Redundant cis-acting elements control expression of the Drosophila affinidisjuncta Adh gene in the larval fat body

Further study on the esterase patterns of sibling species in the Drosophila saltans subgroup (saltans group): intraspecific and interspecific variations in the development

Twenty of the 32 esterase bands previously detected in the adults of D. prosaltans, D. saltans and D. austrosaltans were found in larvae and pupae studied in this work. The results showed that, in addition to expressing the highest number of esterase bands, the adult stage of the three species exhibited the highest degree of expression (amount of synthesis) for most of the bands. Differences between larval and pupal stages were detected in the degree of expression (amount of synthesis) of the bands and in the frequency of samples expressing them. The frequencies of expression of the bands corresponding to genes in loci 1-3 were greater in pupae than in larvae while the frequencies of expression of the bands corresponding to genes in loci 4-9 were predominantly expressed in larvae or were equal in both developmental stages. Like the adults, larvae, pupae and empty pupal cases (which were also studied in this work) showed specific esterases. Taken together, the observations showed that, in the species studied, every developmental stage is characterized by specific bands and by specific frequency and degree of expression of the bands shared with other stages.

The gypsy insulator can act as a promoter-specific transcriptional stimulator

Insulators define chromosomal domains such that an enhancer in one domain cannot activate a promoter in a different domain. We show that the Drosophila gypsy insulator behaves as a cis-stimulatory element in the larval fat body. Transcriptional stimulation by the insulator is distance dependent, as expected for a promoter element as opposed to an enhancer. Stimulation of a test alcohol dehydrogenase promoter requires a binding site for a GATA transcription factor, suggesting that the insulator may be facilitating access of this DNA binding protein to the promoter. Short-range stimulation requires both the Suppressor of Hairy-wing protein and the Mod(mdg4)-62.7 protein encoded by the trithorax group gene mod(mdg4). In the absence of interaction with Mod(mdg4)-62.7, the insulator is converted into a short-range transcriptional repressor but retains some cis-stimulatory activity over longer distances. These results indicate that insulator and promoter sequences share important characteristics and are not entirely distinct. We propose that the gypsy insulator can function as a promoter element and may be analogous to promoter-proximal regulatory modules that integrate input from multiple distal enhancer sequences.

Evolutionary change in the structure of the regulatory region that drives tissue and temporally regulated expression of alcohol dehydrogenase gene in Drosophila funebris

The Adh locus of Drosophilidae is organized as a single gene transcribed from two spatially and temporally regulated promoters except in species of the repleta group, which have two single promoter genes. Here we show that in Drosophila funebris the Adh gene is transcribed from a single promoter, in both larva and adult, with qualitative and quantitative species specific-differences in tissue distribution. The gene is expressed in larval fat body but in other tissues such as gastric caeca, midgut and Malpighian tubules its expression is reduced compared to most Drosophilidae species, and in adults it is almost limited to the fat body. The comparative analysis of gene expression of two strains, which differ by a duplication, indicates that the cis elements necessary for this pattern of expression in larvae are included in the region of 1.55 kb upstream of the transcription initiation site. This new organization reveals the evolution of a different regulatory strategy to express the Adh gene in the subgenus Drosophila.

Polarity of transcriptional enhancement revealed by an insulator element

Transcriptional enhancers for genes transcribed by RNA polymerase II may be localized upstream or downstream of the stimulated promoter in their normal chromosomal context. They stimulate transcription in an orientation-independent manner when assayed on circular plasmids. We describe a transient transformation system to evaluate the orientation preference of transcriptional enhancers in Drosophila. To accomplish this, the gypsy insulator element was used to block bidirectional action of an enhancer on circular plasmids. In this system, as in the chromosome, blocking of enhancer activity requires wild-type levels of the su(Hw) protein. We evaluated the orientation preference for the relatively large (4.4 kb) Adh larval enhancer from Drosophila melanogaster, used in conjunction with a luciferase reporter gene under the control of a minimal Adh promoter. An orientation preference was revealed by insertion of a single copy of the insulator between the enhancer and the promoter. This orientation effect was greatly amplified when the promoter was weakened by removing binding sites for critical transcription factors, consistent with a mechanism of insulator action in which the insulator intercepts signals from the enhancer by competing with the promoter. The orientation preference, as much as 100-fold, is a property of the enhancer itself because it is displayed by gene constructions introduced into the chromosome regardless of the presence of the insulator in a distal location. These findings are most easily reconciled with a facilitated tracking mechanism for enhancer function in a native chromosomal environment.

cis-Acting sequences controlling the adult-specific transcription pattern of the Drosophila affinidisjuncta Adh gene

The cis-acting sequences required for the adult-specific expression pattern of the alcohol dehydrogenase (Adh) gene of the Hawaiian picture-winged fruit fly, Drosophila affinidisjuncta were analyzed by germline transformation. Normally this gene produces two developmentally regulated transcripts. The upstream (distal) promoter produces a distal transcript, which makes up about 80% of the total in adults, while the downstream (proximal) promoter produces a corresponding proximal transcript, which accounts for the remainder. Previously constructed genes lacking regions corresponding to regulatory elements within the Drosophila melanogaster Adh gene or regions known to be required for full expression of the D. affinidisjuncta Adh gene in larvae were analyzed by introduction into the germline of D. melanogaster followed by RNase-protection analysis of RNA levels. In addition, to test a model of preferential promoter utilization by which transcription at the proximal promoter is inhibited by transcription initiated at the upstream distal promoter, a construction lacking the distal promoter was analyzed. Sequences homologous to the adult enhancer of the Adh gene of D. melanogaster appear to play a similar role in the D. affinidisjuncta gene. In contrast to what has been reported for other Drosophila Adh genes, this and some other regulatory elements are shared by the two promoters of the D. affinidisjuncta gene. Taken together, the results favor a model of stage-specific switching between the two promoters of the D. affinidisjuncta gene that involves competition for limiting components stimulating transcription, rather than interference by read-through from the upstream promoter.

Cis-acting sequences contributing to expression of the Drosophila affinidisjuncta Adh gene in both larvae and adults

To characterize the cis-acting sequences required for expression of the alcohol dehydrogenase (Adh) gene of the Hawaiian picture-winged fruit fly Drosophila affinidisjuncta, germ-line transformation was used to introduce altered forms of this gene into Drosophila melanogaster. Genes were constructed lacking regions corresponding to known or putative regulatory elements within the D. melanogaster gene as well as to sequences previously shown to be required for expression of the D. affinidisjuncta gene in the larval fat body as assayed by transient transformation. Measurement of alcohol dehydrogenase (EC 1.1.1.1) activity levels produced by the transfected genes indicates that multiple elements in both the 5' and 3' regions of the gene contribute to expression. The dispersed elements appear to function redundantly to ensure high levels of expression. Moreover, in contrast to what has been reported for other Drosophila Adh genes, some of the regulatory elements influence expression in both larvae and adults. In total, these results reveal a regulatory system in which the transcribed region in imbedded in an extended genomic segment rich in cisacting regulatory information.

Molecular organization of the alcohol dehydrogenase loci of Drosophila grimshawi and Drosophila hawaiiensis

To determine sequences involved in conserved and species-specific aspects of alcohol dehydrogenase (Adh) gene expression in Hawaiian Drosophila, a 3644-base pair (bp) region containing the D. grimshawi gene and the homologous 3335-bp region containing the D. hawaiiensis Adh gene were sequenced. These genes have the two-promoter and exon-intron structure seen for many Drosophila Adh genes. Analysis of putative and known regulatory sequences of the D. grimshawi and D. hawaiiensis genes in comparison to those of D. affinidisjuncta (the only other Hawaiian species for which the promoter organization is known) highlighted elements likely to be involved in conserved aspects of Adh gene expression as well as sequences that may account for species-specific differences in tissue-specific expression. Sequence comparisons, in the context of regulatory roles previously assigned to particular gene fragments, indicated that multiple insertions and deletions in the promoter regions are responsible for differences in tissue-specific regulation displayed by these genes.

The two small introns of the Drosophila affinidisjuncta Adh gene are required for normal transcription

All Drosophila alcohol dehydrogenase (Adh) genes sequenced to date contain two small introns within the coding region. These are conserved in location and, to some extent, in sequence between the various species analyzed. To determine if these introns play a role in Adh gene expression, derivatives of the Drosophila affinidisjuncta Adh gene lacking one or both introns were constructed and analyzed by germline and transient transformation of Drosophila melanogaster. Removal of both introns lowered expression, whether measured by enzyme activity or by RNA levels. The decrease was seen in both germline transformed and transiently transformed larvae, with the effect being larger for germline transformants. Similar decreases (averaging 5-fold) were also seen at the embryonic and adult stages for germline transformants. Nuclear run-off transcription with nuclei from germline transformed embryos indicated that the reduction in RNA levels is due to decreased transcription. However, LacZ fusion constructs designed to test for the presence of a classical enhancer in the introns provided no evidence for such a mechanism. Removal of each intron individually resulted in more complex phenotypes. The introns have smaller, additive effects on expression in adults. In larvae, removal of the upstream intron significantly increases RNA levels but modestly decreases enzyme activity. Removal of the downstream intron lowers expression in both germline and transiently transformed larvae, but also increases position effects in germline transformants. Therefore, the small introns are clearly needed for optimal transcription of this Adh gene, but multiple mechanisms are involved.

Descriptive and functional characterization of variation in the Fundulus heteroclitus Ldh-B proximal promoter

Variation in enzyme expression may be an important mechanism for physiological and evolutionary adaptation. The Ldh-B locus in the teleost fish Fundulus heteroclitus is one of a very few loci for which an evolutionary difference in transcription rate between populations has been demonstrated. To begin to understand the molecular modifications that are responsible for altering transcription, we have characterized the Ldh-B proximal promoter using a combination of sequence analysis, transient transfection, and in vivo footprinting. The Ldh-B gene has several transcription start sites and a TATA-less, Inr (initiator of transcription motif) containing promoter with multiple Sp1-like motifs. Transfection experiments reveal that Sp1 sites, TCC repeats, and Inrs are functional components of the proximal promoter. We find substantial sequence variation between populations within the proximal promoter (250 bp from the transcription start sites) and footprinting analysis indicates that some of this sequence variation is associated with differential protein binding to the apparent TFIID binding site and Sp1 sites. Together, these data suggest that variation in the Ldh-B proximal promoter may play a role in the observed difference in transcription rates between northern and southern populations of F. heteroclitus.

A transcriptional role for conserved footprinting sequences within the larval promoter of a Drosophila alcohol dehydrogenase gene

All Drosophila alcohol dehydrogenase (Adh) genes that are expressed in larvae display strong transcription in the larval fat body. To identify and characterize elements needed for Adh promoter function, footprinting analysis of the Drosophila affinidisjuncta Adh gene was performed with stage-specific nuclear proteins from embryos and larvae. Multiple sites upstream of the larval promoter were protected from deoxyribonuclease digestion by both embryonic and larval extracts. Comparison with foot-printing results for Adh genes from other Drosophila species revealed only one nuclease-protected region that is conserved in both sequence and position. Clustered point mutations in this sequence were analyzed by footprinting analysis, transient transformation and in vitro transcription. Two separate sequences in this footprinting region exerted positive effects on transcription from the Adh proximal promoter in the larval fat body. The effects of these sequences on gene expression were synergistic. One of these sequences, TGATAA, bound in vitro to Drosophila melanogaster box A binding factor protein, as shown by gel mobility shift assays. This is the first direct demonstration of specific protein-DNA interactions influencing transcription of a Drosophila Adh gene in the larval fat body.