Abstract #6

Global Landscape of Protein Complexes in the Yeast Saccharomyces cerevisiae. Nevan Krogan^1,2, Gerard Cagney^1,3, Haiyuan Yu⁴, Gouqing Zhong^1,2, Xinghua Guo^1,2, Alexandr Ignatchenko^1,2, Peter Wong¹, Shuye Pu⁵, Gabe Musso^1,2, Aaron P. Tikuisis¹, Thanuja Punna¹, José M. Peregrín-Alvarez⁵, Dawn P. Richards⁶, James Vlasblom⁵, Samuel Wu⁵, John Parkinson⁵, Marc Gerstein⁴, Shoshana J. Wodak⁵, Jack F. Greenblatt^1,2, Andrew Emili^1,2. 1) Banting & Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research (DCCBR), University of Toronto, Toronto, ON, CANADA; 2) Department of Medical Genetics and Microbiology, University of Toronto, Toronto, ON, CANADA; 3) Conway Institute, University College Dublin, Belfield, Dublin, IRELAND; 4) Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT; 5) Hospital for Sick Children, Toronto, ON, CANADA; 6) Affinium Pharmaceuticals, Toronto, ON, CANADA.
   Identification of protein-protein interactions (PPI) often provides insight into protein function, and many cellular processes are carried out by stable protein complexes. We have used tandem affinity purification (TAP) to process 4562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analyzed by both MALDI-TOF mass spectrometry (MS) and LC-MS/MS, increasing coverage and accuracy and simultaneously enabling identification of thousands of probable sites of post-translational modification. Among 4087 proteins (72% of the yeast proteome) identified with high confidence by MS from successful purifications of 2357 different proteins, our highest confidence dataset (median precision of 0.69) comprises 7123 pair-wise protein interactions involving 2708 proteins. Clustering organized these pair-wise interactions into 552 protein complexes, averaging 4.9 subunits per complex, about half of which are previously unreported. We also identified an additional 429 connections between pairs of protein complexes. All raw and processed data will be available online as a major resource for studies on individual proteins as well as functional genomics and systems biology.

Return to YGM 2006 Home at SGD