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At least 1,657 records · Page 92Linked to original sources
PubMed1994

Transcriptional induction of the mouse metallothionein-I gene in hydrogen peroxide-treated Hepa cells involves a composite major late transcription factor/antioxidant response element and metal response promoter elements.

Synthesis of metallothionein-I (MT-I) and heme oxygenase mRNAs is rapidly and transiently induced by H2O2 in mouse hepatoma cells (Hepa) and this effect is blocked by catalase. Menadione, which generates free radicals, also induces these mRNAs. Deletion mutagenesis revealed that a region between -42 and -153 in the mouse MT-I promoter was essential for induction of a CAT reporter gene. A multimer of a 16 bp sequence (-101 to -86) that includes an antioxidant response element and overlapping adenovirus major late transcription factor binding site elevated basal expression and allowed induction by H2O2 when inserted upstream of a minimal promoter. However, deletion of this region (-100 to -89) from the intact MT-I promoter (-153) did not completely eliminate response. Multiple copies of a metal response element also permitted response to H2O2. These results suggest that induction of MT-I gene transcription by H2O2 is mediated by at least two different elements within the proximal MT-I gene promoter and suggest a previously undescribed function of the MRE. Induction of MT gene transcription by ROS and the subsequent scavenging of ROS by the MT peptide is reminiscent of the metal regulatory loop and is consistent with the hypothesized protective functions of MT.

Animals↗
PubMed1980

Studies of RNA release reaction catalyzed by E. coli transcription termination factor rho using isolated ternary transcription complexes.

Protein factor rho catalyzes site-specific termination of transcription in a reaction requiring hydrolysis of nucleoside triphosphate with eventual release of RNA from RNA polymerase and DNA template. We have characterized the rho-catalyzed RNA release reaction using isolated transcription complexes. Transcription complexes containing T7 D111 DNA, RNA polymerase, and 3H-labeled nascent RNA were formed and isolated by gel filtration on an Agarose 5M column. When the ternary complexes were incubated with rho factor in the presence of ATP, or dATP, significant amounts of nascet RNA were released from the complexes as determined in a membrane filtration assay. Gel electrophoretic analysis of RNA has revealed that rho releases selected species of discrete-sized RNA from among those originally present in the ternary complexes. These results show that rho essentially acts to release RNA from those ternary complexes which have come to pause, and that this reaction proceeds in a discrete step separately from the pausing of RNA synthesis. Under the conditions used, the extent of RNA release widely varied at individual pausing sites and thus the action of rho exhibited certain site-selectivity.

Adenosine Triphosphate↗
PubMed2004

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification.

We have developed a computational method for transcriptional regulatory network inference, CARRIE (Computational Ascertainment of Regu latory Relationships Inferred from Expression), which combines microarray and promoter sequence analysis. CARRIE uses sources of data to identify the transcription factors (TFs) that regulate gene expression changes in response to a stimulus and generates testable hypotheses about the regulatory network connecting these TFs to the genes they regulate. The promoter analysis component of CARRIE, ROVER (Relative OVER-abundance of cis-elements), is highly accurate at detecting the TFs that regulate the response to a stimulus. ROVER also predicts which genes are regulated by each of these TFs. CARRIE uses these transcriptional interactions to infer a regulatory network. To demonstrate our method, we applied CARRIE to six sets of publicly available DNA microarray experiments on Saccharomyces cerevisiae. The predicted networks were validated with comparisons to literature sources, experimental TF binding data, and gene ontology biological process information.

Binding Sites↗
PubMed2006

Studies on transcriptional regulation of endogenous genes by ERF2 transcription factor in tobacco cells.

In this study, we showed that overexpression of ethylene-responsive transcription factor (ERF) 2 activated the expression of endogenous genes that have the GCC box in their promoter region, in tobacco plants. These include not only a defense-related gene, CHN50, encoding class I basic chitinase, but also a transcriptional repressor gene, ERF3. In tobacco plants constitutively expressing ERF2:glucocorticoid receptor fusion protein, treatment with dexamethazone induced a rapid increase of ERF3 mRNA and a slow increase of CHN50 mRNA. These results suggest that an antagonistic interplay of ERF2 and ERF3 is involved in the transcriptional regulation of the class I basic chitinase genes in tobacco.

Chitinases↗
PubMed2026

The transcription factors GmBBX17 and GmSTFs antagonistically regulate shade avoidance in soybean by oppositely modulating GmSRG1 transcription.

High-density planting represents a promising strategy to enhance crop productivity. However, this agronomic practice inevitably triggers shade avoidance responses, manifested as stem and petiole elongation, suppressed branching, and altered petiole angles. Elucidating the molecular underpinnings of shade avoidance remains imperative for rationalizing planting density strategies in crop production. Here, we report that soybean SHADE-REDUCED GENE 1 (GmSRG1) inhibits the stem and petiole growth both in white light and low ratio of Red:Far-red light conditions in soybean. GmSRG1 likely represents a catalytically inactive homolog of xyloglucan endotransglucosylase/hydrolase that lacks the conserved active site. Despite its enzymatic deficiency, it is associated with enhanced xyloglucan-degrading activity and prevents xyloglucan accumulation in soybean. GmBBX17 binds to the GmSRG1 promoter to repress its transcription, whereas GmSTFs (GmSTF1 and GmSTF2) transcriptionally activate GmSRG1. GmBBX17 physically interacts with GmSTFs to antagonistically regulate GmSRG1 expression. Unlike GmSRG1, its close homolog GmXTH23 is associated with increased xyloglucan accumulation and reduced xyloglucan-degrading activity, while GmSRG1 physically interacts with GmXTH23 and counteracts this GmXTH23-associated effect. Our work reveals an integrated regulatory network comprising the GmBBX17-GmSTFs transcriptional module and the GmSRG1-GmXTH23 regulatory module, which collectively govern shade avoidance architecture in soybean.

Glycine max↗
PubMed1989

A 3' exonuclease activity degrades the pseudogene 5S RNA transcript and processes the major oocyte 5S RNA transcript in Xenopus oocytes.

Transcription of the major oocyte 5S RNA gene (o) and pseudogene (psi) of Xenopus laevis yields different RNAs with three different homologous systems: oocyte microinjection, whole oocyte extract, and fractionated TFIIIA + TFIIIB + TFIIIC components. Those peculiar results are caused by a 3' RNA exonuclease activity, which is inhibited in the oocyte extract, that rapidly degrades the pseudogene 5S RNA but does not degrade as readily the chimeric RNA transcripts generated by HindIII-truncated 5S RNA pseudogenes. The same, or a similar, RNase activity processes the 130- and the 142-base-long transcripts of the major oocyte 5S RNA gene into mature 120-base-long 5S RNA. We performed site-specific mutagenesis on the somatic 5S RNA gene and changed specific nucleotides on the somatic 5S RNA. These studies indicated that the structure that confers stability to the 5S RNA in vivo and in vitro is the 9-bp helix formed in 5S RNA, but not in psi 5S RNA, by the complementary 5' and 3' ends of the molecule.

Animals↗
PubMed1990

Transcription-dependent competition for a host factor: the function and optimal sequence of the phage lambda boxA transcription antitermination signal.

Ordered development of lambdoid phages relies on systems of transcription termination and antitermination. The phage-encoded N early regulatory proteins, acting with the Nus proteins of Escherichia coli, modify RNA polymerase to a form that overrides many transcription termination signals. These modifications require cis-acting sites, nut, located downstream of the early phage promoters. The nut sites in phages lambda, 21, and P22, which share similarities but are not identical, contain two signals, boxA and boxB. We demonstrate that although a consensus sequence for the boxA signal (boxAcon), 5'CGCTCTTTA, is found only in P22, changes to consensus in the nutR sites of lambda and 21 create more effective antitermination signals than the wild-type signals. An in vivo competition assay demonstrates that a lambda nut region with boxAcon outcompetes nut regions with wild-type, as well as other variations of the boxA sequence, for the host NusB protein. This suggests that boxA influences NusB activity in N-mediated antitermination. Successful competition by boxAcon requires transcription of the nut site as well as N activation. Nucleotide replacement further demonstrates that bases at both ends of boxA are important for antitermination.

Bacterial Proteins↗
PubMed1991

Cell cycle-specific expression of the SWI4 transcription factor is required for the cell cycle regulation of HO transcription.

Expression of the HO endonuclease triggers mating-type switching in Saccharomyces cerevisiae. Transcription of the HO gene is start-dependent and restricted to the late G1/early S phase of haploid mother cells. The HO promoter contains 10 copies of a cell cycle-regulated upstream activation sequence, which is activated by SWI4 and SWI6. SWI4 mRNA levels vary at least 10-fold throughout the cell cycle and rise sharply just before the rise in HO mRNA levels. Constitutive synthesis of SWI4 mRNA leads to constitutive synthesis of HO mRNA. These data suggest that the cell cycle regulation of SWI4 mRNA is required for the tight cell cycle regulation of HO transcription. High-level constitutive synthesis of SWI4 also suppresses swi5 and swi6 mutations, suggesting that SWI4 is the predominant activator of HO transcription and that mutations in negative regulators of SWI4 could be isolated as suppressors of swi6 mutations. One recessive suppressor of swi6 (ssx1-1) that allowed high-level expression of SWI4 during alpha-factor arrest and constitutive expression of both SWI4 and HO after release from the arrest was isolated. This result suggests that SSX1 has a negative regulatory role in the cell-cycle regulation of SWI4 mRNA accumulation.

Cell Cycle↗
PubMed1995

The bacteriophage T4 middle promoter PuvsX: analysis of regions important for binding of the T4 transcriptional activator MotA and for activation of transcription.

Bacteriophage T4 middle promoters, which are transcribed using phage-modified host RNA polymerase and the T4 transcriptional activator, MotA, match the host sigma 70 consensus sequence at -10, but they have a different consensus ((t/a)(t/a)TGCTT(t/c)A) (a MotA box) at -30. While the T4 middle promoter PuvsX has these -10 and -30 motifs, it also has matches to the MotA box at -35, -51, -70, and -87. We show that MotA binds to PuvsX DNA, footprinting a region that includes the MotA boxes at -30, -35, and -51. Very high levels of MotA are required for footprinting and gel-shift experiments, and protein-DNA complexes formed in the presence of both phage-modified polymerase and MotA are more resistant to HindIII cleavage than those formed with either protein alone. These results suggest that MotA-DNA interactions may be stabilized by phage-modified polymerase. Sequences between -18 and -38 are absolutely required for MotA activation of transcription, but sequences upstream of -38 are stimulatory, particularly when chloride instead of glutamate is the major anion. Our results dissect PuvsX into a core promoter, downstream of -38, which is required for MotA activation, and an upstream region that enhances transcription especially under conditions less favourable for protein-DNA interactions.

Bacteriophage T4↗
PubMed2006

Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling.

In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 h following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 genes were repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are probably upregulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A myb24 mutant was phenotypically wild-type, but production of a myb21myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype. Exogenous jasmonate could not restore fertility to myb21 or myb21myb24 mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development.

Arabidopsis↗
PubMed1998

High levels of transcription factor RpoS (sigma S) in mviA mutants negatively affect 1,2-propanediol-dependent transcription of the cob/pdu regulon of Salmonella typhimurium LT2.

Expression of the cobalamin biosynthetic (cob) and 1,2-propanediol utilization (cob/pdu) regulon of Salmonella typhimurium LT2 is controlled at the transcriptional level by global and specific regulatory proteins. In this paper we show that mutations in the mviA gene negatively affect cob/pdu transcription in response to 1,2-propanediol in the environment. The effects of mviA mutations were consistent with its role in the regulation of RpoS levels in the cell. Null mutations in rpoS eliminated the negative effect of mviA mutations on cob/pdu transcription, and restored growth on succinate, propionate and 1,2-propanediol. In addition, mviA mutants were deficient in the utilization of succinate, propionate and 1,2-propanediol as carbon and energy sources.

Amino Acid Sequence↗
PubMed2004

Regulation of glucocorticoid-inducible hydroxysteroid sulfotransferase (SULT2A-40/41) gene transcription in primary cultured rat hepatocytes: role of CCAAT/enhancer-binding protein liver-enriched transcription factors.

The mechanism responsible for glucocorticoid receptor (GR)-mediated induction of rat hepatic hydroxysteroid sulfotransferase (SULT2A-40/41) gene transcription was investigated. We previously reported that the region of the SULT2A-40/41 5'-flanking region delimited by -158 to -77 nucleotides relative to the transcription start site was sufficient to support GR-inducible expression. This region of the SULT2A-40/41 gene does not contain a consensus glucocorticoid receptor-responsive element, but does contain two consensus sites for liver-enriched CCAAT/enhancer-binding protein (C/EBP) transcription factors. In the present study, incubation of primary cultured rat hepatocytes with a GR-activating concentration (10(-7) M) of a potent glucocorticoid, dexamethasone or triamcinolone acetonide (TA), rapidly produced increases in C/EBPalpha and C/EBPbeta nuclear protein contents, as measured by Western blot or in vitro DNA-binding activity analysis, that preceded increases in SULT2A-40/41 mRNA and protein levels. Transient cotransfection of SULT2A-40/41 reporter plasmids with a dominant negative C/EBP expression plasmid completely blocked TA-inducible SULT2A-40/41 reporter gene expression. Linker scanning and site-directed mutagenesis of the proximal SULT2A-40/41 5'-flanking region, complemented by in vitro DNA-binding analyses, indicated that the more distal C/EBP site was important for controlling SULT2A-40/41 promoter activity. These data support a role for GR-inducible C/EBPalpha and C/EBPbeta expression in the transactivation of hepatic SULT2A-40/41 expression.

Animals↗
PubMed1990

Transcriptional regulation of comC: evidence for a competence-specific transcription factor in Bacillus subtilis.

comC specifies a protein product that is required for genetic competence in Bacillus subtilis. The probable transcriptional start site of comC has been localized by high-resolution primer extension analysis and shown to be preceded by an appropriately positioned sequence that resembles the consensus promoter for the sigma A form of RNA polymerase. Low-resolution S1 nuclease transcription mapping was used to identify the comC terminator, which is located near a palindromic element recognizable in the DNA sequence. Deletion analysis of the sequence upstream from the likely promoter identified a region required in cis for the expression of comC. An overlapping, and possibly identical, sequence was shown to inhibit the expression of competence and of several late competence genes, when present in multiple copies. This was interpreted as due to the titration of a positively acting competence transcription factor (CTF) by multiple copies of the promoter-bearing fragment. In crude lysates of B. subtilis grown to competence, a DNA-binding activity that appeared to be specific for the comC promoter fragment was detected by gel retardation assays. This activity, postulated to be due to CTF, was detected only following growth in competence medium, only in the stationary phase of growth, and was dependent on the expression of ComA, a known competence-regulatory factor. In the presence of the mecA42 mutation, the ComA requirement for CTF activity was bypassed, and CTF activity could be detected in lysates prepared from a strain grown in complex medium. This behavior suggested that either the expression or the activation of CTF was regulated in a competence-specific manner. Comparison of the putative CTF-binding site defined by deletion analysis with a similarly positioned sequence upstream from the start site of the late competence gene comG revealed that both sequences contained palindromes, with 5 of 6 identical base pairs in each arm. It is suggested that these palindromic sequences comprise recognition elements for CTF binding and that CTF binding must occur for the appropriate expression of late competence genes.

Bacillus subtilis↗
PubMed1992

The Agrobacterium tumefaciens vir gene transcriptional activator virG is transcriptionally induced by acid pH and other stress stimuli.

A set of Agrobacterium tumefaciens operons required for pathogenesis is coordinately induced during plant infection by the VirA and VirG proteins. The intracellular concentration of VirG increases in response to acidic media, and this response was proposed to be regulated at the level of transcription at a promoter (P2) that resembles the Escherichia coli heat shock promoters. To test this hypothesis, we first constructed a virG-lacZ transcriptional fusion. A strain containing this fusion had higher levels of beta-galactosidase activity in acidic media than in media at neutral pH. Second, primer extension analysis of virG indicated that acidic media stimulated the transcription of this promoter. To determine whether P2 is a member of a heat shock-like regulon in A. tumefaciens, five agents that induce E. coli heat shock genes were tested for their abilities to induce a P2-lacZ fusion in A. tumefaciens. P2 was most strongly induced by low pH, was moderately stimulated by CdCl2 or mitomycin C, and was slightly induced by P2 as measured by beta-galactosidase activity and primer extension analysis. Induction by these treatments did not require any Ti plasmid-encoded function or the chromosomally encoded RecA protein. We also pulse-labeled cellular proteins after a shift to low pH and detected several proteins whose synthesis was induced by these conditions. We conclude that P2 is primarily induced by acid pH and secondarily by certain other stimuli, each of which is stressful to cell growth. This stress induction is at least partly independent of the heat shock and SOS responses.

Agrobacterium tumefaciens↗
PubMed1996

Transcription of the Anabaena sp. strain PCC 7120 ntcA gene: multiple transcripts and NtcA binding.

The Anabaena sp. strain PCC 7120 ntcA gene showed multiple transcripts with different 5' ends. The relative abundance of transcripts varied in response to nitrogen availability. The ntcA product, NtcA, showed binding to the promoter region of its own gene. The binding site mapped to a region between the transcription start site used under nitrogen-replete conditions and the start sites used under nitrogen-limiting conditions, suggesting that NtcA regulates its own expression.

Amino Acid Sequence↗
PubMed1994

Ordered assembly of a functional preinitiation transcription complex, containing vaccinia virus early transcription factor and RNA polymerase, on an immobilized template.

A functional preinitiation transcription complex was formed by incubating vaccinia virus early transcription factor VETF and RAP94+ RNA polymerase with an early promoter template immobilized on paramagnetic particles. A preferred order of assembly, VETF followed by RNA polymerase, was demonstrated by stepwise addition experiments. ATP was unnecessary for preinitiation transcription complex formation, but divalent cations were required specifically for the association of RNA polymerase.

Base Sequence↗
PubMed1995

Sp1 transcription factor is required for in vitro basal and Tat-activated transcription from the human immunodeficiency virus type 1 long terminal repeat.

Sp1-DNA binding sites have been reported to be essential for basal and Tat-activated transcription of the human immunodeficiency virus type 1 long terminal repeat (LTR). The role of the Sp1 transcription factor itself in regulation of the retroviral LTR, however, has not been clearly defined. It is now known, for instance, that the Sp1-DNA binding sites function also as thyroid hormone receptor response elements (V. Desay-Yajnik and H. H. Samuels, Mol. Cell. Biol. 13:5057-5069, 1993). In this report, we present data that demonstrate a strict requirement for Sp1 for both basal transcription and Tat-mediated trans activation of the human immunodeficiency virus type 1 LTR in vitro.

Adenoviruses, Human↗
PubMed2003

Transcription factor YY1 binds to the murine beta interferon promoter and regulates its transcriptional capacity with a dual activator/repressor role.

The induction of the beta interferon (IFN-beta) gene constitutes one of the first responses of the cell to virus infection. Its regulation is achieved through an intricate combination of virus-induced binding of transcription factors and local chromatin remodeling. In this work, we demonstrate that transcription factor YY1, known to interact with histone deacetylases (HDAC) and histone acetyltransferases, has a dual activator/repressor role during the regulation of the IFN-beta promoter activity. We show that YY1 specifically binds in vitro and in vivo to the murine IFN-beta promoter at positions -90 and -122. Overexpression of YY1 strongly repressed the transcriptional capacity of a stably integrated IFN-beta promoter fused to a chloramphenicol acetyltransferase reporter gene as well as the endogenous IFN activity of murine L929 cells via an HDAC activity. Stably integrated IFN-beta promoters mutated at the -90 site were no longer repressed by YY1, could no longer be activated by trichostatin A, displayed a retarded postinduction turn off, and a reduced virus-induced activity. Introduction of a mutation at the -122 site did not affect YY1-induced repression, but promoters with this mutation displayed a reduced virus-induced activity. Stably integrated full-length promoters (from position -330 to +20) mutated at both YY1-binding sites displayed extremely reduced promoter activities. We conclude that YY1 has a dual activator/repressor role on IFN-beta promoter activity depending on its binding site and time after infection.

Animals↗