Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Abstract

Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.

Prioritizing protein complexes implicated in human diseases by network optimization

“…mTOR complex 1 played a critical role in hematopoiesis and Pten-loss-evoked leukemogenesis [20]. In recent years, several system-level maps of protein complexes have been constructed in yeast [21-23], drosophila melnogaster [24] and human [25], presenting significant efforts towards comprehensive understanding of protein complexes. Effective utilization of these large-scale data has been validated useful in analyzing individual disease proteins or related complexes.…”

Tandem affinity purification of functional TAP-tagged proteins from human cells

“…To streamline the purification of protein complexes from cells, the TAP protocol was developed 1,2 . It has been successfully applied to purify protein complexes from various organisms including bacteria, yeasts, plants as well as mammalian cells [3][4][5][6][7][8][9][10][11][12][13][14] . We used the TAP protocol to purify proteins associated with murine Sgo1 protein 15 .…”

Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions

“…meiosis, cell cycle, stress response) where proteins do not necessarily localize to the same cellular compartment but are nevertheless functionally related. Comprehensive physical interaction datasets (23)(24)(25), are an additional tool for defining gene groups. Such information on the large majority of complexes in the cell, could be used to create an E-MAP in which many cellular functions are represented thus becoming a platform whereby uncharacterized proteins could be genetically implicated in one or more biological processes.…”