Amino acid replacements resulting from super-suppression of nonsense mutants of iso-1-cytochrome c from yeast

Uncovering Wolbachia diversity upon artificial host transfer

The common endosymbiotic Wolbachia bacteria influence arthropod hosts in multiple ways. They are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that Wolbachia also impact host behavior, metabolic pathways and immunity. Besides their biological and evolutionary roles, Wolbachia are new potential biological control agents for pest and vector management. Importantly, Wolbachia-based control strategies require controlled symbiont transfer between host species and predictable outcomes of novel Wolbachia-host associations. Theoretically, this artificial horizontal transfer could inflict genetic changes within transferred Wolbachia populations. This could be facilitated through de novo mutations in the novel recipient host or changes of haplotype frequencies of polymorphic Wolbachia populations when transferred from donor to recipient hosts. Here we show that Wolbachia resident in the European cherry fruit fly, Rhagoletis cerasi, exhibit ancestral and cryptic sequence polymorphism in three symbiont genes, which are exposed upon microinjection into the new hosts Drosophila simulans and Ceratitis capitata. Our analyses of Wolbachia in microinjected D. simulans over 150 generations after microinjection uncovered infections with multiple Wolbachia strains in trans-infected lines that had previously been typed as single infections. This confirms the persistence of low-titer Wolbachia strains in microinjection experiments that had previously escaped standard detection techniques. Our study demonstrates that infections by multiple Wolbachia strains can shift in prevalence after artificial host transfer driven by either stochastic or selective processes. Trans-infection of Wolbachia can claim fitness costs in new hosts and we speculate that these costs may have driven the shifts of Wolbachia strains that we saw in our model system.

Allosuppressors in yeast

Five loci have been identified inSaccharomyces cerevisiaewhose function reduces suppressor activity in strains carrying ochre super-suppressor mutations. Recessive mutations which allow an increased level of suppression occur at these loci. In such mutants, termed allosuppressors, the serine-inserting suppressorSUPQ5suppresses ochre mutations in a [psi−] background and Class I tyrosine-inserting suppressors are lethal or have a reduced viability. Mutations at two allosuppressor loci,sal3 andsal4, have a lethal interaction with one another and with the extrachromosomal determinant [psi+]. This interaction is expressed in the absence of any suppressor mutation. All the mutant alleles of one allosuppressor locussal3 are cold sensitive. One allosuppressor mutation,sal4.2, is temperature-sensitive for growth, as well as for other aspects of its phenotypic expression; namely the expression ofSUPQ5and the lethal interactions with Class I super-suppressors, with [psi+] and withsal3. At low temperature (24 °C),sal3-sal4.2 double mutants weakly suppress the ochre mutationade2.1, but do not suppresshis5.2 orlys1.1. It is argued that the site of function of the products of these loci is ribosomal and that they are involved in chain termination at UAA codons. It is inferred that the [psi+] factor or its product affects protein synthesis by interaction with the ribosome.

[PSI+]: an epigenetic modulator of translation termination efficiency

The [PSI+] factor of the yeast Saccharomyces cerevisiae is an epigenetic regulator of translation termination. More than three decades ago, genetic analysis of the transmission of [PSI+] revealed a complex and often contradictory series of observations. However, many of these discrepancies may now be reconciled by a revolutionary hypothesis: protein conformation-based inheritance (the prion hypothesis). This model predicts that a single protein can stably exist in at least two distinct physical states, each associated with a different phenotype. Propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other. Mounting genetic and biochemical evidence suggests that the determinant of [PSI+] is the nuclear encoded Sup35p, a component of the translation termination complex. Here we review the series of experiments supporting the yeast prion hypothesis and provide another look at the 30 years of work preceding this theory in light of our current state of knowledge.

rar mutations which increase artificial chromosome stability in Saccharomyces cerevisiae identify transcription and recombination proteins

In an attempt to identify trans-acting factors involved in replication origin function, we have characterized the RAR3 and RAR5 genes, identified by mutations which increase the mitotic stability of artificial chromosomes whose replication is dependent on the activity of weak ARS elements. Sequence analysis has shown that the RAR3 gene is identical to GAL11/SPT13, which encodes a putative transcription factor involved in the expression of a wide range of genes. Change-of-function mutations that truncate the RAR3 protein appear to be required to enhance chromosome stability. In contrast, loss of the RAR5 protein results in enhanced chromosome stability, as if the protein is an inhibitor of ARS function. The RAR5 gene encodes the 175 kDa DNA strand transfer protein beta, an activity that can promote the transfer of a strand from a double-stranded DNA molecule to a complementary single strand. This observation implies that a presumed recombination activity can affect eukaryotic chromosomal replication.

Quantitation of readthrough of termination codons in yeast using a novel gene fusion assay

A simple quantitative in vivo assay has been developed for measuring the efficiency of translation of one or other of the three termination codons. UAA, UAG and UGA in Saccharomyces cerevisiae. The assay employs a 3-phosphoglycerate kinase-beta-galactosidase gene fusion, carried on a multicopy plasmid, in which the otherwise retained reading frame is disrupted by one or other of the three termination codons. Termination readthrough is thus quantitated by measuring beta-galactosidase in transformed strains. Using these plasmids to quantitate the endogenous levels of termination readthrough we show that readthrough of all three codons can be detected in a non-suppressor (sup+) strain of S. cerevisiae. The efficiency of this endogenous readthrough is much higher in a [psi+] strain than in a [psi-] strain with the UGA codon being the leakiest in the nucleotide context used. The utility of the assay plasmids for studying genetic modifiers of nonsense suppressors is also shown by their use to demonstrate that the cytoplasmic genetic determinant [psi+] broadens the decoding properties of a serine-inserting UAA suppressor tRNA (SUQ5) to allow it to translate the other two termination codons in the order of efficiency UAA greater than UAG greater than UGA.

A position effect on the expression of a tRNA gene mediated by the SIR genes in Saccharomyces cerevisiae

The SIR genes of Saccharomyces cerevisiae are responsible for the position-dependent regulation of the a and alpha mating-type genes. Previous work by others has shown that the products of the SIR genes prevent the accumulation of stable transcripts of the a and alpha genes at HML and HMR. Results of this study establish that this regulation is a region-specific effect rather than a gene-specific effect since expression of a tRNA gene placed at HMR is repressed by the products of the SIR genes.

The REC46 gene of Saccharomyces cerevisiae controls mitotic chromosomal stability, recombination and sporulation: cell-type and life cycle stage-specific expression of the rec46-1 mutation

The recessive hyperrecombination mutation rec46-1, isolated by ultraviolet light mutagenesis of the MAT alpha n+1 chromosome VII disomic strain LBL1 (Esposito et al. 1982), enhances the mitotic rates of spontaneous gene conversion, intergenic recombination and restitution of haploidy (due to chromosomal loss or mitotic nondisjunction) in MAT alpha n+1 chromosome VII disomic strains. The rec46-1 mutation does not prevent HO directed homothallic interconversion of mating types. MATa/MaT alpha rec46-1/rec46-1 diploids exhibit the same degree of hyperrecombinational activity as MAT alpha rec46-1 n+1 chromosome VII disomics with respect to gene conversion and intragenic recombination resulting in prototrophy. When compared to MAT alpha rec46-1 n+1 disomics however, MATa/MAT alpha rec46-1/rec46-1 diploids exhibit a ten fold reduced level of hyperrecombinational activity with respect to intergenic recombination and present no evidence of chromosomal loss or nondisjunction resulting in 2n-1 monosomic segregants. MATa/MAT alpha rec46-1/rec46-1 diploids are sporulation-deficient. The results obtained demonstrate that the REC46 gene product modulates mitotic chromosomal stability and recombination and is essential for sporulation (meiosis and ascospore formation).

A position effect on the expression of a tRNA gene mediated by the SIR genes in Saccharomyces cerevisiae

The SIR genes of Saccharomyces cerevisiae are responsible for the position-dependent regulation of the a and alpha mating-type genes. Previous work by others has shown that the products of the SIR genes prevent the accumulation of stable transcripts of the a and alpha genes at HML and HMR. Results of this study establish that this regulation is a region-specific effect rather than a gene-specific effect since expression of a tRNA gene placed at HMR is repressed by the products of the SIR genes.

First position wobble in codon-anticodon pairing: amber suppression by a yeast glutamine tRNA

A 2.4-kb fragment of DNA isolated from the Saccharomyces cerevisiae genome was found to suppress amber mutations when its carrier plasmid was present in high copy number. A 1.2-kb subclone of this fragment was sufficient to confer suppressor activity. Sequencing has established that this fragment carries a normal glutamine tRNA gene. Deletion of this tRNA gene from the subclone resulted in the loss of suppressor activity. The tRNAGln has the anticodon CUG that normally recognizes the glutamine codon CAG. We propose that suppression occurs via an inefficient readthrough of the UAG amber stop codons during translation. Such readthrough requires wobble in the first position of the codon.

Interaction of UAG suppressors and omnipotent suppressors in Saccharomyces cerevisiae

Haploids bearing the dominant UAG suppressor, SUP7-a, and various alleles of the omnipotent suppressor sup35 were examined. The presence of the UAG suppressor reduced the efficiency of some alleles of sup35, and caused other sup35 alleles to be lethal. A nonclassical interaction of the dominant suppressor tRNA and the ribosome is proposed to explain these observations.

The amino-acid sequence of two non-toxic mutants of diphtheria toxin: CRM45 and CRM197

The amino-acid sequences of two diphtheria toxin-related, non-toxic proteins, CRM45 and CRM197 , were deduced from the complete sequence of their genes: tox 45 and tox 197. CRM45 lacks the last 149 C-terminal amino-acid residues, but is otherwise identical to diphtheria toxin: a single C----T transition introduces an "ochre" (TAA) termination signal in tox 45, after the codon for threonine-386. A single G----A transition was also found in tox 197, leading to the substitution of glycine-52, present in the wild-type toxin, with glutamic acid in CRM197 . This aminoacid change is responsible for the loss of the NAD:EF2 ADP-ribosyltransferase activity in CRM197 , due most probably to an alteration of the NAD+ binding site.

Uridine-33 in yeast tRNA not essential for amber suppression

The nucleotide at position 33 on the 5' side of the anticodon of almost all tRNAs is a uridine. Crystallographic studies of different tRNAs reveal that although the precise orientation of uridine-33 is not always the same, it connects the anticodon stacked along the 3' side of the loop with the pyrimidine-32 stacked on the 5' side of the loop. The remarkably conserved nature of uridine-33 and its unique position in the anticodon loop structure has led to suggestions that this nucleotide has an essential role in the translational mechanism. We have developed a biochemical procedure to replace nucleotides 33-35 in yeast tRNATyr with any desired sequence and used it to construct amber suppressor tRNAs having different nucleotides at position 33. As all of these synthetic amber suppressor tRNAs functioned well in eukaryotic in vitro suppression assays, we conclude that uridine-33 does not have an obligatory role in the translation mechanism.

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.

The cyc1-11 mutation in yeast reverts by recombination with a nonallelic gene: composite genes determining the iso-cytochromes c

DNA sequence analysis of a cloned fragment directly established that the cyc1-11 mutation of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae is a two-base-pair substitution that changes the CCA proline codon at amino acid position 76 to a UAA nonsense codon. Analysis of 11 revertant proteins and one cloned revertant gene showed that reversion of the cyc1-11 mutation can occur in three ways: a single base-pair substitution, which produces a serine replacement at position 76; recombination with the nonallelic CYC7 gene of iso-2-cytochrome c, which causes replacement of a segment in the cyc1-11 gene by the corresponding segment of the CYC7 gene; and either a two-base-pair substitution or recombination with the CYC7 gene, which causes the formation of the normal iso-1-cytochrome c sequence. These results demonstrate the occurrence of low frequencies of recombination between nonallelic genes having extensive but not complete homology. The formation of composite genes that share sequences from nonallelic genes may be an evolutionary mechanism for producing protein diversities and for maintaining identical sequences at different loci.

Gene expression in eukaryotes

Gene expression in eukaryotes is influenced by a wide variety of mechanisms including the loss, amplification, and rearrangement of genes. Genes are differentially transcribed, and the RNA transcripts are variably utilized. Multigene families regulate the amount, the diversity, and the timing of gene expression. The present level of understanding of gene expression in eukaryotes is attributable mainly to biochemical methods rather than to traditional genetics. The new techniques that permit analysis and modification of purified genes of known function will identify both the control regions in eukaryotic genes as well as the molecules within cell that influence gene expression.

Directed deletion of a yeast transfer RNA intervening sequence

Many eukaryotic genes contain intevening sequences, segments of DNA that interrupt the continuity of the gene. They are removed from RNA transcripts of the gene by a process known as splicing. The intervening sequence in a yeast tyrosine transfer RNA (tRNA Tyr) suppressor gene was deleted in order to test its role in the expression of the gene. The altered gene and its parent were introduced into yeast by transformation. Both genes exhibited suppressor function, showing that the intervening sequence is not absolutely essential for the expression of this gene.

Order and intracellular location of the events involved in the maturation of a spliced tRNA

Microinjected frog oocytes were used to analyse the RNA processing steps which lead to the appearance of a mature cytoplasmic tRNAtyr molecule. The results show that removal of the intervening sequence from within a yeast tRNAtyr precursor, excision of extra 3' and 5' nucleotides, addition of a 3'-terminal CCA and modification of at least seven ribonucleotides all occur in the nucleus before the tRNAtyr is transported to the cytoplasm. Moreover, we find that the ribonucleotide modifications occur in a strict order which precisely correlates with the size alterations of the tRNAtyr precursor.

Isolation and analysis of recombinant DNA molecules containing yeast DNA

2500 recombinant plasmids containing insertions of yeast nuclear DNA have been cloned in Escherichia coli. It can be calculated that about 85% of the yeast genome is represented in this collection. The clones have been characterized by hybridization to purified RNA species. Of the 2000 clones examined, 75 contain insertions of yeast ribosomal DNA, 201 contain insertions of yeast tRNA genes, and 26 contain DNA sequences that are complementary to abundant mRNA species.

Transcription and processing of intervening sequences in yeast tRNA genes

Genes for yeast tRNATyr and tRNAPhe have been sequenced (Goodman, Olson and Hall, 1977; Valenzuela et al., 1978) which contain additional nucleotides (intervening sequences) within the middle of the gene that are not present in the mature tRNA. We have isolated precursors to rRNATyr and tRNAPhe from a yeast temperature-sensitive mutant (at the rna1 locus) which accumulates only certain precursor tRNAs at the nonpermissive temperature. The tRNATyr and tRNAPhe precursors were analyzed by oligonucleotide mapping; they each contain the intervening sequence and fully matured 5' and 3' termini. Furthermore, these precursors were used as substrates to search for an enzymatic activity which can remove the intervening sequences and religate the ends. We have shown that wild-type yeast contains such an activity, and that this activity specifically removes the intervening sequences to produce mature-sized RNAs.

Dynamics of x-ray-induced reversion in heterogeneous S. cerevisiae populations

The survival and frequency of adenine and homoserine revertants after X-irradiation have been studied in starved and growing populations of haploid S. cerevisiae (strain 5483/1b). A growing population is heterogeneous to cell killing, and a mathematical model can be used to determine possible correlation between sensitivity to killing and sensitivity to mutation induction. The results indicate correlation between sensitivity to ade2-1 reversion and sensitivity to cell killing, whereas no such correlation was found between sensitivity to hom3-10 reversion and sensitivity to killing. The difference in the dynamics of homoserine and adenine reversions was reduced by adding caffeine to the post-irradiation media.

Cloning of yeast transfer RNA genes in Escherichia coli

Four thousand Escherichia coli clones containing yeast DNA inserted into the plasmid pBR313 have been isolated. Of these, 175 clones were identified as carrying yeast transfer RNA genes. The initial analysis of the inserted transfer RNA genes via the colony hybridization technique with individual radioactive transfer RNA species is reported. The data indicate that yeast transfer RNA genes are not highly clustered, although some clustering exists. In addition, it was observed that the reiteration number of different transfer RNA genes may vary extensively.

Molecular specificity of x-radiation and its repair in Saccharomyces cerevisiae

Molecular specificity of soft X-radiation has been studied in yeast by analyzing the transitions UAA in equilibrium UAG and nonsense leads to sense mutations in the codon tyr7-1. Synchronized cell populations in the most radiosensitive and radioresistant stages were compared: they did not show any qualitative or quantitative differences in their sensitivities to the mutagenic action of X-rays. We conclude that repair mechanisms, which remain unexpressed in the sensitive cells, do not affect point mutations of the base-substitution type.

Genetic analysis of a transposable suppressor gene in Saccharomyces cerevisiae

We have demonstrated in Saccharomyces cerevisiae the transposition of a gene coding for an efficient ochre (UAA) suppressor from a centromere-linked site on chromosome III to two new sites in the yeast genome. One site is on chromosome VI, very close to, if not allelic with, SUP11, one of eight genes coding for a tyrosine-inserting suppressor. The second site is on chromosome III, unlinked to the centromere and distal to the mating type locus. This site is very close to those mapped for the recessive lethal amber suppressors, SUP-RL1 and SUP61.

Super suppressor action spectrum in Neurospora

The action of super suppressors mapping at eight separate loci upon ten different nonsense mutants is examined. These suppressors can be subdivided into seven classes based upon their capacity to restore function to the test mutants.

Suppressor-specificity of antisuppressors in yeast

Eighteen mutations ofSaccharomyces cerevisiae, at eight loci, isolated as antisuppressors ofSUPQ2, an ochre-suppressing allele ofSUP11, were crossed with three other suppressors.

They were found to abolish the ability ofSUP2(inserting tyrosine), to suppress the ochre mutationsade2.1andcan1.100, but not its ability, to suppresshis5.2orlys1.1.When coupled with any antisuppressor,SUPQ5, inserting serine, was also unable to suppressade2.1, but the suppression of other ochre mutations varied from oneasu-SUPQ5strain to another. No antisuppressor affected the ability ofSUP11-am, an amber-suppressing allele ofSUP11, to suppresstrp1.1, an amber mutation.

Genetic evidence of ribosomal antisuppressors in Podospora anserina

Antisuppressors were screened for with the help of informational suppressors in Podospores anserina. Four mutations in the AS1 locus and two in the AS2 locus were isolated, using allele non specific suppressors supposed to be ribosomal ambiguity mutations. Four mutations in the AS3 locus and 45 in the AS4 locus were obtained, using a nonsense (t-RNA like) suppressor. All antisuppressors are partially dominant. Most mutations in the AS4 locus are lethal. The four mutants at the AS3 locus and 6 out of the 8 viable mutants at the AS4 locus are cold sensitive. Phenotypic properties and action spectra of the antisuppressors suggest that they are restrictive ribosomal mutations.

Killer of Saccharomyces cerevisiae: a double-stranded ribonucleic acid plasmid

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