Complex cis-acting regulatory genes demonstrated in Drosophila hybrids

A synthetic synthesis to explore animal evolution and development

Identifying the general principles by which genotypes are converted into phenotypes remains a challenge in the post-genomic era. We still lack a predictive understanding of how genes shape interactions among cells and tissues in response to signalling and environmental cues, and hence how regulatory networks generate the phenotypic variation required for adaptive evolution. Here, we discuss how techniques borrowed from synthetic biology may facilitate a systematic exploration of evolvability across biological scales. Synthetic approaches permit controlled manipulation of both endogenous and fully engineered systems, providing a flexible platform for investigating causal mechanisms in vivo. Combining synthetic approaches with multi-level phenotyping (phenomics) will supply a detailed, quantitative characterization of how internal and external stimuli shape the morphology and behaviour of living organisms. We advocate integrating high-throughput experimental data with mathematical and computational techniques from a variety of disciplines in order to pursue a comprehensive theory of evolution.

This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.

CONSERVATION OF MOLECULAR PREPATTERNS DURING THE EVOLUTION OF CUTICLE MORPHOLOGY IN DROSOPHILA LARVAE

We are using patterns of cuticle specialization in Drosophila larvae as models to investigate the molecular, genetic, and developmental bases of morphological evolution. Members of the virilis species group differ markedly from one another in the distribution of hairs on the dorsal surface of first instar larvae. In particular, characteristic bands of hairs cover about 20% of each trunk segment in some species but about 70% in others. These major types do not correlate with recently proposed phylogenetic relationships, suggesting that similar phenotypes have arisen independently in different lineages. The patterns of expression of several genes that control or reflect intrasegmental patterning are indistinguishable in species with very different cuticle morphologies. We conclude that, in this case, morphology probably has evolved via altered response to a conserved molecular prepattern.

Evolutionary developmental biology and the problem of variation

One of the oldest problems in evolutionary biology remains largely unsolved. Which mutations generate evolutionarily relevant phenotypic variation? What kinds of molecular changes do they entail? What are the phenotypic magnitudes, frequencies of origin, and pleiotropic effects of such mutations? How is the genome constructed to allow the observed abundance of phenotypic diversity? Historically, the neo-Darwinian synthesizers stressed the predominance of micromutations in evolution, whereas others noted the similarities between some dramatic mutations and evolutionary transitions to argue for macromutationism. Arguments on both sides have been biased by misconceptions of the developmental effects of mutations. For example, the traditional view that mutations of important developmental genes always have large pleiotropic effects can now be seen to be a conclusion drawn from observations of a small class of mutations with dramatic effects. It is possible that some mutations, for example, those in cis-regulatory DNA, have few or no pleiotropic effects and may be the predominant source of morphological evolution. In contrast, mutations causing dramatic phenotypic effects, although superficially similar to hypothesized evolutionary transitions, are unlikely to fairly represent the true path of evolution. Recent developmental studies of gene function provide a new way of conceptualizing and studying variation that contrasts with the traditional genetic view that was incorporated into neo-Darwinian theory and population genetics. This new approach in developmental biology is as important for microevolutionary studies as the actual results from recent evolutionary developmental studies. In particular, this approach will assist in the task of identifying the specific mutations generating phenotypic variation and elucidating how they alter gene function. These data will provide the current missing link between molecular and phenotypic variation in natural populations.

Regulatory differences in developmental expression of alcohol dehydrogenase are related to interspecies differences in ethanol tolerance of Drosophila

Biochemical properties and expression patterns of alcohol dehydrogenase were compared among members of the virilis phylad of Drosophila. Quantitative differences in stage- and tissue-specific expression of ADH of D. virilis, D. novamexicana, D. texana and D. americana were observed. These differences seem to correlate with the temporal differences in ethanol tolerance among these species. Quantitative differences in ADH protein levels account for most, if not all, of the activity differences between species. Analysis of the interspecific hybrids revealed that these differences arise by a mechanism affecting monomer synthesis. A comparison with earlier studies, where independently evolved regulatory differences were related to adaptations, revealed contrasting underlying mechanisms.

Similar tissue-specific expression of the Adh genes from different Drosophila species is mediated by distinct arrangements of cis-acting sequences

In Drosophila melanogaster transformants, the alcohol dehydrogenase (Adh) genes from D. affinidisjuncta and D. grimshawi show similar levels of expression except in the adult midgut where the D. affinidisjuncta gene is expressed about 10- to 20-fold more strongly. To study the arrangement of cis-acting sequences responsible for this regulatory difference, homologous restriction sites were used to create a series of chimeric genes that switched fragments from the 5' and 3' flanking regions of these two genes. Chimeric genes were introduced into the germ-line of D. melanogaster, and Adh gene expression was analyzed by measuring RNA levels. Various gene fragments in the promoter region and elsewhere influence expression in the adult midgut and in whole larvae and adults. Comparison of these results with earlier studies involving chimeras between the D. affinidisjuncta and D. hawaiiensis genes indicates that expression in the adult midgut is influenced by multiple regulatory sequences and that distinct arrangements of regulatory sequences can result in similar levels of expression both in the adult midgut and in the whole organism.

Transgenic animal studies on the evolution of genetic regulatory circuitries

The ability to transfer genes from one species to another provides a powerful method to study genetic regulatory differences between species in a homogeneous genetic background. A survey of several transgenic animal experiments indicates that the vast majority of regulatory differences observed between species are due to differences in the cis-acting elements associated with the genes under study. A corollary is that in almost all cases the host species provides the necessary regulatory proteins for expression of the transgenes in specific tissues in which the endogenous homolog is not expressed. Although the details of the cis-acting differences are unknown for most cases, it appears that these differences may consist of the acquisition or loss of unique elements or subtle variation of conserved elements. It is unknown whether much of this variation is directly related to adaptive evolution. The identification of the promoter/enhancer elements responsible for these differences is an important first step in examining the functional significance of this variation.

A Drosophila CREB/ATF transcriptional activator binds to both fat body- and liver-specific regulatory elements

We have identified a Drosophila transcription factor that binds to fat body-specific enhancers of alcohol dehydrogenase (Adh) and yolk protein genes. DNA sequence analysis of cDNA clones encoding this protein, box B-binding factor-2 (BBF-2), indicates that it is a member of the CREB/ATF family of transcriptional regulatory proteins. A number of observations suggest that BBF-2 is involved in fat body-specific expression: Mutations that disrupt BBF-2 binding to two different Adh fat body enhancers in vitro decrease the activity of these enhancers in transgenic flies. BBF-2 mRNA is present in all cell types examined, and the protein is present in cells that express ADH. Finally, BBF-2 is a transcriptional activator in Drosophila tissue culture cells. Remarkably, BBF-2 also binds specifically to regulatory elements required for liver-specific expression of the human Adh and rat tyrosine aminotransferase genes. Thus, BBF-2 and the DNA sequence to which it binds may be important components of a tissue-specific regulatory mechanism conserved between Drosophila and man.

Species-specific differences in tissue-specific expression of alcohol dehydrogenase are under the control of complex cis-acting loci: evidence from Drosophila hybrids

Differences in the expression of alcohol dehydrogenase in the hindgut and testis of adult Drosophila virilis, D. texana, D. novamexicana and D. borealis flies were observed. These heritable differences do not arise due to chromosomal rearrangements, since the polytene chromosome banding patterns did not reveal any such gross chromosomal rearrangements near the Adh locus in any of the tested species. Analysis of the interspecific hybrids revealed that these differences are controlled by complex cis-acting genetic loci. Further, the cis-acting locus controlling the expression of ADH in testis was found to be separable by crossing-over.

Complexity in evolved regulatory variation for alcohol dehydrogenase genes in Hawaiian Drosophila

The alcohol dehydrogenase gene (Adh gene) of Drosophila affinidisjuncta is expressed at a higher level in the larval midgut and Malpighian tubules than the homologous gene from Drosophila hawaiiensis. This study analyzed the cis-acting sequences responsible for these regulatory differences in larval tissues of Drosophila melanogaster transformants. A series of 10 chimeric and deleted Adh genes was introduced into the germ line of D. melanogaster, and tissue-specific expression levels were quantified by gel electrophoresis of tissue extracts. Sequences in the upstream region of the two genes had the strongest influence on enzyme production in the midgut and Malpighian tubules. Other sequence elements also showed effects, some of which were tissue specific. Most gene fragments displayed context-dependent effects, thus supporting the proposed model of polygenic regulation of Adh gene expression.

Nucleotide sequence of the genomic region encoding alcohol dehydrogenase in Drosophila affinidisjuncta

The DNA sequence of a 3886-bp genomic region containing the alcohol dehydrogenase (Adh) gene from Drosophila affinidisjuncta, and the RNA sequences of the D. affinidisjuncta Adh transcripts, are presented. These data support the conclusion that two Adh promoters generate distinct, developmentally regulated Adh transcripts. Correlations between these sequences and the transcription map are discussed. Comparisons between these and equivalent data from D. melanogaster are also presented. We note the following observations: (1) Except at the extreme 3' end, the two genes are identically organized. (2) Drosophila Adh protein accumulates amino acid replacements at the rate of approximately 0.5 per million years. (3) Among the non-protein-coding DNA sequences, putative homologies occur in the two promoter regions.

Drosophila Adh: a promoter element expands the tissue specificity of an enhancer

Drosophila alcohol dehydrogenase (Adh) genes are expressed in the fat body and in species-specific sets of other tissues during larval and adult development. The Drosophila mulleri Adh-1 gene is expressed in the larval fat body and in three other larval tissues. In this paper, we show that Adh-1 expression in multiple cell types is the result of synergistic interactions between fat body-specific enhancers and a specific Adh-1 promoter element.

Complex developmental regulation of the Drosophila affinidisjuncta alcohol dehydrogenase gene in Drosophila melanogaster

During development, the alcohol dehydrogenase genes of Drosophila melanogaster and D. affinidisjuncta are expressed in similar, yet distinct, tissue- and stage-specific patterns. Transcripts from both of these genes arise from two promoters (distal and proximal) that also display tissue and stage specificity. We used P-element-mediated transformation to introduce the D. affinidisjuncta Adh gene into the germ line of D. melanogaster. We show that the D. affinidisjuncta Adh gene is expressed at comparable overall levels in both species and that the tissue- and stage-specific expression for this gene (including promoter utilization) is similar in the donor and the host species. However, in some details, the expression of the D. affinidisjuncta gene in D. melanogaster resembles the host pattern, and one novel tissue-specific expression phenotype is displayed by transformants. In general, our results suggest that there has been strong conservation of cis- and trans-acting regulatory factors since the divergence of the two species but that this conservation has not been perfect.

Adh expression in species of the mulleri subgroup of Drosophila

The locus encoding the NAD-dependent alcohol dehydrogenase (alcohol:NAD oxidoreductase; EC 1.1.1.1) is duplicated in some species of the cactophilic mulleri subgroup of Drosophila. Here we report a survey on the expression throughout development and in different tissues for this system, its regulation using interspecific hybrids, and the effects induced by 2-propanol in 10 species belonging to four different clusters of the above-mentioned subgroup. Our results indicate different expression throughout development and in different tissues, cis regulation in hybrid ovaries, trans (-) regulation in hybrid adults, and different responses to 2-propanol.

Genetic and developmental characterization of the aldox-2 locus of Drosophila melanogaster

The aldox-2 locus in Drosophila melanogaster has been shown to affect differentially three molybdoenzymes, aldehyde oxidase, pyridoxal oxidase, and xanthine dehydrogenase. These effects are most obvious at times surrounding the pupal-adult boundary, when the normal organism accumulates large amounts of these enzymes in their active form. This locus has been more precisely mapped genetically to 2-82.9 +/- 2.1, with complete concordance between the effects of all recombinant chromosomes on all three enzymes. The cytogenetic location has also been determined to be between 52E and 54E8, with the likelihood that it lies within the region 54B1-54E8. The aldox-2 mutant allele has no visible phenotype and is completely recessive for enzyme effects at all stages tested. Segmental duplication of this region, including the aldox-2+ allele, has no apparent effect on the visible phenotype or the enzymatic activity. The mutant aldox-2 allele has no effect on the developmental expression of two unrelated enzymes, 6-phosphogluconate dehydrogenase and NADP+-dependent isocitrate dehydrogenase. The effects of this locus on aldehyde oxidase, xanthine dehydrogenase, and pyridoxal oxidase suggest that this locus may code for a product involved in the synthesis of the molybdenum cofactor common to these enzymes.

Analysis of Aldoxn alleles isolated from natural populations of Drosophila melanogaster

Aldox "null" alleles which were isolated from natural populations in Great Britain and North Carolina were analyzed for complementation. No complementation was observed between any combinations of "null" alleles for aldehyde oxidase (AO) specific activity in late third-instar larvae and newly emerged adults. AO immunologically cross-reacting material (AO-CRM) was quantitated in all homozygous stocks at both developmental stages as well as all allelic combinations in newly emerged adults. When the adult organism contains only Aldoxn alleles, the polypeptides are not immunologically recognizable or may be rapidly degraded. Larvae and adults have different abilities to degrade mutationally altered enzymatically inactive AO polypeptide or synthesize them differentially. This is indicated by easily measurable AO-CRM levels in late third-instar larvae of Aldoxn homozygotes, while newly emerged adult Aldoxn homozygotes have very little, if any, AO-CRM. Newly emerged adult heterozygotes of Aldoxn/Aldox+ do have increased AO-CRM, indicating that the Aldoxn alleles can code for a polypeptide which can be "rescued" if Aldox+ gene product is present. Heterozygotes containing an Aldox+ allele with a deficiency for the Aldox region produce 74.2% of the AO-CRM found in Aldox+ homozygotes. This may indicate the presence of trans-acting factors which serve to activate gene expression in a system in which each gene copy is not maximally expressed.

Glucosephosphate isomerase (GPI-1) expression in mouse ova: cis regulation of monomer realization

A survey of the glucosephosphate isomerase (GPI-1) activity expressed in mature mouse ova has revealed multiple interstrain differences. Genetic variation at a site either linked to (less than 1.1 cM) or directly associated with Gpi-1 affects the realization of GPI-1 monomers during the later stages of oocyte maturation.

Developmental control of transduced dopa decarboxylase genes in D. melanogaster

Seventeen new euchromatic integration sites of the dopa-decarboxylase gene (Ddc) have been generated using p-mediated transduction. The developmental expression of the integrated genes was examined by monitoring the embryonic induction of dopa decarboxylase enzyme activity (DDC) and by monitoring the developmental pattern of DDC activity from late third instar to eclosion. The majority of inserts are regulated correctly within about 30% of controls. Several cases of multiple insertion events were recovered and these show correspondingly elevated levels of activity and are regulated normally. The pattern of expression of one insert (15C) falls outside the normal range. Multiple copies of transduced Ddc genes are used to test for effects of elevated gene dose on levels of expression. One insert on the X chromosome shows little or no dosage compensation. Possible reasons for the differences between the regulation of transduced genes in Drosophila and the regulation of transformed genes in mammalian systems are discussed.

Relative developmental success of interspecific Lepomis hybrids as an estimate of gene regulatory divergence between species

The developmental success of interspecific Lepomis hybrids is used as an index of gene regulatory divergence between the green sunfish, L. cyanellus, and each of three other parental species, longear sunfish, L. megalotis, warmouth, L. gulosus, and bluegill, L. macrochirus. This gene regulatory divergence is compared to the degree of structural gene divergence among these four species (genetic distance [Nei, '78], D, ranged from 0.206 to 0.586). The developmental success of the hybrid embryos at the level of morphogenesis was higher than expected from the genetic distance between the parental species. The rates of morphogenesis of the hybrid embryos were the same as that for the green sunfish embryos. The percentage of embryos that hatched was relatively high in all crosses. However, two of the hybrid crosses resulted in enhanced percentages of hatched embryos. Slight increases in the extent of morphological abnormalities were observed in hybrids from crosses between more distantly related parental species. The schedules and levels of enzyme locus expression of the hybrids, assessed spectrophotometrically and electrophoretically for nine enzyme systems (encoded in a total of 14 loci), were different from each other and from those of the green sunfish embryos. Alterations in the time of first enzyme appearance and in the time of first increase in enzyme activity in the developing hybrid embryos were not correlated with genetic distance between parental species. However, the extents of alteration of enzyme activities over the entire period of hybrid embryogenesis were correlated with the genetic distance. We attribute the morphological and molecular anomalies observed in the hybrids to gene regulatory incompatibilities between species. Although the exact number of mutational differences and their relative developmental impacts are not known, some inferences can be drawn about the degree of divergence in gene regulation between species. It appears that an uncoupling of the rates of structural and regulatory gene evolution can occur between species of some taxa, an observation that has implications for the roles of gene regulatory differences in organismic evolution.

Ontogenetic patterns of enzyme locus expression in Barbus hybrids (Cypriniformes, Teleostei)

The tissue specific patterns and ontogeny of sorbitol dehydrogenase (SDH, EC 1.1.1.14). lactate dehydrogenase (LDH, EC 1.1.1.27) and isocitrate dehydrogenase (IDH, EC 1.1.1.42) are reported for Barbus tetrazona (tiger barb), B. conchonius (rosy barb), B. nigrofasciatus (black ruby barb), B. titteya (cherry barb), B. sachsi (gold barb), and in interspecific hybrids where B. tetrazona is the maternal parent. The spatial and temporal expression of SDH, LDH and IDH isozymes in Barbus is consistent with those reported for other teleosts. As the genetic distance between the parentals used in forming the hybrid increases, allelic expression proceeds from synchronous to asynchronous, with an increasing delay in embryonic gene expression. These observations are consistent with the hypothesis that parental sensor genes differ in their response to maternally controlled regulatory signals; indicative of species specific effector/activator RNA molecule concentrations and sensor/receptor gene induction thresholds.

Differences in tissue expressions of enzyme activities in interspecific sunfish (Centrarchidae) hybrids and their backcross progeny

The extent of naturally occurring variations of enzyme locus expression was determined for three tissues (liver, muscle, and eye) in two species of sunfish (Centrarchidae), the green sunfish (Lepomis cyanellus) and the redear sunfish (L. microlophus). The genetic basis for species differences in tissue enzyme specific activities of malate dehydrogenase (EC 1.1.1.37), lactate dehydrogenase (EC 1.1.1.27), phosphoglucomutase (EC 2.7.5.1), and glucosephosphate isomerase (EC 5.3.1.9) was investigated by determining enzyme specific activities in the tissues of the reciprocal F1 hybrids and of their backcross progenies. The specific activities for most enzymes in hybrids were intermediate between those of the parental species. Significant differences in enzyme specific activity were detected among the F1 progeny as well as those of backcrosses. Variations in specific activity levels in one tissue were often independent of variations in specific activities in a different tissue. However, the changes in the specific activities of different enzymes within the same tissue were often positively correlated. The tissue glucosephosphate isomerase activity differences appear not to be due to different functional contributions of the glucosephosphate isomerase allelic isozymes. Cluster analysis of distributions of specific activities revealed no simple Mendelian pattern of inheritance for control of tissue enzyme activity. Our results suggest a polygenic control of tissue enzyme specific activity levels.

Regulatory gene evolution: adaptive differences in expression of alcohol dehydrogenase in Drosophila melanogaster and Drosophila simulans

In Drosophila melanogaster X D. simulans hybrids, the alcohol dehydrogenase (ADH) electromorphs characteristic of the two parents display tissue- and stage-specific differences in relative level of expression. This implies distinct cis-acting regulatory elements associated with the respective Adh alleles. These cis-acting elements account in part, but not completely, for markedly different overall patterns of ADH expression in the two species. The regulatory patterns seem to be adaptively significant since they correlate with species-specific patterns of ethanol tolerance. The activity differences are accounted for by different levels of enzyme protein, but the underlying mechanisms have not been fully analysed and may be complex. Independent evolution of various aspects of the ADH developmental programme may relate to use of different promoters for transcription of the Adh locus in different developmental contexts. This system illustrates the potential importance of regulatory genes in evolution and provides a model for investigating the molecular basis of evolved regulatory differences.

Differential regulation of duplicate alcohol dehydrogenase genes in Drosophila mojavensis

These studies report the existence of multiple forms of alcohol dehydrogenase in extracts of Drosophila mojavensis. The existence of these forms can be best explained by the hypothesis of a duplication for the Adh locus in D. mojavensis. Electrophoretic variants at each locus have been identified and crosses between individuals carrying alternative alleles at each locus result in F1 progeny with six bands of ADH. This pattern is consistent with these individuals being heterozygous at two loci. The loci have been named Adh-1 and Adh-2. Examination of the isozyme content during development shows that the two Adh genes are not coordinately controlled but have separate developmental programs. In embryos and first and second instar larvae only Adh-1 is expressed. At about the time of the second molt Adh-2 expression commences in some of the same cells that previously expressed and continue to express Adh-1. This is evidenced by the existence of an interlocus heterodimer in third instar larvae. Both genes are expressed throughout pupation. Shortly after emergence Adh-1 expression declines. In mature males only ADH-2 is present. In mature females both Adh-1 and Adh-2 are expressed but not in the same cells since the interlocus heterodimer is absent. Examination of specific tissues reveals that most of the larval ADH is found in fat body cells and as in most tissues of third instar larvae both Adh-1 and Adh-2 are expressed. The single exception appears to be larval gut which contains ADH-1 but little if any ADH-2. In mature males and female flies all ADH containing tissues have only ADH-2. However, mature ovaries contain substantial quantities of ADH-1 which is apparently deposited into eggs. Given the extensive amount of available information on the Adh gene-enzyme system of D. melanogaster and the tools that can be applied to the analysis of homologous systems, the ADH duplication of D. mojavensis, and its regulation may be a useful one for studying differential gene regulation in specific cell types.

A cis-acting regulator of enzyme tissue specificity in Drosophila is expressed at the RNA level

Alcohol dehydrogenase (ADH) is expressed according to qualitatively different patterns in Drosophila grimshawi and two closely related species, D. orthofascia and D. formella. This regulatory difference is under control of a cis-acting genetic factor. The ADH of these species is very similar to ADH of D. melanogaster and a genomic ADH clone derived from the latter hybridizes specifically to ADH coding sequences of the other species. Using this hybridization probe, it is shown that the above cis-acting regulator acts before or shortly after transcription to control ADH expression.

Aldehyde oxidases of Drosophila: contributions of several enzymes to observed activity patterns

At least four enzymes contribute to histochemically, electrophoretically, or spectrophotometrically detectable aldehyde oxidase (AO) activity in Drosophila melanogaster. The one we designate AO-1 contributes the majority of activity measured in extracts of whole flies. Pyridoxal oxidase (PO) is also a broad range AO. It is prominent only in midgut and Malpighian tubules, where it apparently accounts for a substantial fraction of total AO activity. The tissue distributions of these enzymes are clearly disparate despite close linkage of their structural loci and parallel dependence on the mal, lxd, and cin loci. A similarly related enzyme, xanthine dehydrogenase (XDH), is detected as an AO only in electrophoretic gels. A fourth broad range AO, not dependent on mal, lxd, and cin, is confined to the ejaculatory bulb. A similar array of AO isozymes is present in phylogenetically distant Drosophila species.

Evolution of patterns of gene expression in hawaiian picture-winged Drosophila

The tissue and stage specificity of expression of five enzymes was examined by electrophoretic analysis of relative enzyme levels in extracts of 13 larval and adult tissues in 27 species of Hawaiian picture-winged Drosophila. The developmentally regulated patterns of enzyme expression thus characterized were compared to a modal standard phenotype. About 30% of the pattern features analyzed differed significantly from the standard in one or more species. Many of these regulatory differences are essentially qualitative, with tissue specific differences in enzyme activity in excess of 100 fold for some species pairs. The adaptive significance of these pattern differences in unknown, but the results provide strong direct evidence for rapid evolution of new patterns of gene regulation in this group of organisms.