The ability of a microorganism to adapt changes in its physicochemical (e.g. temperature , pH ) or nutritional [3, 4] environment is crucial for its survival. The yeast, Saccharomyces cerevisiae, has developed mechanisms to respond to such environmental changes in a rapid and effective manner; such responses may demand a widespread re-programming of gene activity [2, 5]. Among other transcription factors, Msn2p and Msn4p regulate the expression of ~200 genes in response to several stresses, including heat shock, osmotic shock, oxidative stress, low pH, glucose starvation, sorbic acid and high ethanol concentrations . This is especially true of changes in the nutrient environment and the ability to sense and respond to changes in nutrient availability is essential for cells from both unicellular and multicellular organisms. Glucose is the most abundant monosaccharide on earth and is the preferred carbon source for most organisms and, accordingly, changes in glucose availability often have profound consequences in many types of cell . A negative regulator of the glucose-sensing signal transduction pathway, Mth1p, is required for repression of transcription by Rgt1p. Mth1p interacts with Rgt1p and the glucose sensors Snf3p and Rgt2p to play one of the key regulatory roles in response to the amount of available glucose in the environment . Gcr1p and Gcr2p are transcription factors that activate genes involved in glycolysis, and are also among the major regulators mediating carbon catabolite repression . The introduction of glucose to a culture of S. cerevisiae cells growing by respiration evokes changes at both the level of gene expression and of metabolism, with several proteins being activated or deactivated and gene expression being completely re-programmed to accommodate the switch from respiration to fermentation. Many transcriptional regulators are involved in the process including the HAP complex, which is a transcriptional activator and a global regulator of respiratory gene expression . Carbon catabolite repression down-regulates the expression of genes that encode enzymes involved in gluconeogenesis, the Krebs cycle, respiration, mitochondrial development, and the utilization of carbon sources other than glucose, fructose or mannose . While the main effect of glucose is exerted at the transcriptional level , changes in mRNA and protein stability are also involved in the process [13, 14].
Ammonium assimilation in yeast occurs through its incorporation into glutamate, the source of nearly 80% of all cellular nitrogen . Growth on ammonium causes a decrease in the activities of the enzymes used to assimilate less favourable nitrogen sources. This phenomenon is termed nitrogen catabolite repression, although the effect is not as well characterised as its carbon counterpart, particularly with respect to sudden changes in ammonium availability. Much less is known of the cellular response to sudden changes in the concentration of ammonium or other nitrogen sources available to the cell. A complex regulatory scheme is invoked in diploid yeast cells when they are deprived of nitrogen, this can result in pseudohyphal growth, a process regulated by a set of transcriptional activators and repressors including Phd1p, Hms1p, Mga1p and Msn1p . It should be noted that, while ammonium is not one of the most preferred nitrogen sources for S. cerevisiae, the yeast grows well on ammonium and its presence evokes nitrogen catabolite repression . Ammonium is taken via two high-affinity permeases (Mep1p and Mep2p) as well as by a low-affinity permease (Mep3p). The expression of the GDH1, GLN1, and GAP1 genes is regulated by the concentration of ammonium present in the growth medium [17, 18]. The expression of nitrogen-regulated genes is controlled by both positively (Gln3p and Nil1p) and negatively acting proteins (Nil2p and Dal80p). In addition, it has been shown that the TOR kinases play an essential role in preventing the expression of nitrogen-regulated genes , and they probably have an important integrative role.
Several investigations of the transient responses of yeast metabolism to a sudden change in nutritional availability have been carried out. Kresnowati et al.  have investigated the transient short-term transcriptome and metabolome response of yeast cells to glucose perturbation in chemostats and have indicated that both the transcriptomic and metabolomic changes mediate two kinds of response - one concerned with the transition from fully respiratory to respiro-fermentative metabolism and the other with the increase in growth rate that is the consequence of an increase in nutrient supply. Ronen and Botstein  have investigated the transient transcriptional response to switching carbon sources between galactose and glucose and concluded that experimental designs that involve short-term transient perturbations may be useful in understanding dynamic metabolic regulatory networks. The transient response to nitrogen catabolite repression was investigated by introducing an ammonium pulse into a glutamine-limited culture  and showed that the ammonium-induced repression was not due to a generalised stress response but, instead, represented a specific signal for nitrogen catabolite regulation. The effect of sulphate or phosphate limitation in the growth medium, together with uracil and leucine deficiency, was also investigated and it has been deduced that the cells adjust their growth rate to nutrient availability and maintain homeostasis in the same way in both batch and steady-state conditions .
In this study, the dynamic re-organization of yeast's cellular activity was analyzed by following the short- and long-term transcriptomic response to a sudden relaxation of either carbon and nitrogen limitation by an impulse of glucose or ammonium, respectively. The experimental design was such that the specific perturbation was uniquely introduced into an otherwise carefully controlled environment. Thus a glucose impulse was given to a steady-state glucose-limited culture and an ammonium impulse to a corresponding ammonium-limited steady-state culture. The response of the yeast cells was monitored at the transcriptomic level until the steady state was re-established. Thus the time-scale of this investigation ranged from seconds to hours, allowing the elucidation of both the metabolic and regulatory switches that enable yeast cells to adapt to, and recover from, a transient change in nutrient availability. We believe that this study makes a significant contribution to our understanding of nutritional control in yeast since the response is studied over both short and long time-scales for two different nutrients under well-controlled physiological conditions.