Open AccessCombinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes
Author(s) -
Lee Kenneth K,
Sardiu Mihaela E,
Swanson Selene K,
Gilmore Joshua M,
Torok Michael,
Grant Patrick A,
Florens Laurence,
Workman Jerry L,
Washburn Michael P
Publication year - 2011
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb.2011.40
Subject(s) - biology , histone acetyltransferase , acetyltransferase , proteomics , computational biology , histone , chromatin , protein subunit , chromatin remodeling , proteome , genetics , acetylation , gene
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.