Genetic analysis of antisuppressor mutants in the fission yeast Schizosaccharomyces pombe

Anticodon Wobble Uridine Modification by Elongator at the Crossroad of Cell Signaling, Differentiation, and Diseases

First identified 20 years ago as an RNA polymerase II-associated putative histone acetyltransferase, the conserved Elongator complex has since been recognized as the central player of a complex, regulated, and biologically relevant epitranscriptomic pathway targeting the wobble uridine of some tRNAs. Numerous studies have contributed to three emerging concepts resulting from anticodon modification by Elongator: the codon-specific control of translation, the ability of reprogramming translation in various physiological or pathological contexts, and the maintenance of proteome integrity by counteracting protein aggregation. These three aspects of tRNA modification by Elongator constitute a new layer of regulation that fundamentally contributes to gene expression and are now recognized as being critically involved in various human diseases.

Elongator, a conserved complex required for wobble uridine modifications in eukaryotes

Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The role of this complex has been controversial as the pleiotropic phenotypes of Elongator mutants have implicated the complex in several cellular processes. However, in yeast there is convincing evidence that the primary and probably only role of this complex is in formation of the 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains on uridines at wobble position in tRNA. In this review we summarize the cellular processes that have been linked to the Elongator complex and discuss its role in tRNA modification and regulation of translation. We also describe additional gene products essential for formation of ncm(5) and mcm(5) side chains at U34 and their influence on Elongator activity.

Putative frameshift suppressors in Schizosaccharomyces pombe

Nine genetically distinct suppressors of ICR-170-induced ade6 and ade7 mutations have been identified in Schizosaccharomyces pombe. The nine suppressors of ICR-170-induced and spontaneous origin have been assigned to the three chromosomes by haploidization and meiotic analysis. They do not suppress missense or nonsense mutations and are therefore likely to be frameshift suppressors. Based on the spectrum of suppression, the nine suppressors fall into two mutually exclusive groups. Group I comprises the two dominant suppressors sufl and suf11. Group II consists of the seven dominant suppressors suf2 through suf8. The suppressors of both groups are inefficient and all lead to a marked reduction of growth rate. Within suppressor groups, combinations of suppressors lead to drastic reductions of growth rates and to an increased efficiency of suppression. Freely segregating modifiers of suppression increasing and decreasing the efficiency of supression have been found for all the suppressors. The two omnipotent suppressors sup1 and sup2 increase the efficiency of suppression of some frameshift suppressors. The suf5 locus is unstable and reverts at very high frequency both meiotically and mitotically.

A revised chromosome map of the fission yeast Schizosaccharomyces pombe

The genetic map of the nuclear genome of the fission yeast Schizosaccharomyces pombe has been extended by mitotic and meiotic mapping data. A total of 158 markers are now assigned to the three linkage groups known in this organism, and 118 of them have been located on the corresponding chromosome map. Chromosome II and III each consist of one linkage group. There is some indication that the two large fragments which define chromosome I are meiotically linked, but the linkage observed is significant at the P = 0.05 level only. The length of the map is at least 1,700 map units, corresponding to an average of about 8 kilobases per map unit. The latter figure is comparable to the one obtained for intragenic recombination in the sup3 gene (Hofer et al. 1979). The basic frequency of gene conversion as measured for 21 genes varies according to a distribution of Poisson (with a modal value of 0.6% conversion per meiosis and per gene), in sharp contrast with Saccharomyces cerevisiae (Fogel et al. 1980) and Ascobolus immersus (Nicolas 1979). This may reflect the rarity of gene or region-specific rec alleles in S. pombe and may be related to the homothallism of this organism.

Yeast alpha-tubulin suppressor Ats1/Kti13 relates to the Elongator complex and interacts with Elongator partner protein Kti11

The alpha-tubulin suppressor 1 (ATS1) gene and the killer toxin-insensitive 13 (KTI13) locus from Saccharomyces cerevisiae are allelic. The Ats1/Kti13 gene product interacts with the cell polarity factor Nap1 and promotes growth inhibition of S. cerevisiae by zymocin, a tRNAse toxin complex from Kluyveromyces lactis. Kti13 removal causes zymocin resistance, a trait that is typical of defects in the Elongator complex. Here, we show that Kti13 co-purifies with the Elongator partner protein Kti11 and that the Kti11 interaction, not the Nap1 partnership, requires the C-terminus of Kti13. Moreover, Kti13 functionally relates to roles of the Elongator complex in tRNA wobble uridine modification, tRNA suppression of nonsense (SUP4) and missense (SOE1) mutations and tRNA restriction by zymocin. Also, inactivation of Kti13 or Elongator rescues the thermosensitive growth defect of secretory mutants (sec2-59(ts), sec12-4(ts)), suggesting that Kti13 and Elongator affect secretion processes that depend on the GTP exchange factors Sec2 and Sec12 respectively. Distinct from tandem deletions in KTI13 and Elongator genes, a kti13Delta kti11Delta double deletion induces synthetic sickness or lethality. In sum, our data suggest that Kti13 and Kti11 support Elongator functions and that they both share Elongator-independent role(s) that are important for cell viability.

Gene database for the fission yeast Schizosaccharomyces pombe

As an aid to the fission yeast genome project, we describe a database for Schizosaccharomyces pombe consisting of both genetic and physical information. As presented, it is therefore both an updated gene list of all the nuclear genes of the fission yeast, and provides an estimate of the physical distance between two mapped genes. Additionally, a field indicates whether the sequence of the gene is available. Currently, sequence information is available for 135 of the 501 known genes.

Antisuppressor mutations in Aspergillus nidulans: cold-resistant revertants of suppressor suaC109

Cold-resistant revertants of the cold-sensitive, ribosomal suppressorsuaC109have been isolated, with a view to obtaining mutations in new ribosomal protein genes. Many revertants had reduced suppressor activity and were classified as antisuppressor mutants. Both intragenic and extragenic reversions were found. In seven strains the extragenic reversion to cold resistance segregated with the antisuppressor phenotype, and these were designatedasumutations. Three of the fiveasugenes, C, B and D were mapped to linkage groups, I, II and V respectively. The antisuppressors are not gene-specific, although they mainly antagonize the activity of ribosomal suppressors. The antisuppressors altered all aspects of the phenotype of suppressorsuaC109including sensitivity to aminoglycoside antibiotics, and are therefore thought to be mutations in ribosomal protein genes.

Inactivation of nonsense suppressor transfer RNA genes in Schizosaccharomyces pombe. Intergenic conversion and hot spots of mutation

Intergenic conversion is a mechanism for the concerted evolution of repeated DNA sequences. A new approach for the isolation of intergenic convertants of serine tRNA genes in the yeast Schizosaccharomyces pombe is described. Contrary to a previous scheme, the intergenic conversion events studied in this case need not result in functional tRNA genes. The procedure utilizes crosses of strains that are homozygous for an active UGA suppressor tRNA gene, and the resulting progeny spores are screened for loss of suppressor activity. In this way, intergenic convertants of a tRNA gene are identified that inherit varying stretches of DNA sequence from either of two other tRNA genes. The information transferred between genes includes anticodon and intron sequences. Two of the three tRNA genes involved in these information transfers are located on different chromosomes. The results indicate that intergenic conversion is a conservative process. No infidelity is observed in the nucleotide sequence transfers. This provides further evidence for the hypothesis that intergenic conversion and allelic conversion are the result of the same molecular mechanism. The screening procedure for intergenic revertants also yields spontaneous mutations that inactivate the suppressor tRNA gene. Point mutations and insertions of A occur at various sites at low frequency. In contrast, A insertions at one specific site occur with high frequency in each of the three tRNA genes. This new type of mutation hot spot is found also in vegetative cells.

Fine tuning of ribosomal accuracy

If the rate constant for peptide bond formation were high just after an amino acid incorporation and occasionally switched to a lower value afterwards, then the ribosome could compensate for tRNA imbalance specifically at hungry codons. A rigorous analysis of the scheme proves its effectiveness. For instance, a 10-fold reduction in cognate tRNA concentration may increase the error rate by only a factor of two.

First identification of an amber nonsense mutation in Schizosaccharomyces pombe: major differences in the efficiency of homologous versus heterologous yeast suppressor tRNA genes

In Saccharomyces cerevisiae ochre and opal, as well as amber mutations are known, whereas in the fission yeast Schizosaccharomyces pombe no amber alleles have been described. We have characterized trp1-566, an amber allele in the trp1 locus of S. pombe. The identification of trp1-566 as an amber allele is based on the following results: (a) The nonsense allele can be converted to an ochre allele by nitrosoguanidine mutagenesis. (b) trp1-566 is suppressed by a bona fide S. pombe amber suppressor tRNA, supSI. The supSI gene was obtained by primer-directed in vitro mutagenesis of a tRNASer from S. pombe. Unexpectedly, an S. cerevisiae amber suppressor tRNASer, supR21, transformed into S. pombe, failed to suppress trp1-566. Northern analysis of S. pombe transformants, containing supRL1 or S. cerevisiae tRNALeu or tRNATyr genes reveals that these genes are not transcribed in the fission yeast. As an additional tool for the analysis of nonsense mutations in S. pombe, we obtained by nitrosoguanidine mutagenesis two unlinked amber suppressor alleles, sup13 and sup14, which act on trp1-566.

Presence and source of free isopentenyladenosine in yeasts

Cytokinins are a class of naturally occurring compounds that regulate growth and differentiation in tissues of higher plants. Many cytokinins are isopentenylated derivatives of adenine and its riboside, adenosine. By virtue of the post-transcriptional isopentenylation of specific anticodon loop adenosine residues in certain tRNA sequences, cytokinins are nearly universal, but tRNA-independent (de novo) cytokinin synthesis has been demonstrated in a few species. Using a radioimmunoassay, we have demonstrated that haploid strains of Saccharomyces cerevisiae and Schizosaccharomyces pombe contain, respectively, 0.8 and 0.9 microgram of the free cytokinin, N6-(delta 2-isopentenyl)adenosine, per g of cells (wet weight). Strains of both species characterized by mutations that result in deficiencies of isopentenylated tRNAs have somewhat elevated levels of free N6-(delta 2-isopentenyl)adenosine. These findings lead to the conclusion that the major, if not exclusive, source of free cytokinins in these two yeasts is a synthetic pathway independent of isopentenylated RNA turnover.

An antisuppressor mutant of Saccharomyces cerevisiae deficient in isopentenylated tRNA has reduced delta 2-isopentenylpyrophosphate: tRNA-delta 2-isopentenyl transferase activity

We have previously reported the isolation and initial characterization of a mutation in Saccharomyces cerevisiae, designated mod5-1, that reduces the capacity of altered tyrosine tRNAs to suppress ochre nonsense mutations. The mutation results in the virtual elimination of the modified tRNA nucleoside, N6-delta 2-(isopentenyl) adenosine, normally found adjacent to the anticodons of certain tRNA species. We demonstrate here that MOD5 codes for delta 2-isopentenylpyrophosphate: tRNA-delta 2-isopentenyl transferase, or a protein that regulates its synthesis.

Does translational ambiguity increase during cell differentiation?

Several observations made in the fungus Podospora anserina suggest that translational ambiguity may increase, and possibly must increase, at specific stages of the life cycle. Such changes in the properties of the translational apparatus seem to occur as well in the yeast S. cerevisiae and in the alga C. reinhardii. A slight increase of the misreading level would allow readthrough or frameshifting necessary to synthesise regulatory proteins in low amount at key points of cellular differentiation.

Mutations relieving hypersensitivity to paromomycin caused by ribosomal suppressors in Podospora anserina

In the fungusPodospora anserina, mutations were selected which relieved the hypersensitivity to paromomycin caused by four suppressors assumed to be ribosomal ambiguity mutations (su1–31,su1–49,su1–60,su2–5). Our first purpose was to isolate new antisuppressor mutations and in fact a new antisuppressor gene,AS7was uncovered. TheAS7–1mutant displays a pleiotropic phenotype and particularly a sporulation defect. On the other hand, a newsu1mutant was obtained which acts as a suppressor and also as an antisuppressor: it can specifically reduce the suppressor effect of certainsu2mutations. This property of somesu1andsu2mutations was already known. Apart from these mutations probably involved in the control of translational fidelity, six mutations conferring cross-resistance to paromomycin and neomycin were isolated. While four of them are localized in thePm1andPm2loci previously identified, the two others define a new gene which controls paromomycin and neomycin resistance,Pm3. Strains carrying thePm3–1allele are sensitive to temperature at the level of growth and sporulation. The three last mutations which were obtained confer no mutant phenotype when separated from thesu1background. They are closely linked to thesu2locus.

Mutations affecting translational fidelity in the eucaryote Podospora anserina: characterization of two ribosomal restrictive mutations

Fifty-nine mutations that restrict suppressor efficiency were selected in the fungus Podospora anserina using four different screening methods. Previous genetic analysis has shown that these antisuppressors lie in six loci and that they could be similar to ribosomal restrictive mutations known in Escherichia coli. The present study deals with the response of two of them, AS1-1 and AS6-1, to paromomycin and low temperature both in vivo and in vitro. The data demonstrate that ribosomes of the mutant and double-mutant strains are equally resistant to the ambiguity effect of paromomycin. These data are the first demonstration of mutations that increase translational fidelity in eucaryotic organism.

Search for ribosomal mutants in Podospora anserina: genetic analysis of cold-sensitive mutants

Twenty-four cold-sensitive (prototrophic) mutants were isolated after UV mutagenesis of protoplasts of the fungusPodospora anserina. Genetic analysis of these mutants was performed in order to detect those among them which were most likely to be impaired in translational fidelity. The 24 mutations belonged to 24 different genes. One half of the mutants were pleiotropic and displayed an altered phenotype: growth rate at the permissive temperature, germination of the spores, fertility and/or sporulation. Nine mutants differed from wild-type in their resistance levels to cycloheximide, trichodermin and/or paromomycin. Several mutations were linked to known ribosomal loci. Two mutations behaved like informational antisuppressors: one is allelic to the previously describedAs3gene and the other one defines a new antisuppressor gene,AS6.

Genetical studies on revertants to sensitivity from a cycloheximide resistant strain of Schizosaccharomyces pombe

Six UV induced cycloheximide-sensitive revertants were isolated from the cyh1-C7 strain of Schizosaccharomyces pombe which is resistant to cycloheximide. In all cases reversion to sensitivity was due to a forward mutation in a second suppressor gene. Genetical analysis showed that at least two genes, designated scr1 and scr2 (scr=suppression of cycloheximide resistance) were involved. Both scr1 and scr2 suppressed the resistance of six independently isolated alleles at the cyh1 locus. They had no effect on two known nonsense mutations in the ade7 locus. The cyh1-C7 strain has an altered 60S ribosomal protein which can be detected by two-dimensional polyacrylamide gel electrophoresis. In two suppressed strains, cyh1-C7 scr1 and cyh1-C7 scr2, the original altered protein was present. However no further ribosomal protein differences were observed which could be correlated with the presence of the scr genes. Both scr mutations conferred cold sensitivity on the organism indicating that they were of the missense type. Hence it seems certain that scr1 and scr2 are not mutations in tRNA genes leading to either nonsense or missense suppression. There is however no direct evidence that they code for ribosomal proteins and exert their effect on cyh1-C7 at the ribosomal level.

Ribosomal suppressors and antisuppressors in Podospora anserina: resistance to cycloheximide

Informational suppressors and antisuppressors have been previously isolated in Podospora anserina, and a range of exclusively genetic arguments have led to the assumption that they correspond to ribosomal mutations. An in vivo and in vitro comparison of the effect of the ribosomal inhibitor cycloheximide on wildtype and mutant strains described in this paper confirms the ribosomal hypothesis for at least some mutants. Indeed, the four mutants in the AS3 gene were cycloheximide resistant, and their ribosomes were found to be resistant when analyzed by polyuridyl-directed polyphenylalanine systhesis. On the other hand, ribosomes from two su 1 mutants were hypersensitive to the drug.