The size and the location of the ribosomal RNA segments in ribosomal precursor RNA of yeast

Heat-sensitive mutant strain of Neurospora crassa, 4M(t), conditionally defective in 25S ribosomal ribonucleic acid production

A heat-sensitive mutant strain of Neurospora crassa, 4M(t), was studied in an attempt to define its molecular lesion. The mutant strain is inhibited in conidial germination and mycelial extension at the nonpermissive temperature (37 degrees C). Macromolecular synthesis studies showed that both ribonucleic acid (RNA) and protein syntheses are inhibited when 4-h cultures are shifted from 20 to 37 degrees C. Density gradient analysis of ribosomal subunits made at 37 degrees C indicated that strain 4M(t) is deficient in the accumulation of 60S ribosomal subunits in that the ratio of 60S/37S subunits was 0.29:1 compared with 1.6:1 for the parental strain. This phenotype was shown to be the result of a slow rate of processing of, and a deficiency in the amount of, the immediate precursor to 25S ribosomal RNA (the large RNA of the 60S subunit) in the sequence of events constituting the production of mature ribosomal RNAs from the primary transcript of the ribosomal deoxyribonucleic acid, the precursor ribosomal RNA molecule. Analysis of polysomes suggested that the heat-sensitive gene product might function in both the assembly and the function of the 60S ribosomal subunit, since there was a smaller proportion of newly made 60S subunits synthesized at 37 degrees C in the polysome region of the gradients than in the monosome-plus-subunit region. The ribosomal RNA processing defect is apparently responsible for the observed defects in germination and macromolecular synthesis at 37 degrees C, but the precise molecular lesion is not known. On the basis of these results, the heat-sensitive mutant allele in the 4M(t) strain is considered to define the rip1 (ribosome production) gene locus.

Syntheses of rRNA, 5.8S, 5S and tRNA are inhibited equally by 8-methoxypsoralen phototreatment of Tetrahymena thermophila

Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose dependent equal inhibition of the synthesis of rRNA, 5.8S, 5S and tRNA. Similar results were obtained with 3-carbethoxy-8-methoxypsoralen which predominantly forms DNA mono-adducts. In contrast the synthesis of tRNA in T. thermophila was much less sensitive than that of rRNA, 5.8S and 5S RNA to treatment with short wavelength ultraviolet irradiation (UVB, lambda approximately 254 nm). These results are interpreted in favor of a mechanism by which psoralen-DNA adducts (crosslinks much greater than monoadducts) inhibit RNA transcription initiation (in contrast to UVB which causes premature chain termination). Furthermore it is argued that RNA synthesis is regulated in equally sized domains regardless of the gene-size.

Inhibition of ribosomal RNA synthesis in yeast by ionizing radiations

The effects of ionizing radiations on transcriptional activity were studied in the diploid yeast Saccharomyces cerevisiae. As experimental indicator the synthesis of ribosomal RNA (r-RNA) was measured for 1 h after exposure of cells to gamma-rays, X-rays or alpha-particles. gamma- or X-ray induced transcription inhibition was always found to decrease exponentially with dose. D0 values of 2150 or 1950 Gy were determined in wild-type cells, corresponding to a mean energy of about 60 eV per r-RNA gene. The finding of differential sensitivities of the two high molecular-weight r-RNA species which are cotranscribed from r-DNA is compatible with the existence of a transcription terminating mechanism. Cells from a mutant strain (rad-9), radiation sensitive with respect to colony forming ability, show an approximately equal sensitivity for transcription inhibition compared to the wild-type (D0 (2095) = 2400 Gy). Inactivation of r-RNA synthesis in cells exposed to alpha-particles at room-temperature showed a decreased sensitivity with higher particle fluences ('resistant tail'). This phenomenon, however, was drastically reduced if the temperature during irradiation was lowered to 4 degrees C, and was completely abolished when dried cells were used. The results may be explained by the presence of recovery processes in vegetative cells during prolonged exposures to alpha-particles at room temperature. An inactivation cross-section for alpha-particle induced transcription inhibition of about 0.02 micron 2 can be derived from the experimental data. When comparing this value with the estimated target volume, it appears that no single genes but the whole cluster of about 120 r-RNA genes on each of the chromosomes XII in the diploid cell may be inactivated by a single alpha-particle.

Inhibition of induced ornithine decarboxylase activity in Chinese hamster cells by gamma radiation, far ultraviolet light and psoralen plus near-ultraviolet light: a comparative study

Inhibition by radiation of the transcriptionally controlled induction of ornithine decarboxylase (ODC) was studied in plateau-phase Chinese hamster cells. The effects of gamma radiation, far ultraviolet (254nm, UV-C) light and psoralen plus near-U.V. light (360nm, PUV-A) were compared. Increasing doses of all three treatments caused an exponential decrease in the capacity for ODC induction. This was preceded by a large shoulder region in the case of PUV-A. There was no shoulder for gamma radiation and possibly none or a small one for UV-C. When compared on the basis of cell killing UV-C is 13 times more efficient in inhibiting ODC induction than PUV-A and 69 times more than gamma radiation. The doses required to produce an inactivating hit for inhibition of ODC induction (D0) are 106 krad for gamma radiation, 2400 J m-2 for PUV-A and 14 J m-2 for UV-C. These doses produce about one gamma ray lesion, one psoralen adduct and one pyrimidine dimer in the structural gene of ODC. However, the number of lesions per transcription unit may be up to 10, depending on the contribution to the effect by lesions in transcribed and non-transcribed spacers and introns. Thus, assuming that most of the inhibition is due to effects on RNA synthesis, the various DNA lesions appear to have a similar efficiency in terminating RNA transcription, in spite of their greatly different efficiency in cell killing.

Heat-sensitive mutant strain of Neurospora crassa, 4M(t), conditionally defective in 25S ribosomal ribonucleic acid production

A heat-sensitive mutant strain of Neurospora crassa, 4M(t), was studied in an attempt to define its molecular lesion. The mutant strain is inhibited in conidial germination and mycelial extension at the nonpermissive temperature (37 degrees C). Macromolecular synthesis studies showed that both ribonucleic acid (RNA) and protein syntheses are inhibited when 4-h cultures are shifted from 20 to 37 degrees C. Density gradient analysis of ribosomal subunits made at 37 degrees C indicated that strain 4M(t) is deficient in the accumulation of 60S ribosomal subunits in that the ratio of 60S/37S subunits was 0.29:1 compared with 1.6:1 for the parental strain. This phenotype was shown to be the result of a slow rate of processing of, and a deficiency in the amount of, the immediate precursor to 25S ribosomal RNA (the large RNA of the 60S subunit) in the sequence of events constituting the production of mature ribosomal RNAs from the primary transcript of the ribosomal deoxyribonucleic acid, the precursor ribosomal RNA molecule. Analysis of polysomes suggested that the heat-sensitive gene product might function in both the assembly and the function of the 60S ribosomal subunit, since there was a smaller proportion of newly made 60S subunits synthesized at 37 degrees C in the polysome region of the gradients than in the monosome-plus-subunit region. The ribosomal RNA processing defect is apparently responsible for the observed defects in germination and macromolecular synthesis at 37 degrees C, but the precise molecular lesion is not known. On the basis of these results, the heat-sensitive mutant allele in the 4M(t) strain is considered to define the rip1 (ribosome production) gene locus.

The transcription termination site of the ribosomal RNA operon in yeast

The site at which transcription of the ribosomal RNA operon in yeast is terminated was precisely localized. First, the exact position of the 3' end of the 26S rRNA gene was mapped on the rDNA on the basis of RNA- and DNA sequence data. Next, the 3' terminus of the primary transcript, 37S precursor rRNA, was established by hybridization experiments and sequence analysis. 37S pre-rRNA appears to be just 7 nucleotides longer at its 3' end than 26S rRNA. The non-coding strand around the termination site is extremely T-rich: 15 out of 18 nucleotides are T-residues. An extensive dyad symmetry is present in the sequence downstream from the termination site; a possible role of this structure in the regulation of transcription termination is discussed. The 3'-terminal 110 nucleotides of yeast 26S rRNA have approx. 50% and 60% homology with the corresponding regions of E. coli 23S rRNA and Xenopus laevis 28S rRNA, respectively.

Some characteristics of processing sites in ribosomal precursor RNA of yeast

The DNA sequences of the intergenic region between the 17S and 5.8S rRNA genes of the ribosomal RNA operon in yeast has been determined. In this region the 37S ribosomal precursor RNA is specifically cleaved at a number of sites in the course of the maturation process. The exact position of these processing sites has been established by sequence analysis of the terminal fragments of the respective RNA species. There appears to be no significant complementarity between the sequences surrounding the two termini of the 18S secondary precursor RNA nor between those surrounding the two termini of 17S mature rRNA. This finding implies that the processing of yeast 37S ribosomal precursor RNA is not directed by a double-strand specific ribonuclease previously shown to be involved in the processing of E. coli ribosomal precursor RNA [see Refs 1,2]. The processing sites of yeast ribosomal precursor RNA described in the present paper are all flanked at one side by a very [A+T]-rich sequence. In addition, sequence repeats are found around the processing sites in this precursor RNA. Finally, sequence homologies are present at the 3'-termini [6 nucleotides] and the 5'-termini [13 nucleotides] of a number of mature rRNA products and intermediate ribosomal RNA precursors. These structural features are discussed in terms of possible recognition sites for the processing enzymes.

Impairment of RNA synthesis and its recovery in angelicin photosensitized mammalian cells. A probe for DNA damage and repair

The template activity of DNA for ribosomal RNA transcription has been investigated in monkey kidney CV-1 cells after angelicin photosensitization in order to monitor the induction of lesions in the DNA and their possible subsequent disappearance, i.e. repair. Separate confluent cultures were submitted to a single angelicin treatment at different time intervals before incubation with [3H]uridine. The labeled RNA prepared from whole cells was analysed by polyacrylamide-agarose gel electrophoresis. The results indicate that: Angelicin monoadditions on DNA constitute transcription-terminating lesions which depress overall RNA synthesis, give rise to shortened RNA chains and modify the expression of transcriptional linked genes. CV-1 cells are able to repair, at least partially, the induced transcription-terminating lesions and progressively recover RNA synthesis with a reversion of the initially observed modifications. The repair seems to be independent of semiconservative DNA synthesis since fluorodeoxyuridine does not affect the recovery of RNA transcription. The present work also confirms the arrangement of rRNA genes in tandem behind a common operator in the order 18--28 S as previously determined in the same cells by a radiological mapping technique and reinforces the potential applicability of transcription analysis to the study of repair processes operating on physically or chemically induced damage in DNA.

Genetic organization of the ribosomal transcription units of the yeast Saccharomyces carlsbergensis

The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S. 73, 2294-2298). Plasmid pBR 322, the molecular weight of which is known, was used as a standard for converting contour length of double-stranded DNA into molecular weight. The 140 yeast RTUs were found to be arrayed in tandem repeats, each repeat containing at most 0.4 X 10(6) D (about 6% of the length of the RTU) of non-transcribed spacer DNA. The repeats, in turn, are arranged in a number of clusters separated by much longer stretches of non-ribosomal DNA.

Synthesis of inducible enzymes in irradiated yeast cells. Ultraviolet effects on transcription and the influence of recovery processes

The induced synthesis of arginase was measured in several yeast strains after ultraviolet light irradiation. There was an exponential dose-related reduction which was the same in all cell lines tested. This sensitivity is compatible with the size of the arginase structural gene if it is assumed that one pyrimidine dimer suffices for blocking transcription. The ultraviolet-induced synthesis inhibition is susceptible to photoreactivation and liquid holding recovery. The latter process is absent in a rad2 mutant and reduced in a rad9 mutant.

Transcriptional units for ribosomal proteins in yeast

The effects of ultraviolet irradiation on the rates of synthesis of individual ribosomal proteins in yeast were examined and compared with the ultraviolet sensitivities of the synthesis of other yeast proteins. It was found that the synthesis of yeast ribosomal proteins is much more sensitive to ultraviolet irradiation than that of other yeast cellular proteins. Taking into account the half-life of yeast mRNA, the results obtained indicate that the genes coding for ribosomal proteins form part of long transcriptional units, which are much longer than the DNA stretch needed to code for a ribosomal protein of average molecular weight. Saturation hybridization of total poly(A)-containing mRNA with yeast nuclear DNA revealed that as much as 30% of DNA is complementary to yeast mRNA. Thus, the primary transcript of a protein gene on the average is about 1.7 times the length of the actual messenger. On the basis of the various experimental data we suggest a clustering of the yeast ribosomal protein genes in a number of common transcriptional units.

Studies of the UV-sensitivity of virus-specific RNA synthesis in cells infected or transformed by adenovirus 5 and SV 40

The effect of UV-irradiation on host and virus-specific RNA synthesis in cells infected or transformed by tumor viruses (Ad 5 and SV 40) was studied. It was found that the synthesis of host and Ad 5 RNA in infected KB cells was almost euqally inhibited upon UV-irradiation; the transcription of the EcoRI produced fragements--fragment B was inhibited to a greater extent than fragment A, suggesting that the transcription of the whole Ad 5 genome starts from the left side. The transcription of viral sequences in transformed cells, on the other hand, was more resistant to UV-irradiation than the transcription of the host ones. The results obtained suggest that the small size of the virus transcriptions, or their location at the beginning of large host transcriptions, may be responsible for the observed data.

Ultraviolet-induced inhibition of ribosomal RNA synthesis in yeast strains differing in radiation sensitivities

The ultraviolet-induced inhibition of rRNA synthesis has been measured during the first hour after irradiation for stationary yeast cells differing in radiation sensitivity. rRNA was isolated and separated on an agarose-polyacrylamide gel. The wild type and a mutant which is possibly defective in recombinational repair show a sigmoidal inhibition curve, an excision-deficient mutant shows an exponential one. From these curves it is deduced that a pyrimidine dimer acts as a transcription terminating lesion as was shown for bacteria. During the first hour after irradiation the excision repair system decreases the number of transcription terminating lesions by 22% in the wild type and 25% in the mutant defective in recombinational repair. An approximation of the repair efficiency gives a value of 7500-10 000 transcription terminating lesions per cell being removed during the first hour after irradiation by excision. Ultraviolet-induced lesions of this kind can partially be removed by photoreactivation. The inhibition coefficients are the same for 26 S and 18 S rRNA in stationary cells, whereas exponentially growing cells show different inhibition coefficients for 26 S and 18 S rRNA leading to the suggestion that the processing of the ribosomal precursor RNA is different in stationary and exponentially growing cells.

Inhibition and recovery of ribosomal RNA synthesis in ultraviolet-irradiation mammalian cells

The effects of ultravilet light on rRNA synthesis were studied in stationary, monkey kidney CV-1 cells. Separate cultures were irradiated with a single ultraviolet dose of up to 525 erg/mm2 at different time intervals before incubation with [3H]uridine. The labeled RNA prepared from whole cells was analyzed by polyacrylamide-agarose gel electrophoresis. In cells ultraviolet irradiated 30 min before transcription analysis, the rate of total RNA and of 45 S RNA synthesis are depressed whereas a synthesis of unusual RNAs, shorter than 45 S RNA, appears. The rates of 28 S and of 18 S RNA synthesis decrease as a function of ultravilet dose and at the same time the ratio of 18 S to 28 S RNA increases. These results are consistent with the idea of a premature RNA chain termination on ultraviolet-damaged DNA. The ultraviolet-induced alterations of transcription disappear progressively with time after irradiation: the rates of total RNA and of 45 S RNA synthesis increase whereas the synthesis of unusual RNAs decreases; in parallel the rates of 28 S and 18 S RNA synthesis recover with a shift of the 18 S to 28 S RNA ratio toward the normal value 1 : 1, probably as a direct consequence of the repair of ultraviolet-induced lesions in the DNA. The kinetics of recovery are dose dependent and are comparable to those of the excision-repair of DNA photoproducts as measured by unscheduled DNA synthesis in ultraviolet-irradiated CV-1 cells. Fluorodeoxyuridine does not affect recovery. The data also show that in CV-1 cells, rRNA genes are arranged after their promotor in the order 18 S rRNA -- 28 S rRNA.

Topographical analysis of yeast ribosomal DNA by cleavage with restriction endonucleases

Yeast ribosomal DNA (rDNA) was digested with the restriction enzymes Hind III, Hind II and a mixture of Hind II and Hind III. The cleavage products were analyzed by electrophoresis on 1.5% agarose gels. Several distinct bands could be observed, which are derived from the redundant ribosomal transcription units. They are superimposed on a rather broad smear of background DNA, representing the heterogenous 'spacer' sequences. From the restriction maps, together with data obtained by partial digestion, a physical map for the ribosomal transcription unit in yeast could be constructed.

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.

Structure and transcription specificity of yeast RNA polymerase A

DNA-dependent RNA polymerase A (Nucleosidetriphosphate: RNA nucleotidyltransferase, EC 2.7.7.6) was isolated from whole yeast cells and purified to a nearly homogeneous state. The subunit structure as well as the transcription specificity of the purified enzyme were investigated. Polyacrylamide gel electrophoresis under denaturating conditions revealed that yeast polymerase A is made up of two large subunits having mol. wts of 190 000 and 135 000, and five smaller subunits with mol. wts of 54 000, 44 000, 35 000, 25 000 and 16 000, respectively. The molar ratios of all these polypeptides were found to be about unity. The transcription specificity of yeast polymerase A was tested using homologous nuclear DNA as a template. The in vitro synthesized RNA was characterized by determining its degree of self-complementarity and its ability to compete with purified ribosomal RNA in hybridization experiments. It was found that yeast polymerase A is capable of a highly selective transcription in vitro of the rRNA cistrons, provided DNA of high integrity is used as a template.