Electrophoretic Experiments Research Articles

A Donnan potential model for metal sorption onto Bacillus subtilis

In this study, we conducted electrophoretic mobility, potentiometric titration, and metal sorption experiments to investigate the surface charge characteristics of Bacillus subtilis and the electrostatic interactions between metal cations and the cell surface electric field. Electrophoretic mobility experiments performed as a function of pH and ionic strength show an isoelectric point of pH 2.4, with the magnitude of the electrokinetic potential increasing with increasing pH, and decreasing with increasing ionic strength. Potentiometric titration experiments conducted from pH 2.4 to 9 yield an average surface charge excess of 1.6 μmol/mg (dry mass). Corresponding cell wall charge density values were used to calculate the Donnan potential (Ψ DON) as function of pH and ionic strength. Metal sorption experiments conducted with Ca(II), Sr(II), and Ba(II) exhibit strong ionic strength dependence, suggesting that the metal ions are bound to the bacterial cell wall via an outer-sphere complexation mechanism. Intrinsic metal sorption constants for the sorption reactions were determined by correcting the apparent sorption constant with the Boltzmann factor. A 1:2 metal-ligand stoichiometry provides the best fit to the experimental data with log K 2 int values of 5.9 ± 0.3, 6.0 ± 0.2, 6.2 ± 0.2 for Ca(II), Sr(II), and Ba(II) respectively. Electrophoretic mobility measurements of cells sorbed with Ca(II), Sr(II), and Ba(II) support the 1:2 sorption stoichiometry. These results indicate that electrical potential parameters derived from the Donnan model can be applied to predict metal binding onto bacterial surfaces over a wide range of pH and ionic strength conditions.

Triple helix formation with Drosophila satellite repeats. Unexpected stabilization by copper ions.

The Drosophila melanogaster (AAGAGAG)(n) satellite repeat represents up to 1.5% of the entire fly genome and may adopt non-B DNA structures such as pyrimidine triple helices. UV melting and electrophoretic mobility shift assay experiments were used to monitor the stability of intermolecular triple helices as a function of size, pH, and backbone or base modification. Three to four repeats of the heptanucleotide motif were sufficient to allow the formation of a stable complex, especially when modified TFOs were used. Unexpectedly, low concentrations (40-100 microM) of Cu(2+) were found to favor strongly pyrimidine triplex formation under near-physiological conditions. In contrast, a much higher magnesium concentration was required to stabilize these triplexes significantly, suggesting that copper may be an essential stabilizing factor for pyrimidine triplexes.

On experimental aspects of electrophoretic NMR

AbstractArtefacts in electrophoretic NMR experiments are investigated in detail. We identify electroosmosis, sample heating, and gas development on the electrodes as main error sources and suggest experimental strategies and setups to suppress their influence on the monitored electrophoretic mobilities. We hereby demonstrate essentially artefact‐free experiments up to currents and electric fields 3 mA and 70 V/cm, respectively. © 2004 Wiley Periodicals, Inc. Concepts Magn Reson Part A 22A: 61–68, 2004

Aggregation and other intermolecular interactions of biological buffers observed by capillary electrophoresis and UV photometry

Electrophoretic and photometric experiments strongly indicate that monovalent anions, which arise by deprotonation of the nitrogen atom in zwitterionic Good’s buffers 3-(cyclohexylamino)-2-hydroxy-1-propanesulfonic acid (CAPSO) and 3-morpholinopropanesulfonic acid (MOPS), spontaneously aggregate. Cationic migration of sanguinarine (SA) and chelerythrine (CHE) in highly alkaline 1,3-bis[tris(hydroxymethyl)methylamino]propane (Bis–Tris–propane), in which the concentration of cations of both alkaloids is negligible, may be explained by the existence of an aggregate, which contains uncharged sanguinarine or chelerythrine and one monovalent cation of Bis–Tris–propane at least. Tendency of tris(hydroxymethyl)aminomethane (Tris), bis (2-hydroxyethyl)iminotris(hydroxymethyl)methane (Bis–Tris) and Bis–Tris–propane cations to ion pairing with synthetic cluster borane anions and with fused silica markedly rises up with the size and charge of these cations. The drop in mobility of cluster borane compounds sometimes exceeds 50% of their mobility found at identical pH and ionic strength in buffers with sodium cation. The electroosmosis drop approached 70% if background electrolyte contained Bis–Tris–propane cations instead of sodium cations. Nitrate, taken as a model inorganic ion, and four randomly chosen organic anions interacted markedly less with Tris, Bis–Tris and Bis–Tris–propane cations than cluster borane anions. 2-( N-morpholino)ethanesulfonic (MES) acid anions present in background electrolyte affect the ion pairing of Tris, Bis–Tris and Bis–Tris–propane cations with anionic analytes and, in this way influence also mobilites of these anionic analytes. Limited hydrophilicity at least one of interacting species appears to be the most probable cause of observed intermolecular interactions of biological buffers.

Positive and Negative Modulation of the Transcriptional Activity of the ETS Factor ESE-1 through Interaction with p300, CREB-binding Protein, and Ku 70/86

Epithelium-specific ETS (ESE)-1 is a prototypic member of a novel subset of the ETS transcription factor family that is predominantly expressed in cells of epithelial origin but can also be induced in other cell types including vascular endothelial and smooth muscle cells in response to inflammatory stimuli. To further define the molecular mechanisms by which the transcriptional activity of ESE-1 is regulated, we have focused our attention on identifying proteins that interact with ESE-1. We have determined that Ku70, Ku86, p300, and CREB-binding protein (CBP) are ESE-1 interacting proteins. The Ku proteins have previously been shown to bind to breaks in DNA where they function to recruit additional proteins that promote DNA repair. Interestingly, Ku70 and Ku 86 negatively regulate the transcriptional activity of ESE-1. Using a series of deletion constructs, we have determined that the Ku proteins bind to the DNA-binding domain of ESE-1. The Ku proteins inhibit the ability of ESE-1 to bind to oligonucleotide probes in gel mobility shift assays. The finding that Ku proteins can interact with other transcription factors and block their function has not been previously demonstrated. In contrast, co-transfection of p300 and CBP with ESE-1 enhances the transcriptional activity of ESE-1. Moreover, the induction of ESE-1 in response to inflammatory cytokine interleukin-1 is associated with a parallel increase of the expression of p300 in vascular endothelial cells, suggesting that in the setting of inflammation, the transcriptional activity of ESE-1 is positively modulated by interaction with the transcriptional co-activator p300. In summary, our results demonstrated that the activity of ESE-1 is positively and negatively modulated by other interacting proteins including Ku70, Ku86, p300, and CBP.

The coffee diterpene kahweol suppress the inducible nitric oxide synthase expression in macrophages

Excessive nitric oxide production by inducible nitric oxide synthase (iNOS) in stimulated inflammatory cells is thought to be a causative factor of cellular injury in cases of inflammation. In recent studies, it has been shown that kahweol, coffee-specific diterpene, exhibit chemoprotective effects. In this study, we investigated the effects of kahweol on the production of and the expression of inducible nitric oxide synthase (iNOS) in lipopolysaccharide (LPS)-activated RAW 264.7 macrophages. The nitrite production induced by LPS was markedly reduced in a dose-dependent manner. In addition, kahweol suppressed the expression of iNOS protein and iNOS mRNA. Since iNOS transcription has been shown to be under the control of the transcription factor, NF-κB, the effects of kahweol on NF-κB activation were examined. Transient transfection experiments showed that kahweol inhibited NF-κB-dependent transcriptional activity. Moreover, electrophoretic mobility shift assay experiments indicated that kahweol blocked the LPS-induced activation of NF-κB. The results of these studies suggest that the suppression of the transcriptional activation of iNOS by kahweol might be mediated through the inhibition of NF-κB activation. Taken together, the results of our study provide evidence that kahweol possess an anti-inflammatory potential, which constitutes a previously unrecognized biologic activity, and which may provide new insights into the inflammatory process.

Stress tolerance and glucose insensitive phenotypes in Arabidopsis overexpressing the CpMYB10 transcription factor gene.

The resurrection plant Craterostigma plantagineum has the ability to survive complete dehydration. In an attempt to further understand desiccation tolerance in this plant, the CpMYB10 transcription factor gene was functionally characterized. CpMYB10 is rapidly induced by dehydration and abscisic acid (ABA) treatments in leaves and roots, but no expression was detected in fully hydrated tissues. Electrophoretic mobility shift assay experiments showed binding of rCpMYB10 to specific mybRE elements within the LEA Cp11-24 and CpMYB10 promoters. Localization of CpMYB10 transcript by in situ reverse transcription-PCR reactions showed expression in vascular tissues, parenchyma, and epidermis both in leaves and roots in response to ABA. Transgenic Arabidopsis plants transformed with CpMYB10 promoter fused to GUS gene showed reporter expression under ABA and stress conditions in several organs. Overexpression of CpMYB10 cDNA in Arabidopsis led to desiccation and salt tolerance of transgenics lines. Interestingly, it was found that plants overexpressing CpMYB10 exhibited Glc-insensitive and ABA hypersensitive phenotypes. Therefore, our results indicate that CpMYB10 in Arabidopsis is mediating stress tolerance and altering ABA and Glc signaling responses.

The coffee diterpene kahweol suppress the inducible nitric oxide synthase expression in macrophages

Excessive nitric oxide production by inducible nitric oxide synthase (iNOS) in stimulated inflammatory cells is thought to be a causative factor of cellular injury in cases of inflammation. In recent studies, it has been shown that kahweol, coffee-specific diterpene, exhibit chemoprotective effects. In this study, we investigated the effects of kahweol on the production of and the expression of inducible nitric oxide synthase (iNOS) in lipopolysaccharide (LPS)-activated RAW 264.7 macrophages. The nitrite production induced by LPS was markedly reduced in a dose-dependent manner. In addition, kahweol suppressed the expression of iNOS protein and iNOS mRNA. Since iNOS transcription has been shown to be under the control of the transcription factor, NF-κB, the effects of kahweol on NF-κB activation were examined. Transient transfection experiments showed that kahweol inhibited NF-κB-dependent transcriptional activity. Moreover, electrophoretic mobility shift assay experiments indicated that kahweol blocked the LPS-induced activation of NF-κB. The results of these studies suggest that the suppression of the transcriptional activation of iNOS by kahweol might be mediated through the inhibition of NF-κB activation. Taken together, the results of our study provide evidence that kahweol possess an anti-inflammatory potential, which constitutes a previously unrecognized biologic activity, and which may provide new insights into the inflammatory process.

A Novel Cyanobacterial SmtB/ArsR Family Repressor Regulates the Expression of a CPx-ATPase and a Metallothionein in Response to Both Cu(I)/Ag(I) and Zn(II)/Cd(II)

A novel SmtB/ArsR family metalloregulator, denoted BxmR, has been identified and characterized from the cyanobacterium Oscillatoria brevis. Genetic and biochemical evidence reveals that BxmR represses the expression of both bxa1, encoding a CPx-ATPase metal transporter, as well as a divergently transcribed operon encoding bxmR and bmtA, a heavy metal sequestering metallothionein. Derepression of the expression of all three genes is mediated by both monovalent (Ag(I) and Cu(I)) and divalent (Zn(II) and Cd(II)) heavy metal ions, a novel property among SmtB/ArsR metal sensors. Electrophoretic gel mobility shift experiments reveal that apoBxmR forms multiple resolvable complexes with oligonucleotides containing a single 12-2-12 inverted repeat derived from one of the two operator/promoter regions with similar apparent affinities. Preincubation with either monovalent or divalent metal ions induces disassembly of both the BxmR-bxa1 and BxmR-bxmR/bmtA operator/promoter complexes. Interestingly, the temporal regulation of expression of bxa1 and bmtA mRNAs is different in O. brevis with bxa1 induced first upon heavy metal treatment, followed by bmtA/bxmR. A dynamic interplay among Bxa1, BmtA, and BxmR is proposed that maintains metal homeostasis in O. brevis by balancing the relative rates of metal storage and efflux of multiple heavy metal ions.

Multiple peak formation of avidin on an iminobiotin affinity support.

When pure avidin is chromatographed on a homemade iminobiotin column, two distinct peaks are observed using a gradient solvent system starting with a pH 9 buffer. Proteins in both peaks are shown to be identical by nondenatured polyacrylamide gel electrophoretic experiment. The weak interaction of the protein with the stationary phase at pH 9 could cause this unusual behavior.

The Escherichia coli transcriptional regulator MarA directly represses transcription of purA and hdeA.

The Escherichia coli MarA protein mediates a response to multiple environmental stresses through the activation or repression in vivo of a large number of chromosomal genes. Transcriptional activation for a number of these genes has been shown to occur via direct interaction of MarA with a 20-bp degenerate asymmetric "marbox" sequence. It was not known whether repression by MarA was also direct. We found that purified MarA was sufficient in vitro to repress transcription of both purA and hdeA. Transcription and electrophoretic mobility shift experiments in vitro using mutant promoters suggested that the marbox involved in the repression overlapped the -35 promoter motif and was in the "backward" orientation. This organization contrasts with that of the class II promoters activated by MarA, in which the marbox also overlaps the -35 motif but is in the "forward" orientation. We conclude that MarA, a member of the AraC/XylS family, can act directly as a repressor or an activator, depending on the position and orientation of the marbox within a promoter.

Polymorphisms in the 5′-untranslated region of the human serotonin receptor 1B (HTR1B) gene affect gene expression

We present evidence of complex balancing regulation of HTR1B transcription by common polymorphisms in its promoter. Computational analysis of the HTR1B gene predicted that a 5' segment, spanning common DNA sequence variations, T-261G, A-161T, and -182INS/DEL-181, contained a putative functional promoter. Using a secreted alkaline phosphatase (SEAP) reporter gene system, we found that the haplotype -261G_-182INS-181_A-161 enhanced transcriptional activity 2.3-fold compared with the haplotype T-261_-182INS-181_A-161. Conversely, -161T reversed this, and the net effect when -261G and -161T were in the same haplotype (-261G_-182INS-181_-161T) was equivalent to the major haplotype (T-261_-182INS-181_A-161). Electrophoretic mobility shift experiments showed that -261G and -161T modify the binding of transcription factors (TFs): -261G generates a new AP2 binding site, while alleles A-161 and -161T exhibit different binding characteristics to AP1. T-261G and A-161T were found to be in linkage disequilibrium (LD) with G861C in a European ancestry population. Interestingly, G861C has been reported to be associated with several psychiatric disorders. Our results indicate that HTR1B is the target of substantial transcriptional genetic regulation by common haplotypes, which are in LD with the HTR1B single-nucleotide polymorphism (SNP) most commonly used in association studies.

Anti-Inflammatory Actions of St. John's Wort: Inhibition of Human Inducible Nitric-Oxide Synthase Expression by Down-Regulating Signal Transducer and Activator of Transcription-1α (STAT-1α) Activation

St. John's wort (SJW) has been described to show anti-inflammatory properties due to its inhibitory effects on the expression of pro-inflammatory genes like cyclooxygenase-2, interleukin-6, and inducible nitric-oxide synthase (iNOS). Since iNOS plays a critical role in chronic inflammatory diseases, we have focused our attention on the regulation of iNOS expression by SJW in two different human epithelial cell lines, alveolar A549/8 and colon DLD-1 cells. SJW extract concentration dependently inhibited human iNOS expression evaluated by measuring the amounts of iNOS mRNA, iNOS protein, and NO production in both cell lines. This inhibitory effect resulted from transcriptional inhibition as shown in reporter gene experiments. With electrophoretic mobility shift experiments, we found a SJW-mediated down-regulation of the DNA binding activity of the transcription factor signal transducer and activator of transcription-1alpha (STAT-1alpha), but not of nuclear factor-kappaB. This down-regulation of the STAT-1alpha DNA binding was shown to result from reduced tyrosine phosphorylation of the STAT-1alpha protein. The diminished STAT-1alpha tyrosine phosphorylation resulted from SJW-mediated reduction of Janus kinase 2 activity. These data suggest that extracts from SJW may be a promising anti-inflammatory principle in chronic inflammatory diseases.

Transcription factor binding to variable nucleotide sequences in 5′-flanking regions of bovine casein genes

Different transcription-factor (TF)-binding sites involved in expression of bovine milk protein genes were identified in their 5′-flanking regions (promoters). Previous studies have identified polymorphism within 5′-flanking regions of bovine milk protein genes resulting from the natural variations in nucleotide sequences. Our computer analysis using the TESS program revealed that in the bovine casein genes at least some of the polymorphic sequences are located in putative TF-binding sites, and thus they may influence gene expression. Moreover, in the 5′-flanking region of the bovine αS1-casein gene two putative mammary gland factor/signal transducer and activator of transcription binding sites were identified differing in the G/A nucleotide substitution. Electrophoretic mobility-shift assays showed quantitative differences in the binding of nuclear proteins to variable sequences in bovine αS1- and αS2-casein gene promoters. The differences in protein binding to variable sites of bovine αS2-casein gene at positions –1101/−1100 and −186 were statistically significant (p<0.05). Results of electrophoretic mobility-shift assays competition experiments suggested that TFs such as activator protein 1, cAMP-response element-binding protein, thyroid receptor and Ying Yang 1 might take part in the formation of DNA–protein complexes. Using reverse transcription PCR method, differences in the transcription rates were found for the αS2-casein gene promoter variants, but not in the case of αS1 gene variants.

Comparing expression level-dependent features in codon usage with protein abundance: An analysis of ‘predictive proteomics’

Synonymous codon usage is a commonly used means for estimating gene expression levels of Escherichia coli genes and has also been used for predicting highly expressed genes for a number of prokaryotic genomes. By comparison of expression level-dependent features in codon usage with protein abundance data from two proteome studies of exponentially growing E. coli and Bacillus subtilis cells, we try to evaluate whether the implicit assumption of this approach can be confirmed with experimental data. Log-odds ratio scores are used to model differences in codon usage between highly expressed genes and genomic average. Using these, the strength and significance of expression level-dependent features in codon usage were determined for the genes of the Escherichia coli, Bacillus subtilis and Haemophilus influenzae genomes. The comparison of codon usage features with protein abundance data confirmed a relationship between these to be present, although exceptions to this, possibly related to functional context, were found. For species with expression level-dependent features in their codon usage, the applied methodology could be used to improve in silico simulations of the outcome of two-dimensional gel electrophoretic experiments.

Effects of FK506 and rapamycin on generation of reactive oxygen species, nitric oxide production and nuclear factor kappa B activation in rat hepatocytes

We investigated the effect of two immunosuppressant drugs, FK506 and rapamycin, on reactive oxygen species (ROS) generation, nitric oxide (NO) production, inducible nitric oxide synthase (iNOS) expression and nuclear factor kappa B (NF-κB) activation in lipopolysaccharide (LPS)-activated rat hepatocytes. Primary culture of rat hepatocytes was treated with LPS in the presence and absence of FK506 or rapamycin. LPS increased the release of lactate dehydrogenase (LDH) and nitrite into the culture medium. Western blot and reverse transcription–polymerase chain reaction analyses demonstrated increased levels of iNOS protein and mRNA. Both immunosuppressant agents inhibited the induction of iNOS mRNA and protein stimulated by LPS. ROS generation, assessed by flow cytometry using dichlorodihydrofluorescein diacetate, was significantly decreased by FK506 and rapamycin. Moreover, electrophoretic mobility shift assay experiments indicated that both drugs blocked the LPS-induced activation of NF-κB. Inhibitor kappa B protein levels were decreased by LPS and this effect was partly blocked by FK506 or rapamycin. In summary, both immunosuppressant agents decreased the intracellular generation of ROS and inhibited NO production and iNOS expression at mRNA level in association to NF-κB activation. In addition to its capacity to reduce acute allograft rejection, this study highlights the anti-inflammatory properties of FK506 and rapamycin.

Upregulation of HMG1 leads to melanoma inhibitory activity expression in malignant melanoma cells and contributes to their malignancy phenotype.

Malignant transformation of melanocytes to melanoma cells closely parallels activation of melanoma inhibitory activity (MIA) expression. We have previously shown that upregulation of MIA occurs on a transcriptional level and involves the highly conserved region (HCR) promoter element. We further observed that the HCR element interacts with the melanoma-associated transcription factor (MATF) and thereby confers strong promoter activation. In this study we identify the peptide sequence of MATF and show that it is identical with the transcription factor HMG1. HMG1 was upregulated in malignant melanoma cells and further activated by hypophosphorylation. Stable antisense-HMG1 expression in melanoma cells led to the reduction of MIA promoter activity and protein expression, indicating that HMG1 is a potent regulator of MIA expression. Interestingly, chromatin immunoprecipitation and electrophoretic mobility shift experiments indicated that HMG1 and the NF-kappa B family member p65 both interact and bind to the HCR promoter element. In summary, our study proves HMG1 and p65 to be important factors in MIA regulation and melanoma progression.

Leptin activates the promoter of the interleukin-1 receptor antagonist through p42/44 mitogen-activated protein kinase and a composite nuclear factor kappa B/PU.1 binding site.

We have recently shown that leptin strongly induces the expression and secretion of the interleukin-1 receptor antagonist (IL-1Ra) [Gabay, Dreyer, Pellegrinelli, Chicheportiche and Meier (2001) J. Clin. Endocrinol. Metab. 86, 783-791] in monocytes. However, the intracellular signalling mechanisms involved remained unknown. We now demonstrate that the activation of the IL-1Ra promoter by leptin is strictly dependent on the presence of the long form of the leptin receptor (OB-Rb), and that it also requires the activation of the p42/44 mitogen-activated protein kinases (MAPKs) as well as the presence of a nuclear factor kappaB (NF-kappa B)/PU.1 composite site at position -80 of the IL-1Ra promoter. Although leptin is capable of activating a NF-kappa B reporter element in transient transfection experiments, the protein complex binding to the NF-kappa B/PU.1 site of the IL-1Ra promoter is not composed of the p65/p50 subunits of NF-kappa B, as is evident in electrophoretic gel mobility-shift experiments. In contrast, a protein complex which does not contain PU.1 binds to this composite element in a leptin-dependent manner. In summary, we characterize the signalling pathway for leptin and OB-Rb involved in the induction of IL-1Ra, involving p42/44 MAPK, and a yet uncharacterized complex of transcription factor(s) binding to a NF-kappa B/PU.1 composite element of the IL-1Ra promoter.

Temperature-dependent conformational changes in herpes simplex virus ICP4 that affect transcription activation.

The C-terminal 500 amino acids of herpes simplex virus type 1 ICP4 are required for full activator function and viral growth and are known to participate in interactions consistent with the role of ICP4 as an activator of transcription. Oligonucleotide mutagenesis was used to target stretches of amino acids that are conserved with the ICP4 analogs of other alphaherpesviruses and were also predicted to be exposed on the surface of the molecule. Seven mutants were isolated that possessed one to three amino acid changes to the residue alanine in four regions between residues 1000 and 1200. The mutants generated were analyzed first in transfection assays and subsequently after introduction into the viral genome. A number of phenotypes representing different degrees of functional impairment were observed. In transient assays conducted at 37 degrees C, mutant M2 was indistinguishable from wild-type ICP4. Mutants M6 and M7 were marginally impaired. M3, M4, and M5 were more significantly impaired but still able to activate transcription, and M1 was completely impaired. In the context of the viral genome, M1, M3, and M7 were found to be temperature sensitive for growth. All three overproduced immediate-early (IE) proteins at the nonpermissive temperature (NPT). M3 and M7 produced early but not late proteins, and M1 produced neither early nor late proteins, at the NPT. The ICP4 proteins synthesized by all of the mutants tested were able to bind to specific ICP4 binding sites in electrophoretic mobility shift experiments. However, the DNA-protein complexes formed with the ICP4 from M1, M3, or M7 produced at the NPT possessed altered mobility. These complexes were not supershifted by a monoclonal antibody that recognizes an epitope in the C terminus; however, they were supershifted by a monoclonal antibody that recognizes the N terminus. The results suggest that the mutant forms of ICP4, while able to bind to DNA, are conformationally altered at the NPT, thus impairing the ability of the protein to activate transcription to different extents. The complete lack of ICP4 function characteristic of the M1 protein, and the inability of all the mutants to attenuate IE gene expression, suggest that the mutations additionally affect functions of the N terminus to different extents.

Transcriptional regulation of the nuclear gene encoding the alpha-subunit of the mammalian mitochondrial F1F0 ATP synthase complex: role for the orphan nuclear receptor, COUP-TFII/ARP-1.

Our laboratory has been studying the transcriptional regulation of the nuclear gene (ATPA) that encodes the alpha-subunit of the mammalian mitochondrial F1F0 ATP synthase complex. We have previously determined that the regulatory factor, upstream stimulatory factor 2 (USF2), can stimulate transcription of the ATPA gene through the cis-acting regulatory element 1 in the upstream promoter of this gene. In this study, we used the yeast one-hybrid screening method to identify another factor, COUP-TFII/ARP-1, which also binds to the ATPA cis-acting regulatory element 1. Binding of the orphan nuclear receptor, COUP-TFII/ARP-1, to the ATPA regulatory element 1 was confirmed using electrophoretic mobility shift experiments, and COUP-TFII/ARP-1-containing complexes were detected in HeLa cell nuclear extracts. A mutational analysis indicated that the binding site for COUP-TFII/ARP-1 in the ATPA regulatory element 1 is an imperfect direct repeat of a nuclear receptor response element (A/GGGTCA) with a spacer of three nucleotides. Functional assays in HeLa cells showed that COUP-TFII/ARP-1 represses the ATPA promoter activity in a dose- and sequence-dependent manner. Furthermore, cotransfection assays demonstrated that COUP-TFII/ARP-1 inhibits the USF2-mediated activation of the wild-type ATPA gene promoter but not a mutant promoter that is defective in COUP-TFII/ARP-1-binding. Overexpression of USF2 reversed the COUP-TFII/ARP-1-mediated repression of the ATPA promoter. Mobility shift assays revealed that COUP-TFII/ARP-1 and USF2 compete for binding to the ATPA regulatory element 1. Thus, the ATPA gene is regulated by a multifunctional binding site through which the transcription factors, COUP-TFII/ARP-1 and USF2, bind and exert their antagonistic effects.