1
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Namba S, Kato H, Shigenobu S, Makino T, Moriya H. Massive expression of cysteine-containing proteins causes abnormal elongation of yeast cells by perturbing the proteasome. G3 (BETHESDA, MD.) 2022; 12:jkac106. [PMID: 35485947 PMCID: PMC9157148 DOI: 10.1093/g3journal/jkac106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022]
Abstract
The enhanced green fluorescent protein (EGFP) is considered to be a harmless protein because the critical expression level that causes growth defects is higher than that of other proteins. Here, we found that overexpression of EGFP, but not a glycolytic protein Gpm1, triggered the cell elongation phenotype in the budding yeast Saccharomyces cerevisiae. By the morphological analysis of the cell overexpressing fluorescent protein and glycolytic enzyme variants, we revealed that cysteine content was associated with the cell elongation phenotype. The abnormal cell morphology triggered by overexpression of EGFP was also observed in the fission yeast Schizosaccharomyces pombe. Overexpression of cysteine-containing protein was toxic, especially at high-temperature, while the toxicity could be modulated by additional protein characteristics. Investigation of protein aggregate formation, morphological abnormalities in mutants, and transcriptomic changes that occur upon overexpression of EGFP variants suggested that perturbation of the proteasome by the exposed cysteine of the overexpressed protein causes cell elongation. Overexpression of proteins with relatively low folding properties, such as EGFP, was also found to promote the formation of SHOTA (Seventy kDa Heat shock protein-containing, Overexpression-Triggered Aggregates), an intracellular aggregate that incorporates Hsp70/Ssa1, which induces a heat shock response, while it was unrelated to cell elongation. Evolutionary analysis of duplicated genes showed that cysteine toxicity may be an evolutionary bias to exclude cysteine from highly expressed proteins. The overexpression of cysteine-less moxGFP, the least toxic protein revealed in this study, would be a good model system to understand the physiological state of protein burden triggered by ultimate overexpression of harmless proteins.
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Affiliation(s)
- Shotaro Namba
- Graduate School of Environmental and Life Sciences, Okayama University, Okayama 700-8530, Japan
| | - Hisaaki Kato
- Graduate School of Environmental and Life Sciences, Okayama University, Okayama 700-8530, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology, Okazaki, 444-8585 Aichi, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Hisao Moriya
- Graduate School of Environmental and Life Sciences, Okayama University, Okayama 700-8530, Japan
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2
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Ascencio D, Diss G, Gagnon-Arsenault I, Dubé AK, DeLuna A, Landry CR. Expression attenuation as a mechanism of robustness against gene duplication. Proc Natl Acad Sci U S A 2021; 118:e2014345118. [PMID: 33526669 PMCID: PMC7970654 DOI: 10.1073/pnas.2014345118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Gene duplication is ubiquitous and a major driver of phenotypic diversity across the tree of life, but its immediate consequences are not fully understood. Deleterious effects would decrease the probability of retention of duplicates and prevent their contribution to long-term evolution. One possible detrimental effect of duplication is the perturbation of the stoichiometry of protein complexes. Here, we measured the fitness effects of the duplication of 899 essential genes in the budding yeast using high-resolution competition assays. At least 10% of genes caused a fitness disadvantage when duplicated. Intriguingly, the duplication of most protein complex subunits had small to nondetectable effects on fitness, with few exceptions. We selected four complexes with subunits that had an impact on fitness when duplicated and measured the impact of individual gene duplications on their protein-protein interactions. We found that very few duplications affect both fitness and interactions. Furthermore, large complexes such as the 26S proteasome are protected from gene duplication by attenuation of protein abundance. Regulatory mechanisms that maintain the stoichiometric balance of protein complexes may protect from the immediate effects of gene duplication. Our results show that a better understanding of protein regulation and assembly in complexes is required for the refinement of current models of gene duplication.
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Affiliation(s)
- Diana Ascencio
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, 36824 Irapuato, Guanajuato, Mexico
| | - Guillaume Diss
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexandre K Dubé
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Alexander DeLuna
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados, 36824 Irapuato, Guanajuato, Mexico
| | - Christian R Landry
- Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC G1V 0A6, Canada;
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, QC G1V 0A6, Canada
- Département de Biologie, Université Laval, Québec, QC G1V 0A6, Canada
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3
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Kintaka R, Makanae K, Namba S, Kato H, Kito K, Ohnuki S, Ohya Y, Andrews BJ, Boone C, Moriya H. Genetic profiling of protein burden and nuclear export overload. eLife 2020; 9:54080. [PMID: 33146608 PMCID: PMC7673788 DOI: 10.7554/elife.54080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 11/01/2020] [Indexed: 12/11/2022] Open
Abstract
Overproduction (op) of proteins triggers cellular defects. One of the consequences of overproduction is the protein burden/cost, which is produced by an overloading of the protein synthesis process. However, the physiology of cells under a protein burden is not well characterized. We performed genetic profiling of protein burden by systematic analysis of genetic interactions between GFP-op, surveying both deletion and temperature-sensitive mutants in budding yeast. We also performed genetic profiling in cells with overproduction of triple-GFP (tGFP), and the nuclear export signal-containing tGFP (NES-tGFP). The mutants specifically interacted with GFP-op were suggestive of unexpected connections between actin-related processes like polarization and the protein burden, which was supported by morphological analysis. The tGFP-op interactions suggested that this protein probe overloads the proteasome, whereas those that interacted with NES-tGFP involved genes encoding components of the nuclear export process, providing a resource for further analysis of the protein burden and nuclear export overload.
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Affiliation(s)
- Reiko Kintaka
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
| | - Shotaro Namba
- Matching Program Course, Okayama University, Okayama, Japan
| | - Hisaaki Kato
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Tokyo, Japan
| | - Shinsuke Ohnuki
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Yoshikazu Ohya
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Brenda J Andrews
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada
| | - Charles Boone
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada.,RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan.,Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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4
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N-terminal deletion of Swi3 created by the deletion of a dubious ORF YJL175W mitigates protein burden effect in S. cerevisiae. Sci Rep 2020; 10:9500. [PMID: 32528012 PMCID: PMC7289859 DOI: 10.1038/s41598-020-66307-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 05/19/2020] [Indexed: 12/28/2022] Open
Abstract
Extreme overproduction of gratuitous proteins can overload cellular protein production resources, leading to growth defects, a phenomenon known as the protein burden/cost effect. Genetic screening in the budding yeast Saccharomyces cerevisiae has isolated several dubious ORFs whose deletions mitigated the protein burden effect, but individual characterization thereof has yet to be delineated. We found that deletion of the YJL175W ORF yielded an N-terminal deletion of Swi3, a subunit of the SWI/SNF chromatin remodeling complex, and partial loss of function of Swi3. The deletion mutant showed a reduction in transcription of genes encoding highly expressed, secreted proteins and an overall reduction in translation. Mutations in the chromatin remodeling complex could thus mitigate the protein burden effect, likely by reallocating residual cellular resources used to overproduce proteins. This cellular state might also be related to cancer cells, as they frequently harbor mutations in the SWI/SNF complex.
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5
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Mori Y, Yoshida Y, Satoh A, Moriya H. Development of an experimental method of systematically estimating protein expression limits in HEK293 cells. Sci Rep 2020; 10:4798. [PMID: 32179769 PMCID: PMC7075890 DOI: 10.1038/s41598-020-61646-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/28/2020] [Indexed: 11/25/2022] Open
Abstract
Protein overexpression sometimes causes cellular defects, although the underlying mechanism is still unknown. A protein's expression limit, which triggers cellular defects, is a useful indication of the underlying mechanism. In this study, we developed an experimental method of estimating the expression limits of target proteins in the human embryonic kidney cell line HEK293 by measuring the proteins' expression levels in cells that survived after the high-copy introduction of plasmid DNA by which the proteins were expressed under a strong cytomegalovirus promoter. The expression limits of nonfluorescent target proteins were indirectly estimated by measuring the levels of green fluorescent protein (GFP) connected to the target proteins with the self-cleaving sequence P2A. The expression limit of a model GFP was ~5.0% of the total protein, and sustained GFP overexpression caused cell death. The expression limits of GFPs with mitochondria-targeting signals and endoplasmic reticulum localization signals were 1.6% and 0.38%, respectively. The expression limits of four proteins involved in vesicular trafficking were far lower compared to a red fluorescent protein. The protein expression limit estimation method developed will be valuable for defining toxic proteins and consequences of protein overexpression.
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Affiliation(s)
- Yoshihiro Mori
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Yuki Yoshida
- Sony Computer Science Laboratories, Tokyo, Japan
| | - Ayano Satoh
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan.
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
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6
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Moriya H. The expression level and cytotoxicity of green fluorescent protein are modulated by an additional N-terminal sequence. AIMS BIOPHYSICS 2020. [DOI: 10.3934/biophy.2020010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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7
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Abstract
A gene duplication can lead to all sorts of problems in a cell. However, it can also lead to all sorts of benefits. Beneficial or not, the gene duplicates might be kept in the genome because of several different reasons. For instance, if natural selection works towards optimizing one function of a gene at the expense of another, then gene duplication could resolve this conflict by separating the functions in two genes. Here, we outline evolutionary incentives to keep a duplicated gene in the genome, focusing on divergence in expression and trade-off resolution as featured in a new and exciting paper published in this edition of PLOS Biology.
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Affiliation(s)
- Johan Hallin
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- PROTEO, Le réseau québécois de recherche sur la fonction, la structure et l’ingénierie des protéines, Université Laval, Québec, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
| | - Christian R. Landry
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Département de biologie, Faculté des sciences et de génie, Université Laval, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- PROTEO, Le réseau québécois de recherche sur la fonction, la structure et l’ingénierie des protéines, Université Laval, Québec, Canada
- Centre de Recherche en Données Massives (CRDM), Université Laval, Québec, Canada
- * E-mail:
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8
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Def1 mediates the degradation of excess nucleolar protein Nop1 in budding yeast. Biochem Biophys Res Commun 2019; 519:302-308. [PMID: 31506176 DOI: 10.1016/j.bbrc.2019.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/01/2019] [Indexed: 01/22/2023]
Abstract
Nucleolar proteins such as Nop1/fibrillarin are degraded by nucleophagy in nutrient-starved conditions. However, whether and how excess nucleolar proteins are removed in normal conditions is unknown. Here we show that overexpressed nucleolar protein Nop1 is toxic and degraded in nutrient-rich conditions in budding yeast. The degradation was dependent on proteasomes. The CUE domain-containing protein Def1 mediated the degradation via the CUE domain and alleviated toxicity of Nop1 overexpression. Def1 was recruited to overexpressed Nop1 in the nucleolus. Ubiquitin mutants compromised this recruitment. This study revealed that Def1 is a novel factor for ubiquitin-dependent degradation of excess nucleolar proteins.
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9
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Eguchi Y, Makanae K, Hasunuma T, Ishibashi Y, Kito K, Moriya H. Estimating the protein burden limit of yeast cells by measuring the expression limits of glycolytic proteins. eLife 2018; 7:34595. [PMID: 30095406 PMCID: PMC6086662 DOI: 10.7554/elife.34595] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 07/01/2018] [Indexed: 11/30/2022] Open
Abstract
The ultimate overexpression of a protein could cause growth defects, which are known as the protein burden. However, the expression limit at which the protein-burden effect is triggered is still unclear. To estimate this limit, we systematically measured the overexpression limits of glycolytic proteins in Saccharomyces cerevisiae. The limits of some glycolytic proteins were up to 15% of the total cellular protein. These limits were independent of the proteins’ catalytic activities, a finding that was supported by an in silico analysis. Some proteins had low expression limits that were explained by their localization and metabolic perturbations. The codon usage should be highly optimized to trigger the protein-burden effect, even under strong transcriptional induction. The S–S-bond-connected aggregation mediated by the cysteine residues of a protein might affect its expression limit. Theoretically, only non-harmful proteins could be expressed up to the protein-burden limit. Therefore, we established a framework to distinguish proteins that are harmful and non-harmful upon overexpression. If a cell makes too much of a given protein, it can sometimes cause problems and impair the cell’s growth. Overproducing some proteins may deplete the cell’s limited resources, meaning it does not have enough to make other more essential proteins. This phenomenon is known as the protein burden effect. Theoretically, only harmless proteins can be overproduced up to a level where growth would be impaired in this way. Conversely, if an overproduced protein causes harm before it becomes a burden on resources, scientists must consider other mechanisms to explain the cell’s problems, namely that the protein itself is harmful. Knowing the ultimate level of protein production that could cause the protein burden effect – the protein burden limit – would allow scientists to distinguish between harmful and non-harmful proteins. However, to date, this limit had not been defined for any cell. Eguchi et al. have now tried to estimate the protein burden limit for budding yeast – one of the best-studied experimental organisms. The experiments first focused on enzymes involved in alcoholic fermentation because they were expected to be non-harmful. Some of these enzymes were overproduced to the level were the made up 15% of all the cell’s proteins before they started to cause growth defects. The same results were seen with versions of the enzymes that had been mutated to be less active, leading Eguchi et al. to conclude that this level is the protein burden limit. In other experiments, harmful enzymes could only be overproduced to levels that were far less than this proposed protein burden limit. These enzymes caused problems for the yeast in several ways, including interfering with biochemical reactions and forming large aggregates in the cell. Lastly, Eguchi et al. looked at the yeast’s genetic code and saw that most of its genes seemed to have evolved to specifically limit the production of proteins to a level that would avoid the unwanted protein burden effect. Together these findings establish a framework to clearly distinguish between harmful and non-harmful proteins. This framework will be useful to understand the different reasons why the overproduction of certain proteins, which is seen in neurodegenerative diseases and cancer cells, can cause problems for cells.
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Affiliation(s)
- Yuichi Eguchi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Yuko Ishibashi
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Hisao Moriya
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.,Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
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10
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Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism. PLoS One 2017; 12:e0172742. [PMID: 28241048 PMCID: PMC5328394 DOI: 10.1371/journal.pone.0172742] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/08/2017] [Indexed: 12/25/2022] Open
Abstract
Central carbon metabolism is controlled by modulating the protein abundance profiles of enzymes that maintain the essential systems in living organisms. In this study, metabolic adaptation mechanisms in the model organism Saccharomyces cerevisiae were investigated by direct determination of enzyme abundance levels in 30 wild type and mutant strains. We performed a targeted proteome analysis using S. cerevisiae strains that lack genes encoding the enzymes responsible for central carbon metabolism. Our analysis revealed that at least 30% of the observed variations in enzyme abundance levels could be explained by global regulatory mechanisms. A enzyme-enzyme co-abundance analysis revealed that the abundances of enzyme proteins involved in the trehalose metabolism and glycolysis changed in a coordinated manner under the control of the transcription factors for global regulation. The remaining variations were derived from local mechanisms such as a mutant-specific increase in the abundances of remote enzymes. The proteome data also suggested that, although the functional compensation of the deficient enzyme was attained by using more resources for protein biosynthesis, available resources for the biosynthesis of the enzymes responsible for central metabolism were not abundant in S. cerevisiae cells. These results showed that global and local regulation of enzyme abundance levels shape central carbon metabolism in S. cerevisiae by using a limited resource for protein biosynthesis.
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11
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Abstract
Overexpression experiments are sometimes considered as qualitative experiments designed to identify novel proteins and study their function. However, in order to draw conclusions regarding protein overexpression through association analyses using large-scale biological data sets, we need to recognize the quantitative nature of overexpression experiments. Here I discuss the quantitative features of two different types of overexpression experiment: absolute and relative. I also introduce the four primary mechanisms involved in growth defects caused by protein overexpression: resource overload, stoichiometric imbalance, promiscuous interactions, and pathway modulation associated with the degree of overexpression.
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Affiliation(s)
- Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama 700-8530, Japan
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12
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Kintaka R, Makanae K, Moriya H. Cellular growth defects triggered by an overload of protein localization processes. Sci Rep 2016; 6:31774. [PMID: 27538565 PMCID: PMC4990933 DOI: 10.1038/srep31774] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022] Open
Abstract
High-level expression of a protein localized to an intracellular compartment is expected to cause cellular defects because it overloads localization processes. However, overloads of localization processes have never been studied systematically. Here, we show that the expression levels of green fluorescent proteins (GFPs) with localization signals were limited to the same degree as a toxic misfolded GFP in budding yeast cells, and that their high-level expression caused cellular defects associated with localization processes. We further show that limitation of the exportin Crm1 determined the expression limit of GFP with a nuclear export signal. Although misfolding of GFP with a vesicle-mediated transport signal triggered endoplasmic reticulum stress, it was not the primary determinant of its expression limit. The precursor of GFP with a mitochondrial targeting signal caused a cellular defect. Finally, we estimated the residual capacities of localization processes. High-level expression of a localized protein thus causes cellular defects by overloading the capacities of localization processes.
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Affiliation(s)
- Reiko Kintaka
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
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13
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Abstract
Dividing cells that experience chromosome mis-segregation generate aneuploid daughter cells, which contain an incorrect number of chromosomes. Although aneuploidy interferes with the proliferation of untransformed cells, it is also, paradoxically, a hallmark of cancer, a disease defined by increased proliferative potential. These contradictory effects are also observed in mouse models of chromosome instability (CIN). CIN can inhibit and promote tumorigenesis. Recent work has provided insights into the cellular consequences of CIN and aneuploidy. Chromosome mis-segregation per se can alter the genome in many more ways than just causing the gain or loss of chromosomes. The short- and long-term effects of aneuploidy are caused by gene-specific effects and a stereotypic aneuploidy stress response. Importantly, these recent findings provide insights into the role of aneuploidy in tumorigenesis.
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14
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Bonney ME, Moriya H, Amon A. Aneuploid proliferation defects in yeast are not driven by copy number changes of a few dosage-sensitive genes. Genes Dev 2015; 29:898-903. [PMID: 25934502 PMCID: PMC4421978 DOI: 10.1101/gad.261743.115] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A central question is whether aneuploid phenotypes are the consequence of copy number changes of a few especially harmful genes that may be present on the extra chromosome or are caused by copy number alterations of many genes that confer no observable phenotype when varied individually. Bonney et al. used the proliferation defect exhibited by budding yeast strains carrying single additional chromosomes (disomes) to show that subtle changes in gene dosage across a chromosome can have significant phenotypic consequences. Aneuploidy—the gain or loss of one or more whole chromosome—typically has an adverse impact on organismal fitness, manifest in conditions such as Down syndrome. A central question is whether aneuploid phenotypes are the consequence of copy number changes of a few especially harmful genes that may be present on the extra chromosome or are caused by copy number alterations of many genes that confer no observable phenotype when varied individually. We used the proliferation defect exhibited by budding yeast strains carrying single additional chromosomes (disomes) to distinguish between the “few critical genes” hypothesis and the “mass action of genes” hypothesis. Our results indicate that subtle changes in gene dosage across a chromosome can have significant phenotypic consequences. We conclude that phenotypic thresholds can be crossed by mass action of copy number changes that, on their own, are benign.
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Affiliation(s)
- Megan E Bonney
- Koch Institute for Integrative Cancer Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama 700-8530, Japan
| | - Angelika Amon
- Koch Institute for Integrative Cancer Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA;
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15
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Small toxic protein encoded on chromosome VII of Saccharomyces cerevisiae. PLoS One 2015; 10:e0120678. [PMID: 25781884 PMCID: PMC4363601 DOI: 10.1371/journal.pone.0120678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/25/2015] [Indexed: 11/19/2022] Open
Abstract
In a previous study, we found an unknown element that caused growth inhibition after its copy number increased in the 3' region of DIE2 in Saccharomyces cerevisiae. In this study, we further identified this element and observed that overexpression of a small protein (sORF2) of 57 amino acids encoded in this region caused growth inhibition. The transcriptional response and multicopy suppression of the growth inhibition caused by sORF2 overexpression suggest that sORF2 overexpression inhibits the ergosterol biosynthetic pathway. sORF2 was not required in the normal growth of S. cerevisiae, and not conserved in related yeast species including S. paradoxus. Thus, sORF2 (designated as OTO1) is an orphan ORF that determines the specificity of this species.
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Sasabe M, Shintani S, Kintaka R, Kaizu K, Makanae K, Moriya H. Evaluation of the lower protein limit in the budding yeast Saccharomyces cerevisiae using TIPI-gTOW. BMC SYSTEMS BIOLOGY 2014; 8:2. [PMID: 24393197 PMCID: PMC3892067 DOI: 10.1186/1752-0509-8-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 12/27/2013] [Indexed: 12/19/2022]
Abstract
Background Identifying permissible limits of intracellular parameters such as protein expression provides important information for examining robustness. In this study, we used the TEV protease-mediated induction of protein instability (TIPI) in combination with the genetic Tug-of-War (gTOW) to develop a method to measure the lower limit of protein level. We first tested the feasibility of this method using ADE2 as a marker and then analyzed some cell cycle regulators to reveal genetic interactions. Results Using TIPI-gTOW, we successfully constructed a strain in which GFP-TDegFAde2 was expressed at the lower limit, just sufficient to support cellular growth under the -Ade condition by accelerating degradation by TEV protease. We also succeeded in constructing a strain in which the minimal level of GFP-TDegFCdc20 was expressed by TIPI-gTOW. Using this strain, we studied genetic interactions between cell cycle regulators and CDC20, and the result was highly consistent with the previously identified interactions. Comparison of the experimental data with predictions of a mathematical model revealed some interactions that were not implemented into the current model. Conclusions TIPI-gTOW is useful for estimating changes in the lower limit of a protein under different conditions, such as different genetic backgrounds and environments. TIPI-gTOW is also useful for analyzing genetic interactions of essential genes whose deletion mutants cannot be obtained.
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Affiliation(s)
| | | | | | | | | | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Kita-ku, Okayama, Japan.
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Cirillo D, Livi CM, Agostini F, Tartaglia GG. Discovery of protein–RNA networks. ACTA ACUST UNITED AC 2014; 10:1632-42. [DOI: 10.1039/c4mb00099d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We review the latest advances and future challenges in experimental and computational investigation of protein–RNA networks.
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Affiliation(s)
- Davide Cirillo
- Gene Function and Evolution
- Centre for Genomic Regulation (CRG)
- 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF)
- 08003 Barcelona, Spain
| | - Carmen Maria Livi
- Gene Function and Evolution
- Centre for Genomic Regulation (CRG)
- 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF)
- 08003 Barcelona, Spain
| | - Federico Agostini
- Gene Function and Evolution
- Centre for Genomic Regulation (CRG)
- 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF)
- 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Gene Function and Evolution
- Centre for Genomic Regulation (CRG)
- 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF)
- 08003 Barcelona, Spain
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Zanzoni A, Marchese D, Agostini F, Bolognesi B, Cirillo D, Botta-Orfila M, Livi CM, Rodriguez-Mulero S, Tartaglia GG. Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein. Nucleic Acids Res 2013; 41:9987-98. [PMID: 24003031 PMCID: PMC3905859 DOI: 10.1093/nar/gkt794] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory mechanisms that control gene expression at the translational level. Using the catRAPID approach to predict the propensity of proteins to bind to RNA, we investigated the occurrence of autogenous associations in the human proteome. Our algorithm correctly identified binding sites in well-known cases such as thymidylate synthase, tumor suppressor P53, synaptotagmin-1, serine/ariginine-rich splicing factor 2, heat shock 70 kDa, ribonucleic particle-specific U1A and ribosomal protein S13. In addition, we found that several other proteins are able to bind to their own mRNAs. A large-scale analysis of biological pathways revealed that aggregation-prone and structurally disordered proteins have the highest propensity to interact with cognate RNAs. These findings are substantiated by experimental evidence on amyloidogenic proteins such as TAR DNA-binding protein 43 and fragile X mental retardation protein. Among the amyloidogenic proteins, we predicted that Parkinson’s disease-related α-synuclein is highly prone to interact with cognate transcripts, which suggests the existence of RNA-dependent factors in its function and dysfunction. Indeed, as aggregation is intrinsically concentration dependent, it is possible that autogenous interactions play a crucial role in controlling protein homeostasis.
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Affiliation(s)
- Andreas Zanzoni
- Gene Function and Evolution, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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Chino A, Makanae K, Moriya H. Relationships between cell cycle regulator gene copy numbers and protein expression levels in Schizosaccharomyces pombe. PLoS One 2013; 8:e73319. [PMID: 24019917 PMCID: PMC3760898 DOI: 10.1371/journal.pone.0073319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/18/2013] [Indexed: 12/02/2022] Open
Abstract
We previously determined the copy number limits of overexpression for cell division cycle (cdc) regulatory genes in the fission yeast Schizosaccharomyces pombe using the “genetic tug-of-war” (gTOW) method. In this study, we measured the levels of tandem affinity purification (TAP)-tagged target proteins when their copy numbers are increased in gTOW. Twenty analyzed genes showed roughly linear correlations between increased protein levels and gene copy numbers, which suggested a general lack of compensation for gene dosage in S. pombe. Cdc16 and Sid2 protein levels but not their mRNA levels were much lower than that expected by their copy numbers, which suggested the existence of a post-transcriptional down regulation of these genes. The cyclin Cig1 protein level and its mRNA level were much higher than that expected by its copy numbers, which suggested a positive feedback mechanism for its expression. A higher Cdc10 protein level and its mRNA level, probably due to cloning its gene into a plasmid, indicated that Cdc10 regulation was more robust than that previously predicted.
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Affiliation(s)
- Ayako Chino
- Graduate School of Science and Technology, Okayama University, Kita-ku, Okayama, Japan
- Research Core for Interdisciplinary Sciences, Okayama University, Kita-ku, Okayama, Japan
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Kita-ku, Okayama, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Kita-ku, Okayama, Japan
- * E-mail:
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Makanae K, Kintaka R, Makino T, Kitano H, Moriya H. Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method. Genome Res 2012; 23:300-11. [PMID: 23275495 PMCID: PMC3561871 DOI: 10.1101/gr.146662.112] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Gene overexpression beyond a permissible limit causes defects in cellular functions. However, the permissible limits of most genes are unclear. Previously, we developed a genetic method designated genetic tug-of-war (gTOW) to measure the copy number limit of overexpression of a target gene. In the current study, we applied gTOW to the analysis of all protein-coding genes in the budding yeast Saccharomyces cerevisiae. We showed that the yeast cellular system was robust against an increase in the copy number by up to 100 copies in >80% of the genes. After frameshift and segmentation analyses, we isolated 115 dosage-sensitive genes (DSGs) with copy number limits of 10 or less. DSGs contained a significant number of genes involved in cytoskeletal organization and intracellular transport. DSGs tended to be highly expressed and to encode protein complex members. We demonstrated that the protein burden caused the dosage sensitivity of highly expressed genes using a gTOW experiment in which the open reading frame was replaced with GFP. Dosage sensitivities of some DSGs were rescued by the simultaneous increase in the copy numbers of partner genes, indicating that stoichiometric imbalances among complexes cause dosage sensitivity. The results obtained in this study will provide basic knowledge about the physiology of chromosomal abnormalities and the evolution of chromosomal composition.
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Affiliation(s)
- Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama 700-8530, Japan
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