When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation

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Abstract
Within the first 5 min after a sudden relief from glucose limitation, Saccharomyces cerevisiae exhibited fast changes of intracellular metabolite levels and a major transcriptional reprogramming. Integration of transcriptome and metabolome data revealed tight relationships between the changes at these two levels. Transcriptome as well as metabolite changes reflected a major investment in two processes: adaptation from fully respiratory to respiro‐fermentative metabolism and preparation for growth acceleration. At the metabolite level, a severe drop of the AXP pools directly after glucose addition was not accompanied by any of the other three NXP. To counterbalance this loss, purine biosynthesis and salvage pathways were transcriptionally upregulated in a concerted manner, reflecting a sudden increase of the purine demand. The short‐term dynamics of the transcriptome revealed a remarkably fast decrease in the average half‐life of downregulated genes. This acceleration of mRNA decay can be interpreted both as an additional nucleotide salvage pathway and an additional level of glucose‐induced regulation of gene expression. ### Synopsis In natural environment, nutrient availability may vary ‘from feast to famine’ and vice versa very suddenly and frequently causing excessive nutritional stresses. The robustness of an organism pictures its ability to cope with these transitions. Among the essential nutrient for growth, the more investigated of all is still the carbon source with a preference for glucose. The sudden increase in glucose concentration causes fast changes in the concentration of metabolites acting as secondary messengers, for example, cAMP. However, with the exception of adenosine nucleotides ([Theobald et al , 1997][1]) and central carbon metabolism intermediates ([Visser et al , 2004][2]), little is known about the fast changes at metabolome level occurring within the first minutes following the addition of excess glucose. By integrating metabolome and transcriptome data collected within the first minutes following the sudden relief of glucose limitation, this work provides the first comprehensive study, clearly picturing how yeast cells adapt to new environmental conditions. For the quantitative systems analysis of the dynamic response to glucose availability, it is essential that experimental conditions are tightly controlled. To achieve such analysis, the yeast Saccharomyces cerevisiae was grown under glucose limitation at a growth rate of 0.05/h in chemostat culture. At steady state, the glucose concentration was instantaneously increased from 0.15 to 5 mM. The culture was sampled after 30, 60, 90, 120, 210, 300 and 330 s for metabolite and transcript analysis. As the metabolites varied within seconds after the addition of glucose to the steady‐state culture, the transcriptome response only changed between 120 and 210 s. Despite this time shift, a very high correlation in the nature of these responses was observed. Among the fast metabolite fluctuations, an important drop in AXP pool was measured. This drop was accompanied by a time‐delayed upregulation of the genes encoding the complete purine biosynthetic pathway. Interestingly, the transcript data revealed that besides the purine biosynthesis genes, purine salvage, one carbon (C1), sulfur assimilation pathways were all coordinately upregulated, strengthening the metabolome data pointing out a requirement of purines ([Figures 3][3] and [4][4]). The coordinated elicitation of purine synthetic and salvage, one carbon (C1) and sulfur assimilation pathways suggests that methylation reactions mediated via S ‐adenosylmethionine might play a crucial role in the growth acceleration process. Further analysis of the transcriptome response by incorporating overrepresentation of functional categories and location analysis data from more than 100 transcription factors allowed mapping of the regulatory circuit taking place in this metabolic transition. It pictured that the cells were gearing up to accelerate growth as shown by the reprogramming of the transcription and translation machinery and were trying to recover from severe redox stress. Very early on (after 120 s), a large part of the genes involved in translation of ribosomal DNA (subunits of the RNA pol I) and ribosome processing were significantly upregulated. In conjunction, fine‐tuning of the translation seems to set up, as many elements of the translation initiation machinery were upregulated as well. In addition to the ‘energetic stress’, as shown by a loss of the cellular energy charge, the cells faced redox stress. Based on the data presented here, we hypothesized that the imbalance in intermediates of the top (high) and the bottom (low) of the glycolysis was a direct consequence of the inhibition of glyceraldehyde‐3‐phosphate dehydrogenase by the increased NADH/NAD ratio. To restore redox homeostasis, the cell used both metabolic and transcriptional regulations. Increase of the intracellular trehalose‐6‐phosphate concentration was in line with its inhibitory role of the hexokinases preventing the cell to die from the so‐called ‘glucose accelerated death’. The modulation of the expression of the genes encoding tricarboxylic acid enzymes was also essential in the restoration of the redox cellular status. More surprising was the rapidity of the transcript turnover. Measurement of mRNA half‐lives undoubtedly showed that a much faster decay of transcript was occurring upon the relief of glucose limitation. The average half‐life of mRNA displaying significant downregulation was nine‐fold shorter than reported earlier (Wang et al , 2001), suggesting that mRNA degradation participates actively in the regulation of translation. Consequently, one could consider that this accelerated mRNA decay represents a widespread regulatory level of...