Influence of genotype and nutrition on survival and metabolism of starving yeast

Abstract

Starvation of yeast cultures limited by auxotrophic requirements results in glucose wasting and failure to achieve prompt cell-cycle arrest when compared with starvation for basic natural nutrients like phosphate or sulfate. We measured the survival of yeast auxotrophs upon starvation for different nutrients and found substantial differences: When deprived of leucine or uracil, viability declined exponentially with a half-life of <2 days, whereas when the same strains were deprived of phosphate or sulfate, the half-life was approximately 10 days. The survival rates of nongrowing auxotrophs deprived of uracil or leucine depended on the carbon source available during starvation, but were independent of the carbon source during prior growth. We performed an enrichment procedure for mutants that suppress lethality during auxotrophy starvation. We repeatedly found loss-of-function mutations in a number of functionally related genes. Mutations in PPM1, which methylates protein phosphatase 2A, and target of rapamycin (TOR1) were characterized further. Deletion of PPM1 almost completely suppressed the rapid lethality and substantially suppressed glucose wasting during starvation for leucine or uracil. Suppression by a deletion of TOR1 was less complete. We suggest that, similar to the Warburg effect observed in tumor cells, starving yeast auxotrophs wastes glucose as a consequence of the failure of conserved growth control pathways. Furthermore, we suggest that our results on condition-dependent chronological lifespan have important implications for the interpretation and design of studies on chronological aging.

Fig. 1.

Survival of strain DB8863, measured as colony-forming units, during starvation for phosphate (triangles), sulfate (diamonds), leucine (circles), and uracil (squares). The number of viable cells was normalized to 100% and measured at the onset of starvation (day 0). The average values and SD for three independent replicate experiments are shown. Survival of prototrophs in limiting phosphate or sulfate is identical to that of auxotrophs and is unaffected by added uracil or leucine (data not shown).

Fig. 2.

Survival of strain DB8863, measured as colony-forming units, during leucine starvation in media containing as carbon source ethanol and glycerol (triangles), galactose (squares), or glucose (circles). Cells were pregrown on leucine-limited media containing, as a carbon source, glucose (black symbols), galactose (gray), or ethanol and glycerol (white).

Fig. 3.

Bulk segregant analysis on tiling arrays reveals a single locus on chromosome IV. The difference in signal intensity (resistant pool–sensitive pool) is shown for chromosome IV and the whole genome (Inset).

Fig. 4.

Survival of strain DBY8863 (circles) and isogenic ppm1Δ0 derivative (squares) during leucine starvation, with mean and SD of six independent replicates.

Fig. 5.

Growth and glucose consumption during phosphate and uracil starvation. Triangles, strain DBY8863 during phosphate starvation; squares, strain DBY8863 during uracil starvation; circles, isogenic ppm1Δ0 deletion strain during uracil starvation; open symbols, OD₆₀₀; closed symbols, glucose concentration. Values represent averages and SD of two (DBY8863) or four (ppm1Δ0 deletion strain) independent experiments.

Fig. 6.

Gene neighborhood of genes affected by mutation in the leucine survival screen (orange) and the top-ranking associated genes (green). *, Methylation site; †, added interaction based on evidence published previously (39). See Materials and Methods for details.