title: Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes.
abstract: Despite the availability of several large-scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild-type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. We applied this technique to determine the organization of two well-studied complexes, Spt-Ada-Gcn5 histone acetyltransferase (SAGA) and ADA, for which no comprehensive high-resolution structures exist. This approach revealed that SAGA/ADA is composed of five distinct functional modules, which can persist separately. Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. Finally, we propose a model for the architecture of the SAGA and ADA complexes, which predicts novel functional associations within the SAGA complex and provides mechanistic insights into phenotypical observations in SAGA mutants.
authors: Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
authors: Kenneth K
authors: KK
authors: Lee
authors: Mihaela E
authors: ME
authors: Sardiu
authors: Selene K
authors: SK
authors: Swanson
authors: Joshua M
authors: JM
authors: Gilmore
authors: Michael
authors: M
authors: Torok
authors: Patrick A
authors: PA
authors: Grant
authors: Laurence
authors: L
authors: Florens
authors: Jerry L
authors: JL
authors: Workman
authors: Michael P
authors: MP
authors: Washburn
mesh_terms: D042002:Chromatin Assembly and Disassembly; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D017353:Gene Deletion; D051548:Histone Acetyltransferases / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D010641:Phenotype; D010957:Plasmids; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism; D015534:Trans-Activators / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: C090575:ADA2 protein, S cerevisiae; C083323:NGG1 protein, S cerevisiae; C507785:SAGA complex, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D015534:Trans-Activators; D014157:Transcription Factors; D051548:Histone Acetyltransferases; C553425:Sgf29 protein, S cerevisiae