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Maksiutenko EM, Barbitoff YA, Danilov LG, Matveenko AG, Zemlyanko OM, Efremova EP, Moskalenko SE, Zhouravleva GA. Gene Expression Analysis of Yeast Strains with a Nonsense Mutation in the eRF3-Coding Gene Highlights Possible Mechanisms of Adaptation. Int J Mol Sci 2024; 25:6308. [PMID: 38928012 PMCID: PMC11203930 DOI: 10.3390/ijms25126308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
In yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 (Sup45) and eRF3 (Sup35), which are essential for viability. Previous studies have revealed that presence of nonsense mutations in these genes leads to amplification of mutant alleles (sup35-n and sup45-n), which appears to be necessary for the viability of such cells. However, the mechanism of this phenomenon remained unclear. In this study, we used RNA-Seq and proteome analysis to reveal the complete set of gene expression changes that occur during cellular adaptation to the introduction of the sup35-218 nonsense allele. Our analysis demonstrated significant changes in the transcription of genes that control the cell cycle: decreases in the expression of genes of the anaphase promoting complex APC/C (APC9, CDC23) and their activator CDC20, and increases in the expression of the transcription factor FKH1, the main cell cycle kinase CDC28, and cyclins that induce DNA biosynthesis. We propose a model according to which yeast adaptation to nonsense mutations in the translation termination factor genes occurs as a result of a delayed cell cycle progression beyond the G2-M stage, which leads to an extension of the S and G2 phases and an increase in the number of copies of the mutant sup35-n allele.
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Affiliation(s)
- Evgeniia M. Maksiutenko
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.B.); (L.G.D.); (A.G.M.); (O.M.Z.); (E.P.E.); (S.E.M.)
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.B.); (L.G.D.); (A.G.M.); (O.M.Z.); (E.P.E.); (S.E.M.)
- Bioinformatics Institute, 197342 St. Petersburg, Russia
| | - Lavrentii G. Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.B.); (L.G.D.); (A.G.M.); (O.M.Z.); (E.P.E.); (S.E.M.)
| | - Andrew G. Matveenko
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.B.); (L.G.D.); (A.G.M.); (O.M.Z.); (E.P.E.); (S.E.M.)
| | - Olga M. Zemlyanko
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.B.); (L.G.D.); (A.G.M.); (O.M.Z.); (E.P.E.); (S.E.M.)
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena P. Efremova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.B.); (L.G.D.); (A.G.M.); (O.M.Z.); (E.P.E.); (S.E.M.)
| | - Svetlana E. Moskalenko
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.B.); (L.G.D.); (A.G.M.); (O.M.Z.); (E.P.E.); (S.E.M.)
- St. Petersburg Branch, Vavilov Institute of General Genetics of the Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Galina A. Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (E.M.M.); (Y.A.B.); (L.G.D.); (A.G.M.); (O.M.Z.); (E.P.E.); (S.E.M.)
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
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Tummler K, Klipp E. Data integration strategies for whole-cell modeling. FEMS Yeast Res 2024; 24:foae011. [PMID: 38544322 PMCID: PMC11042497 DOI: 10.1093/femsyr/foae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Data makes the world go round-and high quality data is a prerequisite for precise models, especially for whole-cell models (WCM). Data for WCM must be reusable, contain information about the exact experimental background, and should-in its entirety-cover all relevant processes in the cell. Here, we review basic requirements to data for WCM and strategies how to combine them. As a species-specific resource, we introduce the Yeast Cell Model Data Base (YCMDB) to illustrate requirements and solutions. We discuss recent standards for data as well as for computational models including the modeling process as data to be reported. We outline strategies for constructions of WCM despite their inherent complexity.
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Affiliation(s)
- Katja Tummler
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany
| | - Edda Klipp
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Institute of Biology, Theoretical Biophysics,, Invalidenstr. 42, 10115 Berlin, Germany
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Lucas M, Morris A, Townsend-Teague A, Tichit L, Habermann B, Barrat A. Inferring cell cycle phases from a partially temporal network of protein interactions. CELL REPORTS METHODS 2023; 3:100397. [PMID: 36936083 PMCID: PMC10014271 DOI: 10.1016/j.crmeth.2023.100397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
The temporal organization of biological systems is key for understanding them, but current methods for identifying this organization are often ad hoc and require prior knowledge. We present Phasik, a method that automatically identifies this multiscale organization by combining time series data (protein or gene expression) and interaction data (protein-protein interaction network). Phasik builds a (partially) temporal network and uses clustering to infer temporal phases. We demonstrate the method's effectiveness by recovering well-known phases and sub-phases of the cell cycle of budding yeast and phase arrests of mutants. We also show its general applicability using temporal gene expression data from circadian rhythms in wild-type and mutant mouse models. We systematically test Phasik's robustness and investigate the effect of having only partial temporal information. As time-resolved, multiomics datasets become more common, this method will allow the study of temporal regulation in lesser-known biological contexts, such as development, metabolism, and disease.
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Affiliation(s)
- Maxime Lucas
- Aix Marseille University, CNRS, I2M UMR 7373, Turing Center for Living Systems, Marseille, France
- Aix Marseille University, CNRS, IBDM UMR 7288, Turing Center for Living Systems, Marseille, France
- Aix Marseille University, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
| | | | | | - Laurent Tichit
- Aix Marseille University, CNRS, I2M UMR 7373, Turing Center for Living Systems, Marseille, France
| | - Bianca Habermann
- Aix Marseille University, CNRS, IBDM UMR 7288, Turing Center for Living Systems, Marseille, France
| | - Alain Barrat
- Aix Marseille University, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France
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A dynamical stochastic model of yeast translation across the cell cycle. Heliyon 2023; 9:e13101. [PMID: 36793957 PMCID: PMC9922973 DOI: 10.1016/j.heliyon.2023.e13101] [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: 03/18/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Translation is a central step in gene expression, however its quantitative and time-resolved regulation is poorly understood. We developed a discrete, stochastic model for protein translation in S. cerevisiae in a whole-transcriptome, single-cell context. A "base case" scenario representing an average cell highlights translation initiation rates as the main co-translational regulatory parameters. Codon usage bias emerges as a secondary regulatory mechanism through ribosome stalling. Demand for anticodons with low abundancy is shown to cause above-average ribosome dwelling times. Codon usage bias correlates strongly both with protein synthesis rates and elongation rates. Applying the model to a time-resolved transcriptome estimated by combining data from FISH and RNA-Seq experiments, it could be shown that increased total transcript abundance during the cell cycle decreases translation efficiency at single transcript level. Translation efficiency grouped by gene function shows highest values for ribosomal and glycolytic genes. Ribosomal proteins peak in S phase while glycolytic proteins rank highest in later cell cycle phases.
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Lázari LC, Wolf IR, Schnepper AP, Valente GT. LncRNAs of Saccharomyces cerevisiae bypass the cell cycle arrest imposed by ethanol stress. PLoS Comput Biol 2022; 18:e1010081. [PMID: 35587936 PMCID: PMC9232138 DOI: 10.1371/journal.pcbi.1010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 06/24/2022] [Accepted: 04/05/2022] [Indexed: 11/19/2022] Open
Abstract
Ethanol alters many subsystems of Saccharomyces cerevisiae, including the cell cycle. Two ethanol-responsive lncRNAs in yeast interact with cell cycle proteins, and here, we investigated the role of these RNAs in cell cycle. Our network dynamic modeling showed that higher and lower ethanol-tolerant strains undergo cell cycle arrest in mitosis and G1 phases, respectively, during ethanol stress. The higher population rebound of the lower ethanol-tolerant phenotype after stress relief responds to the late phase arrest. We found that the lncRNA lnc9136 of SEY6210 (a lower ethanol-tolerant strain) induces cells to skip mitosis arrest. Simulating an overexpression of lnc9136 and analyzing CRISPR–Cas9 mutants lacking this lncRNA suggest that lnc9136 induces a regular cell cycle even under ethanol stress, indirectly regulating Swe1p and Clb1/2 by binding to Gin4p and Hsl1p. Notably, lnc10883 of BY4742 (a higher ethanol-tolerant strain) does not prevent G1 arrest in this strain under ethanol stress. However, lnc19883 circumvents DNA and spindle damage checkpoints, maintaining a functional cell cycle by interacting with Mec1p or Bub1p even in the presence of DNA/spindle damage. Overall, we present the first evidence of direct roles for lncRNAs in regulating yeast cell cycle proteins, the dynamics of this system in different ethanol-tolerant phenotypes, and a new yeast cell cycle model. Ethanol is a cell stressor in yeast that dampen ethanol production. LncRNAs are RNAs that control many cellular processes. Computational simulations allow us to study the dynamism of cell systems. Therefore, we built a computational model of the yeast cell cycle to investigate how cells respond to ethanol stress. Simulations showed that ethanol stress or spindle damage arrests the cell cycle. Furthermore, the performance of higher and lower ethanol-tolerant strains in poststress recovery growth seems to be related to the cell cycle phase in which cells are stalled. However, two lncRNAs maintain the activity of the cell cycle even in yeast cells under these stresses by repressing specific cell cycle proteins. Finally, this model facilitates analyses of the yeast cell cycle for applied or basic science purposes.
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Affiliation(s)
- Lucas Cardoso Lázari
- Department of Parasitology, Institute of Biomedical Sciences, Sāo Paulo University (USP), Sao Paulo, Brazil
- Department of Bioprocess and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Ivan Rodrigo Wolf
- Department of Bioprocess and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Amanda Piveta Schnepper
- Department of Bioprocess and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Guilherme Targino Valente
- Department of Bioprocess and Biotechnology, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- * E-mail: ,
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Cyclin-Dependent Kinases and CTD Phosphatases in Cell Cycle Transcriptional Control: Conservation across Eukaryotic Kingdoms and Uniqueness to Plants. Cells 2022; 11:cells11020279. [PMID: 35053398 PMCID: PMC8774115 DOI: 10.3390/cells11020279] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023] Open
Abstract
Cell cycle control is vital for cell proliferation in all eukaryotic organisms. The entire cell cycle can be conceptually separated into four distinct phases, Gap 1 (G1), DNA synthesis (S), G2, and mitosis (M), which progress sequentially. The precise control of transcription, in particular, at the G1 to S and G2 to M transitions, is crucial for the synthesis of many phase-specific proteins, to ensure orderly progression throughout the cell cycle. This mini-review highlights highly conserved transcriptional regulators that are shared in budding yeast (Saccharomyces cerevisiae), Arabidopsis thaliana model plant, and humans, which have been separated for more than a billion years of evolution. These include structurally and/or functionally conserved regulators cyclin-dependent kinases (CDKs), RNA polymerase II C-terminal domain (CTD) phosphatases, and the classical versus shortcut models of Pol II transcriptional control. A few of CDKs and CTD phosphatases counteract to control the Pol II CTD Ser phosphorylation codes and are considered critical regulators of Pol II transcriptional process from initiation to elongation and termination. The functions of plant-unique CDKs and CTD phosphatases in relation to cell division are also briefly summarized. Future studies towards testing a cooperative transcriptional mechanism, which is proposed here and involves sequence-specific transcription factors and the shortcut model of Pol II CTD code modulation, across the three eukaryotic kingdoms will reveal how individual organisms achieve the most productive, large-scale transcription of phase-specific genes required for orderly progression throughout the entire cell cycle.
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A processive phosphorylation circuit with multiple kinase inputs and mutually diversional routes controls G1/S decision. Nat Commun 2020; 11:1836. [PMID: 32296067 PMCID: PMC7160111 DOI: 10.1038/s41467-020-15685-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 03/23/2020] [Indexed: 12/14/2022] Open
Abstract
Studies on multisite phosphorylation networks of cyclin-dependent kinase (CDK) targets have opened a new level of signaling complexity by revealing signal processing routes encoded into disordered proteins. A model target, the CDK inhibitor Sic1, contains linear phosphorylation motifs, docking sites, and phosphodegrons to empower an N-to-C terminally directed phosphorylation process. Here, we uncover a signal processing mechanism involving multi-step competition between mutually diversional phosphorylation routes within the S-CDK-Sic1 inhibitory complex. Intracomplex phosphorylation plays a direct role in controlling Sic1 degradation, and provides a mechanism to sequentially integrate both the G1- and S-CDK activities while keeping S-CDK inhibited towards other targets. The competing phosphorylation routes prevent premature Sic1 degradation and demonstrate how integration of MAPK from the pheromone pathway allows one to tune the competition of alternative phosphorylation paths. The mutually diversional phosphorylation circuits may be a general way for processing multiple kinase signals to coordinate cellular decisions in eukaryotes. The decision of whether and when a cell divides is tightly controlled. Here, the authors show in yeast that there is a multi-step competition between different phosphorylation states and sites in the S phase CDK-Sic1 complex, which controls Sic1 degradation and coordinates the precise timing of the G1/S transition.
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