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PubMed1995

Structures of genes encoding TATA box-binding proteins from Trimeresurus gramineus and T. flavoviridis snakes.

A cDNA encoding the Trimeresurus gramineus (Tg; green habu snake) TATA-box-binding protein (TgTBP) was cloned and sequenced. The cDNA encodes a 33-kDa protein with an extensive sequence similarity to those derived from other organisms, except for the N-terminal domain. Genes encoding TgTBP and Trimeresurus flavoviridis (Tf; habu snake) TBP (TfTBP) were isolated using a TgTBP cDNA and their nt sequences were determined. They are the first TBP genes entirely sequenced in higher animals. Both genes span over 15 kb and are constructed from eight exons and seven introns. Comparison of the loci of introns on the aligned amino-acid sequences of TBP from six organisms (Tg, Tf, mouse, Arabidopsis thaliana, Schizosaccharomyces pombe and Acanthamoeba castellanii) indicated that there are three highly conserved loci in the C-terminal domain.

Amino Acid Sequence↗
PubMed1989

Binding sites of HeLa cell nuclear proteins on the upstream region of adenovirus type 5 E1A gene.

Twenty one binding sites of HeLa cell nuclear proteins were identified on the upstream region of adenovirus type 5 E1A gene using DNase I footprint assay. The proximal promoter region contained five binding sites that overlapped the cap site, TATA box, TATA-like sequence, CCAAT box, and -100 region relative to the E1A cap site(+1). The -190 region was a potential site for octamer-motif binding proteins, such as NFIII and OBP100. An upstream copy of the E1A enhancer element 1 was the site for a factor (E1A-F) with the binding specificity of XGGAYGT (X = A, C; Y = A, T). E1A-F factor also bound to three other sites, one of which coincided with the distal E1A enhancer element. The distal element also contained a potential site for ATF factor. The adenovirus minimal origin of DNA replication competed for DNA-protein complex formation on the CCAAT and TATA box region and the -190 region, suggesting that these regions interacted with a common or related factor.

Adenovirus Early Proteins↗
PubMed1993

In vitro transcription of a Drosophila U1 small nuclear RNA gene requires TATA box-binding protein and two proximal cis-acting elements with stringent spacing requirements.

Transcription of a Drosophila U1 small nuclear RNA gene was functionally analyzed in cell extracts derived from 0- to 12-h embryos. Two promoter elements essential for efficient initiation of transcription in vitro by RNA polymerase II were identified. The first, termed PSEA, is located between positions -41 and -61 relative to the transcription start site, is crucial for promoter activity, and is the dominant element for specifying the transcription initiation site. PSEA thus appears to be functionally homologous to the proximal sequence element of vertebrate small nuclear RNA genes. The second element, termed PSEB, is located at positions -25 to -32 and is required for an efficient level of transcription initiation because mutation of PSEB, or alteration of the spacing between PSEA and PSEB, severely reduced transcriptional activity relative to that of the wild-type promoter. Although the PSEB sequence does not have any obvious sequence similarity to a TATA box, conversion of PSEB to the canonical TATA sequence dramatically increased the efficiency of the U1 promoter and simultaneously relieved the requirement for the upstream PSEA. Despite these effects, introduction of the TATA sequence into the U1 promoter had no effect on the choice of start site or on the RNA polymerase II specificity of the promoter. Finally, evidence is presented that the TATA box-binding protein is required for transcription from the wild-type U1 promoter as well as from the TATA-containing U1 promoter.

Animals↗
PubMed1986

Protein factor(s) binding independently to two different regions of the adenovirus 2 major late promoter.

The protein factor(s) in a fraction from the HeLa cell nuclear extract required for specific in vitro transcription can specifically bind to adenovirus 2 major late promoter (Ad 2 MLP) DNA. We demonstrate by in vitro footprinting assay that there are two asymmetric protected regions covering the TATA box and the nucleotides upstream from the TATA box. In the coding strand, the DNAse I protected regions span from nucleotides -10 to -50 and from -52 to -68. In the noncoding strand, the protected regions span from nucleotides -10 to -32 and from -45 to -65. Using different Ad 2 MLP point mutants in this assay, we show that the transcriptional down mutants of the TATA box (AC-30 and AC-28) abolish the binding of protein factor(s) to the TATA box but do not affect binding in the upstream region. The new upstream transcriptional down mutant (TA-56) abolishes the binding of protein factor(s) in the upstream region but does not affect binding to the TATA box. The mutants which do not affect transcription efficiency (GA-51 and CG-61) do not modify the binding to either the TATA box or the upstream region. Methylation protection experiments show that the guanosines at -58 and -60 in the coding strand and at -57 (probably also -55) in the noncoding strand are in close contact with protein factor(s). The results indicate that the TATA box and its upstream region of Ad 2 MLP are independently bound by at least two different factors in vitro.

Adenoviruses, Human↗
PubMed1995

Promoter structure and intron-exon organization of a scorpion alpha-toxin gene.

The Androctonus australis scorpion venom contains alpha-toxins for which the complementary DNAs have been cloned [Bougis et al. (1989) J. Biol. Chem. 264, 19259-19265], targeting with high affinity the voltage-sensitive sodium channel. From a genomic library made of this species of scorpion, we have cloned and characterized the gene encoding the toxin AaH I'. The gene transcriptional unit is 793 base pairs long, and the gene has a single intron of 425 base pairs located near the end of the signal peptide of the toxin precursor. The transcription initiation site was determined by primer extension and corresponded to the nucleotide sequence AACAA. Upstream, a promoter region has been identified with positive acting sequence elements at consensus positions, such as a CCAAT box and a TATA box. In addition, putative elements for binding the transcriptional factors MAT-alpha 2, Pit-1, and IEF1 are also present. Analysis of DNA curvature by computer modeling revealed a strong bending centered around the transcription initiation site of the gene. The bending angle (61 degrees) estimated experimentally using polyacrylamide gel electrophoresis correlates well with the value predicted by computer modeling (66 degrees). Other minor deflections of the helix axis cooperate for an overall curvature of nearly 90 degrees, which is significantly stronger than similar structures already reported in eukaryotic cells. It is worth noting that the grooves relative to the CCAAT box and the TATA box lie along the inside of the DNA curve. This observation is in agreement with the previously reported correlation between DNA bending and promoter function.

Amino Acid Sequence↗
PubMed2006

TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences.

We carried out in vitro selection experiments to systematically probe the effects of TATA-box flanking sequences on its interaction with the TATA-box binding protein (TBP). This study validates our previous hypothesis that the effect of the flanking sequences on TBP/TATA-box interactions is much more significant when the TATA box has a context-dependent DNA structure. Several interesting observations, with implications for protein-DNA interactions in general, came out of this study. (i) Selected sequences are selection-method specific and TATA-box dependent. (ii) The variability in binding stability as a function of the flanking sequences for (T-A)4 boxes is as large as the variability in binding stability as a function of the core TATA box itself. Thus, for (T-A)4 boxes the flanking sequences completely dominate and determine the binding interaction. (iii) Binding stabilities of all but one of the individual selected sequences of the (T-A)4 form is significantly higher than that of their mononucleotide-based consensus sequence. (iv) Even though the (T-A)4 sequence is symmetric the flanking sequence pattern is asymmetric. We propose that the plasticity of (T-A)n sequences increases the number of conformationally distinct TATA boxes without the need to extent the TBP contact region beyond the eight-base-pair long TATA box.

Base Pairing↗
PubMed2002

A new class of transcription initiation factors, intermediate between TATA box-binding proteins (TBPs) and TBP-like factors (TLFs), is present in the marine unicellular organism, the dinoflagellate Crypthecodinium cohnii.

Dinoflagellates are marine unicellular eukaryotes that exhibit unique features including a very low level of basic proteins bound to the chromatin and the complete absence of histones and nucleosomal structure. A cDNA encoding a protein with a strong homology to the TATA box-binding proteins (TBP) has been isolated from an expressed sequence tag library of the dinoflagellate Crypthecodinium cohnii. The typical TBP repeat signature and the amino acid motives involved in TFIIA and TFIIB interactions were conserved in this new TBP-like protein. However, the four phenylalanines known to interact with the TATA box were substituted with hydrophilic residues (His(77), Arg(94), Tyr(171), Thr(188)) as has been described for TBP-like factors (TLF)/TBP-related proteins (TRP). A phylogenetic analysis showed that cTBP is intermediate between TBP and TLF/TRP protein families, and the structural similarity of cTBP with TLF was confirmed by low affinity binding to a consensus' TATA box in an equivalent manner to that usually observed for TLFs. Six 5'-upstream gene regions of dinoflagellate genes have been analyzed and neither a TATA box nor a consensus-promoting element could be found within these different sequences. Our results showed that cTBP could bind stronger to a TTTT box sequence than to the canonical TATA box, especially at high salt concentration. Same binding results were obtained with a mutated cTBP (mcTBP), in which the four phenylalanines were restored. To our knowledge, this is the first description of a TBP-like protein in a unicellular organism, which also appears as the major form of TBP present in C. cohnii.

Amino Acid Sequence↗
PubMed1997

Identification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae.

Interaction of the TATA box-binding protein (TBP) with promoters of RNA polymerase II-transcribed genes is an early and essential step in mRNA synthesis. Previous studies have demonstrated that the rate-limiting binding of TBP to a TATA element can be influenced by transcriptional regulatory proteins. To identify additional factors that may regulate DNA binding by TBP in vivo, we performed a genetic selection for extragenic suppressors of a yeast TBP mutant that exhibits altered and relaxed DNA binding specificity. This analysis has led to the discovery of a previously unidentified gene, RTF1. The original rtf1 suppressor mutation, which encodes a single amino acid change in Rtf1, and an rtf1 null allele suppress the effects of the TBP specificity mutant by altering transcription initiation. Differences in the patterns of transcription initiation in these strains strongly suggest that the rtf1 missense mutation is distinct from a simple loss-of-function allele. The results of genetic crosses indicate that suppression of TBP mutants by mutations in RTF1 occurs in an allele-specific fashion. In a strain containing wild-type TBP, the rtf1 null mutation suppresses the transcriptional effects of a Ty delta insertion mutation in the promoter of the HIS4 gene, a phenotype also conferred by the TBP altered-specificity mutant. Finally, as shown by indirect immunofluorescence experiments, Rtf1 is a nuclear protein. Taken together, our findings suggest that Rtf1 either directly or indirectly regulates the DNA binding properties of TBP and, consequently, the relative activities of different TATA elements in vivo.

Amino Acid Sequence↗
PubMed1999

Orientation of the transcription preinitiation complex in archaea.

The basal transcription machinery of Archaea corresponds to the minimal subset of factors required for RNA polymerase II transcription in eukaryotes. Using just two factors, Archaea recruit the RNA polymerase to promoters and define the direction of transcription. Notably, the principal determinant for the orientation of transcription is not the recognition of the TATA box by the TATA-box-binding protein. Instead, transcriptional polarity is governed by the interaction of the archaeal TFIIB homologue with a conserved motif immediately upstream of the TATA box. This interaction yields an archaeal preinitiation complex with the same orientation as the analogous eukaryal complex.

Archaea↗
PubMed1992

Isolation and characterization of a cDNA clone encoding the TATA box-binding protein (TFIID) from wheat.

We isolated a complementary DNA (cDNA) encoding the TATA-binding factor 'TFIID' from a wheat seedling cDNA library. The wheat TFIID transcript of 1.2 kb poly(A)+ RNA was expressed at a low level early in germination, but gradually increased as the seedlings developed. In vitro binding experiments showed that the bacterially expressed wheat TFIID protein could specifically bind to the TATA boxes of the cauliflower mosaic virus (CaMV) 35S, wheat histone H3 and adenovirus major late genes with different affinity. A comparison with Arabidopsis TFIID showed the presence of a plant-specific region consisting of 13 amino acids at the divergent amino terminus and a conserved region (182 amino acids) at the carboxy terminus longer than that observed in yeasts (180 amino acids) and animals (181 amino acids).

Amino Acid Sequence↗
PubMed1997

Local DNA stretching mimics the distortion caused by the TATA box-binding protein.

X-ray structures of the TATA box-binding protein complexed with its DNA target show that the nucleic acid is severely bent away from the protein and also strongly unwound. We have used molecular mechanics and energy mapping to understand how such an unusual conformation can be induced. The results show that simple deformation pathways involving local stretching or unwinding of DNA reproduce many features of the experimental structure. Notably, kinked junctions with the flanking B-DNA regions occur without the need for any specific local

DNA↗
PubMed2001

Ectopic expression of TATA box-binding protein induces shoot proliferation in Arabidopsis.

The TATA box-binding protein (TBP) is an essential component of transcription initiation complexes of all three eukaryotic RNA polymerases. Increasing evidence suggests that the TBP activity and availability may be regulated to precisely control gene transcription and play an important role in cell type-specific regulation. Arabidopsis TBP-2 is up-regulated in apical shoot tissues. Overexpression of TBP-2 in transgenic Arabidopsis induces apical shoot proliferation. The expression of some shoot meristem regulatory genes is altered. These data suggest that the TBP gene dosage and/or expression level may play an important role in controlling shoot production and plant morphology.

Arabidopsis↗
PubMed1988

Constraints on spacing between transcription factor binding sites in a simple adenovirus promoter.

The adenovirus 2 E1B transcription unit has an extremely simple promoter consisting of a TATA box and a closely situated GC box. The interaction between the TATA box and the GC box was analyzed using insertion mutations which expand the distance between the two elements. We observed that the E1B promoter has an unusually rigid architecture. When the GC box, which is a binding site for transcription factor Sp1, was separated further from the TATA box than in the wild-type promoter, in vivo transcription quickly diminished to a level comparable to the elimination of the Sp1 site. Yet all the insertion mutants bound Sp1 factor in vitro with an affinity approximately equal to that of the wild-type promoter. From these results, we argue that Sp1 binding alone is not sufficient to stimulate transcription. The increased distance might disrupt direct contacts between Sp1 and transcription factors bound at the TATA box, contacts required for transcription stimulation by Sp1. The insertion mutations do not interfere with the transcription activation process mediated by the adenovirus large E1A protein or the pseudorabies virus immediate early protein.

Adenoviridae↗
PubMed1992

Structure and expression of a calcium-binding protein gene contained within a calmodulin-regulated protein kinase gene.

We have determined the first genomic structure and characterized the mRNA and protein products of a novel vertebrate gene that encodes a calcium-binding protein with amino acid sequence identity to a protein kinase domain. The elucidation of the complete DNA sequence of this transcription unit and adjacent genomic DNA, Southern blot and polymerase chain reaction analyses of cellular genomic DNA, and examination of mRNA and protein species revealed that the calcium-binding kinase-related protein (KRP)-encoding gene is contained within the gene for a calmodulin-regulated protein kinase, myosin light-chain kinase (MLCK). The KRP gene transcription unit is composed of three exons and a 5'-flanking sequence containing a canonical TATA box motif. The TATA box, the transcription initiation site, and the first 109 nucleotides of the 5' noncoding region of the KRP mRNA correspond to an MLCK gene intron sequence. Both KRP and MLCK are produced in the same adult chicken tissue in relatively high abundance from a single contiguous stretch of genomic DNA and utilize the same reading frame and common exons to produce distinct mRNAs (2.7 and 5.5 kb, respectively) that encode proteins with dissimilar biochemical functions. There appears to be no precedent in vertebrate molecular biology for such a relationship. This may represent a mechanism whereby functional diversity can be achieved within the same vertebrate tissue by use of common exons to produce shuffled domains with identical amino acid sequences in different molecular contexts.

Amino Acid Sequence↗
PubMed1990

Structure of a gene for a lysosomal membrane glycoprotein (LEP100). Housekeeping gene with unexpected exon organization.

Members of a recently described family of glycoproteins constitute the major protein components of the lysosomal membrane. Changes in glycosylation patterns, redistribution to the cell surface, and increased levels of expression of these proteins are associated, in at least some cases, with cell differentiation, transformation, and metastasis. To understand further the regulation of expression of these proteins and their relationships to each other, we have isolated and characterized the gene for one of these proteins, LEP100, from chicken. Two overlapping clones were isolated which contain the nine exons and eight introns of the 17-kilobase gene for LEP 100. The 5'-flanking region of the gene contains CAAT and TATAAA sequences, but these do not appear to be used as promoter elements. Further downstream are three CCAAT boxes, with no corresponding TATA boxes, which represent putative promoter elements. Multiple CCAAT boxes, the apparent lack of a TATA box, and the GC-rich composition of the 5' region support the classification of the LEP100 gene as a TATA box-lacking housekeeping gene. As further evidence of the housekeeping nature of the LEP100 gene, Northern blots of RNA from several adult and embryonic tissues (skeletal muscle, kidney, liver, heart, gizzard, and brain) revealed a single message for LEP100 of the same size (about 3 kilobases) in each tissue. The gene's introns range in size from 104 to 7200 base pairs. Exons do not represent the four disulfide-bonded loops of the protein, but instead each cysteine of each disulfide-linked pair is encoded by a separate exon. The existence of the same sized mRNA in all tissues indicates that no alternate splicing occurs. The exon organization of the LEP100 gene suggests that it may have evolved from a primordial cysteine-containing exon by gene duplication events. It is likely that the genes of the other members of this family diverged from the same ancestral gene and have a gene organization similar to that of LEP100.

Amino Acid Sequence↗
PubMed1989

Accurate, TATA box-dependent polymerase III transcription from promoters of the c-myc gene in injected Xenopus oocytes.

We have investigated the factors that permit a gene normally transcribed by RNA polymerase II to be transcribed by RNA polymerase III. It was shown previously that the human c-myc gene could be transcribed in vitro and in Xenopus oocytes by both alpha-amanitin-sensitive and alpha-amanitin-resistant polymerases, probably corresponding to polymerase II and polymerase III. We confirmed this observation in microinjected oocytes and showed that the alpha-amanitin-resistant transcription of c-myc was competed by known polymerase III genes. Polymerase III transcription of c-myc was very inefficient compared to other polymerase III genes, however, and was observed only when large amounts of template DNA were injected. At lower DNA concentrations the gene was transcribed, exclusively by polymerase II. In contrast, the adenovirus major late promoter was not transcribed by polymerase III. The 5' ends of polymerase III RNAs were almost indistinguishable from those of polymerase II RNAs initiating at the P1 and P2 promoters of the human and mouse c-myc genes. Furthermore, point mutations in the TATA box of the human P2 promoter greatly reduced polymerase III activity. At this promoter, therefore, polymerase II and polymerase III recognize a common element, the TATA box, which probably plays an important role in specifying the start site of transcription for both polymerases. We suggest that the highly accurate though inefficient mimicry of polymerase II by polymerase III at the c-myc promoters reflects the common evolutionary origin of these two enzymes.

Animals↗
PubMed1993

Only the HLA class I gene minimal promoter elements are required for transactivation by human cytomegalovirus immediate early genes.

The immediate early (IE) genes of human cytomegalovirus (HCMV) are expressed in lymphocytes and are known to transactivate both viral and cellular promoters. The mechanism by which IE gene products of HCMV transactivate expression of the HLA A2 gene promoter in Jurkat cells, a T-lymphocyte cell line, was investigated. Transient expression assays were performed using plasmids containing the HLA A2 promoter-regulatory region linked to the bacterial chloramphenicol acetyltransferase (CAT) gene and a plasmid expressing the CMV IE genes. The upregulation of the HLA A2 promoter by HCVM IE gene products was shown not to be secondary to either interferon-gamma or -alpha. Previously described MHC class I regulatory or enhancer elements such as the interferon-stimulated response element (ISRE), NF-kappa B and H2TF1 binding sequences, and the interferon consensus sequence (ICS) were not required for transactivation of the A2 promoter. Rather, the only known regulatory elements in the HLA A2 promoter necessary for both basal expression and transactivation by HCVM IE gene products are the CCAAT box and TATA box motifs. These results support a model in which HCVM IE gene products act through the minimal HLA A2 promoter elements to increase gene expression.

Base Sequence↗
PubMed1996

Nucleotide sequence of 5'-upstream region and expression of a silkworm gene encoding a new member of the attacin family.

A genomic clone encoding a new member of attacin, an insect antibacterial protein, was isolated from a genomic library of the silkworm, Bombyx mori, and the nucleotide sequence of the 5'-upstream region was determined. The region contained Bm 1, a highly repetitive element of B. mori and a lipopolysaccharide (LPS) response element (RE)(NF-kappaB binding site), CAAT box and TATA box. Northern blot analysis showed that the attacin gene expression was rapidly induced by bacterial cell wall components such as LPS from Escherichia coli and peptidoglycan (PG) from Micrococcus luteus, suggesting that attacin plays an important role in an early phase of the self-defense system upon bacterial infection.

Animals↗