Sequence-directed bends of DNA helix axis at the upstream activation sites of alpha-cell-specific genes in yeast

DNA axial rotation and the merge of oppositely supercoiled DNA domains in Escherichia coli: effects of DNA bends

We have examined the issue whether axial rotation of an intracellular DNA segment several thousand base pairs in length is associated with a large friction barrier against the merge of oppositely supercoiled DNA domains. The induction of a site-specific recombinase was used to form intracellular DNA rings bearing different numbers of transcription units, and it was found that DNA rings with a single tetA gene and no other transcription units does not become excessively negatively supercoiled in Escherichia coli cells lacking DNA topoisomerase I. Thus, whereas oppositely supercoiled domains are generated in a tetA-bearing DNA ring through anchoring of the tetA transcripts to cell membrane, these domains appear to readily merge by means of axial rotation of the DNA segment connecting them. The diffusional merge of these oppositely supercoiled domains is not significantly affected by the presence of bent sequences in the intervening DNA segment. Examination of the effects of adding more transcription units to the tetA-bearing ring suggests, however, that DNA bends stabilized by bound protein molecules may significantly impede this process inside E. coli, as suggested by previous in vitro studies.

Intrinsic DNA bends: an organizer of local chromatin structure for transcription

DNA with a curved trajectory of its helix axis is called bent DNA, or curved DNA. Interestingly, biologically important DNA regions often contain this structure, irrespective of the origin of DNA. In the last decade, considerable progress has been made in clarifying one role of bent DNA in prokaryotic transcription and its mechanism of action. However, the role of bent DNA in eukaryotic transcription remains unclear. Our recent study raises the possibility that bent DNA is implicated in the "functional packaging" of transcriptional regulatory regions into chromatin. In this article, I review recent progress in bent DNA research in eukaryotic transcription, and summarize the history of bent DNA research and several subjects relevant to this theme. Finally, I propose a hypothesis that bent DNA structures that mimic a negative supercoil, or have a right-handed superhelical writhe, organize local chromatin infrastructure to help the very first interaction between cis-acting DNA elements and activators that trigger transcription.

Eukaryotic DNA replication

One of the fundamental characteristics of life is the ability of an entity to reproduce itself, which stems from the ability of the DNA molecule to replicate itself. The initiation step of DNA replication, where control over the timing and frequency of replication is exerted, is poorly understood in eukaryotes in general, and in mammalian cells in particular. The cis-acting DNA element defining the position and providing control over initiation is the replication origin. The activation of replication origins seems to be dependent on the presence of both a particular sequence and of structural determinants. In the past few years, the development of new methods for identification and mapping of origins of DNA replication has allowed some understanding of the fundamental elements that control the replication process. This review summarizes some of the major findings of this century, regarding the mechanism of DNA replication, emphasizing what is known about the replication of mammalian DNA. J. Cell. Biochem. Suppls. 32/33:1-14, 1999.

Structure and comparative analysis of the rDNA intergenic spacer of Brassica rapa. Implications for the function and evolution of the Cruciferae spacer

The sequence of the intergenic spacer (IGS) of the Brassica rapa rDNA was determined and compared with those of other Cruciferae species. In the 3012-bp IGS, two segments of mostly unique sequence flank a 1.5-kb region consisting of two tandem arrays of repeats. A putative transcription initiation site (TIS) was identified by sequence comparison, 395 bp downstream from the repeat region. The intercalating segment displays unusual sequence patterns, and modelling of its topology predicts intrinsically bent DNA, with two elements of bending centered at positions -118 and -288 relative to the TIS. Comparative analysis of spacers from Cruciferae, revealed a common organization and high sequence similarity in their 5' and, particularly, 3' regions, whereas the repeat region upstream of TIS diverges rapidly. The conservation of structural elements, including the bent DNA upstream from the TIS, is discussed in light of their possible involvement in the IGS functions and structure of spacers in common ancestors. Examination of the Cruciferae spacers shows that, in addition to unequal crossover and gene conversion, insertional mutagenesis and replication slippage are molecular mechanisms significantly contributing to their evolution.

The bovine papillomavirus type 1 genome contains multiple loci of static DNA bending, but bends are absent from the functional origin of replication

Twenty-four overlapping restriction fragments spanning the entire bovine papillomavirus type 1 (BPV-1) genome were analyzed by electrophoresis to determine the extent of static DNA bending in the BPV-1 genome. Thirteen of 24 fragments contained static bends. Based on known locations of previously mapped bend loci and the overlapping pattern of these 13 fragments, we estimate that there are 8-11 distinct static bend loci in the BPV-1 genome. The bend loci were not uniformly distributed on the genome and with one exception, were clustered from nucleotides 5816 to 2621 on the BPV-1 map. This portion of the BPV-1 genome contains most of the transcriptional regulatory sequences as well as the origin of replication. The concordance between the genomic distribution of DNA bends and cis-active elements is consistent with the possibility that bent sequences may contribute to the function of at least some of these elements. However, unlike SV40, there was no static bend at that functional origin of replication for BPV-1. The nearest bends to the origin were approximately 120 bp to the 5' side and 300 bp to the 3' side. As both of these bends were outside of the sequences required for origin function, it is unlikely that static bending plays a critical role in BPV-1 replication.

On the consensus structure within the E. coli promoters

Using the theoretical model of DNA curvature, we have studied about 112 different E. coli promoters with a view to obtain some common super structures associated with them. Out of the 112 promoters analyzed by theoretical gel electrophoresis permutation about 66 of them have their minima lying between the -10 and the -35 region. The analysis of the bases at the minima reveals strong structural similarities. The differences can account for the varying strengths of the promoters as well as for different degree with which the RNA polymerase binds to these regions. The effects of mutation in each of these 112 promoters and their changes in curvature dispersion have also been evaluated.

A structural analysis of the bent kinetoplast DNA from Crithidia fasciculata by high resolution chemical probing

The chemical probes potassium permanganate (KMnO4) and diethylpyrocarbonate (DEPC) have been used to study the conformation of bent kinetoplast DNA from Crithidia fasciculata at different temperatures. Chemical reactivity data shows that the numerous short A-tracts of this bent DNA adopt a similar structure at 43 degrees C. This conformation appears to be very similar to the conformation of A-tracts in DNA exhibiting normal gel mobility. The A-tract structure detected by chemical probing is characterized by a high degree of base stacking on the thymine strand, and by an abrupt conformational change at the 3' end of the adenine strand. In general, no major alteration of this A-tract specific structure was detected between 4-53 degrees C. However, probing with KMnO4 revealed two unusual features of the C. fasciculata sequence that may contribute to the highly aberrant gel mobility of this DNA: 1) the B DNA/A-tract junction 5' dC/A3-6 3'. 5' dT3-6/G 3' is disproportionately represented and is conformationally distinct from other 5' end junctions, and 2) low temperature favors a novel strand-specific conformational distortion over a 20 base pair region of the bent kinetoplast DNA. Presence of the minor groove binding drug distamycin had little detectable effect on the A-tract conformation. However, distamycin did inhibit formation of the novel KMnO4 sensitive low temperature structure and partially eliminated the anomalous gel mobility of the kinetoplast DNA. Finally, we describe a simple and reproducible procedure for the production of an adenine-specific chemical DNA sequence ladder.

Alteration of the curved helical structure located in the upstream region of the beta-lactamase promoter of plasmid pUC19 and its effect on transcription

The region preceding the beta-lactamase promoter of Escherichia coli plasmid pUC19 has a curved DNA (bent DNA) structure. The center of the curvature was revealed to exist around nucleotide position 2580 of the plasmid, which is just beside RNA polymerase binding region. It was indicated that the identified region is curved even at 60 degrees C. The gross geometry of the curvature was altered by inserting synthetic double-stranded oligonucleotides between positions 2585 and 2586. Effect of the alteration on strength of the promoter was not detected in vitro. However, in vivo analyses showed that the promoter strength is apparently dependent, in part, on the gross geometry of the curvature. Insertions of 4 and 16 bp, both of which altered the gross geometry of the curvature greatly, caused considerable reductions of in vivo level of beta-lactamase mRNA. In vivo, overall three-dimensional structure of the region covering the promoter and the curvature seems to play some significant role in transcription of the gene.

A theoretical method to predict DNA permutation gel electrophoresis from the sequence

The gel electrophoretic permutation assays of DNA fragments experimentally investigated by different authors were theoretically reproduced using our theoretical model of sequence-dependent curvature. The general pattern of agreement obtained suggests that our method can be usefully adopted as an alternative to the experimental assay, in particular where the lack of a sufficient number of unique restriction sites in the fragment prevents the correct localization of the main bend site.

Analysis of the creA gene, a regulator of carbon catabolite repression in Aspergillus nidulans

The complete nucleotide sequence derived from a genomic clone and two cDNA clones of the creA gene of Aspergillus nidulans is presented. The gene contains no introns. The derived polypeptide of 415 amino acids contains two zinc fingers of the C2H2 class, frequent S(T)PXX motifs, and an alanine-rich region indicative of a DNA-binding repressor protein. The amino acid sequence of the zinc finger region has 84% similarity to the zinc finger region of Mig1, a protein involved in carbon catabolite repression in yeast cells, and it is related both to the mammalian Egr1 and Egr2 proteins and to the Wilms' tumor protein. A deletion removing the creA gene was obtained, by using in vitro techniques, in both a heterokaryon and a diploid strain but was unobtainable in a pure haploid condition. Evidence is presented suggesting that the phenotype of such a deletion, when not complemented by another creA allele, is leaky lethality allowing limited germination of the spore but not colony formation. This phenotype is far more extreme than that of any of the in vivo-generated mutations, and thus either the gene product may have an activator activity as well as a repressor function or some residual repressor function may be required for full viability.

Analysis of the creA gene, a regulator of carbon catabolite repression in Aspergillus nidulans

The complete nucleotide sequence derived from a genomic clone and two cDNA clones of the creA gene of Aspergillus nidulans is presented. The gene contains no introns. The derived polypeptide of 415 amino acids contains two zinc fingers of the C2H2 class, frequent S(T)PXX motifs, and an alanine-rich region indicative of a DNA-binding repressor protein. The amino acid sequence of the zinc finger region has 84% similarity to the zinc finger region of Mig1, a protein involved in carbon catabolite repression in yeast cells, and it is related both to the mammalian Egr1 and Egr2 proteins and to the Wilms' tumor protein. A deletion removing the creA gene was obtained, by using in vitro techniques, in both a heterokaryon and a diploid strain but was unobtainable in a pure haploid condition. Evidence is presented suggesting that the phenotype of such a deletion, when not complemented by another creA allele, is leaky lethality allowing limited germination of the spore but not colony formation. This phenotype is far more extreme than that of any of the in vivo-generated mutations, and thus either the gene product may have an activator activity as well as a repressor function or some residual repressor function may be required for full viability.

Lack of a requirement for strict rotational alignment among transcription factor binding sites in yeast

The MF alpha 1 gene of Saccharomyces cerevisiae is an alpha specific gene whose expression is regulated by two upstream activation sites (UASMF alpha 1S), which are the binding sites for activator proteins, MAT alpha 1 and MCM1. UASMF alpha 1 elements act in a synergistic fashion; lack of either element causes reduced expression levels that are 6- to 45-fold less than that of intact promoter in alpha cells. We investigated the effect of manipulating rotational alignments among transcription factor binding sites of MF alpha 1 on the expression of the gene. The expression level of MF alpha 1 decreased with the spacing between the two UASMF alpha 1S and no synergism was observed when the distance of the two elements was longer than 90 base pairs. No strict rotational alignment was required for their synergistic action. We also show that the spacing between UASMF alpha 1 elements and TFIID binding site, the TATA box, had little, if any, effect on MF alpha 1 expression. We chose a sufficient number of positions for UASMF alpha 1S to ensure that, in several of these positions, MAT alpha 1 and MCM1 were on the opposite side of the DNA helix with respect to the TATA box.

Identification of an enhancer element for the endosperm-specific expression of high molecular weight glutenin

Genes encoding high molecular weight (HMW) glutenin, a wheat seed storage protein, are expressed only in the developing endosperm. It was previously demonstrated that sequences essential for endosperm-specific transcription reside within 436 base pairs upstream of the initiation codon for HMW glutenin translation. We have further analyzed this region by testing the ability of a series of truncated HMW glutenin promoter fragments to enhance transcription from an adjacent heterologous promoter. The activity of these hybrid promoters was determined by measuring the expression of a linked beta-glucuronidase (GUS) reporter gene in transgenic tobacco plants. An HMW glutenin promoter fragment spanning nucleotides -375 to -45 relative to the transcription start site was found to stimulate GUS expression in tobacco seeds when inserted in either orientation upstream of the heterologous promoter. Furthermore, this fragment could also potentiate transcription when located 3' to the GUS reporter gene. Stimulation of GUS gene expression in transgenic tobacco seeds did not occur until 9 days to 12 days after anthesis, coincident with the onset of storage protein synthesis in the developing tobacco and wheat seed, and was confined to the endosperm tissue. By testing progressively shorter promoter fragments, the enhancer element responsible for this pattern of expression was localized to a 40-base pair region some 170 base pairs upstream of the start site for HMW glutenin transcription.

Identification of an enhancer element for the endosperm-specific expression of high molecular weight glutenin

Genes encoding high molecular weight (HMW) glutenin, a wheat seed storage protein, are expressed only in the developing endosperm. It was previously demonstrated that sequences essential for endosperm-specific transcription reside within 436 base pairs upstream of the initiation codon for HMW glutenin translation. We have further analyzed this region by testing the ability of a series of truncated HMW glutenin promoter fragments to enhance transcription from an adjacent heterologous promoter. The activity of these hybrid promoters was determined by measuring the expression of a linked beta-glucuronidase (GUS) reporter gene in transgenic tobacco plants. An HMW glutenin promoter fragment spanning nucleotides -375 to -45 relative to the transcription start site was found to stimulate GUS expression in tobacco seeds when inserted in either orientation upstream of the heterologous promoter. Furthermore, this fragment could also potentiate transcription when located 3' to the GUS reporter gene. Stimulation of GUS gene expression in transgenic tobacco seeds did not occur until 9 days to 12 days after anthesis, coincident with the onset of storage protein synthesis in the developing tobacco and wheat seed, and was confined to the endosperm tissue. By testing progressively shorter promoter fragments, the enhancer element responsible for this pattern of expression was localized to a 40-base pair region some 170 base pairs upstream of the start site for HMW glutenin transcription.

Sequence signals in eukaryotic upstream regions

Two DNA sequence elements are known to recur frequently upstream of eukaryotic polymerase II-transcribed genes. The TATAAA, at position -40, specifies the transcription initiation site. The GGCCAATCT is less frequent around -80. Sequence analysis of upstream regions reveals that the underlined yeast UAS2 consensus sequence, TGATTGGT, is also very frequent at -80 in higher polymerase II-transcribed animal sequences. The underlined CCAAT box and yeast UAS sequences are complementary. Structural analysis suggests some symmetry in their DNA structures. Upstream of the TATAAT-rich region there is an abundance of GC sequences. Analysis of nucleotide tracts indicates that these are preferentially flanked by their complementary nucleotides with a pyrimidine-purine junction, i.e., TTAN, CCGn, CnGG, TnAA. Here, I discuss DNA structural consideration in upstream regions along with protein readout of the major and minor groove information content. These sequence-structure aspects are put in the general context of protein (factors)-DNA (elements) recognition and regulation.

Hydroxyl radical footprints reveal novel structural features around the NF I binding site in adenovirus DNA

We have identified a number of as yet unknown structural abnormalities of the NF I-DNA binding site within the inverted terminal repetition of adenovirus DNA by probing it with a hydroxyl radical footprinting technique. NF I binding alters the accessibility of the deoxyribose moieties to hydroxyl radicals both at the 3' and at the 5' side of the recognition sequence 5'-TGG(N)6GCCAA-3'. A smooth bend at the 5' side of the binding sequence is already present in naked linear DNA and it is further enhanced by protein binding. This could be demonstrated not only by hydroxyl radical footprinting but also by studying the temperature dependent mobility during gel electrophoresis of DNA fragments carrying the NF I binding site at circularly permutated positions. We propose that the bent conformation at this site is responsible for facilitating protein/DNA interactions.

Upstream half of adenovirus type 2 enhancer adopts a curved DNA conformation

The putative enhancer domain of human adenovirus type 2 (Ad2) was revealed to contain a bent DNA structure in the upstream half. By using "deletion analysis", this unusual structure was identified experimentally to span from nucleotide 194 to 269 (figures; nucleotide numbers from the left terminal nucleotide of the viral DNA). This region has almost the same nucleotide sequence as the upstream half of the enhancer and packaging region of Ad5 and, therefore, is thought to contain multiple enhancer elements for transcription and the elements required for packaging of Ad2 DNA. The bent DNA structure of this region was further characterized by analyzing temperature-dependent changes in electrophoretic mobility of the DNA fragments used for bending analysis. Ad2 enhancer provides a good system to investigate the relationship between higher order structure of DNA and transcriptional activation.

DNA bending and binding factors of the human beta-actin promoter

Transcription of the beta-actin gene is rapidly inducible in response to serum stimulation. To determine the regions responsible for serum inducible and basal level expression, the human beta-actin promoter was subjected to mutational analysis. Two distinct elements, the CCAAT homology and the beta-actin specific conserved sequences, were found by a chloramphenicol acetyltransferase expression assay and sequence comparisons, and then analyzed for possible functions. Using a DNA bend assay, it was shown that the conserved sequences included the core of a sequence-directed bend of DNA. Gel mobility shift and DNase I protection assays revealed that the conserved sequences and the CCAAT homology were recognized by binding factors in HeLa cell extracts.

Sequence-directed DNA bending upstream of the streptokinase promoter

A 450-base pair (bp) HinfI restriction fragment from the chromosome of Streptococcus equisimilis H46A contains the early coding region of the streptokinase gene (skc), the skc promoter, and a stretch of DNA 5' to the--35 region of the skc promoter. Two-dimensional polyacrylamide (PA) gel electrophoresis at two different temperatures showed that this fragment migrates anomalously slowly on PA gels, suggesting the existence of a bent DNA conformation. Inspection of the nucleotide sequence confirmed this suggestion by revealing numerous oligomeric dA.dT tracts, some of which are in phase with the helix screw. Computer analysis of the sequence predicted the existence of two bending loci, one of which is located upstream of the skc promoter. In addition to showing DNA bending, the 450-bp HinfI fragment contains multiple 13-bp sequences homologous to the Escherichia coli integration host factor DNA-binding consensus sequence. Insertion of IS1 into a site immediately upstream of the--35 region decreased the expression level of skc in E. coli, suggesting that DNA conformation upstream of the promoter has a role in skc expression.