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Sunshine AB, Ong GT, Nickerson DP, Carr D, Murakami CJ, Wasko BM, Shemorry A, Merz AJ, Kaeberlein M, Dunham MJ. Aneuploidy shortens replicative lifespan in Saccharomyces cerevisiae. Aging Cell 2016; 15:317-24. [PMID: 26762766 PMCID: PMC4783355 DOI: 10.1111/acel.12443] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2015] [Indexed: 11/28/2022] Open
Abstract
Aneuploidy and aging are correlated; however, a causal link between these two phenomena has remained elusive. Here, we show that yeast disomic for a single native yeast chromosome generally have a decreased replicative lifespan. In addition, the extent of this lifespan deficit correlates with the size of the extra chromosome. We identified a mutation in BUL1 that rescues both the lifespan deficit and a protein trafficking defect in yeast disomic for chromosome 5. Bul1 is an E4 ubiquitin ligase adaptor involved in a protein quality control pathway that targets membrane proteins for endocytosis and destruction in the lysosomal vacuole, thereby maintaining protein homeostasis. Concurrent suppression of the aging and trafficking phenotypes suggests that disrupted membrane protein homeostasis in aneuploid yeast may contribute to their accelerated aging. The data reported here demonstrate that aneuploidy can impair protein homeostasis, shorten lifespan, and may contribute to age-associated phenotypes.
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Affiliation(s)
- Anna B. Sunshine
- Department of Genome SciencesUniversity of WashingtonFoege Building, Room S403B, 3720 15th Ave NE, Box 355065SeattleWA98195‐5065USA
| | - Giang T. Ong
- Department of Genome SciencesUniversity of WashingtonFoege Building, Room S403B, 3720 15th Ave NE, Box 355065SeattleWA98195‐5065USA
| | - Daniel P. Nickerson
- Departments of Biochemistry and Physiology and BiophysicsUniversity of WashingtonRoom HSB J‐355, 1705 NE Pacific St, UW box 357350SeattleWA98195‐7350USA
| | - Daniel Carr
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Christopher J. Murakami
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Brian M. Wasko
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Anna Shemorry
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Alexey J. Merz
- Departments of Biochemistry and Physiology and BiophysicsUniversity of WashingtonRoom HSB J‐355, 1705 NE Pacific St, UW box 357350SeattleWA98195‐7350USA
| | - Matt Kaeberlein
- Department of PathologyUniversity of WashingtonRoom HSB D‐514, 1705 NE Pacific St, Box 357470SeattleWA98195‐7470USA
| | - Maitreya J. Dunham
- Department of Genome SciencesUniversity of WashingtonFoege Building, Room S403B, 3720 15th Ave NE, Box 355065SeattleWA98195‐5065USA
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2
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McCormick MA, Delaney JR, Tsuchiya M, Tsuchiyama S, Shemorry A, Sim S, Chou ACZ, Ahmed U, Carr D, Murakami CJ, Schleit J, Sutphin GL, Wasko BM, Bennett CF, Wang AM, Olsen B, Beyer RP, Bammler TK, Prunkard D, Johnson SC, Pennypacker JK, An E, Anies A, Castanza AS, Choi E, Dang N, Enerio S, Fletcher M, Fox L, Goswami S, Higgins SA, Holmberg MA, Hu D, Hui J, Jelic M, Jeong KS, Johnston E, Kerr EO, Kim J, Kim D, Kirkland K, Klum S, Kotireddy S, Liao E, Lim M, Lin MS, Lo WC, Lockshon D, Miller HA, Moller RM, Muller B, Oakes J, Pak DN, Peng ZJ, Pham KM, Pollard TG, Pradeep P, Pruett D, Rai D, Robison B, Rodriguez AA, Ros B, Sage M, Singh MK, Smith ED, Snead K, Solanky A, Spector BL, Steffen KK, Tchao BN, Ting MK, Vander Wende H, Wang D, Welton KL, Westman EA, Brem RB, Liu XG, Suh Y, Zhou Z, Kaeberlein M, Kennedy BK. A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging. Cell Metab 2015; 22:895-906. [PMID: 26456335 PMCID: PMC4862740 DOI: 10.1016/j.cmet.2015.09.008] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/31/2015] [Accepted: 09/08/2015] [Indexed: 02/05/2023]
Abstract
Many genes that affect replicative lifespan (RLS) in the budding yeast Saccharomyces cerevisiae also affect aging in other organisms such as C. elegans and M. musculus. We performed a systematic analysis of yeast RLS in a set of 4,698 viable single-gene deletion strains. Multiple functional gene clusters were identified, and full genome-to-genome comparison demonstrated a significant conservation in longevity pathways between yeast and C. elegans. Among the mechanisms of aging identified, deletion of tRNA exporter LOS1 robustly extended lifespan. Dietary restriction (DR) and inhibition of mechanistic Target of Rapamycin (mTOR) exclude Los1 from the nucleus in a Rad53-dependent manner. Moreover, lifespan extension from deletion of LOS1 is nonadditive with DR or mTOR inhibition, and results in Gcn4 transcription factor activation. Thus, the DNA damage response and mTOR converge on Los1-mediated nuclear tRNA export to regulate Gcn4 activity and aging.
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Affiliation(s)
- Mark A McCormick
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Joe R Delaney
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Mitsuhiro Tsuchiya
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Scott Tsuchiyama
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Anna Shemorry
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Sylvia Sim
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Umema Ahmed
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Daniel Carr
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Christopher F Bennett
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Adrienne M Wang
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Brady Olsen
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Richard P Beyer
- Department of Occupational and Environmental Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Theodor K Bammler
- Department of Occupational and Environmental Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Donna Prunkard
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Simon C Johnson
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Elroy An
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Arieanna Anies
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Anthony S Castanza
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Eunice Choi
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Nick Dang
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Shiena Enerio
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Marissa Fletcher
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lindsay Fox
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sarani Goswami
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Sean A Higgins
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Molly A Holmberg
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Di Hu
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Jessica Hui
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Monika Jelic
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Ki-Soo Jeong
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Elijah Johnston
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Emily O Kerr
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jin Kim
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Diana Kim
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Katie Kirkland
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Shannon Klum
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Soumya Kotireddy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Eric Liao
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Michael Lim
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Michael S Lin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Winston C Lo
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Dan Lockshon
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Hillary A Miller
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Richard M Moller
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Brian Muller
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Jonathan Oakes
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Diana N Pak
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Zhao Jun Peng
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Kim M Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tom G Pollard
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Prarthana Pradeep
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Dillon Pruett
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Dilreet Rai
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Brett Robison
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Ariana A Rodriguez
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Bopharoth Ros
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Michael Sage
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Manpreet K Singh
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Erica D Smith
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Katie Snead
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Amrita Solanky
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Benjamin L Spector
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Kristan K Steffen
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Bie Nga Tchao
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Marc K Ting
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Helen Vander Wende
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Dennis Wang
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - K Linnea Welton
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Eric A Westman
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Xin-Guang Liu
- Aging Research Institute, Guangdong Medical College, Dongguan 523808, Guangdong, P.R. China
| | - Yousin Suh
- Aging Research Institute, Guangdong Medical College, Dongguan 523808, Guangdong, P.R. China; Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Zhongjun Zhou
- Department of Biochemistry, University of Hong Kong, Hong Kong
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
| | - Brian K Kennedy
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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3
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Dang W, Sutphin GL, Dorsey JA, Otte GL, Cao K, Perry RM, Wanat JJ, Saviolaki D, Murakami CJ, Tsuchiyama S, Robison B, Gregory BD, Vermeulen M, Shiekhattar R, Johnson FB, Kennedy BK, Kaeberlein M, Berger SL. Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response. Cell Metab 2014; 19:952-66. [PMID: 24814484 PMCID: PMC4106248 DOI: 10.1016/j.cmet.2014.04.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/30/2013] [Accepted: 03/31/2014] [Indexed: 12/16/2022]
Abstract
ATP-dependent chromatin remodeling is involved in all DNA transactions and is linked to numerous human diseases. We explored functions of chromatin remodelers during cellular aging. Deletion of ISW2, or mutations inactivating the Isw2 enzyme complex, extends yeast replicative lifespan. This extension by ISW2 deletion is epistatic to the longevity effect of calorie restriction (CR), and this mechanism is distinct from suppression of TOR signaling by CR. Transcriptome analysis indicates that isw2Δ partially mimics an upregulated stress response in CR cells. In particular, isw2Δ cells show an increased response to genotoxic stresses, and the DNA repair enzyme Rad51 is important for isw2Δ-mediated longevity. We show that lifespan is also extended in C. elegans by reducing levels of athp-2, a putative ortholog of Itc1/ACF1, a critical subunit of the enzyme complex. Our findings demonstrate that the ISWI class of ATP-dependent chromatin remodeling complexes plays a conserved role during aging and in CR.
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Affiliation(s)
- Weiwei Dang
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jean A Dorsey
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriel L Otte
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kajia Cao
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rocco M Perry
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer J Wanat
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | - Brett Robison
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michiel Vermeulen
- Department Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | | | - F Brad Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA.
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4
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Schleit J, Johnson SC, Bennett CF, Simko M, Trongtham N, Castanza A, Hsieh EJ, Moller RM, Wasko BM, Delaney JR, Sutphin GL, Carr D, Murakami CJ, Tocchi A, Xian B, Chen W, Yu T, Goswami S, Higgins S, Holmberg M, Jeong KS, Kim JR, Klum S, Liao E, Lin MS, Lo W, Miller H, Olsen B, Peng ZJ, Pollard T, Pradeep P, Pruett D, Rai D, Ros V, Singh M, Spector BL, Wende HV, An EH, Fletcher M, Jelic M, Rabinovitch PS, MacCoss MJ, Han JDJ, Kennedy BK, Kaeberlein M. Molecular mechanisms underlying genotype-dependent responses to dietary restriction. Aging Cell 2013; 12:1050-61. [PMID: 23837470 DOI: 10.1111/acel.12130] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2013] [Indexed: 01/11/2023] Open
Abstract
Dietary restriction (DR) increases lifespan and attenuates age-related phenotypes in many organisms; however, the effect of DR on longevity of individuals in genetically heterogeneous populations is not well characterized. Here, we describe a large-scale effort to define molecular mechanisms that underlie genotype-specific responses to DR. The effect of DR on lifespan was determined for 166 single gene deletion strains in Saccharomyces cerevisiae. Resulting changes in mean lifespan ranged from a reduction of 79% to an increase of 103%. Vacuolar pH homeostasis, superoxide dismutase activity, and mitochondrial proteostasis were found to be strong determinants of the response to DR. Proteomic analysis of cells deficient in prohibitins revealed induction of a mitochondrial unfolded protein response (mtUPR), which has not previously been described in yeast. Mitochondrial proteotoxic stress in prohibitin mutants was suppressed by DR via reduced cytoplasmic mRNA translation. A similar relationship between prohibitins, the mtUPR, and longevity was also observed in Caenorhabditis elegans. These observations define conserved molecular processes that underlie genotype-dependent effects of DR that may be important modulators of DR in higher organisms.
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5
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Delaney JR, Ahmed U, Chou A, Sim S, Carr D, Murakami CJ, Schleit J, Sutphin GL, An EH, Castanza A, Fletcher M, Higgins S, Jelic M, Klum S, Muller B, Peng ZJ, Rai D, Ros V, Singh M, Wende HV, Kennedy BK, Kaeberlein M. Stress profiling of longevity mutants identifies Afg3 as a mitochondrial determinant of cytoplasmic mRNA translation and aging. Aging Cell 2013; 12:156-66. [PMID: 23167605 DOI: 10.1111/acel.12032] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2012] [Indexed: 01/05/2023] Open
Abstract
Although environmental stress likely plays a significant role in promoting aging, the relationship remains poorly understood. To characterize this interaction in a more comprehensive manner, we examined the stress response profiles for 46 long-lived yeast mutant strains across four different stress conditions (oxidative, ER, DNA damage, and thermal), grouping genes based on their associated stress response profiles. Unexpectedly, cells lacking the mitochondrial AAA protease gene AFG3 clustered strongly with long-lived strains lacking cytosolic ribosomal proteins of the large subunit. Similar to these ribosomal protein mutants, afg3Δ cells show reduced cytoplasmic mRNA translation, enhanced resistance to tunicamycin that is independent of the ER unfolded protein response, and Sir2-independent but Gcn4-dependent lifespan extension. These data demonstrate an unexpected link between a mitochondrial protease, cytoplasmic mRNA translation, and aging.
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Affiliation(s)
| | - Umema Ahmed
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Annie Chou
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Sylvia Sim
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Daniel Carr
- Department of Pathology; University of Washington; Seattle; WA; USA
| | | | - Jennifer Schleit
- Department of Pathology; University of Washington; Seattle; WA; USA
| | | | - Elroy H. An
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Anthony Castanza
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Marissa Fletcher
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Sean Higgins
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Monika Jelic
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Shannon Klum
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Brian Muller
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Zhao J. Peng
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Dilreet Rai
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Vanessa Ros
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Minnie Singh
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Helen V. Wende
- Department of Pathology; University of Washington; Seattle; WA; USA
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6
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Delaney JR, Sutphin GL, Dulken B, Sim S, Kim JR, Robison B, Schleit J, Murakami CJ, Carr D, An EH, Choi E, Chou A, Fletcher M, Jelic M, Liu B, Lockshon D, Moller RM, Pak DN, Peng Q, Peng ZJ, Pham KM, Sage M, Solanky A, Steffen KK, Tsuchiya M, Tsuchiyama S, Johnson S, Raabe C, Suh Y, Zhou Z, Liu X, Kennedy BK, Kaeberlein M. Sir2 deletion prevents lifespan extension in 32 long-lived mutants. Aging Cell 2011; 10:1089-91. [PMID: 21902802 DOI: 10.1111/j.1474-9726.2011.00742.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Activation of Sir2 orthologs is proposed to increase lifespan downstream of dietary restriction. Here, we describe an examination of the effect of 32 different lifespan-extending mutations and four methods of DR on replicative lifespan (RLS) in the short-lived sir2Δ yeast strain. In every case, deletion of SIR2 prevented RLS extension; however, RLS extension was restored when both SIR2 and FOB1 were deleted in several cases, demonstrating that SIR2 is not directly required for RLS extension. These findings indicate that suppression of the sir2Δ lifespan defect is a rare phenotype among longevity interventions and suggest that sir2Δ cells senesce rapidly by a mechanism distinct from that of wild-type cells. They also demonstrate that failure to observe lifespan extension in a short-lived background, such as cells or animals lacking sirtuins, should be interpreted with caution.
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Affiliation(s)
- Joe R Delaney
- Department of Pathology, University of Washington, Seattle, WA, USA
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7
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Murakami CJ, Wall V, Basisty N, Kaeberlein M. Composition and acidification of the culture medium influences chronological aging similarly in vineyard and laboratory yeast. PLoS One 2011; 6:e24530. [PMID: 21949725 PMCID: PMC3176285 DOI: 10.1371/journal.pone.0024530] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 08/11/2011] [Indexed: 11/17/2022] Open
Abstract
Chronological aging has been studied extensively in laboratory yeast by culturing cells into stationary phase in synthetic complete medium with 2% glucose as the carbon source. During this process, acidification of the culture medium occurs due to secretion of organic acids, including acetic acid, which limits survival of yeast cells. Dietary restriction or buffering the medium to pH 6 prevents acidification and increases chronological life span. Here we set out to determine whether these effects are specific to laboratory-derived yeast by testing the chronological aging properties of the vineyard yeast strain RM11. Similar to the laboratory strain BY4743 and its haploid derivatives, RM11 and its haploid derivatives displayed increased chronological life span from dietary restriction, buffering the pH of the culture medium, or aging in rich medium. RM11 and BY4743 also displayed generally similar aging and growth characteristics when cultured in a variety of different carbon sources. These data support the idea that mechanisms of chronological aging are similar in both the laboratory and vineyard strains.
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Affiliation(s)
- Christopher J Murakami
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
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8
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Kruegel U, Robison B, Dange T, Kahlert G, Delaney JR, Kotireddy S, Tsuchiya M, Tsuchiyama S, Murakami CJ, Schleit J, Sutphin G, Carr D, Tar K, Dittmar G, Kaeberlein M, Kennedy BK, Schmidt M. Elevated proteasome capacity extends replicative lifespan in Saccharomyces cerevisiae. PLoS Genet 2011; 7:e1002253. [PMID: 21931558 PMCID: PMC3169524 DOI: 10.1371/journal.pgen.1002253] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 07/06/2011] [Indexed: 12/23/2022] Open
Abstract
Aging is characterized by the accumulation of damaged cellular macromolecules caused by declining repair and elimination pathways. An integral component employed by cells to counter toxic protein aggregates is the conserved ubiquitin/proteasome system (UPS). Previous studies have described an age-dependent decline of proteasomal function and increased longevity correlates with sustained proteasome capacity in centenarians and in naked mole rats, a long-lived rodent. Proof for a direct impact of enhanced proteasome function on longevity, however, is still lacking. To determine the importance of proteasome function in yeast aging, we established a method to modulate UPS capacity by manipulating levels of the UPS–related transcription factor Rpn4. While cells lacking RPN4 exhibit a decreased non-adaptable proteasome pool, loss of UBR2, an ubiquitin ligase that regulates Rpn4 turnover, results in elevated Rpn4 levels, which upregulates UPS components. Increased UPS capacity significantly enhances replicative lifespan (RLS) and resistance to proteotoxic stress, while reduced UPS capacity has opposing consequences. Despite tight transcriptional co-regulation of the UPS and oxidative detoxification systems, the impact of proteasome capacity on lifespan is independent of the latter, since elimination of Yap1, a key regulator of the oxidative stress response, does not affect lifespan extension of cells with higher proteasome capacity. Moreover, since elevated proteasome capacity results in improved clearance of toxic huntingtin fragments in a yeast model for neurodegenerative diseases, we speculate that the observed lifespan extension originates from prolonged elimination of damaged proteins in old mother cells. Epistasis analyses indicate that proteasome-mediated modulation of lifespan is at least partially distinct from dietary restriction, Tor1, and Sir2. These findings demonstrate that UPS capacity determines yeast RLS by a mechanism that is distinct from known longevity pathways and raise the possibility that interventions to promote enhanced proteasome function will have beneficial effects on longevity and age-related disease in humans. The ubiquitin/proteasome system (UPS) is an integral part of the machinery that maintains cellular protein homeostasis and represents the major pathway for specific protein degradation in the cytoplasm and nuclei of eukaryotic cells. Its proteolytic capacity declines with age. In parallel, substrate load for the UPS increases in aging cells due to accumulated protein damage. This imbalance is thought to be an origin for the frequently observed accumulation of protein aggregates in aged cells and is thought to contribute to age-related cellular dysfunction. In this study, we investigated the impact of proteasome capacity on replicative lifespan in Saccharomyces cerevisiae using a genetic system that allows manipulation of UPS abundance at the transcriptional level. The results obtained reveal a positive correlation between proteasome capacity and longevity, with reduced lifespan in cells with low proteasome abundance or activity and strong lifespan extension upon up-regulation of the UPS in a mechanism that is at least partially independent of known yeast longevity modulating pathways. The same correlation is observed for oxidative and protein stress tolerance and clearance of toxic huntingtin fragments in a yeast model for neurodegenerative diseases, suggesting that lifespan extension by increased proteasome capacity is caused by improved protein homeostasis.
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Affiliation(s)
- Undine Kruegel
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Brett Robison
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Buck Institute, Novato, California, United States of America
| | - Thomas Dange
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Günther Kahlert
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Joe R. Delaney
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Soumya Kotireddy
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | | | | | - Christopher J. Murakami
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - George Sutphin
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Daniel Carr
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Krisztina Tar
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Gunnar Dittmar
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (MS); (BKK); (MK)
| | - Brian K. Kennedy
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Buck Institute, Novato, California, United States of America
- * E-mail: (MS); (BKK); (MK)
| | - Marion Schmidt
- Department of Biochemistry, Albert Einstein College of Medicine, New York, New York, United States of America
- * E-mail: (MS); (BKK); (MK)
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Burtner CR, Murakami CJ, Olsen B, Kennedy BK, Kaeberlein M. A genomic analysis of chronological longevity factors in budding yeast. Cell Cycle 2011; 10:1385-96. [PMID: 21447998 DOI: 10.4161/cc.10.9.15464] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chronological life span (CLS) has been studied as an aging paradigm in yeast. A few conserved aging genes have been identified that modulate both chronological and replicative longevity in yeast as well as longevity in the nematode Caenorhabditis elegans; however, a comprehensive analysis of the relationship between genetic control of chronological longevity and aging in other model systems has yet to be reported. To address this question, we performed a functional genomic analysis of chronological longevity for 550 single-gene deletion strains, which accounts for approximately 12% of the viable homozygous diploid deletion strains in the yeast ORF deletion collection. This study identified 33 previously unknown determinants of CLS. We found no significant enrichment for enhanced CLS among deletions corresponding to yeast orthologs of worm aging genes or among replicatively long-lived deletion strains, although a trend toward overlap was noted. In contrast, a subset of gene deletions identified from a screen for reduced acidification of culture media during growth to stationary phase was enriched for increased CLS. These results suggest that genetic control of CLS under the most commonly utilized assay conditions does not strongly overlap with longevity determinants in C. elegans, with the existing confined to a small number of genetic pathways. These data also further support the model that acidification of the culture medium plays an important role in survival during chronological aging in synthetic medium, and suggest that chronological aging studies using alternate medium conditions may be more informative with regard to aging of multicellular eukaryotes.
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Delaney JR, Murakami CJ, Olsen B, Kennedy BK, Kaeberlein M. Quantitative evidence for early life fitness defects from 32 longevity-associated alleles in yeast. Cell Cycle 2011; 10:156-65. [PMID: 21191185 DOI: 10.4161/cc.10.1.14457] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Reduced fecundity has been associated with some alleles that enhance longevity in invertebrate and mammalian models. This observation has been suggested to support the antagonistic pleiotropy theory of aging, which predicts that alleles of some genes promoting fitness early in life have detrimental effects later in life that limit survival. In only a few cases, however, has the relative fitness of long-lived mutants been quantified through direct competition with the wild type genotype. Here we report the first comprehensive analysis of longevity/fitness trade-offs by measuring the relative fitness of 49 long-lived yeast variants in a direct competition assay with wild type cells. We find that 32 (65%) of these variants show a significant defect in fitness in this competition assay. In 26 (81%) of these cases, this reduction in fitness can be partially accounted for by reduced maximal growth rate during early life, usually resulting from a G0/G1-specific cell cycle defect. A majority of the less fit longevity-enhancing variants are associated with reduced mRNA translation. These findings are therefore consistent with the idea that enhanced longevity often comes with a fitness cost and suggest that this cost is often associated with variation in a subset of longevity factors, such as those regulating mRNA translation, growth, and reproduction.
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Affiliation(s)
- Joe R Delaney
- Department of Pathology, University of Washington, Seattle, WA, USA
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11
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Olsen B, Murakami CJ, Kaeberlein M. YODA: software to facilitate high-throughput analysis of chronological life span, growth rate, and survival in budding yeast. BMC Bioinformatics 2010; 11:141. [PMID: 20298554 PMCID: PMC2850362 DOI: 10.1186/1471-2105-11-141] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 03/18/2010] [Indexed: 11/13/2022] Open
Abstract
Background The budding yeast Saccharomyces cerevisiae is one of the most widely studied model organisms in aging-related science. Although several genetic modifiers of yeast longevity have been identified, the utility of this system for longevity studies has been limited by a lack of high-throughput assays for quantitatively measuring survival of individual yeast cells during aging. Results Here we describe the Yeast Outgrowth Data Analyzer (YODA), an automated system for analyzing population survival of yeast cells based on the kinetics of outgrowth measured by optical density over time. YODA has been designed specifically for quantification of yeast chronological life span, but can also be used to quantify growth rate and survival of yeast cells in response to a variety of different conditions, including temperature, nutritional composition of the growth media, and chemical treatments. YODA is optimized for use with a Bioscreen C MBR shaker/incubator/plate reader, but is also amenable to use with any standard plate reader or spectrophotometer. Conclusions We estimate that use of YODA as described here reduces the effort and resources required to measure chronological life span and analyze the resulting data by at least 15-fold.
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Affiliation(s)
- Brady Olsen
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
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12
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Abstract
The molecular mechanisms that cause organismal aging are a topic of intense scrutiny and debate. Dietary restriction extends the life span of many organisms, including yeast, and efforts are underway to understand the biochemical and genetic pathways that regulate this life span extension in model organisms. Here we describe the mechanism by which dietary restriction extends yeast chronological life span, defined as the length of time stationary yeast cells remain viable in a quiescent state. We find that aging under standard culture conditions is the result of a cell-extrinsic component that is linked to the pH of the culture medium. We identify acetic acid as a cell-extrinsic mediator of cell death during chronological aging, and demonstrate that dietary restriction, growth in a non-fermentable carbon source, or transferring cells to water increases chronological life span by reducing or eliminating extracellular acetic acid. Other life span extending environmental and genetic interventions, such as growth in high osmolarity media, deletion of SCH9 or RAS2, increase cellular resistance to acetic acid. We conclude that acetic acid induced mortality is the primary mechanism of chronological aging in yeast under standard conditions.
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Affiliation(s)
- Christopher R Burtner
- Department of Biochemistry, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA
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13
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Abstract
Yeast is a useful model organism to study the genetic and biochemical mechanisms of aging. Genomic studies of aging in yeast have been limited, however, by traditional methodologies that require a large investment of labor and resources. In this chapter, we describe a newly-developed method for quantitatively measuring the chronological life span of each strain contained in the yeast ORF deletion collection. Our approach involves determining population survival by monitoring outgrowth kinetics using a Bioscreen C MBR shaker/incubator/plate reader. This method has accuracy comparable to traditional assays, while allowing for higher throughput and decreased variability in measurement.
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14
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Murakami CJ, Burtner CR, Kennedy BK, Kaeberlein M. A method for high-throughput quantitative analysis of yeast chronological life span. J Gerontol A Biol Sci Med Sci 2008; 63:113-21. [PMID: 18314444 DOI: 10.1093/gerona/63.2.113] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Chronological aging in yeast has been studied by maintaining cells in a quiescent-like stationary phase culture and monitoring cell survival over time. The composition of the growth medium can have a profound influence on chronological aging. For example, dietary restriction accomplished by lowering the glucose concentration of the medium significantly increases life span. Here we report a novel high-throughput method for measuring yeast chronological life span by monitoring outgrowth of aging cells using a Bioscreen C MBR machine. We show that this method provides survival data comparable to traditional methods, but with decreased variability. In addition to reducing the glucose concentration, we find that elevated amino acid levels or increased osmolarity of the growth medium is sufficient to increase chronological life span. We also report that life-span extension from dietary restriction does not require any of the five yeast sirtuins (Sir2, Hst1, Hst2, Hst3, or Hst4) either alone or in combination.
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Affiliation(s)
- Christopher J Murakami
- Department of Pathology, University of Washington, Box 357470, Seattle, WA 98195-7470, USA
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