Turnover of polyadenylated messenger RNA in fission yeast. Evidence for the control of protein synthesis at the translational level

Genome-wide screen for cell growth regulators in fission yeast

Cellular growth control is important for all living organisms, but experimental investigation into this problem is difficult because of the complex range of growth regulatory mechanisms. Here, we have used the fission yeast Schizosaccharomyces pombe to identify potential master regulators of growth. At the restrictive temperature, the S. pombe pat1^ts mei4Δ strain enters the meiotic developmental program, but arrests in meiotic G2 phase as mei4⁺ is essential for meiotic progression. These cells do not grow, even in an abundance of nutrients. To identify regulators of growth that can reverse this growth arrest, we introduced an ORFeome plasmid library into the pat1^tsmei4Δ strain. Overexpression of eight genes promoted cell growth; two of these were core RNA polymerase subunits, and one was sck2⁺ , an S6 kinase thought to contribute to TORC1 signalling. Sck2 had the greatest effect on cell growth, and we also show that it significantly increases the cellular transcription rate. These findings indicate, for the first time, that global transcriptional control mediated through S6 kinase signalling is central to cellular growth control.

Antisense transcription controls cell fate in Saccharomyces cerevisiae

Entry into meiosis is a key developmental decision. We show here that meiotic entry in Saccharomyces cerevisiae is controlled by antisense-mediated regulation of IME4, a gene required for initiating meiosis. In MAT a/alpha diploids the antisense IME4 transcript is repressed by binding of the a1/alpha2 heterodimer at a conserved site located downstream of the IME4 coding sequence. MAT a/alpha diploids that produce IME4 antisense transcript have diminished sense transcription and fail to initiate meiosis. Haploids that produce the sense transcript have diminished antisense transcription and manifest several diploid phenotypes. Our data are consistent with transcription interference as a regulatory mechanism at the IME4 locus that determines cell fate.

Functional analysis of the zinc cluster domain of the CYP1 (HAP1) complex regulator in heme-sufficient and heme-deficient yeast cells

CYP1 determines the expression of several genes whose transcription is heme-dependent in yeast. It exerts regulatory functions even in the absence of heme, usually considered to be its effector. It mediates both positive and negative effects, depending on the target gene and on the redox state of the cell. In the presence of heme, it binds through a cysteine-rich domain in which a histidine residue occupies the position of the sixth and essential cysteine of the otherwise classical zinc cluster DNA-binding domain exemplified by GAL4. We constructed specific missense mutations in the potential CYP1 zinc cluster domain by site-directed mutagenesis and looked for regulatory effects of the mutated proteins under specific physiological conditions. We show that CYP1 does belong to the zinc cluster regulatory family since a sixth essential cysteine residue is indeed present, albeit at a modified position when compared to the consensus sequence. We also show that the amino acid preceding the first cysteine residue of the DNA-binding domain critically affects the efficiency of regulation both in the presence and in the absence of heme: mutations known to affect DNA binding under heme-sufficient conditions also affect regulation under heme-deficient conditions. We therefore surmise that regulation under heme-deficient conditions is dependent upon DNA binding.

The NAM8 gene in Saccharomyces cerevisiae encodes a protein with putative RNA binding motifs and acts as a suppressor of mitochondrial splicing deficiencies when overexpressed

We have characterized the nuclear gene NAM8 in Saccharomyces cerevisiae. It acts as a suppressor of mitochondrial splicing deficiencies when present on a multicopy plasmid. The suppressed mutations affect RNA folding and are located in both group I and group II introns. The gene is weakly transcribed in wild-type strains, its overexpression is a prerequisite for the suppressor action. Inactivation of the NAM8 gene does not affect cell viability, mitochondrial function or mitochondrial genome stability. The NAM8 gene encodes a protein of 523 amino acids which includes two conserved (RNP) motifs common to RNA-binding proteins from widely different organisms. This homology with RNA-binding proteins, together with the intronic location of the suppressed mitochondrial mutations, suggests that the NAM8 protein could be a non-essential component of the mitochondrial splicing machinery and, when present in increased amounts, it could convert a deficient intron RNA folding pattern into a productive one.

CYP1 (HAP1) regulator of oxygen-dependent gene expression in yeast. I. Overall organization of the protein sequence displays several novel structural domains

In the yeast Saccharomyces cerevisiae the CYP1 gene that modulates the expression of iso1-(CYC1) and iso2-cytochrome c (CYP3) structural genes gives rise to two classes of mutated alleles; one class, represented by CYP1-18, has opposite effects on CYC1 and CYP3, it reduces the expression of CYC1 while it stimulates that of CYP3. The other class, represented by cyp1-23 or the related allele hap1-1, reduces the expression of both CYC1 and CYP3 genes. Genetic data suggested that the CYP1 product is a positive regulator of the cytochrome c genes. The CYP1-18 allele has been cloned. We show here that the iso2 overproducer function of CYP1-18 is included in a 5300 base XhoI-PstI fragment. The sequence of this fragment reveals a unique, long, uninterrupted open reading frame of 4449 nucleotides able to encode a protein of 1483 amino acid residues. The predicted product of this open reading frame contains several interesting features. The N-terminal part of the protein resembles a nucleic acid-binding domain, in which two domains can be distinguished. The first is similar to a "finger" DNA binding motif, as found in TFIIIA and other regulatory proteins. The second consists of seven tandemly repeated sequences with a KCPVDH motif. Because of its structure, it is tempting to speculate that this region may act as a "redox sensor" folded around a metal atom or heme and involved in recognition of respiratory effectors. These two domains are separated by an "opa" sequence of 13 Gln residues. Implication of these domains for the function of CYP1-18 is discussed.

Cloning and expression of the OMP decarboxylase gene URA4 from Schizosaccharomyces pombe

URA4, the gene coding for orotidine monophosphate decarboxylase (OMPdecase), has been cloned from the fission yeast by homologous complementation and restricted in an Escherichia coli-Schizosaccharomyces pombe (E. coli-S. pombe) replicative plasmid to a 1.76 kb HindIII fragment. This plasmid is maintained at a high copy number in S. pombe and allows OMPdecase expression in Saccharomyces cerevisiae (S. cerevisiae) as well as in E. coli. After characterisation by restriction mapping and Southern hybridisation, the cloned gene was used as a probe to measure URA4 transcription and to examine its regulation. Messenger RNA levels were measured by DNA/RNA filter-hybridisation with pulse labelled RNAs during 6-azauridine (6-AUR) inhibited growth in wild type and 6-AUR sensitive strains. We found that in S. pombe the OMP analogue 6-AUR does not regulate the level of OMPdecase formation as it does in S. cerevisiae but rather modifies the ratio of total polyA+ to polyA- RNAs in the cell. Based on these results and on corresponding enzyme activities this study demonstrates divergent pyrimidine pathway regulation in the two yeasts S. cerevisiae and S. pombe. Finally, we propose the use of the URA4 gene as a convenient selective marker for genetic engineering in S. pombe.

Isolation, physical characterization and expression analysis of the Saccharomyces cerevisiae positive regulatory gene PHO4

The Saccharomyces cerevisiae PHO4 gene, which positively controls the expression of phosphatase genes, has been isolated by complementation of a pho4 mutation. The isolated DNA directed integration at the chromosomal PHO4 locus. The nucleotide sequence of PHO4 has a coding region of 930 nucleotides, flanked by sequences with typical transcription initiation and termination signals. The 5' region has characteristics of low-expression promoters and carries several uncommon elements, whose significance is not known. The predicted primary structure of the PHO4 protein, of 309 residues, does not show sequence elements typical of DNA-binding proteins. The transcription of PHO4 is independent of inorganic phosphate. Like other regulatory genes, PHO4 is transcribed at a very low level and the translation of its message uses preferentially several codons which are not employed for highly expressed genes.

Transcriptional and translational expression of a chimeric bacterial-yeast plasmid in yeasts

Chimeric plasmids composed of the bacterial plasmid pBR322, 2 micron yeast plasmid fragments and the 1.1 kb ura3+ fragment of yeast chromosomal DNA which codes for orotidine-5'-phosphate (OMP) decarboxylase were constructed and used to transform Escherichia coli and Saccharomyces cerevisiae recipient cells. The expression in yeast of one such plasmid was studied and compared to the expression of a chromosomally integrated bacterial plasmid. In the strain carrying the chimeric plasmid the level of OMP decarboxylase activity is about 25 times that found in either the wild-type strain or in the strain carrying the chromosomally integrated plasmid. The ampicillin gene of pBR322 is expressed in yeast. Labeling kinetics of RNA and measurements of the polyadenylated fractions showed that RNA hybridizing to the pBR322 plasmid was polyadenylated to the same extent as RNA hybridizing to the ura3+ gene. Half-lives of 10 and 20 min were estimated for the ura3+ and pBR322 transcripts respectively.

Level and turnover of polyadenylate-containing ribonucleic acid in Neurospora crassa in different steady states of growth

Mycelia of Neurospora crassa in a steady state of growth in different media have a ribosomal content proportional to the rate of growth. Moreover, both the percentage of polysomes and the average ribosomal activity are about the same at all different growth rates. The content of polyadenylated RNA was determined in three different conditions of exponential growth, which allowed growth rates that ranged from 0.26 to 0.51 duplications/h, and was found to constitute about the same fraction of total RNA (4.5--5.2%). Using a kinetic approach, an equation was derived which allowed determination of the average half-lives of polyadenylated RNA: in each medium the cultures were labeled from the moment of the inoculation with [32P]orthophosphate and were then given a 10-min pulse with [5-3H]uridine when they were in the exponential phase. It was found that the determined half-lives of polyadenylated RNA vary, depending on the growth medium, between 30 and 60 min, but with no direct correlation with the growth rate. Moreover, the rate of synthesis of polyadenylated RNA relative to that of stable RNA decreased with the growth rate. On the basis of previous data on the rates of synthesis of stable RNA, it was possible to make an evaluation of the absolute rate of synthesis of polyadenylated RNA. Whereas the rate of synthesis of stable ribosomal RNA increases as a function of the square of the number of duplications per hour, the increase in the rate of synthesis of polyadenylated RNA with the growth rate is much less consistent. It is concluded that in Neurospora the growth rate does not depend on the rate of synthesis of mRNA but rather on the rate of synthesis of rRNA, which sets both the ribosomal level and the steady-state level of mRNA.

Inhibition of photo-induced Trichoderma viride conidiation by inhibitors of RNA synthesis

The photo-induced conidiation of Trichoderma viride is suppressed by ethidium bromide, acriflavin, lomofungin and 8-quinolinol at concentrations which do not inhibit the colony growth of this deuteromycete.

Yeast temperature-sensitive mutants specifically impaired in processing of poly(A)-containing RNAs

The selection at 22 degrees C of yeast cordycepin (3'-deoxyadenosine) sensitive mutants which would be temperature-sensitive at 37 degrees C allowed the obtention of mutants specifically impaired in processing of Poly(A)-containing RNAs at 37 degrees C. The mutants displaying this phenotype belong to two different loci. The biochemical study of the physiological function which is blocked by the mutation has revealed that the level of radioactive Poly(A)-containing RNAs found in a 5 min pulse after a 10 min shift at 37 degrees C is 6 times less in the mutants than in the wild type without reduction of the non Poly(A)-containing RNAs fraction. Further studies have shown no alteration in the two Poly(A) polymerases activities and suggest strongly a faster decay of Poly(A)-containing RNAs in the mutants.

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.

Large and small invertases and the yeast cell cycle. Pattern of synthesis and sensitivity to tunicamycin

We have examined the pattern of synthesis of the glycoprotein form of invertase and of the smaller carbohydratefree from in synchronous culture to obtain further infromation concerning their biosynthetic relationship. Saccharomyces mutant 1710 was chosen since its invertase production is almost completely derepressed during growth in 0.1 M mannose medium. The large enzyme, unlike the small form, binds to concanavalin A-Sepharose, and on this basis the two types can conveniently be separated for analysis. Large invertase was produced throughout the cell cycle. Synthesis of the small invertase was periodic; the single burst occurred at or close to the budding stage. Tunicamycin, which inhibits the sypthesis of external glycoproteins, halted formation of the large enzyme but not of the small form, and there was no accumulation of invertase activity with the properties of the small enzyme. Hence, it is unlikely that the small form is a precursor of the large one. Despite marked differences in their amino acid compositions, the two enzymes have many similarities. They are probably, in part, the products of the same gene(s), and the differences between them may largely reflect differences in post-translational processing.

Size and turnover of polyadenylic acid-containing ribonucleic acids in a fragile mutant of Saccharomyces cerevisiae

Ribonucleic acid-containing polyadenylic acid [poly(A)+-RNA] was studied in lysates from an osmotic-sensitive mutant of Saccharomyces cerevisiae characterized by low nuclease activity. The poly(A)+-RNA fraction, analyzed by electrophoresis in polyacrylamide-formamide gels, constitutes a heterogeneous population of molecules, with molecular weights ranging from 0.2 X 10(6) to 3 X 10(6) and having an average of 1.2 X 10(6). The turnover rate of poly(A)+-RNA was determined by the decay of radioactivity after a cold uracil chase, and the observed half-life of 21 min corresponds to about 10% of the cell doubling time. Poly(A)+-RNA was analyzed by gel electrophoresis under denaturing and non-denaturing conditions. A correlation was established between the apparent secondary structure and the turnover rate of poly(A)+-RNA species.

Effect of 8-hydroxyquinoline on the uptake of uridine and incorporation into RNA

8-hydroxyquinoline has been previously used as an inhibitor in studies on porphyrin metabolism, where it is thought to act by chelating iron. It is shown that this compound also rapidly inhibits uridine uptake of seedlings or cotyledons of the crucifer Matthiola incana R.Br. RNA synthesis is also affected but the inhibition is not as severe as reported for fission yeast.

The effect of 8-hydroxyquinoline on enzyme synthesis in the fission yeast Schizosaccharomyces pombe

The effect of 8-hydroxyquinoline, a rapid inhibitor of RNA synthesis, was followed on the activity of a number of enzymes in cultures of the fission yeast Schizosaccharomyces pombe. Two types of effect were found. In the first the activity continued to rise for a period and then remained constant. This occurred with alkaline phosphatase, basal and derepressed acid phosphatase, hexokinase, and derepressed sucrase and maltase at low cell density. It is consistent with control being exercised by an unstable mRNA or by an unstable stimulator of translocation. In the second the activity increased above the control values for several hours. This occurred with basal sucrase and maltase, and suggests a stable mRNA and an unstable inhibitor of translation. The extent of 'superproduction' of sucrase varied with cell density and with growth medium and this may be due to differences in the degree of translational inhibition. The possiblilty of a stable mRNA has interesting implications for the control of enzyme synthesis through the cell cycle.