Altered 40 S ribosomal subunits in omnipotent suppressors of yeast

The five suppressors SUP35, SUP43, SUP44, SUP45 and SUP46, each mapping at a different chromosomal locus in the yeast Saccharomyces cerevisiae, suppress a wide range of mutations, including representatives of all three types of nonsense mutations, UAA, UAG and UGA. We have demonstrated that ribosomes from the four suppressors SUP35, SUP44, SUP45 and SUP46 translate polyuridylate templates in vitro with higher errors than ribosomes from the normal stain, and that this misreading is substantially enhanced by the antibiotic paromomycin. Furthermore, ribosomal subunit mixing experiments established that the 40 S ribosomal subunit, and this subunit only, is responsible for the higher levels of misreading. Thus, the gene products of SUP35, SUP44, SUP45 and SUP46 are components of the 40 S subunit or are enzymes that modify the subunit. In addition, a protein from the 40 S subunit of the SUP35 suppressor has an altered electrophoretic mobility; this protein is distinct from the altered protein previously uncovered in the 40 S subunit of the SUP46 suppressor. In contrast to the ribosomes from the four suppressors SUP35, SUP44, SUP45 and SUP46, the ribosomes from the SUP43 suppressor do not significantly misread polyuridylate templates in vitro, suggesting that this locus may not encode a ribosomal component or that the misreading is highly specific.     

Release factor competition is equivalent at strong and weakly suppressed nonsense codons

Summary We have compared the competition between strong or weak suppressor tRNAs and translational release factors (RF) at nonsense codons in the lacI gene of Escherichia coli. Using the F'lacIZ fusions developed by Miller and coworkers, UAG, UAA, and UGA codons at positions 189 and 220 were efficiently suppressed by plasmid-borne tRNAtrp suppressors cognate to each nonsense triplet. Introduction of a compatible RF 1 plasmid competed at UAG and UAA but not UGA codons. An RF2 expressing plasmid competed at UAA and UGA but had little effect at UAG. Release factor competition against weak suppressors was measured using combinations of noncognate suppressors and nonsense codons. In each case, release factor plasmids behaved identically towards poorly suppressed codons as they did when the same codons were efficiently suppressed. The implications for these studies on the role of release factors in nonsense suppression context effects are discussed.     

Serine insertion caused by the ribosomal suppressor SUP46 in yeast

The ribosomal suppressor SUP46 isolated from the yeast Saccharomyces cerevisiae suppresses a broad range of mutations, including at least some UAA, UAG and UGA alleles. The SUP46 suppressor causes the insertion of serine into iso-1-cytochrome c at the site of the UAA mutation in the cyc1-72 allele. It is believed that the altered ribosomes in the SUP46 suppressor allow a serine tRNA to misread UAA codons.     

A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some tRNA nonsense suppressors

Summary A spontaneous mutant was isolated that harbors a weak suppressing activity towards a UAG mutation, together with an inability to grow at 43° C in rich medium. The mutation is shown to be associated with an increased misreading of UAG at certain codon contexts and UAA. UGA, missense or frameshift mutations do not appear to be misread to a similar extent. The mutation gives an increased efficiency to several amber tRNA suppressors with-out increasing their ambiguity towards UAA. The ochre suppressors SuB and Su5 are stimulated in their reading of both UAG and UAA with preference for UAG. An opal suppressor is not affected. The effect of the mutation on the efficiency of amber and ochre suppressors is dependent on the codon context of the nonsense codon.The mutated gene (uar) has been mapped and found to be recessive both with respect to suppressor-enhancing ability as well as for temperature sensitivity. The phenotype is partly suppressed by the ochre suppressor SuC. It is suggested that uar codes for a protein, which is involved in translational termination at UAG and UAA stop codons.     

Frameshift suppression through inactivation of translation termination in yeast Saccharomyces cerevisiae: significance of the local context

Site-directed mutagenesis and nucleotide sequence analysis were used to study the roles of the global and local contexts in suppression of the lys2-90 frameshift (FS) mutation in Saccharomyces cerevisiae. Global context features established for the LYS2 mRNA region containing the extra T (lys2-90) were similar to those characteristic of regions involved in translational frameshifting. These were a potential ability of the region to form a pseudoknot and the presence of heptanucleotide CUU UGA C with the "hungry" UGA nonsense codon in the pseudoknot. Some local context features proved to be essential for the phenotypic expression of FS suppression as a result of translational frameshifting. Two amino acid substitutions determined by the nucleotide sequence between the extra U and the UGA nonsense codon lacked expression. A dependence was observed between the efficiency of FS suppression and the type of the nonsense codon located at a particular position downstream of the extra nucleotide (UGA > UAG > UAA). When translation termination was inactivated, nonsense suppression and FS suppression correlated with each other. These results suggest that translational frameshifting, which underlies suppression in the case of inactivation of translation termination, most likely takes place on the nonsense codon arising as a result of insertion of an extra nucleotide.     

Mutations to nonsense codons in human genetic disease: implications for gene therapy by nonsense suppressor tRNAs.

Nonsense suppressor tRNAs have been suggested as potential agents for human somatic gene therapy. Recent work from this laboratory has described significant effects of 3' codon context on the efficiency of human nonsense suppressors. A rapid increase in the number of reports of human diseases caused by nonsense codons, prompted us to determine how the spectrum of mutation to either UAG, UAA or UGA codons and their respective 3' contexts, might effect the efficiency of human suppressor tRNAs employed for purposes of gene therapy. This paper presents a survey of 179 events of mutations to nonsense codons which cause human germline or somatic disease. The analysis revealed a ratio of approximately 1:2:3 for mutation to UAA, UAG and UGA respectively. This pattern is similar, but not identical, to that of naturally occurring stop codons. The 3' contexts of new mutations to stop were also analysed. Once again, the pattern was similar to the contexts surrounding natural termination signals. These results imply there will be little difference in the sensitivity of nonsense mutations and natural stop codons to suppression by nonsense suppressor tRNAs. Analysis of the codons altered by nonsense mutations suggests that efforts to design human UAG suppressor tRNAs charged with Trp, Gln, and Glu; UAA suppressors charged with Gln and Glu, and UGA suppressors which insert Arg, would be an essential step in the development of suppressor tRNAs as agents of human somatic gene therapy.     

Suppression of nonsense and frameshift mutations obtained by different methods for inactivating the translation termination factor eRF3 in yeast Saccharomyces cerevisiae

Mutations in genes of omnipotent nonsense suppressors SUP35 and SUP45 in yeast Saccharomyces cerevisiae encoding translation termination factors eRF3 and eRF1, respectively, and prionization of the eRF3 protein may lead to the suppression of some frameshift mutations (CPC mutations). Partial inactivation of the translation termination factor eRF3 was studied in strains with unstable genetically modified prions and also in transgenic yeast S. cerevisiae strains with the substitution of the indigenous SUP35 gene for its homolog from Pichia methanolica or for a recombinant S. cerevisiae SUP35 gene. It was shown that this partial inactivation leads not only to nonsense suppression, but also to suppression of the frameshift lys2-90 mutation. Possible reasons for the correlation between nonsense suppression and suppression of the CPC lys2-90 mutation and mechanisms responsible for the suppression of CPC mutations during inactivation of translation termination factors are discussed.     

Suppression of Nonsense and Frameshift Mutations Obtained by Different Methods for Inactivating the Translation Termination Factor eRF3 in Yeast Saccharomyces cerevisiae

Mutations in genes of omnipotent nonsense suppressors SUP35 and SUP45 in yeast Saccharomyces cerevisiae encoding translation termination factors eRF3 and eRF1, respectively, and prionization of the eRF3 protein may lead to the suppression of some frameshift mutations (CPC mutations). Partial inactivation of the translation termination factor eRF3 was studied in strains with unstable genetically modified prions and also in transgenic yeast S. cerevisiae strains with the substitution of the indigenous SUP35 gene for its homolog from Pichia methanolica or for a recombinant S. cerevisiae SUP35gene. It was shown that this partial inactivation leads not only to nonsense suppression, but also to suppression of the frameshift lys2-90 mutation. Possible reasons for the correlation between nonsense suppression and suppression of the CPC lys2-90 mutation and mechanisms responsible for the suppression of CPC mutations during inactivation of translation termination factors are discussed.     

Frameshift Suppression through Inactivation of Translation Termination in Yeast Saccharomyces cerevisiae: Significance of the Local Context

Site-directed mutagenesis and nucleotide sequence analysis were used to study the roles of the global and local contexts in suppression of the lys2-90 frameshift (FS) mutation inSaccharomyces cerevisiae. Global context features established for the LYS2 mRNA region containing the extra T (lys2-90) were similar to those characteristic of regions involved in translational frameshifting. These were a potential ability of the region to form a pseudoknot and the presence of heptanucleotide CUU UGA C with the hungry UGA nonsense codon in the pseudoknot. Some local context features proved to be essential for the phenotypic expression of FS suppression as a result of translational frameshifting. Two amino acid substitutions determined by the nucleotide sequence between the extra U and the UGA nonsense codon lacked expression. A dependence was observed between the efficiency of FS suppression and the type of the nonsense codon located at a particular position downstream of the extra nucleotide (UGA > UAG > UAA). When translation termination was inactivated, nonsense suppression and FS suppression correlated with each other. These results suggest that translational frameshifting, which underlies suppression in the case of inactivation of translation termination, most likely takes place on the nonsense codon arising as a result of insertion of an extra nucleotide.     

Analysis of specific misreading in Escherichia coli

The pattern of specific misreading by nonsense suppressors has been investigated using nonsense mutants in the rIIB gene of phage T4 and in the lacZ gene of Escherichia coli. It is shown that a su⁺ transfer RNA which reads UAG also misreads UAA but not UGA, a su⁺ tRNA which reads UAA (while it also reads UAG by wobble) misreads UGA and a su⁺ tRNA which reads UGA also probably misreads UAA but not UAG.These specific types of errors in translation occur in the absence of streptomycin. The addition of the drug raises their level without altering the pattern described. A ribosomal mutation str A reduces the level of specific misreading; by contrast, a ram mutation strongly increases this level. In all cases the specific pattern is not affected.The rate of specific misreading of nonsense codons in different cases ranges from less than 0.001% to more than 3%. Since the frequency of misreading is sitespecific (unpublished observations), the rates obtained cannot be extrapolated to any other codon at any other site.     

Variation of phenotypic suppression due to the psi+ and psi- extrachromosomal determinants in yeast.

Paromomycin, an aminoglycoside antibiotic, can phenotypically suppress nonsense mutations in the yeast Saccharomyces cerevisiae (Palmer et al., 1979). We report here that the extrachromosomal determinant, ψ⁺, enhances this phenotypic suppression of all three nonsense mutations. UAG. UAA and UGA, by three-to sevenfold.     

Nonsense suppressor and antisuppressor mutations at the 1409-1491 base pair in the decoding region of Escherichia coli 16S rRNA.

Using a genetic selection for suppressors of a UGA nonsense mutation in trpA, we have isolated a G to A transition mutation at position 1491 in the decoding region of 16S rRNA. This suppressor displayed no codon specificity, suppressing UGA, UAG and UAA nonsense mutations and +1 and -1 frameshift mutations in lacZ. Subsequent examination of a series of mutations at G1491 and its base-pairing partner C1409 revealed various effects on nonsense suppression and frameshifting. Mutations that prevented Watson-Crick base pairing between these residues were observed to increase misreading and frameshifting. However, double mutations that retained pairing potential produced an antisuppressor or hyperaccurate phenotype. Previous studies of antibiotic resistance mutations and antibiotic and tRNA footprints have placed G1491 and C1409 near the site of codon-anticodon pairing. The results of this study demonstrate that the nature of the interaction of these two residues influences the fidelity of tRNA selection.     

Aminoglycoside suppression at UAG, UAA and UGA codons in Escherichia coli and human tissue culture cells

Summary We have compared the suppression of nonsense mutations by aminoglycoside antibiotics inEscherichia coli and in human 293 cells. Six nonsense alleles of the chloramphenicol acetyl transferase (cat) gene, in the vector pRSVcat, were suppressed by growth in G418 and paromomycin. Readthrough at UAG, UAA and UGA codons was monitored with enzyme assays for chloramphenicol acetyl transferase (CAT), in stably transformed bacteria and during transient expression from the same plasmid in human 293 tissue culture cells. We have found significant differences in the degree of suppression amongst three UAG codons and two UAA codons in different mRNA contexts. However, the pattern of these effects are not the same in the two organisms. Our data suggest that context effects of nonsense suppression may operate under different rules inE. coli and human cells.     

Recessive Uaa Suppressors of the Yeast SACCHAROMYCES CEREVISIAE

Recessive lysine-independent revertants were isolated from a ψ⁺ haploid strain of the yeast Saccharomyces cerevisiae containing one of the leucine-inserting UAA suppressors, SUP29, and various UAA mutations including lys1-1. The majority of the revertants were found to have recessive suppressors in addition to the pre-existing SUP29 mutation. The recessive suppressors were able to suppress only a very limited number of UAA mutations, and none of the UAG mutations thus far examined. The recessive inefficient UAA suppressors were assigned to three complementation groups, sup111, sup112, and sup113. A high incidence of gene conversion was observed for an allele of sup111. An antisuppressor acting on sup111, but not detectably on SUP29, was inadvertently obtained during the course of the study. Interactions between SUP29, sup111 and the antisuppressor asu12 were studied.     

Nonsense mutations in the can1 locus of Saccharomyces cerevisiae.

Yeast mutants resistant to L-canavanine were selected. All were recessive and fell into the can1 complementation group. Nonsense mutations were identified among them by using a set of different suppressors. Frequencies of UAA, UAG, and presumed UGA mutations were 14.8, 0.8, and 0.4%, respectively. A high incidence of nonsense mutations having discriminatory suppression patterns was characteristic of the locus.     

A novel method for detection and characterization of ochere suppressors in Escherichia coli

Summary We have found a new method for specifically detecting the occurrence of ochre (UAA) suppression in Escherichia coli. It is based on a procedure we used several years ago to distinguish trpA missense mutants from nonsense mutants, and relies on the generally low efficiency of suppression that seems to be characteristic of ochre suppressors in E. coli. Suppressed ochre mutants are distinguishable from trpA revertants by their inability to grow on glucose minimal medium containing a low concentration (1.5 m/ml) of indole and a high concentration (50 g/ml) of 5-methyl-DL-tryptophan (Ind-5MT). The procedure provides a specific and rapid means for detection of UAA derived from missense codons and has also been exploited to obtain different classes of ochre suppressors derived from the amber suppressor supDam and from a glycine tRNA missense suppressor. The Ind-5MT phenotype seems to depend in some way on the location of the ochre codon within the trpA messenger RNA. The method can be put to many uses and should be generally applicable to all low-efficiency nonsense suppressors, including those specific for UAG and UGA.Preliminary reports of portions of this work were presented at the spring meeting of the Texas Branch of the American Society for Microbiology, College Station, Texas, March, 1975     

Nonsense Suppression of the Major Rhodopsin Gene of Drosophila

We placed UAA, UAG and UGA nonsense mutations at two leucine codons, Leu205 and Leu309, in Drosophila's major rhodopsin gene, ninaE, by site-directed mutagenesis, and then created the corresponding mutants by P element-mediated transformation of a ninaE deficiency strain. In the absence of a genetic suppressor, flies harboring any of the nonsense mutations at the 309 site, but not the 205 site, show increased rhodopsin activity. Additionally, all flies with nonsense mutations at either site have better rhabdomere structure than does the ninaE deficiency strain. Construction and analysis of a 3'-deletion mutant of ninaE indicates that translational readthrough accounts for the extra photoreceptor activity of the ninaE309 alleles and that truncated opsins are responsible for the improved rhabdomere structure. The presence of leucine-inserting tRNA nonsense suppressors DtLa Su+ and DtLb Su+ in the mutant strains produced a small increase (less than 0.04%) in functional rhodopsin. The opal (UGA) suppressor derived from the DtLa tRNA gene is more efficient than the amber (UAG) or opal suppressor derived from the DtLb gene, and both DtLa and DtLb derived suppressors are more efficient at site 205 than 309.     

Construction, expression, and function of a new yeast amber suppressor, tRNATrpA

The number of different tRNA species in Saccharomyces cerevisiae known to be capable of suppressing termination of translation at UAG, UAA, and UGA codons is limited to those which insert tyrosine, leucine, and serine. Suppressor tRNAs that insert other amino acids, even those whose anticodons differ from the expected recognition sequences for nonsense codons by a single nucleotide, have never been identified via classical genetic analysis. We have used site-directed mutagenesis to convert the anticodon of a cloned tRNATrp gene from CCA to CTA with the expectation that this gene would produce tRNA molecules capable of interacting with the UAG terminator codon. We show that this form of the gene can be transcribed and spliced in vitro to produce mature tRNA with the expected base sequence. The putative suppressor gene has been introduced into several S. cerevisiae host strains using the centromere vector YCp19. Efficient suppression of amber mutations met8-1, tyr7-1, and lys2-801 results from the presence of the CTA form of tDNATrp. Two UAA mutants, leu2-1 and ade2-101, and the UGA marker his4-260 are not suppressed.     

Defined set of cloned termination suppressors: in vivo activity of isogenetic UAG, UAA, and UGA suppressor tRNAs.

We have cloned an isogenetic set of UAG, UAA, and UGA suppressors. These include the Su7 -UAG, Su7 -UAA, and Su7 -UGA suppressors derived from base substitutions in the anticodon of Escherichia coli tRNATrp and also Su9 , a UGA suppressor derived from a base substitution in the D-arm of the same tRNA. These genes are cloned on high-copy-number plasmids under lac promoter control. The construction of the Su7 -UAG plasmid and the wild-type trpT plasmid have been previously described ( Yarus , et al., Proc. Natl. Acad. Sci. U.S.A. 77:5092-5097, 1980). Su7 -UAA ( trpT177 ) is a weak suppressor which recognizes both UAA and UAG nonsense codons and probably inserts glutamine. Su7 -UGA ( trpT176 ) is a strong UGA suppressor which may insert tryptophan. Su9 ( trpT178 ) is a moderately strong UGA suppressor which also recognizes UGG (Trp) codons, and it inserts tryptophan. The construction of these plasmids is detailed within. Data on the DNA sequences of these trpT alleles and on amino acid specificity of the suppressors are presented. The efficiency of the cloned suppressors at certain nonsense mutations has been measured and is discussed with respect to the context of these codons.