Circadian rhythms govern multiple aspects of animal metabolism. Transcriptome-, proteome-and metabolome-wide measurements have revealed widespread circadian rhythms in metabolism governed by a cellular genetic oscillator, the circadian core clock. However, it remains unclear if and under which conditions transcriptional rhythms cause rhythms in particular metabolites and metabolic fluxes. Here, we analyzed the circadian orchestration of metabolic pathways by direct measurement of enzyme activities, analysis of transcriptome data, and developing a theoretical method called circadian response analysis. Contrary to a common assumption, we found that pronounced rhythms in metabolic pathways are often favored by separation rather than alignment in the times of peak activity of key enzymes. This property holds true for a set of metabolic pathway motifs (e.g., linear chains and branching points) and also under the conditions of fast kinetics typical for metabolic reactions. By circadian response analysis of pathway motifs, we determined exact timing separation constraints on rhythmic enzyme activities that allow for substantial rhythms in pathway flux and metabolite concentrations. Direct measurements of circadian enzyme activities in mouse skeletal muscle confirmed that such timing separation occurs in vivo.circadian rhythms | glucose metabolism | metabolic response analysis | mouse skeletal muscle C ircadian rhythms are ∼24-h cycles in behavior, physiology, and cellular processes that persist in the absence of external cues. In mammals, circadian rhythms in the expression of thousands of genes in various metabolic tissues ensure up-or down-regulation of important metabolic processes in anticipation of daily activity and rest periods (1, 2). Circadian gene expression in mammalian tissues depends on the circadian core clock, a genetic feedback oscillator inducing the transcription of thousands of clock-controlled genes. Additional rhythmicity in gene expression is generated by rhythmic posttranscriptional regulation (3). Circadian rhythms have been detected in mRNA and protein abundances (4-6), enzyme activities (7, 8), and concentrations of metabolites (9-11) in various mammalian tissues. Whereas the mechanisms underlying rhythmic gene expression are relatively well-studied, it remains unclear how circadian gene expression induces rhythms in the abundance of metabolites or metabolic fluxes.A naïve picture of circadian regulation (Fig. 1A) ("central dogma of molecular chronobiology") suggests that the circadian core clock drives rhythmic mRNA expression, resulting in rhythmic protein levels and directly leading to rhythmic enzyme activity (12) and thus, metabolic activity. Here, especially metabolic pathway flux (rate of conversion of substrate into product metabolites measured in concentration per time; an analogy is water flow through a floodgate) has been regarded as a crucial biological function under strong evolutionary selection pressure (13,14). However, it is unclear whether circadian abundances of enzyme trans...