DNA and polyribosome-like structures in lysates of mitochondria of Drosophila melanogaster

A comparison of the ribosomal proteins of Drosophila ovary, adult, and embryo

The proteins in the 80S ribosomes of Drosophila melanogaster ovaries and adults have been characterized by two-dimensional polyacrylamide gel electrophoresis. When ribosomal proteins of ovaries and adults were compared with those from embryos, all 3 tissues showed a similar number of proteins. In addition, qualitatively, the electrophoretograms of proteins extracted from the ribosomes of these 3 tissues were found to be indistinguishable. However, apparent quantitative differences in certain acidic proteins were observed between tissues. Using ribosomes from embryos as a standard for comparison, ribosomes from adult flies that were more than 14 days old appeared to have relatively larger amounts of acidic proteins S7 and S9, and relatively smaller amounts of acidic proteins S14 and S25/S27. The transition period occurred during the ninth to thirteenth day of adult fly development. Significant differences were not detected between ovarian and embryonic acidic ribosomal proteins. In contrast to the differential ratio of acidic proteins in ovaries, adults, and embryos, a similar distribution of basic proteins was found in these tissues.

An electron microscopic method for localization of ribosomal proteins during transcription of ribosomal DNA: a method for studying protein assembly

We describe a method for the localization of ribosomal proteins on electron microscopic spreads of active rRNA genes. The method consists of raising antibodies against Drosophila melanogaster proteins and allowing these antibodies to react with lysates of D. melanogaster egg chambers. The locations of the bound IgGs in the active transcripts are detected with goat anti-rabbit IgGs that have been labeled with electron-dense polymethacrylate spheres. By statistical analysis we can generate a confidence interval for the initial point of protein assembly for a particular protein. The first point of protein assembly for S14 is located near the 5' end of the pre-18S rRNA. In contrast, the first point of protein assembly for L4 is at 0.38 unit from the initiation point (a unit being the length of a ribosomal transcription unit). The binding patterns of S14 and L4 are consistent with the 5' proximal and the 5' distal orientations of the pre-18S and the pre-28S rRNAs. The method described here provides an approach to the elucidation of the assembly of eukaryotic ribosomal proteins in vivo.

The in vivo expression of pseudo ribosomal RNA genes in Drosophila melanogaster

Electron microscopic examination of chromatin has indicated that there are two major classes of ribosomal transcription units (rTUs) in Drosophila melanogaster. (a) a standard class which is about 8 kb in length and (b) a longer class (up to 15 kb) which has been hypothesized as having an intron in the 28S region of the gene. On rare occasions, we have observed a third class of TUs, which we term pseudo rTUs (or pseudo ribosomal RNA genes), distributed among the standard rTUs. Pseudo rTUs are composed of short fiber arrays with clear gradients in their RNP fiber lengths. The pseudo rTUs observed in egg chambers and blastoderm embryos are 4.1 +/- 0.58 kb in length and are found in tandem with non-transcribed spacer regions. The lengths of the non-transcribed spacer regions are found in 2 classes: one at 4.94 +/- 1.78 kb and the other at 19.28 +/- 2.11 kb. The present information suggests that these pseudo rTU fiber arrays are ribosomal in origin as their RNP fibers cross-react with antibodies raised against Drosophila ribosomal proteins. The pattern of distribution of D. melanogaster ribosomal protein L4 on RNP fibers in standard rTUs is compared with that in pseudo rTUs. This was determined by a novel approach involving the use of electron microscopic spreads of rTUs to which had been added IgGs labelled with polymethacrylate spheres. Pseudo ribosomal RNA genes are present in both the X (6%) and in the Y (6%) ribosomal chromatin as is indicated by their existence in nurse cells of both Oregon-R females, and females of the genotype sc4sc8/sc4sc8/y+Y.

DNA-protein interactions in the Drosophila melanogaster mitochondrial genome as deduced from trimethylpsoralen crosslinking patterns

The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila melanogaster was investigated by trimethylpsoralen photoreaction of embryos disrupted by gentle homogenization. After photoreaction, the mtDNA was isolated and the pattern of DNA crosslinking was determined by electron microscopy of the DNA under totally denaturing conditions. In contrast to nuclear DNA, which showed periodic crosslinks indicative of a nucleosome structure, most of each mtDNA molecule exhibited uniformly heavy crosslinking. A 10% region of the mtDNA was, however, protected from psoralen crosslinking in a distinctive manner: five uncrosslinked segments were closely clustered in the mtDNA. Four were 394 +/- 13 (SD) base pairs in size, while the fifth measured about 200 base pairs. These protected segments mapped within the A+T-rich region of the mtDNA, extending from the end of the A+T-rich region near the Bg1 II cleavage site to the center of the A+T-rich region. Protection of this part of the mtDNA from crosslinking was interpreted to be the result of association with proteins in the mitochondrion because mtDNA that was deproteinized before the photoreaction was uniformly crosslinked over its entire length. The origin of replication of the mtDNA is also located at the center of the A+T-rich region, which suggests that the protection from the psoralen photoreaction may be due to proteins involved in membrane attachment or replication.

Group fractionation and determination of the number of ribosomal subunit proteins from Drosophila melanogaster embryos

Proteins were extracted from ribosomes and (for the first time) from ribosomal subunits of Drosophila melanogaster embryos. The ribosomal proteins were analyzed by two-dimensional polyacrylamide gel electrophoresis. The electrophoretograms displayed 78 spots for the 80S monomers, 35 spots for the 60S subunits, and 31 spots for the 40S subunits. On the basis of present information, we propose what we believe to be a reliable and convenient nomenclature for the proteins of the ribosomes and each of the subunits. A pair of acidic proteins from D. melanogaster appears to be very similar in electrophoretic mobility to the acidic proteins L7/L12 from Escherichia coli and L40/L41 from rat liver. The electrophoretogram of proteins from embryonic ribosomes shows both qualitative and quantitative differences from those of larvae, pupae, and adults previously reported by others. The proteins of the 40S subunit range in molecular weight from approximately 10,000 to 50,000, and those from the 60S subunit range from approximately 11,000 to 50,000.

The occurrence of long transcription units among the X and Y ribosomal genes of Drosophila melanogaster: transcription of insertion sequences

Most of the ribosomal transcription units (rTUs) in Drosophila melanogaster observed by electron microscopy measure about 8 kb; a length which corresponds to the size of the 38S precursor to ribosomal RNA in D. melanogaster. However, interspersed among these rTUs are transcription units that are much longer (up to 14.6 kb) than the 8 kb expected for rTUs. Some of these larger length estimates can be attributed to stretching but an important fraction is significantly larger and has up to 60 more fibers per gene.--The following evidence suggests that these larger transcription units are ribosomal genes consisting of insertion sequences. The long transcription units are within the sizes expected for rTUs containing insertion sequences as reported by other workers. Their RNP fibers cross-react with antibodies raised against ribosomal proteins in a manner similar to that observed for ribosomal RNP. They are interspersed among rTUs in the X chromosome.--These putative ribosomal genes carrying insertions are present both in the X and, although to a lesser extent, in the Y ribosomal chromatin as is indicated by their existence in nurse cells of both Oregon R females and females of the genotype sc4sc8/sc4sc8/y+ Y. Analysis of the fiber patterns of "long TUs" supports the hypothesis that the insertion region is being transcribed.--"Long TUs" are found in tandem with non-transcribed spacer regions which are heterogeneous in length with a mean of 1.53+/-0.61 micrometers (or 8.5+/-3.4 kb).

Evolution of Drosophila mitochondrial DNAs. Comparison of denaturation maps

In an approach to the functional anatomy of the mitochondrial genome and its evolution, we have compared buoyant densities, contour lengths, and denaturation maps in circular mitochondrial DNAs of the genus Drosophila. Mitochondrial DNAs from three representatives of the subgenus Drosophila (D. virilis, D. hydei, D. funebris) are similar in size (approx. 5 mum or 1 - 10(7) daltons) and buoyant density (approx. 1.685 g/ml), while in two members of the subgenus Sophophora (D. melanogaster, D. simulans), mitochondrial DNAs are longer (approx. 6 mum or 12.4 - 10(6) daltons) and have a lower buoyant density (approx. 1.681 g/ml). The latter mitochondrial DNAs also share one distinctly large early melting region, which in D. melanogaster is equivalent to 1.54 mum of native DNA. The corresponding (A + T)-rich region in D. virilis or D. hydei mitochondrial DNA is 1 mum shorter. Except for this region, denaturation maps of D. melanogaster and D. virilis mitochondrial DNAs are indistinguishable. The addition or deletion of a single block of (A + T)-rich sequences can fully account for the differences in buoyant density and size between the mitochondrial DNAs we have examined. In an appendix, we show that there is an equivalent discrepancy between the extent of strand separation determined by electron by electron microscopy and the actual extent of DNA denaturation, whether this is determined from absorbance changes or inferred from the reduction in contour lengths of individual circular molecules. The reduction in contour length appears to result exclusively from the uniform foreshortening of single-stranded DNA, not only in regions of visible strand separation but also in denatured regions hidden within putatively native segments of molecules. For molecules showing 15--45% strand separation, we estimate that putatively native segments are approximately 50% denatured.

Analysis of chromatin-associated fiber arrays

Electron microscopic examination of chromatin from embryonic nuclei of Oncopeltus fasciatus and Drosophila melanogaster reveals arrays of chromatin associated fibers. The lengths and spacings of these fibers were analyzed to provide a basis for defining and interpreting regions of transcriptionally active chromatin. The results of the analysis are consistent with the interpretation of some fibers as nascent RNA with associated protein (RNP). The chromatin segments underlying these fiber arrays were classified as ribosomal or non-ribosomal transcription units according to definitions and criteria described by Foe et al. (1976). Nascent fibers on active ribosomal transcription units were analyzed and compared for Drosophila melanogaster, Triturus viridescens, and Oncopeltus fasciatus. A common feature of the fiber patterns on ribosomal TUs is that origin-distal fibers exhibit greater length variability and a lower slope relative to proximal fibers. The region of increased variability in fiber lengths is correlated with the expected location of 28S ribosomal RNA sequences in the distal half of each ribosomal transcription unit. Because 28S ribosomal RNA appears to contain more extensive regions of base sequence complementarity, we suggest that the length of ribosomal RNP fibers is influenced under our spreading conditions by the secondary structure of the nascent RNA. In order to calculate the RNA content of RNP fibers, chromatin morphology was used to estimate lengths of transcribed DNA. The packing ratio of DNA in chromatin, which we express as the length of B-structure DNA divided by length of chromatin, is 1.1-1.2 and 1.6 for the DNA in active ribosomal and non-ribosomal chromatins, respectively. These DNA packing ratios are used to determine the extent to which nascent RNP fibers are shorter than the transcribed DNA (expressed as DNA/RNP length ratio). For non-ribosomal transcription units and for proximal fibers of ribosomal transcription units. DNA/RNP length ratios are relatively constant within each array. However, considerable variability in this ratio (4-23) is observed for different arrays of fibers. Possible sources of this variability are considered by comparing ratios derived from the presumably identical ribosomal transcription units. Further analysis of the morphology of nascent fibers may elucidate the contributions of proteins and successive RNA sequences to RNP structure.