RT Journal Article
SR Electronic
T1 The social architecture of an in-depth cellular protein interactome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.10.24.465633
DO 10.1101/2021.10.24.465633
A1 André C. Michaelis
A1 Andreas-David Brunner
A1 Maximilian Zwiebel
A1 Florian Meier
A1 Maximilian T. Strauss
A1 Isabell Bludau
A1 Matthias Mann
YR 2021
UL http://biorxiv.org/content/early/2021/10/26/2021.10.24.465633.abstract
AB Nearly all cellular functions are mediated by protein-protein interactions and mapping the interactome provides fundamental insights into the regulation and structure of biological systems. In principle, affinity purification coupled to mass spectrometry (AP-MS) is an ideal and scalable tool, however, it has been difficult to identify low copy number complexes, membrane complexes and those disturbed by protein-tagging. As a result, our current knowledge of the interactome is far from complete, and assessing the reliability of reported interactions is challenging. Here we develop a sensitive, high-throughput, and highly reproducible AP-MS technology combined with a quantitative two-dimensional analysis strategy for comprehensive interactome mapping of Saccharomyces cerevisiae. We reduced required cell culture volumes thousand-fold and employed 96-well formats throughout, allowing replicate analysis of the endogenous green fluorescent protein (GFP) tagged library covering the entire expressed yeast proteome. The 4159 pull-downs generated a highly structured network of 3,909 proteins connected by 29,710 interactions. Compared to previous large-scale studies, we double the number of proteins (nodes in the network) and triple the number of reliable interactions (edges), including very low abundant epigenetic complexes, organellar membrane complexes and non-taggable complexes interfered by abundance correlation. This nearly saturated interactome reveals that the vast majority of yeast proteins are highly connected, with an average of 15 interactors, the majority of them unreported so far. Similar to social networks between humans, the average shortest distance is 4.2 interactions. A web portal (www.yeast-interactome.org) enables exploration of our dataset by the network and biological communities and variations of our AP-MS technology can be employed in any organism or dynamic conditions.Competing Interest StatementM. M. is an indirect investor in EvoSep.