Structure and processing of precursor 5 S RNA in Drosophila melanogaster.

The 135-nucleotide-long “5 + S” RNA molecule found in Drosophila tissue culture cells after labelling at 37 °C has been identified as a precursor to 5 S RNA by pulse-chase experiments. The structure of the 15-nucleotide-long 3′-terminal sequence which differentiates this molecule from mature 5 S RNA has been determined. This ends in a stretch of U residues, suggestive of a polymerase termination signal.     

Sequence and heterogeneity in the 5S RNA gene cluster of Drosophila melanogaster.

The sequence of the entire 5S RNA gene of Drosophila melanogaster was determined by sequencing collectively 23 copies contained in a cloned fragment of Drosophila DNA and by sequencing individually four subcloned gene copies. A repetitive heptamer (GCTG CCT) present in variable numbers immediately following the coding sequence, is responsible for the length heterogeneity in the spacer region. Some of the gene copies contain a nucleotide change in the coding region which results in a new site for the restriction enzyme Mn1 I. The variant 5S RNA produced by these gene copies has not been detected in vivo. Two other single nucleotide variations were identified in the spacer region.     

The 5S genes of Drosophila melanogaster.

We have cloned embryonic Drosophila DNA using the poly (dA-DT) connector method (Lobban and Kaiser, 1973) and the ampicillin-resistant plasmid pSF2124 (So, Gill and Falkow, 1975) as a cloning vehicle. Two clones, containing hybrid plasmids with sequences complementary to a 5S RNA probe isolated from Drosophila tissue culture cells, were identified by the Grunstein and Hogness (1975) colony hybridization procedure. One hybrid plasmid has a Drosophila insert which is comprised solely of tandem repeats of the 5S gene plus spacer sequences. The other plasmid contains an insert which has about 20 tandem 5S repeat units plus an additional 4 kilobases of adjacent sequences. The size of the 5S repeat unit was determined by gel electrophoresis and was found to be approximately 375 base pairs. We present a restriction map of both plasmids, and a detailed map of of the5S repeat unit. The 5S repat unit shows slight length and sequence heterogeneity. We present evidence suggesting that the 5S genes in Drosophila melanogaster may be arranged in a single continuous cluster.     

Proportional polyploidization of 5S RNA genes in the ovary of Drosophila melanogaster mutants containing three 5S RNA gene loci

The 5S RNA gene content of polyploid cells of the ovary of Drosophila melanogaster has been compared in animals with two or three gene clusters. The amount of 5S RNA genes is exactly proportional to the number of gene clusters as determined by DNA-RNA filter hybridization. In contrast, the number of rDNA genes in endomitotic cells remains constant regardless of different numbers of nucleolus organizer regions (Spear, 1974).     

The structure of the chromatin at the syncytial stage in Drosophila melanogaster embryos

Chromatin structure of D. melanogaster embryonic nuclei was studied at the stage of preblastoderm using the Miller method. Several levels of chromatin packing were detected after soft nuclei dispersion: individual or clustered compact spherical bodies 0.5-1 micron in diameter, nucleosomic fibers with different nucleosome density, DNA loops and fibers that contain few granules.     

Variability in the molecular organization of the 5S RNA genes among strains of Drosophila melanogaster.

The organization of the 5S RNA cluster has been analyzed in four strains of Drosophila melanogaster by the Southern technique. In some of the strains the 5S RNA cluster appears to be interrupted by an unrelated sequence. In other strains a continuous cluster is present.     

Determination of the secondary structure of Drosophila melanogaster 5 S RNA by hydroxymethyltrimethylpsoralen crosslinking

The secondary structure of Drosophila melanogaster 5 S RNA was probed by 4′-hydroxymethyl-4,5′,8-trimethylpsoralen crosslinking. 5 S RNA was found to have a stable conformation in solution over a wide range of salt conditions. The structure was not affected by the intercalation of HMT. After HMT-crosslinks were formed, oligonucleotides containing the crosslinks were separated by gel electrophoresis and analyzed. Two different crosslinks were identified unambiguously. These crosslinks lead to a model very similar to that already proposed on the basis of evolutionary and enzymatic digestion data. The model proposed is in excellent agreement with all available data on eukaryotic 5 S RNA.     

Transfer RNA genes of Drosophila melanogaster.

Three recombinant plasmids containing randomly sheared genomic D. melanogaster tRNAs have been identified and characterized in detail. One of these, the plasmid 14C4, has a D. melanogaster (Dm) DNA segment of 18 kb, and has three tRNA2Arg and two tRNAAsN genes. The second plasmid, 38B10, has tRNAHis genes, while the third plasmid, 63H5, contains coding sequences for tRNA2Asp. The Dm DNA segments in each recombinant plasmid are derived from unique cytogenetic loci. 14C4 is from 84 F, 38B10 is from 48 F and 63H5 is from 70 A.     

Phosphoproteome analysis of Drosophila melanogaster embryos

Protein phosphorylation is a key regulatory event in most cellular processes and development. Mass spectrometry-based proteomics provides a framework for the large-scale identification and characterization of phosphorylation sites. Here, we used a well-established phosphopeptide enrichment and identification strategy including the combination of strong cation exchange chromatography, immobilized metal affinity chromatography, and high-accuracy mass spectrometry instrumentation to study phosphorylation in developing Drosophila embryos. In total, 13,720 different phosphorylation sites were discovered from 2702 proteins with an estimated false-discovery rate (FDR) of 0.63% at the peptide level. Because of the large size of the data set, both novel and known phosphorylation motifs were extracted using the Motif-X algorithm, including those representative of potential ordered phosphorylation events.     

Osmometric behavior of Drosophila melanogaster embryos

The osmometric behavior of Drosophila melanogaster embryos in permeabilized eggs was studied in a microscope diffusion chamber designed to impose a rapid change in osmotic environment at various temperatures. A numerical model of NaCl diffusion in the chamber predicted that radial variations in concentration arising from the presence of a thin film of solution at the top of the chamber were negligible. On the basis of transient electrical conductance measurements in the chamber, characteristic time constants for the change in concentration averaged over the chamber depth occupied by the eggs were 0.99, 0.77, and 0.60 min at 0, 10, and 20 degrees C, respectively. The chamber response was sufficiently rapid that the characteristic response of the embryo was not masked. Equilibrium volumetric behavior of the embryos indicated that they behaved as nearly ideal osmometers over the range of 0.256 to 2.000 osm, and followed the relation FVeq = 0.123C-1 + 0.541, where FVeq is equilibrium fractional volume and C is osmolality. Nonlinear regression of volumetric data during osmotic contraction yielded an average Lp of 0.722 micron/(min.atm) at 20 degrees C and an apparent activation energy delta E of 8.11 kcal/mol. The coefficients of variation in the Lp estimates among individual embryos were 38, 18, and 47% at 0, 10, and 20 degrees C, respectively. With the use of probability rules and a model for volumetric behavior during freezing, it was determined that the observed variability in Lp (assuming delta E is fixed) considerably broadens the transition range of cooling rates over which the predicted probability of intracellular ice formation goes from 0 to 1. However, experimental observations (21) show the actual transition range is even wider, indicating that there exist other important sources of variability which determine the event of ice formation in D. melanogaster embryos.     

Glycomic studies of Drosophila melanogaster embryos

With the complete genome sequence of Drosophila melanogaster defined a systematic approach towards understanding the function of glycosylation has become possible. Structural assignment of the entire Drosophila glycome during specific developmental stages could provide information that would shed further light on the specific roles of different glycans during development and pinpoint the activity of certain glycosyltransferases and other glycan biosynthetic genes that otherwise might be missed through genetic analyses. In this paper the major glycoprotein N- and O-glycans of Drosophila embryos are described as part of our initial undertaking to characterize the glycome of Drosophila melanogaster. The N-glycans are dominated by high mannose and paucimannose structures. Minor amounts of mono-, bi- and tri-antennary complex glycans were observed with GlcNAc and Galβ1–4GlcNAc non-reducing end termini. O-glycans were restricted to the mucin-type core 1 Galβ1-3GalNAc sequence.     

Isolation of HnRNP particles from Drosophila melanogaster embryos.

HnRNP from nitrogen frozen Drosophila melanogaster embryos were isolated in the presence of EDTA and EGTA cosedimenting in sucrose and density gradients like hnRNP from vertebrates. Four "core" proteins of 23.000, 28.000, 32.000 and 45.000 Da are strongly enriched in these complexes. One could conclude that the basic structural organization of Drosophila melanogaster hnRNP is similar to that described for vertebrates.     

RNA sorting in Drosophila oocytes and embryos.

Many RNAs involved in determination of the oocyte, specification of embryonic axes, and establishment of germ cells in Drosophila are localized asymmetrically within the developing egg or syncytial embryo. Here I review the current state of knowledge about the cis-acting sequences involved in RNA targeting, RNA binding proteins; gene activities implicated in localizing specific RNAs, and the role of the tubulin and actin cytoskeletons in RNA sorting within the oocyte. Targeted RNAs are often under complex translational control, and the translational control of two RNAs that localize to the posterior of the oocyte, oskar and nanos, is also discussed. Prospects for filling gaps in our knowledge about the mechanisms of localizing RNAs and the importance of RNA sorting in regulating gene expression are also explored.     

Delta-type DNA polymerase characterized from Drosophila melanogaster embryos.

Genetic and biochemical evidence suggests there are at least three DNA polymerases required for replication in eukaryotic cells. However, Drosophila embryonic cells have a very short duration S phase which is regulated differently. To address the question of whether embryos utilize different DNA polymerases, we employed Mono Q anion exchange chromatography to resolve the DNA polymerase activities. Two types of DNA polymerase, DNA polymerase delta and DNA polymerase alpha, were distinguished by: 1. copurification of DNA primase or 3'-5'exonuclease activities; 2. immunoblot analysis with alpha-specific polyclonal antisera; 3. sensitivity to aphidicolin and BuPdGTP; and 4. processivity measurements with and without Proliferating Cell Nuclear Antigen. These observations suggest that Drosophila embryos, similar to nonembryonic cells, have both alpha- and delta-type DNA polymerases.