Codon Usage Bias and tRNA Abundance in Drosophila

Codon usage bias of 1,117 Drosophila melanogaster genes, as well as fewer D. pseudoobscura and D. virilis genes, was examined from the perspective of relative abundance of isoaccepting tRNAs and their changes during development. We found that each amino acid contributes about equally and highly significantly to overall codon usage bias, with the exception of Asp which had very low contribution to overall bias. Asp was also the only amino acid that did not show a clear preference for one of its synonymous codons. Synonymous codon usage in Drosophila was consistent with ``optimal' codons deduced from the isoaccepting tRNA availability. Interestingly, amino acids whose major isoaccepting tRNAs change during development did not show as strong bias as those with developmentally unchanged tRNA pools. Asp is the only amino acid for which the major isoaccepting tRNAs change between larval and adult stages. We conclude that synonymous codon usage in Drosophila is well explained by tRNA availability and is probably influenced by developmental changes in relative abundance. Received: 5 December 1996 / Accepted: 14 June 1997     

The Correlation Between Recombination Rate and Dinucleotide Bias in Drosophila melanogaster

Revealing how recombination affects genomic sequence is of great significance to our understanding of genome evolution. The present paper focuses on the correlation between recombination rate and dinucleotide bias in Drosophila melanogaster genome. Our results show that the overall dinucleotide bias is positively correlated with recombination rate for genomic sequences including untranslated regions, introns, intergenic regions, and coding sequences. The correlation patterns of individual dinucleotide biases with recombination rate are presented. Possible mechanisms of interaction between recombination and dinucleotide bias are discussed. Our data indicate that there may be a genome-wide universal mechanism acting between recombination rate and dinucleotide bias, which is likely to be neighbor-dependent biased gene conversion.     

Menin is a regulator of the stress response in Drosophila melanogaster

Menin, the product of the multiple endocrine neoplasia type I gene, has been implicated in several biological processes, including the control of gene expression and apoptosis, the modulation of mitogen-activated protein kinase pathways, and DNA damage sensing or repair. In this study, we have investigated the function of menin in the model organism Drosophila melanogaster. We show that Drosophila lines overexpressing menin or an RNA interference for this gene develop normally but are impaired in their response to several stresses, including heat shock, hypoxia, hyperosmolarity and oxidative stress. In the embryo subjected to heat shock, this impairment was characterized by a high degree of developmental arrest and lethality. The overexpression of menin enhanced the expression of HSP70 in embryos and interfered with its down-regulation during recovery at the normal temperature. In contrast, the inhibition of menin with RNA interference reduced the induction of HSP70 and blocked the activation of HSP23 upon heat shock, Menin was recruited to the Hsp70 promoter upon heat shock and menin overexpression stimulated the activity of this promoter in embryos. A 70-kDa inducible form of menin was expressed in response to heat shock, indicating that menin is also regulated in conditions of stress. The induction of HSP70 and HSP23 was markedly reduced or absent in mutant embryos harboring a deletion of the menin gene. These embryos, which did not express the heat shock-inducible form of menin, were also hypersensitive to various conditions of stress. These results suggest a novel role for menin in the control of the stress response and in processes associated with the maintenance of protein integrity.     

Distribution of a Methionine Enkephalin-Like Substance in Gonads of Drosophila melanogaster

Summary

By means of the peroxidase-antiperoxidase (PAP) technique, methionine enkephalin immunoreactivity was demonstrated in ovaries and testes of Drosophila melanogaster. In all ovaries the germarium is immunopositive. Immunopositivity appears in the follicle cells from stage 6 and 7 and in the ooplasm from stage 7. Increasing immunoreaction was visualised in nurse cells of all successive stages. From stages 11 and 12 on, immunoreactivity is absent. Apart from the mature spermatozoa, all cells of the spermatogenic line are immunopositive. No immunoreactivity is found with antisera against leucine enkephalin and β-endorphin. Possible functions of the methionine enkephalin-like material are discussed.     

Pattern formation in the imaginal discs of a temperature-sensitive cell-lethal mutant of Drosophila melanogaster

To explore the effects of cell death on pattern formation in the developing imaginal discs of Drosophila melanogaster, I have isolated a number of cell-autonomous temperature-sensitive lethal mutants. Sex-linked temperature-sensitive lethals were screened for cell-autonomy by scoring the survival of lethal-bearing clones in genetic mosaics. The mutant with the strongest effect on clone viability gave rise to a high frequency of structural deficiencies and duplications in the derivatives of the eye-antennal discs, when subjected to pulse-treatments at the nonpermissive temperature during the late second and third instars. The patterns produced were nonrandom, with some structures showing a tendency to become deficient, and others a tendency to duplicate. Duplicated structures were only found in heads in which other structures were missing. Genetic tests identified the lethal as a point mutation at the suppressor-of-forked locus. Recombination, and complementation tests with a small duplication of this region showed that a second mutational lesion is in all probability not involved in the generation of abnormal patterns in the imaginal discs. It is therefore proposed that the cell-lethal action of the mutant is sufficient to account for phenotypic effects described. According to this hypothesis, cell death primarily causes deficiencies, and duplications occur as a response of the discs to injury. In agreement with this, it was found that in gynandromorphs, pattern duplications can be found in wild-type tissue in the presence of lethal tissue in the same disc. Thus, a cell-autonomous lethal may affect the process of pattern formation in a nonautonomous way.     

Distribution of dinucleotide microsatellites in the Drosophila melanogaster genome.

Microsatellites, a special class of repetitive DNA, have become one of the most popular genetic markers. The progress of various genome projects has made it possible to study the genomic distribution of microsatellites and to evaluate the potential influence of several parameters on their genesis. We report the distribution of dinucleotide microsatellites in the genome of Drosophila melanogaster. When considering only microsatellites with five or more repeat units, the average length of dinucleotide repeats in D. melanogaster is 6.7 repeats. We tested a wide range of parameters which could potentially influence microsatellite density, and we did not detect a significant influence of recombination rate, number of exons, or total length of coding sequence. In concordance with the neutral expectation for the origin of microsatellites, a significant positive correlation between AT content and (AT/TA)n microsatellite density was detected. While this pattern may indicate that microsatellite genesis is a random process, we also found evidence for a nonrandom distribution of microsatellites. Average microsatellite density was higher on the X chromosome, but extreme heterogeneity was observed between different genomic regions. Such a clumping of microsatellites was also evident on a more local scale, as 38.9% of the contiguous sequences analyzed showed a deviation from a random distribution of microsatellites.     

Pattern Formation in Asymmetrical and Symmetrical Imaginal Discs of Drosophila melanogaster

The polar coordinate model for pattern regulation in epimorphicfields (French et al., 1976) predicts that bilaterally symmetricalfields will show different kinds of regulative behavior dependingon the direction of the cut. These predictions have been testedusing the male genital disc of Drosophila melanogaster. First,a detailed fate map was established by examining the fate ofdisc fragments subjected to immediate metamorphosis in hostlarvae. Then the regulative abilities of various fragments wereexamined by culturing them for seven days in adult abdomens,before transfer to larvae for metamorphosis. When the disc wasbisected by a vertical cut (parallel to the line of symmetry)then fragments smaller than half of the disc underwent duplicationwith some simultaneous regeneration, while fragments largerthan half of the disc underwent regeneration. If the disc wasbisected by a bilaterally symmetrical cut across the line ofsymmetry, wound healing resulted in the confrontation of cellsfrom similar positions on the right and left sides of the fragment,and no regulation occurred. With the exception of regenerationoccurring during duplication of small lateral fragments, theseresults are as predicted by the polar coordinate model.     

Histamine is a major mechanosensory neurotransmitter candidate in Drosophila melanogaster

Histamine is known to be the neurotransmitter of insect photoreceptors. Histamine-like immunoreactivity is also found in a number of interneurons in the central nervous system of various insects. Here, we demonstrate by immunohistochemical techniques that, in Drosophila melanogaster (Acalypterae), most or all mechanosensory neurons of imaginal hair sensilla selectively bind antibodies directed against histamine. The histamine-like staining includes the cell bodies of these neurons as well as their axons, which form prominent fibre bundles in peripheral nerves, and their terminal projections in the central neuropil of head and thoracic ganglia. The specificity of the immunostaining is demonstrated by investigating a Drosophila mutant unable to synthesize histamine. Other mechanosensory organs, such as campaniform sensilla or scolopidial organs, do not stain. In the calypteran flies, Musca and Calliphora, we find no comparable immunoreactivity associated with either hair sensilla or the nerves entering the central nervous system, observations in agreement with earlier studies on Calliphora. Thus, histamine seems to be a major mechanosensory transmitter candidate of the adult nervous system of Drosophila, but apparently not of Musca or Calliphora.     

Distribution of the Sex combs reduced Gene Products in Drosophila melanogaster

The spatial and temporal distribution of RNA and protein encoded by the homeotic Sex combs reduced (Scr) gene were examined during Drosophila development. The gene products are present in the epidermis of both the labial and first thoracic segments as would be predicted from prior genetic studies. However, the pattern in the central nervous system (CNS) and mesoderm is further restricted; the major expression located in the labial neuromere of the CNS and the mesoderm of the first thoracic segment. The spatial restriction within the CNS is correlated with and may be due to a differential timing of expression in the labial and first thoracic ectoderm. The labial ectoderm accumulates the Scr RNA prior to segregation of the neuroblasts while expression in the first thoracic ectoderm occurs after neuroblast segregation. The protein is also observed in the subesophageal ganglia of both larvae and adults, as well as in the labial and first thoracic imaginal discs. Surprisingly, the protein is also present to a lesser extent in second and third thoracic leg discs.     

Pattern formation and determination in the antenna of the homoeotic mutant Antennapedia of Drosophila melanogaster

The development of the antenna in the antennal-leg homoeotic mutant Antennapedia (Antp^R) was investigated using somatic crossing-over to mark clones of cells in Antp^R antennal appendages. Antp^R antennae ranged from a nearly normal antenna to a nearly normal leg. The arrangement of clones of marked bristles and cuticle in the more antennalike antennae was similar to the wild type antenna, and that of the leglike antennae was similar to the wild-type leg. The contiguity of clones argued against extensive individual cell migration. The regions occupied by homoeotic leg varied considerably between different Antp^R antennae. Observation of Antp^R antennae in these phenotypic mosaics showed that specific leg parts replaced specific antennal parts. Even small groups of leg sensilla appeared only at precise locations in the antenna. These results suggest that homoeotic leg cells and antennal cells can both respond to the same positional information or prepattern. An analysis of clone size provided estimates for cell number in the Antp^R antenna. It was found that cell numbers in the wild-type and Antp^R antennae are about the same until the third instar, when the Antp^R cells start dividing more rapidly than wild type. Previous work had shown that clonal inheritance of a commitment for homoeotic leg also did not occur prior to the early third instar. It is suggested that determination for homoeotic leg occurs in the early third instar, and that thereafter this commitment is inherited by the progeny of the determined cells. The increase in growth rate is probably due to a faster growth rate in cells with a leg commitment than in cells with an antennal commitment. The results suggest that, once initiated, determination may be of two types—a clonally inherited determination (for example, to be homoeotic leg) and an environmental determination (for example, to be a specific part of a homoeotic leg). Clonal inheritance of determination in normal embryonic development and in sex determination in intersexes is discussed.     

DFak56 is a novel Drosophila melanogaster focal adhesion kinase

The mammalian focal adhesion kinase (FAK) family of nonreceptor protein-tyrosine kinases have been implicated in controlling a multitude of cellular responses to the engagement of cell surface integrins and G protein-coupled receptors. We describe here a Drosophila melanogaster FAK homologue, DFak56, which maps to band 56D on the right arm of the second chromosome. Full-length DFak56 cDNA encodes a phosphoprotein of 140 kDa, which shares strong sequence similarity not only with mammalian p125(FAK) but also with the more recently described mammalian Pyk2 (also known as CAKbeta, RAFTK, FAK2, and CADTK) FAK family member. DFak56 has intrinsic tyrosine kinase activity and is phosphorylated on tyrosine in vivo. As is the case for FAK, tyrosine phosphorylation of DFak56 is increased upon plating Drosophila embryo cells on extracellular matrix proteins. In situ hybridization and immunofluorescence staining analysis showed that DFak56 is ubiquitously expressed with particularly high levels within the developing central nervous system. We utilized the UAS-GAL4 expression system to express DFak56 and analyze its function in vivo. Overexpression of DFak56 in the wing imaginal disc results in wing blistering in adults, a phenotype also observed with both position-specific integrin loss of function and position-specific integrin overexpression. Our results imply a role for DFak56 in adhesion-dependent signaling pathways in vivo during D. melanogaster development.     

TRAF6 is a novel regulator of Notch signaling in Drosophila melanogaster

Notch signaling pathway unravels a fundamental cellular communication system that plays an elemental role in development. It is evident from different studies that the outcome of Notch signaling depends on signal strength, timing, cell type, and cellular context. Since Notch signaling affects a spectrum of cellular activity at various developmental stages by reorganizing itself in more than one way to produce different intensities in the signaling output, it is important to understand the context dependent complexity of Notch signaling and different routes of its regulation. We identified, TRAF6 (Drosophila homolog of mammalian TRAF6) as an interacting partner of Notch intracellular domain (Notch-ICD). TRAF6 genetically interacts with Notch pathway components in trans-heterozygous combinations. Immunocytochemical analysis shows that TRAF6 co-localizes with Notch in Drosophila third instar larval tissues. Our genetic interaction data suggests that the loss-of-function of TRAF6 leads to the rescue of previously identified Kurtz–Deltex mediated wing notching phenotype and enhances Notch protein survival. Co-expression of TRAF6 and Deltex results in depletion of Notch in the larval wing discs and down-regulates Notch targets, Wingless and Cut. Taken together, our results suggest that TRAF6 may function as a negative regulator of Notch signaling.     

Distribution of MR-induced sex-linked recessive lethal mutations in Drosophila melanogaster

In the ‘doubling-dose’ method currently used in genetic risk evaluation, two principle assumptions are made and these are: (1) there is proportionality between spontaneous and induced mutations and (2) the lesions that lead to spontaneous and induced mutations are essentially similar. The studies reported in this paper were directed at examining the validity of these two assumptions in Drosophila. An analysis was made of the distribution of sex-linked recessive lethals induced by MR, one of the well-studied mutator systems in Drosophila.

Appropriate genetic complementation tests with 15 defined X-chromosome duplications showed that MR-induced lethals occurred at many sites along the X-chromosome (in contrast to the known locus specificity of MR-induced visible-mutations); some, but not all these sites at which recessive lethals arose in the MR-system are the same as those known to be hot-spots for X-ray-induced lethals. With in situ hybridization we were able to demonstrate that a majority of MR-induced lethals is associated with a particular mobile DNA sequence, the P-element, i.e. they arose as a result of transposition.

The differences between the profiles of MR-induced and X-ray-induced recessive lethals, and the nature of MR-induced and X-ray-induced mutations, thus raise questions about the validity of the assumptions involved in the use of the ‘doubling-dose’ method.     

Pattern formation in the wing veins of the fused mutant (Drosophila melanogaster).

In order to analyze the effects of the mutation fused (fu) on vein pattern formation, wings mosaic for fused and non-fused tissue were obtained. Analysis of these wings (1) confirmed that fused does not involve the production of a freely diffusible substance; (2) showed that a genotypically fu fourth longitudinal vein (LV 4) develops a normal phenotype nonautonomously if the third longitudinal vein (LV 3) and most of the first posterior cell are non-fused; (3) showed that in the reciprocal situation, a non-fused fourth longitudinal vein often exhibited autonomous differentiation; (4) demonstrated that small groups of cells (either fu or non-fu) could be incorporated into structures characteristic of the opposite genotype; and (5) offered evidence that the dorsal wing surface may play an important role in the control of vein formation. Additionally, the fused phenotype itself was examined in some detail, and the anterior-posterior compartment border was defined. This examination suggests that in the more extreme cases LV 4 does not fuse with LV 3, but simply fails to form.     

Gamma-tubulin is present in Drosophila melanogaster and Homo sapiens and is associated with the centrosome

The mipA gene of A. nidulans encodes a newly discovered member of the tubulin superfamily of proteins, gamma-tubulin. In A. nidulans, gamma-tubulin is essential for nuclear division and microtubule assembly and is associated with the spindle pole body, the fungal microtubule organizing center. By low stringency hybridizations we have cloned cDNAs from D. melanogaster and H. sapiens, the predicted products of which share more than 66% amino acid identity with A. nidulans gamma-tubulin. gamma-Tubulin-specific antibodies stained centrosomes of Drosophila, human, and mouse cell lines. Staining was most intense in prophase through metaphase when microtubule assembly from centrosomes was maximal. These results demonstrate that gamma-tubulin genes are present and expressed in humans and flies; they suggest that gamma-tubulin may be a universal component of microtubule organizing centers; and they are consistent with an earlier hypothesis that gamma-tubulin is a minus-end nucleator of microtubule assembly.