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PubMed2001

Involvement of two distinct catabolite-responsive elements in catabolite repression of the Bacillus subtilis myo-inositol (iol) operon.

The Bacillus subtilis inositol operon (iolABCDEFGHIJ) is involved in myo-inositol catabolism. Glucose repression of the iol operon induced by inositol is exerted through catabolite repression mediated by CcpA and the iol induction system mediated by IolR. In this study, we identified two iol catabolite-responsive elements (cre's), to which CcpA complexed with P-Ser-HPr or P-Ser-Crh probably binds. One is located in iolB (cre-iolB, nucleotides +2397 to +2411; +1 is the transcription initiation nucleotide), which was the only cre-iol found in the previous cre search of the B. subtilis genome using a query sequence of WTGNAANCGNWNNCW (W stands for A or T, and N stands for any base). Deletion and base substitution analysis of the iol region indicated that cre-iolB functions even if it is located far downstream of the iol promoter. Further deletion and base substitution analysis revealed another cre located between the iol promoter and the iolA gene (cre-iiolA, nucleotides +86 to +100); the prefix "i" indicates a location in the intergenic region. Both cre-iiolA and cre-iolB appeared to be recognized to almost the same extent by CcpA complexed with either P-Ser-HPr or P-Ser-Crh. Sequence alignment of the six known cre's, including cre-iiolA, which were not revealed in the previous cre search, exhibited another consensus sequence of WTGAAARCGYTTWWN (R stands for A or G, and Y stands for C or T); the right two thymines (TT) were found to be essential for the function of cre-iiolA by means of base substitution analysis. A cre search with this query sequence led to the finding of 14 additional putative cre's.

Bacillus subtilis↗
PubMed2001

An IRP-like protein from Plasmodium falciparum binds to a mammalian iron-responsive element.

This study cloned and sequenced the complementary DNA (cDNA) encoding of a putative malarial iron responsive element-binding protein (PfIRPa) and confirmed its identity to the previously identified iron-regulatory protein (IRP)-like cDNA from Plasmodium falciparum. Sequence alignment showed that the plasmodial sequence has 47% identity with human IRP1. Hemoglobin-free lysates obtained from erythrocyte-stage P falciparum contain a protein that binds a consensus mammalian iron-responsive element (IRE), indicating that a protein(s) with iron-regulatory activity was present in the lysates. IRE-binding activity was found to be iron regulated in the electrophoretic mobility shift assays. Western blot analysis showed a 2-fold increase in the level of PfIRPa in the desferrioxamine-treated cultures versus control or iron-supplemented cells. Malarial IRP was detected by anti-PfIRPa antibody in the IRE-protein complex from P falciparum lysates. Immunofluorescence studies confirmed the presence of PfIRPa in the infected red blood cells. These findings demonstrate that erythrocyte P falciparum contains an iron-regulated IRP that binds a mammalian consensus IRE sequence, raising the possibility that the malaria parasite expresses transcripts that contain IREs and are iron-dependently regulated.

Aconitate Hydratase↗
PubMed2001

Heterodimerization of mineralocorticoid and glucocorticoid receptors at a novel negative response element of the 5-HT1A receptor gene.

Negative regulation of neuronal serotonin (5-HT1A) receptor levels by glucocorticoids in vivo may contribute to depression. Both types I (mineralocorticoid) and II (glucocorticoid) receptors (MR and GR, respectively) participate in corticosteroid-induced transcriptional repression of the 5-HT1A gene; however, the precise mechanism is unclear. A direct repeat 6-base pair glucocorticoid response element (GRE) half-site 5'-TGTCCT separated by 6 nucleotides was conserved in human, mouse, and rat 5-HT1A receptor promoters. In SN-48 neuronal cells that express MR, GR, and 5-HT1A receptors, deletion or inactivation of the nGRE (negative GRE) eliminated negative regulation of the rat 5-HT1A or heterologous promoters by corticosteroids, whereas its inclusion conferred corticosteroid-induced inhibition to a heterologous promoter. Bacterially expressed recombinant MR and GR preferentially bound to the nGRE as a heterodimer, as identified in nuclear extracts of MR/GR-transfected COS-7 cells, and with higher affinity than MR or GR homodimers. In SN48 and COS-7 cells, concentration-dependent coactivation of MR and GR was required for maximal inhibitory action by corticosteroids and was abrogated in the L501P-GR mutant lacking DNA binding activity. Corticosteroid-mediated transcriptional inhibition was greater for MR/GR in combination than for MR or GR alone. These data represent the first identification of an nMRE/GRE and indicate that heterodimerization of MR and GR mediates direct corticosteroid-induced transrepression of the 5-HT1A receptor promoter.

Animals↗
PubMed2006

Cyclic AMP stimulates MEG3 gene expression in cells through a cAMP-response element (CRE) in the MEG3 proximal promoter region.

MEG3 is a human maternally expressed gene that potentially acts as a non-coding RNA. Our laboratory found that a cDNA isoform of MEG3, MEG3a, inhibits cell proliferation. MEG3 is highly expressed in the normal human pituitary but not expressed in clinically non-functioning pituitary tumors, suggesting that this imprinted gene may be involved in pituitary tumorigenesis. Previously we demonstrated that hypermethylation of the MEG3 promoter region is associated with the loss of MEG3 expression in pituitary tumors, potentially by blocking the binding of transcription factors to their cis-elements. To further investigate the cis- and trans-factors that are important for the regulation of MEG3, we have characterized the human MEG3 promoter. A single transcription initiation site was identified by 5' RACE. Up to 5kb of the 5'-flanking region of MEG3 gene was cloned into a reporter plasmid. Deletion and mutation analysis suggest that a cAMP response element (CRE), located between -69 and -49 of the MEG3 proximal promoter region, is critical for promoter activity. Consistent with this finding, Northern blot analysis demonstrate that elevated intracellular cAMP levels stimulate MEG3 expression in human fibroblasts in culture. Furthermore, gel shifting, ChIP analysis, and co-transfection experiments show that CREB directly binds to the CRE site and stimulates MEG3 promoter activity. Therefore, MEG3 is a downstream target gene of cAMP. Together with the anti-proliferative function of cAMP, our data suggest that MEG3 may interact with the cAMP-dependent signaling pathway to be involved in the control of cell proliferation and other cAMP-related physiological functions.

Base Sequence↗
PubMed2003

[Changes in the phosphorylation of cAMP response element binding protein in the rat nucleus accumbens after acute and chronic ethanol administration].

To define the molecular basis of ethanol dependence, changes in the phosphorylation of cAMP response element binding protein (CREB) in the nucleus accumbens of rats after acute and chronic ethanol administration were detected using immunohistochemistry. The results demonstrate that the expression of phospho-CREB (p-CREB) protein in the rat nucleus accumbens significantly increased after 15 min of acute ethanol exposure, reaching a peak at 30 min after ethanol administration. The increment remained after 1 or 6 h of ethanol exposure compared to the control rats. In contrast, chronic intake of ethanol solution obviously decreased the expression of p-CREB protein compared to the control rats. The decrement remained 24 h or 72 h after ethanol withdrawal, and returned to the control levels after 7 d of ethanol withdrawal. The results suggest that an acute ethanol administration led to an increase in the phosphorylation of CREB in the nucleus accumbens, but chronic ethanol administration produced a decrement, which is possibly one of the molecular mechanisms of alcohol dependence.

Alcoholism↗
PubMed2005

Regulation of regional expression in rat brain PC2 by thyroid hormone/characterization of novel negative thyroid hormone response elements in the PC2 promoter.

The prohormone convertases (PCs) PC1 and PC2 are involved in the tissue-specific endoproteolytic processing of neuropeptide precursors within the secretory pathway. We previously showed that changes in thyroid status altered pituitary PC2 mRNA and that this regulation was due to triiodothyronine-dependent interaction of the thyroid hormone receptor (TR) with negative thyroid hormone response elements (nTREs) contained in a large proximal region of the human PC2 promoter. In the current study, we examined the in vivo regulation of brain PC2 mRNA by thyroid status and found that 6-n-propyl-2-thiouracil-induced hypothyroidism stimulated, whereas thyroxine-induced hyperthyroidism suppressed, PC2 mRNA levels in the rat hypothalamus and cerebral cortex. To address the mechanism of T3 regulation of the PC2 gene, we used human PC2 (hPC2) promoter constructs transiently transfected into GH3 cells and found that triiodothyronine negatively and 9-cis-retinoic acid positively regulated hPC2 promoter activity. EMSAs, using purified TRalpha1 and retinoid X receptor-beta (RXRbeta) proteins demonstrated that TRalpha bound the distal putative nTRE-containing oligonucleotide in the PC2 promoter, and RXR bound to both nTRE-containing oligonucleotides. EMSAs with oligonucleotides containing deletion mutations of the nTREs demonstrated that the binding to TR and RXR separately is reduced, but specific binding to TR and RXR together persists even with deletion of each putative nTRE. We conclude that there are two novel TRE-like sequences in the hPC2 promoter and that these regions act in concert in a unique manner to facilitate the effects of thyroid hormone and 9-cis-retinoic acid on PC2.

Alitretinoin↗
PubMed2003

Rapid electrical and delayed molecular signals regulate the serum response element after nerve injury: convergence of injury and learning signals.

Axotomy elicits changes in gene expression, but little is known about how information from the site of injury is communicated to the cell nucleus. We crushed nerves in Aplysia californica and the sciatic nerve in the mouse and found short- and long-term activation of an Elk1-SRF transcription complex that binds to the serum response element (SRE). The enhanced short-term binding appeared rapidly and was attributed to the injury-induced activation of an Elk1 kinase that phosphorylates Elk1 at ser383. This kinase is the previously described Aplysia (ap) ERK2 homologue, apMAPK. Nerve crush evoked action potentials that propagated along the axon to the cell soma. Exposing axons to medium containing high K(+), which evoked a similar burst of spikes, or bathing the ganglia in 20 microM serotonin (5HT) for 20 min, activated the apMAPK and enhanced SRE binding. Since 5HT is released in response to electrical activity, our data indicate that the short-term process is initiated by an injury-induced electrical discharge that causes the release of 5HT which activates apMAPK. 5HT is also released in response to noxious stimuli for aversive learning. Hence, apMAPK is a point of convergence for injury signals and learning signals. The delay before the onset of the long-term SRE binding was reduced when the crush was closer to the ganglion and was attributed to an Elk1 kinase that is activated by injury in the axon and retrogradely transported to the cell body. Although this Elk1 kinase phosphorylates mammalian rElk1 at ser383, it is distinct from apMAPK.

Action Potentials↗
PubMed2000

The peroxisome proliferator response element of the gene encoding the peroxisomal beta-oxidation enzyme enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase is a target for constitutive androstane receptor beta/9-cis-retinoic acid receptor-mediated transactivation.

The genes encoding the first two enzymes of the peroxisomal beta-oxidation pathway, acyl-CoA oxidase (AOx) and enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase (HD), contain upstream cis-acting regulatory regions termed peroxisome proliferator response elements (PPRE). Transcription of these genes is mediated through the binding of peroxisome proliferator-activated receptor alpha (PPARalpha), which binds to a PPRE as a heterodimer with the 9-cis-retinoic acid receptor (RXRalpha). Here we demonstrate that the HD-PPRE is also a target for the constitutive androstane receptor beta (CARbeta). In vitro binding analysis showed that CARbeta bound the HD-PPRE, but not the AOx-PPRE, as a heterodimer with RXRalpha. Binding of CARbeta/RXRalpha to the HD-PPRE occurred via determinants that overlap partially with those required for PPARalpha/RXRalpha binding. In vivo, CARbeta/RXRalpha activated transcription from an HD-PPRE luciferase reporter construct. Interestingly, CARbeta was shown to also modulate PPARalpha/RXRalpha-mediated transactivation in a response element-specific manner. In the presence of the peroxisome proliferator, Wy-14,643, CARbeta had no effect on PPARalpha/RXRalpha-mediated transactivation from the HD-PPRE but antagonized transactivation from the AOx-PPRE in both the presence and the absence of proliferator. Our results illustrate that transcription of the AOx and HD genes is differentially regulated by CARbeta and that the HD gene is a specific target for regulation by CARbeta. Overall, this study proposes a novel role for CARbeta in the regulation of peroxisomal beta-oxidation.

Acyl-CoA Oxidase↗
PubMed1991

Changes in cyclic adenosine monophosphate-responsive element binding proteins in rat hepatomas.

We applied Southwestern and Western blotting and gel retardation techniques to investigate the changes that occur in the cyclic adenosine monophosphate (cAMP)-responsive element (CRE) binding (CREB) proteins in rapidly growing, chemically induced 5123tc and 5123D Morris hepatomas. Using the CRE sequences from the c-fos, E2A, and somatostatin gene promoters, we identified in the nuclear proteins from normal unstimulated or proliferating rat liver cells six different protein factors of Mr 34,000, 36,000, 40,000, 47,000, 56,000, and 72,000 capable of binding to the element. The Mr 47,000 protein had the highest specificity for the core CRE, suggesting its importance in cAMP-mediated gene expression. We could not find the Mr 47,000 CREB protein in the 5123tc and 5123D hepatomas. Our efforts to detect this protein in the tumors by (a) using the CRE sequence from different gene promoters, (b) altering the protocol for extracting nuclear proteins, or (c) attempting to restore its DNA-binding property by phosphorylation [with endogenous protein kinase(s), a catalytic subunit of cAMP-dependent protein kinase, and protein kinase C/dephosphorylation (with alkaline phosphatase)] were unsuccessful. The loss of tje Mr 47,000 CREB protein from solid tumors of the Morris hepatoma is likely to be related to the neoplastic properties of the tumor cell rather than to cell growth because the level of this protein remained unchanged during a 6-day period of liver regeneration. The nuclear extract from the Morris hepatoma that did not have the Mr 47,000 CRE-binding factor contained proteins immunologically related to the CREB, c-Jun, and c-Fos proteins. We conclude that the Mr 47,000 factor represents a distinct member of the CRE-binding protein family and that its absence from the hepatomas may lead to aberrant expression of cAMP-inducible genes.

Animals↗
PubMed1997

Defining a functional androgen responsive element in the 5' far upstream flanking region of the prostate-specific antigen gene.

Previously, an androgen responsive element (ARE or promoter ARE) was identified in the proximal promoter region of the prostate-specific antigen (PSA) gene. The proximal promoter fragment could mediate androgen induction of expression of a heterologous reporter gene in androgen receptor (AR)-less cells with exogenous AR in co-transfection assays. However, it exerted little androgen inducibility in androgen sensitive human prostate cells, LNCaP, which produce PSA mRNA and protein. In this study, we have identified a second functional ARE (or upstream ARE) approximately 4 kb upstream of the cap site of the PSA transcript. Interestingly, although the AREs are necessary for androgen induction, the DNA sequences surrounding the upstream ARE are also required for androgen induction by the PSA promoter in LNCaP cells. The results indicated that the upstream DNA sequences can cooperate with either ARE to mediate androgen induced gene expression in LNCaP cells.

Cell Nucleus↗
PubMed2001

Nrf2-dependent activation of the antioxidant responsive element by tert-butylhydroquinone is independent of oxidative stress in IMR-32 human neuroblastoma cells.

The antioxidant responsive element (ARE) is a cis-acting regulatory element located in the 5'-flanking region of several genes encoding phase II detoxification enzymes, including NAD(P)H:quinone oxidoreductase (NQO1). We report here that activation of the NQO1 ARE by tert-butylhydroquinone (tBHQ) is dependent on Nrf2 and not oxidative stress in IMR-32 human neuroblastoma cells. Overexpression of wild-type Nrf2 activated ARE in a dose-dependent manner, and ARE activation by tBHQ or diethyl maleate (DEM) was inhibited by dominant/negative Nrf2 not by dominant/negative c-Jun. According to our observation, the palindromic sequence (5' to the core) and the GC box in the ARE core sequence are essential for maximal inducibility by tBHQ or DEM. Overexpression of Nrf2 selectively activated wild-type ARE up to 24 h. In addition, a dramatic nuclear translocation of Nrf2 by tBHQ supports a role for Nrf2 in ARE activation. Although oxidative stress is hypothesized to be a major driving force for ARE activation, pretreatment of antioxidant or antioxidant enzyme did not block tBHQ-mediated ARE activation. In contrast, ARE activation by DEM was inhibited by antioxidants or catalase. These results suggest that ARE activation signals from tBHQ and DEM converge at Nrf2 transcription factor through independent mechanisms.

Antioxidants↗
PubMed1991

Different superstructural features of the light responsive elements of the pea genes rbcS-3A and rbcS-3.6.

Analyses of the DNA sequences, named Light Responsive Elements (LREs), relevant in the photoactivation of the two pea genes rbcS-3A and rbcS-3.6, encoding the same protein but differently expressed, have been carried out, taking advantage of two complementary methods; a theoretical analysis, based on conformational energy calculations, and an experimental evaluation of LREs curvature, derived from gel electrophoretic mobilities of multimers of the LREs and of oligonucleotides corresponding to the three boxes in which they can be dissected. Theoretical and experimental analyses show that the curvature of the rbcS-3A LRE is larger than that of rbcS-3.6 LRE, and seems to be correlated with rbcS-3A higher transcription efficiency.

Base Sequence↗
PubMed1996

Enhancement of nucleocytoplasmic export of HTLV-1 Rex mRNA through cis and trans interactions of the mRNA with the complex of Rex protein and Rex-responsive element.

p27 rex of HTLV-1 promotes nucleocytoplasmic export of viral mRNAs through binding of the Rex-response element (RexRE) present at the 3' end of the viral transcripts in cis with respect to the ORFs of the viral mRNAs. We have found that expression of the RexRE in trans, as a separate RNA, still allows Rex protein to promote export of viral mRNAs lacking the RexRE. The data suggest the formation of a ternary complex between Rex protein, RexRE and upstream elements of viral mRNA and hence the existence of secondary sites of interaction between Rex protein and viral RNAs.

Animals↗
PubMed1996

Overlapping but unique DNA binding specificities of the Ah receptor and constitutive dioxin-responsive element binding proteins from human keratinocytes.

To understand the relationships between the protein architecture assembled on dioxin-responsive elements (DRE) and transcriptional regulation by dioxin in human keratinocytes, the nuclear DRE-binding proteins from human keratinocytes were identified and characterized. In addition to the aryl hydrocarbon receptor (AHR) complex inducible by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), nuclear extracts from 3 human keratinocyte cell lines also contained one or more proteins that bound specifically to the DRE but whose levels were unaffected by TCDD or by anti-AHR antibody pretreatment. Alteration of a conserved T, within the core DRE sequence needed for transcriptional activation by the AHR complex, did not affect AHR binding but severely affected the ability of the constitutive proteins to bind. These data suggest that the nonidentical interplay of the AHR and constitutive DRE-binding proteins on the DRE is important in the regulation of genes whose expression is controlled by DRE.

Base Sequence↗
PubMed2000

Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression.

Ethylene-responsive element binding factors (ERFs) are members of a novel family of transcription factors that are specific to plants. A highly conserved DNA binding domain known as the ERF domain is the unique feature of this protein family. To characterize in detail this family of transcription factors, we isolated Arabidopsis cDNAs encoding five different ERF proteins (AtERF1 to AtERF5) and analyzed their structure, DNA binding preference, transactivation ability, and mRNA expression profiles. The isolated AtERFs were placed into three classes based on amino acid identity within the ERF domain, although all five displayed GCC box-specific binding activity. AtERF1, AtERF2, and AtERF5 functioned as activators of GCC box-dependent transcription in Arabidopsis leaves. By contrast, AtERF3 and AtERF4 acted as repressors that downregulated not only basal transcription levels of a reporter gene but also the transactivation activity of other transcription factors. The AtERF genes were differentially regulated by ethylene and by abiotic stress conditions, such as wounding, cold, high salinity, or drought, via ETHYLENE-INSENSITIVE2 (EIN2)-dependent or -independent pathways. Cycloheximide, a protein synthesis inhibitor, also induced marked accumulation of AtERF mRNAs. Thus, we conclude that AtERFs are factors that respond to extracellular signals to modulate GCC box-mediated gene expression positively or negatively.

Amino Acid Sequence↗
PubMed1988

Binding of a cytosolic protein to the iron-responsive element of human ferritin messenger RNA.

The human ferritin H chain messenger RNA contains a specific iron-responsive element (IRE) in its 5' untranslated region, which mediates regulation by iron of ferritin translation. An RNA gel retardation assay was used to demonstrate the affinity of a specific cytosolic binding protein for the IRE. A single-base deletion in the IRE eliminated both the interaction of the cytoplasmic protein with the IRE and translational regulation. Thus, the regulatory potential of the IRE correlates with its capacity to specifically interact with proteins. Titration curves of binding activity after treatment of cells with an iron chelator suggest that the factor acts as a repressor of ferritin translation.

Base Composition↗
PubMed1991

3,5,3'-triiodothyronine receptor auxiliary protein (TRAP) enhances receptor binding by interactions within the thyroid hormone response element.

We have previously demonstrated that binding of in vitro synthesized thyroid hormone receptor (TR) to thyroid hormone response elements (TREs) is enhanced by the addition of nuclear extracts from several different cell types, suggesting that binding of TR is partially dependent on a T3 receptor auxiliary protein (TRAP). We have used the avidin-biotin complex DNA-binding assay to discriminate between regions of TREs that bind TR alone and sites that are influenced by interactions with TRAP. Mutations in the TREs from rat GH and glycoprotein hormone alpha-subunit genes show that a specific DNA sequence is required for TRAP-mediated enhancement of TR binding. Mutations in the B half-site of the rat GH TRE or in similar sequences [(T/A)GGGA] in the alpha-subunit TRE ablate the enhancement of TR binding by TRAP. Furthermore, binding of TR to a natural half-site in the TSH beta-subunit gene (bases -16 to 6), which lacks an additional AGGGA-like sequence, is not enhanced by the addition of TRAP. Binding of TR to TREs was also tested at physiological salt concentrations in the avidin-biotin complex DNA-binding assay. Binding of human TR beta to TREs decreases dramatically at 140 mM KCl compared to binding at 50 mM KCl; however, the addition of TRAP enhances the binding to almost 4-fold of basal binding, suggesting that TRAP may be important for stabilization of TR binding to TREs in the cell.

Animals↗