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Spatiotemporal variation of mammalian protein complex stoichiometries

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Official URL:https://doi.org/10.1186/s13059-016-0912-5
PubMed:View item in PubMed
Creators Name:Ori, A. and Iskar, M. and Buczak, K. and Kastritis, P. and Parca, L. and Andres-Pons, A. and Singer, S. and Bork, P. and Beck, M.
Journal Title:Genome Biology
Journal Abbreviation:Genome Biol
Volume:17
Number:1
Page Range:47
Date:14 March 2016
Keywords:Protein Complex, Stoichiometry, Proteomics, Paralog, Epigenetic, Transport, Reprogramming, Cancer
Abstract:Background: Recent large-scale studies revealed cell-type specific proteomes. However, protein complexes, the basic functional modules of a cell, have been so far mostly considered as static entities with well-defined structures. The co-expression of their members has not been systematically charted at the protein level. Results: We used measurements of protein abundance across 11 cell types and five temporal states to analyze the co-expression and the compositional variations of 182 well-characterized protein complexes. We show that although the abundance of protein complex members is generally co-regulated, a considerable fraction of all investigated protein complexes is subject to stoichiometric changes. Compositional variation is most frequently seen in complexes involved in chromatin regulation and cellular transport, and often involves paralog switching as a mechanism for the regulation of complex stoichiometry. We demonstrate that compositional signatures of variable protein complexes have discriminative power beyond individual cell states and can distinguish cancer cells from healthy ones. Conclusions: Our work demonstrates that many protein complexes contain variable members that cause distinct stoichometries and functionally fine-tune complexes spatiotemporally. Only a fraction of these compositional variations is mediated by changes in transcription and other mechanisms regulating protein abundance contribute to determine protein complex stoichiometries. Our work highlights the superior power of proteome profiles to study protein complexes and their variants across cell states.
ISSN:1465-6906
Publisher:BioMed Central (U.K.)
Item Type:Article

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