Nucleotide divergence of the rp49 gene region between Drosophila melanogaster and two species of the Obscura group of Drosophila

Mitochondrial voltage-dependent anion channel gene family in Drosophila melanogaster: complex patterns of evolution, genomic organization, and developmental expression

Voltage-dependent anion channels (VDACs), also known as mitochondrial porins, are a family of small pore-forming proteins of the mitochondrial outer membrane found in all eukaryotes. VDACs play important roles in the regulated flux of metabolites between the cytosolic and mitochondrial compartments, energy metabolism, and apoptosis. Annotation of the genome sequence of Drosophila melanogaster revealed three genes (CG17137, CG31722-A, and CG31722-B) with homology to porin, the previously described Drosophila VDAC. Molecular analysis reveals a complex pattern of organization and expression. The genomic organization of these four genes and sequence comparisons with other insect VDAC homologs indicate that this gene family evolved through a mechanism of duplication and divergence from an ancestral VDAC gene during the radiation of the genus Drosophila. CG17137, CG31722-A, and CG31722-B are expressed in a male-specific pattern on both transcriptional and translational levels, while porin is equally expressed in both male and female flies. Additionally, CG31722-A and CG31722-B are expressed as a dicistronic transcript. Western blot analysis and immunofluorescence microscopy confirm that these proteins localize to the mitochondrion. Further expression analysis showed that CG17137 and CG31722-B are abundant in testes, while porin is ubiquitously expressed. While porin, CG17137, and CG31722-B are expressed to different degrees during embryogenesis, all of these proteins are dramatically reduced relative to cytochrome c content during larvogenesis. These studies illustrate a complex genomic organization and spatiotemporal pattern of expression for Drosophila VDACs as well as an evolutionary history consistent with either a partitioning of VDAC functions or an acquisition of novel functions among isoforms.

The Drosophila fl(2)d gene, required for female-specific splicing of Sxl and tra pre-mRNAs, encodes a novel nuclear protein with a HQ-rich domain

The Drosophila gene female-lethal(2)d [fl(2)d] interacts genetically with the master regulatory gene for sex determination, Sex-lethal. Both genes are required for the activation of female-specific patterns of alternative splicing on transformer and Sex-lethal pre-mRNAs. We have used P-element-mediated mutagenesis to identify the fl(2)d gene. The fl(2)d transcription unit generates two alternatively spliced mRNAs that can encode two protein isoforms differing at their amino terminus. The larger isoform contains a domain rich in histidine and glutamine but has no significant homology to proteins in databases. Several lines of evidence indicate that this protein is responsible for fl(2)d function. First, the P-element insertion that inactivates fl(2)d interrupts this ORF. Second, amino acid changes within this ORF have been identified in fl(2)d mutants, and the nature of the changes correlates with the severity of the mutations. Third, all of the phenotypes associated with fl(2)d mutations can be rescued by expression of this cDNA in transgenic flies. Fl(2)d protein can be detected in extracts from Drosophila cell lines, embryos, larvae, and adult animals, without apparent differences between sexes, as well as in adult ovaries. Consistent with a possible function in posttranscriptional regulation, Fl(2)d protein has nuclear localization and is enriched in nuclear extracts.

The sex-peptide gene (Acp70A) is duplicated in Drosophila subobscura

A 3.1-kb region of Drosphila subobscura homologous to the Acp70A region of D. melanogaster, which contains the sex-peptide gene, was cloned and sequenced. This region contains an approximately 600-bp duplication that includes the sex-peptide and its 5' and 3' flanking regions. The preproteins are 54 and 56 amino acids long, respectively (as compared to 55 amino acids in D. melanogaster), and each includes a 19-amino-acid-long signal peptide. The C-terminal part of the mature peptide is highly conserved between D. melanogaster and the two copies of D. subobscura. In this species, both copies of the gene are transcribed and, like in D. melangaster, only expressed in males. The duplicated region includes 300 bp upstream of the gene that would therefore seem sufficient for their expression in males. This region presents at its 5' end a stretch 93-bp that has a high similarity with the corresponding region of D. melanogaster and could be part of a still unidentified regulatory element of these genes.

Molecular and chromosomal phylogeny in the obscura group of Drosophila inferred from sequences of the rp49 gene region

A region of approximately 1.6 kb encompassing the ribosomal protein 49 gene (rp49) has been sequenced and compared in nine species of the obscura group of Drosophila: four species belonging to the obscura subgroup, three to the pseudoobscura subgroup, and two to the affinis subgroup. Our data provide strong support that the nearctic species (pseudoobscura and affinis subgroups) are monophyletic and place D. bifasciata with the other species of the obscura subgroup. Nucleotide sequence information at the rp49 gene region (located very close to one of the breakpoints of inversion O3) has also been used to infer the phylogeny of the O chromosome in the subobscura species cluster. Analysis based both on parsimony-informative sites and on genetic distances confirms that the O3 gene arrangement, present in D. guanche (together with inversion g) and in D. madeirensis, is ancestral to gene arrangements O3 + 4 and Ost present in extant populations of D. subobscura.

Chromosomal homology and molecular organization of Muller's elements D and E in the Drosophila repleta species group

Thirty-three DNA clones containing protein-coding genes have been used for in situ hybridization to the polytene chromosomes of two Drosophila repleta group species, D. repleta and D. buzzatii. Twenty-six clones gave positive results allowing the precise localization of 26 genes and the tentative identification of another nine. The results were fully consistent with the currently accepted chromosomal homologies and in no case was evidence for reciprocal translocations or pericentric inversions found. Most of the genes mapped to chromosomes 2 and 4 that are homologous, respectively, to chromosome arms 3R and 3L of D. melanogaster (Muller's elements E and D). The comparison of the molecular organization of-these two elements between D. melanogaster and D. repleta (two species that belong to different subgenera and diverged some 62 million years ago) showed an extensive reorganization via paracentric inversions. Using a maximum likelihood procedure, we estimated that 130 paracentric inversions have become fixed in element E after the divergence of the two lineages. Therefore, the evolution rate for element E is approximately one inversion per million years. This value is comparable to previous estimates of the rate of evolution of chromosome X and yields an estimate of 4.5 inversions per million years for the whole Drosophila genome.

A method for estimating the numbers of synonymous and nonsynonymous substitutions per site

A method for estimating the numbers of synonymous (Ks) and nonsynonymous (Ka) substitutions per site is proposed. The method is based on the Li's (J. Mol. Evol. 36:96-99, 1993) and Pamilo and Bianchi's (Mol. Biol. Evol. 10:271-281, 1993) method, but a putative source of bias is solved. It is proposed that the number of synonymous substitutions that are actually transitions or transversions should be computed by separating the twofold degenerate sites into two types of sites, 2S-fold and 2V-fold, where only transitional and transversional substitutions are synonymous, respectively. Kimura's (J. Mol. Evol. 16:111-120, 1980) two-parameter correcting method for multiple substitutions at a site is then applied using the overall observed synonymous transversion frequency to estimate both the numbers of synonymous transversional (Bs) and transitional (As) substitutions per site. This approach, therefore, also minimizes stochastic errors. Computer simulations indicate that the method presented gives more accurate Ks and Ka estimates than the aforementioned methods. Furthermore, the obtention of confidence intervals for divergence estimates by computer simulation is proposed.

Sequence and evolution of the Drosophila pseudoobscura glycerol-3-phosphate dehydrogenase locus

The Gpdh genomic region has been cloned and sequenced in Drosophila pseudoobscura. A total of 6.8 kb of sequence was obtained, encompassing all eight exons of the gene. The exons have been aligned with the sequence from D. melanogaster, and the rates of synonymous and nonsynonymous substitution have been compared to those of other genes sequenced in these two species. Gpdh has the lowest rate of nonsynonymous substitution yet seen in genes sequenced in both D. pseudoobscura and D. melanogaster. No insertion/deletion events were observed, and the overall architecture of the gene (i.e., intron sites, etc.) is conserved. An interesting amino acid reversal was noted between the D. melanogaster Fast allele and the D. pseudoobscura gene.

Separate cis-regulatory sequences control expression of serendipity beta and janus A, two immediately adjacent Drosophila genes

The genes janus (jan) A and B, and serendipity (sry) beta and delta are two pairs of duplicated genes that are adjacent to each other on the third chromosome of Drosophila melanogaster. The jan A and sry beta genes are expressed throughout development in both males and females. They are transcribed in opposite orientations from start sites separated by only 173 bp of DNA. We report here the complete sequence of the jan A and B genes in Drosophila pseudoobscura, a species distantly related to D. melanogaster in which the overall organization of the sry beta, jan A and jan B genes is identical to that in D. melanogaster. Sequence comparison of the jan A-sry beta intergenic region and 5'-transcribed domain of each gene between D. melanogaster and D. pseudoobscura reveals short stretches of conserved sequences that may correspond to cis-acting regulator elements. In order to test the possibility that some cis-acting regulatory sequences are shared by the two genes, we carried out a deletion analysis of the jan A/sry beta intergenic region in D. melanogaster using transgenic lacZ fusion genes. Our results show that sry beta cis-acting sequences are located in the (-117; +137) 5'-region of the gene and that jan A cis-regulatory sequences are included in the (-56; +151) 5'-domain of this gene. Together these data indicate that in spite of the physical proximity of the jan A and sry beta genes, their transcription is regulated by separate cis-acting sequences.

Molecular characterization of the breakpoints of an inversion fixed between Drosophila melanogaster and D. subobscura

The two breakpoints of a chromosomal inversion fixed since the split of Drosophila melanogaster and D. subobscura lineages have been isolated and sequenced in both species. The regions spanning the breakpoints initially were identified by the presence of two signals after interspecific in situ hybridization on polytene chromosomes. Interspecific comparison of the sequenced regions allowed us to delineate the location of the breakpoints. Close to one of these breakpoints a new transcription unit (bcn92) has been identified in both species. The inversion fixed between D. melanogaster and D. subobscura does not seem to have broken any transcription unit. Neither complete nor defective transposable elements were found in the regions encompassing the breakpoints. Short thymine-rich sequences (30-50 bp long) have been found bordering the breakpoint regions. Although alternating Pur-Pyr sequences were detected, these putative target sites for topoisomerase II were not differentially clustered in the breakpoints.

Gene conversion is involved in the transfer of genetic information between naturally occurring inversions of Drosophila

The DNA sequences of the ribosomal protein 49 (rp49) region were determined for 34 isochromosomal strains of Drosophila subobscura representing two chromosomal arrangements, the OST and the O3 + 4 gene arrangements, which differ by two overlapping inversions. The data reveal that gene conversion is a mechanism responsible for the transfer of genetic information between naturally occurring inversions of Drosophila. The estimated rate of gene transfer by gene conversion at this region, which is close to an inversion breakpoint, is lower than previous estimates obtained experimentally at the rosy (ry) gene in Drosophila melanogaster. Our data indicate that gene arrangements OST and O3 + 4 are monophyletic and rather old (0.58 and 0.73 million years old, respectively).

Relationship between expression of serendipity alpha and cellularisation of the Drosophila embryo as revealed by interspecific transformation

A dramatic reorganization of the cytoskeleton underlies the cellularisation of the syncytial Drosophila embryo. Formation of a regular network of acto-myosin filaments, providing a structural framework, and possibly a contractile force as well, appears essential for the synchronous invagination of the plasma membrane between adjacent nuclei. The serendipity alpha (sry alpha) gene is required for this complete reorganization of the microfilaments at the onset of membrane invagination. We compare here the structure and expression of sry alpha between D. pseudoobscura, D. subobscura and D. melanogaster. Interspersion of evolutionarily highly conserved and divergent regions is observed in the protein. One such highly conserved region shows sequence similarities to a motif found in proteins of the ezrin-radixin-moesin (ERM) family. Four 7–13 bp motifs are conserved in the 5′ promoter region; two of these are also found, and at the same position relative to the TATA box, in nullo, another zygotic gene recently shown to be involved in cellularisation. The compared patterns of expression of D. melanogaster sry alpha and nullo, and D. pseudoobscura sry alpha reveal a complex regulation of the spatiotemporal accumulation of their transcripts. The D. pseudoobscura sry alpha gene is able to rescue the cellularisation defects associated with a complete loss of sry alpha function in D. melanogaster embryos, even though species-specific aspects of its expression are maintained. Despite their functional homologies, the D. melanogaster and D. pseudoobscura sry alpha RNAs have different subcellular localisations, suggesting that this specific localization has no conserved role in targeting the sry alpha protein to the apical membranes.