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.
Highlights
Growth of microorganisms in their natural environment and in many industrial applications is often limited by nutrient availability [1, 2]
In Saccharomyces cerevisiae and Escherichia coli, it has been observed that the amino acid composition of the subset of structural enzymes used in the assimilation of sulfur, carbon, or nitrogen have a reduced content of the respective element compared with their average content in the predicted proteome [8]
The concentrations of each excess nutrient were comparable between cultures. This ability to control the concentrations of excess nutrients is a unique feature of chemostat cultivation and one that is especially important for ammonia and glucose in light of their impact on transcriptional regulation via sensors of extracellular nutrients [22]
Summary
Growth of microorganisms in their natural environment and in many industrial applications is often limited by nutrient availability [1, 2]. The medium that is continuously fed into the culture can be designed such that growth is limited by a single, defined nutrient, whereas all other nutrients remain present in excess In conjunction with this continuous feed of fresh media into the vessel, waste media and cells are removed at the same rate. With the use of chemostats, detailed analyses of the transcriptional responses of S. cerevisiae to nutrient limitations may aid in the development of new, DNA array-based approaches for diagnosis of industrial fermentation processes. Such studies provide valuable information for the functional analysis of genes whose encoded protein has no known or only poorly.
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