Thermosensitive mutations affecting ribonucleic acid polymerases in Saccharomyces cerevisiae

Upf1 and Upf2 proteins mediate normal yeast mRNA degradation when translation initiation is limited

mRNA degradation is coupled with the process of mRNA translation. For example, an mRNA molecule, on which translation is prematurely terminated because of a nonsense codon, may be rapidly degraded. This nonsense-mediated mRNA decay in the yeast Saccharomyces cerevisiae is mediated by the Upf1 and Upf2 proteins. Yeast mRNAs can also be selectively destabilized by limiting the rate of translation initiation. Two such destabilized mRNAs, from the SSA1 and SSA2 genes, have been identified using temperature-sensitive mutations affecting the Prt1 component of eukaryotic initiation factor 3. For SSA1 and SSA2 mRNAs, and for structurally modified SSA mRNA derivatives, I show here that degradation is triggered when translation initiation is limited but ongoing. This initiation-dependent mRNA degradation is limited to a subset of mRNAs that includes at least those from the SSA1 and SSA2 genes, and occurs through Upf1- and Upf2-mediated processes, although sequence elements characteristic of nonsense-mediated decay are not evident in these mRNAs.

Mutational analysis of the Prt1 protein subunit of yeast translation initiation factor 3

The Saccharomyces cerevisiae PRT1 gene product Prt1p is a component of translation initiation factor eIF-3, and mutations in PRT1 inhibit translation initiation. We have investigated structural and functional aspects of Prt1p and its gene. Transcript analysis and deletion of the PRT1 5' end revealed that translation of PRT1 mRNA is probably initiated at the second in-frame ATG in the open reading frame. The amino acid changes encoded by six independent temperature-sensitive prt1 mutant alleles were found to be distributed throughout the central and C-terminal regions of Prt1p. The temperature sensitivity of each mutant allele was due to a single missense mutation, except for the prt1-2 allele, in which two missense mutations were required. In-frame deletion of an N-terminal region of Prt1p generated a novel, dominant-negative form of Prt1p that inhibits translation initiation even in the presence of wild-type Prt1p. Subcellular fractionation suggested that the dominant-negative Prt1p competes with wild-type Prt1p for association with a component of large Prt1p complexes and as a result inhibits the binding of wild-type Prt1p to the 40S ribosome.

Starvation for His-tRNAHis in yeast causes translational arrest without a high level of misincorporation of glutamine at histidine codons

The hts1.1 temperature-sensitive histidinyl-tRNA synthetase mutation enables Saccharomyces cerevisiae to be starved for His-tRNAHis by upshift to the non-permissive temperature of 38 degrees C. If yeast behaves similarly to bacterial and mammalian cells, this lack of His-tRNAHis should greatly enhance misreading at histidine codons (CAU/CAC) by Gln-tRNAGln, resulting in substitution of the neutral amino acid glutamine in place of histidine, a basic amino acid. Such misreading causes the isoelectric point (pI) of proteins to shift to lower values, and is readily detectable as "stuttering" on two-dimensional (2D) protein gels. By gel analysis of pulse-labelled proteins of hts1.1 yeast cells that were overexpressing phosphoglycerate kinase (PGK), our study sought to detect this specific translational error in PGK protein. It was not detected by this relatively sensitive technique, indicating that missense errors due to glutamine insertion at histidine codons do not occur in yeast at the readily-detectable level found in bacterial and mammalian cells.

PET genes of Saccharomyces cerevisiae

We describe a collection of nuclear respiratory-defective mutants (pet mutants) of Saccharomyces cerevisiae consisting of 215 complementation groups. This set of mutants probably represents a substantial fraction of the total genetic information of the nucleus required for the maintenance of functional mitochondria in S. cerevisiae. The biochemical lesions of mutants in approximately 50 complementation groups have been related to single enzymes or biosynthetic pathways, and the corresponding wild-type genes have been cloned and their structures have been determined. The genes defined by an additional 20 complementation groups were identified by allelism tests with mutants characterized in other laboratories. Mutants representative of the remaining complementation groups have been assigned to one of the following five phenotypic classes: (i) deficiency in cytochrome oxidase, (ii) deficiency in coenzyme QH2-cytochrome c reductase, (iii) deficiency in mitochondrial ATPase, (iv) absence of mitochondrial protein synthesis, and (v) normal composition of respiratory-chain complexes and of oligomycin-sensitive ATPase. In addition to the genes identified through biochemical and genetic analyses of the pet mutants, we have cataloged PET genes not matched to complementation groups in the mutant collection and other genes whose products function in the mitochondria but are not necessary for respiration. Together, this information provides an up-to-date list of the known genes coding for mitochondrial constituents and for proteins whose expression is vital for the respiratory competence of S. cerevisiae.

On the early evolution of RNA polymerase

The lines of evidence suggesting that RNA preceded double-stranded DNA as an informational macromolecule are briefly reviewed. RNA polymerase is hypothesized to have been one of the earliest proteins to appear. It is argued that an important vestige of the original enzyme is found in the contemporary eubacterial beta' subunit of DNA-dependent RNA polymerase and its homologues among the archaebacterial and eukaryotic enzymes. The evidence that supports a catalytic role in replicase activity of this polypeptide is reviewed. It is suggested that several characteristics of the Escherichia coli transcriptional apparatus are relatively recent evolutionary developments. The phylogenetic importance of the eubacterial beta' subunit from RNA polymerase and its homologues is emphasized, because it allows the study of the evolutionary relationships of the major cellular lines (eubacteria, archaebacteria, and eukaryotes) as well as of some viral lineages.

Regulated arrest of cell proliferation mediated by yeast prt1 mutations

Several temperature-sensitive cell-division-cycle (cdc) mutations differentially affect the regulatory step for cell proliferation in the yeast. Saccharomyces cerevisiae, including one mutation termed cdc63-1, which resides in a previously known gene called PRT1. Other mutations in the PRT1 gene have been shown by others to affect an initiation step in protein synthesis. Here we show that at the appropriate nonpermissive temperature each prt1 mutation can produce a uniform and concerted arrest of cell division; the prt1-1 mutation, like cdc63-1, is shown to arrest cells specifically at the regulatory step for cell proliferation. This response of cessation of cell division is different from the response of cells to an equivalent limitation of protein synthesis using cycloheximide or verrucarin A, which implies that the PRT1 gene product could separately influence both cellular growth via protein synthesis and events in the regulation of cell proliferation.

Isolation and characterization of temperature-sensitive RNA polymerase II mutants of Saccharomyces cerevisiae

Three independent, recessive, temperature-sensitive (Ts-) conditional lethal mutations in the largest subunit of Saccharomyces cerevisiae RNA polymerase II (RNAP II) have been isolated after replacement of a portion of the wild-type gene (RPO21) by a mutagenized fragment of the cloned gene. Measurements of cell growth, viability, and total RNA and protein synthesis showed that rpo21-1, rpo21-2, and rpo21-3 mutations caused a slow shutoff of RNAP II activity in cells shifted to the nonpermissive temperature (39 degrees C). Each mutant displayed a distinct phenotype, and one of the mutant enzymes (rpo21-1) was completely deficient in RNAP II activity in vitro. RNAP I and RNAP III in vitro activities were not affected. These results were consistent with the notion that the genetic lesions affect RNAP II assembly or holoenzyme stability. DNA sequencing revealed that in each case the mutations involved nonconservative amino acid substitutions, resulting in charge changes. The lesions harbored by all three rpo21 Ts- alleles lie in DNA sequence domains that are highly conserved among genes that encode the largest subunits of RNAP from a variety of eucaryotes; one mutation lies in a possible Zn2+ binding domain.

Isolation and characterization of temperature-sensitive RNA polymerase II mutants of Saccharomyces cerevisiae

Three independent, recessive, temperature-sensitive (Ts-) conditional lethal mutations in the largest subunit of Saccharomyces cerevisiae RNA polymerase II (RNAP II) have been isolated after replacement of a portion of the wild-type gene (RPO21) by a mutagenized fragment of the cloned gene. Measurements of cell growth, viability, and total RNA and protein synthesis showed that rpo21-1, rpo21-2, and rpo21-3 mutations caused a slow shutoff of RNAP II activity in cells shifted to the nonpermissive temperature (39 degrees C). Each mutant displayed a distinct phenotype, and one of the mutant enzymes (rpo21-1) was completely deficient in RNAP II activity in vitro. RNAP I and RNAP III in vitro activities were not affected. These results were consistent with the notion that the genetic lesions affect RNAP II assembly or holoenzyme stability. DNA sequencing revealed that in each case the mutations involved nonconservative amino acid substitutions, resulting in charge changes. The lesions harbored by all three rpo21 Ts- alleles lie in DNA sequence domains that are highly conserved among genes that encode the largest subunits of RNAP from a variety of eucaryotes; one mutation lies in a possible Zn2+ binding domain.

Cloning and characterization of the gene coding for cytoplasmic seryl-tRNA synthetase from Saccharomyces cerevisiae

We have screened a Saccharomyces cerevisiae expression library with antibodies against seryl-tRNA synthetase (SerRS) from baker's yeast. In this way we obtained clones which contain serS, the structural gene for seryl-tRNA synthetase. Genomic Southern blots show that the serS gene resides on a 5.0 kb SalI fragment. Nucleotide sequence analysis of the genes revealed a single open reading frame from which we deduced the amino acid sequence of the enzyme consistent with that of two peptides isolated from SerRS. The enzyme is comprised of 462 amino acids consistent with earlier determinations of its molecular weight. The codon usage of serS is typical of abundant yeast proteins. Nuclease S1 analysis of serS mRNA defined the RNA initiation site 20-40 bases downstream from an AT rich sequence containing the TATA box and 21-39 nucleotides upstream of the translation initiation codon. Yeast strains transformed with the cloned gene overproduce seryl-tRNA synthetase in vivo.

The HTS1 gene encodes both the cytoplasmic and mitochondrial histidine tRNA synthetases of S. cerevisiae

The gene encoding the histidine-tRNA synthetase (HTS1) has two in-frame translation start sites located 60 bp apart. One set of HTS1 transcripts (long) initiates upstream of both ATG codons, and the other set (short) initiates between the two ATG codons and therefore contains only the downstream ATG. A mutation that destroys the first AUG on the long message results in the Pet- (respiratory deficient) phenotype, but does not affect either the level of the cytoplasmic histidine-tRNA synthetase or viability. Mutations distal to the second ATG lead to loss of cytoplasmic synthetase function, lethality and respiratory deficiency. These phenotypes can be explained if the longer message were to encode the mitochondrial synthetase and the shorter message were to encode the cytoplasmic histidine-tRNA synthetase.

Patulin degradation in saccharomyces cerevisiae: Sensitive mutants

CONCLUSION

The present experiments (sensitive mutants and transient inhibition of growth) are compatible with the synthesis of an inductible detoxifying substance in the wild type strain. This substance could be glutathione because glutathione detoxification scheme essentially involves properties of the SH group and it is well known that patulin reacts with sulfhy dril groups.Studies are presently being carried out with sensitive mutants to establish definitively the relation between intracellular pool of glutathone and the resistance mechanism of a yeast to patulin.

Eukaryotic RNA polymerases

This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.

Action of patulin on a yeast

The action of patulin on Saccharomyces cerevisiae was studied. At weak doses, the drug inhibited growth, but inhibition was transient. After 10 min, syntheses of rRNA, tRNA, and probably mRNA were blocked; this was shown by radioactive precursor incorporation assays and gel electrophoresis of RNAs. After recovery of growth, patulin disappeared from the medium. It seemed that this degradation resulted from the activity of an inducible enzymatic system. Induced cells resisted very high patulin concentrations.

Quantitative analysis of the heat shock response of Saccharomyces cerevisiae

Transient protein synthesis in Saccharomyces cerevisiae, after shift from 21-23 degrees C to 37 degrees C, was quantitatively analyzed. Pulse-labeled proteins were separated by two-dimensional gel electrophoresis, and autoradiograms of the gels were analyzed by a recently described method involving a computer-coupled film scanning system. In this way, the rate of incorporation of L-[35S]methionine into approximately 500 proteins was followed. The synthesis of more than 80 of these proteins was transiently induced at 37 degrees C, with about 20 being classified as major heat shock proteins (defined as those whose rate of labeling was increased at least eightfold at some time during the response). The synthesis of more than 300 of the proteins was transiently repressed at 37 degrees C, and several general temporal patterns of repression could be distinguished. The influence of temperature-sensitive mutations affecting RNA synthesis and transport on the heat shock response was also examined. A protein whose induction in response to heat shock has a post-transcriptional component could be identified. As previously pointed out, the heat shock repression of certain proteins is so rapid that it also must involve post-transcriptional effects.

A response of protein synthesis to temperature shift in the yeast Saccharomyces cerevisiae

When Saccharomyces cerevisiae are subjected to a sudden increase in temperature (22 degrees C to 37 degrees C) they undergo extensive and, in some cases, extreme alterations in their rates of synthesizing individual polypeptides. These changes were monitored by pulse-labeling cells with [35S]methionine and separating the total soluble proteins by two-dimensional gel electrophoresis. Incorporation of 35S into individual proteins was measured by a computer-coupled autoradiogram-scanning method. The rates of synthesis of most proteins are transiently changed; 10-fold or greater induction or respression is common. This temperature response has also been studied in a mutant strain that is temperature sensitive for the nucleus-to-cytoplasm transport of RNA. In this mutant, not only the induction, but also a part of the repression in response to temperature upshift is largely inhibited. Conceivable mechanisms are discussed.

Isolation and characterisation of a strain of Saccharomyces cerevisiae deficient in in vitro RNA polymerase B(II) activity

Two hundred strains of Saccharomyces cerevisiae temperature sensitive for RNA synthesis were selected and screened in crude extracts for DNA-dependent RNA polymerase activities. One strain was isolated which had only residual in vitro RNA polymerase B activity. In normal growth conditions total RNA, poly A+ RNA and protein synthesis were indistinguishable from those of the wild type strain at 23 degrees C and after shift to 37 degrees C. A temperature sensitive phenotype was detected only when rpoB containing strains were grown in adverse conditions. The mutant character showed mendelian segregation and was coexpressed with the wild type character in heterozygous diploids. Residual enzyme activity was characterised in crude extracts using synthetic polymers and natural templates in different ionic conditions.

Use of 8-hydroxyquinoline to enrich for temperature-sensitive mutants of Tetrahymena

The effects of the chelating agent 8-hydroxyquinoline (Hq) on Tetrahymena thermophila were examined. Cell division was completely inhibited by 5 micrograms of Hq per ml. At this concentration deoxyribonucleic acid, ribonucleic acid, and protein syntheses were also completely and nonselectively inhibited. The inhibition was reversible after 6 h of Hq treatment. At concentrations above 20 micrograms/ml a 10,000-fold decrease in survival as seen after 2 h in the drug. The sensitivity of Tetrahymena to Hq was found to be dependent upon cell concentration, wild-type strain, medium, and length of time the culture is at 38 degrees C before Hq is added. Mutants of Tetrahymena that are unable to divide at the restrictive temperature, but which continue macromolecular synthesis, were found to be resistant to Hq treatment. Conditions were obtained in which more than a 1,000-fold difference in survival was seen between this class of mutant and the wild type. The effect of Hq on three other classes of temperature-sensitive mutants was examined, and the results are discussed.

Concerted repression of the synthesis of the arginine biosynthetic enzymes by aminoacids: a comparison between the regulatory mechanisms controlling aminoacid biosyntheses in bacteria and in yeast

It has been shown that in bacteria, besides specific regulatory mechanisms, the synthesis of aminoacid biosynthetic enzymes is also controlled by the endogenous aminoacid pool. The latter regulates the intracellular level of ppGpp, a positive effector of RNA messenger transcription. A similar regulatory control exists in yeast but does not appear to involve the same general effector. This was established by the observation that derepression of the enzymes belonging to several aminoacid biosynthetic pathways follows aminoacid starvation or tRNA discharging. We now report the repression of the arginine pathway by the total aminoacid pool. New mutations affecting the repressibility of the arginine enzymes as well as enzymes belonging to other aminoacid biosyntheses, when cells are grown in the presence of an excess of aminoacids, were identified.

Structure and processing of yeast precursor tRNAs containing intervening sequences

We have isolated a precursor of yeast tRNATyr and shown that it contains an intervening sequence identical to that found in the gene for tRNATyr. The conformation of pre-tRNATyr is similar to that of mature tRNATyr except for the anticodon loop. The loop is sensitive to endonucleolytic cleavage by S1 nuclease near to the ends of the intervening sequence. This pre-tRNA is functionally inactive as it cannot be aminoacylated and the anticodon is not accessible for hydrogen bonding. A crude nuclear extract from yeast contains an excision-ligase activity which will process pre-tRNATyr into mature tRNATyr.

Mutants of yeast with depressed DNA synthesis

Seven temperature-sensitive mutants have been isolated in Saccharomyces cerevisiae which show a reproducible defect in DNA synthesis at the restrictive temperature. One of these is allelic with rna11 (Hartwell et al., 1970) but the remaining mutants define six complementation groups and probably represent six different genes. The gene symbol dds (for depressed DNA synthesis) is proposed. At the restrictive temperature, rna11-2, dds2-1 and dds6-1 show a rapid and almost total cessation of DNA and RNA synthesis, whilst protein synthesis continues for several hours. The remaining dds mutants show a reduced rate of DNA synthesis from the time of temperature shift (dd1, dds3, dds4) or a cessation of DNA synthesis at a later time (dds5). In some cases, RNA synthesis is affected concomitantly with, or soon after, the depression in DNA synthesis. Possible reasons for the phenotypes of these mutants, and for the relative absence of yeast mutants which are unambiguously and specifically affected in DNA synthesis, are discussed. In addition, we report the isolation of seven new alleles of known cdc genes and ten new mutants with a cell cycle phenotype that complement those already known.

Molecular events associated with induction of arginase in Saccharomyces cerevisiae

Arginase, the enzyme responsible for arginine degradation in Saccharomyces cerevisiae, is an inducible protein whose inhibition of ornithine carbamoyl-transferase has been studied extensively. Mutant strains defective in the normal regulation of arginase production have also been isolated. However, in spite of these studies, the macromolecular biosynthetic events involved in production of arginase remain obscure. We have, therefore, studied the requirements of arginase induction. We observed that: (i) 4 min elapsed between the addition of inducer (homoarginine) and the appearance of arginase activity at 30 degrees C; (ii) induction required ribonucleic acid synthesis and a functional rna1 gene product; and (iii) production of arginase-specific synthetic capacity occurred in the absence of protein synthesis but could be expressed only when protein synthesis was not inhibited. Termination of induction by inducer removal, addition of the ribonucleic acid synthesis inhibitor lomofungin, or resuspension of a culture of organisms containing temperature-sensitive rna1 gene products in a medium at 35 degrees C resulted in loss of ability for continued arginase synthesis with half-lives of 5.5, 3.8, and 4.5 min, respectively. These and other recently published data suggest that a variety of inducible or repressible proteins responding rapidly to the environment may be derived from labile synthetic capacities, whereas constitutively produced proteins needed continuously throughout the cell cycle may be derived from synthetic capacities that are significantly more stable.