Natural variation of chronological aging in the Saccharomyces cerevisiae species reveals diet-dependent mechanisms of life span control

Aging is a complex trait of broad scientific interest, especially because of its intrinsic link with common human diseases. Pioneering work on aging-related mechanisms has been made in Saccharomyces cerevisiae, mainly through the use of deletion collections isogenic to the S288c reference strain. In this study, using a recently published high-throughput approach, we quantified chronological life span (CLS) within a collection of 58 natural strains across seven different conditions. We observed a broad aging variability suggesting the implication of diverse genetic and environmental factors in chronological aging control. Two major Quantitative Trait Loci (QTLs) were identified within a biparental population obtained by crossing two natural isolates with contrasting aging behavior. Detection of these QTLs was dependent upon the nature and concentration of the carbon sources available for growth. In the first QTL, the RIM15 gene was identified as major regulator of aging under low glucose condition, lending further support to the importance of nutrient-sensing pathways in longevity control under calorie restriction. In the second QTL, we could show that the SER1 gene, encoding a conserved aminotransferase of the serine synthesis pathway not previously linked to aging, is causally associated with CLS regulation, especially under high glucose condition. These findings hint toward a new mechanism of life span control involving a trade-off between serine synthesis and aging, most likely through modulation of acetate and trehalose metabolism. More generally it shows that genetic linkage studies across natural strains represent a promising strategy to further unravel the molecular basis of aging.A metabolic block favoring long sweet lifeA Sake yeast strain deficient in producing the protein building block serine lives longer than other yeast strains, especially when exposed to high glucose. A team led by Carole Linster at the University of Luxembourg found a broad variability of lifespan when analyzing more than fifty Saccharomyces cerevisiae strains isolated from around the world. Combining hundreds of lifespan measurements with genotype data from a progeny obtained by crossing the long-lived Sake strain and a short-lived collection strain, they identified two genes playing a pivotal role in causing the contrasting aging behavior of the parents: RIM15, when glucose was limiting and SER1, when glucose was plenty. RIM15 is part of a signaling cascade also regulating aging in mammals; SER1 revealed that a blockage in serine synthesis reprograms metabolism to favor glucose storage and long life.

[1]  Leonid Kruglyak,et al.  Genetic Influences on Translation in Yeast , 2014, bioRxiv.

[2]  Yuya Araki,et al.  A Loss-of-Function Mutation in the PAS Kinase Rim15p Is Related to Defective Quiescence Entry and High Fermentation Rates of Saccharomyces cerevisiae Sake Yeast Strains , 2012, Applied and Environmental Microbiology.

[3]  A. DeLuna,et al.  High-Resolution Profiling of Stationary-Phase Survival Reveals Yeast Longevity Factors and Their Genetic Interactions , 2014, PLoS genetics.

[4]  J. Gancedo Yeast Carbon Catabolite Repression , 1998, Microbiology and Molecular Biology Reviews.

[5]  Robert P. Davey,et al.  Population genomics of domestic and wild yeasts , 2008, Nature.

[6]  Tatiana L. Iouk,et al.  Mitochondrial membrane lipidome defines yeast longevity , 2013, Aging.

[7]  Julien Gagneur,et al.  Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype , 2013, PLoS genetics.

[8]  Michael Davey,et al.  The alternate AP-1 adaptor subunit Apm2 interacts with the Mil1 regulatory protein and confers differential cargo sorting , 2016, Molecular biology of the cell.

[9]  Leopold Parts,et al.  A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes , 2014, Molecular biology and evolution.

[10]  Christopher J. Murakami,et al.  A molecular mechanism of chronological aging in yeast , 2009, Cell cycle.

[11]  Jef D Boeke,et al.  Genome-wide consequences of deleting any single gene. , 2013, Molecular cell.

[12]  G. Kroemer,et al.  Lifespan Extension by Methionine Restriction Requires Autophagy-Dependent Vacuolar Acidification , 2014, PLoS genetics.

[13]  Paul M. Magwene,et al.  The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing , 2011, PLoS Comput. Biol..

[14]  W. G. Hill,et al.  Heritability in the genomics era — concepts and misconceptions , 2008, Nature Reviews Genetics.

[15]  Paul M. Magwene,et al.  The Genetic Architecture of Biofilm Formation in a Clinical Isolate of Saccharomyces cerevisiae , 2013, Genetics.

[16]  Lei M. Li,et al.  Tor1/Sch9-Regulated Carbon Source Substitution Is as Effective as Calorie Restriction in Life Span Extension , 2009, PLoS genetics.

[17]  Júlia Santos,et al.  Dietary Restriction and Nutrient Balance in Aging , 2015, Oxidative medicine and cellular longevity.

[18]  Christopher J. Murakami,et al.  A genomic analysis of chronological longevity factors in budding yeast , 2011, Cell cycle.

[19]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[20]  Christopher J. Murakami,et al.  A method for high-throughput quantitative analysis of yeast chronological life span. , 2008, The journals of gerontology. Series A, Biological sciences and medical sciences.

[21]  Narmada Thanki,et al.  CDD: NCBI's conserved domain database , 2014, Nucleic Acids Res..

[22]  M. Ogur,et al.  Genetic and Physiological Control of Serine and Glycine Biosynthesis in Saccharomyces , 1972, Journal of bacteriology.

[23]  V. Longo,et al.  Regulation of Longevity and Stress Resistance by Sch9 in Yeast , 2001, Science.

[24]  V. Longo,et al.  Chronological aging in Saccharomyces cerevisiae. , 2012, Sub-cellular biochemistry.

[25]  L. Kruglyak,et al.  Genetic Basis of Metabolome Variation in Yeast , 2014, PLoS genetics.

[26]  Anders Blomberg,et al.  Trait Variation in Yeast Is Defined by Population History , 2011, PLoS genetics.

[27]  J. Aris,et al.  Autophagy and amino acid homeostasis are required for chronological longevity in Saccharomyces cerevisiae , 2009, Aging cell.

[28]  Alexander Skupin,et al.  Protocols and Programs for High-Throughput Growth and Aging Phenotyping in Yeast , 2015, PloS one.

[29]  B. Le Bizec,et al.  Simultaneous measurement of plasma concentrations and 13C-enrichment of short-chain fatty acids, lactic acid and ketone bodies by gas chromatography coupled to mass spectrometry. , 2003, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[30]  Matt Kaeberlein,et al.  Lessons on longevity from budding yeast , 2010, Nature.

[31]  L. Kruglyak,et al.  Natural Polymorphism in BUL2 Links Cellular Amino Acid Availability with Chronological Aging and Telomere Maintenance in Yeast , 2011, PLoS genetics.

[32]  L. Kruglyak,et al.  Genetic Dissection of Transcriptional Regulation in Budding Yeast , 2002, Science.

[33]  F Baganz,et al.  Systematic functional analysis of the yeast genome. , 1998, Trends in biotechnology.

[34]  Anders Blomberg,et al.  Ser3p (Yer081wp) and Ser33p (Yil074cp) Are Phosphoglycerate Dehydrogenases in Saccharomyces cerevisiae * , 2003, The Journal of Biological Chemistry.

[35]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[36]  Daniel A. Skelly,et al.  The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen , 2015, Genome research.

[37]  L. Parts,et al.  gitter: A Robust and Accurate Method for Quantification of Colony Sizes From Plate Images , 2014, G3: Genes, Genomes, Genetics.

[38]  Leonid Kruglyak,et al.  Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae , 2009, Nature.

[39]  Jef D. Boeke,et al.  A Microarray-Based Genetic Screen for Yeast Chronological Aging Factors , 2010, PLoS genetics.

[40]  Justin C. Fay,et al.  Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae , 2005, PLoS genetics.

[41]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[42]  Gianni Liti,et al.  Sequence Diversity, Reproductive Isolation and Species Concepts in Saccharomyces , 2006, Genetics.

[43]  S. Oliver,et al.  Chronological Lifespan in Yeast Is Dependent on the Accumulation of Storage Carbohydrates Mediated by Yak1, Mck1 and Rim15 Kinases , 2016, PLoS genetics.

[44]  A. Dudley,et al.  Natural Variation in SER1 and ENA6 Underlie Condition-Specific Growth Defects in Saccharomyces cerevisiae , 2017, G3: Genes, Genomes, Genetics.

[45]  D. Botstein,et al.  Yeast: An Experimental Organism for 21st Century Biology , 2011, Genetics.

[46]  Justin C. Fay,et al.  A Noncomplementation Screen for Quantitative Trait Alleles in Saccharomyces cerevisiae , 2012, G3: Genes | Genomes | Genetics.

[47]  Chao Cheng,et al.  Life Span Extension by Calorie Restriction Depends on Rim15 and Transcription Factors Downstream of Ras/PKA, Tor, and Sch9 , 2007, PLoS genetics.

[48]  K. Entian,et al.  Molecular analysis of the yeast SER1 gene encoding 3-phosphoserine aminotransferase: regulation by general control and serine repression , 1995, Current Genetics.

[49]  Justin C. Fay,et al.  Genomic Sequence Diversity and Population Structure of Saccharomyces cerevisiae Assessed by RAD-seq , 2013, G3: Genes, Genomes, Genetics.

[50]  L. Kruglyak,et al.  Finding the sources of missing heritability in a yeast cross , 2012, Nature.

[51]  B. Kennedy,et al.  Replicative and chronological aging in Saccharomyces cerevisiae. , 2012, Cell metabolism.

[52]  C. Kenyon The genetics of ageing , 2010, Nature.

[53]  B. Kennedy,et al.  Tor-Sch9 deficiency activates catabolism of the ketone body-like acetic acid to promote trehalose accumulation and longevity , 2014, Aging cell.

[54]  Dietmar Schomburg,et al.  MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. , 2009, Analytical chemistry.

[55]  Ruedi Aebersold,et al.  Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A. , 2013, Cell reports.

[56]  Leonid Kruglyak,et al.  Genetic interactions contribute less than additive effects to quantitative trait variation in yeast , 2015, Nature Communications.

[57]  Leonid Kruglyak,et al.  Dissection of genetically complex traits with extremely large pools of yeast segregants , 2010, Nature.

[58]  Daniel R. Richards,et al.  Dissecting the architecture of a quantitative trait locus in yeast , 2002, Nature.

[59]  Dejian Huang,et al.  Independent and Additive Effects of Glutamic Acid and Methionine on Yeast Longevity , 2013, PloS one.