An esterase duplication in Drosophila: differences in expression of duplicate loci within and among related species

Esterase Profile in Drosophila mercatorum pararepleta (Diptera; Drosophilidae), a Non-cactophilic Species of the repleta Group: Development Patterns and Aspects of Genetic Variability

Luciana Paes de Barros Machado, Natalia Silva Alves, Jaqueline de Oliveira Prestes, Gabriela Ronchi Salomón, Daiane Biegai, Thais Wouk, and Rogério Pincela Mateus (2017) Esterases are a diversified group of isozymes that performs several metabolic functions in Drosophila. In the D. repleta group, this class of enzymes was well described in cactophilic species, existing a lack of studies considering substrate speci city and life cycle expression in the non-cactophilic species. The larvae of cactophilic species of the D. repleta group develop in rotting cacti cladodes, but adults are generalists. Thus, different patterns expression can be found for esterases throughout development. In this work we analyzed esterase pro le and substrate speci city during development, and genetic variability aspects in D. mercatorum pararepleta, a non-cactophilic and generalist species of D. repleta group that was understudied hitherto. Samples of 3rd (F3) and 104th (F104) generations of three D. mercatorum pararepleta strains, obtained after collections in xerophytic enclaves of southeastern Brazil (ITI and SER in São Paulo state and RIP in Paraná state), and of D33 strain (obtained from Cristalina-GO, Midwest of Brazil, and established in the laboratory in 1987) were analyzed. Eight esterase loci, EST-1 to EST-8, were detected. EST-1 and EST-2 were adult exclusive. Only EST-3 and EST-8 were monomorphic; all the others presented between two (EST-6) and six (EST-7) alleles. EST-7 was the only dimeric locus and also the only one that showed to be a preferably β-esterase regarding affinity to α- and β-naphthyl acetates as substrates. The other seven loci were divided into three classes: α-esterase exclusive (EST-2); preferably α-esterase (EST-3, EST-4, EST-5 and EST-8); and α/β-esterase (EST-1 and EST-6). The EST-3, EST-5 and EST-6 loci were not detected in all samples, suggesting that they could have become pseudogenes due to the mutation accumulation after the gene duplication. The allele frequency of EST-7 locus, which showed the highest number of alleles, in adults of D33 and SER-F3 evidenced a higher variability and diversity in the oldest strain (six alleles, Ho = 0.46) than in the youngest ( five alleles, Ho = 0.26). Moreover, the analysis of SER-F104 revealed that this locus became monomorphic. The higher variability in the strain established in the laboratory at least two decades ago, together with the allele fixation in the SER-F104, indicate that the SER strain probably suffered a more severe action of founder effect/bottleneck when it was established in the laboratory and, therefore, even if the maintenance afterwards was performed using a high number of individuals, it did not assured the conservation of the existing genetic variability.

Purification and characterization of a specific late-larval esterase from two species of the Drosophila repleta group: contributions to understand its evolution

Background

After duplication, one copy of an original gene can become redundant and decay toward a pseudogene status or functionally diverge. Here, we performed the purification and biochemical characterization of EST-4 (a late larval β-esterase) from two Drosophila repleta group species, Drosophila mulleri and Drosophila arizonae, in order to establish comparative parameters between these enzymes in these species and to contribute to better understand their evolution.

Results

In D. mulleri, EST-4 had an optimal activity in temperatures ranging from 40° to 45°C and at pH 7.5, maintaining stability in alkaline pH (8.0 to 10.0). It was classified as serine esterase as its activity was inhibited by PMSF. No ion negatively modulated EST-4 activity, and iron had the most positive modulating effect. In D. arizonae, it showed similar optimum temperature (40°C), pH (8.0), and was also classified as a serine esterase, but the enzymatic stability was maintained in an acidic pH (5.5 to 6.5). Fe+2 had the opposite effect found in D. mulleri, that is, negative modulation. Al+3 almost totally inhibited the EST-4 activity, and Na+ and Cu+2 had a positive modulation effect. Kinetic studies, using ρ-nitrophenyl acetate as substrate, showed that EST-4 from D. mulleri had higher affinity, while in D. arizonae, it showed higher V max and catalytic efficiency in optimal reaction conditions.

Conclusions

EST-4 from D. mulleri and D. arizonae are very closely related and still maintain several similar features; however, they show some degree of differentiation. Considering that EST-4 from D. mulleri has more conspicuous gel mobility difference among all EST-4 studied so far and a lower catalytic efficiency was observed here, we proposed that after duplication, this new copy of the original gene became redundant and started to decay toward a pseudogene status in this species, which probably is not occurring in D. arizonae.

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.

Developmental expression and gene/enzyme identifications in the alpha esterase gene cluster of Drosophila melanogaster

Here we show how the 10 genes of the alpha esterase cluster of Drosophila melanogaster have diverged substantially in their expression profiles. Together with previously described sequence divergence this suggests substantial functional diversification. By peptide mass fingerprinting and in vitro gene expression we have also shown that two of the genes encode the isozymes EST9 (formerly ESTC) and EST23. EST9 is the major 'alpha staining' esterase in zymograms of gut tissues in feeding stages while orthologues of EST23 confer resistance to organophosphorus insecticides in other higher Diptera. The results for EST9 and EST23 concur with previous suggestions that the products of the alpha esterase cluster function in digestion and detoxification of xenobiotic esters. However, many of the other genes in the cluster show developmental or tissue-specific expression that seems inconsistent with such roles. Furthermore, there is generally poor correspondence between the mRNA expression patterns of the remaining eight genes and isozymes previously characterized by standard techniques of electrophoresis and staining, suggesting that the alpha cluster might only account for a small minority of the esterase isozyme profile.

Evolutionary genetics of Drosophila esterases

Over 30 carboxylester hydrolases have been identified in D. melanogaster. Most are classified as acetyl, carboxyl or cholinesterases. Sequence similarities among most of the carboxyl and all the cholinesterases so far characterised from D. melanogaster and other eukaryotes justify recognition of a carboxyl/cholinesterase multigene family. This family shows minimal sequence similarities with other esterases but crystallographic data for a few non-drosophilid enzymes show that the family shares a distinctive overall structure with some other carboxyl and aryl esterases, so they are all put in one superfamily of/beta hydrolases. Fifteen esterase genes have been mapped in D. melanogaster and twelve are clustered at two chromosomal sites. The constitution of each cluster varies across Drosophila species but two carboxyl esterases in one cluster are sufficiently conserved that their homologues can be identified among enzymes conferring insecticide resistance in other Diptera. Sequence differences between two other esterases, the EST6 carboxyl esterase and acetylcholinesterase, have been interpreted against the consensus super-secondary structure for the carboxyl/cholinesterase multigene family; their sequence differences are widely dispersed across the structure and include substantial divergence in substrate binding sites and the active site gorge. This also applies when EST6 is compared across species where differences in its expression indicate a difference in function. However, comparisons within and among species where EST6 expression is conserved show that many aspects of the predicted super-secondary structure are tightly conserved. Two notable exceptions are a pair of polymorphisms in the substrate binding site of the enzyme in D. melanogaster. These polymorphisms are associated with differences in substrate interactions in vitro and demographic data indicate that the alternative forms are not selectively equivalent in vivo.

An evolutionary model for the duplication and divergence of esterase genes in Drosophila

The esterase 5 (Est-5 = gene, EST 5 = protein) enzyme in Drosophila pseudoobscura is encoded by one of three paralogous genes, Est-5A, Est-5B, and Est-5C, that are tightly clustered on the right arm of the X chromosome. The homologous Est-6 locus in Drosophila melanogaster has only one paralogous neighbor, Est-P. Comparisons of coding and flanking DNA sequences among the three D. pseudoobscura and two D. melanogaster genes suggest that two paralogous genes were present before the divergence of D. pseudoobscura from D. melanogaster and that, later, a second duplication occurred in D. pseudoobscura. Nucleotide sequences of the coding regions of the three D. pseudoobscura genes showed 78-85% similarity in pairwise comparisons, whereas the relatedness between Est-6 and Est-P was only 67%. The higher degree of conservation in D. pseudoobscura likely results from the comparatively recent divergence of Est-5B and Est-5C and from possible gene conversion events between Est-5A and Est-5B. Analyses of silent and replacement site differences in the two exons of the paralogous and orthologous genes in each species indicate that common selective forces are acting on all five loci. Further evidence for common purifying selective constraints comes from the conservation of hydropathy profiles and proposed catalytic residues. However, different levels of amino acid substitution between the paralogous genes in D. melanogaster relative to those in D. pseudoobscura suggest that interspecific differences in selection also exist.

A biochemical genetic study of alcohol dehydrogenase isozymes of the medfly, Ceratitis capitata Wied

A concerted effort is under way to analyze, at the genetic, biochemical, and molecular level, the Adh gene system in the medfly Ceratitis capitata, an important agricultural pest. The isoelectric focusing (IEF) pattern of alcohol dehydrogenase (ADH) of the medfly demonstrates the presence of two well-differentiated, genetically independent dimeric proteins, called ADH-1 and ADH-2. These proteins do not exhibit interlocus heterodimeric isozymes, and the genes are not controlled coordinately during development, Adh1 and Adh2 being expressed mainly in muscle or in fat body and ovary, respectively. From the intensity of the IEF isozyme patterns, primary alcohols are judged to be better substrates than secondary alcohols, in contrast with Drosophila melanogaster ADH, and ethanol is probably the most efficient substrate for both sets of isozymes. The isoelectric points of ADH-1 (pI = 5.4) and ADH-2 (pI = 8.6) are different from D. melanogaster ADH (pI = 7.6), but the medfly ADH-1 has a native molecular weight (approx. 58 kD) close to that of D. melanogaster. A population survey of samples both from laboratory strains and from wild geographically different populations showed that the Adh1 locus is more polymorphic than Adh2. The most variable populations are from Africa, the supposed source area of the species. Further, a case of selection at the Adh1 locus under laboratory conditions is reported. The hypothesis of Adh gene duplication and the degree of similarity between medfly and Drosophila ADH are also discussed.

Evidence for a genetic duplication involving alcohol dehydrogenase genes in Ceratitis capitata

An Adh duplication is described in the medfly Ceratitis capitata. Evidence is presented for two separate Adh1 and Adh2 structural loci mapping at a distance of 0.49 recombination unit from each other. By deletion mapping the Adh region has been cytologically located near the free end of the left arm of the second chromosome within an area between 2C;3A segments of the polytene chromosome. The genetic analysis of the region around Adh has identified seven neighboring genes (Acon1, Mpi, Est6, Aox, Xdh, Mdh2, Lsp1) which identify the linkage group D. The orientation of loci with regard to the centromere sets the origin of the map of the left arm of the second chromosome close to the two Adh loci.

Physical mapping of the Esterase-6 locus of Drosophila melanogaster

The Esterase-6 gene locus of Drosophila melanogaster although well-characterized, has not been definitely mapped by in situ hybridization. In this paper, a high resolution in situ hybridization protocol using an avidin/biotinylated-horseradish peroxidase/diaminobenzidine system was adopted to refine the physical map position of the Esterase-6 locus. Clarity of signal, detail of banding pattern and absence of background allowed the assignment of a 1.8 kb cDNA encoding Esterase-6 to three bands within subsections 69 A1-A3 on the left arm of polytene chromosome 3. These data refine earlier deletion mapping and low resolution in situ hybridization results, which assigned Esterase-6 to 69A1-A5. The potential use of this high resolution in situ hybridization technique in the analysis of the physical organization of the Esterase-6 gene duplication and surrounding region is discussed.

Structural comparison of two esterases from Drosophila mojavensis isolated by immunoaffinity chromatography

Antibodies raised against esterase-4 and esterase-5 from Drosophila mojavensis were coupled to Protein A-Sepharose CL-4B to prepare high-efficiency immunomatrices used for their purification. Final purification was achieved by anion-exchange h.p.l.c., in the case of esterase-5 followed by gel-filtration h.p.l.c. The resultant esterase preparations were homogeneous, as judged by gel-filtration h.p.l.c., SDS/polyacrylamide-gel electrophoresis and non-denaturing gel electrophoresis. Esterase-4 and esterase-5 are the products of a duplicated gene. They are differently localized in the insect's body and expressed in different periods during development. Although both enzymes exhibit little immunological cross-reactivity, their amino acid compositions show few significant differences and their N-terminal sequences are largely identical, which clearly show their common origin.

Esterase-23 (ES-23): characterization of a new carboxylesterase isozyme (EC 3.1.1.1) of the house mouse, genetically linked to ES-2 on chromosome 8

Genetic variation of a carboxylesterase isozyme (EC 3.1.1.1) of the house mouse, designated ES-23, is described. ES-23 was found in kidney, liver, and intestine. The isozyme was resistant to inhibition by 10(-3) mol/liter eserine and was stained using alpha-naphthyl butyrate or 5-bromoindoxyl acetate as substrate. Five different phenotypes, ES-23A to ES-23E, could be distinguished by disc electrophoresis and by isoelectric focusing. ES-23 is controlled by a structural locus situated within the esterase gene cluster 2 on chromosome 8. An analysis of allele distribution among different strains suggested a separate structural locus for the isozyme, Es-23e, which is closely linked to the loci Es-2, Es-5, Es-7, and Es-11. Of the five phenotypes, only ES-23B was expressed in lung. This variation is apparently controlled by a cis-acting regulatory element, presumably a temporal locus, Es-23t, closely linked to the presumed structural locus Es-23e.