A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes

Abstract

The respiratory metabolic cycle in budding yeast (Saccharomyces cerevisiae) consists of two phases that are most simply defined phenomenologically: low oxygen consumption (LOC) and high oxygen consumption (HOC). Each phase is associated with the periodic expression of thousands of genes, producing oscillating patterns of gene expression found in synchronized cultures and in single cells of slowly growing unsynchronized cultures. Systematic variation in the durations of the HOC and LOC phases can account quantitatively for well-studied transcriptional responses to growth rate differences. Here we show that a similar mechanism-transitions from the HOC phase to the LOC phase-can account for much of the common environmental stress response (ESR) and for the cross-protection by a preliminary heat stress (or slow growth rate) to subsequent lethal heat stress. Similar to the budding yeast metabolic cycle, we suggest that a metabolic cycle, coupled in a similar way to the ESR, in the distantly related fission yeast, Schizosaccharomyces pombe, and in humans can explain gene expression and respiratory patterns observed in these eukaryotes. Although metabolic cycling is associated with the G0/G1 phase of the cell division cycle of slowly growing budding yeast, transcriptional cycling was detected in the G2 phase of the division cycle in fission yeast, consistent with the idea that respiratory metabolic cycling occurs during the phases of the cell division cycle associated with mass accumulation in these divergent eukaryotes.

FIGURE 1:

Correlation between metabolic cycling, transcriptional ESR, and sensitivity to lethal heat shock. (A) Left, phase-ordered metabolic genes expressed periodically in a budding yeast culture that was YMC synchronized (Tu et al., 2005). The bars on the top correspond to dissolved oxygen in the medium. Right, the corresponding expression levels of the genes, measured by Gasch et al. (2000) during stress (H₂O₂, heat). The gene expression data in this and all other figures are displayed on a log₂ scale (Eisen et al., 1998). (B) Percentage of the cells surviving after 50°C heat shock with duration indicated on the x-axis. Samples were taken from the HOC phase and from the LOC phase of a metabolically synchronized culture growing at μ = 0.10 h⁻¹. The counting error is <10%; see Materials and Methods. The inset shows the same type of heat shock applied to a phosphate-limited asynchronous culture growing at μ = 0.3 h⁻¹ (Lu et al., 2009).

FIGURE 2:

The magnitude of the ESR increases with the growth rate. (A) Comparison of the magnitude of the transcriptional heat shock response at growth rates μ = 0.05 and μ = 0.25 h⁻¹ for all YMC-periodic genes peaking in expression either during the LOC or during the HOC phase. (B) Distribution of fold change in the levels of genes from A whose expression levels change more than fourfold in at least one of the cultures after the heat shock. The p value is computed from a rank sum test. (C) Mechanism that can account for the observed increase in the magnitude of the ESR with growth rate. The gene expression data and the magnitude of the heat-shock response are displayed on a log₂ scale.

FIGURE 3:

CDC periodic genes in fission yeast. Genes expressed periodically in the CDC of fission yeast are arranged by phase of peak expression based on correlation analysis; see Materials and Methods. The data were collected from two independent cultures that were CDC synchronized by elutriation (Rustici et al., 2004). The gene expression data are displayed on a log₂ scale.

FIGURE 4:

Phases of the fission yeast CDC. Mean expression levels of three gene clusters obtained by unsupervised K-means clustering. The gene sets are named after the most significantly enriched GO terms in each cluster. Table 1 lists more significantly enriched GO terms in the biosynthesis cluster. The data were collected from two independent cultures that have been CDC synchronized by elutriation (Rustici et al., 2004) and are converted to z-scores (zero mean and unit variance) and displayed on a log₂ scale.

FIGURE 5:

Correlation between metabolic cycling and stress response. (A) Left, phase-ordered metabolic genes expressed periodically in a budding yeast culture that was YMC synchronized (Tu et al., 2005). Right, their corresponding expression levels measured by Gasch et al. (2000) during stress (H₂O₂, heat). (B) Left, phase-ordered metabolic genes expressed periodically in two fission yeast cultures that were CDC synchronized by elutriation (Rustici et al., 2004). Right, their corresponding expression levels measured by Chen et al. (2003) during stress (H₂O₂, heat, and cadmium). The labels of the two large clusters (biosynthesis and stress) are derived from the most highly enriched GO terms within each cluster. The genes in both panels are ordered based only on their phase of peak expression in the synchronized cultures, and the gene expression data are displayed on a log₂ scale.

FIGURE 6:

Reciprocal regulation of biosynthetic and stress and developmental genes in humans. Clustered gene expression from small sets of stochastically profiled human epithelial cells in a three-dimensional culture model of mammary acinar morphogenesis (Janes et al., 2010). The labels of the clusters (biosynthesis and stress) correspond to the most highly enriched GO terms in each cluster; see Table 2. The gene expression data are displayed on a log₂ scale.

FIGURE 7:

The common ESR in human fibroblasts indicates a reciprocal regulation of biosynthetic and stress genes. The expression levels of ∼6000 genes either increased or decreased consistently across all stress types applied to primary human fibroblasts (Murray et al., 2004). The labels of the clusters (biosynthesis and stress) correspond to highly enriched GO terms in each cluster. The solid red circles correspond to one-, two-, and three-dimensional crowding (Murray et al., 2004). The gene expression data are displayed on a log₂ scale.