Regulation of eukaryotic transcription factors by post-translational modification

Transcriptional regulation by the Set7 lysine methyltransferase

Posttranslational histone modifications define chromatin structure and function. In recent years, a number of studies have characterized many of the enzymatic activities and diverse regulatory components required for monomethylation of histone H3 lysine 4 (H3K4me1) and the expression of specific genes. The challenge now is to understand how this specific chemical modification is written and the Set7 methyltransferase has emerged as a key regulatory enzyme mediating methylation of lysine residues of histone and non-histone proteins. In this review, we comprehensively explore the regulatory proteins modified by Set7 and highlight mechanisms of specific co-recruitment of the enzyme to activating promoters. With a focus on signaling and transcriptional control in disease we discuss recent experimental data emphasizing specific components of diverse regulatory complexes that mediate chromatin modification and reinterpretation of Set7-mediated gene expression.

Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis

Transcription factor activity is largely regulated through post-translational modification. Here, we report the first integrative model of transcription that includes both interactions between transcription factors and promoters, and between transcription factors and modifying enzymes. Simulations indicate that our method is robust against noise. We validated our tool on a well-studied stress response network in yeast and on a STAT1-mediated regulatory network in human B cells. Our work represents a significant step toward a comprehensive model of gene transcription.

An overview of stress response and hypometabolic strategies in Caenorhabditis elegans: conserved and contrasting signals with the mammalian system

Studies of the molecular mechanisms that are involved in stress responses (environmental or physiological) have long been used to make links to disease states in humans. The nematode model organism, Caenorhabditis elegans, undergoes a state of hypometabolism called the 'dauer' stage. This period of developmental arrest is characterized by a significant reduction in metabolic rate, triggered by ambient temperature increase and restricted oxygen/ nutrients. C. elegans employs a number of signal transduction cascades in order to adapt to these unfavourable conditions and survive for long times with severely reduced energy production. The suppression of cellular metabolism, providing energetic homeostasis, is critical to the survival of nematodes through the dauer period. This transition displays molecular mechanisms that are fundamental to control of hypometabolism across the animal kingdom. In general, mammalian systems are highly inelastic to environmental stresses (such as extreme temperatures and low oxygen), however, there is a great deal of conservation between the signal transduction pathways of nematodes and mammals. Along with conserving many of the protein targets in the stress response, many of the critical regulatory mechanisms are maintained, and often differ only in their level of expression. Hence, the C. elegans model outlines a framework of critical molecular mechanisms that may be employed in the future as therapeutic targets for addressing disease states.

Regulating the regulators: modulators of transcription factor activity

Gene transcription is largely regulated by DNA-binding transcription factors (TFs). However, the TF activity itself is modulated via, among other things, post-translational modifications (PTMs) by specific modification enzymes in response to cellular stimuli. TF-PTMs thus serve as "molecular switchboards" that map upstream signaling events to the downstream transcriptional events. An important long-term goal is to obtain a genome-wide map of "regulatory triplets" consisting of a TF, target gene, and a modulator gene that specifically modulates the regulation of the target gene by the TF. A variety of genome-wide data sets can be exploited by computational methods to obtain a rough map of regulatory triplets, which can guide directed experiments. However, a prerequisite to developing such computational tools is a systematic catalog of known instances of regulatory triplets. We first describe PTM-Switchboard, a recent database that stores triplets of genes such that the ability of one gene (the TF) to regulate a target gene is dependent on one or more PTMs catalyzed by a third gene, the modifying enzyme. We also review current computational approaches to infer regulatory triplets from genome-wide data sets and conclude with a discussion of potential future research. PTM-Switchboard is accessible at http://cagr.pcbi.upenn.edu/PTMswitchboard /

Transcription factor functionality and transcription regulatory networks

Now that numerous high-quality complete genome sequences are available, many efforts are focusing on the "second genomic code", namely the code that determines how the precise temporal and spatial expression of each gene in the genome is achieved. In this regard, the elucidation of transcription regulatory networks that describe combined transcriptional circuits for an organism of interest has become valuable to our understanding of gene expression at a systems level. Such networks describe physical and regulatory interactions between transcription factors (TFs) and the target genes they regulate under different developmental, physiological, or pathological conditions. The mapping of high-quality transcription regulatory networks depends not only on the accuracy of the experimental or computational method chosen, but also relies on the quality of TF predictions. Moreover, the total repertoire of TFs is not only determined by the protein-coding capacity of the genome, but also by different protein properties, including dimerization, co-factor interactions and post-translational modifications. Here, we discuss the factors that influence TF functionality and, hence, the functionality of the networks in which they operate.

From genotype to olfactory neuron phenotype: the role of the Olf-1-binding site

The highly organized pattern of gene expression leading to the determination of cellular phenotype derives from the interplay between genetic and epigenetic factors. This is mediated in part by distinctive DNA sequence motifs present in the regulatory regions of various genes and the transcription factors with which they interact. The phenotype of olfactory neurons is determined in part by the selective expression of novel isoforms of several genes involved in chemosensory transduction. To characterize the mechanisms determining olfactory neuron phenotype we have been studying the olfactory marker protein (OMP), the first olfactory-specific protein to be isolated and cloned. The temporal and spatial expression of OMP is regulated stringently and is highly restricted to mature olfactory neurons in all vertebrates from amphibians to humans. Identification of the specific elements responsible for regulating the expression of the OMP gene will elucidate the mechanisms leading to the determination of olfactory neuron phenotype. Using a combined in vivo (transgenic mice) and in vitro (electrophoretic mobility shift assays and DNase I footprinting) approach, we have identified and characterized a novel genomic motif that binds an olfactory tissue nuclear protein(s) that we designate Olf-1. We propose that Olf-1 is a novel olfactory-specific transacting factor responsible for directing the expression of genes containing the Olf-1 motif in olfactory neurons. Thus it may play a role in regulating the expression of genes associated with neuronal turnover and olfactory transduction.

The effect of glucosamine concentration on the development and sex ratio of bovine embryos

Glucosamine is a component of hyaluronic acid and an alternative substrate to glucose for the extracellular matrix synthesis of COCs. Its addition to an IVM medium reduces the glucose consumption of bovine COCs. Glucosamine is also metabolized to UDP-N-acetyl glucosamine (UDP-GlcNAc) via the hexosamine biosynthesis pathway and is utilized for O-linked glycosylation by the X-linked enzyme, O-linked GlcNAc transferase (OGT). Moreover, the inactivation of the second X chromosome in female embryos is influential in producing the sex ratio bias observed in vitro when embryos are cultured in the presence of glucose above 2.5mM. Accordingly, the aim of this study is to examine whether the presence of glucosamine during maturation or embryo culture causes a sex ratio bias in bovine blastocysts. Glucosamine was added to the medium in three different embryo developmental periods: in vitro maturation, the one-cell to eight-cell stage (before the maternal-zygotic transition, MZT), and the eight-cell to blastocyst stage (after MZT). When glucosamine was added during in vitro maturation, the developmental competence of oocytes was severely compromised. However, the sex ratio of embryos was not influenced. When glucosamine was added to embryo culture medium during development from one-cell to eight-cell stage (before MZT), it affected neither the development nor the sex ratio of bovine embryos. Finally, when glucosamine was added after MZT, the development rate of embryos was severely decreased, and the sex ratio was skewed toward males. Moreover, an inhibitor of OGT, benzyl-2-acetamido-2-deoxy-alpha-D-galactopyranoside (BADGP), negated the effect of glucosamine on the sex ratio when it was added to embryo culture medium from the eight-cell to blastocyst stage (after MZT). These results suggest that, like glucose, the supplementation of glucosamine into the medium skewed the sex ratio to males and that OGT, an X-linked enzyme, was involved in this phenomenon. Moreover, this effect of glucosamine was limited only to when it was present in the embryo culture medium after MZT.

Signal transduction by the antigen receptors of B and T lymphocytes

B and T lymphocytes of the immune system recognize and destroy invading microorganisms but are tolerant to the cells and tissues of one's own body. The basis for this self/non-self-discrimination is the clonal nature of the B and T cell antigen receptors. Each lymphocyte has antigen receptors with a single unique antigen specificity. Multiple mechanisms ensure that self-reactive lymphocytes are eliminated or silenced whereas lymphocytes directed against foreign antigens are activated only when the appropriate antigen is present. The key element in these processes is the ability of the antigen receptors to transmit signals to the interior of the lymphocyte when they bind the antigen for which they are specific. Whether these signals lead to activation, tolerance, or cell death is dependent on the maturation state of the lymphocytes as well as on signals from other receptors. We review the role of antigen receptor signaling in the development and activation of B and T lymphocytes and also describe the biochemical signaling mechanisms employed by these receptors. In addition, we discuss how signal transduction pathways activated by the antigen receptors may alter gene expression, regulate the cell cycle, and induce or prevent programmed cell death.

A majority of casein kinase II alpha subunit is tightly bound to intranuclear components but not to the beta subunit

Nuclear casein kinase II (CK II) was purified from an epithelial cell line of Chironomus tentans and characterized. The intracellular distribution of CK II and its two intracellular subunits (alpha and beta) was analysed by immunoblotting. The apparent molecular weights of the alpha and beta subunits were estimated to be 36 and 28 kDa, respectively. Like other purified CK II preparations, CK II from Chironomus tentans is able to use ATP or GTP for phosphorylation of casein and phosvitin, and its activity is strongly inhibited by heparin and by the transcription inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). Due to their differential solubilities in NaCl and (NH4)2SO4 solutions, individual alpha and beta subunit pools could be detected. More than 85% of the total immunostainable alpha subunit and essentially all immunoreactive individual beta subunit and heterooligomeric enzyme molecules were localised to the nucleus. Unexpectedly, more than 80% of this nuclear alpha subunit was insoluble in 0.35 M NaCl, while all individual beta subunit and heterooligomeric enzyme molecules were solubilized under the same conditions. Of the 0.35 M NaCl soluble kinase fractions, the active multisubunit form of CK II precipitated in 50% (NH4)2SO4 and could thus be separated from the free beta subunit, which precipitated at 60% and 80% (NH4)2SO4. These results suggest that a major portion of the nuclear CK II alpha subunit does not form heterooligomeric structures with the beta subunit, but binds tightly to nuclear components.

DNA-binding specificity of the S8 homeodomain

The murine S8 homeobox gene is expressed in a mesenchyme-specific pattern in embryos, as well as in mesodermal cell lines. The S8 homeodomain is overall similar to paired type homeodomains, but at position 50, which is crucial for specific DNA recognition, it contains a Gln, as is found in Antennapedia (Antp)-type homeodomains. We determined the DNA-binding specificity of the purified S8 homeodomain by in vitro selection of random oligonucleotides. The resulting 11-bp consensus binding site, ANC/TC/TAATTAA/GC resembles, but subtly differs from, the recognition sequences of Antp-type homeodomains. Equilibrium binding constants of down to 6.0 x 10(-10) M were found for binding of the S8 homeodomain to selected oligonucleotides. Using specific antibodies and an oligonucleotide containing an S8-site, we detected by band-shift two abundant DNA binding activities in mesodermal cell lines that correspond to S8 and two more that correspond to its close relative MHox. These S8 protein forms are differentially expressed in retinoic acid-treated P19 EC cells.

Purification and biochemical characterization of proteins which bind to the H-box cis-element implicated in transcriptional activation of plant defense genes

The H-box (CCTACC(N)7CT(N)4A), which occurs three times within the -154 to -42 region of the bean chalcone synthase chs15 promoter, is important for developmental regulation of chs15, and induction of chs15 and coordinately regulated defense genes by elicitors and other stress stimuli. Two protein factors, KAP-1 and KAP-2, which recognize conserved features in the H-box motif, were purified from bean cell suspension cultures by a combination of ion exchange chromatography and DNA affinity chromatography. KAP-1 is a 97 kDa polypeptide, whereas KAP-2 comprises two polypeptides of 76 and 56 kDa. KAP-1 and KAP-2 also differ in the sensitivity of their DNA-bound forms to trypsin. Dephosphorylation of KAP-1 or KAP-2 affects the mobility of the protein/H-box binding complex in gel shift assays but does not inhibit DNA binding. Elicitation of bean cell suspensions with glutathione does not affect the total cellular activities of KAP-1 or KAP-2, but causes a rapid increase in the specific activities of both factors in the nuclear fraction, consistent with a role for these factors in the signal pathway for elicitor induction of chs15 and related defense genes.

Olf-1-binding site: characterization of an olfactory neuron-specific promoter motif

We report characterization of several domains within the 5' flanking region of the olfactory marker protein (OMP) gene that may participate in regulating transcription of this and other olfactory neuron-specific genes. Analysis by electrophoretic mobility shift assay and DNase I footprinting identifies two regions that contain a novel sequence motif. Interactions between this motif and nuclear proteins were detected only with nuclear protein extracts derived from olfactory neuroepithelium, and this activity is more abundant in olfactory epithelium enriched in immature neurons. We have designated a factor(s) involved in this binding as Olf-1. The Olf-1-binding motif consensus sequence was defined as TCCCC(A/T)NGGAG. Studies with transgenic mice indicate that a 0.3-kb fragment of the OMP gene containing one Olf-1 motif is sufficient for olfactory tissue-specific expression of the reporter gene. Some of the other identified sequence motifs also interact specifically with olfactory nuclear protein extracts. We propose that Olf-1 is a novel, olfactory neuron-specific trans-acting factor involved in the cell-specific expression of OMP.

Olf-1-binding site: characterization of an olfactory neuron-specific promoter motif

We report characterization of several domains within the 5' flanking region of the olfactory marker protein (OMP) gene that may participate in regulating transcription of this and other olfactory neuron-specific genes. Analysis by electrophoretic mobility shift assay and DNase I footprinting identifies two regions that contain a novel sequence motif. Interactions between this motif and nuclear proteins were detected only with nuclear protein extracts derived from olfactory neuroepithelium, and this activity is more abundant in olfactory epithelium enriched in immature neurons. We have designated a factor(s) involved in this binding as Olf-1. The Olf-1-binding motif consensus sequence was defined as TCCCC(A/T)NGGAG. Studies with transgenic mice indicate that a 0.3-kb fragment of the OMP gene containing one Olf-1 motif is sufficient for olfactory tissue-specific expression of the reporter gene. Some of the other identified sequence motifs also interact specifically with olfactory nuclear protein extracts. We propose that Olf-1 is a novel, olfactory neuron-specific trans-acting factor involved in the cell-specific expression of OMP.

Biochemistry of B lymphocyte activation

The activation of B lymphocytes from resting cells proceeds from the events of early activation to clonal proliferation to final differentiation into either an antibody-secreting plasma cell or a memory B cell. This is a complex activation process marked by several alternative pathways, depending on the nature of the initial antigenic stimulus. Over the past 5-10 years, there has been an explosion of studies examining the biochemical nature of various steps in these pathways. Some of that progress is reviewed here. In particular, we have described in detail what is known about the structure and function of the AgR, as this molecule plays a pivotal role in B cell responses of various types. We have also reviewed recent progress in understanding the mechanism of action of contact-dependent T cell help and of the cytokine receptors, particularly the receptors for IL-2, IL-4, and IL-6. Clearly, all of these areas represent active areas of investigation and great progress can be anticipated in the next few years.

GEBF-I in Drosophila species and hybrids: the co-evolution of an enhancer and its cognate factor

The activation of the Drosophila melanogaster salivary gland secretion protein gene Sgs-3 is marked by important changes in chromatin structure in the distal regulatory region at -600 bp from the Sgs-3 start site. A stage- and tissue-specific glue enhancer binding factor, GEBF-I, binds in vitro to sequences from this region. Previous studies have revealed considerable variation in the DNA sequences of comparable regions in the related Drosophila species, D. simulans, D. erecta and D. yakuba. We detected GEBF-I-like proteins in these species, which appear to evolve as rapidly as the corresponding DNA sequences, and studied in detail the binding characteristics of the GEBF-I proteins of the two most closely related species, D. melanogaster and D. simulans. In crosses between these species, certain strains produce hybrid larvae which, unexpectedly, synthesised a single intermediate form of the protein. This suggests that the factor is subject to species-specific post-transcriptional modifications. In these hybrid larvae, which carry one D. melanogaster and one D. simulans Sgs-3 gene, the hybrid GEBF-I protein appears equally effective in the induction of both target genes.

The induction of adipose conversion in 3T3-L1 cells is associated with early phosphorylation of a 60-kDa nuclear protein

The induction of adipose conversion in 3T3-L1 cells by bezafibrate has been shown to be enhanced by dibutyryl-cAMP. We here report that the induction of adipose conversion in 3T3-L1 cells, by either bezafibrate and dibutyryl cAMP, or isobutylmethyxanthine alone, is associated with a very early phosphorylation of a 60-kDa acidic protein found in the nuclear fraction.

The nuclear 42-kDa phosphoprotein preferentially binds promoter-containing single-stranded DNA

The DNA-binding activity of a 42-kDa phosphoprotein from salivary gland cells and cultured epithelial cells of Chironomus tentans have been analyzed by the Southwestern technique. Both the salivary gland and the epithelial cell 42-kDa polypeptides were found to be single-stranded DNA-binding proteins. They bind to single-stranded promoter-containing restriction fragments including sequences from -204 to +74 from the ecdysterone controlled I-18C gene as well as sequences including the joint histone H2A/H2B promoters in a sequence selective manner. By contrast, the 42-kDa polypeptides show no significant binding to intragenic restriction fragments from +71 to +351 from the I-18C gene. Previous and present data taken together suggest that the 42-kDa protein has a general role in the regulation of protein coding genes.

Expression and interactions of human adenovirus oncoproteins

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Regulation of hsp70 mRNA levels during oocyte maturation and zygotic gene activation in the mouse

Protein phosphorylation catalyzed by the cAMP-dependent protein kinase is implicated in transcriptional activation of the embryonic genome in the two-cell mouse embryo, while heat shock protein (hsp70) has been identified as one of the first products of zygotic gene activation. Using reverse transcription-polymerase chain reaction we have analyzed relative changes in the amount of hsp70 mRNA during oocyte maturation and early embryogenesis. We report that the amount of hsp70 mRNA decreases after germinal vesicle breakdown, while inhibiting germinal vesicle breakdown inhibits this maturation-associated decrease. The amount of hsp70 mRNA increases between the one- and two-cell stages. This increase is inhibited by either alpha-amanitin or the cAMP-dependent protein kinase inhibitor H-8; the same concentration of H-7, which is a more potent inhibitor of protein kinase C, has little inhibitory effect on this increase in the relative amount of hsp70 mRNA. Last, addition of cycloheximide to one-cell embryos late in G2 inhibits neither cleavage to the two-cell stage nor the increase in the relative amount of hsp70 mRNA. These results strengthen the previous proposal that protein phosphorylation is involved in zygotic gene activation in the two-cell mouse embryo.

Cyclic AMP induces activity increase of kinase FA (a transmembrane signal of insulin) during NG108-15 hybrid cell differentiation

The ATP.Mg-dependent protein phosphatase activating factor (protein kinase FA) has been identified to exist in neuroblastoma x glioma hybrid 108-15 cells (NG108-15 cells). More importantly, when NG cells were induced to differentiate with N6, O2'-dibutyryl adenosine 3',5'-cyclic monophosphate (dibutyryl cAMP), the cellular activity of kinase FA was found to increase dramatically. Time course study further revealed that induction of differentiation in NG cells by dibutyryl cAMP treatment increased the FA activity to over 3 times the levels found in undifferentiated cells and in a linear day-dependent manner, indicating that the FA activity level is correlated with the state of differentiation of NG108-15 cells. This is the first report providing initial evidence that protein kinase FA (a transmembrane signal of insulin) is involved in the induction of neuronal cell differentiation.