The Genome-wide Transcriptional Responses of Saccharomyces cerevisiae Grown on Glucose in Aerobic Chemostat Cultures Limited for Carbon, Nitrogen, Phosphorus, or Sulfur

Abstract

Profiles of genome-wide transcriptional events for a given environmental condition can be of importance in the diagnosis of poorly defined environments. To identify clusters of genes constituting such diagnostic profiles, we characterized the specific transcriptional responses of Saccharomyces cerevisiae to growth limitation by carbon, nitrogen, phosphorus, or sulfur. Microarray experiments were performed using cells growing in steady-state conditions in chemostat cultures at the same dilution rate. This enabled us to study the effects of one particular limitation while other growth parameters (pH, temperature, dissolved oxygen tension) remained constant. Furthermore, the composition of the media fed to the cultures was altered so that the concentrations of excess nutrients were comparable between experimental conditions. In total, 1881 transcripts (31% of the annotated genome) were significantly changed between at least two growth conditions. Of those, 484 were significantly higher or lower in one limitation only. The functional annotations of these genes indicated cellular metabolism was altered to meet the growth requirements for nutrient-limited growth. Furthermore, we identified responses for several active transcription factors with a role in nutrient assimilation. Finally, 51 genes were identified that showed 10-fold higher or lower expression in a single condition only. The transcription of these genes can be used as indicators for the characterization of nutrient-limited growth conditions and provide information for metabolic engineering strategies.Growth of microorganisms in their natural environment and in many industrial applications is often limited by nutrient availability (1, 2). In these situations the specific growth rate of the organism is determined by the low (non-saturating) concentration of a single nutrient. For example, in the industrial production of bakers' yeast sugar-limited, aerobic cultivation at relatively low specific growth rates is essential to achieve high biomass yields. On the other hand processes such as beer fermentation occur at high concentrations of fermentable sugars and are limited by other nutrients (e.g. oxygen, nitrogen). As a result the yeast's metabolic activities are altered. This situation is different from nutrient starvation in which the absence of a nutritional component is often the cause of stress responses that result in growth arrest or cell death (3, 4).In the laboratory, cultivation of microorganisms is predominantly performed in shake-flasks, in which all relevant nutrients are at least initially present in excess. During the course of batch cultivation the physical and chemical environment constantly changes, which directly affects the specific growth rate and the regulation of many metabolic processes (5). With

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“…Carefully designed studies such as those of Boer et al (2003) have allowed removal of ambiguity from experimental datasets. Chemostat cultures provide nutrient-limiting conditions specific for a single nutrient in a medium that has stable levels of the non-limiting components.…”

“…The analysis of transcriptional responses to specific nutrients in chemostat culture of S. cerevisiae was investigated by Boer et al (2003) to determine the functions of unknown genes and to map unknown regulons that correlated with nutrient limitation. Transcriptional responses to carbon, nitrogen, phosphorus or sulphur limitation were studied in glucose-grown cultures at a dilution rate of 0?1 h 21 .…”