1
|
Takallou S, Hajikarimlou M, Al-Gafari M, Wang J, Kazmirchuk TDD, Said KB, Samanfar B, Golshani A. The Involvement of YNR069C in Protein Synthesis in the Baker's Yeast, Saccharomyces cerevisiae. BIOLOGY 2024; 13:138. [PMID: 38534408 DOI: 10.3390/biology13030138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/28/2024]
Abstract
Maintaining translation fidelity is a critical step within the process of gene expression. It requires the involvement of numerous regulatory elements to ensure the synthesis of functional proteins. The efficient termination of protein synthesis can play a crucial role in preserving this fidelity. Here, we report on investigating a protein of unknown function, YNR069C (also known as BSC5), for its activity in the process of translation. We observed a significant increase in the bypass of premature stop codons upon the deletion of YNR069C. Interestingly, the genomic arrangement of this ORF suggests a compatible mode of expression reliant on translational readthrough, incorporating the neighboring open reading frame. We also showed that the deletion of YNR069C results in an increase in the rate of translation. Based on our results, we propose that YNR069C may play a role in translation fidelity, impacting the overall quantity and quality of translation. Our genetic interaction analysis supports our hypothesis, associating the role of YNR069C to the regulation of protein synthesis.
Collapse
Affiliation(s)
- Sarah Takallou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Maryam Hajikarimlou
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Mustafa Al-Gafari
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiashu Wang
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Thomas David Daniel Kazmirchuk
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Kamaledin B Said
- Department of Pathology and Microbiology, College of Medicine, University of Hail, Hail 55476, Saudi Arabia
| | - Bahram Samanfar
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (ORDC), Ottawa, ON K1A 0C6, Canada
| | - Ashkan Golshani
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| |
Collapse
|
2
|
Processing of Fluorescent Proteins May Prevent Detection of Prion Particles in [ PSI+] Cells. BIOLOGY 2022; 11:biology11121688. [PMID: 36552198 PMCID: PMC9774836 DOI: 10.3390/biology11121688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022]
Abstract
Yeast is a convenient model for studying protein aggregation as it is known to propagate amyloid prions. [PSI+] is the prion form of the release factor eRF3 (Sup35). Aggregated Sup35 causes defects in termination of translation, which results in nonsense suppression in strains carrying premature stop codons. N-terminal and middle (M) domains of Sup35 are necessary and sufficient for maintaining [PSI+] in cells while preserving the prion strain's properties. For this reason, Sup35NM fused to fluorescent proteins is often used for [PSI+] detection and investigation. However, we found that in such chimeric constructs, not all fluorescent proteins allow the reliable detection of Sup35 aggregates. Particularly, transient overproduction of Sup35NM-mCherry resulted in a diffuse fluorescent pattern in the [PSI+] cells, while no loss of prions and no effect on the Sup35NM prion properties could be observed. This effect was reproduced in various unrelated strain backgrounds and prion variants. In contrast, Sup35NM fused to another red fluorescent protein, TagRFP-T, allowed the detection of [PSI+] aggregates. Analysis of protein lysates showed that Sup35NM-mCherry is actively degraded in the cell. This degradation was not caused by vacuolar proteases and the ubiquitin-proteasomal system implicated in the Sup35 processing. Even though the intensity of this proteolysis was higher than that of Sup35NM-GFP, it was roughly the same as in the case of Sup35NM-TagRFP-T. Thus, it is possible that, in contrast to TagRFP-T, degradation products of Sup35NM-mCherry still preserve their fluorescent properties while losing the ability to decorate pre-existing Sup35 aggregates. This results in diffuse fluorescence despite the presence of the prion aggregates in the cell. Thus, tagging with fluorescent proteins should be used with caution, as such proteolysis may increase the rate of false-negative results when detecting prion-bearing cells.
Collapse
|
3
|
Pastukhov A, Kovaleva V, Kaverin D. Microbial Community Structure in Ancient European Arctic Peatlands. PLANTS (BASEL, SWITZERLAND) 2022; 11:2704. [PMID: 36297728 PMCID: PMC9607101 DOI: 10.3390/plants11202704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Northern peatlands, which are crucial reservoirs of carbon and nitrogen (415 ± 150 and 10 ± 7 Pg, respectively), are vulnerable to microbial mineralization after permafrost thaw. This study was carried out in four key sites containing northern permafrost peatland, which are located along the southern cryolithozone. The aim of this study is to characterize amino acids and the microbial community composition in peat strata along a climate gradient. Amino acids and microbiota diversity were studied by liquid chromatography and a quantitative polymerase chain reaction. The share of amino acid fragments was 2.6-7.8, and it is highly significantly correlated (r = 0.87, -0.74 and 0.67, p ˂ 0.05) with the organic nitrogen concentration in the soil, the C/N ratio, and δ15N. The data shows the existence of a large pool of microorganisms concentrated in permafrost peatlands, and a vertical continuum of bacteria, archaea, and microscopic fungi along the peat profile, due to the presence of microorganisms in each layer, throughout all the peat strata. There is no significant correlation between microorganism distribution and the plant macrofossil composition of the peat strata. Determining factors for the development of microorganism abundance are aeration and hydrothermal conditions. The availability of nitrogen will limit the ability of plants and microorganisms to respond to changing environmental conditions; however, with the increased decomposition of organic matter, amino acids will be released as organic sources of nitrogen stored in the protein material of peat-forming plants and microbial communities, which can also affect the organic nitrogen cycle.
Collapse
Affiliation(s)
- Alexander Pastukhov
- Institute of Biology Komi Science Centre Ural Branch Russian Academy of Sciences, Kommunisticheskaya 28, 167982 Syktyvkar, Russia
- BIO-GEO-CLIM Laboratory, National Research Tomsk State University, Lenina 36, 634050 Tomsk, Russia
| | - Vera Kovaleva
- Institute of Biology Komi Science Centre Ural Branch Russian Academy of Sciences, Kommunisticheskaya 28, 167982 Syktyvkar, Russia
| | - Dmitry Kaverin
- Institute of Biology Komi Science Centre Ural Branch Russian Academy of Sciences, Kommunisticheskaya 28, 167982 Syktyvkar, Russia
| |
Collapse
|
4
|
Zhouravleva GA, Bondarev SA, Zemlyanko OM, Moskalenko SE. Role of Proteins Interacting with the eRF1 and eRF3 Release Factors in the Regulation of Translation and Prionization. Mol Biol 2022. [DOI: 10.1134/s0026893322010101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
5
|
Gene Amplification as a Mechanism of Yeast Adaptation to Nonsense Mutations in Release Factor Genes. Genes (Basel) 2021; 12:genes12122019. [PMID: 34946968 PMCID: PMC8701342 DOI: 10.3390/genes12122019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Protein synthesis (translation) is one of the fundamental processes occurring in the cells of living organisms. Translation can be divided into three key steps: initiation, elongation, and termination. In the yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 and eRF3. These factors are encoded by the SUP45 and SUP35 genes, which are essential; deletion of any of them leads to the death of yeast cells. However, viable strains with nonsense mutations in both the SUP35 and SUP45 genes were previously obtained in several groups. The survival of such mutants clearly involves feedback control of premature stop codon readthrough; however, the exact molecular basis of such feedback control remain unclear. To investigate the genetic factors supporting the viability of these SUP35 and SUP45 nonsense mutants, we performed whole-genome sequencing of strains carrying mutant sup35-n and sup45-n alleles; while no common SNPs or indels were found in these genomes, we discovered a systematic increase in the copy number of the plasmids carrying mutant sup35-n and sup45-n alleles. We used the qPCR method which confirmed the differences in the relative number of SUP35 and SUP45 gene copies between strains carrying wild-type or mutant alleles of SUP35 and SUP45 genes. Moreover, we compare the number of copies of the SUP35 and SUP45 genes in strains carrying different nonsense mutant variants of these genes as a single chromosomal copy. qPCR results indicate that the number of mutant gene copies is increased compared to the wild-type control. In case of several sup45-n alleles, this was due to a disomy of the entire chromosome II, while for the sup35-218 mutation we observed a local duplication of a segment of chromosome IV containing the SUP35 gene. Taken together, our results indicate that gene amplification is a common mechanism of adaptation to nonsense mutations in release factor genes in yeast.
Collapse
|
6
|
Sergeeva AV, Belashova TA, Bondarev SA, Velizhanina ME, Barbitoff YA, Matveenko AG, Valina AA, Simanova AL, Zhouravleva GA, Galkin AP. Direct proof of the amyloid nature of yeast prions [PSI+] and [PIN+] by the method of immunoprecipitation of native fibrils. FEMS Yeast Res 2021; 21:6360323. [PMID: 34463335 DOI: 10.1093/femsyr/foab046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/28/2021] [Indexed: 12/12/2022] Open
Abstract
Prions are proteins that can exist in several structurally and functionally distinct states, one or more of which is transmissible. Yeast proteins Sup35 and Rnq1 in prion state ([PSI+] and [PIN+], respectively) form oligomers and aggregates, which are transmitted from parents to offspring in a series of generations. Several pieces of indirect evidence indicate that these aggregates also possess amyloid properties, but their binding to amyloid-specific dyes has not been shown in vivo. Meanwhile, it is the specific binding to the Congo Red dye and birefringence in polarized light after such staining that is considered the gold standard for proving the amyloid properties of a protein. Here, we used immunoprecipitation to extract native fibrils of the Sup35 and Rnq1 proteins from yeast strains with different prion status. These fibrils are detected by electron microscopy, stained with Congo Red and exhibit yellow-green birefringence after such staining. All these data show that the Sup35 and Rnq1 proteins in prion state form amyloid fibrils in vivo. The technology of fibrils extraction in combination with standard cytological methods can be used to identify new pathological and functional amyloids in any organism and to analyze the structural features of native amyloid fibrils.
Collapse
Affiliation(s)
- Aleksandra V Sergeeva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Tatyana A Belashova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation.,Laboratory of Amyloid Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Marya E Velizhanina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation.,Laboratory of Signal Regulation, All-Russia Research Institute for Agricultural Microbiology, Podbelsky Chaussee, 3 , Pushkin, St. Petersburg, Russian Federation
| | - Yury A Barbitoff
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Anna A Valina
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Angelina L Simanova
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| | - Alexey P Galkin
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation.,Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russian Federation
| |
Collapse
|
7
|
Barbitoff YA, Matveenko AG, Matiiv AB, Maksiutenko EM, Moskalenko SE, Drozdova PB, Polev DE, Beliavskaia AY, Danilov LG, Predeus AV, Zhouravleva GA. Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage. G3-GENES GENOMES GENETICS 2021; 11:6129118. [PMID: 33677552 PMCID: PMC8759820 DOI: 10.1093/g3journal/jkab029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/22/2021] [Indexed: 01/23/2023]
Abstract
Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences. In our study, we applied Oxford Nanopore and Illumina technologies to assemble complete genomes of two widely used members of a distinct laboratory yeast lineage, the Peterhof Genetic Collection (PGC), and investigate the structural features of these genomes including transposable element content, copy number alterations, and structural rearrangements. We identified numerous notable structural differences between genomes of PGC strains and the reference S288C strain. We discovered a substantial enrichment of mid-length insertions and deletions within repetitive coding sequences, such as in the SCH9 gene or the NUP100 gene, with possible impact of these variants on protein amyloidogenicity. High contiguity of the final assemblies allowed us to trace back the history of reciprocal unbalanced translocations between chromosomes I, VIII, IX, XI, and XVI of the PGC strains. We show that formation of hybrid alleles of the FLO genes during such chromosomal rearrangements is likely responsible for the lack of invasive growth of yeast strains. Taken together, our results highlight important features of laboratory yeast strain evolution using the power of long-read sequencing.
Collapse
Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Anton B Matiiv
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Bioinformatics Institute, St. Petersburg 197342, Russia
| | - Evgeniia M Maksiutenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Svetlana E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg 199034, Russia
| | | | | | - Alexandra Y Beliavskaia
- Department of Invertebrate Zoology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Lavrentii G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Alexander V Predeus
- Bioinformatics Institute, St. Petersburg 197342, Russia.,University of Liverpool, Liverpool, UK, L7 3EA
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| |
Collapse
|
8
|
Trubitsina NP, Zemlyanko OM, Bondarev SA, Zhouravleva GA. Nonsense Mutations in the Yeast SUP35 Gene Affect the [ PSI+] Prion Propagation. Int J Mol Sci 2020; 21:E1648. [PMID: 32121268 PMCID: PMC7084296 DOI: 10.3390/ijms21051648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
The essential SUP35 gene encodes yeast translation termination factor eRF3. Previously, we isolated nonsense mutations sup35-n and proposed that the viability of such mutants can be explained by readthrough of the premature stop codon. Such mutations, as well as the prion [PSI+], can appear in natural yeast populations, and their combinations may have different effects on the cells. Here, we analyze the effects of the compatibility of sup35-n mutations with the [PSI+] prion in haploid and diploid cells. We demonstrated that sup35-n mutations are incompatible with the [PSI+] prion, leading to lethality of sup35-n [PSI+] haploid cells. In diploid cells the compatibility of [PSI+] with sup35-n depends on how the corresponding diploid was obtained. Nonsense mutations sup35-21, sup35-74, and sup35-218 are compatible with the [PSI+] prion in diploid strains, but affect [PSI+] properties and lead to the formation of new prion variant. The only mutation that could replace the SUP35 wild-type allele in both haploid and diploid [PSI+] strains, sup35-240, led to the prion loss. Possibly, short Sup351-55 protein, produced from the sup35-240 allele, is included in Sup35 aggregates and destabilize them. Alternatively, single molecules of Sup351-55 can stick to aggregate ends, and thus interrupt the fibril growth. Thus, we can conclude that sup35-240 mutation prevents [PSI+] propagation and can be considered as a new pnm mutation.
Collapse
Affiliation(s)
- Nina P. Trubitsina
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
| | - Olga M. Zemlyanko
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, 199034 St. Petersburg, Russia; (N.P.T.); (O.M.Z.); (S.A.B.)
- Laboratory of Amyloid Biology, Saint Petersburg State University, 199034 St. Petersburg, Russia
| |
Collapse
|
9
|
Matveenko AG, Drozdova PB, Moskalenko SE, Tarasov OV, Zhouravleva GA. Whole genome sequencing data and analyses of the underlying SUP35 transcriptional regulation for a Saccharomyces cerevisiae nonsense suppressor mutant. Data Brief 2019; 23:103694. [PMID: 30788402 PMCID: PMC6369104 DOI: 10.1016/j.dib.2019.01.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/06/2019] [Accepted: 01/18/2019] [Indexed: 11/18/2022] Open
Abstract
Termination of translation in eukaryotes is governed by two release factors encoded by the SUP45 and SUP35 genes in Saccharomyces cerevisiae. Previously, a set of mutations in these genes had been obtained. However, the exact sequence change associated with one mutation, sup35-222, was not identified by Sanger sequencing of the SUP35 region. Presented here are whole-genome sequencing data for the sup35-222 strain, data on copy number variation in its genome along with supporting pulse-field gel electrophoresis experiment data, and the list of single-nucleotide variations that differentiate this strain and its wild-type ancestor. One substitution upstream the SUP35 gene was located in a sequence corresponding to the Abf1-binding site. Data obtained from the introduction of this variation from sup35-222 strain into a different wild-type strain, specifically, detection of a nonsense-suppressor phenotype accompanied by a decrease in the Sup35 protein level, are also presented in this article.
Collapse
Affiliation(s)
- Andrew G. Matveenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Polina B. Drozdova
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Svetlana E. Moskalenko
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Oleg V. Tarasov
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg 199034, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, St. Petersburg 199034, Russia
- Corresponding author at: Department of Genetics and Biotechnology, Saint-Petersburg State University, Universitetskaya emb., 7/9, St. Petersburg 199034, Russia.
| |
Collapse
|
10
|
Barbitoff YA, Matveenko AG, Moskalenko SE, Zemlyanko OM, Newnam GP, Patel A, Chernova TA, Chernoff YO, Zhouravleva GA. To CURe or not to CURe? Differential effects of the chaperone sorting factor Cur1 on yeast prions are mediated by the chaperone Sis1. Mol Microbiol 2017; 105:242-257. [PMID: 28431189 DOI: 10.1111/mmi.13697] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2017] [Indexed: 02/06/2023]
Abstract
Yeast self-perpetuating protein aggregates (prions) provide a convenient model for studying various components of the cellular protein quality control system. Molecular chaperones and chaperone-sorting factors, such as yeast Cur1 protein, play key role in proteostasis via tight control of partitioning and recycling of misfolded proteins. In this study, we show that, despite the previously described ability of Cur1 to antagonize the yeast prion [URE3], it enhances propagation and phenotypic manifestation of another prion, [PSI+ ]. We demonstrate that both curing of [URE3] and enhancement of [PSI+ ] in the presence of excess Cur1 are counteracted by the cochaperone Hsp40-Sis1 in a dosage-dependent manner, and show that the effect of Cur1 on prions parallels effects of the attachment of nuclear localization signal to Sis1, indicating that Cur1 acts on prions via its previously reported ability to relocalize Sis1 from the cytoplasm to nucleus. This shows that the direction in which Cur1 influences a prion depends on how this specific prion responds to relocalization of Sis1.
Collapse
Affiliation(s)
- Yury A Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Andrew G Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Svetlana E Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,St. Petersburg Branch, Vavilov Institute of General Genetics, Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Olga M Zemlyanko
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia.,Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Gary P Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Ayesha Patel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yury O Chernoff
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg 199034, Russia.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332-2000, USA.,Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg 199034, Russia
| |
Collapse
|
11
|
Drozdova P, Mironova L, Zhouravleva G. Haploid yeast cells undergo a reversible phenotypic switch associated with chromosome II copy number. BMC Genet 2016; 17:152. [PMID: 28105933 PMCID: PMC5249023 DOI: 10.1186/s12863-016-0464-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SUP35 and SUP45 are essential genes encoding polypeptide chain release factors. However, mutants for these genes may be viable but display pleiotropic phenotypes which include, but are not limited to, nonsense suppressor phenotype due to translation termination defect. [PSI +] prion formation is another Sup35p-associated mechanism leading to nonsense suppression through decreased availability of functional Sup35p. [PSI +] differs from genuine sup35 mutations by the possibility of its elimination and subsequent re-induction. Some suppressor sup35 mutants had also been shown to undergo a reversible phenotypic switch in the opposite direction. This reversible switching had been attributed to a prion termed [ISP +]. However, even though many phenotypic and molecular level features of [ISP +] were revealed, the mechanism behind this phenomenon has not been clearly explained and might be more complex than suggested initially. RESULTS Here we took a genomic approach to look into the molecular basis of the difference between the suppressor (Isp-) and non-suppressor (Isp+) phenotypes. We report that the reason for the difference between the Isp+ and the Isp- phenotypes is chromosome II copy number changes and support our finding with showing that these changes are indeed reversible by reproducing the phenotypic switch and tracking karyotypic changes. Finally, we suggest mechanisms that mediate elevation in nonsense suppression efficiency upon amplification of chromosome II and facilitate switching between these states. CONCLUSIONS (i) In our experimental system, amplification of chromosome II confers nonsense suppressor phenotype and guanidine hydrochloride resistance at the cost of overall decreased viability in rich medium. (ii) SFP1 might represent a novel regulator of chromosome stability, as SFP1 overexpression elevates frequency of the additional chromosome loss in our system. (iii) Prolonged treatment with guanidine hydrochloride leads to selection of resistant isolates, some of which are disomic for chromosome II.
Collapse
Affiliation(s)
- Polina Drozdova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, Universitetskaya nab. 7-9, St. Petersburg, Russia
| | - Ludmila Mironova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, Universitetskaya nab. 7-9, St. Petersburg, Russia
| | - Galina Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034, Universitetskaya nab. 7-9, St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034, Universitetskaya nab. 7-9, St. Petersburg, Russia
| |
Collapse
|
12
|
Matveenko AG, Belousov MV, Bondarev SA, Moskalenko SE, Zhouravleva GA. Identification of new genes that affect [PSI +] prion toxicity in Saccharomyces cerevisiae yeast. Mol Biol 2016. [DOI: 10.1134/s0026893316050113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
13
|
Matveenko AG, Drozdova PB, Belousov MV, Moskalenko SE, Bondarev SA, Barbitoff YA, Nizhnikov AA, Zhouravleva GA. SFP1-mediated prion-dependent lethality is caused by increased Sup35 aggregation and alleviated by Sis1. Genes Cells 2016; 21:1290-1308. [DOI: 10.1111/gtc.12444] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew G. Matveenko
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Polina B. Drozdova
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Mikhail V. Belousov
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Svetlana E. Moskalenko
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Stanislav A. Bondarev
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| | - Yury A. Barbitoff
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
| | - Anton A. Nizhnikov
- St Petersburg Branch; Vavilov Institute of General Genetics of the Russian Academy of Sciences; St Petersburg Russia
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- All-Russia Research Institute for Agricultural Microbiology; Pushkin St Petersburg Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology; Saint Petersburg State University; St Petersburg Russia
- Laboratory of Amyloid Biology; Saint Petersburg State University; St Petersburg Russia
| |
Collapse
|
14
|
Drozdova PB, Tarasov OV, Matveenko AG, Radchenko EA, Sopova JV, Polev DE, Inge-Vechtomov SG, Dobrynin PV. Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PLoS One 2016; 11:e0154722. [PMID: 27152522 PMCID: PMC4859572 DOI: 10.1371/journal.pone.0154722] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/18/2016] [Indexed: 01/09/2023] Open
Abstract
The Peterhof genetic collection of Saccharomyces cerevisiae strains (PGC) is a large laboratory stock that has accumulated several thousands of strains for over than half a century. It originated independently of other common laboratory stocks from a distillery lineage (race XII). Several PGC strains have been extensively used in certain fields of yeast research but their genomes have not been thoroughly explored yet. Here we employed whole genome sequencing to characterize five selected PGC strains including one of the closest to the progenitor, 15V-P4, and several strains that have been used to study translation termination and prions in yeast (25-25-2V-P3982, 1B-D1606, 74-D694, and 6P-33G-D373). The genetic distance between the PGC progenitor and S288C is comparable to that between two geographically isolated populations. The PGC seems to be closer to two bakery strains than to S288C-related laboratory stocks or European wine strains. In genomes of the PGC strains, we found several loci which are absent from the S288C genome; 15V-P4 harbors a rare combination of the gene cluster characteristic for wine strains and the RTM1 cluster. We closely examined known and previously uncharacterized gene variants of particular strains and were able to establish the molecular basis for known phenotypes including phenylalanine auxotrophy, clumping behavior and galactose utilization. Finally, we made sequencing data and results of the analysis available for the yeast community. Our data widen the knowledge about genetic variation between Saccharomyces cerevisiae strains and can form the basis for planning future work in PGC-related strains and with PGC-derived alleles.
Collapse
Affiliation(s)
- Polina B. Drozdova
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- Bioinformatics Institute, St. Petersburg, Russia
| | - Oleg V. Tarasov
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Scientific Center of RAS, St. Petersburg, Russia
| | - Andrew G. Matveenko
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
- Laboratory of Amyloid Biology, Saint Petersburg State University, St. Petersburg, Russia
| | - Elina A. Radchenko
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- Bioinformatics Institute, St. Petersburg, Russia
| | - Julia V. Sopova
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
- Institute of Translational Biomedicine, Saint Petersburg State University, St. Petersburg, Russia
| | - Dmitrii E. Polev
- Research Resource Center for Molecular and Cell Technologies, Research Park, Saint-Petersburg State University, St. Petersburg, Russia
| | - Sergey G. Inge-Vechtomov
- Dept. of Genetics and Biotechnology, Saint Petersburg State University, St. Petersburg, Russia
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Pavel V. Dobrynin
- Bioinformatics Institute, St. Petersburg, Russia
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
15
|
Petrova A, Kiktev D, Askinazi O, Chabelskaya S, Moskalenko S, Zemlyanko O, Zhouravleva G. The translation termination factor eRF1 (Sup45p) of Saccharomyces cerevisiae is required for pseudohyphal growth and invasion. FEMS Yeast Res 2015; 15:fov033. [PMID: 26054854 DOI: 10.1093/femsyr/fov033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 01/16/2023] Open
Abstract
Mutations in the essential genes SUP45 and SUP35, encoding yeast translation termination factors eRF1 and eRF3, respectively, lead to a wide range of phenotypes and affect various cell processes. In this work, we show that nonsense and missense mutations in the SUP45, but not the SUP35, gene abolish diploid pseudohyphal and haploid invasive growth. Missense mutations that change phosphorylation sites of Sup45 protein do not affect the ability of yeast strains to form pseudohyphae. Deletion of the C-terminal part of eRF1 did not lead to impairment of filamentation. We show a correlation between the filamentation defect and the budding pattern in sup45 strains. Inhibition of translation with specific antibiotics causes a significant reduction in pseudohyphal growth in the wild-type strain, suggesting a strong correlation between translation and the ability for filamentous growth. Partial restoration of pseudohyphal growth by addition of exogenous cAMP assumes that sup45 mutants are defective in the cAMP-dependent pathway that control filament formation.
Collapse
Affiliation(s)
- Alexandra Petrova
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Denis Kiktev
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Olga Askinazi
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Svetlana Chabelskaya
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Svetlana Moskalenko
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Olga Zemlyanko
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Galina Zhouravleva
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| |
Collapse
|
16
|
Samanfar B, Tan LH, Shostak K, Chalabian F, Wu Z, Alamgir M, Sunba N, Burnside D, Omidi K, Hooshyar M, Galván Márquez I, Jessulat M, Smith ML, Babu M, Azizi A, Golshani A. A global investigation of gene deletion strains that affect premature stop codon bypass in yeast, Saccharomyces cerevisiae. MOLECULAR BIOSYSTEMS 2014; 10:916-24. [PMID: 24535059 DOI: 10.1039/c3mb70501c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Protein biosynthesis is an orderly process that requires a balance between rate and accuracy. To produce a functional product, the fidelity of this process has to be maintained from start to finish. In order to systematically identify genes that affect stop codon bypass, three expression plasmids, pUKC817, pUKC818 and pUKC819, were integrated into the yeast non-essential loss-of-function gene array (5000 strains). These plasmids contain three different premature stop codons (UAA, UGA and UAG, respectively) within the LacZ expression cassette. A fourth plasmid, pUKC815 that carries the native LacZ gene was used as a control. Transformed strains were subjected to large-scale β-galactosidase lift assay analysis to evaluate production of β-galactosidase for each gene deletion strain. In this way 84 potential candidate genes that affect stop codon bypass were identified. Three candidate genes, OLA1, BSC2, and YNL040W, were further investigated, and were found to be important for cytoplasmic protein biosynthesis.
Collapse
Affiliation(s)
- Bahram Samanfar
- Department of Biology and Ottawa Institute of Systems Biology, Carleton University, Ottawa, Ontario, Canada.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Matveenko AG, Zemlyanko OM, Zhouravleva GA. Identification of Saccharomyces cerevisiae genes leading to synthetic lethality of prion [PSI +] with SUP45 mutations. Mol Biol 2013. [DOI: 10.1134/s0026893313040110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
18
|
Drozdova PB, Radchenko EA, Rogoza TM, Khokhrina MA, Mironova LN. The SFP1 controls translation termination in Saccharomyces cerevisiae via regulation of Sup35p (eRF3) level. Mol Biol 2013. [DOI: 10.1134/s0026893313010044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
19
|
Betney R, de Silva E, Mertens C, Knox Y, Krishnan J, Stansfield I. Regulation of release factor expression using a translational negative feedback loop: a systems analysis. RNA (NEW YORK, N.Y.) 2012; 18:2320-34. [PMID: 23104998 PMCID: PMC3504682 DOI: 10.1261/rna.035113.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The essential eukaryote release factor eRF1, encoded by the yeast SUP45 gene, recognizes stop codons during ribosomal translation. SUP45 nonsense alleles are, however, viable due to the establishment of feedback-regulated readthrough of the premature termination codon; reductions in full-length eRF1 promote tRNA-mediated stop codon readthrough, which, in turn, drives partial production of full-length eRF1. A deterministic mathematical model of this eRF1 feedback loop was developed using a staged increase in model complexity. Model predictions matched the experimental observation that strains carrying the mutant SUQ5 tRNA (a weak UAA suppressor) in combination with any of the tested sup45(UAA) nonsense alleles exhibit threefold more stop codon readthrough than that of an SUQ5 yeast strain. The model also successfully predicted that eRF1 feedback control in an SUQ5 sup45(UAA) mutant would resist, but not completely prevent, imposed changes in eRF1 expression. In these experiments, the introduction of a plasmid-borne SUQ5 copy into a sup45(UAA) SUQ5 mutant directed additional readthrough and full-length eRF1 expression, despite feedback. Secondly, induction of additional sup45(UAA) mRNA expression in a sup45(UAA) SUQ5 strain also directed increased full-length eRF1 expression. The autogenous sup45 control mechanism therefore acts not to precisely control eRF1 expression, but rather as a damping mechanism that only partially resists changes in release factor expression level. The validated model predicts that the degree of feedback damping (i.e., control precision) is proportional to eRF1 affinity for the premature stop codon. The validated model represents an important tool to analyze this and other translational negative feedback loops.
Collapse
MESH Headings
- Binding, Competitive
- Codon, Terminator/genetics
- Codon, Terminator/metabolism
- Feedback, Physiological
- Genes, Fungal
- Models, Biological
- Mutation
- Peptide Termination Factors/genetics
- Peptide Termination Factors/metabolism
- Protein Biosynthesis
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Systems Analysis
Collapse
Affiliation(s)
- Russell Betney
- University of Aberdeen, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Eric de Silva
- Chemical Engineering and Chemical Technology, Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Christina Mertens
- University of Aberdeen, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Yvonne Knox
- University of Aberdeen, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - J. Krishnan
- Chemical Engineering and Chemical Technology, Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Ian Stansfield
- University of Aberdeen, School of Medical Sciences, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
- Corresponding authorE-mail
| |
Collapse
|
20
|
|
21
|
[NSI+] determinant has a pleiotropic phenotypic manifestation that is modulated by SUP35, SUP45, and VTS1 genes. Curr Genet 2012; 58:35-47. [PMID: 22215010 DOI: 10.1007/s00294-011-0363-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 12/19/2011] [Accepted: 12/22/2011] [Indexed: 10/14/2022]
Abstract
We recently discovered the novel non-chromosomal determinant in Saccharomyces cerevisiae [NSI(+)] (nonsense suppression inducer), which causes omnipotent nonsense suppression in strains where the Sup35 N-terminal domain is deleted. [NSI(+)] possesses yeast prion features and does not correspond to previously identified yeast prion determinants. Here, we show that [NSI(+)] enhances nonsense codon read-through and inhibits vegetative growth in S. cerevisiae. Using a large-scale overexpression screen to identify genes that impact the phenotypic effects of [NSI(+)], we found that the SUP35 and SUP45 genes encoding the translation termination factors eRF3 and eRF1, respectively, modulate nonsense suppression in [NSI(+)] strains. The VTS1 gene encodes an NQ-enriched RNA-binding protein that enhances nonsense suppression in [NSI(+)] and [nsi(-)] strains. We demonstrate that VTS1 overexpression, like [NSI(+)] induction, causes translational read-through and growth defects in S. cerevisiae.
Collapse
|
22
|
Kiktev DA, Chernoff YO, Archipenko AV, Zhouravleva GA. Identification of genes influencing synthetic lethality of genetic and epigenetic alterations in translation termination factors in yeast. DOKL BIOCHEM BIOPHYS 2011; 438:117-9. [PMID: 21725886 DOI: 10.1134/s1607672911030021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Indexed: 11/23/2022]
Affiliation(s)
- D A Kiktev
- Department of Genetic and Breeding, St. Petersburg State University, St. Petersburg, 199034, Russia
| | | | | | | |
Collapse
|
23
|
Zhouravleva GA, Petrova AV. The role of translation termination factor eRF1 in the regulation of pseudohyphal growth in Saccharomyces cerevisiae cells. DOKL BIOCHEM BIOPHYS 2010; 433:209-11. [PMID: 20714858 DOI: 10.1134/s1607672910040162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Indexed: 11/23/2022]
|
24
|
Murina OA, Moskalenko SE, Zhouravleva GA. Overexpression of genes encoding tRNATyr and tRNAGln increases the viability of Saccharomyces cerevisiae strains with nonsense mutations in the SUP45 gene. Mol Biol 2010. [DOI: 10.1134/s0026893310020123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
25
|
Betney R, de Silva E, Krishnan J, Stansfield I. Autoregulatory systems controlling translation factor expression: thermostat-like control of translational accuracy. RNA (NEW YORK, N.Y.) 2010; 16:655-63. [PMID: 20185543 PMCID: PMC2844614 DOI: 10.1261/rna.1796210] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In both prokaryotes and eukaryotes, the expression of a large number of genes is controlled by negative feedback, in some cases operating at the level of translation of the mRNA transcript. Of particular interest are those cases where the proteins concerned have cell-wide function in recognizing a particular codon or RNA sequence. Examples include the bacterial translation termination release factor RF2, initiation factor IF3, and eukaryote poly(A) binding protein. The regulatory loops that control their synthesis establish a negative feedback control mechanism based upon that protein's RNA sequence recognition function in translation (for example, stop codon recognition) without compromising the accurate recognition of that codon, or sequence during general, cell-wide translation. Here, the bacterial release factor RF2 and initiation factor IF3 negative feedback loops are reviewed and compared with similar negative feedback loops that regulate the levels of the eukaryote release factor, eRF1, established artificially by mutation. The control properties of such negative feedback loops are discussed as well as their evolution. The role of negative feedback to control translation factor expression is considered in the context of a growing body of evidence that both IF3 and RF2 can play a role in stimulating stalled ribosomes to abandon translation in response to amino acid starvation. Here, we make the case that negative feedback control serves primarily to limit the overexpression of these translation factors, preventing the loss of fitness resulting from an unregulated increase in the frequency of ribosome drop-off.
Collapse
Affiliation(s)
- Russell Betney
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | | | | | | |
Collapse
|
26
|
Chabelskaya SV, Zhouravleva GA. Mutations in the SUP35 gene impair nonsense-mediated mRNA decay. Mol Biol 2010. [DOI: 10.1134/s0026893310010073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
27
|
de Silva E, Krishnan J, Betney R, Stansfield I. A mathematical modelling framework for elucidating the role of feedback control in translation termination. J Theor Biol 2010; 264:808-21. [PMID: 20176033 DOI: 10.1016/j.jtbi.2010.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2009] [Revised: 11/27/2009] [Accepted: 01/13/2010] [Indexed: 11/15/2022]
Abstract
Translation is the final stage of gene expression where messenger RNA is used as a template for protein polymerization from appropriate amino acids. Release of the completed protein requires a release factor protein acting at the termination/stop codon to liberate it. In this paper we focus on a complex feedback control mechanism involved in the translation and synthesis of release factor proteins, which has been observed in different systems. These release factor proteins are involved in the termination stage of their own translation. Further, mutations in the release factor gene can result in a premature stop codon. In this case translation can result either in early termination and the production of a truncated protein or readthrough of the premature stop codon and production of the complete release factor protein. Thus during translation of the release factor mRNA containing a premature stop codon, the full length protein negatively regulates its production by its action on a premature stop codon, while positively regulating its production by its action on the regular stop codon. This paper develops a mathematical modelling framework to investigate this complex feedback control system involved in translation. A series of models is established to carefully investigate the role of individual mechanisms and how they work together. The steady state and dynamic behaviour of the resulting models are examined both analytically and numerically.
Collapse
Affiliation(s)
- Eric de Silva
- Department of Chemical Engineering and Chemical Technology, Centre for Process Systems Engineering, Institute for Systems and Synthetic Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | | | | |
Collapse
|
28
|
The paradox of viable sup45 STOP mutations: a necessary equilibrium between translational readthrough, activity and stability of the protein. Mol Genet Genomics 2009; 282:83-96. [PMID: 19370360 DOI: 10.1007/s00438-009-0447-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 03/26/2009] [Indexed: 10/20/2022]
Abstract
The mechanisms leading to non-lethality of nonsense mutations in essential genes are poorly understood. Here, we focus on the factors influencing viability of yeast cells bearing premature termination codons (PTCs) in the essential gene SUP45 encoding translation termination factor eRF1. Using a dual reporter system we compared readthrough efficiency of the natural termination codon of SUP45 gene, spontaneous sup45-n (nonsense) mutations, nonsense mutations obtained by site-directed mutagenesis (76Q --> TAA, 242R --> TGA, 317L --> TAG). The nonsense mutations in SUP45 gene were shown to be situated in moderate contexts for readthrough efficiency. We showed that readthrough efficiency of some of the mutations present in the sup45 mutants is not correlated with full-length Sup45 protein amount. This resulted from modification of both sup45 mRNA stability which varies 3-fold among sup45-n mutants and degradation rate of mutant Sup45 proteins. Our results demonstrate that some substitutions in the place of PTCs decrease Sup45 stability. The viability of sup45 nonsense mutants is therefore supported by diverse mechanisms that control the final amount of functional Sup45 in cells.
Collapse
|
29
|
Studte P, Zink S, Jablonowski D, Bär C, von der Haar T, Tuite MF, Schaffrath R. tRNA and protein methylase complexes mediate zymocin toxicity in yeast. Mol Microbiol 2008; 69:1266-77. [PMID: 18657261 DOI: 10.1111/j.1365-2958.2008.06358.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Modification of Saccharomyces cerevisiae tRNA anticodons at the wobble uridine (U34) position is required for tRNA cleavage by the zymocin tRNase killer toxin from Kluyveromyces lactis. Hence, U34 modification defects including lack of the U34 tRNA methyltransferase Trm9 protect against tRNA cleavage and zymocin. Using zymocin as a tool, we have identified toxin-resistant mutations in TRM9 that are likely to affect the U34 methylation reaction. Most strikingly, C-terminal truncations in Trm9 abolish interaction with Trm112, a protein shown to individually purify with Lys9 and two more methylases, Trm11 and Mtq2. Downregulation of a GAL1-TRM112 allele protects against zymocin whereas LYS9, TRM11 and MTQ2 are dosage suppressors of zymocin. Based on immune precipitation studies, the latter scenario correlates with competition for Trm112 and in excess, some of these Trm112 partners interfere with formation of the toxin-relevant Trm9.Trm112 complex. In contrast to trm11Delta or lys9Delta cells, trm112Delta and mtq2Delta null mutants are zymocin resistant. In line with the identified role that methylation of Sup45 by Mtq2 has for translation termination by the release factor dimer Sup45.Sup35, we observe that SUP45 overexpression and sup45 mutants suppress zymocin. Intriguingly, this suppression correlates with upregulated levels of tRNA species targeted by zymocin's tRNase activity.
Collapse
Affiliation(s)
- Patrick Studte
- Institut für Biologie, Bereich Genetik, Martin-Luther-Universität, Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany
| | | | | | | | | | | | | |
Collapse
|
30
|
Ivanov MS, Aksenova AY, Burdaeva YV, Radchenko EA, Mironova LN. Overexpression of gene PPZ1 in the yeast Saccharomyces cerevisiae affects the efficiency of nonsense suppression. RUSS J GENET+ 2008. [DOI: 10.1134/s102279540802004x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
31
|
Zhouravleva GA, Moskalenko SE, Murina OA, Inge-Vechtomov SG. Viable nonsense mutants for the SUP45 gene in the yeast Saccharomyces cerevisiae are lethal at increased temperature. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407100079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
32
|
Chabelskaya S, Gryzina V, Moskalenko S, Le Goff C, Zhouravleva G. Inactivation of NMD increases viability of sup45 nonsense mutants in Saccharomyces cerevisiae. BMC Mol Biol 2007; 8:71. [PMID: 17705828 PMCID: PMC2039749 DOI: 10.1186/1471-2199-8-71] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Accepted: 08/16/2007] [Indexed: 11/10/2022] Open
Abstract
Background The nonsense-mediated mRNA decay (NMD) pathway promotes the rapid degradation of mRNAs containing premature termination codons (PTCs). In yeast Saccharomyces cerevisiae, the activity of the NMD pathway depends on the recognition of the PTC by the translational machinery. Translation termination factors eRF1 (Sup45) and eRF3 (Sup35) participate not only in the last step of protein synthesis but also in mRNA degradation and translation initiation via interaction with such proteins as Pab1, Upf1, Upf2 and Upf3. Results In this work we have used previously isolated sup45 mutants of S. cerevisiae to characterize degradation of aberrant mRNA in conditions when translation termination is impaired. We have sequenced his7-1, lys9-A21 and trp1-289 alleles which are frequently used for analysis of nonsense suppression. We have established that sup45 nonsense and missense mutations lead to accumulation of his7-1 mRNA and CYH2 pre-mRNA. Remarkably, deletion of the UPF1 gene suppresses some sup45 phenotypes. In particular, sup45-n upf1Δ double mutants were less temperature sensitive, and more resistant to paromomycin than sup45 single mutants. In addition, deletion of either UPF2 or UPF3 restored viability of sup45-n double mutants. Conclusion This is the first demonstration that sup45 mutations do not only change translation fidelity but also acts by causing a change in mRNA stability.
Collapse
Affiliation(s)
- Svetlana Chabelskaya
- Department of Genetics and Breeding, St Petersburg State University, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
- CNRS UMR 6061 Génétique et Développement, Université de Rennes 1, IFR 140, Faculté de Médecine, 2 av. Pr. Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Valentina Gryzina
- Department of Genetics and Breeding, St Petersburg State University, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Svetlana Moskalenko
- Department of Genetics and Breeding, St Petersburg State University, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
- CNRS UMR 6061 Génétique et Développement, Université de Rennes 1, IFR 140, Faculté de Médecine, 2 av. Pr. Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Catherine Le Goff
- CNRS UMR 6061 Génétique et Développement, Université de Rennes 1, IFR 140, Faculté de Médecine, 2 av. Pr. Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Galina Zhouravleva
- Department of Genetics and Breeding, St Petersburg State University, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
- CNRS UMR 6061 Génétique et Développement, Université de Rennes 1, IFR 140, Faculté de Médecine, 2 av. Pr. Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| |
Collapse
|
33
|
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.
Collapse
Affiliation(s)
- Denis Kiktev
- Department of Genetics and Breeding, St Petersburg State University, St. Petersburg, Russia
| | | | | |
Collapse
|
34
|
Aksenova AY, Volkov KV, Rovinsky NS, Svitin AV, Mironova LN. Phenotypic expression of epigenetic determinant [ISP +] in Saccharomyces cerevisiae depends on the combination of sup35 and sup45 mutations. Mol Biol 2006. [DOI: 10.1134/s0026893306050104] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
35
|
Zhouravleva GA, Moskalenko SE, Chabelskaya SV, Philippe M, Inge-Vechtomov SG. Increased tRNA level in yeast cells with mutant translation termination factors eRF1 and eRF3. Mol Biol 2006. [DOI: 10.1134/s0026893306040170] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
36
|
Rospert S, Rakwalska M, Dubaquié Y. Polypeptide chain termination and stop codon readthrough on eukaryotic ribosomes. REVIEWS OF PHYSIOLOGY BIOCHEMISTRY AND PHARMACOLOGY 2006; 155:1-30. [PMID: 15928926 DOI: 10.1007/3-540-28217-3_1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
During protein translation, a variety of quality control checks ensure that the resulting polypeptides deviate minimally from their genetic encoding template. Translational fidelity is central in order to preserve the function and integrity of each cell. Correct termination is an important aspect of translational fidelity, and a multitude of mechanisms and players participate in this exquisitely regulated process. This review explores our current understanding of eukaryotic termination by highlighting the roles of the different ribosomal components as well as termination factors and ribosome-associated proteins, such as chaperones.
Collapse
Affiliation(s)
- S Rospert
- Universität Freiburg, Institut für Biochemie und Molekularbiologie, Hermann-Herder-Strasse 7, 79104 Freiburg, Germany.
| | | | | |
Collapse
|
37
|
Salas-Marco J, Fan-Minogue H, Kallmeyer AK, Klobutcher LA, Farabaugh PJ, Bedwell DM. Distinct paths to stop codon reassignment by the variant-code organisms Tetrahymena and Euplotes. Mol Cell Biol 2006; 26:438-47. [PMID: 16382136 PMCID: PMC1346903 DOI: 10.1128/mcb.26.2.438-447.2006] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The reassignment of stop codons is common among many ciliate species. For example, Tetrahymena species recognize only UGA as a stop codon, while Euplotes species recognize only UAA and UAG as stop codons. Recent studies have shown that domain 1 of the translation termination factor eRF1 mediates stop codon recognition. While it is commonly assumed that changes in domain 1 of ciliate eRF1s are responsible for altered stop codon recognition, this has never been demonstrated in vivo. To carry out such an analysis, we made hybrid proteins that contained eRF1 domain 1 from either Tetrahymena thermophila or Euplotes octocarinatus fused to eRF1 domains 2 and 3 from Saccharomyces cerevisiae. We found that the Tetrahymena hybrid eRF1 efficiently terminated at all three stop codons when expressed in yeast cells, indicating that domain 1 is not the sole determinant of stop codon recognition in Tetrahymena species. In contrast, the Euplotes hybrid facilitated efficient translation termination at UAA and UAG codons but not at the UGA codon. Together, these results indicate that while domain 1 facilitates stop codon recognition, other factors can influence this process. Our findings also indicate that these two ciliate species used distinct approaches to diverge from the universal genetic code.
Collapse
Affiliation(s)
- Joe Salas-Marco
- Department of Microbiology, BBRB 432/Box 8, 1530 Third Avenue South, The University of Alabama at Birmingham, Birmingham, Alabama 35294-2170, USA
| | | | | | | | | | | |
Collapse
|
38
|
Rospert S, Rakwalska M, Dubaquié Y. Polypeptide chain termination and stop codon readthrough on eukaryotic ribosomes. Rev Physiol Biochem Pharmacol 2005. [DOI: 10.1007/s10254-005-0039-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
39
|
Chabelskaya S, Kiktev D, Inge-Vechtomov S, Philippe M, Zhouravleva G. Nonsense mutations in the essential gene SUP35 of Saccharomyces cerevisiae are non-lethal. Mol Genet Genomics 2004; 272:297-307. [PMID: 15349771 DOI: 10.1007/s00438-004-1053-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Accepted: 08/05/2004] [Indexed: 10/26/2022]
Abstract
In the present work we have characterized for the first time non-lethal nonsense mutations in the essential gene SUP35, which codes for the translation termination factor eRF3 in Saccharomyces cerevisiae. The screen used was based on selection for simultaneous suppression of two auxotrophic nonsense mutations. Among 48 mutants obtained, sixteen were distinguished by the production of a reduced amount of eRF3, suggesting the appearance of nonsense mutations. Fifteen of the total mutants were sequenced, and the presence of nonsense mutations was confirmed for nine of them. Thus a substantial fraction of the sup35 mutations recovered are nonsense mutations located in different regions of SUP35, and such mutants are easily identified by the fact that they express reduced amounts of eRF3. Nonsense mutations in the SUP35 gene do not lead to a decrease in levels of SUP35 mRNA and do not influence the steady-state level of eRF1. The ability of these mutations to complement SUP35 gene disruption mutations in different genetic backgrounds and in the absence of any tRNA suppressor mutation was demonstrated. The missense mutations studied, unlike nonsense mutations, do not decrease steady-state amounts of eRF3.
Collapse
Affiliation(s)
- S Chabelskaya
- Department of Genetics and Breeding, St Petersburg State University, Universitetskaya Emb. 7/9, 199034 St Petersburg, Russia
| | | | | | | | | |
Collapse
|