1
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Ölmez TT, Moreno DF, Liu P, Johnson ZM, McGinnis MM, Tu BP, Hochstrasser M, Acar M. Sis2 regulates yeast replicative lifespan in a dose-dependent manner. Nat Commun 2023; 14:7719. [PMID: 38012152 PMCID: PMC10682402 DOI: 10.1038/s41467-023-43233-y] [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: 08/30/2022] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
Application of microfluidic platforms facilitated high-precision measurements of yeast replicative lifespan (RLS); however, comparative quantification of lifespan across strain libraries has been missing. Here we microfluidically measure the RLS of 307 yeast strains, each deleted for a single gene. Despite previous reports of extended lifespan in these strains, we found that 56% of them did not actually live longer than the wild-type; while the remaining 44% showed extended lifespans, the degree of extension was often different from what was previously reported. Deletion of SIS2 gene led to the largest RLS increase observed. Sis2 regulated yeast lifespan in a dose-dependent manner, implying a role for the coenzyme A biosynthesis pathway in lifespan regulation. Introduction of the human PPCDC gene in the sis2Δ background neutralized the lifespan extension. RNA-seq experiments revealed transcriptional increases in cell-cycle machinery components in sis2Δ background. High-precision lifespan measurement will be essential to elucidate the gene network governing lifespan.
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Affiliation(s)
- Tolga T Ölmez
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
- Koç University Research Center for Translational Medicine, Koç University, Rumelifeneri Yolu, Sarıyer, İstanbul, 34450, Turkey
- Department of Basic Medical Sciences, Koc University Rumelifeneri Yolu, Sarıyer, İstanbul, 34450, Turkey
| | - David F Moreno
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, 67400, France
| | - Ping Liu
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA
| | - Zane M Johnson
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06520, USA
| | - Madeline M McGinnis
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mark Hochstrasser
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06520, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT, 06511, USA.
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT, 06516, USA.
- Department of Basic Medical Sciences, Koc University Rumelifeneri Yolu, Sarıyer, İstanbul, 34450, Turkey.
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2
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Mouton SN, Boersma AJ, Veenhoff LM. A physicochemical perspective on cellular ageing. Trends Biochem Sci 2023; 48:949-962. [PMID: 37716870 DOI: 10.1016/j.tibs.2023.08.007] [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: 04/21/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Cellular ageing described at the molecular level is a multifactorial process that leads to a spectrum of ageing trajectories. There has been recent discussion about whether a decline in physicochemical homeostasis causes aberrant phase transitions, which are a driver of ageing. Indeed, the function of all biological macromolecules, regardless of their participation in biomolecular condensates, depends on parameters such as pH, crowding, and redox state. We expand on the physicochemical homeostasis hypothesis and summarise recent evidence that the intracellular milieu influences molecular processes involved in ageing.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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3
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Gastelum S, Michael AF, Bolger TA. Saccharomyces cerevisiae as a research tool for RNA-mediated human disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1814. [PMID: 37671427 DOI: 10.1002/wrna.1814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023]
Abstract
The budding yeast, Saccharomyces cerevisiae, has been used for decades as a powerful genetic tool to study a broad spectrum of biological topics. With its ease of use, economic utility, well-studied genome, and a highly conserved proteome across eukaryotes, it has become one of the most used model organisms. Due to these advantages, it has been used to study an array of complex human diseases. From broad, complex pathological conditions such as aging and neurodegenerative disease to newer uses such as SARS-CoV-2, yeast continues to offer new insights into how cellular processes are affected by disease and how affected pathways might be targeted in therapeutic settings. At the same time, the roles of RNA and RNA-based processes have become increasingly prominent in the pathology of many of these same human diseases, and yeast has been utilized to investigate these mechanisms, from aberrant RNA-binding proteins in amyotrophic lateral sclerosis to translation regulation in cancer. Here we review some of the important insights that yeast models have yielded into the molecular pathology of complex, RNA-based human diseases. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Stephanie Gastelum
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Allison F Michael
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Timothy A Bolger
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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4
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Zhou Z, Liu Y, Feng Y, Klepin S, Tsimring LS, Pillus L, Hasty J, Hao N. Engineering longevity-design of a synthetic gene oscillator to slow cellular aging. Science 2023; 380:376-381. [PMID: 37104589 PMCID: PMC10249776 DOI: 10.1126/science.add7631] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 03/03/2023] [Indexed: 04/29/2023]
Abstract
Synthetic biology enables the design of gene networks to confer specific biological functions, yet it remains a challenge to rationally engineer a biological trait as complex as longevity. A naturally occurring toggle switch underlies fate decisions toward either nucleolar or mitochondrial decline during the aging of yeast cells. We rewired this endogenous toggle to engineer an autonomous genetic clock that generates sustained oscillations between the nucleolar and mitochondrial aging processes in individual cells. These oscillations increased cellular life span through the delay of the commitment to aging that resulted from either the loss of chromatin silencing or the depletion of heme. Our results establish a connection between gene network architecture and cellular longevity that could lead to rationally designed gene circuits that slow aging.
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Affiliation(s)
- Zhen Zhou
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yuting Liu
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yushen Feng
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Stephen Klepin
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Lev S. Tsimring
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Lorraine Pillus
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
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5
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Deprez MA, Caligaris M, Rosseels J, Hatakeyama R, Ghillebert R, Sampaio-Marques B, Mudholkar K, Eskes E, Meert E, Ungermann C, Ludovico P, Rospert S, De Virgilio C, Winderickx J. The nutrient-responsive CDK Pho85 primes the Sch9 kinase for its activation by TORC1. PLoS Genet 2023; 19:e1010641. [PMID: 36791155 PMCID: PMC9974134 DOI: 10.1371/journal.pgen.1010641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/28/2023] [Accepted: 01/27/2023] [Indexed: 02/16/2023] Open
Abstract
Yeast cells maintain an intricate network of nutrient signaling pathways enabling them to integrate information on the availability of different nutrients and adjust their metabolism and growth accordingly. Cells that are no longer capable of integrating this information, or that are unable to make the necessary adaptations, will cease growth and eventually die. Here, we studied the molecular basis underlying the synthetic lethality caused by loss of the protein kinase Sch9, a key player in amino acid signaling and proximal effector of the conserved growth-regulatory TORC1 complex, when combined with either loss of the cyclin-dependent kinase (CDK) Pho85 or loss of its inhibitor Pho81, which both have pivotal roles in phosphate sensing and cell cycle regulation. We demonstrate that it is specifically the CDK-cyclin pair Pho85-Pho80 or the partially redundant CDK-cyclin pairs Pho85-Pcl6/Pcl7 that become essential for growth when Sch9 is absent. Interestingly, the respective three CDK-cyclin pairs regulate the activity and distribution of the phosphatidylinositol-3 phosphate 5-kinase Fab1 on endosomes and vacuoles, where it generates phosphatidylinositol-3,5 bisphosphate that serves to recruit both TORC1 and its substrate Sch9. In addition, Pho85-Pho80 directly phosphorylates Sch9 at Ser726, and to a lesser extent at Thr723, thereby priming Sch9 for its subsequent phosphorylation and activation by TORC1. The TORC1-Sch9 signaling branch therefore integrates Pho85-mediated information at different levels. In this context, we also discovered that loss of the transcription factor Pho4 rescued the synthetic lethality caused by loss of Pho85 and Sch9, indicating that both signaling pathways also converge on Pho4, which appears to be wired to a feedback loop involving the high-affinity phosphate transporter Pho84 that fine-tunes Sch9-mediated responses.
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Affiliation(s)
- Marie-Anne Deprez
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Marco Caligaris
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Joëlle Rosseels
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Riko Hatakeyama
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Ruben Ghillebert
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal
| | - Kaivalya Mudholkar
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elja Eskes
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Els Meert
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
| | - Christian Ungermann
- Department of Biology/Chemistry & Center of Cellular Nanoanalytics (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Braga, Portugal
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudio De Virgilio
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail: (CDV); (JW)
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, Heverlee, Belgium
- * E-mail: (CDV); (JW)
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6
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Hu X, Jin X, Cao X, Liu B. The Anaphase-Promoting Complex/Cyclosome Is a Cellular Ageing Regulator. Int J Mol Sci 2022; 23:ijms232315327. [PMID: 36499653 PMCID: PMC9740938 DOI: 10.3390/ijms232315327] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/11/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a complicated cellular component that plays significant roles in regulating the cell cycle process of eukaryotic organisms. The spatiotemporal regulation mechanisms of APC/C in distinct cell cycle transitions are no longer mysterious, and the components of this protein complex are gradually identified and characterized. Given the close relationship between the cell cycle and lifespan, it is urgent to understand the roles of APC/C in lifespan regulation, but this field still seems to have not been systematically summarized. Furthermore, although several reviews have reported the roles of APC/C in cancer, there are still gaps in the summary of its roles in other age-related diseases. In this review, we propose that the APC/C is a novel cellular ageing regulator based on its indispensable role in the regulation of lifespan and its involvement in age-associated diseases. This work provides an extensive review of aspects related to the underlying mechanisms of APC/C in lifespan regulation and how it participates in age-associated diseases. More comprehensive recognition and understanding of the relationship between APC/C and ageing and age-related diseases will increase the development of targeted strategies for human health.
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Affiliation(s)
- Xiangdong Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiuling Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Correspondence: (X.C.); (B.L.)
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- Correspondence: (X.C.); (B.L.)
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7
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Suvorov A. Modalities of aging in organisms with different strategies of resource allocation. Ageing Res Rev 2022; 82:101770. [PMID: 36330930 PMCID: PMC10435286 DOI: 10.1016/j.arr.2022.101770] [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: 06/23/2022] [Revised: 08/17/2022] [Accepted: 10/24/2022] [Indexed: 01/31/2023]
Abstract
Although the progress of aging research relies heavily on a theoretical framework, today there is no consensus on many critical questions in aging biology. I hypothesize that a systematic analysis of the intersection of different evolutionary mechanisms of aging with diverse resource allocation strategies in different organisms may reconcile aging hypotheses. The application of disposable soma, mutation accumulation, antagonistic pleiotropy, and life-history theory is considered across organisms with asexual reproduction, organisms with sexual reproduction and indeterminate growth in different conditions of extrinsic mortality, and organisms with determinate growth, with endotherms/homeotherms as a subgroup. This review demonstrates that different aging mechanisms are complementary to each other, and in organisms with different resource allocation strategies they form aging modalities ranging from immortality to suicidal programs. It also revamps the role of growth arrest in aging. Growth arrest evolved in many different groups of organisms as a result of resource reallocation from growth to reproduction (e.g., semelparous animals, holometabolic insects), or from growth to nutrient storage (endotherms/homeotherms). Growth arrest in different animal lineages has similar molecular mechanisms and similar consequences for longevity due to the conflict between growth-promoting and growth-suppressing programs and suppression of regenerative capacity.
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Affiliation(s)
- Alexander Suvorov
- Environmental Health Sciences, University of Massachusetts, Amherst 240B Goessmann, 686 Noth Pleasant Str., Amherst, MA 01003, USA.
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8
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Sing TL, Brar GA, Ünal E. Gametogenesis: Exploring an Endogenous Rejuvenation Program to Understand Cellular Aging and Quality Control. Annu Rev Genet 2022; 56:89-112. [PMID: 35878627 PMCID: PMC9712276 DOI: 10.1146/annurev-genet-080320-025104] [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] [Indexed: 01/07/2023]
Abstract
Gametogenesis is a conserved developmental program whereby a diploid progenitor cell differentiates into haploid gametes, the precursors for sexually reproducing organisms. In addition to ploidy reduction and extensive organelle remodeling, gametogenesis naturally rejuvenates the ensuing gametes, leading to resetting of life span. Excitingly, ectopic expression of the gametogenesis-specific transcription factor Ndt80 is sufficient to extend life span in mitotically dividing budding yeast, suggesting that meiotic rejuvenation pathways can be repurposed outside of their natural context. In this review, we highlight recent studies of gametogenesis that provide emerging insight into natural quality control, organelle remodeling, and rejuvenation strategies that exist within a cell. These include selective inheritance, programmed degradation, and de novo synthesis, all of which are governed by the meiotic gene expression program entailing many forms of noncanonical gene regulation. Finally, we highlight critical questions that remain in the field and provide perspective on the implications of gametogenesis research on human health span.
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Affiliation(s)
- Tina L Sing
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA;
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9
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Kang PJ, Mullner R, Li H, Hansford D, Shen HW, Park HO. Upregulation of the Cdc42 GTPase limits the replicative lifespan of budding yeast. Mol Biol Cell 2022; 33:br5. [PMID: 35044837 PMCID: PMC9250358 DOI: 10.1091/mbc.e21-04-0208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cdc42, a conserved Rho GTPase, plays a central role in polarity establishment in yeast and animals. Cell polarity is critical for asymmetric cell division, and asymmetric cell division underlies replicative aging of budding yeast. Yet how Cdc42 and other polarity factors impact life span is largely unknown. Here we show by live-cell imaging that the active Cdc42 level is sporadically elevated in wild type during repeated cell divisions but rarely in the long-lived bud8 deletion cells. We find a novel Bud8 localization with cytokinesis remnants, which also recruit Rga1, a Cdc42 GTPase activating protein. Genetic analyses and live-cell imaging suggest that Rga1 and Bud8 oppositely impact life span likely by modulating active Cdc42 levels. An rga1 mutant, which has a shorter life span, dies at the unbudded state with a defect in polarity establishment. Remarkably, Cdc42 accumulates in old cells, and its mild overexpression accelerates aging with frequent symmetric cell divisions, despite no harmful effects on young cells. Our findings implicate that the interplay among these positive and negative polarity factors limits the life span of budding yeast.
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Affiliation(s)
- Pil Jung Kang
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Rachel Mullner
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Haoyu Li
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Derek Hansford
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Han-Wei Shen
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Hay-Oak Park
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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10
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Feng MW, Adams PD. A new mechanistic insight into fate decisions during yeast cell aging process. Mech Ageing Dev 2021; 198:111542. [PMID: 34273382 DOI: 10.1016/j.mad.2021.111542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Despite massive technological advances in mammalian models in recent years, studies in yeast still have the power to inform on the basic mechanisms of aging. Illustrating this, in Nan Hao's recent article published in the journal Science, he and his lab use microfluidics and fluorescent imaging technology to analyze the dynamics and interactions of aging mechanisms within yeast cells. They focused in on the Sir2 gene and the heme activator protein and, through the manipulation of these two molecular aging pathways, were able to determine that yeast cells can undergo one of three modes of aging, with one of them having a significantly longer lifespan than the others. These findings provide unexpected insights into mechanisms of aging, apparently as regulated fate-decision process, and open up avenues for future research.
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Affiliation(s)
- Morgan W Feng
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, United States
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, United States.
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11
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Dawes IW, Perrone GG. Stress and ageing in yeast. FEMS Yeast Res 2021; 20:5670642. [PMID: 31816015 DOI: 10.1093/femsyr/foz085] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023] Open
Abstract
There has long been speculation about the role of various stresses in ageing. Some stresses have beneficial effects on ageing-dependent on duration and severity of the stress, others have negative effects and the question arises whether these negative effects are causative of ageing or the result of the ageing process. Cellular responses to many stresses are highly coordinated in a concerted way and hence there is a great deal of cross-talk between different stresses. Here the relevant aspects of the coordination of stress responses and the roles of different stresses on yeast cell ageing are discussed, together with the various functions that are involved. The cellular processes that are involved in alleviating the effects of stress on ageing are considered, together with the possible role of early stress events on subsequent ageing of cells.
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Affiliation(s)
- Ian W Dawes
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Gabriel G Perrone
- School of Science and Health, Western Sydney University, Campbelltown, NSW 2560, Australia
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12
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Guo HB, Ghafari M, Dang W, Qin H. Protein interaction potential landscapes for yeast replicative aging. Sci Rep 2021; 11:7143. [PMID: 33785798 PMCID: PMC8010020 DOI: 10.1038/s41598-021-86415-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 03/15/2021] [Indexed: 11/17/2022] Open
Abstract
We proposed a novel interaction potential landscape approach to map the systems-level profile changes of gene networks during replicative aging in Saccharomyces cerevisiae. This approach enabled us to apply quasi-potentials, the negative logarithm of the probabilities, to calibrate the elevation of the interaction landscapes with young cells as a reference state. Our approach detected opposite landscape changes based on protein abundances from transcript levels, especially for intra-essential gene interactions. We showed that essential proteins play different roles from hub proteins on the age-dependent interaction potential landscapes. We verified that hub proteins tend to avoid other hub proteins, but essential proteins prefer to interact with other essential proteins. Overall, we showed that the interaction potential landscape is promising for inferring network profile change during aging and that the essential hub proteins may play an important role in the uncoupling between protein and transcript levels during replicative aging.
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Affiliation(s)
- Hao-Bo Guo
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- SimCenter, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH, 45433, USA.
| | - Mehran Ghafari
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hong Qin
- Department of Computer Science and Engineering, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- SimCenter, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
- Department of Biology, Geology and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, 37405, USA.
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13
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Synergistic effects of repair, resilience and retention of damage determine the conditions for replicative ageing. Sci Rep 2020; 10:1556. [PMID: 32005954 PMCID: PMC6994596 DOI: 10.1038/s41598-020-58444-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 01/15/2020] [Indexed: 12/31/2022] Open
Abstract
Accumulation of damaged proteins is a hallmark of ageing, occurring in organisms ranging from bacteria and yeast to mammalian cells. During cell division in Saccharomyces cerevisiae, damaged proteins are retained within the mother cell, resulting in an ageing mother while a new daughter cell exhibits full replicative potential. The cell-specific features determining the ageing remain elusive. It has been suggested that the replicative ageing is dependent on the ability of the cell to repair and retain pre-existing damage. To deepen the understanding of how these factors influence the life of individual cells, we developed and experimentally validated a dynamic model of damage accumulation accounting for replicative ageing on the single cell level. The model includes five essential properties: cell growth, damage formation, damage repair, cell division and cell death, represented in a theoretical framework describing the conditions allowing for replicative ageing, starvation, immortality or clonal senescence. We introduce the resilience to damage, which can be interpreted as the difference in volume between an old and a young cell. We show that the capacity to retain damage deteriorates with high age, that asymmetric division allows for retention of damage, and that there is a trade-off between retention and the resilience property. Finally, we derive the maximal degree of asymmetry as a function of resilience, proposing that asymmetric cell division is beneficial with respect to replicative ageing as it increases the lifespan of a given organism. The proposed model contributes to a deeper understanding of the ageing process in eukaryotic organisms.
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14
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O'Laughlin R, Jin M, Li Y, Pillus L, Tsimring LS, Hasty J, Hao N. Advances in quantitative biology methods for studying replicative aging in Saccharomyces cerevisiae. TRANSLATIONAL MEDICINE OF AGING 2019; 4:151-160. [PMID: 33880425 PMCID: PMC8054985 DOI: 10.1016/j.tma.2019.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Aging is a complex, yet pervasive phenomenon in biology. As human cells steadily succumb to the deteriorating effects of aging, so too comes a host of age-related ailments such as neurodegenerative disorders, cardiovascular disease and cancer. Therefore, elucidation of the molecular networks that drive aging is of paramount importance to human health. Progress toward this goal has been aided by studies from simple model organisms such as Saccharomyces cerevisiae. While work in budding yeast has already revealed much about the basic biology of aging as well as a number of evolutionarily conserved pathways involved in this process, recent technological advances are poised to greatly expand our knowledge of aging in this simple eukaryote. Here, we review the latest developments in microfluidics, single-cell analysis and high-throughput technologies for studying single-cell replicative aging in S. cerevisiae. We detail the challenges each of these methods addresses as well as the unique insights into aging that each has provided. We conclude with a discussion of potential future applications of these techniques as well as the importance of single-cell dynamics and quantitative biology approaches for understanding cell aging.
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Affiliation(s)
- Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Meng Jin
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nan Hao
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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15
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Gulli J, Cook E, Kroll E, Rosebrock A, Caudy A, Rosenzweig F. Diverse conditions support near-zero growth in yeast: Implications for the study of cell lifespan. MICROBIAL CELL 2019; 6:397-413. [PMID: 31528631 PMCID: PMC6717879 DOI: 10.15698/mic2019.09.690] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Baker's yeast has a finite lifespan and ages in two ways: a mother cell can only divide so many times (its replicative lifespan), and a non-dividing cell can only live so long (its chronological lifespan). Wild and laboratory yeast strains exhibit natural variation for each type of lifespan, and the genetic basis for this variation has been generalized to other eukaryotes, including metazoans. To date, yeast chronological lifespan has chiefly been studied in relation to the rate and mode of functional decline among non-dividing cells in nutrient-depleted batch culture. However, this culture method does not accurately capture two major classes of long-lived metazoan cells: cells that are terminally differentiated and metabolically active for periods that approximate animal lifespan (e.g. cardiac myocytes), and cells that are pluripotent and metabolically quiescent (e.g. stem cells). Here, we consider alternative ways of cultivating Saccharomyces cerevisiae so that these different metabolic states can be explored in non-dividing cells: (i) yeast cultured as giant colonies on semi-solid agar, (ii) yeast cultured in retentostats and provided sufficient nutrients to meet minimal energy requirements, and (iii) yeast encapsulated in a semisolid matrix and fed ad libitum in bioreactors. We review the physiology of yeast cultured under each of these conditions, and explore their potential to provide unique insights into determinants of chronological lifespan in the cells of higher eukaryotes.
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Affiliation(s)
- Jordan Gulli
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Emily Cook
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Eugene Kroll
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Adam Rosebrock
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Present address: Stony Brook School of Medicine, Stony Brook University, Stony Brook, NY 11794
| | - Amy Caudy
- Donnelly Centre for Cellular and Biological Research and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Frank Rosenzweig
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
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16
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Chen KL, Ven TN, Crane MM, Chen DE, Feng YC, Suzuki N, Russell AE, de Moraes D, Kaeberlein M. An inexpensive microscopy system for microfluidic studies in budding yeast. TRANSLATIONAL MEDICINE OF AGING 2019; 3:52-56. [PMID: 31511839 PMCID: PMC6738973 DOI: 10.1016/j.tma.2019.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Recently, microfluidic technologies have been developed to allow higher throughput collection of yeast replicative lifespan data. Adoption of these devices has been limited, in part, due to the high cost of the motorized microscopy instrumentation from mainline manufacturers. Inspired by recent development of open source microscopy hardware and software, we developed minimal-cost hardware attachments to provide long-term focus stabilization for lower-cost microscopes and open source software to manage concurrent time-lapse image acquisition from multiple microscopes. We hope that these tools will help spur the wider adoption of microfluidic technologies for the study of aging in yeast.
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Affiliation(s)
- Kenneth L. Chen
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, School of Medicine, University of Washington, Seattle, WA, USA
| | - Toby N. Ven
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matthew M. Crane
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Dexter E. Chen
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Yen-Chi Feng
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Nozomi Suzuki
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Adam E. Russell
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Diogo de Moraes
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA, USA
- Corresponding author. Department of Pathology, School of Medicine, University of Washington, Seattle, WA, USA. (M. Kaeberlein)
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17
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Structure Characterization and Action Mechanism of an Antiaging New Compound from Gastrodia elata Blume. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:5459862. [PMID: 31198492 PMCID: PMC6526511 DOI: 10.1155/2019/5459862] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/23/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
A new compound, bis(4-hydroxybenzyl)ether mono-β-L-galactopyranoside (1), was isolated from the rhizome of Gastrodia elata Blume. Its structure was elucidated using extensive spectroscopic analysis, including 1D and 2D NMR, HR-ESI-TOF-MS, and chemical derivatization. Compound 1 extended the replicative lifespan of K6001 and the chronological lifespan of YOM36 yeast strains. To understand the mechanism of action, oxidative stress assessment, reactive oxygen species (ROS) and malondialdehyde (MDA) levels, catalase (CAT) and total glutathione peroxidase (GPx) activity assays, and replicative lifespan assay of sod1, sod2, uth1, and skn7 yeast mutant strains were performed. Results indicated the significant increase in the survival rate of yeast under oxidative stress after treatment with 1. ROS and MDA levels were reduced significantly. Meanwhile, the activity of CAT and GPx was significantly increased. The lifespan of sod1, sod2, uth1, and skn7 mutants of K6001 was not affected by 1. Furthermore, we investigated the gene expression related to longevity after administrating 1. The significant increase of Sir2 and reduction of Uth1 gene expression in the 1-treated group were observed. These results indicated that antioxidative stress played an important role in the antiaging effect of 1; Sir2 and Uth1 genes were involved in antiaging effects of 1.
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18
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Fine RD, Maqani N, Li M, Franck E, Smith JS. Depletion of Limiting rDNA Structural Complexes Triggers Chromosomal Instability and Replicative Aging of Saccharomyces cerevisiae. Genetics 2019; 212:75-91. [PMID: 30842210 PMCID: PMC6499517 DOI: 10.1534/genetics.119.302047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/01/2019] [Indexed: 12/12/2022] Open
Abstract
Sir2 is a highly conserved NAD+-dependent histone deacetylase that functions in heterochromatin formation and promotes replicative life span (RLS) in the budding yeast, Saccharomyces cerevisiae Within the yeast rDNA locus, Sir2 is required for efficient cohesin recruitment and maintaining the stability of the tandem array. In addition to the previously reported depletion of Sir2 in replicatively aged cells, we discovered that subunits of the Sir2-containing complexes silent information regulator (SIR) and regulator of nucleolar silencing and telophase (RENT) were depleted. Several other rDNA structural protein complexes also exhibited age-related depletion, most notably the cohesin complex. We hypothesized that mitotic chromosome instability (CIN) due to cohesin depletion could be a driver of replicative aging. Chromatin immunoprecipitation assays of the residual cohesin (Mcd1-Myc) in moderately aged cells showed strong depletion from the rDNA and initial redistribution to the point centromeres, which was then lost in older cells. Despite the shift in cohesin distribution, sister chromatid cohesion was partially attenuated in aged cells and the frequency of chromosome loss was increased. This age-induced CIN was exacerbated in strains lacking Sir2 and its paralog, Hst1, but suppressed in strains that stabilize the rDNA array due to deletion of FOB1 or through caloric restriction. Furthermore, ectopic expression of MCD1 from a doxycycline-inducible promoter was sufficient to suppress rDNA instability in aged cells and to extend RLS. Taken together, we conclude that age-induced depletion of cohesin and multiple other nucleolar chromatin factors destabilize the rDNA locus, which then results in general CIN and aneuploidy that shortens RLS.
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Affiliation(s)
- Ryan D Fine
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Nazif Maqani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Mingguang Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908
- Department of Laboratory Medicine, Jilin Medical University, 132013, China
| | - Elizabeth Franck
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908
| | - Jeffrey S Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908
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19
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Abstract
A new device for isolating large quantities of old yeast cells expands the experimental boundaries of aging research.
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Affiliation(s)
- Troy K Coody
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Adam L Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
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20
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Yaku K, Okabe K, Nakagawa T. NAD metabolism: Implications in aging and longevity. Ageing Res Rev 2018; 47:1-17. [PMID: 29883761 DOI: 10.1016/j.arr.2018.05.006] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 12/20/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) is an important co-factor involved in numerous physiological processes, including metabolism, post-translational protein modification, and DNA repair. In living organisms, a careful balance between NAD production and degradation serves to regulate NAD levels. Recently, a number of studies have demonstrated that NAD levels decrease with age, and the deterioration of NAD metabolism promotes several aging-associated diseases, including metabolic and neurodegenerative diseases and various cancers. Conversely, the upregulation of NAD metabolism, including dietary supplementation with NAD precursors, has been shown to prevent the decline of NAD and exhibits beneficial effects against aging and aging-associated diseases. In addition, many studies have demonstrated that genetic and/or nutritional activation of NAD metabolism can extend the lifespan of diverse organisms. Collectively, it is clear that NAD metabolism plays important roles in aging and longevity. In this review, we summarize the basic functions of the enzymes involved in NAD synthesis and degradation, as well as the outcomes of their dysregulation in various aging processes. In addition, a particular focus is given on the role of NAD metabolism in the longevity of various organisms, with a discussion of the remaining obstacles in this research field.
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21
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Sarnoski EA, Song R, Ertekin E, Koonce N, Acar M. Fundamental Characteristics of Single-Cell Aging in Diploid Yeast. iScience 2018; 7:96-109. [PMID: 30267689 PMCID: PMC6135869 DOI: 10.1016/j.isci.2018.08.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/01/2018] [Accepted: 08/10/2018] [Indexed: 11/26/2022] Open
Abstract
Single-cell-level experimentation can elucidate key biological insights about cellular aging that are masked in population-level studies. However, the extensive time requirement of tracking single cells has historically prevented their long-term longitudinal observation. Using a microfluidic device that automates microscopic monitoring of diploid Saccharomyces cerevisiae cells throughout their replicative lifespan, here we report the fundamental characteristics of single-cell aging for diploid yeast. We find that proteins with short versus long half-lives exhibit distinct dynamics as cells age and that the intercellular gene expression noise increases during aging, whereas the intracellular noise stays unchanged. A stochastic model provides quantitative mechanistic insights into the observed noise dynamics and sheds light on the age-dependent intracellular noise differences between diploid and haploid yeast. Our work elucidates how a set of canonical phenotypes dynamically change while the host cells are aging in real time, providing essential insights for a comprehensive understanding on and control of lifespan at the single-cell level. A microfluidic device facilitates longitudinal observation of aging diploid yeast Proteins with short versus long half-lives exhibit distinct dynamics as cells age Intercellular gene expression noise increases during replicative aging Unlike haploid yeast, intracellular noise is unchanged during aging in diploid yeast
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Affiliation(s)
- Ethan A Sarnoski
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Ruijie Song
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA
| | - Ege Ertekin
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Noelle Koonce
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA.
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22
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Smith JT, White JW, Dungrawala H, Hua H, Schneider BL. Yeast lifespan variation correlates with cell growth and SIR2 expression. PLoS One 2018; 13:e0200275. [PMID: 29979754 PMCID: PMC6034835 DOI: 10.1371/journal.pone.0200275] [Citation(s) in RCA: 10] [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: 03/07/2018] [Accepted: 06/22/2018] [Indexed: 11/19/2022] Open
Abstract
Isogenic wild type yeast cells raised in controlled environments display a significant range of lifespan variation. Recent microfluidic studies suggest that differential growth or gene expression patterns may explain some of the heterogeneity of aging assays. Herein, we sought to complement this work by similarly examining a large set of replicative lifespan data from traditional plate assays. In so doing, we reproduced the finding that short-lived cells tend to arrest at senescence with a budded morphology. Further, we found that wild type cells born unusually small did not have an extended lifespan. However, large birth size and/or high inter-generational growth rates significantly correlated with a reduced lifespan. Finally, we found that SIR2 expression levels correlated with lifespan and intergenerational growth. SIR2 expression was significantly reduced in large cells and increased in small wild type cells. A moderate increase in SIR2 expression correlated with reduced growth, decreased proliferation and increased lifespan in plate aging assays. We conclude that cellular growth rates and SIR2 expression levels may contribute to lifespan variation in individual cells.
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Affiliation(s)
- Jessica T. Smith
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
| | - Jill W. White
- Center for the Integration of STEM Education & Research, Texas Tech University, Lubbock, TX, United States of America
| | - Huzefa Dungrawala
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Hui Hua
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
| | - Brandt L. Schneider
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
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23
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Jones SK, Spivey EC, Rybarski JR, Finkelstein IJ. A Microfluidic Device for Massively Parallel, Whole-lifespan Imaging of Single Fission Yeast Cells. Bio Protoc 2018; 8:e2783. [PMID: 29770351 DOI: 10.21769/bioprotoc.2783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Whole-lifespan single-cell analysis has greatly increased our understanding of fundamental cellular processes such as cellular aging. To observe individual cells across their entire lifespan, all progeny must be removed from the growth medium, typically via manual microdissection. However, manual microdissection is laborious, low-throughput, and incompatible with fluorescence microscopy. Here, we describe assembly and operation of the multiplexed-Fission Yeast Lifespan Microdissector (multFYLM), a high-throughput microfluidic device for rapidly acquiring single-cell whole-lifespan imaging. multFYLM captures approximately one thousand rod-shaped fission yeast cells from up to six different genetic backgrounds or treatment regimens. The immobilized cells are fluorescently imaged for over a week, while the progeny cells are removed from the device. The resulting datasets yield high-resolution multi-channel images that record each cell's replicative lifespan. We anticipate that the multFYLM will be broadly applicable for single-cell whole-lifespan studies in the fission yeast (Schizosaccharomyces pombe) and other symmetrically-dividing unicellular organisms.
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Affiliation(s)
- Stephen K Jones
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Eric C Spivey
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - James R Rybarski
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, USA
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24
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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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25
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Baldi S, Bolognesi A, Meinema AC, Barral Y. Heat stress promotes longevity in budding yeast by relaxing the confinement of age-promoting factors in the mother cell. eLife 2017; 6:28329. [PMID: 29283340 PMCID: PMC5771669 DOI: 10.7554/elife.28329] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 12/27/2017] [Indexed: 12/16/2022] Open
Abstract
Although individuals of many species inexorably age, a number of observations established that the rate of aging is modulated in response to a variety of mild stresses. Here, we investigated how heat stress promotes longevity in yeast. We show that upon growth at higher temperature, yeast cells relax the retention of DNA circles, which act as aging factors in the mother cell. The enhanced frequency at which circles redistribute to daughter cells was not due to changes of anaphase duration or nuclear shape but solely to the downregulation of the diffusion barrier in the nuclear envelope. This effect depended on the PKA and Tor1 pathways, downstream of stress-response kinase Pkc1. Inhibition of these responses restored barrier function and circle retention and abrogated the effect of heat stress on longevity. Our data indicate that redistribution of aging factors from aged cells to their progeny can be a mechanism for modulating longevity.
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Affiliation(s)
- Sandro Baldi
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Alessio Bolognesi
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | | | - Yves Barral
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
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26
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Singh P, Li R. Emerging roles for sphingolipids in cellular aging. Curr Genet 2017; 64:761-767. [PMID: 29260307 DOI: 10.1007/s00294-017-0799-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 02/07/2023]
Abstract
Aging is a gradual loss of physiological functions as organisms' progress in age. Although aging in multicellular organisms is complex, some fundamental mechanisms and pathways may be shared from the single cellular yeast to human. Budding yeast Saccharomyces cerevisiae has been established model system for aging studies. A yeast cell divides asymmetrically to produce two cells that differ in size and age. The one that is smaller coming from bud is a newborn cell that with a full replicative potential head irrespective of the replicative age of its mother-the larger cell from which the bud grows out before division. The age asymmetry between daughter and mother is thought to be dependent on asymmetric segregation of certain factors such as protein aggregates, extrachromosomal DNA (ERCs) and dysfunctional organelles during successive cell divisions of the yeast replicative lifespan (RLS). It is also thought that certain plasma membrane proteins, in particular multidrug-resistant (MDR) proteins, asymmetrically partition between the mother and the bud based on the age of the polypeptides. Functional decline associated with the molecular aging of those proteins contributes to the fitness decline at advance age. In our recent study, we showed that sphingolipids facilitate the age-dependent segregation of MDRs between daughter and mother cell. In this review, we highlight and discuss the potential mechanisms by which sphingolipids regulate the aging process in yeast and cells of vertebrate animals including human.
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Affiliation(s)
- Pushpendra Singh
- Laboratory of Adjuvant and Antigen Research, US Military HIV Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD, 20910, USA. .,US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, MD, 20817, USA.
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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27
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The paths of mortality: how understanding the biology of aging can help explain systems behavior of single cells. ACTA ACUST UNITED AC 2017; 8:25-31. [PMID: 29552673 DOI: 10.1016/j.coisb.2017.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Aging is a fundamental aspect of life, yet also one of the most confounding. In individual cells, aging results in a progressive decline which affects all organelles and reduces a cell's ability to maintain homeostasis. Because of the interconnected nature of cellular systems, the failure of even a single organelle can have cascading effects. We are just beginning to understand the dramatic physiological changes that occur during aging. Because most aging research has focused on population dynamics, or differences between wild-type and mutant populations, single-cell behavior has been largely overlooked. An open question is whether aging cells are defined by predictable sequences of physiological changes, or whether they proceed along divergent aging trajectories defined by whichever system begins to fail first. Can aging be best characterized by a cell-cycle like model with stereotyped states all cells progress through, or a Waddington landscape with divergent trajectories? Here we present work on understanding the changing physiological states of aging cells, why it will impact systems and synthetic biologists, and how the systems community can contribute significantly to the study of aging.
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28
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Streubel MK, Bischof J, Weiss R, Duschl J, Liedl W, Wimmer H, Breitenbach M, Weber M, Geltinger F, Richter K, Rinnerthaler M. Behead and live long or the tale of cathepsin L. Yeast 2017; 35:237-249. [PMID: 29044689 PMCID: PMC5808862 DOI: 10.1002/yea.3286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/12/2017] [Accepted: 10/04/2017] [Indexed: 12/31/2022] Open
Abstract
In recent decades Saccharomyces cerevisiae has proven to be one of the most valuable model organisms of aging research. Pathways such as autophagy or the effect of substances like resveratrol and spermidine that prolong the replicative as well as chronological lifespan of cells were described for the first time in S. cerevisiae. In this study we describe the establishment of an aging reporter that allows a reliable and relative quick screening of substances and genes that have an impact on the replicative lifespan. A cDNA library of the flatworm Dugesia tigrina that can be immortalized by beheading was screened using this aging reporter. Of all the flatworm genes, only one could be identified that significantly increased the replicative lifespan of S.cerevisiae. This gene is the cysteine protease cathepsin L that was sequenced for the first time in this study. We were able to show that this protease has the capability to degrade such proteins as the yeast Sup35 protein or the human α‐synuclein protein in yeast cells that are both capable of forming cytosolic toxic aggregates. The degradation of these proteins by cathepsin L prevents the formation of these unfolded protein aggregates and this seems to be responsible for the increase in replicative lifespan.
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Affiliation(s)
- Maria Karolin Streubel
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Johannes Bischof
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Richard Weiss
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Jutta Duschl
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Wolfgang Liedl
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Herbert Wimmer
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Michael Breitenbach
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Manuela Weber
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Florian Geltinger
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Klaus Richter
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
| | - Mark Rinnerthaler
- Department of Cell Biology and Physiology, Division of Genetics, University of Salzburg, Salzburg, Austria
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29
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Cabral M, Cheng X, Singh S, Ivessa AS. Absence of Non-histone Protein Complexes at Natural Chromosomal Pause Sites Results in Reduced Replication Pausing in Aging Yeast Cells. Cell Rep 2017; 17:1747-1754. [PMID: 27829146 DOI: 10.1016/j.celrep.2016.10.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/08/2016] [Accepted: 10/14/2016] [Indexed: 11/26/2022] Open
Abstract
There is substantial evidence that genomic instability increases during aging. Replication pausing (and stalling) at difficult-to-replicate chromosomal sites may induce genomic instability. Interestingly, in aging yeast cells, we observed reduced replication pausing at various natural replication pause sites (RPSs) in ribosomal DNA (rDNA) and non-rDNA locations (e.g., silent replication origins and tRNA genes). The reduced pausing occurs independent of the DNA helicase Rrm3p, which facilitates replication past these non-histone protein-complex-bound RPSs, and is independent of the deacetylase Sir2p. Conditions of caloric restriction (CR), which extend life span, also cause reduced replication pausing at the 5S rDNA and at tRNA genes. In aged and CR cells, the RPSs are less occupied by their specific non-histone protein complexes (e.g., the preinitiation complex TFIIIC), likely because members of these complexes have primarily cytosolic localization. These conditions may lead to reduced replication pausing and may lower replication stress at these sites during aging.
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Affiliation(s)
- Marleny Cabral
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Xin Cheng
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA.
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30
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Singh P, Ramachandran SK, Zhu J, Kim BC, Biswas D, Ha T, Iglesias PA, Li R. Sphingolipids facilitate age asymmetry of membrane proteins in dividing yeast cells. Mol Biol Cell 2017; 28:2712-2722. [PMID: 28768828 PMCID: PMC5620378 DOI: 10.1091/mbc.e17-05-0335] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/21/2017] [Accepted: 07/28/2017] [Indexed: 01/20/2023] Open
Abstract
One proposed mechanism of cellular aging is the gradual loss of certain cellular components that are insufficiently renewed. In an earlier study, multidrug resistance transporters (MDRs) were postulated to be such aging determinants during the yeast replicative life span (RLS). Aged MDR proteins were asymmetrically retained by the aging mother cell and did not diffuse freely into the bud, whereas newly synthesized MDR proteins were thought to be deposited mostly in the bud before cytokinesis. In this study, we further demonstrate the proposed age asymmetry of MDR proteins in dividing yeast cells and investigate the mechanism that controls diffusive properties of MDR proteins to maintain this asymmetry. We found that long-chain sphingolipids, but not the septin/endoplasmic reticulum-based membrane diffusion barrier, are important for restricting MDR diffusion. Depletion of sphingolipids or shortening of their long acyl chains resulted in an increase in the lateral mobility of MDR proteins, causing aged MDR protein in the mother cell to enter the bud. We used a mathematical model to understand the effect of diminished MDR age asymmetry on yeast cell aging, the result of which was qualitatively consistent with the observed RLS shortening in sphingolipid mutants.
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Affiliation(s)
- Pushpendra Singh
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Sree Kumar Ramachandran
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Jin Zhu
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Byoung Choul Kim
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218.,Howard Hughes Medical Institute, Baltimore, MD 21218.,Division of Nano-bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Debojyoti Biswas
- Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD 21205.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218.,Howard Hughes Medical Institute, Baltimore, MD 21218
| | - Pablo A Iglesias
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218.,Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 .,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
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31
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Ohtsuka H, Takinami M, Shimasaki T, Hibi T, Murakami H, Aiba H. Sulfur restriction extends fission yeast chronological lifespan through Ecl1 family genes by downregulation of ribosome. Mol Microbiol 2017; 105:84-97. [PMID: 28388826 DOI: 10.1111/mmi.13686] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/20/2017] [Accepted: 03/30/2017] [Indexed: 01/11/2023]
Abstract
Nutritional restrictions such as calorie restrictions are known to increase the lifespan of various organisms. Here, we found that a restriction of sulfur extended the chronological lifespan (CLS) of the fission yeast Schizosaccharomyces pombe. The restriction decreased cellular size, RNA content, and ribosomal proteins and increased sporulation rate. These responses depended on Ecl1 family genes, the overexpression of which results in the extension of CLS. We also showed that the Zip1 transcription factor results in the sulfur restriction-dependent expression of the ecl1+ gene. We demonstrated that a decrease in ribosomal activity results in the extension of CLS. Based on these observations, we propose that sulfur restriction extends CLS through Ecl1 family genes in a ribosomal activity-dependent manner.
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Affiliation(s)
- Hokuto Ohtsuka
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Masahiro Takinami
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Takafumi Shimasaki
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Takahide Hibi
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Hiroshi Murakami
- Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Hirofumi Aiba
- Laboratory of Molecular Microbiology, Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Chikusa-ku, Nagoya, 464-8601, Japan
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32
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Speldewinde SH, Grant CM. The frequency of yeast [ PSI+] prion formation is increased during chronological ageing. MICROBIAL CELL 2017; 4:127-132. [PMID: 28435839 PMCID: PMC5376352 DOI: 10.15698/mic2017.04.568] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ageing involves a time-dependent decline in a variety of intracellular mechanisms and is associated with cellular senescence. This can be exacerbated by prion diseases which can occur in a sporadic manner, predominantly during the later stages of life. Prions are infectious, self-templating proteins responsible for several neurodegenerative diseases in mammals and several prion-forming proteins have been found in yeast. We show here that the frequency of formation of the yeast [PSI+ ] prion, which is the altered form of the Sup35 translation termination factor, is increased during chronological ageing. This increase is exacerbated in an atg1 mutant suggesting that autophagy normally acts to suppress age-related prion formation. We further show that cells which have switched to [PSI+ ] have improved viability during chronological ageing which requires active autophagy. [PSI+ ] stains show increased autophagic flux which correlates with increased viability and decreased levels of cellular protein aggregation. Taken together, our data indicate that the frequency of [PSI+ ] prion formation increases during yeast chronological ageing, and switching to the [PSI+ ] form can exert beneficial effects via the promotion of autophagic flux.
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Affiliation(s)
- Shaun H Speldewinde
- University of Manchester, Faculty of Biology, Medicine and Health, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Chris M Grant
- University of Manchester, Faculty of Biology, Medicine and Health, The Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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33
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Molina-Serrano D, Schiza V, Demosthenous C, Stavrou E, Oppelt J, Kyriakou D, Liu W, Zisser G, Bergler H, Dang W, Kirmizis A. Loss of Nat4 and its associated histone H4 N-terminal acetylation mediates calorie restriction-induced longevity. EMBO Rep 2016; 17:1829-1843. [PMID: 27799288 PMCID: PMC5167350 DOI: 10.15252/embr.201642540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/21/2016] [Accepted: 09/30/2016] [Indexed: 01/07/2023] Open
Abstract
Changes in histone modifications are an attractive model through which environmental signals, such as diet, could be integrated in the cell for regulating its lifespan. However, evidence linking dietary interventions with specific alterations in histone modifications that subsequently affect lifespan remains elusive. We show here that deletion of histone N‐alpha‐terminal acetyltransferase Nat4 and loss of its associated H4 N‐terminal acetylation (N‐acH4) extend yeast replicative lifespan. Notably, nat4Δ‐induced longevity is epistatic to the effects of calorie restriction (CR). Consistent with this, (i) Nat4 expression is downregulated and the levels of N‐acH4 within chromatin are reduced upon CR, (ii) constitutive expression of Nat4 and maintenance of N‐acH4 levels reduces the extension of lifespan mediated by CR, and (iii) transcriptome analysis indicates that nat4Δ largely mimics the effects of CR, especially in the induction of stress‐response genes. We further show that nicotinamidase Pnc1, which is typically upregulated under CR, is required for nat4Δ‐mediated longevity. Collectively, these findings establish histone N‐acH4 as a regulator of cellular lifespan that links CR to increased stress resistance and longevity.
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Affiliation(s)
| | - Vassia Schiza
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | | | - Emmanouil Stavrou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Dimitris Kyriakou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Wei Liu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Gertrude Zisser
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Graz, Austria
| | - Helmut Bergler
- Institut für Molekulare Biowissenschaften, Karl-Franzens-Universität, Graz, Austria
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Antonis Kirmizis
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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34
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CLD1 Reverses the Ubiquinone Insufficiency of Mutant cat5/coq7 in a Saccharomyces cerevisiae Model System. PLoS One 2016; 11:e0162165. [PMID: 27603010 PMCID: PMC5014327 DOI: 10.1371/journal.pone.0162165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/16/2016] [Indexed: 11/23/2022] Open
Abstract
Ubiquinone (Qn) functions as a mobile electron carrier in mitochondria. In humans, Q biosynthetic pathway mutations lead to Q10 deficiency, a life threatening disorder. We have used a Saccharomyces cerevisiae model of Q6 deficiency to screen for new modulators of ubiquinone biosynthesis. We generated several hypomorphic alleles of coq7/cat5 (clk-1 in Caenorhabditis elegans) encoding the penultimate enzyme in Q biosynthesis which converts 5-demethoxy Q6 (DMQ6) to 5-demethyl Q6, and screened for genes that, when overexpressed, suppressed their inability to grow on non-fermentable ethanol—implying recovery of lost mitochondrial function. Through this approach we identified Cardiolipin-specific Deacylase 1 (CLD1), a gene encoding a phospholipase A2 required for cardiolipin acyl remodeling. Interestingly, not all coq7 mutants were suppressed by Cld1p overexpression, and molecular modeling of the mutant Coq7p proteins that were suppressed showed they all contained disruptions in a hydrophobic α-helix that is predicted to mediate membrane-binding. CLD1 overexpression in the suppressible coq7 mutants restored the ratio of DMQ6 to Q6 toward wild type levels, suggesting recovery of lost Coq7p function. Identification of a spontaneous Cld1p loss-of-function mutation illustrated that Cld1p activity was required for coq7 suppression. This observation was further supported by HPLC-ESI-MS/MS profiling of monolysocardiolipin, the product of Cld1p. In summary, our results present a novel example of a lipid remodeling enzyme reversing a mitochondrial ubiquinone insufficiency by facilitating recovery of hypomorphic enzymatic function.
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35
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Mitochondrial translation and cellular stress response. Cell Tissue Res 2016; 367:21-31. [DOI: 10.1007/s00441-016-2460-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/20/2016] [Indexed: 01/08/2023]
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36
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Parishin from Gastrodia elata Extends the Lifespan of Yeast via Regulation of Sir2/Uth1/TOR Signaling Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:4074690. [PMID: 27429709 PMCID: PMC4939362 DOI: 10.1155/2016/4074690] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/11/2016] [Accepted: 05/29/2016] [Indexed: 11/17/2022]
Abstract
Parishin is a phenolic glucoside isolated from Gastrodia elata, which is an important traditional Chinese medicine; this glucoside significantly extended the replicative lifespan of K6001 yeast at 3, 10, and 30 μM. To clarify its mechanism of action, assessment of oxidative stress resistance, superoxide dismutase (SOD) activity, malondialdehyde (MDA), and reactive oxygen species (ROS) assays, replicative lifespans of sod1, sod2, uth1, and skn7 yeast mutants, and real-time quantitative PCR (RT-PCR) analysis were conducted. The significant increase of cell survival rate in oxidative stress condition was observed in parishin-treated groups. Silent information regulator 2 (Sir2) gene expression and SOD activity were significantly increased after treating parishin in normal condition. Meanwhile, the levels of ROS and MDA in yeast were significantly decreased. The replicative lifespans of sod1, sod2, uth1, and skn7 mutants of K6001 yeast were not affected by parishin. We also found that parishin could decrease the gene expression of TORC1, ribosomal protein S26A (RPS26A), and ribosomal protein L9A (RPL9A) in the target of rapamycin (TOR) signaling pathway. Gene expression levels of RPS26A and RPL9A in uth1, as well as in uth1, sir2 double mutants, were significantly lower than those of the control group. Besides, TORC1 gene expression in uth1 mutant of K6001 yeast was inhibited significantly. These results suggested that parishin exhibited antiaging effects via regulation of Sir2/Uth1/TOR signaling pathway.
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37
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Abstract
Recently, efforts have been made to characterize the hallmarks that accompany and
contribute to the phenomenon of aging, as most relevant for humans 1. Remarkably, studying the finite lifespan
of the single cell eukaryote budding yeast (recently reviewed in 2 and 3) has been paramount for our understanding of aging. Here, we
compile observations from literature over the past decades of research on
replicatively aging yeast to highlight how the hallmarks of aging in humans are
present in yeast. We find strong evidence for the majority of these, and
summarize how yeast aging is especially characterized by the hallmarks of
genomic instability, epigenetic alterations, loss of proteostasis, deregulated
nutrient sensing, and mitochondrial dysfunction.
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Affiliation(s)
- Georges E Janssens
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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38
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Hughes AL, Hughes CE, Henderson KA, Yazvenko N, Gottschling DE. Selective sorting and destruction of mitochondrial membrane proteins in aged yeast. eLife 2016; 5. [PMID: 27097106 PMCID: PMC4889329 DOI: 10.7554/elife.13943] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 04/18/2016] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial dysfunction is a hallmark of aging, and underlies the development of many diseases. Cells maintain mitochondrial homeostasis through a number of pathways that remodel the mitochondrial proteome or alter mitochondrial content during times of stress or metabolic adaptation. Here, using yeast as a model system, we identify a new mitochondrial degradation system that remodels the mitochondrial proteome of aged cells. Unlike many common mitochondrial degradation pathways, this system selectively removes a subset of membrane proteins from the mitochondrial inner and outer membranes, while leaving the remainder of the organelle intact. Selective removal of preexisting proteins is achieved by sorting into a mitochondrial-derived compartment, or MDC, followed by release through mitochondrial fission and elimination by autophagy. Formation of MDCs requires the import receptors Tom70/71, and failure to form these structures exacerbates preexisting mitochondrial dysfunction, suggesting that the MDC pathway provides protection to mitochondria in times of stress.
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Affiliation(s)
- Adam L Hughes
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Casey E Hughes
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Kiersten A Henderson
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Nina Yazvenko
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Daniel E Gottschling
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
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39
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Chen KL, Crane MM, Kaeberlein M. Microfluidic technologies for yeast replicative lifespan studies. Mech Ageing Dev 2016; 161:262-269. [PMID: 27015709 DOI: 10.1016/j.mad.2016.03.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 01/02/2023]
Abstract
The budding yeast Saccharomyces cerevisiae has been used as a model organism for the study of aging for over 50 years. In this time, the canonical aging experiment-replicative lifespan analysis by manual microdissection-has remained essentially unchanged. Recently, microfluidic technologies have been developed that may be able to substitute for this time- and labor-intensive procedure. These technologies also allow cell physiology to be observed throughout the entire lifetime. Here, we review these devices, novel observations they have made possible, and some of the current system limitations.
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Affiliation(s)
- Kenneth L Chen
- Department of Pathology, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Matthew M Crane
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, USA.
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40
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Kakolyri M, Margaritou A, Tiligada E. Dimethyl sulphoxide modifies growth and senescence and induces the non-revertible petite phenotype in yeast. FEMS Yeast Res 2016; 16:fow008. [PMID: 26833420 DOI: 10.1093/femsyr/fow008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 11/12/2022] Open
Abstract
Dimethyl sulphoxide is extensively used in chemical, pharmaceutical and biomedical applications, but its specific biological actions remain largely elusive. The aim of this study was to comprehensively explore the effects of dimethyl sulphoxide on eukaryotic growth and senescence by using the budding yeast Saccharomyces cerevisiae as a reliable model organism. Rather than focusing on single cells or on either the replicative or the chronological lifespan approach, well-established microbiological procedures were integrated to monitor a combination of physiological parameters. Cell proliferation, survival, reproductive competence and morphology were recorded at various time points during incubation of asynchronous yeast populations with increasing concentrations of dimethyl sulphoxide. The findings demonstrated a dose-dependent inhibitory effect of the compound on yeast proliferation, survival and reproduction. In parallel, dimethyl sulphoxide induced the acquisition of the non-revertible petite phenotype and promoted morphological alterations that characterize senescence, driving the yeast populations towards the reproductive incompetent state. These findings point to the need for the investigation of the complex cellular and/or molecular mechanisms underlying the actions of dimethyl sulphoxide in eukaryotic cells and for the evaluation of their exploitation potential.
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Affiliation(s)
- Maria Kakolyri
- Department of Pharmacology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece
| | - Aikaterini Margaritou
- Department of Pharmacology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece
| | - Ekaterini Tiligada
- Department of Pharmacology, Medical School, National and Kapodistrian University of Athens, GR-11527 Athens, Greece
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41
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Janssens GE, Meinema AC, González J, Wolters JC, Schmidt A, Guryev V, Bischoff R, Wit EC, Veenhoff LM, Heinemann M. Protein biogenesis machinery is a driver of replicative aging in yeast. eLife 2015; 4:e08527. [PMID: 26422514 PMCID: PMC4718733 DOI: 10.7554/elife.08527] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/29/2015] [Indexed: 12/22/2022] Open
Abstract
An integrated account of the molecular changes occurring during the process of cellular aging is crucial towards understanding the underlying mechanisms. Here, using novel culturing and computational methods as well as latest analytical techniques, we mapped the proteome and transcriptome during the replicative lifespan of budding yeast. With age, we found primarily proteins involved in protein biogenesis to increase relative to their transcript levels. Exploiting the dynamic nature of our data, we reconstructed high-level directional networks, where we found the same protein biogenesis-related genes to have the strongest ability to predict the behavior of other genes in the system. We identified metabolic shifts and the loss of stoichiometry in protein complexes as being consequences of aging. We propose a model whereby the uncoupling of protein levels of biogenesis-related genes from their transcript levels is causal for the changes occurring in aging yeast. Our model explains why targeting protein synthesis, or repairing the downstream consequences, can serve as interventions in aging.
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Affiliation(s)
- Georges E Janssens
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anne C Meinema
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Javier González
- Probability and Statistics, Johann Bernoulli Institute of Mathematics and Computer Science, University of Groningen, Groningen, The Netherlands
| | - Justina C Wolters
- Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | | | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ernst C Wit
- Probability and Statistics, Johann Bernoulli Institute of Mathematics and Computer Science, University of Groningen, Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Sen P, Dang W, Donahue G, Dai J, Dorsey J, Cao X, Liu W, Cao K, Perry R, Lee JY, Wasko BM, Carr DT, He C, Robison B, Wagner J, Gregory BD, Kaeberlein M, Kennedy BK, Boeke JD, Berger SL. H3K36 methylation promotes longevity by enhancing transcriptional fidelity. Genes Dev 2015; 29:1362-76. [PMID: 26159996 PMCID: PMC4511212 DOI: 10.1101/gad.263707.115] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Sen et al. find that lack of sustained histone H3K36 methylation is commensurate with increased cryptic transcription in a subset of genes in old cells and with shorter life span. In contrast, deletion of the K36me2/3 demethylase Rph1 increases H3K36me3 within these genes, suppresses cryptic transcript initiation, and extends life span. Epigenetic mechanisms, including histone post-translational modifications, control longevity in diverse organisms. Relatedly, loss of proper transcriptional regulation on a global scale is an emerging phenomenon of shortened life span, but the specific mechanisms linking these observations remain to be uncovered. Here, we describe a life span screen in Saccharomyces cerevisiae that is designed to identify amino acid residues of histones that regulate yeast replicative aging. Our results reveal that lack of sustained histone H3K36 methylation is commensurate with increased cryptic transcription in a subset of genes in old cells and with shorter life span. In contrast, deletion of the K36me2/3 demethylase Rph1 increases H3K36me3 within these genes, suppresses cryptic transcript initiation, and extends life span. We show that this aging phenomenon is conserved, as cryptic transcription also increases in old worms. We propose that epigenetic misregulation in aging cells leads to loss of transcriptional precision that is detrimental to life span, and, importantly, this acceleration in aging can be reversed by restoring transcriptional fidelity.
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Affiliation(s)
- Payel Sen
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Weiwei Dang
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Junbiao Dai
- High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jean Dorsey
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Xiaohua Cao
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wei Liu
- High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Kajia Cao
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Rocco Perry
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jun Yeop Lee
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Daniel T Carr
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Chong He
- The Buck Institute of Research on Aging, Novato, California 94945, USA
| | - Brett Robison
- The Buck Institute of Research on Aging, Novato, California 94945, USA
| | - John Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Brian K Kennedy
- The Buck Institute of Research on Aging, Novato, California 94945, USA
| | - Jef D Boeke
- High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; Institute for Systems Genetics, New York University Langone Medical Center, New York, New York 10016, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Fontana L, Partridge L. Promoting health and longevity through diet: from model organisms to humans. Cell 2015; 161:106-118. [PMID: 25815989 DOI: 10.1016/j.cell.2015.02.020] [Citation(s) in RCA: 768] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 12/19/2022]
Abstract
Reduced food intake, avoiding malnutrition, can ameliorate aging and aging-associated diseases in invertebrate model organisms, rodents, primates, and humans. Recent findings indicate that meal timing is crucial, with both intermittent fasting and adjusted diurnal rhythm of feeding improving health and function, in the absence of changes in overall intake. Lowered intake of particular nutrients rather than of overall calories is also key, with protein and specific amino acids playing prominent roles. Nutritional modulation of the microbiome can also be important, and there are long-term, including inter-generational, effects of diet. The metabolic, molecular, and cellular mechanisms that mediate both improvement in health during aging to diet and genetic variation in the response to diet are being identified. These new findings are opening the way to specific dietary and pharmacological interventions to recapture the full potential benefits of dietary restriction, which humans can find difficult to maintain voluntarily.
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Affiliation(s)
- Luigi Fontana
- Division of Geriatrics and Nutritional Science, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Clinical and Experimental Science, Brescia University, 25123 Brescia, Italy; CEINGE Biotecnologie Avanzate, 80145 Napoli, Italy.
| | - Linda Partridge
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Institute of Healthy Ageing and Department of Genetics, Environment, and Evolution, University College London, London WC1E 6BT, UK.
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He C, Tsuchiyama SK, Nguyen QT, Plyusnina EN, Terrill SR, Sahibzada S, Patel B, Faulkner AR, Shaposhnikov MV, Tian R, Tsuchiya M, Kaeberlein M, Moskalev AA, Kennedy BK, Polymenis M. Enhanced longevity by ibuprofen, conserved in multiple species, occurs in yeast through inhibition of tryptophan import. PLoS Genet 2014; 10:e1004860. [PMID: 25521617 PMCID: PMC4270464 DOI: 10.1371/journal.pgen.1004860] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/29/2014] [Indexed: 11/29/2022] Open
Abstract
The common non-steroidal anti-inflammatory drug ibuprofen has been associated with a reduced risk of some age-related pathologies. However, a general pro-longevity role for ibuprofen and its mechanistic basis remains unclear. Here we show that ibuprofen increased the lifespan of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster, indicative of conserved eukaryotic longevity effects. Studies in yeast indicate that ibuprofen destabilizes the Tat2p permease and inhibits tryptophan uptake. Loss of Tat2p increased replicative lifespan (RLS), but ibuprofen did not increase RLS when Tat2p was stabilized or in an already long-lived strain background impaired for aromatic amino acid uptake. Concomitant with lifespan extension, ibuprofen moderately reduced cell size at birth, leading to a delay in the G1 phase of the cell cycle. Similar changes in cell cycle progression were evident in a large dataset of replicatively long-lived yeast deletion strains. These results point to fundamental cell cycle signatures linked with longevity, implicate aromatic amino acid import in aging and identify a largely safe drug that extends lifespan across different kingdoms of life. Aging is the greatest risk factor for many diseases, which together account for the majority of global deaths and healthcare costs. Here we show that the common drug ibuprofen increases the lifespan of yeast, worms and flies, indicative of conserved longevity effects. In budding yeast, an excellent model of cellular longevity mechanisms, ibuprofen's pro-longevity action is independent of its known anti-inflammatory role. We show that the critical function of ibuprofen in longevity is to inhibit the uptake of aromatic amino acids, by destabilizing the high-affinity tryptophan permease. We further show that ibuprofen alters cell cycle progression. Mirroring the effects of ibuprofen, we found that most yeast long-lived mutants were also similarly affected in cell cycle progression. These findings identify a safe drug that extends the lifespan of divergent organisms and reveal fundamental cellular properties associated with longevity.
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Affiliation(s)
- Chong He
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Scott K. Tsuchiyama
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Quynh T. Nguyen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Ekaterina N. Plyusnina
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
- Syktyvkar State University, Syktyvkar, Russia
| | - Samuel R. Terrill
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Sarah Sahibzada
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Bhumil Patel
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Alena R. Faulkner
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Mikhail V. Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
- Syktyvkar State University, Syktyvkar, Russia
| | - Ruilin Tian
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Mitsuhiro Tsuchiya
- Buck Institute for Research on Aging, Novato, California, United States of America
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Alexey A. Moskalev
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia
- Syktyvkar State University, Syktyvkar, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - Brian K. Kennedy
- Buck Institute for Research on Aging, Novato, California, United States of America
- * E-mail: (BKK); (MP)
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (BKK); (MP)
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Spivey EC, Xhemalce B, Shear JB, Finkelstein IJ. 3D-printed microfluidic microdissector for high-throughput studies of cellular aging. Anal Chem 2014; 86:7406-12. [PMID: 24992972 PMCID: PMC4636036 DOI: 10.1021/ac500893a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to their short lifespan, rapid division, and ease of genetic manipulation, yeasts are popular model organisms for studying aging in actively dividing cells. To study replicative aging over many cell divisions, individual cells must be continuously separated from their progeny via a laborious manual microdissection procedure. Microfluidics-based soft-lithography devices have recently been used to automate microdissection of the budding yeast Saccharomyces cerevisiae. However, little is known about replicative aging in Schizosaccharomyces pombe, a rod-shaped yeast that divides by binary fission and shares many conserved biological functions with higher eukaryotes. In this report, we develop a versatile multiphoton lithography method that enables rapid fabrication of three-dimensional master structures for polydimethylsiloxane (PDMS)-based microfluidics. We exploit the rapid prototyping capabilities of multiphoton lithography to create and characterize a cell-capture device that is capable of high-resolution microscopic observation of hundreds of individual S. pombe cells. By continuously removing the progeny cells, we demonstrate that cell growth and protein aggregation can be tracked in individual cells for over ~100 h. Thus, the fission yeast lifespan microdissector (FYLM) provides a powerful on-chip microdissection platform that will enable high-throughput studies of aging in rod-shaped cells.
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Affiliation(s)
- Eric C. Spivey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712
| | - Blerta Xhemalce
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
| | - Jason B. Shear
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, Texas 78712
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46
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Affiliation(s)
- Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
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47
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Spivey EC, Finkelstein IJ. From cradle to grave: high-throughput studies of aging in model organisms. MOLECULAR BIOSYSTEMS 2014; 10:1658-67. [PMID: 24535099 DOI: 10.1039/c3mb70604d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aging-the progressive decline of biological functions-is a universal fact of life. Decades of intense research in unicellular and metazoan model organisms have highlighted that aging manifests at all levels of biological organization - from the decline of individual cells, to tissue and organism degeneration. To better understand the aging process, we must first aim to integrate quantitative biological understanding on the systems and cellular levels. A second key challenge is to then understand the many heterogeneous outcomes that may result in aging cells, and to connect cellular aging to organism-wide degeneration. Addressing these challenges requires the development of high-throughput aging and longevity assays. In this review, we highlight the emergence of high-throughput aging approaches in the most commonly used model organisms. We conclude with a discussion of the critical questions that can be addressed with these new methods.
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Affiliation(s)
- Eric C Spivey
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
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Ganley ARD, Kobayashi T. Ribosomal DNA and cellular senescence: new evidence supporting the connection between rDNA and aging. FEMS Yeast Res 2014; 14:49-59. [DOI: 10.1111/1567-1364.12133] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 12/10/2013] [Accepted: 12/19/2013] [Indexed: 12/19/2022] Open
Affiliation(s)
- Austen R. D. Ganley
- Institute of Natural and Mathematical Sciences; Massey University; Auckland New Zealand
| | - Takehiko Kobayashi
- Division of Cytogenetics; National Institute of Genetics; Mishima Shizuoka Japan
- Department of Genetics; The Graduate University for Advanced Studies; SOKENDAI; Mishima Shizuoka Japan
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49
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Sorokin MI, Knorre DA, Severin FF. Early manifestations of replicative aging in the yeast Saccharomyces cerevisiae. MICROBIAL CELL 2014; 1:37-42. [PMID: 28357208 PMCID: PMC5349164 DOI: 10.15698/mic2014.01.122] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The yeast Saccharomyces cerevisiae is successfully used as a model organism to find genes responsible for lifespan control of higher organisms. As functional decline of higher eukaryotes can start as early as one quarter of the average lifespan, we asked whether S. cerevisiae can be used to model this manifestation of aging. While the average replicative lifespan of S. cerevisiae mother cells ranges between 15 and 30 division cycles, we found that resistances to certain stresses start to decrease much earlier. Looking into the mechanism, we found that knockouts of genes responsible for mitochondria-to-nucleus (retrograde) signaling, RTG1 or RTG3, significantly decrease the resistance of cells that generated more than four daughters, but not of the younger ones. We also found that even young mother cells frequently contain mitochondria with heterogeneous transmembrane potential and that the percentage of such cells correlates with replicative age. Together, these facts suggest that retrograde signaling starts to malfunction in relatively young cells, leading to accumulation of heterogeneous mitochondria within one cell. The latter may further contribute to a decline in stress resistances.
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Affiliation(s)
- Maksim I Sorokin
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Vorobyevy Gory 1, Moscow, Russia. ; Institute of Mitoengineering, Moscow State University, Vorobyevy Gory 1, Moscow, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Vorobyevy Gory 1, Moscow, Russia. ; Institute of Mitoengineering, Moscow State University, Vorobyevy Gory 1, Moscow, Russia
| | - Fedor F Severin
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Vorobyevy Gory 1, Moscow, Russia. ; Institute of Mitoengineering, Moscow State University, Vorobyevy Gory 1, Moscow, Russia
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