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At least 1,261 records · Page 70Linked to original sources
PubMed2000

A developmentally regulated GAGA box-binding factor and Sp1 are required for transcription of the hsp70.1 gene at the onset of mouse zygotic genome activation.

We have investigated the onset of zygotic genome transcription in early two-cell mouse embryos by analyzing the regulation of hsp70.1, one of the first genes expressed after fertilization. The transcriptional activation of both an episomic hsp70 promoter and the endogenous hsp70.1 gene requires the contiguity of the GC box proximal to the TATA box with a GAGA box and involves GC box- and GAGA box-binding factors. In vivo transcription factor titrations with double-stranded oligodeoxyribonucleotides and antibodies pinpoint these factors as Sp1 and a novel murine GAGA box-binding factor, which is structurally related to the Drosophila GAGA factor and acts as transcriptional coactivator/potentiator of Sp1. Mouse unfertilized eggs and one-cell and two-cell embryos display a GAGA box-binding activity of maternal origin that disappears at the four-cell stage and is also abundant in the gonads, but is barely detectable in other adult tissues. In light of the well-established nucleosome-disruption role of the Drosophila GAGA factor, these findings suggest a novel mechanism of enhancer-independent gene derepression in early mouse embryos.

Animals↗
PubMed1993

Gene structure of bovine adrenodoxin reductase.

The gene structure of bovine adrenodoxin reductase, a component of the mitochondrial steroid hydroxylating system in the adrenal cortex, was determined. When we screened a bovine genomic DNA library, using bovine adrenodoxin reductase cDNA as a probe, we isolated 10 genomic clones covering a continuous 30 kilobase (kb) region of bovine chromosomal DNA in which the adrenodoxin reductase gene spanned approximately 12 kb. The adrenodoxin reductase gene consisted of 12 exons and all the donor and acceptor sites of the exon/intron junction followed the GT/AG rule. The transcription initiation site was found to be 79 bases upstream of the translation initiation site by primer extension analysis and putative CAAT and GC boxes, but no typical TATA box, were present in the 5'-flanking region. The 5'-flanking region of this gene showed several features characteristic of promoters of house-keeping genes. The CCAGGG sequence present in the 5'-flanking region of genes for adrenodoxin and the steroid hydroxylating cytochromes P-450 in the adrenal cortex was present 13 bases upstream from the transcription initiation site. We analyzed the promoter activity of the 5'-upstream region of this gene, using as a reporter the chloramphenicol acetyltransferase gene. The region between position -757 to -376 was proved necessary for expression of this gene in mouse Y-1 tumor cells. Adrenocorticotropin did not enhance the expression of this bovine gene in the cells.

Amino Acid Sequence↗
PubMed1999

Isolation and characterization of the glyceraldehyde-3-phosphate dehydrogenase gene of Lentinus edodes.

The glyceraldehyde-3-phosphate dehydrogenase (GPD) gene of Lentinus edodes was isolated from a genomic DNA library and cDNA corresponding to this gene was isolated from a mycelium cDNA library. The L. edodes GPD gene was found to encode a 337-aa protein. By comparison of the cDNA and genomic DNA sequences, the presence of eight introns in the GPD gene was confirmed. The putative amino acid sequence of the L. edodes GPD gene product showed high similarity to those of other basidiomycetes. The results of Southern blot analyses suggested that only one copy of the GPD gene is present in the genome of L. edodes. The promoter region was found to contain a CT-rich stretch, two CAAT boxes and a consensus TATA box. In addition, the transcript of the GPD gene was found to be expressed constitutively and strongly. These results suggest that the promoter of the L. edodes GPD gene may be very useful as a component of transformation vectors.

3' Untranslated Regions↗
PubMed2003

Testis-specific expression of the nuclear form of phospholipid hydroperoxide glutathione peroxidase (PHGPx).

The selenoprotein phospholipid hydroperoxide glutathione peroxidase (PHGPx) is present in at least three different isoforms in testis: as a cytosolic, as a mitochondrial, and as a nuclear protein. We have recently shown that a sperm nucleus-specific glutathione peroxidase (snGPx) is identical to the mitochondrial and cytosolic forms of PHGPx apart from its N-terminus. This arginine-rich N-terminus of snGPx, reminiscent of protamines, is encoded by an alternative exon located in the first intron of the PHGPx gene and is responsible for nuclear localisation and chromatin binding of snGPx [Pfeifer et al., FASEB J. 15 (2001), pp. 1236-1238]. By using a combination of techniques including selective cloning of mRNA 5'-ends, RT-PCR, and S1 analyses, we provide evidence that the transcript encoding the nuclear form is generated by transcription initiation at an alternative promoter and not by alternative splicing. We show that the major transcription start region is located at -12 to -14 upstream of the AUG translation initiation site of the sperm nucleus-specific exon and lacks a TATA box. Two minor TATA-less transcription initiation sites are located at around -30 and -45. We have shown by in situ hybridisation that snGPx expression in testis, like protamine expression, is restricted to late stages of spermatogenesis whereas PHGPx expression is only found in spermatocytes and early spermatids. These findings have to be taken into account when studying either the differential regulation of PHGPx and snGPx expression in testis or the impact of putative mutations in snGPx on male fertility in man.

3' Untranslated Regions↗
PubMed1991

Identification of a basal promoter for the human Mr 72,000 type IV collagenase gene and enhanced expression in a highly metastatic cell line.

A basal promoter for the Mr 72,000 type IV collagenase gene was specifically defined by chloramphenicol acetyltransferase assays of a nested set of 5' upstream fragments containing the promoter region. This core promoter is TACATCT and is a noncanonical TATA box that fits the TATA consensus sequence. This sequence begins 26 base pairs in the upstream direction from the start site of transcription for the type IV collagenase gene. This basal promoter is active in the highly metastatic A2058 melanoma cell line. A putative enhancer was found between nucleotides -223 to -422 that produces a 7-fold increase in transcriptional activity in the A2058 melanoma cell line. The region immediately 5' of the basal promoter, upstream to position -422, contains a silencer and represses transcriptional activity in the nonmetastatic HT144 melanoma cell line. The results of this study are consistent with previous data that found high expression of Mr 72,000 type IV collagenase mRNA and enzymatic activity in the A2058 cell line, whereas low mRNA expression and type IV collagenase activity were found in the HT144 cell line.

Base Sequence↗
PubMed2006

Cloning and sequence analysis of a glyceraldehyde-3-phosphate dehydrogenase gene from Ganoderma lucidum.

A cDNA library of Ganoderma lucidum has been constructed using a Zap Express cloning vector. A glyceraldehyde-3-phosphate dehydrogenase gene (gpd) was isolated from this library by hybridization of the recombinant phage clones with a gpd-specific gene probe generated by PCR. By comparison of the cDNA and the genomic DNA sequences, it was found that the complete nucleotide sequence encodes a putative polypeptide chain of 338 amino acids interrupted by 6 introns. The predicted amino acid sequence of this gene shows a high degree of sequence similarity to the GPD proteins from yeast and filamentous fungi. The promoter region contains a CT-rich stretch, two CAAT boxes, and a consensus TATA box. The possibility of using the gpd promoter in the construction of new transformation vectors is discussed.

Amino Acid Sequence↗
PubMed1998

TATA binding protein discriminates between different lesions on DNA, resulting in a transcription decrease.

DNA damage recognition by basal transcription factors follows different mechanisms. Using transcription-competition, nitrocellulose filter binding, and DNase I footprinting assays, we show that, although the general transcription factor TFIIH is able to target any kind of lesion which can be repaired by the nucleotide excision repair pathway, TATA binding protein (TBP)-TFIID is more selective in damage recognition. Only genotoxic agents which are able to induce kinked DNA structures similar to the one for the TATA box in its TBP complex are recognized. Indeed, DNase I footprinting patterns reveal that TBP protects equally 4 nucleotides upstream and 6 nucleotides downstream from the A-T (at position -29 of the noncoding strand) of the adenovirus major late promoter and from the G-G of a cisplatin-induced 1,2-d(GpG) cross-link. Together, our results may partially explain differences in transcription inhibition rates following DNA damage.

Adenoviridae↗
PubMed1998

Overexpression of C/EBPbeta represses human papillomavirus type 18 upstream regulatory region activity in HeLa cells by interfering with the binding of TATA-binding protein.

The human papillomavirus type 18 (HPV-18) upstream regulatory region (URR) controls cell type-specific expression of viral oncoproteins E6 and E7. The HPV-18 URR is highly active in HeLa cells, but its activity is virtually undetectable in HepG2 cells. Previous work has shown that YY1 plays an important role in activation of the HPV-18 URR in HeLa cells, and this activating activity is dependent on its physical interaction with C/EBPbeta, which binds to the switch region adjacent to the YY1 site in the URR. Overexpression of C/EBPbeta in HepG2 cells restores C/EBPbeta-YY1 interaction, resulting in strong activation of the HPV-18 URR activity. In this report, we show that, in contrast to the effect in HepG2 cells, overexpression of C/EBPbeta represses the HPV-18 URR in HeLa cells. This C/EBPbeta-induced repression of the HPV-18 URR in HeLa cells is binding site independent. It is also promoter specific, since it activates the albumin promoter under conditions in which it represses the URR in the same cells. Biochemical analysis shows that overexpression of C/EBPbeta in HeLa cells specifically interferes with binding of TATA-binding protein to the TATA box of the HPV-18 URR, but its overexpression in HepG2 cells leads to activation of the HPV-18 URR. These results suggest that a molecular mechanism underlies the ability of C/EBPbeta to regulate transcription in a cell type-specific manner and indicate the potential of using C/EBPbeta to manipulate the activity of the HPV-18 URR in cervical carcinoma cells.

Albumins↗
PubMed1993

Binding activity of the human transcription factor TFIID.

In order to investigate the conformational state of the human TFIID, we studied the structure of the TATA-box binding protein (TBP) which is the DNA-binding subunit of the transcription factor TFIID required for transcriptional initiation by RNA polymerase II. We showed that TBP was able to form dimers and tetramers by chemical crosslinking, subunit exchange, ultracentrifugation and gel shift experiment. These findings indicate that the TBP homodimers could be the inactive binding form of TFIID and therefore could explain the lack of Gal4-activated transcriptional activity of the E. coli-expressed human TBP.

Base Sequence↗
PubMed1994

Drosophila TFIIA directs cooperative DNA binding with TBP and mediates transcriptional activation.

Drosophila transcription factor IIA (TFIIA) is composed of three subunits (30, 20, and 14 kD) that function during initiation of transcription. We reported previously the characterization of cDNAs that encode a precursor (dTFIIA-L) of the Drosophila TFIIA 30- and 20-kD subunits. In the absence of the smallest subunit, dTFIIA-S (14 kD), the unprocessed large subunit failed to exhibit any detectable promoter binding or transcriptional activity. Here, we report the molecular cloning and expression of dTFIIA-S, which has allowed the assembly of holo-dTFIIA (dTFIIA-L/S). Subunit interaction studies indicate that dTFIIA-S binds to an amino-terminal domain of dTFIIA-L, which likely corresponds to the endogenous 30-kD processed species. In addition, both dTFIIA-S and the carboxy-terminal domain of dTFIIA-L, which corresponds to the 20-kD species, independently interact weakly with the TATA-binding protein (TBP). In contrast, the holo-dTFIIA (L/S) binds TBP with high affinity. The dTFIIA-L/S complex also binds cooperatively with TBP to TATA box DNA sequences, generating an extended DNase footprint pattern. The reconstituted holo-dTFIIA is able to stimulate basal transcription of several core promoter templates. Interestingly, dTFIIA-L/S is also able to significantly enhance transcriptional activation by upstream transcription factors including Sp1, VP16, and NTF-1. These results suggest that dTFIIA is a multifunctional transcription factor capable of influencing DNA binding as well as interactions with the basal machinery, thereby enhancing activator-dependent transcription.

Amino Acid Sequence↗
PubMed2001

Nucleosome sliding via TBP DNA binding in vivo.

Here, we show that a nucleosome obstructing transcription from the IFN-beta promoter slides in vivo in response to virus infection, thus exposing the previously masked TATA box and the initiation site, a requirement for transcriptional activation. Our experiments also revealed that this mode of chromatin remodeling is a two-step reaction. First, the enhanceosome recruits the SWI/SNF chromatin-remodeling complex that modifies the nucleosome to allow binding of TBP. Second, DNA bending is induced by TBP binding, and the nucleosome slides to a new position. Experiments with other DNA binding proteins demonstrated a strong correlation between the ability to bend DNA and nucleosome sliding, suggesting that the sliding is induced by the bend.

Chloramphenicol O-Acetyltransferase↗
PubMed2005

The yeast FACT complex has a role in transcriptional initiation.

A crucial step in eukaryotic transcriptional initiation is recognition of the promoter TATA by the TATA-binding protein (TBP), which then allows TFIIA and TFIIB to be recruited. However, nucleosomes block the interaction between TBP and DNA. We show that the yeast FACT complex (yFACT) promotes TBP binding to a TATA box in chromatin both in vivo and in vitro. The SPT16 gene encodes a subunit of yFACT, and we show that certain spt16 mutations are synthetically lethal with TBP mutants. Some of these genetic defects can be suppressed by TFIIA overexpression, strongly suggesting a role for yFACT in TBP-TFIIA complex formation in vivo. Mutations in the TOA2 subunit of TFIIA that disrupt TBP-TFIIA complex formation in vitro are also synthetically lethal with spt16. In some cases this spt16 toa2 lethality is suppressed by overexpression of TBP or the Nhp6 architectural transcription factor that is also a component of yFACT. The Spt3 protein in the SAGA complex has been shown to regulate TBP binding at certain promoters, and we show that some spt16 phenotypes can be suppressed by spt3 mutations. Chromatin immunoprecipitations show TBP binding to promoters is reduced in single spt16 and spt3 mutants but increases in the spt16 spt3 double mutant, reflecting the mutual suppression seen in the genetic assays. Finally, in vitro studies show that yFACT promotes TBP binding to a TATA sequence within a reconstituted nucleosome in a TFIIA-dependent manner. Thus, yFACT functions in establishing transcription initiation complexes in addition to the previously described role in elongation.

Cell Cycle Proteins↗
PubMed1995

Molecular cloning of the transcription factor TFIIB homolog from Sulfolobus shibatae.

The Archaea (archaebacteria) constitute a group of prokaryotes that are phylogenetically distinct from Eucarya (eukaryotes) and Bacteria (eubacteria). Although Archaea possess only one RNA polymerase, evidence suggests that their transcriptional apparatus is similar to that of Eucarya. For example, Archaea contain a homolog of the TATA-binding protein which interacts with the TATA-box like A-box sequence upstream of many archaeal genes. Here, we report the cloning of a Sulfolobus shibatae gene that encodes a protein (transcription factor TFB) with striking homology to the eukaryotic basal transcription factor TFIIB. We show by primer extension analysis that transcription of the S. shibatae TFB gene initiates 27 bp downstream from a consensus A-box element. Significantly, S. shibatae TFB contains an N-terminal putative metal-binding region and two imperfect direct repeats--structural features that are well conserved in eukaryotic TFIIBs. This suggests that TFB may perform analogous functions in Archaea and Eucarya. Consistent with this, we demonstrate that S. shibatae TFB promotes the binding of S. shibatae TBP to the A-box element of the Sulfolobus 16S/23S rRNA gene. Finally, we show that S. shibatae TFB is significantly more related to TFB of the archaeon Pyrococcus woesei than it is to eukaryotic TFIIBs. These data suggest that TFB arose in the common archaeal/eukaryotic ancestor and that the lineages leading to P. woesei and S. shibatae separated after the divergence of the archaeal and eukaryotic lines of descent.

Amino Acid Sequence↗
PubMed2000

A constitutive active MEK --> ERK pathway negatively regulates NF-kappa B-dependent gene expression by modulating TATA-binding protein phosphorylation.

Endotoxin-induced cytokine gene expression is regulated, in part, by NF-kappaB. We have shown that both the ERK and p38 mitogen-activated protein (MAP) kinases are necessary for cytokine gene transcription and that the p38 MAP kinase is required for NF-kappaB-driven transcription, so we hypothesized that the MEK --> ERK pathway regulated NF-kappaB-driven transcription as well. We found that a constitutive active MEK --> ERK pathway inhibited NF-kappaB-driven transcription. In addition, both PD 98059 and a dominant negative ERK2 augmented NF-kappaB-driven transcription; however, neither PD 98059 nor MEK1 altered NF-kappaB activation at any level. The constitutive active MEK --> ERK pathway inhibited the phosphorylation of TBP, which is necessary for both interaction with RelA and binding to the TATA box. Due to the fact that we have shown that the p38 MAP kinase modulates TBP activation, we evaluated the effect of the constitutive active MEK --> ERK pathway on p38 MAP kinase activity. We found that the MEK --> ERK pathway negatively regulates NF-kappaB-driven transcription, in part, by inhibiting p38 MAP kinase activity. Thus, the ERK and p38 MAP kinases have differential effects on NF-kappaB-driven transcription.

Cell Line↗
PubMed1993

The novel purification of functional RNA polymerase III VAI transcription preinitiation complexes.

A novel purification scheme employing high-performance liquid chromatography (HPLC) gel filtration chromatography on a 4000 A methacrylate-based polymer and preparative gel mobility shift fractionation on 2% agarose gels with continuous elution allowed for a 10(5) fold enrichment in RNA polymerase III transcription preinitiation complexes from NTP-depleted HeLa whole cell extracts. Purified preinitiation complexes from the TATA-less Class III (Internal Control Region) adenovirus VAI gene contain the TATA-Box binding protein (TBP) by the criterion of comigration on sodium dodecyl sulfate (SDS) gels with the 43 kd TBP present in a purified B-TFIID fraction, and by Western blot analysis. Purified VAI preinitiation complex preparations lacking RNA polymerase III consistently contain a number of additional polypeptides with apparent molecular weights of 17, 20, 29, 32, 39, 55, 105, 120, and 140 kDa which appear to be specific components, since they are not detected in the corresponding fractions isolated using a VAI gene B-block mutant promoter.

Adenoviridae↗
PubMed1996

Retinoid-dependent transcription: the RAR/RXR-TBP-EIA/EIA-LA connection.

Retinoids play a fundamental role in regulating normal cell proliferation and differentiation. The most spectacular effects of retinoids in vitro can be observed with embryonal carcinoma (EC) cells that can be induced to differentiate into endodermal, mesodermal and neuroectodermal lineages. An early and essential step in the differentiation process is the activation of the retinoic acid receptor-beta 2 (RAR beta 2) promoter that requires a co-operation between RAR, the EC-cell specific adenovirus early gene product 1A (E1A)-like activity and the TATA-binding protein (TBP). In differentiated cells, this signalling pathway can be mimicked by ectopic expression of the adenoviral E1A protein. Here we show that E1A13S but not E1A12S augments the level of transcription. Analysis of the binding kinetics of E1A13S to TBP by the surface plasmon resonance (SPR) technique reveals that the affinity of TBP for a consensus TATA-box sequence is significantly and specifically increased by E1A13S only. Intriguingly, a specific interaction can only be obtained with crude TBP overexpressed in HeLa cells via vaccinia virus as opposed to bacterially expressed TBP, suggesting a cofactor requirement for the interaction. Co-immunoprecipitation experiments show that E1A13S is an integral component of the RNA polymerase II-specific TBP-containing complex in adenovirus transformed embryonal kidney 293 cells. Taken together the results suggest that E1A13S mediates transcriptional activation by providing a physical bridge between TBP/transcription factor IID (TFIID) and retinoic acid receptor.

Adenovirus E1A Proteins↗
PubMed1998

The TATA-binding protein (TBP) from the human fungal pathogen Candida albicans can complement defects in human and yeast TBPs.

Candida albicans is the major fungal pathogen in humans, yet little is known about transcriptional regulation in this organism. Therefore, we have isolated, characterized, and expressed the C. albicans TATA-binding protein (TBP) gene (TBP1), because this general transcription initiation factor plays a key role in the activation and regulation of eukaryotic promoters. Southern and Northern blot analyses suggest that a single C. albicans TBP1 locus is expressed at similar levels in the yeast and hyphal forms of this fungus. The TBP1 open reading frame is 716 bp long and encodes a functional TBP of 27 kDa. C. albicans TBP is capable of binding specifically to a TATA box in vitro, substituting for the human TBP to activate basal transcription in vitro, and suppressing the lethal delta spt15 mutation in Saccharomyces cerevisiae. The predicted amino acid sequences of TBPs from C. albicans and other organisms reveal a striking pattern of C-terminal conservation and N-terminal variability: the C-terminal DNA-binding domain displays at least 80% amino acid sequence identity to TBPs from fungi, flies, nematodes, slime molds, plants, and humans. Sequence differences between human and fungal TPBs in the DNA-binding domain may represent potential targets for antifungal therapy.

Amino Acid Sequence↗
PubMed1993

Expression of the carcinoma-associated keratin K6 and the role of AP-1 proto-oncoproteins.

The normal pattern of keratin expression in epidermis is altered in carcinomas as well as in nonmalignant diseases such as psoriasis and wound healing. Under these circumstances, the transcription of differentiation-specific keratins K1 and K10 is suppressed, whereas the activation- and hyperproliferation-associated keratins K6 and K16 are induced. Very little is known regarding transcriptional regulators involved in this switch. To investigate the nuclear factors that participate in regulation of expression of the K6 gene, we have characterized the binding sites for nuclear proteins on the promoter DNA of the K6 gene by gel retardation assays and site-specific deletion mutagenesis. We found four nuclear protein binding sites in the K6 gene promoter. Two are near the TATA box, but their ability to bind HeLa or keratinocyte nuclear extracts is independent of the TATA box-binding protein complex. The third binding site is a large palindrome. The sequences of these three sites do not correspond to any described target sequences for characterized transcriptional factors. The fourth is an AP-1 site, the target sequence for the proto-oncoproteins fos and jun. All four sites are independent of the previously characterized epidermal growth factor-responsive element, EGF-RE. These findings suggest that there may be two parallel pathways of induction of K6 transcription. One proceeds through the EGF-RE, which may be involved in nonmalignant hyperproliferation processes; the other, through the AP-1 site and the fos-jun proto-oncoproteins, may be related to induction in malignant processes.

Animals↗