guided by evidence-based trends, probabilities and cautionary notes that have emerged from large-... more guided by evidence-based trends, probabilities and cautionary notes that have emerged from large-scale structural genomics studies. In this review, which is targeted to the researcher with limited experience in protein expression and purification, we draw on our collective experiences to suggest a 'consensus' starting point for soluble protein expression and purification. Over the past decade, our laboratories have collectively targeted and purified tens of thousands of different proteins from the Eubacteria and Archaea, and thousands from the Eukarya, including fungal, nematode, parasite, plant and human proteins (Table 1). These proteins belong to many different classes, including proteins with no predictable structure, human proteins of therapeutic relevance, proteins from parasites and viruses, integral membrane proteins and multiprotein complexes. A near-complete list of these proteins is available in a database (TargetDB) maintained by the Protein Data Bank
Members of the ternary complex factor (TCF) subfamily of the ETS-domain transcription factors are... more 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 TCFmediated 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.
The rules that specify how the information contained in DNA is translated into amino acid "l... more 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 t...
Pea3 subfamily of E-twenty six transcription factors consist of three major -exhibit branching mo... more Pea3 subfamily of E-twenty six transcription factors consist of three major -exhibit branching morphogenesis, the function of Pea3 family in nervous system development and regeneration is only beginning to unfold. In this study, we provide evidence that Pea3 can directs neurite extension and axonal outgrowth in different model systems, and that Serine 90 is important for this function. We have also identified neurofilament-L and neurofilament-M as two putative novel targets for Pea3.
The International Journal of Biochemistry & Cell Biology, 2012
Please cite this article in press as: Mut M, et al. Both mitogen-activated protein kinase (MAPK)/... more Please cite this article in press as: Mut M, et al. Both mitogen-activated protein kinase (MAPK)/extracellular-signal-regulated kinases (ERK) 1/2 and phosphatidylinositide-3-OH kinase (PI3K)/Akt pathways regulate activation of E-twenty-six (ETS)-like transcription factor 1 (Elk-1) in U138 glioblastoma cells.
Elk-1, an ETS domain transcription factor of the TCF (ternary complex factor) subfamily, is known... more Elk-1, an ETS domain transcription factor of the TCF (ternary complex factor) subfamily, is known to be involved in the regulation of immediate-early genes such as c-fos upon mitogen activation, and thus commonly implied in cell proliferation. Early growth response-1, Egr-1, which was known to be an immediate-early gene, has recently been shown to be pro-apoptotic for SH-SY5Y neuroblastoma cells. In that respect, it was not clear whether Elk-1 would activate or repress from this promoter, since Elk-1 is mostly associated with proliferation and not apoptosis. In this study, we wanted to address whether Elk-1 activates or represses egr-1 promoter in neuroblastoma cells, and using a combination of RNA interference and reporter analyses, we present evidence that egr-1 gene is repressed by Elk-1 in normally cycling SH-SY5Y neuroblastoma cell line in a SUMO (small ubiquitin-related modifier)-dependent manner, a potential mechanism used by these cells to bypass apoptosis.
ETS domain transcription factor Elk-1 has been primarily studied in the regulation of genes in re... more 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 colocalization 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.
Cytoplasmic volume undergoes a series of changes during mitosis in eukaryotes; in turn, signaling... more 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.
ABSTRACT Just like all physical systems, biological systems also obey laws of thermodynamics, and... more ABSTRACT Just like all physical systems, biological systems also obey laws of thermodynamics, and as such the useful work potential of a biological system is its exergy. In some studies, exergy of living systems is considered with respect to work performance of humans in offices or buildings; however the exergy analysis of biochemical reactions in a cell as a closed system goes largely untouched. In this study, exergy analysis was applied to glucose metabolism of a model neuron, and dynamic exergy destructions were calculated for four different conditions, namely normoxia, hypoxia, glucose starvation and excess glucose. Our results showed that neuronal metabolism achieved a new steady state under each condition within 5 min. This dynamic model predicts that, both exergy destruction and work potential rates increase with increasing blood glucose concentration. The ratio of exergy destruction rate to work potential nrate increases logarithmically with increasing blood glucose concentration. The neuronal metabolism is thus found to function in an efficient way and switches to lower exergy destruction under stress conditions such as glucose starvation. This behavior seen in this exergy analysis study confirms the assumption of minimum entropy production in living systems.
Glucose and galactose are two alternative carbon sources in yeast for energy production, producin... more Glucose and galactose are two alternative carbon sources in yeast for energy production, producing CO 2 and alcohol. The yeast needs to switch from glucose to galactose metabolism as required, by transcriptional regulation of the respective metabolic enzymes. This regulation is achieved mainly through the GAL genetic switch, in addition to glucose repression mechanism. This study integrates the two metabolic pathways with the genetic regulatory circuit using the GEPASI 3.30 simulation environment, and investigates the model behavior under various nutrient conditions. Our system is successful in achieving transcriptional upregulation of the galactose metabolizing enzymes as required. Under high glucose and high galactose concentrations, the in silico yeast chooses to metabolize glucose first, after which it resorts to using the galactose available. We also show what the preferred storage macromolecules are in different metabolic pathways.
Immediate early gene activation upon mitogenic activation occurs through the serum response eleme... more Immediate early gene activation upon mitogenic activation occurs through the serum response element (SRE), which makes the delineation of the upstream pathways a powerful means to engineer cellular responses. The malfunctioning of this system leads to a variety of disorders, ranging from neurological disorders such as Coffin-Lowry syndrome (RSK2 mutations) to cancer (c-fos mutations). We therefore investigated the SRE activation mechanism in a typical mammalian cell. Mitogenic signaling uses the mitogen-activated protein kinase (MAPK) module through increased binding of the ternary complex factor (TCF), such as Elk-1, to the promoter DNA (the SRE element) and subsequent transcriptional activation, as well as through activation of a histone kinase, such as the MAPK-activated protein kinase (MAPKAP-K) ribosomal S6 kinase (RSK2). This computational model uses the biochemical simulation environment GEPASI 3.30 to investigate three major models of interaction for Elk-1 and RSK2, and to study the effect of histone acetyl transferase (HAT) recruitment in each of these models on the local chromatin modifications in the presence and absence of MAPK activation. We show that the quickest response on the chromatin can be achieved in the presence of a preformed complex of RSK2, Elk-1 and HAT, with HAT being activated upon dissociation from the complex upon activation of the MAPK cascade. This study presents critical components in the pathway that can be targeted for engineering of specific inhibitors or activators of the system. B
The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, 2009
Receptor tyrosine kinase activation by binding of neurotrophic factors determines neuronal morpho... more Receptor tyrosine kinase activation by binding of neurotrophic factors determines neuronal morphology and identity, migration of neurons to appropriate destinations, and integration into functional neural circuits as well as synapse formation with appropriate targets at the right time and at the right place. This review summarizes the most important aspects of intraneuronal signaling mechanisms and induced gene expression changes that underlie morphological and neurochemical consequences of receptor tyrosine kinase activation in central and peripheral neurons.
The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, 2009
Neurogenesis in the embryo involves many signaling pathways and transcriptional programs and an e... more 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.
The phenotypes of biological systems are to some extent robust to genotypic changes. Such robustn... more 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.
Elk-1 belongs to the ternary complex factors (TCFs) subfamily of the ETS domain proteins, and pla... more 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.
guided by evidence-based trends, probabilities and cautionary notes that have emerged from large-... more guided by evidence-based trends, probabilities and cautionary notes that have emerged from large-scale structural genomics studies. In this review, which is targeted to the researcher with limited experience in protein expression and purification, we draw on our collective experiences to suggest a 'consensus' starting point for soluble protein expression and purification. Over the past decade, our laboratories have collectively targeted and purified tens of thousands of different proteins from the Eubacteria and Archaea, and thousands from the Eukarya, including fungal, nematode, parasite, plant and human proteins (Table 1). These proteins belong to many different classes, including proteins with no predictable structure, human proteins of therapeutic relevance, proteins from parasites and viruses, integral membrane proteins and multiprotein complexes. A near-complete list of these proteins is available in a database (TargetDB) maintained by the Protein Data Bank
Members of the ternary complex factor (TCF) subfamily of the ETS-domain transcription factors are... more 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 TCFmediated 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.
The rules that specify how the information contained in DNA is translated into amino acid "l... more 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 t...
Pea3 subfamily of E-twenty six transcription factors consist of three major -exhibit branching mo... more Pea3 subfamily of E-twenty six transcription factors consist of three major -exhibit branching morphogenesis, the function of Pea3 family in nervous system development and regeneration is only beginning to unfold. In this study, we provide evidence that Pea3 can directs neurite extension and axonal outgrowth in different model systems, and that Serine 90 is important for this function. We have also identified neurofilament-L and neurofilament-M as two putative novel targets for Pea3.
The International Journal of Biochemistry & Cell Biology, 2012
Please cite this article in press as: Mut M, et al. Both mitogen-activated protein kinase (MAPK)/... more Please cite this article in press as: Mut M, et al. Both mitogen-activated protein kinase (MAPK)/extracellular-signal-regulated kinases (ERK) 1/2 and phosphatidylinositide-3-OH kinase (PI3K)/Akt pathways regulate activation of E-twenty-six (ETS)-like transcription factor 1 (Elk-1) in U138 glioblastoma cells.
Elk-1, an ETS domain transcription factor of the TCF (ternary complex factor) subfamily, is known... more Elk-1, an ETS domain transcription factor of the TCF (ternary complex factor) subfamily, is known to be involved in the regulation of immediate-early genes such as c-fos upon mitogen activation, and thus commonly implied in cell proliferation. Early growth response-1, Egr-1, which was known to be an immediate-early gene, has recently been shown to be pro-apoptotic for SH-SY5Y neuroblastoma cells. In that respect, it was not clear whether Elk-1 would activate or repress from this promoter, since Elk-1 is mostly associated with proliferation and not apoptosis. In this study, we wanted to address whether Elk-1 activates or represses egr-1 promoter in neuroblastoma cells, and using a combination of RNA interference and reporter analyses, we present evidence that egr-1 gene is repressed by Elk-1 in normally cycling SH-SY5Y neuroblastoma cell line in a SUMO (small ubiquitin-related modifier)-dependent manner, a potential mechanism used by these cells to bypass apoptosis.
ETS domain transcription factor Elk-1 has been primarily studied in the regulation of genes in re... more 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 colocalization 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.
Cytoplasmic volume undergoes a series of changes during mitosis in eukaryotes; in turn, signaling... more 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.
ABSTRACT Just like all physical systems, biological systems also obey laws of thermodynamics, and... more ABSTRACT Just like all physical systems, biological systems also obey laws of thermodynamics, and as such the useful work potential of a biological system is its exergy. In some studies, exergy of living systems is considered with respect to work performance of humans in offices or buildings; however the exergy analysis of biochemical reactions in a cell as a closed system goes largely untouched. In this study, exergy analysis was applied to glucose metabolism of a model neuron, and dynamic exergy destructions were calculated for four different conditions, namely normoxia, hypoxia, glucose starvation and excess glucose. Our results showed that neuronal metabolism achieved a new steady state under each condition within 5 min. This dynamic model predicts that, both exergy destruction and work potential rates increase with increasing blood glucose concentration. The ratio of exergy destruction rate to work potential nrate increases logarithmically with increasing blood glucose concentration. The neuronal metabolism is thus found to function in an efficient way and switches to lower exergy destruction under stress conditions such as glucose starvation. This behavior seen in this exergy analysis study confirms the assumption of minimum entropy production in living systems.
Glucose and galactose are two alternative carbon sources in yeast for energy production, producin... more Glucose and galactose are two alternative carbon sources in yeast for energy production, producing CO 2 and alcohol. The yeast needs to switch from glucose to galactose metabolism as required, by transcriptional regulation of the respective metabolic enzymes. This regulation is achieved mainly through the GAL genetic switch, in addition to glucose repression mechanism. This study integrates the two metabolic pathways with the genetic regulatory circuit using the GEPASI 3.30 simulation environment, and investigates the model behavior under various nutrient conditions. Our system is successful in achieving transcriptional upregulation of the galactose metabolizing enzymes as required. Under high glucose and high galactose concentrations, the in silico yeast chooses to metabolize glucose first, after which it resorts to using the galactose available. We also show what the preferred storage macromolecules are in different metabolic pathways.
Immediate early gene activation upon mitogenic activation occurs through the serum response eleme... more Immediate early gene activation upon mitogenic activation occurs through the serum response element (SRE), which makes the delineation of the upstream pathways a powerful means to engineer cellular responses. The malfunctioning of this system leads to a variety of disorders, ranging from neurological disorders such as Coffin-Lowry syndrome (RSK2 mutations) to cancer (c-fos mutations). We therefore investigated the SRE activation mechanism in a typical mammalian cell. Mitogenic signaling uses the mitogen-activated protein kinase (MAPK) module through increased binding of the ternary complex factor (TCF), such as Elk-1, to the promoter DNA (the SRE element) and subsequent transcriptional activation, as well as through activation of a histone kinase, such as the MAPK-activated protein kinase (MAPKAP-K) ribosomal S6 kinase (RSK2). This computational model uses the biochemical simulation environment GEPASI 3.30 to investigate three major models of interaction for Elk-1 and RSK2, and to study the effect of histone acetyl transferase (HAT) recruitment in each of these models on the local chromatin modifications in the presence and absence of MAPK activation. We show that the quickest response on the chromatin can be achieved in the presence of a preformed complex of RSK2, Elk-1 and HAT, with HAT being activated upon dissociation from the complex upon activation of the MAPK cascade. This study presents critical components in the pathway that can be targeted for engineering of specific inhibitors or activators of the system. B
The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, 2009
Receptor tyrosine kinase activation by binding of neurotrophic factors determines neuronal morpho... more Receptor tyrosine kinase activation by binding of neurotrophic factors determines neuronal morphology and identity, migration of neurons to appropriate destinations, and integration into functional neural circuits as well as synapse formation with appropriate targets at the right time and at the right place. This review summarizes the most important aspects of intraneuronal signaling mechanisms and induced gene expression changes that underlie morphological and neurochemical consequences of receptor tyrosine kinase activation in central and peripheral neurons.
The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, 2009
Neurogenesis in the embryo involves many signaling pathways and transcriptional programs and an e... more 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.
The phenotypes of biological systems are to some extent robust to genotypic changes. Such robustn... more 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.
Elk-1 belongs to the ternary complex factors (TCFs) subfamily of the ETS domain proteins, and pla... more 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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Papers by Isil Kurnaz
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.
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.