Metabolic-State-Dependent Remodeling of the Transcriptome in Response to Anoxia and Subsequent Reoxygenation in Saccharomyces cerevisiae

Abstract

We conducted a comprehensive genomic analysis of the temporal response of yeast to anaerobiosis (six generations) and subsequent aerobic recovery (Ϸ2 generations) to reveal metabolic-state (galactose versus glucose)-dependent differences in gene network activity and function. Analysis of variance showed that far fewer genes responded (raw P value of <10 ؊8 ) to the O 2 shifts in glucose (1,603 genes) than in galactose (2,388 genes). Gene network analysis reveals that this difference is due largely to the failure of "stress"-activated networks controlled by Msn2/4, Fhl1, MCB, SCB, PAC, and RRPE to transiently respond to the shift to anaerobiosis in glucose as they did in galactose. After Ϸ1 generation of anaerobiosis, the response was similar in both media, beginning with the deactivation of Hap1 and Hap2/3/4/5 networks involved in mitochondrial functions and the concomitant derepression of Rox1-regulated networks for carbohydrate catabolism and redox regulation and ending (>2 generations) with the activation of Upc2-and Mot3-regulated networks involved in sterol and cell wall homeostasis. The response to reoxygenation was rapid (<5 min) and similar in both media, dominated by Yap1 networks involved in oxidative stress/redox regulation and the concomitant activation of heme-regulated ones. Our analyses revealed extensive networks of genes subject to combinatorial regulation by both heme-dependent (e.g., Hap1, Hap2/3/4/5, Rox1, Mot3, and Upc2) and heme-independent (e.g., Yap1, Skn7, and Puf3) factors under these conditions. We also uncover novel functions for several cis-regulatory sites and trans-acting factors and define functional regulons involved in the physiological acclimatization to changes in oxygen availability.Although the majority of yeasts cannot grow in the absence of oxygen, many of the Saccharomyces sensu stricto yeasts, as well as other Saccharomyces members, are facultative anaerobes capable of sustained anaerobic growth (3,4,75,86). From genomic comparisons of obligate aerobic and facultative anaerobic yeasts, it would appear that this capacity coincides with a genome duplication event that occurred Ϸ100 to 150 million years ago in the Saccharomyces lineage (75, 83), followed by the subsequent evolution of new protein variants and the rewiring of transcriptional networks (44, 93). Interestingly, even under oxygen-replete conditions, these Crabtree-positive yeasts preferentially dissimilate hexoses to the C 3 and C 2 compounds pyruvate and ethanol. This is due in part to the evolution of a glucose repression circuit, which represses the transcription of respiratory genes in the presence of high concentrations of glucose (reviewed in reference 31). Although thermodynamically less efficient, glucose fermentation provides a much higher power output (ATP · min Ϫ1 · glycosyl unit Ϫ1 ) than glucose oxidation, which confers an obvious selective advantage to these fast-growing, ethanol-producing yeasts in certain environments (84). In addition to maximizing fermentation capacity, facultative anaerobic ye...

Hypoxia elicits broad and systematic changes in protein subcellular localization

“…These results show that oxygen can act, at a rate comparable to rapamycin, to induce changes in protein localization. This result, showing that changes induced by reoxygenation occur much more quickly than those induced by hypoxia, is consistent with a previous time course experiment of the transcriptome response to hypoxia and subsequent reoxygenation (25). Supplemental Figure S3 shows the time courses of transcriptome changes in response to hypoxia and reoxygenation based on principal component analysis, which suggests that changes induced by air occur much more quickly than changes induced by hypoxia.…”

“…For example, it can change the transcript levels of over 1,000 genes in yeast and mammalian cells (24,25,29,31,40). It is conceivable that hypoxia may induce changes in protein distribution, and such changes may contribute to the changes in gene expression and other processes.…”

“…To gain a global understanding of hypoxiainduced molecular events, many labs have applied genomewide approaches. Particularly, several groups, including ours, have performed a series of detailed studies to characterize hypoxia-induced genomewide changes in gene expression by combining microarray gene expression profiling with computational analyses (24,25,29,31,40). Such studies have provided useful insights into transcriptional regulatory programs.…”

The Yeast Genes ROX1, IXR1, SKY1 and Their Effect upon Enzymatic Activities Related to Oxidative Stress

“…It is believed that they are not directly repressed by Rox1 because these genes are down-regulated under anoxia, when Rox1 levels diminish; but probably, they change their expression by complex interactions of regulatory networks affected by Rox1 (Lai et al, 2006). Rox1 also appears to play a role in the control of redox balance through the genes GPM2, GMP3 and CDC19 of the late steps of glycolysis and ADH1 or ADH5 of ethanol biosynthesis (Lai et al, 2006). It has been proposed that caloric restriction extends life span by a process that initially raises ROS levels.…”

Penalized Clustering of Large-Scale Functional Data With Multiple Covariates

“…To study the oxygen-responsive gene networks, Lai et al (2006) ) is the gene specific random effect. We fit the model using the penalty (2.5) with a = 2.…”