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Zubčić K, Franić D, Pravica M, Hof PR, Šimić G, Boban M. Effects of heterologous human tau protein expression in yeast models of proteotoxic stress response. CNS Neurosci Ther 2024; 30:e14304. [PMID: 37341072 PMCID: PMC11163194 DOI: 10.1111/cns.14304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The primary histological characteristic of Alzheimer's disease is the presence of neurofibrillary tangles, which are large aggregates of tau protein. Aging is the primary risk factor for the development of Alzheimer's disease, however, the underlying causes of tau protein aggregation and toxicity are unclear. AIMS Here we investigated tau aggregation and toxicity under the conditions of compromised protein homeostasis. METHODS We used heterologous expression of human tau protein in the unicellular eukaryote yeast Saccharomyces cerevisiae with evolutionarily conserved protein quality control pathways and examined tau-dependent toxicity and aggregation using growth assays, fluorescence microscopy, and a split luciferase-based reporter NanoBiT. RESULTS Tau protein expressed in yeast under mild proteotoxic stress, or in mutants with impaired pathways for proteotoxic stress response, did not lead to synthetic toxicity or the formation of obvious aggregates. Chronologically old cells also did not develop observable tau aggregates. Our examination of tau oligomerization in living cells using NanoBiT reporter suggests that tau does not form significant levels of oligomers under basal conditions or under mild proteotoxic stress. CONCLUSION Together our data suggest that human tau protein does not represent a major burden to the protein quality control system in yeast cells.
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Affiliation(s)
- Klara Zubčić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Dina Franić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Mihaela Pravica
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's DiseaseFriedman Brain Institute, Icahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Goran Šimić
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
| | - Mirta Boban
- Croatian Institute for Brain Research, University of Zagreb School of MedicineZagrebCroatia
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2
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Pradhan SS, R SS, Kanikaram SP, V M DD, Pargaonkar A, Dandamudi RB, Sivaramakrishnan V. Metabolic deregulation associated with aging modulates protein aggregation in the yeast model of Huntington's disease. J Biomol Struct Dyn 2023:1-18. [PMID: 37732342 DOI: 10.1080/07391102.2023.2257322] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023]
Abstract
Huntington's disease is associated with increased CAG repeat resulting in an expanded polyglutamine tract in the protein Huntingtin (HTT) leading to its aggregation resulting in neurodegeneration. Previous studies have shown that N-terminal HTT with 46Q aggregated in the stationary phase but not the logarithmic phase in the yeast model of HD. We carried out a metabolomic analysis of logarithmic and stationary phase yeast model of HD expressing different polyQ lengths attached to N-terminal HTT tagged with enhanced green fluorescent protein (EGFP). The results show significant changes in the metabolic profile and deregulated pathways in stationary phase cells compared to logarithmic phase cells. Comparison of metabolic pathways obtained from logarithmic phase 46Q versus 25Q with those obtained for presymptomatic HD patients from our previous study and drosophila model of HD showed considerable overlap. The arginine biosynthesis pathway emerged as one of the key pathways that is common in stationary phase yeast compared to logarithmic phase and HD patients. Treatment of yeast with arginine led to a significant decrease, while transfer to arginine drop-out media led to a significant increase in the size of protein aggregates in both logarithmic and stationary phase yeast model of HD. Knockout of arginine transporters in the endoplasmic reticulum and vacuole led to a significant decrease in mutant HTT aggregation. Overall our results highlight arginine as a critical metabolite that modulates the aggregation of mutant HTT and disease progression in HD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Swaroop R
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Sai Phalguna Kanikaram
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Datta Darshan V M
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
| | - Ashish Pargaonkar
- Application Division, Agilent Technologies Ltd., Bengaluru, Karnataka, India
| | | | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Anantapur, Andhra Pradesh, India
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3
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Opalek M, Tutaj H, Pirog A, Smug BJ, Rutkowska J, Wloch-Salamon D. A Systematic Review on Quiescent State Research Approaches in S. cerevisiae. Cells 2023; 12:1608. [PMID: 37371078 DOI: 10.3390/cells12121608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Quiescence, the temporary and reversible arrest of cell growth, is a fundamental biological process. However, the lack of standardization in terms of reporting the experimental details of quiescent cells and populations can cause confusion and hinder knowledge transfer. We employ the systematic review methodology to comprehensively analyze the diversity of approaches used to study the quiescent state, focusing on all published research addressing the budding yeast Saccharomyces cerevisiae. We group research articles into those that consider all cells comprising the stationary-phase (SP) population as quiescent and those that recognize heterogeneity within the SP by distinguishing phenotypically distinct subpopulations. Furthermore, we investigate the chronological age of the quiescent populations under study and the methods used to induce the quiescent state, such as gradual starvation or abrupt environmental change. We also assess whether the strains used in research are prototrophic or auxotrophic. By combining the above features, we identify 48 possible experimental setups that can be used to study quiescence, which can be misleading when drawing general conclusions. We therefore summarize our review by proposing guidelines and recommendations pertaining to the information included in research articles. We believe that more rigorous reporting on the features of quiescent populations will facilitate knowledge transfer within and between disciplines, thereby stimulating valuable scientific discussion.
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Affiliation(s)
- Monika Opalek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Hanna Tutaj
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Adrian Pirog
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Joanna Rutkowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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4
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Watchaputi K, Somboon P, Phromma-in N, Ratanakhanokchai K, Soontorngun N. Actin cytoskeletal inhibitor 19,20-epoxycytochalasin Q sensitizes yeast cells lacking ERG6 through actin-targeting and secondarily through disruption of lipid homeostasis. Sci Rep 2021; 11:7779. [PMID: 33833332 PMCID: PMC8032726 DOI: 10.1038/s41598-021-87342-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Repetitive uses of antifungals result in a worldwide crisis of drug resistance; therefore, natural fungicides with minimal side-effects are currently sought after. This study aimed to investigate antifungal property of 19, 20-epoxycytochalasin Q (ECQ), derived from medicinal mushroom Xylaria sp. BCC 1067 of tropical forests. In a model yeast Saccharomyces cerevisiae, ECQ is more toxic in the erg6∆ strain, which has previously been shown to allow higher uptake of many hydrophilic toxins. We selected one pathway to study the effects of ECQ at very high levels on transcription: the ergosterol biosynthesis pathway, which is unlikely to be the primary target of ECQ. Ergosterol serves many functions that cholesterol does in human cells. ECQ's transcriptional effects were correlated with altered sterol and triacylglycerol levels. In the ECQ-treated Δerg6 strain, which presumably takes up far more ECQ than the wild-type strain, there was cell rupture. Increased actin aggregation and lipid droplets assembly were also found in the erg6∆ mutant. Thereby, ECQ is suggested to sensitize yeast cells lacking ERG6 through actin-targeting and consequently but not primarily led to disruption of lipid homeostasis. Investigation of cytochalasins may provide valuable insight with potential biopharmaceutical applications in treatments of fungal infection, cancer or metabolic disorder.
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Affiliation(s)
- Kwanrutai Watchaputi
- grid.412151.20000 0000 8921 9789Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, 10150 Thailand
| | - Pichayada Somboon
- grid.419784.70000 0001 0816 7508Division of Fermentation Technology, Faculty of Food Industry, King Mongkut’s Institute of Technology Ladkrabang (KMITL), Bangkok, 10520 Thailand
| | - Nipatthra Phromma-in
- grid.412151.20000 0000 8921 9789Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, 10150 Thailand
| | - Khanok Ratanakhanokchai
- grid.412151.20000 0000 8921 9789Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, 10150 Thailand
| | - Nitnipa Soontorngun
- grid.412151.20000 0000 8921 9789Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (KMUTT), Bangkok, 10150 Thailand
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5
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Denkiewicz-Kruk M, Jedrychowska M, Endo S, Araki H, Jonczyk P, Dmowski M, Fijalkowska IJ. Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase-Pol ε Interaction. Int J Mol Sci 2020; 21:ijms21249484. [PMID: 33322195 PMCID: PMC7762974 DOI: 10.3390/ijms21249484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 11/22/2022] Open
Abstract
The CMG complex (Cdc45, Mcm2–7, GINS (Psf1, 2, 3, and Sld5)) is crucial for both DNA replication initiation and fork progression. The CMG helicase interaction with the leading strand DNA polymerase epsilon (Pol ε) is essential for the preferential loading of Pol ε onto the leading strand, the stimulation of the polymerase, and the modulation of helicase activity. Here, we analyze the consequences of impaired interaction between Pol ε and GINS in Saccharomyces cerevisiae cells with the psf1-100 mutation. This significantly affects DNA replication activity measured in vitro, while in vivo, the psf1-100 mutation reduces replication fidelity by increasing slippage of Pol ε, which manifests as an elevated number of frameshifts. It also increases the occurrence of single-stranded DNA (ssDNA) gaps and the demand for homologous recombination. The psf1-100 mutant shows elevated recombination rates and synthetic lethality with rad52Δ. Additionally, we observe increased participation of DNA polymerase zeta (Pol ζ) in DNA synthesis. We conclude that the impaired interaction between GINS and Pol ε requires enhanced involvement of error-prone Pol ζ, and increased participation of recombination as a rescue mechanism for recovery of impaired replication forks.
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Affiliation(s)
- Milena Denkiewicz-Kruk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Malgorzata Jedrychowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Shizuko Endo
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Hiroyuki Araki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Michal Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
| | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
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6
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Lai WF, Wong WT. Roles of the actin cytoskeleton in aging and age-associated diseases. Ageing Res Rev 2020; 58:101021. [PMID: 31968269 DOI: 10.1016/j.arr.2020.101021] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/06/2020] [Accepted: 01/17/2020] [Indexed: 12/12/2022]
Abstract
The integrity of the cytoskeleton is essential to diverse cellular processes such as phagocytosis and intracellular trafficking. Disruption of the organization and dynamics of the actin cytoskeleton leads to age-associated symptoms and diseases, ranging from cancer to neurodegeneration. In addition, changes in the integrity of the actin cytoskeleton disrupt the functioning of not only somatic and stem cells but also gametes, resulting in aberrant embryonic development. Strategies to preserve the integrity and dynamics of the cytoskeleton are, therefore, potentially therapeutic to age-related disorders. The objective of this article is to revisit the current understanding of the roles played by the actin cytoskeleton in aging, and to review the opportunities and challenges for the transition of basic research into intervention development. It is hoped that, with the snapshot of evidence regarding changes in actin dynamics with advanced age, insights into future research directions can be attained.
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Affiliation(s)
- Wing-Fu Lai
- School of Pharmaceutical Sciences, Shenzhen University, PR China; School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, PR China; Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, PR China.
| | - Wing-Tak Wong
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, PR China
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7
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Dastpeyman S, Godin R, Cosa G, English AM. Quantifying Heme-Protein Maturation from Ratiometric Fluorescence Lifetime Measurements on the Single Fluorophore in Its GFP Fusion. J Phys Chem A 2020; 124:746-754. [PMID: 31894984 DOI: 10.1021/acs.jpca.9b11901] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein maturation by heme insertion is a common post-translation modification of key biological importance. Nonetheless, where and when this maturation occurs in eukaryotic cells remain unknown for most heme proteins. Here, we demonstrate for the first time that the maturation of a chromosomally expressed, endogenous heme protein fused to a green fluorescent protein (GFP) can be tracked in live cells. Selecting yeast cytochrome c peroxidase (Ccp1) as our model heme-binding protein, we first characterized the emission in vitro of recombinant Ccp1-GFP with GFP fused C-terminally to Ccp1 by the linker GRRIPGLIN. Time-correlated single-photon counting reveals a single fluorescence lifetime for heme-free apoCcp1-GFP, τ0 = 2.84 ± 0.01 ns. Heme bound to Ccp1 only partially quenches GFP fluorescence since holoCcp1-GFP exhibits two lifetimes, τ1 = 0.95 ± 0.02 and τ2 = 2.46 ± 0.03 ns with fractional amplitudes a1 = 38 ± 1.5% and a2 = 62 ± 1.5%. Also, τ and a are independent of Ccp1-GFP concentration and solution pH between 5.5 and 8.0, and a standard plot of a1 vs % holoCcp1-GFP in mixtures with apoCcp1-GFP is linear, establishing that the fraction of Ccp1-GFP with heme bound can be determined from a1. Fluorescence lifetime imaging microscopy (FLIM) of live yeast cells chromosomally expressing the same Ccp1-GFP fusion revealed 30% holoCcp1-GFP (i.e., mature Ccp1) and 70% apoCcp1-GFP in agreement with biochemical measurements on cell lysates. Thus, ratiometric fluorescence lifetime measurements offer promise for probing heme-protein maturation in live cells, and we can dispense with the reference fluorophore required for ratiometric intensity-based measurements.
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Affiliation(s)
- Samaneh Dastpeyman
- PROTEO and Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke St West , Montreal , Canada H4B 1R6
| | - Robert Godin
- Department of Chemistry , McGill University , 801 Sherbrooke St West , Montreal , Canada H3A 0B8
| | - Gonzalo Cosa
- Department of Chemistry , McGill University , 801 Sherbrooke St West , Montreal , Canada H3A 0B8
| | - Ann M English
- PROTEO and Department of Chemistry and Biochemistry , Concordia University , 7141 Sherbrooke St West , Montreal , Canada H4B 1R6
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8
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In Saccharomyces cerevisiae, withdrawal of the carbon source results in detachment of glycolytic enzymes from the cytoskeleton and in actin reorganization. Fungal Biol 2020; 124:15-23. [DOI: 10.1016/j.funbio.2019.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/20/2019] [Accepted: 10/09/2019] [Indexed: 11/19/2022]
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9
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Cell organelles and yeast longevity: an intertwined regulation. Curr Genet 2019; 66:15-41. [PMID: 31535186 DOI: 10.1007/s00294-019-01035-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022]
Abstract
Organelles are dynamic structures of a eukaryotic cell that compartmentalize various essential functions and regulate optimum functioning. On the other hand, ageing is an inevitable phenomenon that leads to irreversible cellular damage and affects optimum functioning of cells. Recent research shows compelling evidence that connects organelle dysfunction to ageing-related diseases/disorders. Studies in several model systems including yeast have led to seminal contributions to the field of ageing in uncovering novel pathways, proteins and their functions, identification of pro- and anti-ageing factors and so on. In this review, we present a comprehensive overview of findings that highlight the role of organelles in ageing and ageing-associated functions/pathways in yeast.
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10
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Effect of Ethanol-Derived Clove Leaf Extract on the Oxidative Stress Response in Yeast Schizosaccharomyces pombe. Int J Microbiol 2019; 2019:2145378. [PMID: 31485231 PMCID: PMC6710797 DOI: 10.1155/2019/2145378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/02/2019] [Indexed: 12/28/2022] Open
Abstract
Compared to the widely explored antioxidant activity from the clove bud extract, less data are available regarding the potential pharmacological use of clove leaves. Our study aimed to explore the antioxidant activity of clove leaves extract in the cellular level. Thus, we used the yeast Schizosaccharomyces pombe as model organisms. Our data indicate that, following extract treatment (100 ppm), the viability of the stationary phase cells of S. pombe was higher than without extract and that of calorie restriction treatments. 100 ppm extract treatment also increased cell viability against H2O2-induced oxidative stress. Those data indicate that the extract could promote oxidative stress tolerance response in yeast cells, which occurred either during the stationary phase or due to exogenous exposure. Higher dose of extract (500 ppm) showed opposite effects, as cell viability was lower than that without treatment. Analysis toward the mitochondrial activity revealed that the extract did not induce mitochondrial activity unlike the calorie restriction treatment. Based on our data, clove leaf extract promotes oxidative stress tolerance response in the yeast S. pombe, independent to that mitochondrial adaptive ROS signaling which commonly occurs in calorie restriction-induced oxidative stress tolerance response.
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Laporte D, Gouleme L, Jimenez L, Khemiri I, Sagot I. Mitochondria reorganization upon proliferation arrest predicts individual yeast cell fate. eLife 2018; 7:35685. [PMID: 30299253 PMCID: PMC6177259 DOI: 10.7554/elife.35685] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Most cells spend the majority of their life in a non-proliferating state. When proliferation cessation is irreversible, cells are senescent. By contrast, if the arrest is only temporary, cells are defined as quiescent. These cellular states are hardly distinguishable without triggering proliferation resumption, hampering thus the study of quiescent cells properties. Here we show that quiescent and senescent yeast cells are recognizable based on their mitochondrial network morphology. Indeed, while quiescent yeast cells display numerous small vesicular mitochondria, senescent cells exhibit few globular mitochondria. This allowed us to reconsider at the individual-cell level, properties previously attributed to quiescent cells using population-based approaches. We demonstrate that cell’s propensity to enter quiescence is not influenced by replicative age, volume or density. Overall, our findings reveal that quiescent cells are not all identical but that their ability to survive is significantly improved when they exhibit the specific reorganization of several cellular machineries.
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Affiliation(s)
- Damien Laporte
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Laëtitia Gouleme
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Laure Jimenez
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Ines Khemiri
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
| | - Isabelle Sagot
- Centre National de la Recherche Scientifique, Université de Bordeaux - Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
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12
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Lipids and lipid domains of the yeast vacuole. Biochem Soc Trans 2018; 46:1047-1054. [PMID: 30242116 DOI: 10.1042/bst20180120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 11/17/2022]
Abstract
The membrane raft has been a focus of intensive research for the past two decades. Liquid-ordered domains form in artificial liposomes containing sterol and saturated lipids, but their presence in living cell membranes has been controversial. The yeast vacuole is exceptional in that micron-sized raft-like domains form in the stationary phase and under several other conditions. The sterol content of the vacuole in the log phase is much lower than that of liposomes showing liquid-ordered domains, suggesting that sterols may need to be supplied to the vacuole for the raft-like domain formation. We will discuss how lipids and lipid domains are organized in the vacuolar membrane and examine whether evidence is strong enough to conclude that the observed micron-sized domains are rafts.
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13
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Lee HY, Chao JC, Cheng KY, Leu JY. Misfolding-prone proteins are reversibly sequestered to an Hsp42-associated granule upon chronological aging. J Cell Sci 2018; 131:jcs.220202. [PMID: 30054385 DOI: 10.1242/jcs.220202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/20/2018] [Indexed: 12/19/2022] Open
Abstract
Alteration of protein localization is an important strategy for cells to regulate protein homeostasis upon environmental stresses. In the budding yeast Saccharomyces cerevisiae, many proteins relocalize and form cytosolic granules during chronological aging. However, the functions and exact components of these protein granules remain uncharacterized in most cases. In this study, we performed a genome-wide analysis of protein localization in stationary phase cells, leading to the discovery of 307 granule-forming proteins and the identification of new components in the Hsp42-stationary phase granule (Hsp42-SPG), P-bodies, Ret2 granules and actin bodies. We further characterized the Hsp42-SPG, which contains the largest number of protein components, including many molecular chaperones, metabolic enzymes and regulatory proteins. Formation of the Hsp42-SPG efficiently downregulates the activities of sequestered components, which can be differentially released from the granule based on environmental cues. We found a similar structure in the pre-whole genome duplication yeast species, Lachancea kluyveri, suggesting that the Hsp42-SPG is a common machinery allowing chronologically aged cells to contend with changing environments when available energy is limited. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Hsin-Yi Lee
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 114, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jung-Chi Chao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Kuo-Yu Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.,Department of Life Sciences, Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Jun-Yi Leu
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei 114, Taiwan .,Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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14
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Bisschops MMM, Luttik MAH, Doerr A, Verheijen PJT, Bruggeman F, Pronk JT, Daran-Lapujade P. Extreme calorie restriction in yeast retentostats induces uniform non-quiescent growth arrest. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:231-242. [PMID: 27818273 DOI: 10.1016/j.bbamcr.2016.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/24/2016] [Accepted: 11/01/2016] [Indexed: 11/16/2022]
Abstract
Non-dividing Saccharomyces cerevisiae cultures are highly relevant for fundamental and applied studies. However, cultivation conditions in which non-dividing cells retain substantial metabolic activity are lacking. Unlike stationary-phase (SP) batch cultures, the current experimental paradigm for non-dividing yeast cultures, cultivation under extreme calorie restriction (ECR) in retentostat enables non-dividing yeast cells to retain substantial metabolic activity and to prevent rapid cellular deterioration. Distribution of F-actin structures and single-cell copy numbers of specific transcripts revealed that cultivation under ECR yields highly homogeneous cultures, in contrast to SP cultures that differentiate into quiescent and non-quiescent subpopulations. Combined with previous physiological studies, these results indicate that yeast cells subjected to ECR survive in an extended G1 phase. This study demonstrates that yeast cells exposed to ECR differ from carbon-starved cells and offer a promising experimental model for studying non-dividing, metabolically active, and robust eukaryotic cells.
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Affiliation(s)
- Markus M M Bisschops
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Anne Doerr
- Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Peter J T Verheijen
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Frank Bruggeman
- Systems Bioinformatics, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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15
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Vasicova P, Rinnerthaler M, Haskova D, Novakova L, Malcova I, Breitenbach M, Hasek J. Formaldehyde fixation is detrimental to actin cables in glucose-depleted S. cerevisiae cells. MICROBIAL CELL 2016; 3:206-214. [PMID: 28357356 PMCID: PMC5349148 DOI: 10.15698/mic2016.05.499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Actin filaments form cortical patches and emanating cables in fermenting cells of
Saccharomyces cerevisiae. This pattern has been shown to be
depolarized in glucose-depleted cells after formaldehyde fixation and staining
with rhodamine-tagged phalloidin. Loss of actin cables in mother cells was
remarkable. Here we extend our knowledge on actin in live glucose-depleted cells
co-expressing the marker of actin patches (Abp1-RFP) with the marker of actin
cables (Abp140-GFP). Glucose depletion resulted in appearance of actin patches
also in mother cells. However, even after 80 min of glucose deprivation these
cells showed a clear network of actin cables labeled with Abp140-GFP in contrast
to previously published data. In live cells with a mitochondrial dysfunction
(rho0 cells), glucose depletion resulted in almost immediate
appearance of Abp140-GFP foci partially overlapping with Abp1-RFP patches in
mother cells. Residual actin cables were clustered in patch-associated bundles.
A similar overlapping “patchy” pattern of both actin markers was observed upon
treatment of glucose-deprived rho+ cells with FCCP (the inhibitor of
oxidative phosphorylation) and upon treatment with formaldehyde. While the
formaldehyde-targeted process stays unknown, our results indicate that published
data on yeast actin cytoskeleton obtained from glucose-depleted cells after
fixation should be considered with caution.
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Affiliation(s)
- Pavla Vasicova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Mark Rinnerthaler
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Danusa Haskova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Lenka Novakova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Ivana Malcova
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
| | - Michael Breitenbach
- Department of Cell Biology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology of the CAS, v.v.i., Prague, Czech Republic
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16
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Sauer M, Mattanovich D. Non-genetic impact factors on chronological lifespan and stress resistance of baker's yeast. MICROBIAL CELL 2016; 3:232-235. [PMID: 28362008 PMCID: PMC5348990 DOI: 10.15698/mic2016.06.504] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Survival under nutrient limitation is an essential feature of microbial cells, and it is defined by the chronological lifespan. We summarize recent findings, illustrating how crucial the choice of the experimental setup is for the interpretation of data in this field. Especially the impact of oxygen supply differs depending on the culture type, highlighting the differences of alternatives like the retentostat to classical batch cultures. Finally the importance of culture conditions on cell aging and survival in biotechnological processes is highlighted.
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Affiliation(s)
- Michael Sauer
- Department of Biotechnology, BOKU - VIBT, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria. ; Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU - VIBT, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria. ; Austrian Centre of Industrial Biotechnology, Muthgasse 11, 1190 Vienna, Austria
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17
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Malcova I, Farkasovsky M, Senohrabkova L, Vasicova P, Hasek J. New integrative modules for multicolor-protein labeling and live-cell imaging in Saccharomyces cerevisiae. FEMS Yeast Res 2016; 16:fow027. [PMID: 26994102 DOI: 10.1093/femsyr/fow027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2016] [Indexed: 12/30/2022] Open
Abstract
Live-imaging analysis is performed in many laboratories all over the world. Various tools have been developed to enable protein labeling either in plasmid or genomic context in live yeast cells. Here, we introduce a set of nine integrative modules for the C-terminal gene tagging that combines three fluorescent proteins (FPs)-ymTagBFP, mCherry and yTagRFP-T with three dominant selection markers: geneticin, nourseothricin and hygromycin. In addition, the construction of two episomal modules for Saccharomyces cerevisiae with photostable yTagRFP-T is also referred to. Our cassettes with orange, red and blue FPs can be combined with other fluorescent probes like green fluorescent protein to prepare double- or triple-labeled strains for multicolor live-cell imaging. Primers for PCR amplification of the cassettes were designed in such a way as to be fully compatible with the existing PCR toolbox representing over 50 various integrative modules and also with deletion cassettes either for single or repeated usage to enable a cost-effective and an easy exchange of tags. New modules can also be used for biochemical analysis since antibodies are available for all three fluorescent probes.
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Affiliation(s)
- Ivana Malcova
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., 142 20 Prague 4, Czech Republic
| | - Marian Farkasovsky
- Laboratory of Molecular Microbiology, Institute of Molecular Biology SAS, 845 51 Bratislava, Slovakia
| | - Lenka Senohrabkova
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., 142 20 Prague 4, Czech Republic
| | - Pavla Vasicova
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., 142 20 Prague 4, Czech Republic
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology CAS, v.v.i., 142 20 Prague 4, Czech Republic
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