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Pea3 transcription factor belongs to the PEA3 subfamily within the ETS domain transcription factor superfamily, and has been largely studied in relation to its role in breast cancer metastasis. Nonetheless, Pea3 plays a role not only in breast tumor, but also in other tissues with branching morphogenesis, including kidneys, blood vasculature, bronchi and the developing nervous system. Identification of Pea3 target promoters in these systems are important for a thorough understanding of how Pea3 functions. Present study particularly focuses on the identification of novel neuronal targets of Pea3 in a combinatorial approach, through curation, computational analysis and microarray studies in a neuronal model system, SH-SY5Y neuroblastoma cells. We not only show that quite a number of genes in cancer, immune system and cell cycle pathways, among many others, are either up- or down-regulated by Pea3, but also identify novel targets including ephrins and ephrin receptors, semaphorins, cell adhesion molecules, as well as metalloproteases such as kallikreins, to be among potential target promoters in neuronal systems. Our overall results indicate that rather than early stages of neurite extension and axonal guidance, Pea3 is more involved in target identification and synaptic maturation. © 2017 Kandemir et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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. © 2014 Kandemir, Caglayan, Hausott, Erdogan, Dag, Demir, Sogut, Klimaschewski and Kurnaz.

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. © Mary Ann Liebert, Inc.

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. © 2013 John Wiley & Sons, Ltd.

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. © Springer Science+Business Media, LLC 2011. Acknowledgments The authors would like to thank interns Basak Kandemir and Betul Bitir for their technical assistance. This study was supported by grants no. 109S230 and 106S247 (COST B-30 action) by TUBITAK, as well as Turkish Fight-Against-Cancer Foundation Terry Fox Project Award; IAK is a TUBA GEBIP awardee.

Transcription factors (TFs) are the proteins which regulates the expression of their target genes either in a positive or negative manner. TFs realize this task by binding to a specific DNA sequence contained in promoter regions, via their DNA binding motifs. Among ETS family TFs, Pea3 proteins are involved in the regulation of expression of genes, which are important for cell growth, development, differentiation, oncogenic transformation and apoptosis. In silico studies should be done to find out the novel target genes for this TF. Even though a few bioinformatics tools are available for this purpose, the user needs to go back and forth between different tools, and to repeat these steps for each of their candidate gene. Here we combined these tools and constituted a new tool which examines the affinity of any TF towards the selected target genes' promoter sequences. The tool is tested on several genes, which are predicted to be regulated by Pea3 TF. © 2011 IEEE. Intron;Lufthansa;Top;TUBA 6th International Symposium on Health Informatics and Bioinformatics, HIBIT 2011 -- 2 May 2011 through 5 May 2011 -- Izmir -- 95808

Nucleic acids are composed of nucleotides, the building blocks, and essentially contain a fi vecarbon sugar, a phosphate group, and nitrogen-containing bases. There are two major groups of nucleic acids, DNA, or deoxyribonucleic acid; and RNA, or ribonucleic acid. DNA serves as the genetic material, in other words, genes are made up of DNA. The DNA molecule has four major building blocks, adenine (A), thymine (T), cytosine (C), and guanine (G), attached to a deoxyribose sugar. RNA is also composed of nucleotide building blocks, with one letter difference: it uses A, C, and G, but uracil (U) instead of thymine, all attached to a ribose sugar. Both DNA and RNA are polar compounds due to the many negative charges they contain in the phosphate groups of the sugar-phosphate backbone of each DNA and RNA strand [1]. © 2010 by Taylor and Francis Group, LLC.

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 antiangiogenic drugs. The key component in hypoxia sensing in tumor cells is the hypoxia-inducible factor, HIF-1?, which is inactivated through proteosome-mediated degradation under normoxic conditions. Two enzymes have been reported to hydroxylate HIF-1?, namely prolyl hydroxylase (PH), recruiting the proetasome complex and degrading cytoplasmic HIF-1?, and asparaginyl hydroxylase/factor inhibiting HIF-1? (FIH-1), downregulating the recruitment of p300 to the promoter, thereby reducing the transcriptional activity of HIF-1?. 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-1? 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. © 2006 Wiley Periodicals, Inc.

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 (MARK) 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. © 2004 Wiley Periodicals, Inc.

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.

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. Anat Rec, 292:1953-1961, 2009. (C) 2009 Wiley-Liss, Inc.

The rules that specify how the information contained in DNA is translated into amino acid “language†during protein synthesis are called “the genetic codeâ€Â, commonly called the “Standard†or “Universal†Genetic Code Table. As a matter of fact, this coding table is not at all “universalâ€Â: 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.

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. © 2013 Springer Science+Business Media New York.

Background Neuro-glial interactions are important for normal functioning of the brain as well as brain energy metabolism. There are two major working models - in the classical view, both neurons and astrocytes can utilize glucose as the energy source through oxidative metabolism, whereas in the astrocyte-neuron lactate shuttle hypothesis (ANLSH) it is the astrocyte which can consume glucose through anaerobic glycolysis to pyruvate and then to lactate, and this lactate is secreted to the extracellular space to be taken up by the neuron for further oxidative degradation. Results In this computational study, we have included hypoxia-induced genetic regulation of these enzymes and transporters, and analyzed whether the ANLSH model can provide an advantage to either cell type in terms of supplying the energy demand. We have based this module on our own experimental analysis of hypoxia-dependent regulation of transcription of key metabolic enzymes. Using this experimentation-supported in silico modeling, we show that under both normoxic and hypoxic conditions in a given time period ANLSH model does indeed provide the neuron with more ATP than in the classical view. Conclusions Although the ANLSH is energetically more favorable for the neuron, it is not the case for the astrocyte in the long term. Considering the fact that astrocytes are more resilient to hypoxia, we would propose that there is likely a switch between the two models, based on the energy demand of the neuron, so as to maintain the survival of the neuron under hypoxic or glucose-and-oxygen-deprived conditions.

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. © 2011. 106S247 Wellcome Trust We would like to thank members of the Kurnaz, Ozturk and Sharrocks laboratories for helpful discussions and Prof. M.L. Kurnaz for help with statistics. We also would like to thank our anonymous reviewers for their helpful criticisms for the improvement of this study. This work was supported by TUBITAK-SBAG project no 106S247 as a partner of the ESF COST B-30 Action (neural plasticity and neuroregeneration, NEREPLAS), and TUBA Young Investigator Award to I.A.K. Funding for ADS was from the Wellcome Trust and a Royal Society-Wolfson award.

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. © 2009 Springer Science+Business Media, LLC.

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. © 2008 Elsevier Inc. All rights reserved. 106S247 The Academy of Sciences for the Developing World: 04-375 RG/BIO/AS 104T221 We would like to acknowledge Prof. A.D. Sharrocks for the Elk-1 constructs and critical discussions, as well as Prof. Aziz Sancar for critical reading of the manuscript. We would also like to acknowledge our anonymous reviewers for their valuable contributions towards the improvement of this study. This work was supported by TUBITAK-SBAG project no.106S247 as a partner of the ESF COST B-30 Action (Neural Plasticity and Neuroregeneration, NEREPLAS), and TUBA Young Investigator Award to I.A.K, as well as TUBITAK Career Award (Project no. 104T221) and TWAS grant (04-375 RG/BIO/AS) to A.K.

The steady increase in the incidence of cutaneous (skin) malignant melanoma worldwide generates the necessity to understand the key molecular events underlying melanogenesis and melanoma. Melanogenesis has two main stages: immediate pigmentation occurs through the redistribution of pigment-containing melanosomes to the dendrites of melanocytes, and subsequently to the surrounding keratinocytes, without the need for any new melanin synthesis. The effect is therefore subtle and transient. Delayed and sustained tanning, however, requires (a) an increase in melanocyte number and dendricity, (b) an increase in melanosome number, and (c) an increase in melanin content. This computer-based model focuses on the sustained eumelanin (black/brown pigment) production through melanocyte-specific gene expression in response to external stimulus. We find in our model that high levels of melanin can be reached within an hour of stimulation. Furthermore we successfully show metabolic downregulation of pigment synthesis through employing in our simulations an experimentally-described inhibitor for melanogenic enzymes. We see this model as a starting point for in silico drug screening for skin lightening agents, sun-tanning agents, and eventually for anti-melanoma agents that are under development.