A major challenge in systems biology lies in the integration of processes occurring at different levels, such as transcription, translation, and metabolism, to understand the functioning of a living cell in its environment. We studied the high temperatureinduced glycolytic flux increase in Saccharomyces cerevisiae and investigated the regulatory mechanisms underlying this increase. We used glucose-limited chemostat cultures to separate regulatory effects of temperature from effects on growth rate. Growth at increased temperature (38°C versus 30°C) resulted in a strongly increased glycolytic flux, accompanied by a switch from respiration to a partially fermentative metabolism. We observed an increased flux through all enzymes, ranging from 5-to 10-fold. We quantified the contributions of direct temperature effects on enzyme activities, the gene expression cascade and shifts in the metabolic network, to the increased flux through each enzyme. To do this we adapted flux regulation analysis. We show that the direct effect of temperature on enzyme kinetics can be included as a separate term. Together with hierarchical regulation and metabolic regulation, this term explains the total flux change between two steady states. Surprisingly, the effect of the cultivation temperature on enzyme catalytic capacity, both directly through the Arrhenius effect and indirectly through adapted gene expression, is only a moderate contribution to the increased glycolytic flux for most enzymes. The changes in flux are therefore largely caused by changes in the interaction of the enzymes with substrates, products, and effectors.Microorganisms encounter environmental changes, which they have to withstand and adapt to in order to survive. Changes in ambient temperature are common to almost every ecological niche. Temperature influences the structural and functional properties of cellular components, both physically and chemically. Physically, temperature affects membrane fluidity (1, 2) and diffusion rates, as well as protein folding and stability (3). Chemically, temperature directly affects reaction rates in the cell. This study focuses on the adaptation of cells to temperatures higher than that optimal for growth.Microbes adapt to high temperature by altering their cellular make-up such as lipid composition, membrane fluidity, and the induction of large numbers of heat shock genes (3-11), which have a wide variety of functions. Many encode protein chaperones involved in protein (un)folding (12, 13) or degradation of damaged proteins (14). Others are involved in the synthesis of the thermoprotecting disaccharide trehalose, which is known to be involved in stabilization of membranes and proteins (15, 16) as well as in storage of free energy (17). Many of these adaptive responses put a significant additional energy burden on the cells (18).There still is little clarity on the actual mechanisms by which cells maintain a balance between the energy needs for adaptive responses to stress survival and those for processes indispensable for grow...