Substrate targeting by the Gcn5 acetyltransferase: mechanisms and consequences

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Problem: Acetylation of lysine residues is catalyzed by histone acetyltransferases (HATs) and removed by histone deacetylases (HDACs). As reflected by their names, these enzymes are best characterized as modifiers of histones. Yet, recent work from our lab and others suggests the need for a paradigm shift in how we think about acetylation as a post-translational modification. Specifically, acetylation is now thought to rival phosphorylation, with 1000s of substrates having been identified in organisms from bacteria to humans. How these substrates are chosen and what their acetylations do is not understood. Our overarching goal is to advance knowledge by determining the regulation and consequences of acetylation on a proteome-wide scale. To achieve this goal, it is necessary for us to move away from old models for acetylation based on the now-outdated assumption that histones are the only important targets. ***Recent Progress: HAT and HDAC enzymes exist in large protein complexes with many subunits. Our data in yeast show that these complexes hold the key to understanding HATs and HDACs as global regulators. We focused on a complex called SAGA that contains an important HAT called Gcn5. Non-catalytic components of SAGA are usually assumed to be uniform and obligate promoters of acetylation by this HAT. Our data show that while this is true for histones, the impact of non-catalytic subunits on the acetylation of other proteins is target specific. Based on these data, we propose a new model wherein SAGA acts as a substrate selection platform. In this model, individual subunits promote or inhibit the acetylation of distinct sets of non-histone targets mediating diverse functions in the cell. ***Approach and Significance: In this program, we will exploit our new model for the SAGA HAT complex to uncover mechanisms of substrate targeting and to link substrate acetylation to downstream functions. In the short term, trainees in my lab will use proteomics and functional genomics technologies in yeast to achieve three objectives. They will: (1) Determine how each subunit of SAGA impacts acetylation of Gcn5 targets; (2) identify novel genetic interactions for SAGA mutants; and (3) elucidate the function of SAGA-regulated acetylations on non-histone substrates. In the long term, we will extend what we learn from these experiments to the study of other HAT and HDAC complexes and determine how mechanisms of substrate targeting are impacted by changes to a cell's environment. Our program will facilitate research by other labs around the world by providing the first comprehensive picture of acetylation targeting and function to date. ***Training: This program will train at least 2 graduate students and up to 10 undergrads over the next 5 years. They will gain experience in proteomics, high-throughput genetics and bioinformatics. These skills will make them highly qualified for positions in both academia and industry.**