Genomic organization and functional analysis of a deletion variant of the 87A7 heat shock locus of Drosophila melanogaster

Variation at the 87A heat shock locus in Drosophila melanogaster

Restriction maps for 25 kilobases of DNA around the 87A7 heat shock locus have been determined in 29 chromosomes isolated from a natural population. The heterozygosity per nucleotide and the proportion of polymorphic nucleotide sites were estimated to be 0.0024 and 0.007, respectively. The mean number of insertional differences in this region between random pairs of chromosomes was 0.95. A significant amount of this variation was due to the insertion of large transposable elements. All the insertion/deletion events were found in a region less than 2 kilobases in size. This could either be due to nonrandom integration or to differences in the intensity of selection against DNA insertion at different sites.

Genomic deletions of the Drosophila melanogaster Hsp70 genes

Homologous recombination can produce directed mutations in the genomes of a number of model organisms, including Drosophila melanogaster. One of the most useful applications has been to delete target genes to generate null alleles. In Drosophila, specific gene deletions have not yet been produced by this method. To test whether such deletions could be produced by homologous recombination in D. melanogaster we set out to delete the Hsp70 genes. Six nearly identical copies of this gene, encoding the major heat-shock protein in Drosophila, are found at two separate but closely linked loci. This arrangement has thwarted standard genetic approaches to generate an Hsp70-null fly, making this an ideal test of gene targeting. In this study, ends-out targeting was used to generate specific deletions of all Hsp70 genes, including one deletion that spanned approximately 47 kb. The Hsp70-null flies are viable and fertile. The results show that genomic deletions of varied sizes can be readily generated by homologous recombination in Drosophila.

Sequence dependence of Drosophila topoisomerase II in plasmid relaxation and DNA binding

The sequence dependence of Drosophila topoisomerase II supercoil relaxation and binding activities has been examined. The DNA substrates used in binding experiments were two fragments from Drosophila heat shock locus 87A7. One of these DNA fragments includes the coding region for the heat shock protein hsp70, and the other includes the intergenic non-coding region that separates two divergently transcribed copies of the hsp70 gene at the locus. The intergenic region was previously shown to have a much higher density of topoisomerase cleavage sites than the hsp70 coding region. Competition nitrocellulose filter binding assays demonstrate a preferential binding of the intergene fragment, and that binding specificity increases with increasing ionic strength. Dissociation kinetics indicate a greater kinetic stability of topoisomerase II complexes with the intergene DNA fragment. To study topoisomerase II relaxation activity, we used supercoiled plasmids that contained the same fragments from locus 87A7 cloned as inserts. The relative relaxation rates of the two plasmids were determined under several conditions of ionic strength, and when the plasmid substrates were included in separate reactions or when they were mixed in a single reaction. The relaxation properties of these two plasmids can be explained by a coincidence of high-affinity binding sites, strong cleavage sites, and sites used during the catalysis of strand passage events by topoisomerase II. Sequence dependence of topoisomerase II catalytic activity may therefore parallel the sequence dependence of DNA cleavage by this enzyme.

Topoisomerase II cleavage in chromatin

We have examined the effect of the anti-tumor drug VM-26 on purified Drosophila topoisomerase II, and used this drug to map (putative) topoisomerase II cleavage sites in chromatin. These studies indicate that VM-26 interferes with the strand breakage-rejoining catalytic cycle. VM-26 appears to stabilize the topoisomerase-II-cleavable complex and markedly enhances the formation of double-strand breaks in naked DNA. VM-26 also stimulates the formation of double-strand breaks in isolated Drosophila nuclei. Analysis of the parameters of the VM-26-stimulated cleavage reaction in nuclei strongly suggests that the double-strand scissions are generated by endogenous topoisomerase II. Finally, we have examined the distribution of (putative) cleavage sites for endogenous topoisomerase II in the chromatin of the 87A7 heat shock locus and the histone repeat unit. We have found that there are prominent VM-26-induced cleavage products from the 5' ends of the 87A7, the two heat shock protein 70 genes, and in the intergenic spacer separating these genes. Moreover, the pattern of VM-26-induced cleavage products is altered in nuclei prepared from heat-shocked cells. In the case of the histone repeat unit, only minor VM-26-induced cleavage products are observed in nuclei (in spite of the fact that experiments on naked DNA indicate that the histone repeat contains many major cleavage sites for purified topoisomerase II). These findings suggest that the nucleoprotein organization of different DNA segments may be important in determining whether specific sites are accessible to endogenous topoisomerase II in nuclei.

Expression of the major heat shock gene of Drosophila melanogaster in Saccharomyces cerevisiae

A copy of the gene which encodes the major heat shock protein (hsp70) of D. melanogaster was integrated in both orientations into the genome of S. cerevisiae at the leu2 locus. The level of transcript from the D. melanogaster gene was measured under both normal conditions and conditions which are known to give rise to the heat shock response in S. cerevisiae. In both orientations the D. melanogaster gene gave rise to an abundant transcript in uninduced cells. The level of this transcript was increased transiently on heat shock, peaking after about 30 min at the elevated temperature. The average induction observed was around 5-fold. Although the D. melanogaster gene is heat inducible in S. cerevisiae, the transcripts are initiated at several sites which lie between 10 and 40 base pairs downstream of the initiation site in D. melanogaster. Thus, the transcriptional apparatus of S. cerevisiae appears to recognize the promoter and regulatory elements of the D. melanogaster major heat shock gene, although the manner in which transcription is initiated differs between the two species.

Chromatin structure of the 87A7 heat-shock locus during heat induction and recovery from heat shock

We have examined the chromatin organization of the 87A7 heat-shock locus (which contains two hsp 70 genes transcribed in opposite orientation) as a function of the time of heat induction and during the course of recovery from heat shock. Our studies show that both induction and recovery from heat shock are accompanied by highly specific alterations in the nucleoprotein structure of this locus. Moreover, these changes parallel the transcriptional activity of the hsp 70 heat-shock genes. We have also examined the effect of inhibitors of transcription and translation. Cycloheximide, an inhibitor of translation, blocks both the attenuation of the heat-shock response (which occurs after a long-term incubation at elevated temperatures) and the re-establishment of the pre-induced chromatin organization of the locus during recovery from heat shock. Actinomycin D, an inhibitor of transcription, prevents some but not all of the alterations in chromatin structure which normally accompany heat induction.

Novobiocin blocks the Drosophila heat shock response

In the studies reported here we show that the antibiotic novobiocin, an in vitro inhibitor of topoisomerase II, blocks the Drosophila heat shock response. If novobiocin is added prior to induction, there is no detectable expression of the Drosophila heat shock genes. Moreover, analysis of the chromatin organization of the 87A7 heat shock locus indicates that the antibiotic prevents the structural alterations which normally accompany heat induction. When novobiocin is added after induction, transcription appears to be rapidly turned off, and the chromatin organization of the 87A7 locus is "fixed" in an "active" configuration. Novobiocin also prevents the re-establishment of the pre-induced 87A7 chromatin organization which occurs during recovery from heat shock. We have also presented data suggesting that this antibiotic blocks transcription at 25 degrees C. These findings raise the possibility that topoisomerase II may be required in eukaryotes for both gene activation and deactivation.

Novel partitioning of DNA cleavage sites for Drosophila topoisomerase II

We have examined the long-range distribution of double-stranded DNA cleavage sites for Drosophila melanogaster topoisomerase II. These studies reveal a novel partitioning of preferred topoisomerase II cleavage sites. In the eukaryotic DNAs examined, major cleavage sites were typically found in nontranscribed spacer segments and close to the 5' and 3' boundaries of genes. In contrast, there were few if any prominent cleavage sites within genes. In addition, most of the major topoisomerase II cleavage sites closely corresponded to naked DNA hypersensitive sites for the prokaryotic enzyme, micrococcal nuclease.

The heat shock response

The response of cells to a heat shock or other stresses is the activation of a small number of genes which were previously inactive or transcribed at low levels. This response has been observed in a wide variety of bacterial, plant, and animal species. Evidence is accumulating that at least some of the proteins found in diverse species are similar, indicating a conservation of the response and the proteins in evolution. In a number of organisms a strong positive correlation has been found between the presence of heat shock proteins and ability of the organism to withstand thermal stress. This review attempts to assess the available data concerning the homology of proteins in different species, the localization of the proteins in cells, and the relationship between heat shock proteins and thermoresistance.

Transcriptionally active chromatin is sensitive to Neurospora crassa and S1 nucleases

We have examined the distribution of Neurospora crassa and S1 nuclease cleavage products in the chromatin of the 87A7 heat shock locus of Drosophila melanogaster. Both of these nucleases generate single and double-strand breaks in chromatin at specific sites in the 87A7 locus. Before heat induction, we find that the 5' ends of the two 87A7 hsp 70 genes contain N. crassa and S1 nuclease hypersensitive sites, while there are only a few cleavage products from elsewhere in the locus. With N. crassa nuclease, we observe one major 5' fragment, and this is derived from cleavage in a DNA segment mapping about 90 to 115 base-pairs from the beginning of the transcription unit. With S1 nuclease, we find two 5' cleavage products. The first maps about 120 to 130 base-pairs from the beginning of the gene. Interestingly, this site is also sensitive to S1 nuclease in supercoiled but not linear naked DNA. The other fragment maps very close to the transcription start site (approximately 0 to -15 base-pairs). After heat induction, there is a transition in the chromatin architecture of 87A7. First, there is a marked reduction in the yield of the prominent 5' N. crassa and S1 nuclease fragments. Second, the entire hsp 70 gene, as well as the spacer DNA just downstream from the 3' end of the gene, becomes highly sensitive to both of these nucleases.

Integration of Drosophila heat-shock genes transfected into cultured Drosophila melanogaster cells

We have used DNA-mediated gene transfer to introduce into Drosophila melanogaster cells DNA sequences for which no selective criteria exist. We have introduced a Drosophila heat-shock locus into cultured Drosophila cells by calcium phosphate cotransfection with the copia vector pCV31gpt and selection for xanthine utilization. We recovered cell lines containing between three and about 50 copies of both pCV31gpt and pMH10A, a cloned 87 A7 hsp70 heat-shock locus that encodes a mutant 40,000-dalton heat-shock protein (hsp40). The stable inheritance of the transformed DNAs argues that the input DNAs have integrated into the genome. We show that this is indeed the case for one cell line by cloning back the transfected DNA and detecting the flanking chromocentral sequences by in situ hybridization. Surprisingly, the integrated hsp70 genes are not expressed. This report represents the first example of the cointroduction of DNA sequences into Drosophila cells by cotransfection with a dominant selectable marker.

Transcription, export and turnover of Hsp70 and alpha beta, two Drosophila heat shock genes sharing a 400 nucleotide 5' upstream region

A highly homologous 400 nucleotide sequence flanks the 5' end and extends 64 NT into the transcribed portion of all five hsp70 and seven alpha beta heat shock genes in Drosophila melanogaster (1-4). To determine the extent to which this sequence dictates coordinate regulation, we compared the total mass, continuous labeling and pulse-labeling of hsp70 and alpha beta RNAs at different times and temperatures of heat shock. By all these measurements, expression of both hsp70 and alpha beta genes increased and decreased in parallel. Hsp70 RNA was generally synthesized at a higher rate and accumulated to a greater extent than alpha beta RNA. As the temperature of heat shock increased, however, the rate of synthesis and accumulation of hsp70 relative to alpha beta RNA decreased. Another difference was that a larger fraction of hsp 70, as compared to alpha beta RNA was exported from the nucleus. For both RNAs, export decreased as the heat shock temperature was increased. The hsp70 and alpha beta genes are thus expressed in parallel, but the homologous 5' upstream sequences do not dictate equal rates of transcription or export from the nucleus.

Chromatin organization of the 87A7 heat shock locus of Drosophila melanogaster

We have examined the chromatin structure of the hsp 70 gene complex at the 87A7 heat shock locus of Drosophila melanogaster. Our results indicate that this locus has a complex chromatin organization. Heat induction causes highly specific alterations in the chromatin throughout the locus. There are major changes within the heat shock gene transcription units, and in both the upstream and downstream flanking spacers.

Localization of the hsp83 transcript within a 3292 nucleotide sequence from the 63B heat shock locus of D. melanogaster

We have determined the complete nucleotide sequence of a 3292 bp cloned segment derived from the 63B heat shock cytogenetic locus of D. melanogaster. Within this segment we have positioned the start of transcription and RNA splice sites of the unique gene that encodes the 83,000 d heat shock polypeptide (hsp83 gene) by S1 mapping and synthesis of cDNA from restriction fragment primed mRNA. The sequence begins at a point 879 bp upstream from the transcription start and includes the 149 bp nontranslated first exon, the 1139 bp intron and extends 1125 bp into the protein coding region. These data identify a single open translation reading frame for the first 375 amino acids of the 83,000 d polypeptide, beginning with the first ATG codon located at the 3' intron-exon junction. We discuss and demonstrate the use of E. coli exonuclease III generated single-strand DNA probes as an alternative to strand separation for S1 mapping of mRNA. We also use homology search criteria based upon known protein-DNA binding sites to compare our hsp83 sequence with other sequenced Drosophila heat shock genes. These comparisons indicate that a large region of approximately 80 bp centered around the transcription initiation point of the hsp83 gene shares only a 31% homology with the corresponding region of the hsp70 gene, whereas the hsp22, 23, 26, and 27 genes share a 54% homology with hsp70 in this region. The lower homology of the hsp83 gene is consistent with the deviant nature of this heat shock gene.

Expression of Drosophila heat shock genes is regulated in Rat-cells

We have introduced a Drosophila 87A heat shock locus into the genome of Rat-1 cells. A brief heat shock of a resultant transformed line, Rhs11, induces the transcription of the Drosophila heat shock genes from the Drosophila heat shock promoter. This suggests that the induction mechanism and regulatory sequences for the heat shock response have been conserved between Drosophila and mammals.