A Microarray-Based Genetic Screen for Yeast Chronological Aging Factors

Abstract

Model organisms have played an important role in the elucidation of multiple genes and cellular processes that regulate aging. In this study we utilized the budding yeast, Saccharomyces cerevisiae, in a large-scale screen for genes that function in the regulation of chronological lifespan, which is defined by the number of days that non-dividing cells remain viable. A pooled collection of viable haploid gene deletion mutants, each tagged with unique identifying DNA “bar-code” sequences was chronologically aged in liquid culture. Viable mutants in the aging population were selected at several time points and then detected using a microarray DNA hybridization technique that quantifies abundance of the barcode tags. Multiple short- and long-lived mutants were identified using this approach. Among the confirmed short-lived mutants were those defective for autophagy, indicating a key requirement for the recycling of cellular organelles in longevity. Defects in autophagy also prevented lifespan extension induced by limitation of amino acids in the growth media. Among the confirmed long-lived mutants were those defective in the highly conserved de novo purine biosynthesis pathway (the ADE genes), which ultimately produces IMP and AMP. Blocking this pathway extended lifespan to the same degree as calorie (glucose) restriction. A recently discovered cell-extrinsic mechanism of chronological aging involving acetic acid secretion and toxicity was suppressed in a long-lived ade4Δ mutant and exacerbated by a short-lived atg16Δ autophagy mutant. The identification of multiple novel effectors of yeast chronological lifespan will greatly aid in the elucidation of mechanisms that cells and organisms utilize in slowing down the aging process.

The role of protein clearance mechanisms in organismal ageing and age-related diseases

“…Similarly, PA28g deficiency promotes premature ageing in mice 56 . In yeast, a genetic screen searching for ageing factors identified multiple short-lived mutants with autophagy defects 57 . In C. elegans, decreased expression of several autophagic genes (atg1, atg7, atg12, bec1 and atg18) shortens its lifespan, supporting the role of autophagy in longevity 58,59 .…”

Genomewide mechanisms of chronological longevity by dietary restriction in budding yeast

“…S3b). Notably, the rate of validation is considerably higher compared to screening assays that have used pooled yeast deletion strains (6–31% hits validated) (Fabrizio et al., 2010; Matecic et al., 2010). To directly compare the results obtained with the conventional single culture CLS assay and with our high‐throughput screen, we modeled a survival curve from the survival coefficients of the corresponding knockout strains (Fig.…”

“…For instance, a recent systematic study of replicative lifespan of most viable deletion strains revealed that translation, the SAGA complex, and the TCA cycle mediate longevity (McCormick et al., 2015). Several studies have aimed to estimate the stationary‐phase survival of single deletion mutants in parallel (Fabrizio et al., 2010; Garay et al., 2014; Gresham et al., 2011; Matecic et al., 2010; Powers et al., 2006), showing that autophagy, vacuolar protein sorting, regulation of translation, purine metabolism, chromatin remodeling, and the SWR1 complex are major determinants of longevity. However, we are still missing a direct comparison of the lifespan effects of such gene deletions under nutrient‐rich and restricted conditions that would allow to systematically address the mechanisms of longevity by dietary restriction.…”

Model-based identification of drug targets that revert disrupted metabolism and its application to ageing

“…5a, a highly significant enrichment for all treatments was found (Hypergeometric test, P-valueo9.99e-5). Further, we find that MTA's common predictions set is enriched with human orthologs of known lifespan-extending genes in yeast and Caenorhabditis elegans, collated from the SGD database and from the literature 28,[31][32][33]41 (Supplementary Data 4, Permutation test, empirical P-valueo0.02). Finally, a recently published study has examined the correlation between gene expression measured in mice livers and lifespan extension across different diet regimens 42 .…”

“…S4 for a detailed stoichiometric explanation underlying the eicosanoids metabolism prediction). MTA's predictions also include the inosine monophosphate biosynthesis pathway whose inhibition was previously found to extend the CLS of yeast via the allosteric regulation of phosphofructokinase 31 (see Supplementary Note 1 and Supplementary Methods).…”