Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures

Abstract

Transcriptional responses of the yeast Saccharomyces cerevisiae to Zn availability were investigated at a fixed specific growth rate under limiting and abundant Zn concentrations in chemostat culture. To investigate the context dependency of this transcriptional response and eliminate growth rate-dependent variations in transcription, yeast was grown under several chemostat regimens, resulting in various carbon (glucose), nitrogen (ammonium), zinc, and oxygen supplies. A robust set of genes that responded consistently to Zn limitation was identified, and the set enabled the definition of the Zn-specific Zap1p regulon, comprised of 26 genes and characterized by a broader zinc-responsive element consensus (MHHAACCBYNMRGGT) than so far described. Most surprising was the Zn-dependent regulation of genes involved in storage carbohydrate metabolism. Their concerted down-regulation was physiologically relevant as revealed by a substantial decrease in glycogen and trehalose cellular content under Zn limitation. An unexpectedly large number of genes were synergistically or antagonistically regulated by oxygen and Zn availability. This combinatorial regulation suggested a more prominent involvement of Zn in mitochondrial biogenesis and function than hitherto identified.

FIG. 1.

Consensus ZRE sequence identified by MEME using module 1 as input.

FIG. 2.

Venn diagram of chemostat-based transcriptome data in comparison with data obtained by Lyons and coworkers (50). (A) Zap1p regulon (modules 1 and 3 in comparison with 46 genes from Lyons and coworkers [50]). (B) Genome-wide comparison (modules 1, 3, and 5 in comparison with all up-regulated genes from Lyons and coworkers [50]). anae, anaerobic; ae, aerobic.

FIG. 3.

Combinatorial regulation of gene expression by Zn and oxygen availability: constraints for the selection of the discretized patterns and average expression profile of these selected patterns. Only the oxygen-induced genes are represented. Error bars indicate standard deviations. lim, limited.

FIG. 4.

(A) Glycogen and trehalose metabolism in S. cerevisiae. Genes indicated in green are clustered in module 2. The four boxes indicate the following n-fold changes from left to right: zinc versus carbon anaerobic, zinc versus nitrogen anaerobic, zinc versus carbon aerobic, and zinc versus nitrogen aerobic. Intensities of n-fold changes are indicated by the color key. (B) Normalized expression profile of genes involved in glycogen and trehalose metabolism and intracellular glycogen and trehalose concentrations. Error bars indicate standard deviations. anae, anaerobic; ae, aerobic.