Mapping the Protein Interaction Network of the Human COP9 Signalosome Complex Using a Label-free QTAX Strategy

• Published in: Molecular & cellular proteomics Vol. 11; no. 5; pp. 138 - 147
• Main Authors: Fang, Lei, Kaake, Robyn M., Patel, Vishal R., Yang, Yingying, Baldi, Pierre, Huang, Lan
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2012; The American Society for Biochemistry and Molecular Biology
• Subjects: Autoantigens - chemistry; Autoantigens - isolation & purification; Autoantigens - metabolism; Chromatography, Affinity; COP9 Signalosome Complex; Cross-Linking Reagents - chemistry; Formaldehyde - chemistry; HeLa Cells; Humans; Immunoprecipitation; Molecular Sequence Annotation; Multiprotein Complexes - isolation & purification; Multiprotein Complexes - metabolism; Peptide Fragments - chemistry; Peptide Hydrolases - isolation & purification; Peptide Hydrolases - metabolism; Peptide Mapping; Proteasome Endopeptidase Complex - chemistry; Proteasome Endopeptidase Complex - isolation & purification; Proteasome Endopeptidase Complex - metabolism; Protein Binding; Protein Interaction Mapping; Protein Interaction Maps; Proteolysis
• ISSN: 1535-9476; 1535-9484; 1535-9484
• DOI: 10.1074/mcp.M111.016352

The COP9 signalosome (CSN) is a multi-subunit protein complex that performs critical roles in controlling diverse cellular and developmental processes. Aberrant regulation of the CSN complex has been shown to lead to tumorigenesis. Despite its biological significance, our current knowledge of the function and regulation of the CSN complex is very limited. To explore CSN biology, we have developed and employed a new version of the tag team-based QTAX strategy (quantitative analysis of tandem affinity purified in vivo cross-linked (X) protein complexes) by incorporating a label-free MS method for quantitation. Coupled with protein interaction network analysis, this strategy produced a comprehensive and detailed assessment of the protein interaction network of the human CSN complex. In total, we quantitatively characterized 825 putative CSN-interacting proteins, with 270 classified as core interactors (captured by all three bait purifications). Biochemical validation further confirms the validity of selected identified interactors. This work presents the most complete analysis of the CSN interaction network to date, providing an inclusive set of physical interaction data consistent with physiological roles for the CSN. Moreover, the methodology described here is a general proteomic tool for the comprehensive study of protein interaction networks.