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Jonak K, Suppanz I, Bender J, Chacinska A, Warscheid B, Topf U. Ageing-dependent thiol oxidation reveals early oxidation of proteins with core proteostasis functions. Life Sci Alliance 2024; 7:e202302300. [PMID: 38383455 PMCID: PMC10881836 DOI: 10.26508/lsa.202302300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024] Open
Abstract
Oxidative post-translational modifications of protein thiols are well recognized as a readily occurring alteration of proteins, which can modify their function and thus control cellular processes. The development of techniques enabling the site-specific assessment of protein thiol oxidation on a proteome-wide scale significantly expanded the number of known oxidation-sensitive protein thiols. However, lacking behind are large-scale data on the redox state of proteins during ageing, a physiological process accompanied by increased levels of endogenous oxidants. Here, we present the landscape of protein thiol oxidation in chronologically aged wild-type Saccharomyces cerevisiae in a time-dependent manner. Our data determine early-oxidation targets in key biological processes governing the de novo production of proteins, protein folding, and degradation, and indicate a hierarchy of cellular responses affected by a reversible redox modification. Comparison with existing datasets in yeast, nematode, fruit fly, and mouse reveals the evolutionary conservation of these oxidation targets. To facilitate accessibility, we integrated the cross-species comparison into the newly developed OxiAge Database.
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Affiliation(s)
- Katarzyna Jonak
- https://ror.org/034tvp782 Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ida Suppanz
- CIBSS Centre for Integrative Biological Signalling Research, University of Freiburg, Freiburg, Germany
| | - Julian Bender
- https://ror.org/00fbnyb24 Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Bettina Warscheid
- CIBSS Centre for Integrative Biological Signalling Research, University of Freiburg, Freiburg, Germany
- https://ror.org/00fbnyb24 Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany
| | - Ulrike Topf
- https://ror.org/034tvp782 Laboratory of Molecular Basis of Aging and Rejuvenation, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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2
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Li Q, Wu H, Tian M, Li D, Zheng P, Zhang X, Qing Tang B. Delayed luminescence to monitor growth stages and assess the entropy of Saccharomyces cerevisiae. Heliyon 2024; 10:e27866. [PMID: 38623220 PMCID: PMC11016582 DOI: 10.1016/j.heliyon.2024.e27866] [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: 07/31/2023] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/17/2024] Open
Abstract
Delayed luminescence (DL) refers to the photon-induced ultra-weak luminescence emitted by samples after the light source is switched off. As a noninvasive method for health monitoring and disease diagnosis, DL has attracted increasing attention. The further development of this technology is valuable for the study of complex biological processes, such as different growth stages. If such studies were to be conducted in humans, large numbers of subjects of all ages would need to be recruited, and individual differences would be inevitable. The budding yeast Saccharomyces cerevisiae (S. cerevisiae) has a short population lifespan, and the growth phases can be monitored within dozens of hours. Therefore, S. cerevisiae is an ideal model organism for research. In this study, we investigated the physiological characteristics and DL emission of S. cerevisiae during growth in glucose-based media and entry into stationary phase, and the results showed that DL kinetic curves of yeast cells in the growing phase were obviously separated from those of stationary phase cells. Moreover, the metabolic and physiological characteristics of the yeast cell population were discussed using the DL emission parameters I0, τ and γ. We also discussed the possibility of assessing entropy using DL emission parameters. Our research demonstrates the potential of this technology to be used in wider applications.
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Affiliation(s)
- Qing Li
- ENNOVA Institute of Life Science & Technology, ENN Group, Langfang 065001, China
| | - Hong Wu
- ENNOVA Institute of Life Science & Technology, ENN Group, Langfang 065001, China
| | - Miao Tian
- ENNOVA Institute of Life Science & Technology, ENN Group, Langfang 065001, China
| | - Danyu Li
- ENNOVA Institute of Life Science & Technology, ENN Group, Langfang 065001, China
| | - Peng Zheng
- ENNOVA Institute of Life Science & Technology, ENN Group, Langfang 065001, China
| | - Xiaochun Zhang
- ENNOVA Institute of Life Science & Technology, ENN Group, Langfang 065001, China
| | - Bruce Qing Tang
- ENNOVA Institute of Life Science & Technology, ENN Group, Langfang 065001, China
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3
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Abbiati F, Garagnani SA, Orlandi I, Vai M. Sir2 and Glycerol Underlie the Pro-Longevity Effect of Quercetin during Yeast Chronological Aging. Int J Mol Sci 2023; 24:12223. [PMID: 37569599 PMCID: PMC10419316 DOI: 10.3390/ijms241512223] [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: 07/06/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Quercetin (QUER) is a natural polyphenolic compound endowed with beneficial properties for human health, with anti-aging effects. However, although this flavonoid is commercially available as a nutraceutical, target molecules/pathways underlying its pro-longevity potential have yet to be fully clarified. Here, we investigated QUER activity in yeast chronological aging, the established model for simulating the aging of postmitotic quiescent mammalian cells. We found that QUER supplementation at the onset of chronological aging, namely at the diauxic shift, significantly increases chronological lifespan (CLS). Consistent with the antioxidant properties of QUER, this extension takes place in concert with a decrease in oxidative stress. In addition, QUER triggers substantial changes in carbon metabolism. Specifically, it promotes an enhancement of a pro-longevity anabolic metabolism toward gluconeogenesis due to improved catabolism of C2 by-products of yeast fermentation and glycerol. The former is attributable to the Sir2-dependent activity of phosphoenolpyruvate carboxykinase and the latter to the L-glycerol 3-phosphate pathway. Such a combined increased supply of gluconeogenesis leads to an increase in the reserve carbohydrate trehalose, ensuring CLS extension. Moreover, QUER supplementation to chronologically aging cells in water alone amplifies their long-lived phenotype. This is associated with intracellular glycerol catabolism and trehalose increase, further indicating a QUER-specific influence on carbon metabolism that results in CLS extension.
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Affiliation(s)
- Francesco Abbiati
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
| | - Stefano Angelo Garagnani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
| | - Ivan Orlandi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
- SYSBIO Centre for Systems Biology, 20126 Milano, Italy
| | - Marina Vai
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy; (F.A.); (S.A.G.); (I.O.)
- SYSBIO Centre for Systems Biology, 20126 Milano, Italy
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4
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Meng X, Liu H, Zhao N, Yang Y, Zhao K, Dai Y. Molecular Dynamics Study of the Effect of Charge and Glycosyl on Superoxide Anion Distribution near Lipid Membrane. Int J Mol Sci 2023; 24:10926. [PMID: 37446103 DOI: 10.3390/ijms241310926] [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: 05/23/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
To examine the effects of membrane charge, the electrolyte species and glycosyl on the distribution of negatively charged radical of superoxide anion (·O2-) around the cell membrane, different phospholipid bilayer systems containing ·O2- radicals, different electrolytes and phospholipid bilayers were constructed through Charmm-GUI and Amber16. These systems were equilibrated with molecular dynamics by using Gromacs 5.0.2 to analyze the statistical behaviors of ·O2- near the lipid membrane under different conditions. It was found that in the presence of potassium rather than sodium, the negative charge of the phospholipid membrane is more likely to rarefy the superoxide anion distribution near the membrane surface. Further, the presence of glycosyl significantly reduced the density of ·O2- near the phospholipid bilayer by 78.3% compared with that of the neutral lipid membrane, which may have a significant contribution to reducing the lipid peroxidation from decreasing the ·O2- density near the membrane.
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Affiliation(s)
- Xuan Meng
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Huiyu Liu
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Ning Zhao
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yajun Yang
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Kai Zhao
- Hebei Kingsci Pharmaceutical Technology Co., Ltd., Shijiazhuang 050035, China
- Jangxi Ourshi Pharmaceutical Co., Ltd., Xinyu 338012, China
| | - Yujie Dai
- Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
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Correia-Melo C, Kamrad S, Tengölics R, Messner CB, Trebulle P, Townsend S, Jayasree Varma S, Freiwald A, Heineike BM, Campbell K, Herrera-Dominguez L, Kaur Aulakh S, Szyrwiel L, Yu JSL, Zelezniak A, Demichev V, Mülleder M, Papp B, Alam MT, Ralser M. Cell-cell metabolite exchange creates a pro-survival metabolic environment that extends lifespan. Cell 2023; 186:63-79.e21. [PMID: 36608659 DOI: 10.1016/j.cell.2022.12.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/07/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
Metabolism is deeply intertwined with aging. Effects of metabolic interventions on aging have been explained with intracellular metabolism, growth control, and signaling. Studying chronological aging in yeast, we reveal a so far overlooked metabolic property that influences aging via the exchange of metabolites. We observed that metabolites exported by young cells are re-imported by chronologically aging cells, resulting in cross-generational metabolic interactions. Then, we used self-establishing metabolically cooperating communities (SeMeCo) as a tool to increase metabolite exchange and observed significant lifespan extensions. The longevity of the SeMeCo was attributable to metabolic reconfigurations in methionine consumer cells. These obtained a more glycolytic metabolism and increased the export of protective metabolites that in turn extended the lifespan of cells that supplied them with methionine. Our results establish metabolite exchange interactions as a determinant of cellular aging and show that metabolically cooperating cells can shape the metabolic environment to extend their lifespan.
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Affiliation(s)
- Clara Correia-Melo
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.
| | - Stephan Kamrad
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Roland Tengölics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged 6726, Hungary; HCEMM-BRC Metabolic Systems Biology Lab, Szeged 6726, Hungary
| | - Christoph B Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland
| | - Pauline Trebulle
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - StJohn Townsend
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | | | - Anja Freiwald
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Benjamin M Heineike
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Quantitative Gene Expression Research Group, MRC London Institute of Medical Sciences (LMS), London W12 0HS, UK; Quantitative Gene Expression Research Group, Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London SW2 2AZ, UK
| | - Kate Campbell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Lucía Herrera-Dominguez
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Simran Kaur Aulakh
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Lukasz Szyrwiel
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Jason S L Yu
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Aleksej Zelezniak
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Vadim Demichev
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Michael Mülleder
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged 6726, Hungary; HCEMM-BRC Metabolic Systems Biology Lab, Szeged 6726, Hungary
| | - Mohammad Tauqeer Alam
- Department of Biology, College of Science, United Arab Emirates University, P.O.Box 15551, Al-Ain, United Arab Emirates
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK; Department of Biochemistry, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.
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6
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Bari KA, Berg MD, Genereaux J, Brandl CJ, Lajoie P. Tra1 controls the transcriptional landscape of the aging cell. G3 (BETHESDA, MD.) 2022; 13:6782959. [PMID: 36315064 PMCID: PMC9836359 DOI: 10.1093/g3journal/jkac287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Gene expression undergoes considerable changes during the aging process. The mechanisms regulating the transcriptional response to cellular aging remain poorly understood. Here, we employ the budding yeast Saccharomyces cerevisiae to better understand how organisms adapt their transcriptome to promote longevity. Chronological lifespan assays in yeast measure the survival of nondividing cells at stationary phase over time, providing insights into the aging process of postmitotic cells. Tra1 is an essential component of both the yeast Spt-Ada-Gcn5 acetyltransferase/Spt-Ada-Gcn5 acetyltransferase-like and nucleosome acetyltransferase of H4 complexes, where it recruits these complexes to acetylate histones at targeted promoters. Importantly, Tra1 regulates the transcriptional response to multiple stresses. To evaluate the role of Tra1 in chronological aging, we took advantage of a previously characterized mutant allele that carries mutations in the TRA1 PI3K domain (tra1Q3). We found that loss of functions associated with tra1Q3 sensitizes cells to growth media acidification and shortens lifespan. Transcriptional profiling reveals that genes differentially regulated by Tra1 during the aging process are enriched for components of the response to stress. Notably, expression of catalases (CTA1, CTT1) involved in hydrogen peroxide detoxification decreases in chronologically aged tra1Q3 cells. Consequently, they display increased sensitivity to oxidative stress. tra1Q3 cells are unable to grow on glycerol indicating a defect in mitochondria function. Aged tra1Q3 cells also display reduced expression of peroxisomal genes, exhibit decreased numbers of peroxisomes, and cannot grow on media containing oleate. Thus, Tra1 emerges as an important regulator of longevity in yeast via multiple mechanisms.
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Affiliation(s)
- Khaleda Afrin Bari
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Matthew D Berg
- Present address for Matthew D Berg: Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Julie Genereaux
- Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada,Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Patrick Lajoie
- Corresponding author: Department of Anatomy and Cell Biology, The University of Western Ontario, London, ON N6A 5C1, Canada.
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Zhao W, Guo F, Kong L, Liu J, Hong X, Jiang Z, Song H, Cui X, Ruan J, Liu X. Yeast YPK9 deficiency results in shortened replicative lifespan and sensitivity to hydrogen peroxide. Biogerontology 2021; 22:547-563. [PMID: 34524607 DOI: 10.1007/s10522-021-09935-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/26/2021] [Indexed: 11/26/2022]
Abstract
YPK9/YOR291W of Saccharomyces cerevisiae encodes a vacuolar membrane protein. Previous research has suggested that Ypk9p is similar to the yeast P5-type ATPase Spf1p and that it plays a role in the sequestration of heavy metals. In addition, bioinformatics analysis has suggested that Ypk9p is a homolog of human ATP13A2, which encodes a protein of the subfamily of P5 ATPases. However, no specific function of Ypk9p has been described to date. In this study, we found, for the first time, that YPK9 is involved in the oxidative stress response and modulation of the replicative lifespan (RLS). We found that YPK9 deficiency confers sensitivity to the oxidative stress inducer hydrogen peroxide accompanied by increased intracellular ROS levels, decreased mitochondrial membrane potential, abnormal mitochondrial function, and increased incidence of early apoptosis in budding yeast. More importantly, YPK9 deficiency can lead to a shortened RLS. In addition, we found that overexpression of the catalase-encoding gene CTA1 can reverse the phenotypic abnormalities of the ypk9Δ yeast strain. Collectively, these findings highlight the involvement of Ypk9p in the oxidative stress response and modulation of RLS.
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Affiliation(s)
- Wei Zhao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Fang Guo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Lingyue Kong
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Jiaxin Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Xiaoshan Hong
- Institute of Gynecology, Women and Children's Hospital of Guangdong Province, Guangzhou, 511442, China
| | - Zhiwen Jiang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Haochang Song
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Xiaojing Cui
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China
| | - Jie Ruan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China.
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China.
| | - Xinguang Liu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Institute of Aging Research, Guangdong Medical University, Dongguan, 523808, China.
- Institute of Biochemistry and Molecular Biology, Guangdong Medical University, Dongguan, 523808, China.
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8
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SPOCK, an R based package for high-throughput analysis of growth rate, survival, and chronological lifespan in yeast. TRANSLATIONAL MEDICINE OF AGING 2021; 4:141-148. [PMID: 33542965 DOI: 10.1016/j.tma.2020.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Plate reader-based methods for high-throughput measurement of growth rate, cellular survival, and chronological lifespan are a compelling addition to the already powerful toolbox of budding yeast Saccharomyces cerevisiae genetics. These methods have overcome many of the limits of traditional yeast biology techniques, but also present a new bottleneck at the point of data-analysis. Herein, we describe SPOCK (Survival Percentage and Outgrowth Collection Kit), an R-based package for the analysis of data created by high-throughput plate reader based methods. This package allows for the determination of chronological lifespan, cellular growth rate, and survival in an efficient, robust, and reproducible fashion.
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Enriquez-Hesles E, Smith DL, Maqani N, Wierman MB, Sutcliffe MD, Fine RD, Kalita A, Santos SM, Muehlbauer MJ, Bain JR, Janes KA, Hartman JL, Hirschey MD, Smith JS. A cell-nonautonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism. J Biol Chem 2021; 296:100125. [PMID: 33243834 PMCID: PMC7949035 DOI: 10.1074/jbc.ra120.015402] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/26/2020] [Accepted: 11/25/2020] [Indexed: 12/30/2022] Open
Abstract
Caloric restriction (CR) improves health span and life span of organisms ranging from yeast to mammals. Understanding the mechanisms involved will uncover future interventions for aging-associated diseases. In budding yeast, Saccharomyces cerevisiae, CR is commonly defined by reduced glucose in the growth medium, which extends both replicative and chronological life span (CLS). We found that conditioned media collected from stationary-phase CR cultures extended CLS when supplemented into nonrestricted (NR) cultures, suggesting a potential cell-nonautonomous mechanism of CR-induced life span regulation. Chromatography and untargeted metabolomics of the conditioned media, as well as transcriptional responses associated with the longevity effect, pointed to specific amino acids enriched in the CR conditioned media (CRCM) as functional molecules, with L-serine being a particularly strong candidate. Indeed, supplementing L-serine into NR cultures extended CLS through a mechanism dependent on the one-carbon metabolism pathway, thus implicating this conserved and central metabolic hub in life span regulation.
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Affiliation(s)
- Elisa Enriquez-Hesles
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Daniel L Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA; Department of Nutrition Science, Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nazif Maqani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Matthew D Sutcliffe
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Ryan D Fine
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Agata Kalita
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Sean M Santos
- Department of Genetics, Nutrition and Obesity Research Center, Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael J Muehlbauer
- Department of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - James R Bain
- Department of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Kevin A Janes
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA; Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - John L Hartman
- Department of Genetics, Nutrition and Obesity Research Center, Nathan Shock Center of Excellence in the Basic Biology of Aging, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Matthew D Hirschey
- Department of Medicine, Duke Molecular Physiology Institute, Duke University, Durham, North Carolina, USA
| | - Jeffrey S Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
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Santos SM, Laflin S, Broadway A, Burnet C, Hartheimer J, Rodgers J, Smith DL, Hartman JL. High-resolution yeast quiescence profiling in human-like media reveals complex influences of auxotrophy and nutrient availability. GeroScience 2020; 43:941-964. [PMID: 33015753 PMCID: PMC8110628 DOI: 10.1007/s11357-020-00265-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022] Open
Abstract
Yeast cells survive in stationary phase culture by entering quiescence, which is measured by colony-forming capacity upon nutrient re-exposure. Yeast chronological lifespan (CLS) studies, employing the comprehensive collection of gene knockout strains, have correlated weakly between independent laboratories, which is hypothesized to reflect differential interaction between the deleted genes, auxotrophy, media composition, and other assay conditions influencing quiescence. This hypothesis was investigated by high-throughput quiescence profiling of the parental prototrophic strain, from which the gene deletion strain libraries were constructed, and all possible auxotrophic allele combinations in that background. Defined media resembling human cell culture media promoted long-term quiescence and was used to assess effects of glucose, ammonium sulfate, auxotrophic nutrient availability, target of rapamycin signaling, and replication stress. Frequent, high-replicate measurements of colony-forming capacity from cultures aged past 60 days provided profiles of quiescence phenomena such as gasping and hormesis. Media acidification was assayed in parallel to assess correlation. Influences of leucine, methionine, glucose, and ammonium sulfate metabolism were clarified, and a role for lysine metabolism newly characterized, while histidine and uracil perturbations had less impact. Interactions occurred between glucose, ammonium sulfate, auxotrophy, auxotrophic nutrient limitation, aeration, TOR signaling, and/or replication stress. Weak correlation existed between media acidification and maintenance of quiescence. In summary, experimental factors, uncontrolled across previous genome-wide yeast CLS studies, influence quiescence and interact extensively, revealing quiescence as a complex metabolic and developmental process that should be studied in a prototrophic context, omitting ammonium sulfate from defined media, and employing highly replicable protocols.
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Affiliation(s)
- Sean M Santos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Samantha Laflin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Audrie Broadway
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Cosby Burnet
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joline Hartheimer
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John Rodgers
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daniel L Smith
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John L Hartman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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11
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Orlandi I, Alberghina L, Vai M. Nicotinamide, Nicotinamide Riboside and Nicotinic Acid-Emerging Roles in Replicative and Chronological Aging in Yeast. Biomolecules 2020; 10:E604. [PMID: 32326437 PMCID: PMC7226615 DOI: 10.3390/biom10040604] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
Nicotinamide, nicotinic acid and nicotinamide riboside are vitamin B3 precursors of NAD+ in the human diet. NAD+ has a fundamental importance for cellular biology, that derives from its essential role as a cofactor of various metabolic redox reactions, as well as an obligate co-substrate for NAD+-consuming enzymes which are involved in many fundamental cellular processes including aging/longevity. During aging, a systemic decrease in NAD+ levels takes place, exposing the organism to the risk of a progressive inefficiency of those processes in which NAD+ is required and, consequently, contributing to the age-associated physiological/functional decline. In this context, dietary supplementation with NAD+ precursors is considered a promising strategy to prevent NAD+ decrease and attenuate in such a way several metabolic defects common to the aging process. The metabolism of NAD+ precursors and its impact on cell longevity have benefited greatly from studies performed in the yeast Saccharomyces cerevisiae, which is one of the most established model systems used to study the aging processes of both proliferating (replicative aging) and non-proliferating cells (chronological aging). In this review we summarize important aspects of the role played by nicotinamide, nicotinic acid and nicotinamide riboside in NAD+ metabolism and how each of these NAD+ precursors contribute to the different aspects that influence both replicative and chronological aging. Taken as a whole, the findings provided by the studies carried out in S. cerevisiae are informative for the understanding of the complex dynamic flexibility of NAD+ metabolism, which is essential for the maintenance of cellular fitness and for the development of dietary supplements based on NAD+ precursors.
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Affiliation(s)
- Ivan Orlandi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 2016 Milan, Italy;
| | | | - Marina Vai
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, 2016 Milan, Italy;
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12
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Garcia EJ, de Jonge JJ, Liao PC, Stivison E, Sing CN, Higuchi-Sanabria R, Boldogh IR, Pon LA. Reciprocal interactions between mtDNA and lifespan control in budding yeast. Mol Biol Cell 2019; 30:2943-2952. [PMID: 31599702 PMCID: PMC6857569 DOI: 10.1091/mbc.e18-06-0356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 01/01/2023] Open
Abstract
Loss of mitochondrial DNA (mtDNA) results in loss of mitochondrial respiratory activity, checkpoint-regulated inhibition of cell cycle progression, defects in growth, and nuclear genome instability. However, after several generations, yeast cells can adapt to the loss of mtDNA. During this adaptation, rho0 cells, which have no mtDNA, exhibit increased growth rates and nuclear genome stabilization. Here, we report that an immediate response to loss of mtDNA is a decrease in replicative lifespan (RLS). Moreover, we find that adapted rho0 cells bypass the mtDNA inheritance checkpoint, exhibit increased mitochondrial function, and undergo an increase in RLS as they adapt to the loss of mtDNA. Transcriptome analysis reveals that metabolic reprogramming to compensate for defects in mitochondrial function is an early event during adaptation and that up-regulation of stress response genes occurs later in the adaptation process. We also find that specific subtelomeric genes are silenced during adaptation to loss of mtDNA. Moreover, we find that deletion of SIR3, a subtelomeric gene silencing protein, inhibits silencing of subtelomeric genes associated with adaptation to loss of mtDNA, as well as adaptation-associated increases in mitochondrial function and RLS extension.
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Affiliation(s)
- Enrique J. Garcia
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Janeska J. de Jonge
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Pin-Chao Liao
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Elizabeth Stivison
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Cierra N. Sing
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Ryo Higuchi-Sanabria
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Istvan R. Boldogh
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
| | - Liza A. Pon
- Department of Pathology and Cell Biology and Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, NY 10032
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13
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Kwong MMY, Lee JW, Samian MR, Watanabe N, Osada H, Ong EBB. Comparison of microplate- and bottle-based methods to age yeast for chronological life span assays. J Microbiol Methods 2019; 167:105743. [PMID: 31629019 DOI: 10.1016/j.mimet.2019.105743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 11/28/2022]
Abstract
This study compared the chronological life span and survival of Saccharomyces cerevisiae aged in a microplate or bottle, under different aeration and calorie restriction conditions. Our data shows that limited aeration in the microplate-aged culture contributed to slower outgrowth but extended yeast CLS compared to the bottle-aged culture.
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Affiliation(s)
- Mandy Mun Yee Kwong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Malaysia
| | - Jee Whu Lee
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Malaysia
| | - Mohammed Razip Samian
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Malaysia; School of Biological Sciences, Universiti Sains Malaysia, Malaysia
| | - Nobumoto Watanabe
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Malaysia; Bioprobe Application Research Unit, RIKEN Centre for Sustainable Resource Science, RIKEN, Japan
| | - Hiroyuki Osada
- USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Malaysia; Chemical Biology Research Group, RIKEN Centre for Sustainable Resource Science, RIKEN, Japan
| | - Eugene Boon Beng Ong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Malaysia; USM-RIKEN International Centre for Ageing Science (URICAS), Universiti Sains Malaysia, Malaysia.
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14
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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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15
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Orlandi I, Stamerra G, Vai M. Altered Expression of Mitochondrial NAD + Carriers Influences Yeast Chronological Lifespan by Modulating Cytosolic and Mitochondrial Metabolism. Front Genet 2018; 9:676. [PMID: 30619489 PMCID: PMC6305841 DOI: 10.3389/fgene.2018.00676] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/04/2018] [Indexed: 01/07/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) represents an essential cofactor in sustaining cellular bioenergetics and maintaining cellular fitness, and has emerged as a therapeutic target to counteract aging and age-related diseases. Besides NAD+ involvement in multiple redox reactions, it is also required as co-substrate for the activity of Sirtuins, a family of evolutionary conserved NAD+-dependent deacetylases that regulate both metabolism and aging. The founding member of this family is Sir2 of Saccharomyces cerevisiae, a well-established model system for studying aging of post-mitotic mammalian cells. In this context, it refers to chronological aging, in which the chronological lifespan (CLS) is measured. In this paper, we investigated the effects of changes in the cellular content of NAD+ on CLS by altering the expression of mitochondrial NAD+ carriers, namely Ndt1 and Ndt2. We found that the deletion or overexpression of these carriers alters the intracellular levels of NAD+ with opposite outcomes on CLS. In particular, lack of both carriers decreases NAD+ content and extends CLS, whereas NDT1 overexpression increases NAD+ content and reduces CLS. This correlates with opposite cytosolic and mitochondrial metabolic assets shown by the two types of mutants. In the former, an increase in the efficiency of oxidative phosphorylation is observed together with an enhancement of a pro-longevity anabolic metabolism toward gluconeogenesis and trehalose storage. On the contrary, NDT1 overexpression brings about on the one hand, a decrease in the respiratory efficiency generating harmful superoxide anions, and on the other, a decrease in gluconeogenesis and trehalose stores: all this is reflected into a time-dependent loss of mitochondrial functionality during chronological aging.
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Affiliation(s)
- Ivan Orlandi
- SYSBIO Centre for Systems Biology, Milan, Italy.,Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Giulia Stamerra
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Marina Vai
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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16
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Ruetenik A, Barrientos A. Exploiting Post-mitotic Yeast Cultures to Model Neurodegeneration. Front Mol Neurosci 2018; 11:400. [PMID: 30450036 PMCID: PMC6224518 DOI: 10.3389/fnmol.2018.00400] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/12/2018] [Indexed: 12/19/2022] Open
Abstract
Over the last few decades, the budding yeast Saccharomyces cerevisiae has been extensively used as a valuable organism to explore mechanisms of aging and human age-associated neurodegenerative disorders. Yeast models can be used to study loss of function of disease-related conserved genes and to investigate gain of function activities, frequently proteotoxicity, exerted by non-conserved human mutant proteins responsible for neurodegeneration. Most published models of proteotoxicity have used rapidly dividing cells and suffer from a high level of protein expression resulting in acute growth arrest or cell death. This contrasts with the slow development of neurodegenerative proteotoxicity during aging and the characteristic post-mitotic state of the affected cell type, the neuron. Here, we will review the efforts to create and characterize yeast models of neurodegeneration using the chronological life span model of aging, and the specific information they can provide regarding the chronology of physiological events leading to neurotoxic proteotoxicity-induced cell death and the identification of new pathways involved.
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Affiliation(s)
- Andrea Ruetenik
- Department of Neurology, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States.,Neuroscience Graduate Program, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Antonio Barrientos
- Department of Neurology, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States.,Neuroscience Graduate Program, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States.,Department of Biochemistry, School of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
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17
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Mara P, Fragiadakis GS, Gkountromichos F, Alexandraki D. The pleiotropic effects of the glutamate dehydrogenase (GDH) pathway in Saccharomyces cerevisiae. Microb Cell Fact 2018; 17:170. [PMID: 30384856 PMCID: PMC6211499 DOI: 10.1186/s12934-018-1018-4] [Citation(s) in RCA: 23] [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: 08/14/2018] [Accepted: 10/29/2018] [Indexed: 12/19/2022] Open
Abstract
Ammonium assimilation is linked to fundamental cellular processes that include the synthesis of non-essential amino acids like glutamate and glutamine. In Saccharomyces cerevisiae glutamate can be synthesized from α-ketoglutarate and ammonium through the action of NADP-dependent glutamate dehydrogenases Gdh1 and Gdh3. Gdh1 and Gdh3 are evolutionarily adapted isoforms and cover the anabolic role of the GDH-pathway. Here, we review the role and function of the GDH pathway in glutamate metabolism and we discuss the additional contributions of the pathway in chromatin regulation, nitrogen catabolite repression, ROS-mediated apoptosis, iron deficiency and sphingolipid-dependent actin cytoskeleton modulation in S.cerevisiae. The pleiotropic effects of GDH pathway in yeast biology highlight the importance of glutamate homeostasis in vital cellular processes and reveal new features for conserved enzymes that were primarily characterized for their metabolic capacity. These newly described features constitute insights that can be utilized for challenges regarding genetic engineering of glutamate homeostasis and maintenance of redox balances, biosynthesis of important metabolites and production of organic substrates. We also conclude that the discussed pleiotropic features intersect with basic metabolism and set a new background for further glutamate-dependent applied research of biotechnological interest.
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Affiliation(s)
- P. Mara
- Department of Chemistry, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Present Address: Woods Hole Oceanographic Institution, Woods Hole, MA 02543 USA
| | - G. S. Fragiadakis
- Institute of Molecular Biology & Biotechnology, FORTH, Nikolaou Plastira 100 GR-70013, Heraklion, Crete Greece
| | - F. Gkountromichos
- Department of Biology, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Faculty of Biology, Biocenter, Ludwig-Maximilians-University of Munich, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - D. Alexandraki
- Department of Biology, University of Crete, Voutes University Campus, 71003 Heraklion, Crete Greece
- Institute of Molecular Biology & Biotechnology, FORTH, Nikolaou Plastira 100 GR-70013, Heraklion, Crete Greece
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18
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Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells. Genetics 2018; 210:733-744. [PMID: 30072377 PMCID: PMC6216586 DOI: 10.1534/genetics.118.301262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/31/2018] [Indexed: 01/24/2023] Open
Abstract
Chronological lifespan of non-dividing yeast cells is a quantitative trait that reflects cellular aging. By monitoring allele frequencies in aging segregant pools, Ellis et al. uncover regulatory variants in the 5'-untranslated regions of two genes... Quantitative traits often show large variation caused by multiple genetic factors . One such trait is the chronological lifespan of non-dividing yeast cells, serving as a model for cellular aging. Screens for genetic factors involved in aging typically assay mutants of protein-coding genes. To identify natural genetic variants contributing to cellular aging, we exploited two strains of the fission yeast, Schizosaccharomyces pombe, that differ in chronological lifespan. We generated segregant pools from these strains and subjected them to advanced intercrossing over multiple generations to break up linkage groups. We chronologically aged the intercrossed segregant pool, followed by genome sequencing at different times to detect genetic variants that became reproducibly enriched as a function of age. A region on Chromosome II showed strong positive selection during aging. Based on expected functions, two candidate variants from this region in the long-lived strain were most promising to be causal: small insertions and deletions in the 5′-untranslated regions of ppk31 and SPBC409.08. Ppk31 is an ortholog of Rim15, a conserved kinase controlling cell proliferation in response to nutrients, while SPBC409.08 is a predicted spermine transmembrane transporter. Both Rim15 and the spermine-precursor, spermidine, are implicated in aging as they are involved in autophagy-dependent lifespan extension. Single and double allele replacement suggests that both variants, alone or combined, have subtle effects on cellular longevity. Furthermore, deletion mutants of both ppk31 and SPBC409.08 rescued growth defects caused by spermidine. We propose that Ppk31 and SPBC409.08 may function together to modulate lifespan, thus linking Rim15/Ppk31 with spermidine metabolism.
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19
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Molon M, Panek A, Molestak E, Skoneczny M, Tchorzewski M, Wnuk M. Daughters of the budding yeast from old mothers have shorter replicative lifespans but not total lifespans. Are DNA damage and rDNA instability the factors that determine longevity? Cell Cycle 2018; 17:1173-1187. [PMID: 29895191 DOI: 10.1080/15384101.2018.1464846] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Although a lot of effort has been put into the search for factors responsible for aging in yeast mother cells, our knowledge of cellular changes in daughter cells originating from old mothers is still very limited. It has been shown that an old mother is not able to compensate for all negative changes within its cell and therefore transfers them to the bud. In this paper, we show for the first time that daughter cells of an old mother have a reset lifespan expressed in units of time despite drastic reduction of their budding lifespan, which suggests that a single yeast cell has a fixed programmed longevity regardless of the time point at which it was originated. Moreover, in our study we found that longevity parameters are not correlated with the rDNA level, DNA damage, chromosome structure or aging parameters (budding lifespan and total lifespan).
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Affiliation(s)
- Mateusz Molon
- a Department of Biochemistry and Cell Biology , University of Rzeszow , Rzeszow , Poland
| | - Anita Panek
- b Department of Genetics , University of Rzeszow , Rzeszow , Poland
| | - Eliza Molestak
- c Department of Molecular Biology , Maria Curie-Sklodowska University , Lublin , Poland
| | - Marek Skoneczny
- d Department of Genetics , Institute of Biochemistry and Biophysics, Polish Academy of Sciences , Warsaw , Poland
| | - Marek Tchorzewski
- c Department of Molecular Biology , Maria Curie-Sklodowska University , Lublin , Poland
| | - Maciej Wnuk
- b Department of Genetics , University of Rzeszow , Rzeszow , Poland
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20
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Baccolo G, Stamerra G, Coppola DP, Orlandi I, Vai M. Mitochondrial Metabolism and Aging in Yeast. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 340:1-33. [PMID: 30072089 DOI: 10.1016/bs.ircmb.2018.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondrial functionality is one of the main factors involved in cell survival, and mitochondrial dysfunctions have been identified as an aging hallmark. In particular, the insurgence of mitochondrial dysfunctions is tightly connected to mitochondrial metabolism. During aging, both mitochondrial oxidative and biosynthetic metabolisms are progressively altered, with the development of malfunctions, in turn affecting mitochondrial functionality. In this context, the relation between mitochondrial pathways and aging is evolutionarily conserved from single-celled organisms, such as yeasts, to complex multicellular organisms, such as humans. Useful information has been provided by the yeast Saccharomyces cerevisiae, which is being increasingly acknowledged as a valuable model system to uncover mechanisms underlying cellular longevity in humans. On this basis, we review the impact of specific aspects of mitochondrial metabolism on aging supported by the contributions brought by numerous studies performed employing yeast. Initially, we will focus on the tricarboxylic acid cycle and oxidative phosphorylation, describing how their modulation has consequences on cellular longevity. Afterward, we will report information regarding the importance of nicotinamide adenine dinucleotide (NAD) metabolism during aging, highlighting its relation with mitochondrial functionality. The comprehension of these key points regarding mitochondrial metabolism and their physiological importance is an essential first step for the development of therapeutic interventions that point to increase life quality during aging, therefore promoting "healthy aging," as well as lifespan itself.
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Affiliation(s)
- Giacomo Baccolo
- SYSBIO Centre for Systems Biology, Milano, Italy; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Giulia Stamerra
- SYSBIO Centre for Systems Biology, Milano, Italy; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | | | - Ivan Orlandi
- SYSBIO Centre for Systems Biology, Milano, Italy; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Marina Vai
- SYSBIO Centre for Systems Biology, Milano, Italy; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
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21
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Lee MB, Kaeberlein M. Translational Geroscience: From invertebrate models to companion animal and human interventions. TRANSLATIONAL MEDICINE OF AGING 2018; 2:15-29. [PMID: 32368707 PMCID: PMC7198054 DOI: 10.1016/j.tma.2018.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Translational geroscience is an interdisciplinary field descended from basic gerontology that seeks to identify, validate, and clinically apply interventions to maximize healthy, disease-free lifespan. In this review, we describe a research pipeline for the identification and validation of lifespan extending interventions. Beginning in invertebrate model systems, interventions are discovered and then characterized using other invertebrate model systems (evolutionary translation), models of genetic diversity, and disease models. Vertebrate model systems, particularly mice, can then be utilized to validate interventions in mammalian systems. Collaborative, multi-site efforts, like the Interventions Testing Program (ITP), provide a key resource to assess intervention robustness in genetically diverse mice. Mouse disease models provide a tool to understand the broader utility of longevity interventions. Beyond mouse models, we advocate for studies in companion pets. The Dog Aging Project is an exciting example of translating research in dogs, both to develop a model system and to extend their healthy lifespan as a goal in itself. Finally, we discuss proposed and ongoing intervention studies in humans, unmet needs for validating interventions in humans, and speculate on how differences in survival among human populations may influence intervention efficacy.
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Affiliation(s)
- Mitchell B. Lee
- Department of Pathology, University of Washington, Seattle, WA USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA USA
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22
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Orlandi I, Stamerra G, Strippoli M, Vai M. During yeast chronological aging resveratrol supplementation results in a short-lived phenotype Sir2-dependent. Redox Biol 2017; 12:745-754. [PMID: 28412652 PMCID: PMC5397018 DOI: 10.1016/j.redox.2017.04.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/05/2017] [Accepted: 04/08/2017] [Indexed: 01/13/2023] Open
Abstract
Resveratrol (RSV) is a naturally occurring polyphenolic compound endowed with interesting biological properties/functions amongst which are its activity as an antioxidant and as Sirtuin activating compound towards SIRT1 in mammals. Sirtuins comprise a family of NAD+-dependent protein deacetylases that are involved in many physiological and pathological processes including aging and age-related diseases. These enzymes are conserved across species and SIRT1 is the closest mammalian orthologue of Sir2 of Saccharomyces cerevisiae. In the field of aging researches, it is well known that Sir2 is a positive regulator of replicative lifespan and, in this context, the RSV effects have been already examined. Here, we analyzed RSV effects during chronological aging, in which Sir2 acts as a negative regulator of chronological lifespan (CLS). Chronological aging refers to quiescent cells in stationary phase; these cells display a survival-based metabolism characterized by an increase in oxidative stress. We found that RSV supplementation at the onset of chronological aging, namely at the diauxic shift, increases oxidative stress and significantly reduces CLS. CLS reduction is dependent on Sir2 presence both in expired medium and in extreme Calorie Restriction. In addition, all data point to an enhancement of Sir2 activity, in particular Sir2-mediated deacetylation of the key gluconeogenic enzyme phosphoenolpyruvate carboxykinase (Pck1). This leads to a reduction in the amount of the acetylated active form of Pck1, whose enzymatic activity is essential for gluconeogenesis and CLS extension.
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Affiliation(s)
- Ivan Orlandi
- SYSBIO Centre for Systems Biology Milano, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.
| | - Giulia Stamerra
- SYSBIO Centre for Systems Biology Milano, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.
| | - Maurizio Strippoli
- SYSBIO Centre for Systems Biology Milano, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.
| | - Marina Vai
- SYSBIO Centre for Systems Biology Milano, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.
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Saini P, Beniwal A, Vij S. Comparative Analysis of Oxidative Stress During Aging of Kluyveromyces marxianus in Synthetic and Whey Media. Appl Biochem Biotechnol 2017; 183:348-361. [DOI: 10.1007/s12010-017-2449-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 02/28/2017] [Indexed: 12/19/2022]
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Kazi RS, Banarjee RM, Deshmukh AB, Patil GV, Jagadeeshaprasad MG, Kulkarni MJ. Glycation inhibitors extend yeast chronological lifespan by reducing advanced glycation end products and by back regulation of proteins involved in mitochondrial respiration. J Proteomics 2017; 156:104-112. [DOI: 10.1016/j.jprot.2017.01.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/27/2016] [Accepted: 01/23/2017] [Indexed: 11/26/2022]
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de Carvalho MDC, De Mesquita JF, Eleutherio ECA. In Vivo Characterization of I91T Sod2 Polymorphism of Saccharomyces cerevisiae. J Cell Biochem 2017; 118:1078-1086. [DOI: 10.1002/jcb.25720] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/30/2016] [Indexed: 11/09/2022]
Affiliation(s)
| | - Joelma Freire De Mesquita
- Department of Genetics and Molecular Biology; Federal University of the State of Rio de Janeiro (UNIRIO); Rio de Janeiro 22290-240 Brazil
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Metal-based superoxide dismutase and catalase mimics reduce oxidative stress biomarkers and extend life span of Saccharomyces cerevisiae. Biochem J 2017; 474:301-315. [DOI: 10.1042/bcj20160480] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 11/17/2022]
Abstract
Aging is a natural process characterized by several biological changes. In this context, oxidative stress appears as a key factor that leads cells and organisms to severe dysfunctions and diseases. To cope with reactive oxygen species and oxidative-related damage, there has been increased use of superoxide dismutase (SOD)/catalase (CAT) biomimetic compounds. Recently, we have shown that three metal-based compounds {[Fe(HPClNOL)Cl2]NO3, [Cu(HPClNOL)(CH3CN)](ClO4)2 and Mn(HPClNOL)(Cl)2}, harboring in vitro SOD and/or CAT activities, were critical for protection of yeast cells against oxidative stress. In this work, treating Saccharomyces cerevisiae with these SOD/CAT mimics (25.0 µM/1 h), we highlight the pivotal role of these compounds to extend the life span of yeast during chronological aging. Evaluating lipid and protein oxidation of aged cells, it becomes evident that these mimics extend the life expectancy of yeast mainly due to the reduction in oxidative stress biomarkers. In addition, the treatment of yeast cells with these mimics regulated the amounts of lipid droplet occurrence, consistent with the requirement and protection of lipids for cell integrity during aging. Concerning SOD/CAT mimics uptake, using inductively coupled plasma mass spectrometry, we add new evidence that these complexes, besides being bioabsorbed by S. cerevisiae cells, can also affect metal homeostasis. Finally, our work presents a new application for these SOD/CAT mimics, which demonstrate a great potential to be employed as antiaging agents. Taken together, these promising results prompt future studies concerning the relevance of administration of these molecules against the emerging aging-related diseases such as Parkinson's, Alzheimer's and Huntington's.
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Orlandi I, Pellegrino Coppola D, Strippoli M, Ronzulli R, Vai M. Nicotinamide supplementation phenocopies SIR2 inactivation by modulating carbon metabolism and respiration during yeast chronological aging. Mech Ageing Dev 2016; 161:277-287. [PMID: 27320176 DOI: 10.1016/j.mad.2016.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/10/2016] [Accepted: 06/15/2016] [Indexed: 02/06/2023]
Abstract
Nicotinamide (NAM), a form of vitamin B3, is a byproduct and noncompetitive inhibitor of the deacetylation reaction catalyzed by Sirtuins. These represent a family of evolutionarily conserved NAD+-dependent deacetylases that are well-known critical regulators of metabolism and aging and whose founding member is Sir2 of Saccharomyces cerevisiae. Here, we investigated the effects of NAM supplementation in the context of yeast chronological aging, the established model for studying aging of postmitotic quiescent mammalian cells. Our data show that NAM supplementation at the diauxic shift results in a phenocopy of chronologically aging sir2Δ cells. In fact, NAM-supplemented cells display the same chronological lifespan extension both in expired medium and extreme Calorie Restriction. Furthermore, NAM allows the cells to push their metabolism toward the same outcomes of sir2Δ cells by elevating the level of the acetylated Pck1. Both these cells have the same metabolic changes that concern not only anabolic pathways such as an increased gluconeogenesis but also respiratory activity in terms both of respiratory rate and state of respiration. In particular, they have a higher respiratory reserve capacity and a lower non-phosphorylating respiration that in concert with a low burden of superoxide anions can affect positively chronological aging.
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Affiliation(s)
- Ivan Orlandi
- SYSBIO Centre for Systems Biology Milano, Italy; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Damiano Pellegrino Coppola
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Maurizio Strippoli
- SYSBIO Centre for Systems Biology Milano, Italy; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Rossella Ronzulli
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Marina Vai
- SYSBIO Centre for Systems Biology Milano, Italy; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy.
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Chadwick SR, Pananos AD, Di Gregorio SE, Park AE, Etedali-Zadeh P, Duennwald ML, Lajoie P. A Toolbox for Rapid Quantitative Assessment of Chronological Lifespan and Survival inSaccharomyces cerevisiae. Traffic 2016; 17:689-703. [DOI: 10.1111/tra.12391] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/01/2016] [Accepted: 03/01/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Sarah R. Chadwick
- Department of Anatomy and Cell Biology; The University of Western Ontario; London N6A 5C1 Canada
| | | | - Sonja E. Di Gregorio
- Department of Pathology and Laboratory Medicine; The University of Western Ontario; London N6A 5C1 Canada
| | - Anna E. Park
- Department of Anatomy and Cell Biology; The University of Western Ontario; London N6A 5C1 Canada
| | - Parnian Etedali-Zadeh
- Department of Anatomy and Cell Biology; The University of Western Ontario; London N6A 5C1 Canada
| | - Martin L. Duennwald
- Department of Anatomy and Cell Biology; The University of Western Ontario; London N6A 5C1 Canada
- Department of Pathology and Laboratory Medicine; The University of Western Ontario; London N6A 5C1 Canada
| | - Patrick Lajoie
- Department of Anatomy and Cell Biology; The University of Western Ontario; London N6A 5C1 Canada
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Dhawan J, Laxman S. Decoding the stem cell quiescence cycle--lessons from yeast for regenerative biology. J Cell Sci 2015; 128:4467-74. [PMID: 26672015 PMCID: PMC5695657 DOI: 10.1242/jcs.177758] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In the past decade, major advances have occurred in the understanding of mammalian stem cell biology, but roadblocks (including gaps in our fundamental understanding) remain in translating this knowledge to regenerative medicine. Interestingly, a close analysis of the Saccharomyces cerevisiae literature leads to an appreciation of how much yeast biology has contributed to the conceptual framework underpinning our understanding of stem cell behavior, to the point where such insights have been internalized into the realm of the known. This Opinion article focuses on one such example, the quiescent adult mammalian stem cell, and examines concepts underlying our understanding of quiescence that can be attributed to studies in yeast. We discuss the metabolic, signaling and gene regulatory events that control entry and exit into quiescence in yeast. These processes and events retain remarkable conservation and conceptual parallels in mammalian systems, and collectively suggest a regulated program beyond the cessation of cell division. We argue that studies in yeast will continue to not only reveal fundamental concepts in quiescence, but also leaven progress in regenerative medicine.
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Affiliation(s)
- Jyotsna Dhawan
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India CSIR Center for Cellular and Molecular Biology, Hyderabad, India
| | - Sunil Laxman
- Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
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30
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da Silva CR, Almeida GS, Caldeira-de-Araújo A, Leitão AC, de Pádula M. Influence of Ogg1 repair on the genetic stability of ccc2 mutant of Saccharomyces cerevisiae chemically challenged with 4-nitroquinoline-1-oxide (4-NQO). Mutagenesis 2015; 31:107-14. [PMID: 26275420 DOI: 10.1093/mutage/gev062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In Saccharomyces cerevisiae, disruption of genes by deletion allowed elucidation of the molecular mechanisms of a series of human diseases, such as in Wilson disease (WD). WD is a disorder of copper metabolism, due to inherited mutations in human copper-transporting ATPase (ATP7B). An orthologous gene is present in S. cerevisiae, CCC2 gene. Copper is required as a cofactor for a number of enzymes. In excess, however, it is toxic, potentially carcinogenic, leading to many pathological conditions via oxidatively generated DNA damage. Deficiency in ATP7B (human) or Ccc2 (yeast) causes accumulation of intracellular copper, favouring the generation of reactive oxygen species. Thus, it becomes important to study the relative importance of proteins involved in the repair of these lesions, such as Ogg1. Herein, we addressed the influence Ogg1 repair in a ccc2 deficient strain of S. cerevisiae. We constructed ccc2-disrupted strains from S. cerevisiae (ogg1ccc2 and ccc2), which were analysed in terms of viability and spontaneous mutator phenotype. We also investigated the impact of 4-nitroquinoline-1-oxide (4-NQO) on nuclear DNA damage and on the stability of mitochondrial DNA. The results indicated a synergistic effect on spontaneous mutagenesis upon OGG1 and CCC2 double inactivation, placing 8-oxoguanine as a strong lesion-candidate at the origin of spontaneous mutations. The ccc2 mutant was more sensitive to cell killing and to mutagenesis upon 4-NQO challenge than the other studied strains. However, Ogg1 repair of exogenous-induced DNA damage revealed to be toxic and mutagenic to ccc2 deficient cells, which can be due to a detrimental action of Ogg1 on DNA lesions induced in ccc2 cells. Altogether, our results point to a critical and ambivalent role of BER mediated by Ogg1 in the maintenance of genomic stability in eukaryotes deficient in CCC2 gene.
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Affiliation(s)
- Claudia R da Silva
- Laboratório de Radio e Fotobiologia, Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, UERJ, Rio de Janeiro CEP 20551-030, Brasil, Laboratório de Radiobiologia Molecular; Instituto de Biofísica Carlos Chagas Filho, UFRJ, Rio de Janeiro CEP 21.941-902, Brasil and
| | - Gabriella S Almeida
- Laboratório de Radio e Fotobiologia, Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, UERJ, Rio de Janeiro CEP 20551-030, Brasil, Laboratório de Radiobiologia Molecular; Instituto de Biofísica Carlos Chagas Filho, UFRJ, Rio de Janeiro CEP 21.941-902, Brasil and Laboratório de Microbiologia e Avaliação Genotóxica, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, UFRJ, Rio de Janeiro CEP 21.941-902, Brasil
| | - Adriano Caldeira-de-Araújo
- Laboratório de Radio e Fotobiologia, Departamento de Biofísica e Biometria, Instituto de Biologia Roberto Alcantara Gomes, UERJ, Rio de Janeiro CEP 20551-030, Brasil
| | - Alvaro C Leitão
- Laboratório de Radiobiologia Molecular; Instituto de Biofísica Carlos Chagas Filho, UFRJ, Rio de Janeiro CEP 21.941-902, Brasil and
| | - Marcelo de Pádula
- Laboratório de Radiobiologia Molecular; Instituto de Biofísica Carlos Chagas Filho, UFRJ, Rio de Janeiro CEP 21.941-902, Brasil and Laboratório de Microbiologia e Avaliação Genotóxica, Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, UFRJ, Rio de Janeiro CEP 21.941-902, Brasil
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Abstract
The field of aging research has progressed rapidly over the past few decades. Genetic modulators of aging rate that are conserved over a broad evolutionary distance have now been identified. Several physiological and environmental interventions have also been shown to influence the rate of aging in organisms ranging from yeast to mammals. Here we briefly review these conserved pathways and interventions and highlight some key unsolved challenges that remain. Although the molecular mechanisms by which these modifiers of aging act are only partially understood, interventions to slow aging are nearing clinical application, and it is likely that we will begin to reap the benefits of aging research prior to solving all of the mysteries that the biology of aging has to offer. Old age is the single greatest risk factor for the leading causes of death in the developed world. Advances in aging research promise to alleviate the diseases of aging by targeting aging itself.
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32
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A yeast model of the Parkinson's disease-associated protein Parkin. Exp Cell Res 2015; 333:73-9. [PMID: 25728007 DOI: 10.1016/j.yexcr.2015.02.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/20/2022]
Abstract
Mutations in Parkin, an E3 ubiquitin ligase, are associated to autosomal recessive Parkinson's disease (PD). Parkin has been mainly implicated, along with Pink1, in mitochondrial autophagy in response to stress. In this study, a yeast model was developed to analyse the biological function of human Parkin. We observed that Parkin increases yeast chronological lifespan and oxidative stress resistance, through a mitochondrial-dependent pathway. Moreover, in response to H2O2, Parkin translocate to mitochondria, leading to a higher mitochondrial degradation. Parkin-induced H2O2 resistance is dependent on the autophagic pathway and on the mitochondrial protein Por1p. Although expression of Pink1 induces an H2O2 resistance phenotype similar to Parkin, co-expression of both proteins does not result in a synergistic effect. Concerning H2O2 resistance, this may indicate that these two proteins independently affect the same pathway. Altogether, this work establishes a yeast model for Parkin, which may provide new insights on Parkin function and potential mechanisms of pathogenicity.
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33
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Orlandi I, Coppola DP, Vai M. Rewiring yeast acetate metabolism through MPC1 loss of function leads to mitochondrial damage and decreases chronological lifespan. ACTA ACUST UNITED AC 2014; 1:393-405. [PMID: 28357219 PMCID: PMC5349135 DOI: 10.15698/mic2014.12.178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During growth on fermentable substrates, such as glucose, pyruvate, which is the
end-product of glycolysis, can be used to generate acetyl-CoA in the cytosol via
acetaldehyde and acetate, or in mitochondria by direct oxidative
decarboxylation. In the latter case, the mitochondrial pyruvate carrier (MPC) is
responsible for pyruvate transport into mitochondrial matrix space. During
chronological aging, yeast cells which lack the major structural subunit Mpc1
display a reduced lifespan accompanied by an age-dependent loss of autophagy.
Here, we show that the impairment of pyruvate import into mitochondria linked to
Mpc1 loss is compensated by a flux redirection of TCA cycle intermediates
through the malic enzyme-dependent alternative route. In such a way, the TCA
cycle operates in a “branched” fashion to generate pyruvate and is depleted of
intermediates. Mutant cells cope with this depletion by increasing the activity
of glyoxylate cycle and of the pathway which provides the nucleocytosolic
acetyl-CoA. Moreover, cellular respiration decreases and ROS accumulate in the
mitochondria which, in turn, undergo severe damage. These acquired traits in
concert with the reduced autophagy restrict cell survival of the mpc1∆ mutant
during chronological aging. Conversely, the activation of the carnitine shuttle
by supplying acetyl-CoA to the mitochondria is sufficient to abrogate the
short-lived phenotype of the mutant.
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Affiliation(s)
- Ivan Orlandi
- SYSBIO Centre for Systems Biology Milano, Italy. ; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Damiano Pellegrino Coppola
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Marina Vai
- SYSBIO Centre for Systems Biology Milano, Italy. ; Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
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Kawałek A, van der Klei IJ. At neutral pH the chronological lifespan of Hansenula polymorpha increases upon enhancing the carbon source concentrations. MICROBIAL CELL 2014; 1:189-202. [PMID: 28357243 PMCID: PMC5354561 DOI: 10.15698/mic2014.06.149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dietary restriction is generally assumed to increase the lifespan in most
eukaryotes, including the simple model organism Saccharomyces
cerevisiae. However, recent data questioned whether this phenomenon
is indeed true for yeast. We studied the effect of reduction of the carbon
source concentration on the chronological lifespan of the yeast
Hansenula polymorpha using four different carbon sources.
Our data indicate that reduction of the carbon source concentration has a
negative (glucose, ethanol, methanol) or positive (glycerol) effect on the
chronological lifespan. We show that the actual effect of carbon source
concentrations largely depends on extracellular factor(s). We provide evidence
that H. polymorpha acidifies the medium and that a low pH of
the medium alone is sufficient to significantly decrease the chronological
lifespan. However, glucose-grown cells are less sensitive to low pH compared to
glycerol-grown cells, explaining why only the reduction of the
glycerol-concentration (which leads to less medium acidification) has a positive
effect on the chronological lifespan. Instead, the positive effect of enhancing
the glucose concentrations is much larger than the negative effect of the medium
acidification at these conditions, explaining the increased lifespan with
increasing glucose concentrations. Importantly, at neutral pH, the chronological
lifespan also decreases with a reduction in glycerol concentrations. We show
that for glycerol cultures this effect is related to acidification independent
changes in the composition of the spent medium. Altogether, our data indicate
that in H. polymorpha at neutral pH the chronological lifespan
invariably extends upon increasing the carbon source concentration.
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Affiliation(s)
- Adam Kawałek
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Metabolism and Ageing, University of Groningen, the Netherlands
| | - Ida J van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, Systems Biology Centre for Metabolism and Ageing, University of Groningen, the Netherlands
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35
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Lewinska A, Miedziak B, Kulak K, Molon M, Wnuk M. Links between nucleolar activity, rDNA stability, aneuploidy and chronological aging in the yeast Saccharomyces cerevisiae. Biogerontology 2014; 15:289-316. [PMID: 24711086 PMCID: PMC4019837 DOI: 10.1007/s10522-014-9499-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 03/25/2014] [Indexed: 12/20/2022]
Abstract
The nucleolus is speculated to be a regulator of cellular senescence in numerous biological systems (Guarente, Genes Dev 11(19):2449–2455, 1997; Johnson et al., Curr Opin Cell Biol 10(3):332–338, 1998). In the budding yeast Saccharomyces cerevisiae, alterations in nucleolar architecture, the redistribution of nucleolar protein and the accumulation of extrachromosomal ribosomal DNA circles (ERCs) during replicative aging have been reported. However, little is known regarding rDNA stability and changes in nucleolar activity during chronological aging (CA), which is another yeast aging model used. In the present study, the impact of aberrant cell cycle checkpoint control (knock-out of BUB1, BUB2, MAD1 and TEL1 genes in haploid and diploid hemizygous states) on CA-mediated changes in the nucleolus was studied. Nucleolus fragmentation, changes in the nucleolus size and the nucleolus/nucleus ratio, ERC accumulation, expression pattern changes and the relocation of protein involved in transcriptional silencing during CA were revealed. All strains examined were affected by oxidative stress, aneuploidy (numerical rather than structural aberrations) and DNA damage. However, the bub1 cells were the most prone to aneuploidy events, which may contribute to observed decrease in chronological lifespan. We postulate that chronological aging may be affected by redox imbalance-mediated chromosome XII instability leading to both rDNA instability and whole chromosome aneuploidy. CA-mediated nucleolus fragmentation may be a consequence of nucleolus enlargement and/or Nop2p upregulation. Moreover, the rDNA content of chronologically aging cells may be a factor determining the subsequent replicative lifespan. Taken together, we demonstrated that the nucleolus state is also affected during CA in yeast.
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Affiliation(s)
- Anna Lewinska
- Department of Biochemistry and Cell Biology, University of Rzeszow, Rzeszow, Poland
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36
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Uncoupling reproduction from metabolism extends chronological lifespan in yeast. Proc Natl Acad Sci U S A 2014; 111:E1538-47. [PMID: 24706810 DOI: 10.1073/pnas.1323918111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Studies of replicative and chronological lifespan in Saccharomyces cerevisiae have advanced understanding of longevity in all eukaryotes. Chronological lifespan in this species is defined as the age-dependent viability of nondividing cells. To date this parameter has only been estimated under calorie restriction, mimicked by starvation. Because postmitotic cells in higher eukaryotes often do not starve, we developed a model yeast system to study cells as they age in the absence of calorie restriction. Yeast cells were encapsulated in a matrix consisting of calcium alginate to form ∼3 mm beads that were packed into bioreactors and fed ad libitum. Under these conditions cells ceased to divide, became heat shock and zymolyase resistant, yet retained high fermentative capacity. Over the course of 17 d, immobilized yeast cells maintained >95% viability, whereas the viability of starving, freely suspended (planktonic) cells decreased to <10%. Immobilized cells exhibited a stable pattern of gene expression that differed markedly from growing or starving planktonic cells, highly expressing genes in glycolysis, cell wall remodeling, and stress resistance, but decreasing transcription of genes in the tricarboxylic acid cycle, and genes that regulate the cell cycle, including master cyclins CDC28 and CLN1. Stress resistance transcription factor MSN4 and its upstream effector RIM15 are conspicuously up-regulated in the immobilized state, and an immobilized rim15 knockout strain fails to exhibit the long-lived, growth-arrested phenotype, suggesting that altered regulation of the Rim15-mediated nutrient-sensing pathway plays an important role in extending yeast chronological lifespan under calorie-unrestricted conditions.
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37
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High-resolution profiling of stationary-phase survival reveals yeast longevity factors and their genetic interactions. PLoS Genet 2014; 10:e1004168. [PMID: 24586198 PMCID: PMC3937222 DOI: 10.1371/journal.pgen.1004168] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 12/23/2013] [Indexed: 01/09/2023] Open
Abstract
Lifespan is influenced by a large number of conserved proteins and gene-regulatory pathways. Here, we introduce a strategy for systematically finding such longevity factors in Saccharomyces cerevisiae and scoring the genetic interactions (epistasis) among these factors. Specifically, we developed an automated competition-based assay for chronological lifespan, defined as stationary-phase survival of yeast populations, and used it to phenotype over 5,600 single- or double-gene knockouts at unprecedented quantitative resolution. We found that 14% of the viable yeast mutant strains were affected in their stationary-phase survival; the extent of true-positive chronological lifespan factors was estimated by accounting for the effects of culture aeration and adaptive regrowth. We show that lifespan extension by dietary restriction depends on the Swr1 histone-exchange complex and that a functional link between autophagy and the lipid-homeostasis factor Arv1 has an impact on cellular lifespan. Importantly, we describe the first genetic interaction network based on aging phenotypes, which successfully recapitulated the core-autophagy machinery and confirmed a role of the human tumor suppressor PTEN homologue in yeast lifespan and phosphatidylinositol phosphate metabolism. Our quantitative analysis of longevity factors and their genetic interactions provides insights into the gene-network interactions of aging cells.
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38
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Wierman MB, Smith JS. Yeast sirtuins and the regulation of aging. FEMS Yeast Res 2014; 14:73-88. [PMID: 24164855 PMCID: PMC4365911 DOI: 10.1111/1567-1364.12115] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/09/2013] [Accepted: 10/13/2013] [Indexed: 11/29/2022] Open
Abstract
The sirtuins are a phylogenetically conserved family of NAD(+) -dependent protein deacetylases that consume one molecule of NAD(+) for every deacetylated lysine side chain. Their requirement for NAD(+) potentially makes them prone to regulation by fluctuations in NAD(+) or biosynthesis intermediates, thus linking them to cellular metabolism. The Sir2 protein from Saccharomyces cerevisiae is the founding sirtuin family member and has been well characterized as a histone deacetylase that functions in transcriptional silencing of heterochromatin domains and as a pro-longevity factor for replicative life span (RLS), defined as the number of times a mother cell divides (buds) before senescing. Deleting SIR2 shortens RLS, while increased gene dosage causes extension. Furthermore, Sir2 has been implicated in mediating the beneficial effects of caloric restriction (CR) on life span, not only in yeast, but also in higher eukaryotes. While this paradigm has had its share of disagreements and debate, it has also helped rapidly drive the aging research field forward. S. cerevisiae has four additional sirtuins, Hst1, Hst2, Hst3, and Hst4. This review discusses the function of Sir2 and the Hst homologs in replicative aging and chronological aging, and also addresses how the sirtuins are regulated in response to environmental stresses such as CR.
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Affiliation(s)
- Margaret B Wierman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
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39
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Cabiscol E, Tamarit J, Ros J. Protein carbonylation: proteomics, specificity and relevance to aging. MASS SPECTROMETRY REVIEWS 2014; 33:21-48. [PMID: 24114980 DOI: 10.1002/mas.21375] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/13/2013] [Accepted: 02/13/2013] [Indexed: 06/02/2023]
Abstract
Detection and quantification of protein carbonyls present in biological samples has become a popular, albeit indirect, method to determine the existence of oxidative stress. Moreover, the rise of proteomics has allowed the identification of the specific proteins targeted by protein carbonylation. This review discusses these methodologies and proteomic strategies and then focuses on the relationship between protein carbonylation and aging and the parameters that may explain the increased sensitivity of certain proteins to protein carbonylation.
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Affiliation(s)
- Elisa Cabiscol
- Departament de Ciències Mèdiques Bàsiques, IRB Lleida, Universitat de Lleida, Av. Rovira Roure, 80, 25198, Lleida, Catalonia, Spain
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40
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Palková Z, Wilkinson D, Váchová L. Aging and differentiation in yeast populations: elders with different properties and functions. FEMS Yeast Res 2013; 14:96-108. [PMID: 24119061 DOI: 10.1111/1567-1364.12103] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 09/23/2013] [Accepted: 09/26/2013] [Indexed: 01/08/2023] Open
Abstract
Over the past decade, it has become evident that similarly to cells forming metazoan tissues, yeast cells have the ability to differentiate and form specialized cell types. Examples of yeast cellular differentiation have been identified both in yeast liquid cultures and within multicellular structures occupying solid surfaces. Most current knowledge on different cell types comes from studies of the spatiotemporal internal architecture of colonies developing on various media. With a few exceptions, yeast cell differentiation often concerns nongrowing, stationary-phase cells and leads to the formation of cell subpopulations differing in stress resistance, cell metabolism, respiration, ROS production, and others. These differences can affect longevity of particular subpopulations. In contrast to liquid cultures, where various cell types are dispersed within stationary-phase populations, cellular differentiation depends on the specific position of particular cells within multicellular colonies. Differentiated colonies, thus, resemble primitive multicellular organisms, in which the gradients of certain compounds and the position of cells within the structure affect cellular differentiation. In this review, we summarize and compare the properties of diverse types of differentiated chronologically aging yeast cells that have been identified in colonies growing on different media, as well as of those found in liquid cultures.
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Affiliation(s)
- Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
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41
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Wasko BM, Carr DT, Tung H, Doan H, Schurman N, Neault JR, Feng J, Lee J, Zipkin B, Mouser J, Oudanonh E, Nguyen T, Stetina T, Shemorry A, Lemma M, Kaeberlein M. Buffering the pH of the culture medium does not extend yeast replicative lifespan. F1000Res 2013; 2:216. [PMID: 24555104 PMCID: PMC3886788 DOI: 10.12688/f1000research.2-216.v1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/10/2013] [Indexed: 12/19/2022] Open
Abstract
During chronological aging of budding yeast cells, the culture medium can become acidified, and this acidification limits cell survival. As a consequence, buffering the culture medium to pH 6 significantly extends chronological life span under standard conditions in synthetic medium. In this study, we assessed whether a similar process occurs during replicative aging of yeast cells. We find no evidence that buffering the pH of the culture medium to pH levels either higher or lower than the initial pH of the medium is able to significantly extend replicative lifespan. Thus, we conclude that, unlike chronological life span, replicative life span is not limited by acidification of the culture medium or by changes in the pH of the environment.
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Affiliation(s)
- Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Daniel T Carr
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Herman Tung
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Ha Doan
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Nathan Schurman
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jillian R Neault
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Joey Feng
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Janet Lee
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Ben Zipkin
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jacob Mouser
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Edward Oudanonh
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Tina Nguyen
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Torin Stetina
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Anna Shemorry
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Mekedes Lemma
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
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42
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Lefevre SD, Roermund CW, Wanders RJA, Veenhuis M, Klei IJ. The significance of peroxisome function in chronological aging of Saccharomyces cerevisiae. Aging Cell 2013; 12:784-93. [PMID: 23755917 PMCID: PMC3824234 DOI: 10.1111/acel.12113] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2013] [Indexed: 12/01/2022] Open
Abstract
We studied the chronological lifespan of glucose-grown Saccharomyces cerevisiae in relation to the function of intact peroxisomes. We analyzed four different peroxisome-deficient (pex) phenotypes. These included Δpex3 cells that lack peroxisomal membranes and in which all peroxisomal proteins are mislocalized together with Δpex6 in which all matrix proteins are mislocalized to the cytosol, whereas membrane proteins are still correctly sorted to peroxisomal ghosts. In addition, we analyzed two mutants in which the peroxisomal location of the β-oxidation machinery is in part disturbed. We analyzed Δpex7 cells that contain virtually normal peroxisomes, except that all matrix proteins that contain a peroxisomal targeting signal type 2 (PTS2, also including thiolase), are mislocalized to the cytosol. In Δpex5 cells, peroxisomes only contain matrix proteins with a PTS2 in conjunction with all proteins containing a peroxisomal targeting signal type 1 (PTS1, including all β-oxidation enzymes except thiolase) are mislocalized to the cytosol. We show that intact peroxisomes are an important factor in yeast chronological aging because all pex mutants showed a reduced chronological lifespan. The strongest reduction was observed in Δpex5 cells. Our data indicate that this is related to the complete inactivation of the peroxisomal β-oxidation pathway in these cells due to the mislocalization of thiolase. Our studies suggest that during chronological aging, peroxisomal β-oxidation contributes to energy generation by the oxidation of fatty acids that are released by degradation of storage materials and recycled cellular components during carbon starvation conditions.
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Affiliation(s)
- Sophie D. Lefevre
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) University of Groningen P.O. Box 111039700CC Groningen The Netherlands
| | - Carlo W. Roermund
- Departments of Pediatrics and Clinical Chemistry Laboratory of Genetic Metabolic Diseases Academic Medical Centre University of Amsterdam 1105 AZ Amsterdam The Netherlands
| | - Ronald J. A. Wanders
- Departments of Pediatrics and Clinical Chemistry Laboratory of Genetic Metabolic Diseases Academic Medical Centre University of Amsterdam 1105 AZ Amsterdam The Netherlands
| | - Marten Veenhuis
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) University of Groningen P.O. Box 111039700CC Groningen The Netherlands
| | - Ida J. Klei
- Molecular Cell Biology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) University of Groningen P.O. Box 111039700CC Groningen The Netherlands
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43
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Ethanol and acetate acting as carbon/energy sources negatively affect yeast chronological aging. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:802870. [PMID: 24062879 PMCID: PMC3767056 DOI: 10.1155/2013/802870] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/09/2013] [Indexed: 12/20/2022]
Abstract
In Saccharomyces cerevisiae, the chronological lifespan (CLS) is defined as the length of time that a population of nondividing cells can survive in stationary phase. In this phase, cells remain metabolically active, albeit at reduced levels, and responsive to environmental signals, thus simulating the postmitotic quiescent state of mammalian cells. Many studies on the main nutrient signaling pathways have uncovered the strong influence of growth conditions, including the composition of culture media, on CLS. In this context, two byproducts of yeast glucose fermentation, ethanol and acetic acid, have been proposed as extrinsic proaging factors. Here, we report that ethanol and acetic acid, at physiological levels released in the exhausted medium, both contribute to chronological aging. Moreover, this combined proaging effect is not due to a toxic environment created by their presence but is mainly mediated by the metabolic pathways required for their utilization as carbon/energy sources. In addition, measurements of key enzymatic activities of the glyoxylate cycle and gluconeogenesis, together with respiration assays performed in extreme calorie restriction, point to a long-term quiescent program favoured by glyoxylate/gluconeogenesis flux contrary to a proaging one based on the oxidative metabolism of ethanol/acetate via TCA and mitochondrial respiration.
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44
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Chen BR, Li Y, Eisenstatt JR, Runge KW. Identification of a lifespan extending mutation in the Schizosaccharomyces pombe cyclin gene clg1+ by direct selection of long-lived mutants. PLoS One 2013; 8:e69084. [PMID: 23874875 PMCID: PMC3711543 DOI: 10.1371/journal.pone.0069084] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 06/12/2013] [Indexed: 11/30/2022] Open
Abstract
Model organisms such as budding yeast, worms and flies have proven instrumental
in the discovery of genetic determinants of aging, and the fission yeast
Schizosaccharomyces
pombe is a promising new system for these
studies. We devised an approach to directly select for long-lived
S.
pombe mutants from a random DNA insertion
library. Each insertion mutation bears a unique sequence tag called a bar code
that allows one to determine the proportion of an individual mutant in a culture
containing thousands of different mutants. Aging these mutants in culture
allowed identification of a long-lived mutant bearing an insertion mutation in
the cyclin gene clg1+. Clg1p, like
Pas1p, physically associates with the cyclin-dependent kinase Pef1p. We
identified a third Pef1p cyclin, Psl1p, and found that only loss of Clg1p or
Pef1p extended lifespan. Genetic and co-immunoprecipitation results indicate
that Pef1p controls lifespan through the downstream protein kinase Cek1p. While
Pef1p is conserved as Pho85p in Saccharomyces
cerevisiae, and as cdk5 in humans, genome-wide
searches for lifespan regulators in S. cerevisiae have
never identified Pho85p. Thus, the S. pombe system
can be used to identify novel, evolutionarily conserved lifespan extending
mutations, and our results suggest a potential role for mammalian cdk5 as a
lifespan regulator.
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Affiliation(s)
- Bo-Ruei Chen
- Department of Molecular Genetics, Cleveland Clinic Lerner College of
Medicine at Case Western Reserve University, Cleveland, Ohio,
USA
- Department of Genetics and Genome Sciences, Case Western Reserve
University School of Medicine, Cleveland, Ohio, United States of
America
- Department of Biochemistry, Case Western Reserve University School of
Medicine, Cleveland, Ohio, United States of America
| | - Yanhui Li
- Department of Molecular Genetics, Cleveland Clinic Lerner College of
Medicine at Case Western Reserve University, Cleveland, Ohio,
USA
- Department of Genetics and Genome Sciences, Case Western Reserve
University School of Medicine, Cleveland, Ohio, United States of
America
| | - Jessica R. Eisenstatt
- Department of Molecular Genetics, Cleveland Clinic Lerner College of
Medicine at Case Western Reserve University, Cleveland, Ohio,
USA
- Department of Biochemistry, Case Western Reserve University School of
Medicine, Cleveland, Ohio, United States of America
| | - Kurt W. Runge
- Department of Molecular Genetics, Cleveland Clinic Lerner College of
Medicine at Case Western Reserve University, Cleveland, Ohio,
USA
- Department of Genetics and Genome Sciences, Case Western Reserve
University School of Medicine, Cleveland, Ohio, United States of
America
- * E-mail:
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Brasil AA, Belati A, Mannarino SC, Panek AD, Eleutherio ECA, Pereira MD. The involvement of GSH in the activation of human Sod1 linked to FALS in chronologically aged yeast cells. FEMS Yeast Res 2013; 13:433-40. [DOI: 10.1111/1567-1364.12045] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/11/2013] [Accepted: 03/11/2013] [Indexed: 11/27/2022] Open
Affiliation(s)
- Aline A. Brasil
- Departamento de Bioquímica; Instituto de Química; Universidade Federal do Rio de Janeiro; Rio de Janeiro; Brazil
| | - Allan Belati
- Departamento de Bioquímica; Instituto de Química; Universidade Federal do Rio de Janeiro; Rio de Janeiro; Brazil
| | - Sérgio C. Mannarino
- Departamento de Bioquímica; Instituto de Química; Universidade Federal do Rio de Janeiro; Rio de Janeiro; Brazil
| | - Anita D. Panek
- Departamento de Bioquímica; Instituto de Química; Universidade Federal do Rio de Janeiro; Rio de Janeiro; Brazil
| | - Elis C. A. Eleutherio
- Departamento de Bioquímica; Instituto de Química; Universidade Federal do Rio de Janeiro; Rio de Janeiro; Brazil
| | - Marcos D. Pereira
- Departamento de Bioquímica; Instituto de Química; Universidade Federal do Rio de Janeiro; Rio de Janeiro; Brazil
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Mazzoni C, Mangiapelo E, Palermo V, Falcone C. Hypothesis: is yeast a clock model to study the onset of humans aging phenotypes? Front Oncol 2012; 2:203. [PMID: 23293770 PMCID: PMC3533236 DOI: 10.3389/fonc.2012.00203] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 12/11/2012] [Indexed: 12/19/2022] Open
Abstract
In this paper we report the growth and aging of yeast colonies derived from single cells isolated by micromanipulation and seeded one by one on separated plates to avoid growth interference by surrounding colonies. We named this procedure clonal life span, and it could represent a third way of studying aging together with the replicative life span and chronological life span. In this study we observed over time the formation of cell mass similar to the human “senile warts” (seborrheic keratoses), the skin lesions that often appear after 30 years of life and increase in number and size over the years. We observed that similar signs of aging appear in yeast colonies after about 27 days of growth and increase during aging. In this respect we hypothesize to use yeast as a clock to study the onset of human aging phenotypes.
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Affiliation(s)
- Cristina Mazzoni
- Department of Biology and Biotechnology "Charles Darwin", University of Rome "La Sapienza" Rome, Italy ; Pasteur Institute-Cenci Bolognetti Foundation, University of Rome "La Sapienza" Rome, Italy
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Kumar S, Lefevre SD, Veenhuis M, van der Klei IJ. Extension of yeast chronological lifespan by methylamine. PLoS One 2012; 7:e48982. [PMID: 23133668 PMCID: PMC3487785 DOI: 10.1371/journal.pone.0048982] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 10/03/2012] [Indexed: 12/28/2022] Open
Abstract
Background Chronological aging of yeast cells is commonly used as a model for aging of human post-mitotic cells. The yeast Saccharomyces cerevisiae grown on glucose in the presence of ammonium sulphate is mainly used in yeast aging research. We have analyzed chronological aging of the yeast Hansenula polymorpha grown at conditions that require primary peroxisome metabolism for growth. Methodology/Principal Findings The chronological lifespan of H. polymorpha is strongly enhanced when cells are grown on methanol or ethanol, metabolized by peroxisome enzymes, relative to growth on glucose that does not require peroxisomes. The short lifespan of H. polymorpha on glucose is mainly due to medium acidification, whereas most likely ROS do not play an important role. Growth of cells on methanol/methylamine instead of methanol/ammonium sulphate resulted in further lifespan enhancement. This was unrelated to medium acidification. We show that oxidation of methylamine by peroxisomal amine oxidase at carbon starvation conditions is responsible for lifespan extension. The methylamine oxidation product formaldehyde is further oxidized resulting in NADH generation, which contributes to increased ATP generation and reduction of ROS levels in the stationary phase. Conclusion/Significance We conclude that primary peroxisome metabolism enhanced chronological lifespan of H. polymorpha. Moreover, the possibility to generate NADH at carbon starvation conditions by an organic nitrogen source supports further extension of the lifespan of the cell. Consequently, the interpretation of CLS analyses in yeast should include possible effects on the energy status of the cell.
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Affiliation(s)
- Sanjeev Kumar
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kluyver Centre for Genomics of Industrial Fermentation, Groningen, The Netherlands
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Volejníková A, Hlousková J, Sigler K, Pichová A. Vital mitochondrial functions show profound changes during yeast culture ageing. FEMS Yeast Res 2012; 13:7-15. [PMID: 22938652 DOI: 10.1111/1567-1364.12001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 08/22/2012] [Accepted: 08/27/2012] [Indexed: 12/25/2022] Open
Abstract
During a 10-day culture ageing, cells of the wild-type Saccharomyces cerevisiae strain JC 482 retain their viability, while mitochondrial function and morphology change. Cell routine and uncoupled respiration rates increase to a maximum on day 4 and then decline to near zero. The decline, which occurs also in mitochondria isolated from cells of different age, is not due to increasing proportion of petites. Rhodamine 123 fluorescence intensity reporting on mitochondrial membrane potential appears to drop slightly for 4 days and then more sharply at the time when respiration rate also decreases. The MitoTracker Green fluorescent signal related to the mitochondrial content per cell also decreases. The branched tubular mitochondrial network of 1-day-old cells dissolves into short fragments; during the first 4 days, this fragmentation is associated with increasing function of mitochondria, while later on, it accompanies functional decline, which is also indicated by the decreasing ratio of Rhodamine 123 fluorescence to MitoTracker Green fluorescence. As shown by cell counting, microscopy and flow cytometry, the cell size distribution in the population broadens, and the population thus becomes more heterogeneous. The changes in respiration rate, mitochondrial membrane potential, mass and structure point to changes in the mitochondrial status during ageing.
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Affiliation(s)
- Andrea Volejníková
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Yeast colonies: a model for studies of aging, environmental adaptation, and longevity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:601836. [PMID: 22928081 PMCID: PMC3425895 DOI: 10.1155/2012/601836] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 07/09/2012] [Indexed: 11/18/2022]
Abstract
When growing on solid surfaces, yeast, like other microorganisms, develops organized multicellular populations (colonies and biofilms) that are composed of differentiated cells with specialized functions. Life within these populations is a prevalent form of microbial existence in natural settings that provides the cells with capabilities to effectively defend against environmental attacks as well as efficiently adapt and survive long periods of starvation and other stresses. Under such circumstances, the fate of an individual yeast cell is subordinated to the profit of the whole population. In the past decade, yeast colonies, with their complicated structure and high complexity that are also developed under laboratory conditions, have become an excellent model for studies of various basic cellular processes such as cell interaction, signaling, and differentiation. In this paper, we summarize current knowledge on the processes related to chronological aging, adaptation, and longevity of a colony cell population and of its differentiated cell constituents. These processes contribute to the colony ability to survive long periods of starvation and mostly differ from the survival strategies of individual yeast cells.
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50
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Growth culture conditions and nutrient signaling modulating yeast chronological longevity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2012; 2012:680304. [PMID: 22928083 PMCID: PMC3425870 DOI: 10.1155/2012/680304] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 07/10/2012] [Indexed: 01/27/2023]
Abstract
The manipulation of nutrient-signaling pathways in yeast has uncovered the impact of environmental growth conditions in longevity. Studies using calorie restriction show that reducing glucose concentration of the culture media is sufficient to increase replicative and chronological lifespan (CLS). Other components of the culture media and factors such as the products of fermentation have also been implicated in the regulation of CLS. Acidification of the culture media mainly due to acetic acid and other organic acids production negatively impacts CLS. Ethanol is another fermentative metabolite capable of inducing CLS reduction in aged cells by yet unknown mechanisms. Recently, ammonium was reported to induce cell death associated with shortening of CLS. This effect is correlated to the concentration of NH4+ added to the culture medium and is particularly evident in cells starved for auxotrophy-complementing amino acids. Studies on the nutrient-signaling pathways regulating yeast aging had a significant impact on aging-related research, providing key insights into mechanisms that modulate aging and establishing the yeast as a powerful system to extend knowledge on longevity regulation in multicellular organisms.
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