Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

Highly conserved among eukaryotic cells, the AMP‐activated kinase (AMPK) is a central regulator of carbon metabolism. To map the complete network of interactions around AMPK in yeast (Snf1) and to evaluate the role of its regulatory subunit Snf4, we measured global mRNA, protein and metabolite levels in wild type, Δ snf1 , Δ snf4 , and Δ snf1 Δ snf4 knockout strains. Using four newly developed computational tools, including novel DOGMA sub‐network analysis, we showed the benefits of three‐level ome‐data integration to uncover the global Snf1 kinase role in yeast. We for the first time identified Snf1's global regulation on gene and protein expression levels, and showed that yeast Snf1 has a far more extensive function in controlling energy metabolism than reported earlier. Additionally, we identified complementary roles of Snf1 and Snf4. Similar to the function of AMPK in humans, our findings showed that Snf1 is a low‐energy checkpoint and that yeast can be used more extensively as a model system for studying the molecular mechanisms underlying the global regulation of AMPK in mammals, failure of which leads to metabolic diseases. Synopsis AMP‐activated kinases (AMPKs) are highly conserved among yeast, plants, and mammals and are central regulators involved in cellular development and survival (Polge and Thomas, 2007 ). Mammalian AMPK, for example, is a master regulator of energy metabolism (Kahn et al , 2005 ). Its function is linked to metabolic and aging diseases and it is a key drug target against obesity and diabetes (Hardie, 2007a ). Through homology studies, yeast AMPK (Snf1) has been used as a model to study the function of human AMPK (Hardie, 2007a , 2007b ). The yeast Snf1 regulates carbon metabolism during growth on various carbon sources (Celenza and Carlson, 1986 ; Carlson, 1999 ). Growing evidence, however, suggests a much broader role for Snf1 as a master regulator of both carbon and energy metabolism. Elucidating the organization and interactions of the Snf1 regulatory network is important for uncovering the complexity of global AMPK function and, ultimately, for using yeast as a model to study the role of AMPK in humans. To achieve this goal, a systems approach combining global measurements across different levels of the cellular hierarchy (mRNAs, proteins, and metabolites) is required. Here, we integrated data from genome‐wide expression profiling and protein measurements with different networks comprising protein–protein interactions, pr