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PubMed1997

Isolation of the gene encoding Pyrococcus furiosus ornithine carbamoyltransferase and study of its expression profile in vivo and in vitro.

The gene coding for ornithine carbamoyltransferase (OTCase, argF) in the hyperthermophilic archaea Pyrococcus furiosus was cloned by complementation of an OTCase mutant of Escherichia coli. The cloned P. furiosus argF gene also complemented a similar mutant of Saccharomyces cerevisiae. Sequencing revealed an open reading frame of 314 amino acids homologous to known OTCases and preceded by a TATA box showing only limited similarity with the Euryarchaeota consensus sequence. This is in accordance with the comparatively low in vitro promoter activity observed in a cell-free purified transcription system. Transcription initiates in vivo as well as in vitro at a guanine, 22 nucleotides downstream of the TATA box. Upstream from argF is a putative gene for diphthine synthetase, a eukaryotic enzyme assumed to occur also in archaea but not in bacteria.

Amino Acid Sequence↗

PubMed1987

Mutations in the adenovirus major late promoter: effects on viability and transcription during infection.

We developed an experimental system to examine the effects of mutations in the adenovirus major late promoter in its correct genomic location during a productive infection. A virus was constructed whose genome could be digested to give a rightward terminal DNA fragment extending from the XhoI site at 22.9 map units, which can be ligated or recombined with plasmid DNA containing adenovirus sequences extending from 0 to 22.9 or 26.5 map units, respectively. Mutations were made by bisulfite mutagenesis in the region between base pairs -52 and -12 with respect to the cap site at +1 and transferred to the appropriate plasmids for viral reconstruction. Of 19 mutant plasmid sequences containing single or multiple G-to-A transitions, 14 could be placed in the viral genome with no apparent change in phenotype. These mutant sequences included those which contained four transitions in the string of G residues immediately downstream of the TATA box. There were no alterations in rates of transcription from the major late promoter, sites of transcription initiation, or steady-state levels of late mRNAs. All of the five mutant sequences which could not be placed in virus contained multiple transitions both up- and downstream of the TATA box. Two of these apparently lethal mutant sequences were used in promoter fusion experiments to test their ability to promote transcription of rabbit beta-globin sequences placed in the dispensable E1 region of the virus. Both sequences showed diminished ability compared with wild-type sequences to promote transcription in this context. Comparisons between these two sequences and the viable mutant sequences suggest a role for the string of G residues located between -38 and -33 in promoting transcription from the major late promoter. The data as a whole also demonstrate that the specific nucleotide sequence of this region of the major late promoter, which overlaps transcription elements of the divergent IVa2 transcription unit and coding sequences of the adenovirus DNA polymerase, is not rigidly constrained but can mutate extensively without loss of these several functions.

Adenoviridae↗

PubMed1996

Cloning, characterization and transient expression of the gene encoding a rice U3 small nuclear RNA.

A rice U3 small nuclear RNA (snRNA)-encoding gene has been isolated. The coding region of this gene contains all five conserved sequence boxes common to plant U3 snRNAs. The upstream and downstream regions of the gene harbour characteristic sequence elements required for transcription with RNA polymerase III (pol III), as well as three monocot-specific promoter (MSP) elements [Connelly et al., Mol. Cell Biol.14 (1994) 5910-5919], two of them comprising a palindromic G+C-rich segment. The sequence (TTTAAAA) of the TATA-box in this gene does not fit the established consensus [Marshallsay et al., Plant Mol. Biol. 19(1992) 973-983], making this gene unique among reported snRNA-encoding genes of plants. An RNase protection assay showed that the gene is expressed properly in cucumber protoplasts. We thus suggest that, with other promoter elements present, the TATA-box for RNA pol III-specific snRNA-encoding genes may not be as well conserved as that for RNA pol II-specific genes.

Base Sequence↗

PubMed1987

Reversible silencing of enhancers by sequences derived from the human IFN-alpha promoter.

The virus-responsive element of the IFN-alpha 1 promoter, VRE(IFN alpha), comprises two imperfect 19 bp repeats, repA and repB. VRE(IFN alpha), tetrameric repA, and tetrameric GAAAGT (a subsequence of repB) or tetrameric AAGTGA conferred inducibility on a reporter gene when placed upstream of a complete or truncated promoter. Induced transcription was weak with a minimal promoter (TATA box only), but was strongly stimulated by the SV40 enhancer placed immediately upstream of the inducible element. Surprisingly, under noninduced conditions, tetrameric repA, GAAAGT, and AAGTGA (but not VRE(IFN alpha)) completely silenced enhancement of constitutive transcription by the SV40 72 bp repeat when interposed between the latter and the TATA box; silencing was fully abrogated by induction.

Animals↗

PubMed2004

[Cloning and analysis of the promoter region of Schistosoma japonicum 8k CaBP gene].

OBJECTIVE: To clone and analyze the promoter sequence of Schistosoma japonicum 8k Calcium binding protein(CaBP) (Sj8CaBP) gene. METHODS: The genomic DNA was extracted from S. japonicum adult worms. The DNA library was constructed according to the user's manual for Clontech Universal Genome Walker(TM) Kit, and the gene-specific primer 1 and 2 (GSP1 and GSP2) of Sj8CaBP gene were designed and synthesized. GSP1 and GSP2 were coupled with the adaptor primer 1 and 2 (AP1 and AP2), then nested PCR was performed. After proper purification, the PCR product was linked to pMD-18 T vector, and the recombinant T-vector was sequenced, analyzed with the promoter prediction software and compared with the cDNA sequence of Sj8CaBP. RESULTS: The cloned Sj8CaBP gene was about 1 079 bp in length ( GenBank accession No.AY262018), which contained a full open-reading frame with 1 intron and 2 exons. The 5'UTR has a putative promoter region including a TATA-box and a CCAAT-box. The GC-box binding region was not found in this gene, nor was that for active protein 1 (AP-1) often seen in other schistosome genes. CONCLUSION: A 1 079 bp Sj8CaBP gene fragment (GenBank accession No.AY262018) was obtained from a S. japonicum genomic DNA library, containing a promoter region with TATA-box, CCAAT-box, 1 intron and 2 extrons.

Animals↗

PubMed1984

DNA sequence comparison of the regulatory signals at the 5' end of the mouse and chick alpha 2 type I collagen genes.

We have isolated a DNA segment that contains the presumptive transcriptional and translational control signals located at the 5' end of the mouse alpha 2(I) collagen gene. The DNA sequence of the first exon of this gene and of 400 base pairs preceding the start of transcription was compared with an analogous sequence in the chick alpha 2(I) collagen gene. The most striking similarity is a block of 68 nucleotides surrounding the translation initiation site which is perfectly conserved except for four contiguous nucleotides in the middle of the conserved sequence. These four nonconserved bases lie between the arms of a perfect inverted repeat with nine nucleotides in each arm. The very high degree of sequence conservation of this segment suggests that both the inverted repeat and the rest of the perfectly conserved sequence have a regulatory role, possibly in translation. The segment preceding the transcription start shows blocks of similarities interspersed with dissimilar sequences. The conserved sequences include the TATA box, CAT box, a G/C rich sequence around -110, a segment that contains almost exclusively pyrimidines on one strand and is sensitive to endonuclease S1 in both promoters, and several other segments that extend to 350 base pairs preceding the start of transcription. Although the distances between these regions of similarity and the TATA box are not the same in the two promoters, we believe the conserved sequences play a role in the transcriptional activation of this gene.

Amino Acid Sequence↗

PubMed1994

Complex organization of CTF/NF-I, C/EBP, and HNF3 binding sites within the promoter of the liver-specific vitellogenin gene.

Vitellogenin genes are expressed specifically in the liver of female oviparous vertebrates under the strict control of estrogen. To explain this tissue-specific expression, we performed a detailed analysis of the Xenopus laevis vitellogenin gene B1 promoter by DNase I footprinting and gel mobility-shift assays. We characterized five binding sites for the ubiquitous factor CTF/NF-I. Two of these sites are close to the TATA-box, whereas the others are located on both sides of the estrogen responsive unit formed by two imperfect estrogen response elements. Moreover two liver-enriched factors, C/EBP and HNF3, were found to interact with multiple closely spaced proximal promoter elements in the first 100 base pairs upstream of the TATA-box. To confirm the physiological significance of this in vitro analysis, in vivo DNase I footprinting experiments were carried out using the ligation-mediated polymerase chain reaction technique. The various cis-elements characterized in vitro as binding sites for known transcription factors and more particularly for liver-enriched transcription factors are efficiently recognized in vivo as well, suggesting that they play an important role in the control of the liver-specific vitellogenin gene B1 expression.

Animals↗

PubMed1987

Human muscle carbonic anhydrase: gene structure and DNA methylation patterns in fetal and adult tissues.

We report the isolation and analysis of genomic clones comprising the entire gene coding for the human muscle carbonic anhydrase, CAIII. The gene spans 10.3 kb and has a seven-exon/six-intron structure. A noncanonical TATA box, a CCAAT motif, and two CCGCCC elements are present in the sequences upstream of exon 1. Although the expression of CAIII shows strict tissue specificity, the gene exhibits a number of features normally associated with housekeeping enzymes. For example, there is 48% homology with a 25-bp consensus sequence between the TATA box and the cap site and there is a CpG-rich island spanning a 469-bp sequence near to the origin of transcription. Methylation studies suggest that some CCGG sites clustered in the CpG-rich island are undermethylated in DNA from fetal and adult muscle and in other tissues irrespective of CAIII expression. In contrast, several nonclustered CCGG sites show a methylation pattern that correlates with gene expression. However DNA from differentiated type II adult muscle fibers is undermethylated at these sites even though CAIII is not expressed.

Adult↗

PubMed1981

T antigen repression of SV40 early transcription from two promoters.

The SV40 early mRNAs encode large (T) and small (t) tumor antigens. During the lytic cycle, the 5' termini of the early mRNAs undergo a shift: shortly after infection only an initiation site downstream from the TATA box is utilized; later an upstream initiation site becomes prominent. Both initiation sites are utilized in an in vitro transcription extract. D2T, a T antigen analog, specifically represses transcription in vitro from both initiation sites, but at different concentrations. Binding of D2T to site I suppresses initiation from the site downstream of the TATA box; binding to sites II and I suppresses initiation from the upstream site. The role of T antigen binding in repression of transcription and in the shift of initiation sites on the early strand is discussed.

Antigens, Polyomavirus Transforming↗

PubMed1994

The herpes simplex virus type 1 major capsid protein (VP5-UL19) promoter contains two cis-acting elements influencing late expression.

The herpes simplex virus type 1 (HSV-1) major capsid protein VP5 gene (UL19) is expressed with beta gamma (gamma 1 [leaky late]) kinetics. We have previously described the construction of recombinant HSV-1 in which the VP5 promoter was engineered to control the expression of the bacterial beta-galactosidase gene as a reporter (C.-J. Huang, S. A. Goodart, M. K. Rice, J. F. Guzowski, and E. K. Wagner, J. Virol. 67:5109-5116, 1993). Here we describe further mutational analysis in recombinant viruses. We have precisely defined the boundaries of the VP5 promoter and identified two regions important for both the level and the kinetics of expression. The 5' boundary was located at -48 relative to the initiation site of transcription by analyzing a series of nested deletions in the upstream sequence, and although a number of cis-acting sites influencing transient expression have been identified upstream of this point, these sites have no role in promoter activity during productive infection. Deletion of an Sp1-binding site located between -48 and the TATA box at -30 greatly reduced VP5 promoter activity late but not early after infection. A cis-acting element whose sequence resembles the human immunodeficiency virus type 1 initiator was located between -2 and +10 in the VP5 sequence by characterizing a series of deletions and site-directed block mutations downstream the TATA box. This element defines the 3' limit of the VP5 promoter, and like the upstream element, disruption of this element also inhibited promoter activity late in the productive cycle.

Base Sequence↗

PubMed1992

Structure of the genes encoding Hordeum vulgare (1----3,1----4)-beta-glucanase isoenzymes I and II and functional analysis of their promoters in barley aleurone protoplasts.

Barley (1----3,1----4)-beta-glucanase isoenzyme II is synthesized in the aleurone cells during germination and secreted into the endosperm for hydrolysis of the cell walls. Its synthesis is stimulated by gibberellic acid (GA3) and repressed by abscisic acid. The gene for isoenzyme I is expressed in the aleurone, scutellum and prominently in young leaves. Close functional relatedness between the two enzymes is attested by 92% identity at the level of the amino acid sequence. The structural genes for the two enzymes each contain a large intron of 2505 bp and 2952 bp, respectively, in the codon for amino acid 25 of the 28-residue signal peptide. During evolution, homologous regions of the two introns have changed position and orientation. Furthermore, a large palindromic sequence of 327 bp in the 5' end of the intron is present only in the gene for isoenzyme II. In transient expression assays using barley aleurone protoplasts and chloramphenicol acetyl transferase as reporter the promoter of the isoenzyme I gene showed no response to GA3. However, removal of a unique 151 bp region extending from positions -402 to -552 upstream of the TATA box permitted low levels of GA3-induced expression of the reporter gene, suggesting a silencer function for this domain. High levels of GA3-responsive expression were obtained in aleurone protoplasts using the promoter of the gene encoding isoenzyme II. Truncation of this promoter revealed that sequences located within 253 bp upstream from the TATA box are sufficient to direct GA3-stimulated expression. Using the homologous barley aleurone protoplast transfection assay, it was possible to reproduce the in vivo expression characteristics of the genes for the barley (1----3,1----4)-beta-glucanase isoenzymes I and II with reporter gene constructs.

Amino Acid Sequence↗

PubMed1992

A 10-base-pair element of the human immunodeficiency virus type 1 long terminal repeat (LTR) is an absolute requirement for transactivation by the human cytomegalovirus 72-kilodalton IE1 protein but can be compensated for by other LTR regions in transactivation by the 80-kilodalton IE2 protein.

Transient gene expression studies have indicated that human cytomegalovirus (HCMV) specifically transactivates the human immunodeficiency virus (HIV) long terminal repeat (LTR). We show here, by a specific mutational analysis, that only the TATA box region is obligatory for transactivation of the HIV-1 LTR by HCMV. Similarly, this element is also sufficient for transactivation by either the HCMV 72-kDa major immediate-early 1 (IE1) or 80-kDa IE2 gene product independently. However, deletion of a 10-bp region from the minimal responsive element, 5' to the TATA box, dramatically reduced the level of HCMV 72-kDa IE1 or 80-kDa IE2 transactivation, indicating a crucial role for this element in transactivation. Whereas inclusion of the TAR element or Sp1 sites on this 10-bp-deleted minimal promoter had no effect on the removal of IE1 transactivation, TAR and Sp1 elements did compensate for the 10-bp element in transactivation by IE2 and HCMV. Consequently, the sequence requirements of the HIV-1 LTR for transactivation by HCMV can be reproduced by these IE1 and IE2 gene products of HCMV.

Base Sequence↗

PubMed2002

Functional characterization of the 5' flanking region of human ubiquitin fusion degradation 1 like gene (UFD1L).

UFD1L (Ubiquitin Fusion Degradation 1 Like) gene encodes for a component of a multi-complex involved in the degradation of ubiquitin fusion proteins. The gene maps on chromosome 22q11, in a region commonly deleted in severe congenital disorders such as DiGeorge (DGS) and velo-cardio-facial (VCFS) syndromes. UFD1L is a single copy gene ubiquitously expressed in high levels in the pharyngeal pouches and fourth branchial arch artery during development. To understand the regulation of UFD1L expression we performed a functional analysis of its 5' regulatory region. 5'-RACE and primer extension analyses revealed the presence of different transcription start sites in adult and fetal tissues. UFD1L 5' flanking region contains a TATA-box motif and is also very GC-rich with a CpG island encompassing exon 1. Transcriptional activity of this region was examined by transfection experiments of promoter-GFP reporter gene constructs in a human epithelial cell line. These experiments revealed the importance of the region between -17 and -463 nt which contains the TATA-box. EMSA assay resulted in the detection of five functional consensus sequences respectively for the transcription complex TFIID and for the transcription factors AP-1 (one site), AP-2 (one) and Sp1 (two).

5' Flanking Region↗

PubMed2001

The 5'-flanking regions of CYP19A1 and CYP19A2 in zebrafish.

This report describes the structure of the 5'-flanking regions of both the CYP19A1 and A2 genes that were isolated from the genome of the zebrafish (Danio rerio). Consensus sequences of three cAMP-responsive elements (CRE), an aryl hydrocarbon-responsive element (AhR/Arnt), a steroidogenic factor 1 (SF-1) site, and a TATA box were observed in the 5'-flanking region of CYP19A1. In contrast, the 5'-flanking region of CYP19A2 was located upstream of an untranslated exon and possessed consensus sequences of a single CRE, an estrogen-responsive element (ERE), a peroxisome proliferator-activated receptor alpha/retinoid X receptor alpha heterodimer-responsive element (PPARalpha/RXRalpha), and a TATA box. Primer extension analysis revealed that the predominant transcription initiation sites for CYP19A1 and A2 transcripts were 28 and 91 bp upstream from the putative translation initiation codon, respectively. These analyses indicate that substantially different regulators, including a variety of environmental xenobiotics, control the expression the two CYP19 genes.

5' Untranslated Regions↗

PubMed1996

The 22 bp W1 element in the pea lectin promoter is necessary and, as a multimer, sufficient for high gene expression in tobacco seeds.

The pea lectin (Psl) gene encodes an abundant seed protein. Its seed-specific expression pattern is conserved in transgenic tobacco plants. Progressive 5' promoter deletions resulted in a gradual decrease of transcriptional activity in tobacco seed. A fragment of 115 bp still conferred seed-specific expression albeit at a low level. This fragment contains a 22 bp element (W1), which has been demonstrated to be important for seed-specific expression when coupled as a trimer to a heterologous TATA box (de Pater et al., Plant Cell 5:877-886, 1993). Here we show that deletion of W1 in the natural promoter context resulted in a strongly decreased level of gene expression. A 4 bp mutation of W1 reduced the expression of truncated derivatives of the Psl promoter. A single copy of W1 coupled to the TATA box of the CaMV 35S promoter directed low gene expression in seeds and leaves. Multimerization enhanced the expression in seeds up to 100-fold, to levels found with the Psl promoter, whereas the expression level in leaves remained low. These results demonstrate that the W1 element is an essential control element in the Psl promoter. When taken out of its natural context and multimerized, it is sufficient for high expression in seeds.

Base Sequence↗

PubMed1992

Cooperativity in transactivation between retinoic acid receptor and TFIID requires an activity analogous to E1A.

In embryonal carcinoma (EC) cells retinoic acid (RA) strongly induces transcription from the RA receptor beta 2 (RAR beta 2) promoter through an RA response element (RARE) located in close proximity to the TATA box. Here we demonstrate that recombinant human TATA box-binding protein, hTFIID, and RAR functionally cooperate in transactivation of the RAR beta 2 promoter in EC cells in a strictly RA-dependent manner. We demonstrate that the core domain of hTFIID is sufficient to mediate RAR-dependent transcription and that Drosophila, but not yeast, TFIID can substitute for hTFIID. In COS cells ectopic expression of the E1A protein is a prerequisite for hTFIID and RAR to cooperate in transactivation. We propose a model for transcriptional regulation of the RAR beta 2 promoter in EC cells in which RAR, following activation by RA, functionally interacts with hTFIID via an E1A-like activity present in EC cells.

Adenovirus Early Proteins↗

PubMed1996

Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: implications for start site selection and initiation complex formation.

SUMMARY: Transcription factors IIB (TFIIB) and IIE (TFIIE) bound to RNA polymerase II have been revealed by electron crystallography in projection at 15.7 A resolution. The results lead to simple hypotheses for the roles of these factors in the initiation of transcription. TFIIB is suggested to define the distance from TATA box to transcription start site by bringing TATA DNA in contact with polymerase at that distance from the active center of the enzyme. TFIIE is suggested to participate in a key conformational switch occurring at the active center upon polymerase-DNA interaction.

Binding Sites↗

PubMed1995

An Sp1 binding site and the minimal promoter contribute to overexpression of the cytokeratin 18 gene in tumorigenic clones relative to that in nontumorigenic clones of a human carcinoma cell line.

Clones of cells tumorigenic or nontumorigenic in nude mice have been previously isolated from the SW613-S human colon carcinoma cell line. We have already reported that tumorigenic cells overexpress the cytokeratin 18 (K18) gene in comparison with nontumorigenic cells and that this difference is mainly due to a transcriptional regulation. We now report that a 2,532-bp cloned human K18 gene promoter drives the differential expression of a reporter gene in a transient assay. A 62-bp minimal K18 promoter (TATA box and initiation site) has a low but differential activity. Analysis of deletion and substitution mutants as well as hybrid SV40-K18 promoters and reconstructed K18 promoters indicated that an important element for the activity of the K18 promoter is a high-affinity binding site for transcription factor Sp1 located just upstream of the TATA box. This Sp1 binding element, as well as the intron 1 enhancer element, stimulates the basal activity of the minimal promoter through mechanisms that maintain the differential activity. Gel shift assays and the use of an anti-Sp1 antibody have shown that both tumorigenic and nontumorigenic SW613-S cells contain three factors able to bind to the Sp1 binding element site and that one of them is Sp1. A hybrid GAL4-Sp1 protein transactivated to comparable extents in tumorigenic and nontumorigenic cells a reconstructed K18 promoter containing GAL4 binding sites and therefore without altering its differential behavior. These results indicate that the Sp1 transcription factor is involved in the overexpression of the K18 gene in tumorigenic SW613-S cells through its interaction with a component of the basal transcription machinery.

Base Sequence↗