Evolution of thedec-1 eggshell locus inDrosophila. I. Restriction site mapping and limited sequence comparison in themelanogaster species subgroup

Summary We have analyzed 18 kb of DNA in and upstream of thedefective chorion-1 (dec-1) locus of the eight known species of themelanogaster species subgroup ofDrosophila. The restriction maps ofD. simulans, D. mauritiana, D. sechellia, D. erecta, andD. orena are shown to have basically the restriction map ofD. melanogaster, whereas the maps ofD. teissieri andD. yakuba were more difficult to align. However, the basic amount of DNA and sequence arrangement appear to have been conserved in these species. A small deletion of varying length (65–200 bp) is found in a repeated sequence of the central transcribed region ofD. melanogaster, D. simulans, andD. erecta. Restriction site mapping indicated that thedec-1 gene is highly conserved in themelanogaster species subgroup. However, sequence comparison revealed that the amount of nucleotide and amino acid substitution in the repeated region is much larger than in the 5 translated region. The 5 flanking region showed noticeable restriction site polymorphisms between species. Based on calculations from the restriction maps a dendrogram was derived that supports earlier published phylogenetic relationships within themelanogaster species subgroup except that theerecta-orena pair is placed closer to themelanogaster complex than toD. teissieri andD. yakuba.     

Concerted evolution of sequence repeats inDrosophila mitochondrial DNA

Summary In the eightDrosophila species of themelanogaster subgroup, the mitochondrial DNA (mtDNA) contains an A+T-rich region in which replication originates. The length of this region, in contrast with that of the coding part of the genome, varies extensively among these species. The A+T-rich region ranges from about 1kbp inD. yakuba, D. teissieri, D. erecta, andD. orena to 5 kbp inD. melanogaster, D. simulans, D. mauritiana, andD. sechellia. The difference in size is due in part to the amplification, in the species with long genomes, of a 470-bp sequence that is present only once in each of the four species with short genomes.Usually three to six repeats of this sequence occur in direct tandem repetition in the species with long genomes. The sequence is characterized by the relative positions of the Hpa I and Acc I cleavage sites. Comparative study of the genomes found in the species with long mtDNA molecules reveals relative homogeneity of the repeat units within a given genome, which contrasts with the variability found among the repeats of different genomes. This result is suggestive of a process of a concerted evolution.The examination of heteroplasmic flies of three species (D. simulans, D. mauritiana, andD. sechellia) has shed light on this process. In most cases the molecular types of mtDNA present in a heteroplasmic individual differ by one repeat unit. Addition or deletion of this sequence appears to be the original mutational event generating transient heteroplasmy. Cycles of addition or deletion may consequently maintain the intragenomic homogeneity of the repeats.Finally, we have analyzed an exceptional isofemale line in which three molecular lengths of mtDNA are found (molecules with four, five, and six repeats, respectively). Individual offspring of this line carry from one to three of the molecular types, in all combinations. This indicates that the remodeling of the mitochondrial genome occurs through a mechanism that is at present unknown, but that is site specific and rather frequent.Presented at the FEBS Symposium on Genome Organization and Evolution, held in Crete, Greece, September 1–5, 1986     

Phenotypic and developmental analysis of mutations at thecrumbs locus,a gene required for the development of epithelia inDrosophila melanogaster

Summary The genecrumbs (crb) ofDrosophila melanogaster provides an essential function for the embryonic development of ectodermally derived epithelia. Complete loss of function alleles of thecrb gene are recessive embryonic lethals and lead to a disorganization of the primordia of these epithelia, followed by cell death in some tissues. Incrb mutant embryos, different organs are affected to a different extent. Some tissues die almost completely (as the epidermis, the atrium and the pharynx) while others partially survive and conserve their basic epithelial structure (as the tracheal system, the oesophagus, the proventriculus, the salivary glands, the hindgut and the Malpighian tubules). Degeneration is first visible at stage 11 and continues successively throughout development. There is evidence that the loss of epithelial cell polarity may be the cause for the degeneration of these tissues, suggesting that thecrb gene product is involved in stabilizing the apico-basal polarity of epithelial cells. As previously shown, thecrb protein is specifically expressed on the apical side of embryonic epithelia in a reticular pattern outlining the borders of the cells. Here we demonstrate that thecrb protein shows the same subcellular localization in epithelial cells of imaginal discs and in follicle cells, indicating a similar function ofcrb during the development of embryonic, imaginal and follicle epithelia. Clonal analysis experiments indicate that the genecrb is not cell-autonomous in its expression, suggesting that the gene product may act as a diffusible factor and may serve as a signal in a cell-cell communication process. This signal is thought to be required for the formation and/or maintenance of the cell and tissue structure of the respective epithelia.     

Naturally occurring quantitative variants of acid phosphatase-1 in Drosophila melanogaster

We have examined 111 wild Drosophila melanogaster lines for cis-acting quantitative variants of the Acph-1 gene, which codes for acid phosphatase-1 (ACPH). Three variants with obvious, reproducible phenotypes were isolated. All variants acted equally on all tissues and developmental stages examined. No recombinants were detected between one quantitative variant and the site determining the electrophoretic mobility of Acph-1 among 3885 flies examined. Several enzymatic properties of the variant enzymes were tested, including the K _m values for two substrates, inhibition by three different inhibitors, and thermal stability; the variant enzymes behaved identically to the wild-type enzyme in all cases. Immunological titration experiments showed that the variant enzymes had the same enzyme activity per molecule of ACPH as the wild-type enzyme. These results suggest that the quantitative variants we have identified are altered in the regulatory portion of Acph-1 so as to produce altered numbers of normal ACPH molecules.This work was supported by NIH Grant 21548. MAJ was supported by NIH Predoctoral Training Grant GM07413.     

Fine sequence analysis of 60 kb around the Arabidopsis thaliana AtEm1 locus on chromosome III

The Arabidopsis thaliana Em1 gene has been mapped to the lower arm of chromosome III. Fine analysis of 60 kb around this gene, based largely on identification and sequencing of cognate cDNAs, has allowed us to identify 15 genes or putative genes. Cognate cDNAs exist for ten of these genes, indicating that they are effectively expressed. Analysis by sequence alignment and intracellular localization prediction programs allows attribution of a potential protein product to these genes which show no obvious functional relationship. Comparison of the true exon/intron structure based on cDNA sequences with that proposed by three commonly used prediction programs shows that, in the absence of further information, the results of these predictions on anonymous genomic sequences should be interpreted with caution. Examination of the non-coding sequence showed the presence of a novel repeated, palindromic element. The results of this detailed analysis show that in-depth studies will be necessary to exploit correctly the complete A. thaliana genome sequence.     

Length polymorphism in the threonine-glycine-encoding repeat region of theperiod gene inDrosophila

Summary Single-fly polymerase chain reaction amplification and direct DNA sequencing revealed high levels of length polymorphism in the threonine-glycine encoding repeat region of theperiod (per) gene in natural populations ofDrosophila melanogaster. DNA comparison of two alleles of identical lengths gave a high number of synonymous substitutions suggesting an ancient time of separation. However detailed examination of the sequences of different Thr-Gly length variants indicated that this divergence could be understood in terms of four deletion/insertion events. InDrosophila pseudoobscura a length polymorphism is observed in a five-amino acid degenerate repeat, which corresponds tomelanogaster's Thr-Gly domain. In spite of the differences betweenD. melanogaster andD. pseudoobscura in the amino acid sequence of the repeats, the predicted secondary structures suggest evolutionary and mechanistic constraints on theper protein of these two species.     

Phylogenetic analysis of DNA length mutations in a repetitive region of the Hawaiiandrosophila yolk protein geneYp2

Nucleotide sequence analysis has demonstrated that interspecific size variation in the YP2 yolk protein among HawaiianDrosophila is due to in-frame insertions and deletions in two repetitive segments of the coding region of the Yp2 gene. Sequence comparisons of the complex repetitive region close to the 5′ end of this gene across 34 endemic Hawaiian taxa revealed five length morphs, spanning a length difference of 21 nucleotides (nt). A phylogenetic character reconstruction of the length mutations on an independently derived molecular phylogeny showed clade-specific length variants arising from six ancient events: two identical insertions of 6 nt, and four deletions, one of 6 nt, one of 12 nt, and two identical but independent deletions of 15 nt. These mutations can be attributed to replication slippage with nontandem trinucleotide repeats playing a major role in the slipped-strand mispairing. Geographic analysis suggests that the 15 nt deletion which distinguishes theplanitibia subgroup from thecyrtoloma subgroup occurred on Oahu about 3 million years ago. The homoplasies observed caution against relying too heavily on nucleotide insertions/deletions for phylogenetic inference. In contrast to the extensive repeat polymorphisms within otherDrosophila and the human species, the more complex 5′Yp2 repetitive region analyzed here appears to lack polymorphism among HawaiianDrosophila, perhaps due to founder effects, low population sizes, and hitchhiking effects of selection on the immediately adjacent 5′ region. Correspondence to: M.P. Kambysellis     

Characterization by isoelectric focusing of chorion protein variants inDrosophila melanogaster and their use in developmental and linkage analysis

Summary Drosophila melanogaster chorion proteins are characterized on one-dimensional isoelectric focusing (IF) gels. The six major chorion components previously identified on SDS gels are shown to resolve into at least 11 components in our IF system. IF screening of 102 geographic strains ofDrosophila melanogaster revealed seven cases of variation in major chorion components. Two strains, Crimea and Falsterbo, which were monomorphic for a variant B1 protein and two strains, Skafto and Lausanne, which were monomorphic for a variant C1 protein, were chosen for further study. After IF developmental analysis of F1 hybrids had indicated that the sources of the variation resided in the structural genes for these proteins, each variant was crossed to a multiply marked and inverted strain (BLT) to determine the linkage group of the variant gene. To localize genes to more specific sites multiply marked 3rd (SKERO) or X-chromosomal (CB1) (X-PLE) mapping strains were used. In both Crimea and Falsterbo the gene for the B1 protein is located near map location 26 on the 3rd chromosome. In both Lausanne and Skafto the C1 gene is located on the X chromosome. Hence, for the first time, we have demonstrated genetically the non-linkage of two chorion genes, B1 and C1.     

Evidence for the wide distribution of repetitive DNA sequences in the genusStreptomyces

Summary Repeated DNA sequences were detected as rapidly reannealing sequences in the chromosomal DNA of 13 out of 14Streptomyces species using either hypochromicity measurements or hydroxyapatite chromatography. These sequences made up between approximately 4% and 11% of the total DNA of these species; only inStreptomyces rimosus were repeated DNA sequences not detected. The repeated sequences fall into a number of distinct percentage G+C (%G+C) classes, many being of rather low %G+C. Analytical density ultracentrifugation of the DNA of these species indicated satellite bands of low %G+C, and high-resolution thermal denaturation profiles indicated the presence of blocks of DNA of low G+C content too. No such satellite band could be found inStreptomyces coelicolor and no low-%G+C DNA could be detected in its thermal denaturation profile. The possible relationship of this repeated DNA, an unusual occurrence in a procaryote, to genetic instability and genetic control mechanisms inStreptomyces is discussed.     

Structural and functional analysis of the scute locus in Drosophila melanogaster

Summary The functional expression of 12 scute alleles in homozygotes and compounds of Drosophila melanogaster at 14°, 22°, 30°C is analysed. Based on the data obtained, linear maps for bristles and mutations are built. The basic features of the maps, clustering and polarity, are invariable with respect to temperature, scute gene dosage and cross direction. In addition local dominance of the norm over bristle reduction was produced by the scute mutation; different types of complementation reactions were established for each bristle. The gene scute is treated as an operon-like system, composed of 3–4 cistrons with each controlling the formation of bristles on a particular region of the fly's body. This model argues well with the structure of maps constructed and implies a post-translational level of initial events of bristle-formation process.This paper is based on the report presented at XIV International Congress of Genetics (Moscow, August 1978)     

Distribution of polymorphic gene duplication at theGpdh locus in natural populations ofDrosophila melanogaster

Summary The glycerol-3-phosphate dehydrogenase (GPDH, E. C. 1.1.1.8) gene ofDrosophila melanogaster contains a tandem duplication of a 4.5-kb-long DNA fragment. Survey of theGpdh gene region by the Southern blot analysis revealed the following features of this gene duplication: (1) The duplication was not observed in chromosome lines that carryIn(2L)t, a cosmopolitan chromosomal inversion in this species. The duplication and the inversion are in linkage disequilibrium. (2) The duplication is polymorphic in the Japan and US natural populations examined. Its frequency is 0.26 on an average inIn(2L)t-free chromosomes. (3) Triplication is absent or has not become frequent in the populations surveyed. Possible evolutionary factors of this duplication polymorphism are discussed.     

The DNA content of polytene nuclei in midgut and Malpighian tubule cells of adultDrosophila melanogaster

Summary The amounts of DNA in midgut and Malpighian tubule cells of adult maleDrosophila melanogaster have been determined by Feulgen-DNA cytophotometry. The DNA values fall into discrete classes reflecting different levels of polyteny. The maximum level is 64C in the midgut, 256C in Malpighian tubules, and the modal values are 32C and 128C respectively. The data provide no evidence for extensive underreplication of heterochromatin. It is suggested that the reduced amount of satellite DNA found in the tissues of young adult flies may be a consequence of the fact that cycles of DNA replication started in the pre-adult stages are not completed until some hours after eclosion.     

Complete replication of DNA in polytene nuclei of salivary glands ofDrosophila melanogaster

Summary Combined cytophotometric and autoradiographic experiments are performed on individual polytene salivary gland nuclei of X/X-female and X/Y-male larvae ofDrosophila melanogaster, DNA measurements of unlabeled nuclei reveal complete douplings of all 4C DNA quantity during polytenization. These new data do not agree with the hypothesis of heterochromatic underreplication.