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The transcription factor NFAT (nuclear factor of activated T cells) controls the expression of many immunomodulatory proteins. African swine fever virus inhibits proinflammatory cytokine expression in infected macrophages, and a vital protein A238L was found to display the activity of the immunosuppressive drug cyclosporin A by inhibiting NFAT-regulated gene transcription in vivo. This it does by binding the catalytic subunit of calcineurin and inhibiting calcineurin phosphatase activity., Viruses encode many proteins that interfere with host defense systems (1). Nucleotide sequence analysis of the African swine fever virus (ASFV) genome (2) identified genes encoding proteins that are potentially [...]

The plant hormone auxin regulates plant physiology by modulating the interaction of transcription factors with auxin response elements (AuxREs) of the affected genes. A transcription factor, Auxin Response Factor 1 [...]

Members of the myocyte enhancer factor-2 (MEF2) family of MADS (MCM1, agamous, deficiens, serum response factor)-box transcription factors bind an A-T-rich DNA sequence associated with muscle-specific genes. The murine MEF2C gene is expressed in heart precursor cells before formation of the linear heart tube. In mice homozygous for a null mutation of MEF2C, the heart tube did not undergo looping morphogenesis, the future right ventricle did not form, and a subset of cardiac muscle genes was not expressed. The absence of the, right ventricular region of the mutant heart correlated with down-regulation of the dHAND gene, which encodes a basic helix-loop-helix transcription factor required for cardiac morphogenesis. Thus, MEF2C is an essential regulator of cardiac myogenesis and right ventricular development., The mechanisms that regulate heart formation during embryogenesis are only beginning to be elucidated (1). Members of the MEF2 family of transcription factors bind a conserved A-T-rich DNA sequence associated [...]

Many cells are resistant to stimuli that can induce apoptosis, but the mechanisms involved are not fully understood. The activation of the transcription factor nuclear factor-kappa B (NF-κB) by tumor necrosis factor (TNF), ionizing radiation, or daunorubicin (a cancer chemotherapeutic compound), was found to protect from cell killing. Inhibition of NF-κB nuclear translocation enhanced apoptotic killing bythesereagents but not by apoptotic stimuli that do not activate NF-κB. These results provide a mechanism of cellular resistance to killing by some apoptotic reagents, offer insight into a new role for NF-κB, and have potential for improvement of the efficacy of cancer therapies., Observations that NF--κb (1) is activated by certain apoptotic stimuli has led to the speculation that this transcription factor may mediate aspects of programmed cell death An anti-apoptotic function of [...]

PHO4, a transcription factor required for induction of the PHO5 gene in response to phosphate starvation, is phosphorylated by the PHO80-PHO85 cyclin-CDK (cyclin-dependent kinase) complex when yeast are grown in [...]

The template and coactivator requirements for synergistic transcription directed single activator, Bicoid (BCD), bound to multiple sites have been determined. Mutagenesis studies in combination with protein binding experiments and reconstituted transcription, reactions identified two independent activation domains of BCD that target different coactivator subunits ([TAF.sub.II]110 and [TAF.sub.II]60) of the basal transcription factor IID (TFIID). The presence of both coactivators is required for BCD to recruit the TATA binding protein (TBP)T-TAF complex to the promoter and direct synergistic activation of transcription. Thus, contact between multiple activation domains of BCD and different targets within the TFIID complex can mediate transcriptional synergism., A generally accepted model for transcriptional activation postulates that activator proteins bind selectively to enhancer elements of target genes, thereby positioning one more activation domains for contact with specific targets [...]

Coordinate activation of transcription by multiple enhancer binding factors is essential for the regulation of pattern formation during development of Drosophila melanogaster. Cell-free transcription reactions are described that recapitulate transcriptional synergism directed by the Drosophila developmental regulators Bicoid (BCD) and Hunchback (HB). Within the basal transcription factor complex TFIID, two specific targets, [TAF.sub.II]110 and [TAF.sub.II]60, served as coactivators to mediate transcriptional activation by these two enhancer binding proteins. A quadruple complex containing TATA binding protein (TBP), [TAF.sub.II]250, [TAF.sub.II]110, and [TAF.sub.II]60 mediated transcriptional synergism by BCD and HB, whereas triple TBP-[TAF.sub.II] complexes lacking one or the other target coactivator failed to support synergistic activation. Deoxyribonuclease I footprint protection experiments revealed that art integral step leading to transcriptional synergism involves the recruitment of TBP-[TAF.sub.II] complexes to the promoter by way of multivalent contacts between activators and selected [TAF.sub.II]s. Thus, the concerted action of multiple regulators with different coactivators helps to establish the pattern and level of segmentation gene transcription during Drosophila development., The segmented body pattern of Drosophila melanogaster is established by a hierarchic network of maternal and zygotic segmentation gene activities that progressively subdivide the embryo into its final metameric pattern. [...]

Human ribosomal RNA synthesis by RNA polymerase I requires the activator UBF and the promoter selectivity factor SL1, which consists of the TATA binding protein (TBP) and three associated subunits, [TAF.sub.1]110, [TAF.sub.1]63, and [TAF.sub.1]48. Here it is shown that both [TAF.sub.1]110 and [TAF.sub.1]63 contact the promoter, whereas [TAF.sub.1]48 serves as a target for interaction with UBF and is required to form a transcriptionally active SL1 complex responsive to UBF in vitro. [TAF.sub.1]48 also alters the ability of TBP to interact with TATA box elements, and the resulting complex fails to support transcription by RNA polymerase II. Thus, [TAF.sub.1]48 may function both as a target to mediate UBF activation and as a class-specific promoter selectivity factor., Enhancement of transcription initiation by sequence-specific DNA binding proteins is a principal mechanism for regulating gene expression in animal cells (1). Promoter-selective transcriptional activators bind DNA and interact with specific [...]

The crystal structure of restriction endonuclease Bam HI complexed to DNA has been determined at 2.2 angstrom resolution. The DNA binds in the cleft and retains a B-DNA type of [...]

The ternary complex factor (TCF) subfamily of ETS-domain transcription factors bind with serum response factor (SRF) to the serum response element (SRE) and mediate increased gene expression. The TCF protein Elk-1 is phosphorylated by the JNK and ERK groups of mitogen-activated protein (MAP) kinases causing increased DNA binding, ternary complex formation, and transcriptional activation. Activated SRE-dependent gene expression is induced by JNK in cells treated with interleukin-1 and by ERK after treatment with phorbol ester. The Elk-1 transcription factor therefore integrates MAP kinase signaling pathways in vivoto coordinate biological responses to different extracellular stimuli., The SRE mediates increased immediate-early gene expression (for example, c-fos) in cells treated with growth factors or cytokines or subjected to environmental stress[1]. The SRF binds to the SRE along [...]

DCoH, the dimerization cofactor of hepatocyte nuclear factor-1, stimulates gene expression by associating with specific DNA binding proteins and also catalyzes the dehydration of the biopterin cofactor of phenylalanine hydroxylase. The x-ray crystal structure determined at 3 angstrom resolution reveals that DCoH forms a tetramer containing two saddle-shaped grooves that comprise likely macromolecule binding sites. Two equivalent enzyme active sites flank each saddle, suggesting that there is a spatial connection between the catalytic and binding activities. Structural similarities between the DCoH fold and nucleic acid-binding proteins argue that the saddle motif has evolved to bind diverse ligands or that DCoH unexpectedly may bind nucleic acids., Transcription depends on interactions among numerous proteins, including regulatory proteins bound at specific DNA sites. Homeodomain transcription factors, for example, are recognized by protein-binding coactivators[1, 2]. Little is known, however, [...]

RNA encoding the B subunit of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) subtype of ionotropic glutamate receptor (GluR-B) undergoes a posttranscriptional modification in which a genomically encoded adenosine is represented as a guanosine in the GluR-B complementary DNA. In vitro editing of GluR-B RNA transcripts with HeLa cell nuclear extracts was found to result from an activity that converts adenosine to inosine in regions of double-stranded RNA by enzymatic base modification. This activity is consistent with that of a double-stranded RNA-specific adenosine deaminase previously described in Xenopus oocytes and widely distributed in mammalian tissues., The editing of MRNA transcripts is an important mechanism for augmenting the flexibility of eukaryotic gene expression (1). The A[equivalence]G conversion seen in mRNAs encoding glutamatergic ion channet subunits exemplifies [...]

IκB-α inhibits transcription factor NF-κB by retaining it in the cytoplasm. Various stimuli, typically those associated with stress or pathogens, rapidly inactivate IκB-α. This liberates NF-κB to translocate to the nucleus and initiate transcription of genes important for the defense of the organism. Activation of NF-κB correlates with phosphorylation of IκB-α and requires the proteolysis of this inhibitor. When either serine-32 or serine-36 Of IκB-α was mutated, the protein did not undergo signal-induced phosphorylation or degradation, and NF-κB could not be activated. These results suggest that phosphorylation at one or both of these residues is critical for activation of NF-κB., Proteolytic degradation of IκB-α is essential for activation of NF-κB [1-4]. When degradation is blocked by certain protease inhibitors that target proteasomes, activation of NF-κB is prevented. Physiologic stimulation also [...]

Drosophila dorsoventral (DV) patterning and mammalian hematopoiesis are regulated by related signaling pathways (Toll, interleukin-1) and transcription factors dorsal, nuclear factor - κB). These factors interact with related enhancers, such as the rhomboid NEE and κlight chain enhancer, that contain similar arrangements of activator and repressor binding sites. it is shown that the κ enhancer can generate lateral stripes of gone expression in transgenic drosophila embryos in a pattern similar to that directed by the rhomboid NEE. Drosophila DV determinants direct these stripes through the corresponding mammalian cis regulatory elements in the κ enhancer, including the κB site and κE boxes. These results suggest that enhancers can couple conserved signaling pathways to divergent gene functions., There are numerous parallels between the regulation of gene expression along the DV axis of the Drosophila embryo and the regulation of lymphoid-restricted expression in the mammalian immune system [1-4]. [...]

The structure of the DNA binding domain, determined at 1.8 angstrom resolution, contains a three-helix bundle that is capped by a four-stranded antiparallel β sheet. This structure is a variant of the helix-turn-helix motif, typified by catabolite activator protein. In th, heat shock transcription factor, the first helix of the motif (α2) has an α-helical bulge and a proline-induced kink. The angle between the two helices of the motif (α2 and α3) is about 20° smaller than the average for canonical helix-turn-helix proteins. Nevertheless, the relative positions of the first and third helices of the bundle (α1 and α3) are conserved. It is proposed here that the first helix of the three-helix bundle be considered a componeot of the helix-turn-helix motif., All cells respond to stress, such as heat shock or chemical or environmeotal perturbations, by rapidly expressing a small number of proteins known as th, heat shock proteins. Th,se proteins [...]

Interferons induce transcriptional activation through tyrosine phosphorylation of the latent, cytoplasmic transcription factor interferon-stimulated gene factor-3 (ISGF-3). Growth factors and cytokines were found to use a similar pathway: The 91-kilodalton subunit of ISGF-3 was activated and tyrosine phosphorylated in response to epidermal growth factor (EGF), platelet-derived growth factor, and colony stimulating factor-1. The tyrosine phosphorylated factor acquired DNA binding activity and accumulated in nuclei. Activation required the major sites for autophosphorylation on the EGF receptor that bind Src homology region 2 domain-containing proteins implicated in Ras activation. However, activation of this factor was independent of the normal functioning of Ras., Cell surface receptors for extracellular polypeptide ligands transduce proliferative and differentiation signals to the cell's interior. Many growth factor receptors are tyrosine kinases, containing a cytoplasmic catalytic domain capable of [...]

Intraperitoneal injection of epidermal growth factor (EGF) into mice resulted in the appearance in liver nuclei of three tyrosine phosphorylated proteins (84, 91, and 92 kilodaltons) within minutes after administration of EGF. Administration of interteron-γ (IFN-γ) resulted in the appearance in liver nuclei of two tyrosine phosphorylated proteins (84 and 91 kilodaltons). The 84- and 91-kilodalton proteins detected after either EGF or IFN-γ administration were identified as the IFN-γ activation factors (GAF). Furthermore, gel shift analysis revealed that these GAF proteins, detected after either EGF or IFN-γ administration, specifically bound to the sis-inducible element of the c-fos promoter. Thus, GAF proteins participate in nuclear signaling in both IFN-γ and EGF pathways., Epidermal growth factor elicits a wide range of physiological responses from a variety of cell types[1-3]. All of these responses are believed to be mediated by the membrane-spanning receptor for [...]

interferon-α (IFN-α) and IFN-γ regulate gene expression by tyrosine phosphorylation of several transcripton factors that have the 91-kilodalton (p91) protein of interferon-stimulated gene factor-3 (ISGF-3) as a common component. Interferon-activated protein complexes bind enhancers present in the promoters of early response genes such as the high-affinity Fc γ receptor gene (Fc γ RI). Treatment of human peripheral blood monocytes or basophils with interleukin-3 (IL-3), IL-5, IL-10, or granulocyte-macrophage colony-stimulating factor (GM-CSF) activated DNA binding proteins that recognized the IFN-γ response region (GRR) located in the promoter of the Fc γ RI gene. Although tyrosine phosphorylation was required for the assembly of each of these GRR binding complexes, only those formed as a result at treatment with IFN-γ or IL-10 contained p91. Instead, complexes activated by IL-3 or GM-CSF contained a tyrosine-phosphorylated protein of 80 kilodaltons. Induction of Fc γ RI RNA occurred only with IFN-γ and IL-10, whereas pretreatment of cells with GM-CSF or IL-3 inhibited IFN-γ induction of Fc γ RI RNA. Thus, several cytokines other than interferons can activate putative transcription factors by tyrosine phosphorylation., Nuclear or whole-cell extracts prepared from human monocytes incubated with either IFN-γ or IFN-α contain a protein or proteins (FcRF γ) that specifically recognize the GRR in the promoter of [...]

Transcription-dependent DNA melting on the yeast GAL1 and GAL10 promoters was found to be more closely correlated with the TATA box than the transcription start site. On both these genes, melting begins about 20 base pairs downstream of the TATA box. Physical and genetic analyses suggest that RNA polymerase II associates with this region. Thus, the distance between promoter melting and the TATA box in yeast may be similar to that in higher eukaryotes, even though transcription initiates in a region about 10 to 90 base pairs farther downstream in yeast, In prokaryotes, the melting of the DNA helix at the commencement of transcription often requires only the RNA polymerase and promoter sequence elements[1]. For eukaryotic RNA polymerase II genes, this [...]

Phosphorothioate oligodeoxynucleotides containing the C-5 propyne analogs of uridine and cytidine bind RNA with high affinity and are potent antisense inhibitors of gene expression. In a cellular assay, gene-specific antisense inhibition occurred at nanomolar concentrations of oligonucleotide, was dose-dependent and exquisitely sensitive to sequence mismatches, and was correlated with the melting temperature and length of oligonucleotide. Activity was independent of RNA target site and cell type but was detectable only when the oligonucleotides were microinjected or delivered with cell-permeabilizing agents. These oligonucleotides may have important applications in therapy and in studies of gene function., Oligodeoxynucleotides (ODNs) offer great promise as antisense agents for the sequence-specific inhibition of gene expression (1). Previously, high concentrations of ODNs have been required to elicit biological effects, frequently leading [...]

PU.1 recruits the binding of a second B cell--restricted nuclear factor, NF-EM5, to a DNA site in the immunoglobulin Κ 3' enhancer. DNA binding by NF-EM5 requires a protein-protein interaction with PU.1 and specific DNA contacts. Dephosphorylated PU.1 bound to DNA but did not interact with NF-EM5. Analysis of serine-to-alanine mutations in PU.1 indicated that serine 148 [Ser.sup.148] is required for protein-protein interaction. PU.1 produced in bacteria did not interact with NF-EM5. Phosphorylation of bacterially produced PU.1 by purified casein kinase II modified it to a form that interacted with NF-EM5 and that recruited NF-EM5 to bind to DNA. Phosphopeptide analysis of bacterially produced PU.1 suggested that [Ser.sup.148]is phosphorylated by casein kinase II. This site is also phosphorylated in vivo. Expression of wild-type PU. 1 increased expression of a reporter construct containing the PU.1 and NF-EM5 binding sites nearly sixfold, whereas the [Ser.sup.148] mutant form only weakly activated transcription. These results demonstrate that phosphorylation of PU.1 at [Ser.sup.148] is necessary for interaction with NF-EM5 and suggest that this phosphorylation can regulate transcriptional activity., Modification by phosphorylation can influence either the binding to DNA or the functional activity of a number of transcription factors including SRF, Myb, Max, c-Jun, and cyclic adenosine monophosphate response [...]

The signal transducer and activator of transcription-3 (Stat3) protein is activated by the interleukin 6 (IL-6) family of cytokines, epidermal growth factor, and leptin. A protein named PIAS3 (protein inhibitor [...]

STAT (signal transducers and activators of transcription) proteins undergo cytokine-dependent phosphorylation on serine and tyrosine. STAT3, a transcription factor for acute phase response genes, was found to act as an adapter molecule in signal transduction from the type I interferon receptor. STAT3 bound to a conserved sequence in the cytoplasmic tail of the IFNAR1 chain of the receptor and underwent interferon-dependent tyrosine phosphorylation. The p85 regulatory subunit of phosphatidylinositol 3-kinase, which activates a series of serine kinases, bound to phosphorylated STAT3 and subsequently underwent tyrosine phosphorylation. Thus, STAT3 acts as an adapter to couple another signaling pathway to the interferon receptor., Interferons (IFNs) are cytokines that block the viral infection of cells, inhibit cell proliferation, and modulate cell differentiation. Type I IFNs (IFN-[Alpha], -Β, and -Ω) compete with each other for [...]

During translation errors of aminoacylation are corrected in editing reactions which ensure that an amino acid is stably attached to its corresponding transfer RNA (tRNA). Previous studies have not shown whether the tRNA nucleotides needed for effecting translational editing are the same as or distinct from those required for aminoacylation, but several considerations have suggested that they are the same. Here, designed tRNAs that are highly active for aminoacylation but are not active in translational editing are presented. The editing reaction can be controlled by manipulation of nucleotides at the corner of the L-shaped tRNA. In contrast, these manipulations do not affect aminoacylation. These results demonstrate the segregation of nucleotide determinants for the editing and aminoacylation functions of tRNA., During aminoacylation of tRNAs for protein synthesis, errors of amino acid activation (by tRNA synthetases) can occur. These errors are corrected by translational editing reactions, some of which require the [...]

The proto-oncogen-encoded transcription factor c-Jun activates genes in response to a number of inducers that act through mitogen-activated protein kinase (MAPK) signal transduction pathways. The activation of c-Jun after phosphorylation by MAPK is accompanied by a reduction in c-Jun ubiquitination and consequent stabilization of the protein. These results illustrate the relevance of regulated protein degradation in the signal-dependent control of gene expression., The ubiquitin-dependent protein degradation system is used in the cell not just to eliminate proteins that are either damaged or no longer needed. Instead, it fulfills important functions in cell [...]

For decades, molecular biologists bent on understanding how the cell controls the activity of its genes rarely paid much attention to the genes' milieu. In the living cell, the DNA [...]

The structure of the carboxyl-terminal domain of the Escherichia coli RNA polymerase α subunit (αCTD), which is regarded as the contact site for transcription activator proteins and for the promoter UP element, was determined by nuclear magnetic resonance spectroscopy. Its compact structure of four helices and two long arms enclosing its hydrophobic core shows a folding topology distinct from those of other DNA-binding proteins. The UP element binding site was found on the surface comprising helix 1, the amino-terminal end of helix 4, and the preceding loop. Mutation experiments indicated that the contact sites for transcription activator proteins are also on the same surface., Activation of gene transcription in a prokaryote system is triggered by several kinds of transcription activators (1). In the E. coli RNA polymerase holoenzyme-composed of a core enzyme, [α.sub.2]ββ', and [...]

Interferon-γ (IFN-γ) stimulates transcription of specific genes by inducing tyrosine phosphorylation of a 91-kilodalton cytoplasmic protein (termed STAT for signal transducer and activator of transcription). Stat91 was phosphorylated on a single site ([Tyr.sup.701]), and phosphorylation of this site was required for nuclear translocation, DNA binding, and gene activation. Stat84, a differentially spliced product of the same gene that lacks the 38 carboxyl-terminal amino acids of Stat91, did not activate transcription, although it was phosphorylated and translocated to the nucleus and bound DNA. Thus, Stat91 mediates activation of transcription in response to IFN-γ., Signaling from a ligand-bound cell surface receptor to the nucleus can be accomplished by tyrosine phosphorylation of latent cytoplasmic transcriptional factors that are transported to the nucleus[1, 2]. In cells [...]

In metazoans, two distinct spliceosomes catalyzing pre-messenger RNA splicing have been identified. Here, the human U11/U12 small nuclear ribonucleoprotein (snRNP), a subunit of the minor (U12-dependent) spliceosome, was isolated. Twenty U11/U12 proteins were identified, including subsets unique to the minor spliceosome or common to both spliceosomes. Common proteins include four U2 snRNP polypeptides that constitute the essential splicing factor SF3b. A 35-kilodalton U11-associated protein homologous to the U1 snRNP 70K protein was also identified. These data provide fundamental information about proteins of the minor spliceosome and shed light on its evolutionary relationship to the major spliceosome., The minor (U12-dependent) spliceosome is required for splicing a rare class of nuclear pre-mRNA introns (1). These so-called U12-type introns contain highly conserved sequence elements at the 5' splice site [...]

Bile acids regulate the transcription of genes that control cholesterol homeostasis through molecular mechanisms that are poorly understood. Physiological concentrations of free and conjugated chenodeoxycholic acid, lithocholic acid, and deoxycholic acid activated the farnesoid X receptor (FXR; NR1H4), an orphan nuclear receptor. As ligands, these bile acids and their conjugates modulated interaction of FXR with a peptide derived from steroid receptor coactivator 1. These results provide evidence for a nuclear bile acid signaling pathway that may regulate cholesterol homeostasis., Cholesterol homeostasis is achieved through the coordinate regulation of dietary cholesterol uptake, endogenous biosynthesis, and the disposal of cholesterol in the form of bile acids. Bile acids are not simply [...]

Transcription factors are often phosphorylated at multiple sites. Here it is shown that multiple phosphorylation sites on the budding yeast transcription factor Pho4 play distinct and separable roles in regulating the factor's activity. Phosphorylation of Pho4 at two sites promotes the factor's nuclear export and phosphorylation at a third site inhibits its nuclear import. Phosphorylation of a fourth site blocks the interaction of Pho4 with the transcription factor Pho2. Multiple phosphorylation sites provide overlapping and partially redundant layers of regulation that function to efficiently control the activity of Pho4., Many signaling pathways rapidly and reversibly convert extracellular signals into changes in gene expression. Phosphorylation of a transcription factor, often at multiple sites, is a common mechanism for responding to [...]

How can we know the dancer from the dance? In the field of growth factors, key intermediates in a signal transduction pathway are often identified by their association with activated [...]

Aminoglycoside antibiotics such as neomycin, getamicin, and streptomycin bind to the 16S RNA component of prokaryotic ribosomes and disturb their ability to decode mRNA and synthesize the specified new protein [...]

ZIPPING UP HORMONE ACTION Although biologists are only beginning to unravel the molecular mechanisms by which plant hormones influence gene expression, they have already discovered an astonishing evolutionary conservation between [...]

In eukaryotic cells, chromosomal genes are first transcribed into RNA as large precursors and processed into mature RNAs in the cell's nucleus. These mature RNAs are then exported out of [...]

Early in Drosophila embryogenesis, gap gene products directly repress transcription of homeotic (HOX) genes and thereby delimit HOX expression domains. Subsequently, Polycomb-group proteins maintain this repression. Currently, there is no known molecular link between gap and Polycomb-group proteins. Here, dMi-2 is identified as a protein that binds to a domain in the gap protein Hunchback that is specifically required for the repression of HOX genes. Genetic analyses show that dMi-2 participates in both Hunchback and Polycomb repression in vivo. Hence, recruitment of dMi-2 may serve as a Link between repression of HOX genes by Hunchback and Polycomb proteins., The design of animals depends on spatially restricted expression of HOX genes (1). In the early Drosophila embryo, segmentation gene products that are locally expressed delimit the domains of HOX [...]

Transcription, the making of RNA polymers inside cells, is a multi-step process. It begins with the binding of a DNA-dependent RNA polymerase to the DNA and terminates with the generation [...]