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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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2
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Wickner RB, Edskes HK, Kryndushkin D, Shewmaker FP. Genetic Methods for Studying Yeast Prions. Cold Spring Harb Protoc 2017; 2017:2017/2/pdb.prot089029. [PMID: 28148848 DOI: 10.1101/pdb.prot089029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The recognition that certain long-known nonchromosomal genetic elements were actually prions was based not on the specific phenotypic manifestations of those elements, but rather on their unusual genetic properties. Here, we outline methods of prion assay, methods for showing the nonchromosomal inheritance, and methods for determining whether a nonchromosomal trait has the unusual characteristics diagnostic of a prion. Finally, we discuss genetic methods often useful in the study of yeast prions.
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Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830;
| | - Herman K Edskes
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830
| | - Dmitry Kryndushkin
- Department of Pharmacology, Uniformed Services University of Health Sciences, Bethesda, Maryland 20814
| | - Frank P Shewmaker
- Department of Pharmacology, Uniformed Services University of Health Sciences, Bethesda, Maryland 20814
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3
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Abstract
Sup35p of Saccharomyces cerevisiae can form the [PSI+] prion, an infectious amyloid in which the protein is largely inactive. The part of Sup35p that forms the amyloid is the region normally involved in control of mRNA turnover. The formation of [PSI+] by Sup35p's from other yeasts has been interpreted to imply that the prion-forming ability of Sup35p is conserved in evolution, and thus of survival/fitness/evolutionary value to these organisms. We surveyed a larger number of yeast and fungal species by the same criteria as used previously and find that the Sup35p from many species cannot form prions. [PSI+] could be formed by the Sup35p from Candida albicans, Candida maltosa, Debaromyces hansenii, and Kluyveromyces lactis, but orders of magnitude less often than the S. cerevisiae Sup35p converts to the prion form. The Sup35s from Schizosaccharomyces pombe and Ashbya gossypii clearly do not form [PSI+]. We were also unable to detect [PSI+] formation by the Sup35ps from Aspergillus nidulans, Aspergillus fumigatus, Magnaporthe grisea, Ustilago maydis, or Cryptococcus neoformans. Each of two C. albicans SUP35 alleles can form [PSI+], but transmission from one to the other is partially blocked. These results suggest that the prion-forming ability of Sup35p is not a conserved trait, but is an occasional deleterious side effect of a protein domain conserved for another function.
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4
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Hasin N, Cusack SA, Ali SS, Fitzpatrick DA, Jones GW. Global transcript and phenotypic analysis of yeast cells expressing Ssa1, Ssa2, Ssa3 or Ssa4 as sole source of cytosolic Hsp70-Ssa chaperone activity. BMC Genomics 2014; 15:194. [PMID: 24628813 PMCID: PMC4022180 DOI: 10.1186/1471-2164-15-194] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 03/07/2014] [Indexed: 11/18/2022] Open
Abstract
Background Cytosolic Hsp70 is a ubiquitous molecular chaperone that is involved in responding to a variety of cellular stresses. A major function of Hsp70 is to prevent the aggregation of denatured proteins by binding to exposed hydrophobic regions and preventing the accumulation of amorphous aggregates. To gain further insight into the functional redundancy and specialisation of the highly homologous yeast Hsp70-Ssa family we expressed each of the individual Ssa proteins as the sole source of Hsp70 in the cell and assessed phenotypic differences in prion propagation and stress resistance. Additionally we also analysed the global gene expression patterns in yeast strains expressing individual Ssa proteins, using microarray and RT-qPCR analysis. Results We confirm and extend previous studies demonstrating that cells expressing different Hsp70-Ssa isoforms vary in their ability to propagate the yeast [PSI+] prion, with Ssa3 being the most proficient. Of the four Ssa family members the heat inducible isoforms are more proficient in acquiring thermotolerance and we show a greater requirement than was previously thought, for cellular processes in addition to the traditional Hsp104 protein disaggregase machinery, in acquiring such thermotolerance. Cells expressing different Hsp70-Ssa isoforms also display differences in phenotypic response to exposure to cell wall damaging and oxidative stress agents, again with the heat inducible isoforms providing better protection than constitutive isoforms. We assessed global transcriptome profiles for cells expressing individual Hsp70-Ssa isoforms as the sole source of cytosolic Hsp70, and identified a significant difference in cellular gene expression between these strains. Differences in gene expression profiles provide a rationale for some phenotypic differences we observed in this study. We also demonstrate a high degree of correlation between microarray data and RT-qPCR analysis for a selection of genes. Conclusions The Hsp70-Ssa family provide both redundant and variant-specific functions within the yeast cell. Yeast cells expressing individual members of the Hsp70-Ssa family as the sole source of Ssa protein display differences in global gene expression profiles. These changes in global gene expression may contribute significantly to the phenotypic differences observed between the Hsp70-Ssa family members. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-194) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Gary W Jones
- Yeast Genetics Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland.
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5
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Singh A, Helms C, Sherman F. Mutation of the non-Mendelian suppressor, Psi, in yeast by hypertonic media. Proc Natl Acad Sci U S A 2010; 76:1952-6. [PMID: 16592643 PMCID: PMC383511 DOI: 10.1073/pnas.76.4.1952] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Psi(+) extrachromosomal determinant in the yeast Saccharomyces cerevisiae suppresses certain UAA markers and increases the efficiency of suppression of UAA suppressors and certain frameshift suppressors. Although the exact nature of Psi(+) determinant is unknown, it is believed to be a self-replicating cytoplasmic factor affecting some component of the translational machinery. In this report we describe growth conditions for efficient mutation or elimination of the Psi(+) determinant. Incubation of Psi(+) cultures in hypertonic nutrient medium resulted in rapid conversion to a culture containing predominantly Psi(-) cells during the growth cycle. The kinetics of Psi(+) to Psi(-) conversion established that the occurrence of Psi(-) cells was due to induction and not to selection of pre-existing Psi(-) cells. The results suggest that the replication of the Psi(+) determinant is sensitive to hypertonic conditions.
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Affiliation(s)
- A Singh
- Department of Radiation Biology and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
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6
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Abstract
SUMMARYFive 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.
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Kiktev D, Vechtomov SI, Zhouravleva G. Prion-dependent lethality of sup45 mutants in Saccharomyces cerevisiae. Prion 2007; 1:136-43. [PMID: 19164896 DOI: 10.4161/pri.1.2.4533] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In yeast Saccharomyces cerevisiae translation termination factors eRF1 (Sup45) and eRF3 (Sup35) are encoded by the essential genes SUP45 and SUP35 respectively. Heritable aggregation of Sup35 results in formation of the yeast prion [PSI(+)]. It is known that combination of [PSI(+)] with some mutant alleles of the SUP35 or SUP45 genes in one and the same haploid yeast cell causes synthetic lethality. In this study, we perform detailed analysis of synthetic lethality between various sup45 nonsense and missense mutations on one hand, and different variants of [PSI(+)] on the other hand. Synthetic lethality with sup45 mutations was detected for [PSI(+)] variants of different stringencies. Moreover, we demonstrate for the first time that in some combinations, synthetic lethality is dominant and occurs at the postzygotic stage after only a few cell divisions. The tRNA suppressor SUQ5 counteracts the prion-dependent lethality of the nonsense alleles but not of the missense alleles of SUP45, indicating that the lethal effect is due to the depletion of Sup45. Synthetic lethality is also suppressed in the presence of the C-proximal fragment of Sup35 (Sup35C) that lacks the prion domain and cannot be included into the prion aggregates. Remarkably, the production of Sup35C in a sup45 mutant strain is also accompanied by an increase in the Sup45 levels, suggesting that translationally active Sup35 up-regulates Sup45 or protects it from degradation.
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Affiliation(s)
- Denis Kiktev
- Department of Genetics and Breeding, St Petersburg State University, St. Petersburg, Russia
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8
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Manogaran AL, Kirkland KT, Liebman SW. An engineered nonsense URA3 allele provides a versatile system to detect the presence, absence and appearance of the [PSI+] prion in Saccharomyces cerevisiae. Yeast 2006; 23:141-7. [PMID: 16491470 PMCID: PMC2600413 DOI: 10.1002/yea.1341] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Common methods to identify yeast cells containing the prion form of the Sup35 translation termination factor, [PSI+], involve a nonsense suppressor phenotype. Decreased function of Sup35p in [PSI+] cells leads to read-through of certain nonsense mutations in a few auxotrophic markers, e.g. ade1-14. This read-through results in growth on adenine-deficient media. While this powerful tool has dramatically facilitated the study of [PSI+], it is limited to a narrow range of laboratory strains and cannot easily be used to screen for cells that have lost the [PSI+] prion. Therefore we have engineered a nonsense mutation in the widely used URA3 gene, termed the ura3-14 allele. Introduction of the ura3-14 allele into an array of genetic backgrounds, carrying a loss-of-function URA3 mutation and [PSI+], allows for growth on media lacking uracil, indicative of decreased translational termination efficiency. This ura3-14 allele is able to distinguish various forms of the [PSI+] prion, called variants, and is able to detect the de novo appearance of [PSI+] in strains carrying the prion form of Rnq1p, [PIN+]. Furthermore, 5-fluoroorotic acid, which kills cells making functional Ura3p, provides a means to select for [psi-] derivatives in a population of [PSI+] cells marked with the ura3-14 allele, making this system much more versatile than previous methods.
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Affiliation(s)
| | | | - Susan W. Liebman
- Correspondence author: Susan W. Liebman, Phone: (312) 996-4662, Fax: (312) 413-2691,
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9
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Wickner RB, Edskes HK, Roberts BT, Baxa U, Pierce MM, Ross ED, Brachmann A. Prions: proteins as genes and infectious entities. Genes Dev 2004; 18:470-85. [PMID: 15037545 DOI: 10.1101/gad.1177104] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Reed B Wickner
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0830, USA.
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10
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Serio TR, Lindquist SL. The yeast prion [PSI+]: molecular insights and functional consequences. ADVANCES IN PROTEIN CHEMISTRY 2002; 59:391-412. [PMID: 11868278 DOI: 10.1016/s0065-3233(01)59012-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- T R Serio
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
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11
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Van Everbroeck B, Pals P, Martin JJ, Cras P. Transmissible spongiform encephalopathies: the story of a pathogenic protein. Peptides 2002; 23:1351-9. [PMID: 12128092 DOI: 10.1016/s0196-9781(02)00071-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An overview is provided from the first description of the transmissible spongiform encephalopathies (TSE) to recent major discoveries in this research field. The TSE are a group of diseases in animal and in man caused by a unique pathogen: the prion protein. The exact nature of the etiological agent or the prion protein is thought to be a misfolded protein. Although current research has provided a wealth of data indicating that a structural isoform of the prion protein is the responsible pathogen, this hypothesis is not yet experimentally proven.
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Affiliation(s)
- Bart Van Everbroeck
- Laboratory of Neurobiology, Born Bunge Foundation, University of Antwerp (UIA), Universiteitsplein 1, B-2610 Antwerp, Belgium
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12
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Jung G, Jones G, Wegrzyn RD, Masison DC. A role for cytosolic hsp70 in yeast [PSI(+)] prion propagation and [PSI(+)] as a cellular stress. Genetics 2000; 156:559-70. [PMID: 11014806 PMCID: PMC1461277 DOI: 10.1093/genetics/156.2.559] [Citation(s) in RCA: 176] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
[PSI(+)] is a prion (infectious protein) of Sup35p, a subunit of the Saccharomyces cerevisiae translation termination factor. We isolated a dominant allele, SSA1-21, of a gene encoding an Hsp70 chaperone that impairs [PSI(+)] mitotic stability and weakens allosuppression caused by [PSI(+)]. While [PSI(+)] stability is normal in strains lacking SSA1, SSA2, or both, SSA1-21 strains with a deletion of SSA2 cannot propagate [PSI(+)]. SSA1-21 [PSI(+)] strains are hypersensitive to curing of [PSI(+)] by guanidine-hydrochloride and partially cured of [PSI(+)] by rapid induction of the heat-shock response but not by growth at 37 degrees. The number of inheritable [PSI(+)] particles is significantly reduced in SSA1-21 cells. SSA1-21 effects on [PSI(+)] appear to be independent of Hsp104, another stress-inducible protein chaperone known to be involved in [PSI(+)] propagation. We propose that cytosolic Hsp70 is important for the formation of Sup35p polymers characteristic of [PSI(+)] from preexisting material and that Ssa1-21p both lacks and interferes with this activity. We further demonstrate that the negative effect of heat stress on [PSI(+)] phenotype directly correlates with solubility of Sup35p and find that in wild-type strains the presence of [PSI(+)] causes a stress that elevates basal expression of Hsp104 and SSA1.
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Affiliation(s)
- G Jung
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0851, USA
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13
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Abstract
Recent work suggests that two unrelated phenotypes, [PSI+] and [URE3], in the yeast Saccharomyces cerevisiae are transmitted by non-covalent changes in the physical states of their protein determinants, Sup35p and Ure2p, rather than by changes in the genes that encode these proteins. The mechanism by which alternative protein states are self-propagating is the key to understanding how proteins function as elements of epigenetic inheritance. Here, we focus on recent molecular-genetic analysis of the inheritance of the [PSI+] factor of S. cerevisiae. Insights into this process might be extendable to a group of mammalian diseases (the amyloidoses), which are also believed to be a manifestation of self-perpetuating changes in protein conformation.
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Affiliation(s)
- T R Serio
- Dept of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
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14
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Serio TR, Cashikar AG, Moslehi JJ, Kowal AS, Lindquist SL. Yeast prion [psi +] and its determinant, Sup35p. Methods Enzymol 1999; 309:649-73. [PMID: 10507053 DOI: 10.1016/s0076-6879(99)09043-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- T R Serio
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
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15
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Derkatch IL, Bradley ME, Liebman SW. Overexpression of the SUP45 gene encoding a Sup35p-binding protein inhibits the induction of the de novo appearance of the [PSI+] prion. Proc Natl Acad Sci U S A 1998; 95:2400-5. [PMID: 9482897 PMCID: PMC19355 DOI: 10.1073/pnas.95.5.2400] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
[PSI+], a non-Mendelian element found in some strains of Saccharomyces cerevisiae, is presumed to be the manifestation of a self-propagating prion conformation of eRF3 (Sup35p). Translation termination factor eRF3 enhances the activity of release factor eRF1 (Sup45p). As predicted by the prion model, overproduction of Sup35p induces the de novo appearance of [PSI+]. However, another non-Mendelian determinant, [PIN+], is required for this induction. We now show that SUP45 overexpression inhibits the induction of [PSI+] by Sup35p overproduction in [PIN+] strains, but has no effect on the propagation of [PSI+] or on the [PIN] status of the cells. We also show that SUP45 overexpression counteracts the growth inhibition usually associated with overexpression of SUP35 in [PSI+] strains. We argue that excess Sup45p inhibits [PSI+] seed formation. Because Sup45p complexes with Sup35p, we hypothesize that excess Sup45p may sequester Sup35p, thereby reducing the opportunity for Sup35p conformational flips and/or self-interactions leading to prion formation. This in vivo yeast result is reminiscent of the in vitro finding by investigators of Alzheimer disease that apolipoprotein E inhibits amyloid nucleation, but does not reduce seeded growth of amyloid.
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Affiliation(s)
- I L Derkatch
- Laboratory for Molecular Biology, Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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16
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Paushkin SV, Kushnirov VV, Smirnov VN, Ter-Avanesyan MD. Interaction between yeast Sup45p (eRF1) and Sup35p (eRF3) polypeptide chain release factors: implications for prion-dependent regulation. Mol Cell Biol 1997; 17:2798-805. [PMID: 9111351 PMCID: PMC232131 DOI: 10.1128/mcb.17.5.2798] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The SUP45 and SUP35 genes of Saccharomyces cerevisiae encode polypeptide chain release factors eRF1 and eRF3, respectively. It has been suggested that the Sup35 protein (Sup35p) is subject to a heritable conformational switch, similar to mammalian prions, thus giving rise to the non-Mendelian [PSI+] nonsense suppressor determinant. In a [PSI+] state, Sup35p forms high-molecular-weight aggregates which may inhibit Sup35p activity, leading to the [PSI+] phenotype. Sup35p is composed of the N-terminal domain (N) required for [PSI+] maintenance, the presumably nonfunctional middle region (M), and the C-terminal domain (C) essential for translation termination. In this study, we observed that the N domain, alone or as a part of larger fragments, can form aggregates in [PSI+] cells. Two sites for Sup45p binding were found within Sup35p: one is formed by the N and M domains, and the other is located within the C domain. Similarly to Sup35p, in [PSI+] cells Sup45p was found in aggregates. The aggregation of Sup45p is caused by its binding to Sup35p and was not observed when the aggregated Sup35p fragments did not contain sites for Sup45p binding. The incorporation of Sup45p into the aggregates should inhibit its activity. The N domain of Sup35p, responsible for its aggregation in [PSI+] cells, may thus act as a repressor of another polypeptide chain release factor, Sup45p. This phenomenon represents a novel mechanism of regulation of gene expression at the posttranslational level.
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Affiliation(s)
- S V Paushkin
- Institute of Experimental Cardiology, Cardiology Research Center, Moscow, Russia
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17
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Abstract
Saccharomyces cerevisiae is host to the dsRNA viruses L-A (including its killer toxin-encoding satellite, M) and L-BC, the 20S and 23S ssRNA replicons, and the putative prions, [URE3] and [PSI]. review the genetic and biochemical evidence indicating that [URE3] and [PSI] are prion forms of Ure2p and Sup35p, respectively. Each has an N-terminal domain involved in propagation or generation of the prion state and a C-terminal domain responsible for the protein's normal function, nitrogen regulation, or translation termination, respectively. The L-A dsRNA virus expression, replication, and RNA packaging are reviewed. L-A uses a -1 ribosomal frameshift to produce a Gag-Pol fusion protein. The host SK12, SK13 and SK18 proteins block translation of nonpoly(A) mRNAs (such as viral mRNA). Mutants deficient in 60S ribosomal subunits replicate L-A poorly, but not if cells are also ski-. Interaction of 60S subunits with the 3' polyA is suggested. SKI1/XRN1 is a 5'--> 3' exoribonuclease that degrades uncapped mRNAs. The viral Gag protein decapitates cellular mRNAs apparently to decoy this enzyme from working on viral mRNA.
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Affiliation(s)
- R B Wickner
- National Institute of Diabetes, Digestive and Kidney Disease, National Institute of Health, Bethesda, Maryland 20892-0830, USA
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18
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Affiliation(s)
- R B Wickner
- Section on Genetics of Simple Eukaryotes, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
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19
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Abstract
[URE3] is a non-Mendelian genetic element that mimics recessive mutations in the chromosomal URE2 gene making cells derepressed for nitrogen catabolic enzymes. [PSI] is a non-Mendelian enhancer of readthrough of translational termination similar in its effects to some mutations in the chromosomal SUP35 gene. Three lines of evidence led to the proposal that both [URE3] and [PSI] are prions, infectious proteins analogous to the scrapie agent mediating transmissible spongiform encephalopathies of mammals. 1) Both [PSI] and [URE3] are reversibly curable. 2) [PSI] propagation requires SUP35 and [URE3] propagation requires URE2 with recessive chromosomal mutants having the same phenotypes as the presence of the respective dominant non-Mendelian element. 3) Overproduction of Sup35p and Ure2p increases the frequency of cells acquiring [PSI] or [URE3], respectively.
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Affiliation(s)
- R B Wickner
- Section on Genetics of Simple Eukaryotes, National Institute of Diabetes, Digestive and Kidney Diseases, Bethesda, MD 20892-0830, USA
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20
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Ter-Avanesyan MD, Kushnirov VV, Dagkesamanskaya AR, Didichenko SA, Chernoff YO, Inge-Vechtomov SG, Smirnov VN. Deletion analysis of the SUP35 gene of the yeast Saccharomyces cerevisiae reveals two non-overlapping functional regions in the encoded protein. Mol Microbiol 1993; 7:683-92. [PMID: 8469113 DOI: 10.1111/j.1365-2958.1993.tb01159.x] [Citation(s) in RCA: 252] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
SUP35 is an omnipotent suppressor gene of Saccharomyces cerevisiae coding for a protein consisting of a C-terminal part similar to the elongation factor EF-1 alpha and a unique N-terminal sequence of 253 amino acids. Twelve truncated versions of the SUP35 gene were generated by the deletion of fragments internal to the coding sequence. Functional studies of these deletion mutants showed that: (i) only the EF-1 alpha-like C-terminal part of the Sup35 protein is essential for the cell viability; (ii) overexpression of either the N-terminal part of the Sup35 protein or the full-length Sup35 protein decreases translational fidelity, resulting in omnipotent suppression and reduced growth of [psi+] strains; (iii) expression of the C-terminal part of the Sup35 protein generates an antisuppressor phenotype; and (iv) both the N- or C-terminal segments of the Sup35 protein can bind to 80S ribosomes. Thus, the data obtained define two domains within the Sup35 protein which are responsible for different functions.
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Affiliation(s)
- M D Ter-Avanesyan
- Institute of Experimental Cardiology, Cardiology Research Centre, Moscow, Russia
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21
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All-Robyn JA, Kelley-Geraghty D, Griffin E, Brown N, Liebman SW. Isolation of omnipotent suppressors in an [eta+] yeast strain. Genetics 1990; 124:505-14. [PMID: 2311916 PMCID: PMC1203944 DOI: 10.1093/genetics/124.3.505] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Omnipotent suppressors decrease translational fidelity and cause misreading of nonsense codons. In the presence of the non-Mendelian factor [eta+], some alleles of previously isolated omnipotent suppressors are lethal. Thus the current search was conducted in an [eta+] strain in an effort to identify new suppressor loci. A new omnipotent suppressor, SUP39, and alleles of sup35, sup45, SUP44 and SUP46 were identified. Efficiencies of the dominant suppressors were dramatically reduced in strains that were cured of non-Mendelian factors by growth on guanidine hydrochloride. Wild-type alleles of SUP44 and SUP46 were cloned and these clones were used to facilitate the genetic analyses. SUP44 was shown to be on chromosome VII linked to cyh2, and SUP46 was clearly identified as distinct from the linked sup45.
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Affiliation(s)
- J A All-Robyn
- Department of Biological Sciences, University of Illinois, Chicago 60680
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22
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Affiliation(s)
- B S Cox
- Plant Sciences Department, Oxford, U.K
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23
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Tuite MF, McLaughlin CS. The effects of paromomycin on the fidelity of translation in a yeast cell-free system. BIOCHIMICA ET BIOPHYSICA ACTA 1984; 783:166-70. [PMID: 6388640 DOI: 10.1016/0167-4781(84)90009-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The effects of the aminoglycoside antibiotic paromomycin on the fidelity of translation of the synthetic template poly(U), and two natural mRNAs (rabbit globin mRNA and Brome Mosaic virus RNA), were examined in an mRNA-dependent cell-free system from the yeast Saccharomyces cerevisiae. At antibiotic concentrations that did not inhibit translation (100 microM) optimal mistranslation of all three templates was observed, with the effects declining at higher antibiotic concentrations. Synthesis of the opal termination read-through protein of rabbit beta-globin mRNA was induced by paromomycin, but only in lysates prepared from a [psi+] strain of yeast. The antibiotic did not induce detectable levels of either ochre or amber read-through, but did induce general misreading of Brome Mosaic virus RNA to the same degree in both [psi+] and [psi-] lysates. This misreading was enhanced by addition of the polyamine spermidine.
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25
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A non-Mendelian factor, [eta+], causes lethality of yeast omnipotent-suppressor strains. Curr Genet 1984; 8:567-73. [DOI: 10.1007/bf00395701] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/1984] [Indexed: 11/26/2022]
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26
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Laten HM. Antisuppression of class I suppressors in an isopentenylated-transfer RNA deficient mutant of Saccharomyces cerevisiae. Curr Genet 1984; 8:29-32. [DOI: 10.1007/bf00405428] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/1983] [Indexed: 11/25/2022]
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27
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Polyamines enhance the efficiency of tRNA-mediated readthrough of amber and UGA termination codons in a yeast cell-free system. Curr Genet 1983; 7:421-6. [DOI: 10.1007/bf00377606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/1983] [Indexed: 10/26/2022]
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28
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Endogenous read-through of a UGA termination codon in a Saccharomyces cerevisiae cell-free system: evidence for involvement of both a mitochondrial and a nuclear tRNA. Mol Cell Biol 1982. [PMID: 7050674 DOI: 10.1128/mcb.2.5.490] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Globin mRNA, translated in a Saccharomyces cerevisiae cell-free protein synthesizing system prepared from a [psi+ rho+] strain, primarily directed the synthesis of alpha- and beta-globin. A third globin mRNA-specific polypeptide was also synthesized, representing approximately 10% of the total translation products. This polypeptide (beta') was synthesized by translational read-through of the beta- globin mRNA UGA terminator and was mediated primarily by an endogenous tRNA coded for by the mitochondria. This mitochondrial tRNA, when charged, could be preferentially bound, in high salt, to benzoylated DEAE-cellulose, a characteristic of a tRNATrp. The synthesis of beta- mediated by this mitochondrial tRNATrp was significantly reduced when the translation system was prepared from an isogenic [psi-] strain. Evidence for a nuclear-coded tRNA, also able to suppress the beta-globin mRNA UGA terminator in [psi+] but not [psi-] lysates, was also obtained. The presence of these endogenous UGA suppressor activities in the yeast cell-free system should allow successful in vitro translation of mitochondrial mRNAs.
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30
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Tuite MF, Lund PM, Futcher AB, Dobson MJ, Cox BS, McLaughlin CS. Relationship of the [psi] factor with other plasmids of Saccharomyces cerevisiae. Plasmid 1982; 8:103-11. [PMID: 6757991 DOI: 10.1016/0147-619x(82)90048-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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31
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Etcheverry T, Salvato M, Guthrie C. Recessive lethality of yeast strains carrying the SUP61 suppressor results from loss of a transfer RNA with a unique decoding function. J Mol Biol 1982; 158:599-618. [PMID: 6750138 DOI: 10.1016/0022-2836(82)90251-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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32
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Tuite MF, McLaughlin CS. Endogenous read-through of a UGA termination codon in a Saccharomyces cerevisiae cell-free system: evidence for involvement of both a mitochondrial and a nuclear tRNA. Mol Cell Biol 1982; 2:490-7. [PMID: 7050674 PMCID: PMC369818 DOI: 10.1128/mcb.2.5.490-497.1982] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Globin mRNA, translated in a Saccharomyces cerevisiae cell-free protein synthesizing system prepared from a [psi+ rho+] strain, primarily directed the synthesis of alpha- and beta-globin. A third globin mRNA-specific polypeptide was also synthesized, representing approximately 10% of the total translation products. This polypeptide (beta') was synthesized by translational read-through of the beta- globin mRNA UGA terminator and was mediated primarily by an endogenous tRNA coded for by the mitochondria. This mitochondrial tRNA, when charged, could be preferentially bound, in high salt, to benzoylated DEAE-cellulose, a characteristic of a tRNATrp. The synthesis of beta- mediated by this mitochondrial tRNATrp was significantly reduced when the translation system was prepared from an isogenic [psi-] strain. Evidence for a nuclear-coded tRNA, also able to suppress the beta-globin mRNA UGA terminator in [psi+] but not [psi-] lysates, was also obtained. The presence of these endogenous UGA suppressor activities in the yeast cell-free system should allow successful in vitro translation of mitochondrial mRNAs.
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33
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Glass RE, Nene V, Hunter MG. Informational suppression as a tool for the investigation of gene structure and function. Biochem J 1982; 203:1-13. [PMID: 7049160 PMCID: PMC1158186 DOI: 10.1042/bj2030001] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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34
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Ernst JF, Stewart JW, Sherman F. The cyc1-11 mutation in yeast reverts by recombination with a nonallelic gene: composite genes determining the iso-cytochromes c. Proc Natl Acad Sci U S A 1981; 78:6334-8. [PMID: 6273865 PMCID: PMC349033 DOI: 10.1073/pnas.78.10.6334] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
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.
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Ono BI, Wills N, Stewart JW, Gesteland RF, Sherman F. Serine-inserting UAA suppression mediated by yeast tRNASer. J Mol Biol 1981; 150:361-73. [PMID: 6795356 DOI: 10.1016/0022-2836(81)90552-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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36
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Waldron C, Cox BS, Wills N, Gesteland RF, Piper PW, Colby D, Guthrie C. Yeast ochre suppressor SUQ5-ol is an altered tRNA Ser UCA. Nucleic Acids Res 1981; 9:3077-88. [PMID: 7024909 PMCID: PMC327332 DOI: 10.1093/nar/9.13.3077] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Ochre suppressor tRNA was partially purified from strains of Saccharomyces cerevisiae containing the serine-inserting class III suppressor SUQ5-ol. RNA sequence analysis of this tRNA indicated that the suppressor is derived from a UCA-decoding tRNA Ser by a G leads to U substitution in the middle position of the anticodon. The suppressor further differs from the wild-type UCA-decoding tRNA Ser in that the mutant anticodon lacks the modified uridine found in the wobble position of the wild-type tRNA and contains instead another modification in or near the anticodon.
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37
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Olson MV, Page GS, Sentenac A, Piper PW, Worthington M, Weiss RB, Hall BD. Only one of two closely related yeast suppressor tRNA genes contains an intervening sequence. Nature 1981; 291:464-9. [PMID: 6262655 DOI: 10.1038/291464a0] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The yeast genes that code for the serine-inserting SUP-RL1 amber and SUQ5 ochre suppressors have been cloned and sequenced. These two unlinked genes differ by only three base pairs in their coding regions yet they encode tRNAs of different translational specificities, and while the SUP-RL1 gene has a 19-base pair intervening sequence, the SUQ5 gene has none.
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39
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Colby D, Sherman F. Nucleotide modification of tRNA in. the yeast Saccharomyces cerevisiae is not Affected by the ψ factor which modulates suppression efficiency. Curr Genet 1981; 3:163-5. [PMID: 24190063 DOI: 10.1007/bf00365721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/1980] [Indexed: 11/25/2022]
Abstract
We have examined the tRNAs of two related strains of Saccharomyces cerevisiae, ψ (+) and ψ (-), which differ with respect to an extrachromosomal genetic element that modulates the expression of genotypic and phenotypic suppression. Both the pattern of tRNAs synthesized and the level of nucleotide modification of several selected tRNA species were found to be the same in the ψ (+) and ψ (-) strains.
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Affiliation(s)
- D Colby
- Department of Biochemistry and Biophysics, University of California School of Medicine, 94143, San Francisco, California, USA
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Abstract
SUMMARYMutants of [psi] a cytoplasmically inherited factor in the yeastSaccharomyces cerevisiaewere isolated after treatment with a variety of agents including conventional mutagens and a number of compounds which cause loss of [psi] at high frequencies, namely methanol, KCl, dimethyl sulphoxide and guanidine hydrochloride. In [psi−] mutants the suppressorSUQ5does not suppress ochre mutations such asade.2.1.Reversion analysis of the [psi−] mutants revealed three classes: (1) a class of agents producing [psi−] mutations which could readily revert to [psi+] (methanol, KCl and dimethyl sulphoxide belong to this class), (2) those which could not be shown to revert (GuHCl) and (3) the conventional mutagens which produced both revertible and apparently non-revertible [psi−] mutations. We conclude that GuHCl causes a deletion or loss of the [psi] factor. Methanol may cause an alteration of ‘state’ for example, of a promoter, and KCl may be selecting or inducing low copy number variants of [psi+] strains. It is possible that DMSO may be involved in regulation of [psi].
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Ono BI, Stewart JW, Sherman F. Yeast UAA suppressors effective in psi+ strains: leucine-inserting suppressors. J Mol Biol 1979; 132:507-20. [PMID: 392110 DOI: 10.1016/0022-2836(79)90272-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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43
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Characterization of a UGA-suppressing serine tRNA from Schizosaccharomyces pombe with the help of a new in vitro assay system for eukaryotic suppressor tRNAs. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(17)37806-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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44
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Palmer E, Wilhelm JM, Sherman F. Variation of phenotypic suppression due to the psi+ and psi- extrachromosomal determinants in yeast. J Mol Biol 1979; 128:107-10. [PMID: 372547 DOI: 10.1016/0022-2836(79)90311-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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45
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Ono BI, Stewart JW, Sherman F. Yeast UAA suppressors effective in psi+ strains serine-inserting suppressors. J Mol Biol 1979; 128:81-100. [PMID: 372549 DOI: 10.1016/0022-2836(79)90309-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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46
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Singh A, Ursic D, Davies J. Phenotypic suppression and misreading Saccharomyces cerevisiae. Nature 1979; 277:146-8. [PMID: 366438 DOI: 10.1038/277146a0] [Citation(s) in RCA: 183] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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47
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Leibowitz MJ, Wickner RB. Pet18: a chromosomal gene required for cell growth and for the maintenance of mitochondrial DNA and the killer plasmid of yeast. MOLECULAR & GENERAL GENETICS : MGG 1978; 165:115-21. [PMID: 366371 DOI: 10.1007/bf00269899] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mutations in the pet18 gene of Saccharomyces cerevisiae (formerly denoted pets) confer three phenotypes on mutant strains: (i) inability to respire (petite), (ii) inability to maintain the double-stranded RNA killer plasmid (sensitive), and (iii) temperature sensitivity for growth. We find that pet18 mutants lack mitochondrial DNA. However, despite their inability to maintain the killer RNA plasmid and mitochondrial DNA, pet18 mutants still can carry the other yeast plasmids, [URE3--1], [PSI], and 2-micron DNA. The temperature sensitivity of the pet18 mutants is not expressed as a selective defect in total DNA, RNA, or protein synthesis.
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48
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Piper PW. A correlation between a recessive lethal amber suppressor mutation in Saccharomyces cerevisiae and an anticodon change in a minor serine transfer RNA. J Mol Biol 1978; 122:217-35. [PMID: 355641 DOI: 10.1016/0022-2836(78)90037-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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49
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Waldron C, Cox BS. Ribosomal proteins of yeast strains carrying mutations which affect the efficiency of nonsense suppression. MOLECULAR & GENERAL GENETICS : MGG 1978; 159:223-5. [PMID: 345095 DOI: 10.1007/bf00270898] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have examined the ribosomal proteins of strains of Saccharomyces cerevisiae which differ in the efficiency with which ochre nonsense mutations are suppressed. The strains in which ochre suppression is poor were [psi]- or carried antisuppressor mutations; those in which suppression was highly efficient were [psi]+ or carried allosuppressor mutations. The ribosomal proteins of these strains, as judged by two-dimensional polyacrylamide gel electrophoresis, were indistinguishable from those of wild-type.
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50
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Schweingruber M, Stewart J, Sherman F. Amino acid replacements of the evolutionarily invariant tryptophan at position 64 in mutant forms of iso-1-cytochrome c from Saccharomyces cerevisiae. J Mol Biol 1978. [DOI: 10.1016/0022-2836(78)90286-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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