Nutritional Homeostasis in Batch and Steady-State Culture of Yeast

Abstract

We studied the physiological response to limitation by diverse nutrients in batch and steady-state (chemostat) cultures of S. cerevisiae. We found that the global pattern of transcription in steady-state cultures in limiting phosphate or sulfate is essentially identical to that of batch cultures growing in the same medium just before the limiting nutrient is completely exhausted. The massive stress response and complete arrest of the cell cycle that occurs when nutrients are fully exhausted in batch cultures is not observed in the chemostat, indicating that the cells in the chemostat are "poor, not starving." Similar comparisons using leucine or uracil auxotrophs limited on leucine or uracil again showed patterns of gene expression in steady-state closely resembling those of corresponding batch cultures just before they exhaust the nutrient. Although there is also a strong stress response in the auxotrophic batch cultures, cell cycle arrest, if it occurs at all, is much less uniform. Many of the differences among the patterns of gene expression between the four nutrient limitations are interpretable in light of known involvement of the genes in stress responses or in the regulation or execution of particular metabolic pathways appropriate to the limiting nutrient. We conclude that cells adjust their growth rate to nutrient availability and maintain homeostasis in the same way in batch and steady state conditions; cells in steady-state cultures are in a physiological condition normally encountered in batch cultures.

Revisiting the role of yeast Sfp1 in ribosome biogenesis and cell size control: a chemostat study

“…Downregulation of the RP genes observed in sfp1D mutants during growth in shake flasks might be a secondary effect due to growth rate defects. Finally, several expression profiles published elsewhere (Saldanha et al, 2004;Wade et al, 2001) together with the observed differences in the promoter regions lend further support to our hypothesis on the differential regulation of RiBi and RP gene clusters.…”

“…In addition, very slow growth rates can be reached while maintaining continuous exponential growth and an optimal physiology (Regenberg et al, 2006;Saldanha et al, 2004). This approach allowed us to grow the reference strain and the sfp1D mutant at the same specific growth rate.…”

“…No evidence of starvation characterizes these slow-growing cultures and the transcription of ribosomal protein genes, an indicator of cellular fitness, is fully active (see Supplementary Table S3, available with the online version of this paper) (Regenberg et al, 2006;Saldanha et al, 2004).…”

Budding YeastSSD1-VRegulates Transcript Levels of Many Longevity Genes and Extends Chronological Life Span in Purified Quiescent Cells

“…Starved auxotrophs have short but variable life spans, depending on the limiting nutrient (Henry, 1973;Boer et al, 2008). They also have a nonuniform arrest (Saldanha et al, 2004), accumulate more reactive oxygen species and DNA fragmentation (Gomes et al, 2007)¤ and exhaust their …”

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns

“…Microarray data have been analyzed by using a variety of statistical tools to detect significant differences in gene expression levels and identify meaningful subgroups of genes exhibiting similar expression patterns (1,2). Correlations and other statistical measures that group genes by profile similarity identify functionally interconnected groups of genes because proteins encoded by genes involved in the same biological process are often coregulated (3,4). However, correlation measures do not provide direct insight into the identity or nature of the gene interactions that give rise to the observed expression patterns.…”