Synthesis of amplified DNA that codes for ribosomal RNA

Ribosomal RNA genes of Neurospora crassa: multiple copies and specificities

Ribosomal RNA genes were isolated from the germinated conidial and mycelial cells of N. crassa by repeated cycles of 3H-DNA:rRNA reactions followed by hydroxyapatite chromatography. Specificity of multiple copies of those rDNAs with respect to N. crassa cell types was studied. The fraction of N. crassa germinated conidial in vitro labelled 3H-DNA recovered in the presence of rRNA isolated from the same cell type was about 2.2%, when compared with approximately 1.2% rDNAs obtained in mycelial cells. These isolated rDNAs reacted specifically to 26S and 17S rRNAs of eukaryotic (N. crassa) organisms and did not react with 4S tRNAs. rRNA:rDNA reassociation kinetics studies indicate that 90% of the rRNA genes were homogeneous and not identical with the other 10% rRNA genes isolated from N. crassa mycelia. These studies suggest that the possible heterogeneity of rDNA sequences of N. crassa cannot be attributed to inclusion of any tDNA sequences as has been shown in the heterogeneity of rDNA sequences of the bacterium Escherichia coli. The heterogeneity of multiple copies of N. crassa rDNAs could be due to differences in internal or external spacer regions of N. crassa rRNA genes.

Possible role of RNA-dependent DNA-polymerase in early stages of evolution

The tDNA cistrons have permuted sequences of triplets corresponding to anti-codons in tRNA at specific regions in their sequences. We invoke reverse transcription for the generation of such sequences in the genome during early stages of evolution. Making the assumption that a single tDNA cistron, in a genome might have come into existence by an 'accident', after transcription, tRNA is expected to fold into a three-dimensional shape analogous to the contemporary tRNA, where the anti-codon triplet bases are sticking out well-exposed for chemical mutagens. The mutated tRNAs would have been reverse-transcribed into the genome by crude analogs of now-known reverse-transcriptases. The back and forth process of transcription and reverse transcription would give rise to all the tDNA cistrons with the required anti-codons. This process may act as an important feedback mechanism for the efficient progress of evolution.

Circular ribosomal DNA and ribosomal DNA: replication in somatic amphibian cells

Pulse labelled rDNA from cultured somatic cells of Xenopus laevis was examined by electron microscope autoradiography. The pattern of replication closely resembles that of bulk chromosomal DNA and differs considerably from rDNA synthesis during amplification in the oocyte. - About 0.15% of the rDNA molecules in the purified preparations were circular. The presence of interlocked circles of equal size indicates that the circles are not in vitro cyclization artefacts, but may represent free rRNA genes. A low frequency of circles was also seen in Xenopus blood rDNA. Their stability in high concentration of formamide suggests that they too did not arise after DNA extraction.

Differential gene activity and segregation of cell lines: an attempt at a molecular interpretation of the primary events of embryonic development

The study of differentiation is concerned with the analysis of the processes responsible for ‘the cellular changes in macromolecular synthesis and composition, patterned in time and space and resulting in specialized functions, forms and organization’ (Moscona, 1973).

Lymphocyte stimualtion by a mammary carcinoma assoicated glycoprotein

A glycoprotein was isolated from 3M KCl extracts of mammary carcinoma. Addition of an optimal amount of the carcinoma associated glycoprotein induces proliferation of both peripheral blood lymphocytes from normal donors and from patients with mammary carcinoma. RNA-dependent DNA-polymerase levels were found to be markedly increased in glycoprotein-untreated lymphocytes from patients with mammary carcinoma and in glycoprotein-treated lymphocytes of both normal donors and tumor-bearing patients. A factor ("Blocking Factor") was eluted at pH 3.1 from the cell membrane of the mammary carcinoma cells. Addition of an optimal amount of this factor inhibits the glycoprotein induced stimulation of the RNA-dependent DNA-polymerase activity in glycoprotein-treated lymphocytes of both normal donors and tumor-bearing patients.

The three-dimensional organization of the amplified ribosomal DNA complex in Acheta

The major chromomere of pachytene chromosome 6 in the oocytes of Acheta (Orthoptera) is a region of amplification for ribosomal RNA cistrons (28 S and 18 S). This chromomere was isolated and studied with the scanning electron microscope. It has an outer shell that is smooth at early stages but divides into polygonal plates as indentations appear on its surface. These indentations increase in number as the DNA copies separate from each other and as the ribosomal RNA synthesis progresses. The vertices of the polygonal plates coincide with the positions at which the DNA copies reach the surface of the chromomere during their "puffing" process. The combined information gained from scanning and transmission electron microscopy, DNA measurements, DNA.RNA hybridization, and cytochemistry, leads to a three-dimensional picture of the organization of the amplified ribosomal DNA in its association with ribosomal RNA and protein.

Estimation of the number of genes coding for the constant part of the mouse immunoglobulin kappa light chain

As previously shown, purified 14S RNA of mouse myeloma MOPC-41 forms a single peak on sucrose gradients and gel electrophoresis and codes for a single polypeptide chain, the immunoglobulin light chain produced by the same myeloma in vivo. This 14S mRNA was used for the enzymatic synthesis of DNA (cDNA) which is complementary to the RNA template. A DNA fraction was isolated which has an average size of 300 nucleotides. Kinetic studies of the hybridization of the 14S RNA with the cDNA indicate that about 40% of the RNA consists of a single RNA sequence. From the size of the cDNA fraction and from the direction of DNA synthesis, it can be concluded that the cDNA includes the sequence complementary to the constant region of light chain mRNA. This radioactive cDNA was used for DNA.DNA reannealing experiments with unlabeled DNA from mouse liver or myeloma tumor in 3 x 10(6)-fold excess. This allowed the determination of the number of copies in the mouse genome of those sequences represented in the cDNA. The data show no significant reiteration in either liver or myeloma DNA and suggest that the gene coding for the constant part of immunoglobins is present in the haploid genome in one to five copies. Furthermore, this gene is not "amplified" in nuclear DNA of myeloma plasmocytes.

The amplification of ribosomal RNA genes involves a rolling circle intermediate

During the development of Xenopus oocytes there is a special DNA synthesis that leads to a thousandfold amplification of the genes that code for ribosomal RNA. We have used the electron microscope to study this process. Our primary observation is the presence of ribosomal DNA in rolling-circle intermediates at the time of amplification. We believe that these intermediates are involved in the amplification process, and as such offer the first example of the involvement of a rolling circle in the replication of eukaryotic DNA.

Stimulated normal human lymphocytes contain a ribonuclease-sensitive DNA polymerase distinct from viral RNA-directed DNA polymerase

Ribonuclease-sensitive DNA synthesis is demonstrated in a cytoplasmic particulate fraction of normal human blood lymphocytes stimulated with phytohemagglutinin, but not in unstimulated lymphocytes. DNA polymerase purified from this fraction does not transcribe the heteropolymeric regions of 70S RNA from RNA tumor viruses, thus distinguishing this enzyme from the RNA-directed DNA polymerase (reverse transcriptase) found in oncogenic RNA viruses and human leukemic cells.

Coupling of replication to transcription in vitro

In a coupled system consisting of RNA polymerase and DNA polymerase I of Escherichia coli, the four deoxyribo- and the four ribonucleoside triphosphates, and DNA of bacteriophage f1 as template, DNA synthesis depends on the concomitant synthesis of RNA. Over a wide range of concentrations of the two polymerases, RNA synthesis was unaffected by the simultaneous synthesis of DNA, whereas the rate of DNA synthesis depended on the level of RNA synthesis. In the coupled reaction, RNA synthesis starts immediately at a high rate, which subsequently decreases, whereas DNA synthesis starts after a lag and its rate increases as the reaction proceeds. Upon addition of rifampicin, the rate of RNA synthesis falls abruptly, while that of DNA declines only gradually. The base composition of the DNA synthesized in the coupled reaction is complementary to that of f1 DNA template. It is suggested that the RNA synthesized by the RNA polymerase serves as a primer rather than as a template for the DNA polymerase.

[On the role of RNA in gene amplification]

A complex of ribosomal DNA with RNA has been isolated from ovaries of metamorphosing tadpoles of Xenopus laevis. The complex is disrupted by treatments that destroy hydrogen bonds, and the sedimentation of the DNA within the complex is sensitive to RNase. We suggest that the RNA-ribosomal DNA complex is an intermediate in the synthesis of amplified ribosomal DNA and that the RNA is a template. In addition, in a preliminary attempt to mimic the amplification process in vitro, we have demonstrated the use of this RNA from the complex as a template for DNA synthesis by a DNA polymerase isolated from ovaries of Xenopus.

An RNA-DNA complex intermediate in ribosomal gene amplification

An RNA-ribosomal DNA complex can be isolated from ovaries of Xenopus laevis incubated in vitro during the amplification stage. A part of the RNA present in the complex is resistent to RNase but becomes completely sensitive after heat denaturation, a treatment that also allows the separation of the RNA from the DNA. The size of the RNA-ribosomal DNA complex is strongly reduced after treatment with RNase. A small fraction of the RNA present in the complex is complementary to the spacer region of the strand, which is not transcribed in vivo into cytoplasmic 18S and 28S ribosomal RNA.

Endogenous RNA-directed DNA polymerase activity in uninfected chicken embryos

Early chicken embryos that are either positive or negative for group-specific antigens of avian leukosis viruses contained endogenous RNA-directed DNA polymerase activity. This endogenous DNA polymerase activity was not increased after mixture of soluble DNA polymerases isolated from chicken embryos with disrupted chicken embryo cells. The endogenous activity was resistant to treatment with deoxyribonuclease, and the initial rate of DNA synthesis was partially resistant to actinomycin D. In contrast, over 90% of the endogenous polymerase activity was destroyed by ribonuclease in medium with high salt concentration. The DNA product of the endogenous DNA polymerase activity from chicken embryos did not hybridize with RNA of Rous sarcoma virus or reticuloendotheliosis virus, whereas about 40% of this DNA product hybridized with the RNA from the same chicken-cell fraction. Antibody against DNA polymerase of avian myeloblastosis virus did not neutralize the chicken endogenous DNA polymerase activity. These results demonstrate that uninfected chicken embryo cells contain endogenous RNA-directed DNA polymerase activity that is not derived from avian leukosis or reticuloendotheliosis viruses.

Action of DNA polymerase I of Escherichia coli with DNA-RNA hybrids as templates

Experiments indicating the ability of the ribo strand of a DNA-RNA template to guide polydeoxynucleotide synthesis by highly purified DNA polymerase I of E. coli (EC 2.7.7.7) are presented. With poly(rA).poly(dT) as template, poly(dT) is formed with a high efficiency, but almost no poly(dA). The specific activity of the enzyme, when tested with this template under suitable conditions, is eight times greater than that found for the poly(dA-dT) template. Single-stranded DNA fractions, with no template activity for DNA polymerase, are converted to efficient templates after their transcription by RNA polymerase. A concerted polymerization reaction, in which the action of DNA polymerase is dependent on that of RNA polymerase, can also be demonstrated with synthetic polydeoxynucleotides and single-stranded fractions of denatured DNA as templates.

RNA-dependent DNA polymerase: possible role in the amplification of ribosomal DNA in Xenopus oocytes

2',5' - dimethyl - N(4')benzyl - N(4') - [desmethyl]rifampicin, a derivative of rifampicin, is used to acquire autoradiographic evidence that RNA-dependent DNA synthesis is involved in gene amplification during the early oogenesis of Xenopus laevis.