Location of ribosomal RNA cistrons in yeast

The modest beginnings of one genome project

One of the top things on a geneticist's wish list has to be a set of mutants for every gene in their particular organism. Such a set was produced for the yeast, Saccharomyces cerevisiae near the end of the 20th century by a consortium of yeast geneticists. However, the functional genomic analysis of one chromosome, its smallest, had already begun more than 25 years earlier as a project that was designed to define most or all of that chromosome's essential genes by temperature-sensitive lethal mutations. When far fewer than expected genes were uncovered, the relatively new field of molecular cloning enabled us and indeed, the entire community of yeast researchers to approach this problem more definitively. These studies ultimately led to cloning, genomic sequencing, and the production and phenotypic analysis of the entire set of knockout mutations for this model organism as well as a better concept of what defines an essential function, a wish fulfilled that enables this model eukaryote to continue at the forefront of research in modern biology.

The detection of mitotic and meiotic aneuploidy in yeast using a gene dosage selection system

A system is described in which spontaneous and chemically-induced mitotic and meiotic hyperploidy can be assayed in the same diploid culture of Saccharomyces cerevisiae. Monitoring gene dosage changes at two loci on chromosome VIII, the test utilizes a leaky temperature-sensitive allele arg4-8 and low level copper resistance conferred by the single copy allele cup1s. An extra chromosome VIII provides simultaneous increased dosage for both genes, resulting in colonies that are both prototrophic for arginine at 30 degrees C and copper resistant. During mitotic cell divisions in diploids, spontaneous chromosome VIII hyperploids (trisomes and tetrasomes) occur at a frequency of 6.4 x 10(-6) per viable cell. Among ascospores, the spontaneous chromosome VIII disome frequency is 5.5 x 10(-6) per viable spore. The tubulin-binding reagent methyl benzimidazol-2-yl carbamate (MBC) elicits enhanced levels of mitotic and meiotic aneuploidy relative to control levels. The system represents a novel model for examining chromosome behavior during mitosis and meiosis and provides a sensitive and quantifiable procedure for examining chemically induced aneuploidy.

3 micron DNA - an extrachromosomal ribosomal DNA in the yeast Saccharomyces cerevisiae

A new class of extrachromosomal DNA which consists predominantly of covalently closed molecules with lengths around 3 micron, has been detected in Saccharomyces cerevisiae strain 6-1G-P188 from the Peterhof collection. Restriction analysis of the 3 micron DNA as well as of recombinant plasmids carrying HindIII fragments of the 3 micron DNA permitted construction of a physical map of the new extrachromosomal DNA species, and detection of two types differing by one EcoRI restriction site. Molecular hybridization, as well as comparison of the restriction maps, revealed the complete structural identity of the 3 micron DNA with a chromosomal repetitive unit of rDNA containing the genes for 25 S, 18 S, 5.8 S and 5 S rRNAs.

Replication and meiotic transmission of yeast ribosomal RNA genes

The yeast Saccharomyces cerevisiae has approximately 120 genes for the ribosomal RNAs (rDNA) which are organized in tandem within chromosomal DNA. These multiple-copy genes are homogeneous in sequence but can undergo changes in copy number and topology. To determine if these changes reflect unusual features of rDNA metabolism, we have examined both the replication of rDNA in the mitotic cell cycle and the inheritance of rDNA during meiosis. The results indicate that rDNA behaves identically to chromosomal DNA: each rDNA unit is replicated once during the S phase of each cell cycle and each unit is conserved through meiosis. Therefore, the flexibility in copy number and topology of rDNA does not arise from the selective replication of units in each S phase nor by the selective inheritance of units in meiosis.

Evidence that the ribosomal DNA genes of yeast are not on chromosome I

Several workers have reported that most of the ribosomal DNA genes (rDNA) of the yeast Saccharomyces cerevisiae are located on chromosome I. More recently, data indicating that the yeast rDNA genes are located on chromosome XII has been presented. In this report, we present additional evidence indicating that most of the yeast rDNA genes are not on chromosome I. Starting from a diploid yeast strain, we isolated ten strains which were monosomic (2n-1) for chromosome I. We found that each of these ten strains contained two copies of the rDNA-containing chromosome. In addition, we show that the earlier evidence indicating that the yeast rDNA genes were on chromosome I cannot be explained by a difference in the yeast strains which were used in the different experiments.

Radiation-induced mitotic and meiotic aneuploidy in the yeast Saccharomyces cerevisiae

A number of genetic systems are described which in yeast may be used to monitor the induction of chromosome aneuploidy during both mitotic and meiotic cell division. Using these systems we have been able to demonstrate the induction of both monosomic and trisomic cells in mitotically dividing cells and disomic spores in meiotically dividing cells after both UV light and X-ray exposure. The frequency of UV-light-induced monosomic colonies were reduced by post-treatment with photoreactivity light and both UV-light- and X-ray-induced monosomic colonies were reduced by liquid holding post-treatment under non-nutrient conditions. Both responses indicate an involvement of DNA-repair mechanisms in the removal of lesions which may lead to monosomy in yeast. This was further confirmed by the response of an excision-defective yeast strain which showed considerably increased sensitivity to the induction of monosomic colonies by UV-light treatment at low doses. Yeast cultures irradiated at different stages of growth showed variation in their responses to both UV-light and X-rays, cells at the exponential phase of growth show maximum sensitivity to the induction of monosomic colonies at low doses whereas stationary phase cultures showed maximum induction of monosomic colonies at high does. The frequencies of X-ray-induced chromosome aneuploidy during meiosis leading to the production of disomic spores was shown to be dependent upon the stage of meiosis at which the yeast cells were exposed to radiation. Cells which had proceeded beyond the DNA synthetic stage of meiosis were shown to produce disomic spores at considerably lower radiation doses than those cells which had only recently been inoculated into sporulation medium. The results obtained suggest that the yeast sustem may be suitable for the study of sensitivities of the various stages of meiotic cell division to the induction of chromosome aneuploidy after radiation exposure.

Study of a haploid yeast strain with an unusually high rDNA content. III. Unequal meiotic segregation of the gamma-DNA fraction

DNA from different strains of Saccharomyces cerevisiae has been fractionated in preparative Ag+/Cs2-SO4 density gradients. The results show that there are real differences in amount of the nuclear satellite component, the gamma-DNA, from one strain to the other. The gamma-DNA forms a homogeneous dense band that contains all the rDNA, and the amount of gamma-DNA estimated from the gradients can be correlated to amount of rDNA derived from rRNA-DNA hybridizations. By various crossings and sporulations we have obtained diploid and haploid strains with gamma-DNA contents ranging from 7 to 20% of the nuclear DNA. During meiosis, the amount of gamma-DNA appears to segregate in a pattern that indicates unequal crossing over as a possible mechanism for differences in gamma-DNA contents.

Characterization of two types of yeast ribosomal DNA genes

The intragenic organization of ribosomal DNA from a diploid strain of Saccharomyces cerevisiae was analyzed by using recombinant DNA molecules constructed in vitro. Restriction analysis of the yeast ribosomal DNA with the EcoRI restriction enzyme indicated that eight restriction fragments were present in the ribosomal DNA of this strain: X' (1.87 X 10(6) daltons), A (1.77 X 10(6) daltons), B (1.48 X 10(6) daltons), C (1.22 X 10(6) daltons), D (0.39 X 10(6) daltons), E (0.36 X 10(6) daltons), F (0.22 X 10(6) daltons), and G (0.17 X 10(6) daltons). These fragments were distributed between two different types of ribosomal DNA genes, which had the restriction maps: (formula: see text) in which the underlined region shows the repeating unit. The diploid yeast strain contained approximately equal amounts of each of these two types of genes. The analysis of the recombinant DNA molecules also indicated that the yeast ribosomal genes are homogeneous and extensively clustered.

Ribosomal RNA cistrons in Allomyces arbuscula

Bulk and nuclear DNA have been fractionated by preparative neutral CsCl equilibrium density gradient centrifugation and each fraction hybridized to labeled rRNA (25 + 18 S). The cistrons coding for rRNA appeared on the light side of the main peak. Hybridization of the nuclear DNA fractionated by preparative Ag+-Cs2SO4 gradients at different pHs showed that the banding profile did not change as compared to the CsCl pattern. In Hg2+-Cs2SO4 gradients, however, the peak of the fRNA-DNA hybrids shifted on the heavier side of the profile. This indicates that the ribosomal RNA cistrons in Allomyces are A-T-rich. Hybridization with homologous rRNA showed that, at saturation, 3.25% of the DNA is complementary to rRNA. With the genome size of 1.7-10(10) daltons, the multiplicity of rRNA cistrons has been found to be close to 270.

Construction and restriction endonuclease mapping of hybrid plasmids containing Saccharomyces cerevisiae ribosomal DNA

Fragments produced by partial digestion of Saccharomyces cerevisiae ribosomal DNA (rDNA) with the restriction endonuclease EcoRI were ligated in vitro to the bacterial plasmid RSF2124. The resulting hybrid plasmids were cloned in Escherichia coli. Three hybrid plasmids which contain at least one intact repetitive unit of the multiple, tandem sequences of the yeast rDNA genes have been further characterized. These plasmids have been used to construct a map of the EcoRI, SmaI, HindII and HindIII restriction sites in the individual repetitive units of yeast rDNA.

The extrachromosomal control of nonsense suppression in yeast: an analysis of the elimination of [psi+] in the presence of a nuclear gene PNM

When a [psi-] strain of yeast mutates to [psi+], the efficiency of suppression by certain ochre suppressors is increased. The [psi+] phenotype is inherited extrachromosomally. There is a nuclear gene, PNM, which, when mutant, causes loss of the [psi+] phenotype. PNM- is dominant to PNM+ and a heterozygous diploid gradually loses the ability over successive generations, to produce PNM+ [psi+] spores. This paper describes the kinetics of this elimination and the data obtained are discussed in relation to two models of the molecular nature of the [psi] genetic determinant--one considering the [psi] determinant as an autonomous nucleic acid, the other treating the possibility that the [psi] nucleic acid is that which codes for rRNA in the nuclear genome.

Restriction endonuclease analysis of ribosomal DNA from Saccharomyces cerevisiae

The size and degree of homogeneity of the repetitive units in purified ribosomal DNA (gamma DNA) from Saccharomyces cerevisiae have been analyzed by restriction endonuclease digestion and heteroduplex mapping. Digestion of the gamma DNA with EcoRI yields seven fragments, digestion with Hind II+III yields five fragments, digestion with Hind III alone yields two fragments, and digestion with Sma I yields one fragment. The sum of the fragment molecular weights after digestion with each of the endonucleases is 5.5-5.6 x 10(6). When the DNA strands of the Sma I fragment are dissociated and reannealed, only homoduplexes are formed. We have concluded from these results that the repeating units in yeast ribosomal DNA are 5.6 x 10(6) datons and are homogeneous in size and composition.

Characterization of yeast ribosomal DNA fragments generated by EcoR1 restriction endonuclease

The action of Escherichia coli restriction endonuclease R1 (EcoR1) on DNA isolated from Saccharomyces cerevisiae (strain MAR-33) generates three predominent homogenously sized DNA fragments (species of 1.8, 2.2 and 2.5 kilo nucleotide base pairs (KB). Many DNA species of molecular weight greater than 2 million daltons can be recognized upon incomplete EcoR1 digestion of yeast DNA. Four additional DNA species ranging from 0.3--0.9 KB can be identified as the second major class of EcoR1-yeast DNA products. Hybridization with radioactive ribosomal RNA (rRNA) and competition with nonradioactive rRNA show that of the three predominent EcoR1-yeast DNA species, the 2.5 KB species hybridizes only with the 25S rRNA while the lighter 1.8 KB species hybridizes with the 18S rRNA. The intermediate DNA species of 2.2 KB hybridizes to a small extent with the 25S rRNA and could be a result of the presence of the 2.5 KB DNA species. The mass proportions and hybridization values of these 3 DNA species account for about 60% of the total ribosomal DNA (rDNA). The 5 Eco-R1-yeast DNA species of less than 0.9 KB (4 major and 1 minor species) hybridize to varying degrees with the 2 rRNA and can be grouped in two classes. In one class there are 3 DNA species that hybridize exclusively with the 18S rRNA. In the second class there are 2 DNA species that besides hybridizing predominently with the 25S rRNA also hybridize with the 18S rRNA. The 7 EcoR1-yeast DNA species (excluding the 2.2 KB DNA species) that hybridize with the two rRNA account for nearly a 5 million dalton DNA segment, which is very close to the anticipated gene size of rRNA precursor molecule. If the 2.2 KB DNA species is a part of the rDNA that is not transcribed or 5 sRNA then the cistron encoding the rRNA in S. cerevisiae has at least 8 EcoR1 recognition sites resulting in 8 DNA fragments upon digestion with the EcoR1. Consideration is given to the relationship of the rRNA species generated by EcoR1 digestion and the chromosomes containing ribosomal cistrons.

Naturally occurring cross-links in yeast chromosomal DNA

Chromosome-size yeast DNA molecules with a number average molecular weight (Mn) of 3-4 X 10(8) were isolated from sucrose gradients after sedimentation of lysed yeast spheroplasts. Resedimentation showed that the molecules were isolated without introducing appreciable single-strand or double-strand breaks. The presence of cross-links in these molecules was suggested by the observation that the apparent Mn in alkali was greater than expected for separated single strands. Since cross-linked molecules would have strands which fail to separate upon denaturation, this was tested more directly. Neutralization of alkaline denaturing conditions resulted in up to 70% of the intact molecules rapidly reforming duplex structures, as shown by equilibrium banding in CsCI. Experiments with larger E. coli DNA molecules (Mn = 5.2 X 10(8)) indicated that the conditions used were sufficient to denature completely molecules of this size. Results of enzyme treatments suggest that the cross-links are not RNA or protein. Experiments with density-labeled yeast DNA molecules showed that the rapid reformation of duplex DNA is not the consequence either of a bimolecular reaction between separated DNA strands or of intrastrand renaturation. The data indicate that when the yeast DNA molecules are completely denatured, the strands fail to separate. Hence they must be cross-linked. Experiments with sheared DNA show that there are small number of cross-links, one to four, permolecule.

Abundant species of poly(A)-containing RNA from Saccharomyces cerevisiae

Hybridization experiments using uniformly labeled poly(A) RNA derived from Saccharomyces cerevisiae strains carrying the "killer character" showed that (1) these molecules appear to be transcribed from repetitive DNA sequences. (2) there are approximately 35 DNA template sequences that are transcribed into poly(A) RNA. It is concluded that under the RNA extraction procedure used, most of the poly (A) RNA represents killer-RNA as judged by the dependence of the kinetic complexity of poly(A) RNA on the genomic complexity of killer-RNA.

Electron microscopic observations on the meiotic karyotype of diploid and tetraploid Saccharomyces cerevisiae

Certain strains of Saccharomyces cerevisiae contain visible segments of synaptonemal complex which are apparent components of bivalents in pachytene of meiotic prophase. The synaptonemal complex has the typical width in the frontal plane but is unusually thin in the sagittal plane, thus accounting for its poor visibility. Amorphous densities situated adjacent to the central element occur at intervals suggesting their coincidence with sites of crossing over. Reconstruction of the synaptonemal complex from serial sections has permitted karyotypic analysis. The number of segments of synaptonemal complex and the distribution of their legths is consistent with the genetic map. Two, possibly three, segments enter the nucleolus as if bearing sequences encoding ribosomal RNA. Reconstruction of tetraploid nuclei reveals an approximate doubling of the diploid chromosome number and confirms the pattern of nucleolar entry. Quadrivalent pairing is evident between the pairs of synaptonemal complex segments in the tetraploid nuclei.

Isolation, characterization, and stability of the 30S ribosomal RNA complex from HeLa cells

The HeLa 30S rRNA molecule (historically designated 28S rRNA) can be dissociated into two components, a 7S rRNA and a large rRNA component which we call 29S rRNA. To evaluate conformational differences between the 30S rRNA complex and the isolated 29S rRNA component of the complex, viscosity, sedimentation velocity, circular dichroism, and ultraviolet absorption measurements with the two species were performed. Sedimentation equilibrium studies were also carried out with the 30S rRNA complex. In addition, the kinetics of the reaction which dissociates the 30S rRNA complex were characterized. The removal of glycogen-like molecules by cetyltrimethylammonium bromide prescipitation of the rRNA and the preequilibration of rRNA with solvent by Sephadex column chromatography were found to be essential for reproducibility. The s20,2o values for the 30S rRNA complex and the isolated 29S rRNA were determined from the experimental data obtained at various rRNA concentrations as 29.89 plus or minus 0.40 and 29.09 plus or minus 0.14, respectively. The corresponding intrinsic viscosity values were 74 plus or minus 5 and 67 plus or minus 5 cm3/g, respectively. The optical properties of the 30S rRNA and 29S rRNA were not significantly different. These results indicate that there is no significant conformational difference between 30S rRNA and 29S rRNA under the conditions studied. We conclude from the sedimentation equilibrium data that the molecular weight of 30S rRNA is 2.1 x 10-6. From the kinetic data, the 30S rRNA dissociation appears to be an irreversible, cooperative, and ionic strength dependent reaction which at an ionic strength of 0.051 has an activation enthalpy of 123.5 kcal/mol and an activation entropy of 0.21 kcal/(mol deg).

Cryptopleurine resistance: genetic locus for a 40S ribosomal component in Saccharomyces cerevisiae

Mutants resistant to the phenanthrene alkaloids tylophorine, tylocrebrine, and cryptopleurine have been isolated from the yeast Saccharomyces cerevisiae. A single recessive nuclear gene was responsible for resistance. This resistance locus, cry, was closely linked to the mating locus (2.2 centimorgans). The resistance was ribosomal and was due to an altered 40S ribosomal subunit. The mode of action of these drugs has been examined, and they appear to inhibit the translocation phase of protein synthesis.

Control of RNA synthesis in yeast

During the cell cycle in Saccharomyces cerevisiae there is an ordered appearance of a number of enzymes and various physiological properties but a continuous increase in the rate of rRNA synthesis. A detailed study of rRNA synthesis has shown that there are reiterated genes for rRNA which are largely clustered on chromosome I and appear to be transcribed continuously during the cell cycle. However, the level of activity of polymerase I is proportional to the level of rRNA during the cell cycle and is correlated with the growth rate of the culture. In contrast, the level of polymerase II, thought to be involved in mRNA synthesis, increases during a definite period of the cell cycle characteristic of step enzymes in yeast. It would appear that the level of the activity of polymerase I is involved in the regulation of rRNA synthesis. Possible other mechanisms for the regulation of rRNA are discussed.

Saccharomyces cerevisiae cell cycle

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Lethal sectoring and the delayed induction of aneuploidy in yeast

Persistent lethal sectoring in a homothallic strain of yeast has been ascribed to tetrasomy for chromosome I. Such aneuploids can appear many generations after irradiation. The data thus indicate that an induced predisposition towards aneuploidy can be prolonged through successive post-irradiation cell divisions. Sporadic cell death in tetrasomics for chromosome I was found to result from a metabolic imbalance and not from a genetic instability conseqent to aneuploidy. This imbalance may be due to a dosage effect involving cistrons for ribosomal RNA since many of these are known to be located on chromosome I. Tetrasomy is not the only cause of persistent lethal sectoring; the phenomenon has been initiated through genetic recombination involving normal diploids. It has also been concluded that, in trisomics, equational division of the supernumerary chromosome sometimes occurs at the first meiotic division.

Distribution of ribosomal ribonucleic acid cistrons among yeast chromosomes

High-molecular-weight deoxyribonucleic acid (DNA) of Saccharomyces carls bergensis has been fractionated by sucrose density gradient centrifugation. The main DNA fraction has an average molecular weight of about 500 x 10(6). A major fraction of the DNA molecules containing sequences homologous to ribosomal ribonucleic acid (RNA) sediments as material of this molecular weight. The remainder sediments as material of a molecular weight of about 250 x 10(6). The latter fraction contains relatively more ribosomal RNA cistrons than the former. Studies on the buoyant density of high-molecular-weight DNA homologous to ribosomal RNA have led to the conclusion that the ribosomal RNA cistrons occur in groups attached to a relatively large amount of nonribosomal RNA and suggest that ribosomal RNA cistrons are distributed over a number of yeast chromosomes.