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PubMed1999

An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region.

A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species. Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926

Alcohol Dehydrogenase↗
PubMed1993

20-OH-ecdysone swells nuclear volume by alkalinization in salivary glands of Drosophila melanogaster.

Ecdysteroids play an important role in the larval moulting process of insects. Ecdysone-induced stimulation causes specific "puffs" in polytene chromosomes of salivary gland cells resulting in nuclear swelling. During this process, changes of intracellular ion composition are thought to act as an early regulatory mechanism of gene activation. By use of video-imaging analysis and electrophysiological techniques, we examined ecdysone-induced nuclear swelling in Drosophila salivary glands in situ and its dependence on pH and calcium. Isolated glands of the third larval stage were superfused with a solution mimicking the haemolymph. Addition of 5 x 10(-6) mol/1 20-OH-ecdysone led, after a lag period of 50 min, to a sustained Ca(2+)-dependent increase of nuclear volume by 23.0 +/- 2.3%. Amiloride, a blocker of plasma membrane Na+/H+ exchange, prevented 20-OH-ecdysone-induced nuclear swelling. Decreasing pH in the superfusate from 7.15 to 6.8 led to nuclear shrinkage by 16.9 +/- 3.9%. Measurements of pH in salivary gland cells with ion-sensitive microelectrodes disclosed an alkalinization of 0.23 +/- 0.05 pH units after stimulation with 20-OH-ecdysone. We postulate that 20-OH-ecdysone activates the amiloride-sensitive plasma membrane Na+/H+ exchanger. This leads to intracellular alkalinization and concomitant decondensation of the nuclear chromatin visible as nuclear swelling. Thus, cell alkalinization could be a potentially important stimulatory mechanism in mediating ecdysteroid-induced activation of the cell nucleus.

Alkalies↗
PubMed1996

In vivo assay for protein-protein interactions using Drosophila chromosomes.

The ability of a chimeric HP1-Polycomb (Pc) protein to bind both to heterochromatin and to euchromatic sites of Pc protein binding was exploited to detect stable protein-protein interactions in vivo. Previously, we showed that endogenous Pc protein was recruited to ectopic heterochromatic binding sites by the chimeric protein. Here, we examine the association of other Pc group (Pc-G) proteins. We show that Posterior sex combs (Psc) protein also is recruited to heterochromatin by the chimeric protein, demonstrating that Psc protein participates in direct protein-protein interaction with Pc protein or Pc-associated protein. In flies carrying temperature-sensitive alleles of Enhancer of zeste[E(z)] the general decondensation of polytene chromosomes that occurs at the restrictive temperature is associated with loss of binding of endogenous Pc and chimeric HP1-Polycomb protein to euchromatin, but binding of HP1 and chimeric HP1-Polycomb protein to the heterochromatin is maintained. The E(z) mutation also results in the loss of chimera-dependent binding to heterochromatin by endogenous Pc and Psc proteins at the restrictive temperature, suggesting that interaction of these proteins is mediated by E(z) protein. A myc-tagged full-length Suppressor 2 of zeste [Su(z)2] protein interacts poorly or not at all with ectopic Pc-G complexes, but a truncated Su(z)2 protein is strongly recruited to all sites of chimeric protein binding. Trithorax protein is not recruited to the heterochromatin by the chimeric HP1-Polycomb protein, suggesting either that this protein does not interact directly with Pc-G complexes or that such interactions are regulated. Ectopic binding of chimeric chromosomal proteins provides a useful tool for distinguishing specific protein-protein interactions from specific protein-DNA interactions important for complex assembly in vivo.

Animals↗
PubMed1996

Phosphorylation dependence of the initiation of productive transcription of Balbiani ring 2 genes in living cells.

Using polytene chromosomes of salivary gland cells of Chironomus tentans, phosphorylation state-sensitive antibodies and the transcription and protein kinase inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), we have visualized the chromosomal distribution of RNA polymerase II (pol II) with hypophosphorylated (pol IIA) and hyperphosphorylated (pol II0) carboxyl-terminal repeat domain (CTD). DRB blocks labeling of the CTD with 32Pi within minutes of its addition, and nuclear pol II0 is gradually converted to IIA; this conversion parallels the reduction in transcription of protein-coding genes. DRB also alters the chromosomal distribution of II0: there is a time-dependent clearance from chromosomes of phosphoCTD (PCTD) after addition of DRB, which coincides in time with the completion and release of preinitiated transcripts. Furthermore, the staining of smaller transcription units is abolished before that of larger ones. The staining pattern of chromosomes with anti-CTD antibodies is not detectably influenced by the DRB treatment, indicating that hypophosphorylated pol IIA is unaffected by the transcription inhibitor. Microinjection of synthetic heptapeptide repeats, anti-CTD and anti-PCTD antibodies into salivary gland nuclei hampered the transcription of BR2 genes, indicating the requirement for CTD and PCTD in transcription in living cells. The results demonstrate that in vivo the protein kinase effector DRB shows parallel effects on an early step in gene transcription and the process of pol II hyperphosphorylation. Our observations are consistent with the proposal that the initiation of productive RNA synthesis is CTD-phosphorylation dependent and also with the idea that the gradual dephosphorylation of transcribing pol II0 is coupled to the completion of nascent pol II gene transcripts.

Amanitins↗
PubMed1993

HSP90 associates with specific heat shock puffs (hsr omega) in polytene chromosomes of Drosophila and Chironomus.

The heat shock protein HSP90, which is mainly cytoplasmic, has recently been reported to be present in the nucleus. We have found a specific chromosomal localization of HSP90 in different species of Drosophila and Chironomus using immunocytochemical techniques with different mono- and polyclonal antibodies for this hsp. HSP90 was found associated with heat shock-induced puffs at 93D and 48B in salivary gland chromosomes of Drosophila melanogaster and Drosophila hydei, respectively. The localization of HSP90 to locus 93D occurred rapidly after the onset of heat shock and disappeared during recovery, concomitant with puff regression. The association of HSP90 with the 93D locus was strictly heat shock dependent as shown by the absence of HSP90 in puff 93D induced by either benzamide or colchicine. No specific nuclear staining was observed in unstressed control cells. HSP90 was also found in the temperature-induced telomeric Balbiani ring puffs (T-BRs) in Chironomus thummi and in one heat shock puff at I-1C in Chironomus tentans. Other heat shock puffs also appeared lightly stained with the HSP90 polyclonal antibody in both species of Chironomus. HSP90 was absent from the T-BRs when RNA synthesis was inhibited with Actinomycin D suggesting that the localization of HSP90 is dependent on transcription. Inhibition of protein synthesis did not prevent association of this hsp with the T-BRs, indicating that pre-existing HSP90 can associate with this locus. HSP90 did not associate with any telomeric chromosomal regions of unstressed cells. The present observations suggest that heat shock gene products such as HSP90 may somehow be involved in the regulation at the chromosomal level of other members of the heat shock gene family. Puffs 93D (D. melanogaster) and 48B (D. hydei) are equivalent and correspond to homologous gene loci (hsr omega) that have unusual features that distinguish them from other heat shock puffs. The binding of HSP90 at T-BRs and at puff I-1C in the genus Chironomus is the first demonstration, albeit indirect, of the existence of hsr omega analogous loci in species other than Drosophila.

Animals↗
PubMed1995

Transcription of heat shock gene loci versus non-heat shock loci in Chironomus polytene chromosomes: evidence for heat-induced formation of novel putative ribonucleoprotein particles (hsRNPs) in the major heat shock puffs.

The heat shock response of Chironomus polytene chromosomes was reexamined. The in vivo effects of heat shock on chromosomal [3H]uridine labeling, RNA polymerase II distribution and ribonucleoprotein (RNP) formation were investigated. One primary result is a clarification of the number and location of chromosomal sites strongly induced by treatment at 37 degrees C for 60 min. In total, seven major heat shock loci were identified by transcription autoradiography in Chironomus tentans: I-20A, II-16B, II-10C, II-4B, II-1C, III-12B, and IV-5C. Secondly, combining immunofluorescence with transcription autoradiography, I find RNA polymerase II occurring after heat shock at multiple chromosomal sites that were also active under normal conditions (20 degrees C). Furthermore, the results demonstrate conclusively that the presence of RNA polymerase II at heat shock and non-heat shock loci is generally correlated with [3H]uridine labeling during heat shock. These latter results extend and corroborate previous findings. Thirdly, the most striking result of this study was revealed in ultrathin sections of puffs by electron microscopy: I discerned a site-specific ultrastructural difference in putative RNP particles between heat shock versus non-heat shock loci. At least three of the seven induced major heat shock puffs (I-20A, III-12B, IV-5C) were observed to contain globular particles that were different, i.e. significantly larger, 250-1,000 A in diameter with a prominent 500-750 A class, than RNP particles of other loci under non-heat shock conditions. These large heat shock puff particles presumably represent nascent or newly synthesized heat shock RNA associated with protein(s) to form heat shock RNPs (hsRNPs). This finding suggests the possible involvement of novel RNPs (hsRNPs) in transcriptional regulation or heat shock RNA turnover and may stimulate further molecular investigations on this subject in both cell physiological and structural terms. I conclude that the locus-specific putative hsRNPs are an intrinsic property of greatly increased heat shock gene transcription.

Animals↗
PubMed1995

A species specific satellite DNA family of Drosophila subsilvestris appearing predominantly in B chromosomes.

This paper describes a species specific satellite DNA family (pSsP216) of Drosophila subsilvestris, a palearctic species of the D. obscura group. The pSsP216 family consists of tandemly arranged 216 bp repetitive units that are predominantly localized on B chromosomes. These chromosomes appear in variable numbers in the karyotype of this species. Some pSsP216 repeats can also be detected in the centromeric heterochromatin of the acrocentric A chromosomes. Two strains, one with and the other without B chromosomes, were investigated for sequence variability and for the location of this satellite DNA on the chromosomes. Among 16 clones of the 216 bp basic repeat unit an overall similarity of about 93% and no strain specific differences were found, indicating that the B chromosomes may have derived from the A chromosomes (probably the dots) by spontaneous amplification of the pSsP216 satellite DNA family.

Animals↗
PubMed1993

Use of recombinant inbred strains to map genes of aging.

Recombinant inbred strains have been used in a number of organisms for segregation and linkage analysis of quantitative traits. One major advantage of the recombinant inbred (RI) methodology is that the genetic identity of individuals within a strain permits replicate measures of the same recombinant genotype. Such replicability is important for traits such as aging in Drosophila, where phenotypic expression is highly influenced by different environmental conditions. RI strain methodology has an added advantage for DNA marker-based linkage analysis of traits measured over the lifespan of the organism. The DNA can be extracted from individuals of the same genotype as those measured in a longevity study. In this paper an argument is presented for the use of a set of recombinant inbred strains to map the quantitative trait loci involved in the aging process in Drosophila. A unique use of a set of stable, transposable molecular markers to trace the quantitative trait loci involved is suggested.

Aging↗
PubMedDate not supplied

Organization of the Drosophila genome in mutants with changes in second messenger metabolism and learning ability.

Mechanisms modifying the structural-functional organization of polytene chromosomes were studied in a Drosophila line in which the activating properties of calmodulin were altered and learning ability was increased, by treating mutants with homeopathic preparations which affect Ca2+ and F- ion metabolism. The results indicated a dominant role for Ca2+ ions and calmodulin in determining the chromocentric organization of the nucleus. F- ions, which stimulate the adenylate cyclase complex, were found not to have a role.

Animals↗
PubMed2006

A specific SR protein binds preferentially to the secretory protein gene transcripts in salivary glands of Chironomus tentans.

The members of the serine-arginine (SR) family of proteins play multiple roles in posttranscriptional gene expression. Initially considered as essential splicing factors confined to the nucleus and regulating constitutive and alternative splicing, SR proteins are now known to shuttle between the nucleus and the cytoplasm and to be involved in mRNA biogenesis, transport, and translation. In Chironomus tentans, hrp45 is an SR protein structurally similar to the Drosophila SRp55/B52 SR protein. We have studied how hrp45, hrp36 [a heterogenous nuclear ribonucleoprotein (hnRNP) protein], and small nuclear RNP (snRNP) proteins are distributed in the transcriptionally active loci of polytene chromosomes in C. tentans. Immunofluorescence visualization of the proteins in double-labeling experiments revealed that hrp45 preferentially associates with a small number of puffs. On the other hand, hrp36 and snRNP proteins were found distributed in a large number of loci with little quantitative difference. Remarkably, hrp45-labeled loci coincide with the sites of transcription of premessenger RNPs of secretory protein (sp) genes. Because the labeling was found sensitive to RNase A treatment, we conclude that the SR protein hrp45 preferentially binds to sp gene transcripts in salivary gland cells. The preferential association of a specific SR protein with a particular type of gene transcripts reflects substrate-specific function(s) of an SR protein, in vivo. The possible roles that hrp45 might be playing in speedy and efficient processing of sp gene transcripts are discussed.

Animals↗
PubMed2005

Genetic approaches for the identification of apoptotic components.

Jun amino-terminal kinase (JNK) mediates a physiological stress signal that leads to cell death. However, the role of the JNK pathway in intrinsic cell death execution mechanisms is largely unknown. In a genetic screen for dominant suppressors of Reaper (Rpr)-induced cell death, we identified Drosophila chromosomal regions that contain genes which are homologous to apoptosis signal-regulating kinase (ASK1) and Drosophila tumor necrosis factor receptor-associated factor 1 (DTRAF1). We present evidence that the killer signal initiates the JNK pathway via proteasome-mediated degradation of Drosophila inhibitor of apoptosis protein 1 (DIAP1) to promote cell death.

Animals↗
PubMed1995

Localization of centromere function in a Drosophila minichromosome.

The DNA elements responsible for centromere activity in a metazoan have been localized using the Drosophila minichromosome Dp1187. Deleted minichromosomes were generated by irradiation mutagenesis, and their molecular structures were determined by pulsed-field Southern blot analysis. Analyses of the transmission behavior of Dp1187 derivatives localized sequences necessary for chromosome inheritance within the centric heterochromatin. The essential core of the centromere is contained within a 220 kb region that includes significant amounts of complex DNA. Completely normal inheritance also requires approximately 200 kb on either side of the essential core. This flanking DNA predominantly contains highly repeated sequences, and the amount required for normal transmission differs among division types and between the sexes. We propose that the essential core is the site of kinetochore formation and that flanking DNA provides two functions: sister chromatid cohesion and indirect assistance in kinetochore formation or function.

Animals↗