor, serum response factor (SRF). The association of TCFs with SREs within immediate-early gene promoters is suggestive of a role for the ternary TCF-SRF complex in promoting cell cycle entry and proliferation in response to mitogenic signaling. Here we have investigated the downstream gene regulatory and phenotypic effects of inhibiting the activity of genes regulated by TCFs by expressing a dominantly acting repressive form of the TCF, Elk-1. Inhibition of ternary complex activity leads to the downregulation of several immediate-early genes. Furthermore, blocking TCF-mediated gene expression leads to growth arrest and triggers apoptosis. By using mutant Elk-1 alleles, we demonstrated that these effects are via an SRF-dependent mechanism. The antiapoptotic gene Mcl-1 is identified as a key target for the TCF-SRF complex in this system. Thus, our data confirm a role for TCF-SRF-regulated gene activity in regulating proliferation and provide further evidence to indicate a role in protecting cells from apoptotic cell death.