The ribosomal RNA cistrons

Characterization of yeast ribosomal DNA

High-molecular-weight yeast ribosomal DNA, purified by preparative Hg2+/Cs2SO4 gradient centrifugation, was characterized using RNA-DNA hybridization, CsC1 gradient analysis and denaturation-renaturation experiments. The following conclusions are drawn from the results of these studies. 1. 55--60% of the total yeast rDNA is made up of sequences coding for 42-S ribosomal precursor RNA. 2. The mean length of the 42-S precursor cistrons corresponds to a molecular weight of 6.2 X 10(6). 3. The overall G + C content fo yeast rDNA is 42%. On the hand, both the segments coding for the nonribosomal excess RNA of the 42-S precursor and those specifying 26-S and 17-S rRNA have a higher G + C content of 46.9--47.5%. 4. The 42-S precursor cistrons are closely bound up with sequences rather low in G + C content (34--35%), which account for 40--45% of the total yeast rDNA. In contrast to the multiple 42-S precurosr cistrons which show very little or no base sequence divergence these intervening (A + T)-rich sequences display a considerable heterogeneity in base sequence.

Isolation of a DNA fraction highly enriched in transfer RNA genes from Xenopus laevis

A DNA fraction highly enriched in tRNA genes can be isolated from the Xenopus laevis genome by the use of Ag+/Cs2SO4 density gradients. Ag+ shows a low affinity for some tRNA cistrons, allowing their separation from bulk DNA upon equilibrium centrifugation in a Cs2SO4 density gradient. Contaminating DNA in the resulting tDNA fraction is further removed by two additional CsCl density gradient centrifugations. The final DNA fraction is 60-fold enriched in tRNA genes, compared to the starting DNA material.

Effects of actinomycin D on the association of newly formed ribonucleoproteins with the cistrons of ribosomal RNA in Triturus oocytes

The effect of actinomycin D(AMD) on the association of the nascent ribonucleo-protein (RNP) fibrils containing the precursors of ribosomal RNA (pre-rRNA) with their template deoxyribonucleoprotein (rDNP) strands has been studied in lampbrush stage oocytes from Triturus alpestris. Ovary pieces were incubated in vitro either in media containing radioactive ribonucleosides and then, for various times, in solutions containing 25 mug/ml AMD, or were directly exposed to the drug. The ultrastructure of the nucleoli and the nuclear periphery was studied by electron microscopy of thin sections and positively stained spread preparations of isolated nuclear contents, and by light and electron microscope autoradiography. The fate of the labeled pre-rRNA was followed by gel electrophoresis of RNA extracted from manually isolated nuclei. Our results show that the growing fibrils which contain the nascent pre-rRNA progressively detach from the DNP strands, the majority being released between 45 and 180 min after application of the drug. The release pattern seems to be random and does not show preference for regions close to the initiator or terminator sites of the transcribed rDNP units. There is a pronounced tendency to removal of groups of adjacent mascent fibrils. The effect of the drug is very heterogeneous. Even after 3 h of treatment with AMD the nucleoli exhibit several individual transcriptional units which appear almost completely covered with lateral fibrils. Autoradiography revealed that most of this released RNP remains within the confinements of the nucleoli which show some foci of aggregation and condensation of fibrillar components but no clear "segregation" phenomenon. In the gel-electrophoretic analysis, a significant but moderate decrease of labeled pre-rRNA was noted only in the first stable pre-rRNA component, whereas pre-rRNA classes of lower molecular weight are very stable under these conditions. The results are discussed in relation to the stability of rDNA transcription complexes and as a basis for an explanation of the ultrastructural changes which are generally observed in nucleoli of AMD-treated cells. It is postulated that inhibition of transcription results in a slow but progressive release of the arrested incomplete RNP fibrils from the template.

Hybridization of ribosomal RNA labeled to high specific radioactivity with dimethyl sulfate

RNA radioactively methylated with dimethyl sulfate has the advantage of relatively low background noise level when utilized in DNA saturation hybridization employing the membrane filter technique. In addition, the RNA can be methylated with either 3H- or 14C-labeled methyl groups. However, the low specific radioactivity usually obtained with dimethyl sulfate has limited the use of this labeling technique. We describe a detailed characterization of the methylation of rRNA with dimethyl sulfate giving specific radioactivities on the order 10-5 cpm/mug. Kinetics and optimum conditions for the methylation reaction of rRNA were studied. The methylation did not cause excessive degradation of RNA in neutral aqueous solution, and the methyl derivative of RNA was stable under normal hybridization conditions. Specific radioactivitiy of the methylated RNA was found to be a linear function of the product of RNA concentration and specific radioactivity of the dimethyl sulfate in the reaction mixture at a constant incubation time. The methylated bases of the RNA lowered the thermal stability of the DNA-RNA hybrids by 1 degree in Tm per 1.6 per cent methylated RNA bases. rRNA gene dosage values using high specific radioactive methylated RNA were found to be 81 and 180 genes/haploid genome, respectively. Dissociation constants of the hybridization reaction ranged from 0.90 times 10-10 to 2.37 times 10-10 M.

Replication and expression of constructed plasmid chimeras in transformed Escherichia coli--a review

EcoRI restriction-endonuclease-generated fragments of bacterial plasmids isolated from Staphylococcus aureus or Escherichia coli, or of amplified DNA coding for the 18S and 28S ribosomal RNA of Xenopus laevis, have been linked to the pSC101 plasmid replicon and introduced into E. coli by transformation. The constructed plasmid chimeras can be cloned as stable replicons in E. coli, where they synthesize RNA and/or protein products specified by their component genes.

Ribosomal DNA in different members of a family of green algae (Chlorophyta, Dasycladaceae): an electron microscopisal study

Active cistrons and non-transcribed spacers of rDNA were made visible in spread preparations of nucleolar material from different species of the green alga family Dasycladaceae (Chlorophyta). The data observed show a difference in length in transcribed rDNA regions between Acetabularia peniculus Solms-Laubach, Acetabularia dentata Solms-Laubach on the one hand and Acetabularia ryukyuensis Okamura et Yamada, Dasycladus clavaeformis J. Agardh, Cymopolia van bosseae Solms-Laubach and Batophora oerstedii J. Agardh on the other: The large size difference between spacer intercepts of different species is very conspicuous. While the Acetabularia species have long non-transcribed spacers they are very short or even not observable in the other Dasycladaceen species studied. Peculiarities found in rDNA include extra long spacers between cistrons, single extra long cistrons together with rDNA cistrons on the same strand and rDNA-sized cistrons alternately arranged on one strand with larger sized cistrons. In spite of extensive searching, inversions were never found in spread nucleolar material. However, they were frequent in spread material of whole nuclei.

Morphology of nucleolar cistrons in a plant cell, Acetabularia mediterranea

The structural organization of transcriptionally active DNA that contains cistrons for precursor molecules of ribosomal RNA is described in positively stained spread preparations from nuclei and nucleoli isolated from the green alga, Acetabularia mediterranea Lmx. These nuclei contain large aggregates of nucleolar subunits in which fibril-covered regions, the putative active cistrons for precursors of ribosomal RNA, alternate with fibril-free intercepts, the "spacers." The length distribution of the different intercepts of this DNA is given, and the pattern is compared with those shown in animal cell systems. The data are discussed in relation to problems of transcription and of amplification of ribosomal RNA genes.

A small number of cistrons for ribosomal RNA in the germinal nucleus of a eukaryote, Tetrahymena pyriformis

The percentage of DNA complementary to 25S and 17S rRNA has been determined for both the macro- and micronucleus of the ciliated protozoan, Tetrahymena pyriformis. Saturation levels obtained by DNA.RNA hybridization indicate that approximately 200 copies of the gene for rRNA per haploid genome were present in macronuclei. The saturation level obtained with DNA extracted from isolated micronuclei was only 5-10% of the level obtained with DNA from macronuclei. After correction for contamination of micronuclear DNA by DNA from macronuclei, only a few copies (possibly only 1) of the gene for rRNA are estimated to be present in micronuclei. Micronuclei are germinal nuclei. Macronuclei serve as somatic nuclei during vegetative growth but are destroyed every sexual generation and are reformed from products of meiosis, fertilization, and division of the micronuclei. Thus, the hybridization data suggest that the gene for rRNA must be amplified during macronuclear formation with each sexual generation. These observations also demonstrate that the multiple copies of a repeated gene in a somatic nucleus of a eukaryote can be generated from a small number of copies of that gene in a germinal nucleus.

Under-replication of ribosomal cistrons in polytene chromosomes of Rhynchosciara

DNA preparations obtained from several tissues of Rhynchosciara americana and two related species, R. milleri and R. papaveroi, were hybridized to R. americana rRNA. The percentage of hybridization was found to be higher in tissues with low polyteny than in tissues with high polyteny, suggesting a relationship between the amount of rDNA and the tissue polyteny. This could be explained by under-replication of ribosomal cistrons in polytene cells, such as those from the salivary gland. Only slight tissue-dependent changes in the percentages of hybridization can be observed in heterologous hybridization using Xenopus laevis rRNA. The possibility that these experiments could not detect differences in the amount of ribosomal cistrons among tissues is discussed. The female:male ratio for the percentages of hybridization in the salivary gland of R. americana agrees with the results obtained by in situ hybridization experiments (16, 17) which have shown that the rRNA cistrons are distributed among chromosomes other than chromosome X.

Replication and transcription of eukaryotic DNA in Escherichia coli

Fragments of amplified Xenopus laevis DNA, coding for 18S and 28S ribosomal RNA and generated by EcoRI restriction endonuclease, have been linked in vitro to the bacterial plasmid pSC101; and the recombinant molecular species have been introduced into E. coli by transformation. These recombinant plasmids, containing both eukaryotic and prokaryotic DNA, replicate stably in E. coli. RNA isolated from E. coli minicells harboring the plasmids hybridizes to amplified X. laevis rDNA.

Discontinuous variability, in the form of a geometric progression, of albumin production in hepatoma and hybrid cells

A clonal rat hepatoma cell line (Fu5) produces rat serum albumin at a constant rate over at least 3 months of continuous cultivation. Ten hybrid cell clones derived from the fusion of Fu5 cells and mouse fibroblasts, as well as 14 hepatoma subclones of Fu5 cells, all produce albumin but at different rates, ranging from about 0.09 to 36.7 mug/mg of protein per 72 hr. Despite this variability in albumin production, the distribution of clones is not random but discontinuous, with both hepatoma and hybrid clones clustering around discrete values that can be fitted to the geometric progression: a, a( radical2)(1), a( radical2)(2)..... a( radical2)(n). The values of the majority of clones fall into alternate members of this geometric progression, which differ by a factor of 2. Hepatoma subclones with indistinguishable karyotypes differ in level of albumin production by as much as 4-fold. In contrast to hepatoma clones, albumin production in hybrid clones decreases with increasing cell generations. A survey of 28 enzymes of different hepatomas reveals a large variability in enzyme levels which, for most enzymes, can be arranged into classes that form a geometric progression. The apparent widespread nature of this discontinuous phenotypic variability suggests that it may reflect a basic mechanism of control of gene expression in animal cells.

Control of 5S RNA synthesis during early development of anucleolate and partial nucleolate mutants of Xenopus laevis

Ribosomes of all eukaryotes contain a single molecule of 5S, 18S, and 28S RNA. In the frog Xenopus laevis the genes which code for 18S and 28S RNA are located in the nucleolar organizer, but these genes are not linked to the 5S RNA genes. Therefore the synthesis of the three ribosomal RNAs provides a model system for studying interchromosomal aspects of gene regulation. In order to determine if the synthesis of the three ribosomal RNAs are interdependent, the relative rate of 5S RNA synthesis was measured in anucleolate mutants (o/o), which do not synthesize any 18S or 28S RNA, and in partial nucleolate mutants (p(l-1)/o), which synthesize 18S and 28S RNA at 25% of the normal rate. Since the o/o and p(l-1)/o mutants have a complete and partial deletion of 18S and 28S RNA genes respectively, but the normal number of 5S RNA genes, they provide a unique system in which to study the dependence of 5S RNA synthesis on the synthesis of 18S and 28S RNA. Total RNA was extracted from embryos labeled during different stages of development and analyzed by polyacrylamide gel electrophoresis. Quite unexpectedly it was found that 5S RNA synthesis in o/o and p(l-1)/o mutants proceeds at the same rate as it does in normal embryos. Furthermore, 5S RNA synthesis is initiated normally at gastrulation in o/o mutants in the complete absence of 18S and 28S RNA synthesis.

Crossing-over between X AND Y chromosomes during ribosomal DNA magnification in Drosophila melanogaster

In genetic combinations undergoing ribosomal DNA magnification, the frequency of crossing-over between X and Y chromosomes is increased at least 20-fold above that in similar combinations not undergoing magnification. Such recombination occurs at the ribosomal DNA level. The data are consistent with a model where extra copies of ribosomal DNA are formed which, after circularization, are integrated into the chromosome.

Ribonucleic acid synthesis in chloroplasts

Chloroplasts isolated from young spinach leaves incorporate [(3)H]uridine into RNA. This incorporation shows an absolute requirement for light and does not occur in lysed chloroplasts. Fractionation by polyacrylamide-gel electrophoresis of the RNA synthesized in vitro reveals a major discrete product of molecular weight 2.7x10(6) and two minor products of molecular weight 1.2x10(6) and 0.47x10(6). These discrete products are super-imposed on a background of polydisperse RNA. The incorporation of (32)P(i) into chloroplast rRNA species (mol.wt. 1.05x10(6) and 0.56x10(6)) in excised spinach leaves proceeds after a distinct lag period compared with the incorporation into cytoplasmic rRNA species (mol.wt. 1.34x10(6) and 0.7x10(6)). Incorporation of (32)P(i) into chloroplast RNA species of molecular weight 2.7x10(6), 1.2x10(6), 0.65x10(6) and 0.47x10(6) proceeds without such a time-lag. The kinetics of labelling of the individual RNA components is consistent with the rapidly labelled RNA species of molecular weight 1.2x10(6) and 0.65x10(6) being precursors to the more slowly labelled rRNA species of molecular weight 1.05x10(6) and 0.56x10(6) respectively.

DNA Complementary to Ribosomal RNA: Relation between Genomic Proportion and Ploidy

Ten Nicotiana species were assayed for the proportion of DNA that is complementary to ribosomal RNA. This proportion varies from 0.27 to 0.9 percent, with tetraploid species having lower values than the diploid species. The tetraploid species have about twice as much DNA per cell as do diploid species. Thus, the absolute number of genes for ribosomal RNA varies less than the proportion of complementary DNA. Further, the number of genes for the RNA in 80S ribosomes varies less among species than does that for the RNA in 70S ribosomes. The data indicate that loss of DNA complementary to ribosomal RNA is associated with tetraploidy in the genus Nicotiana.