Systematic Localization of Escherichia coli Membrane Proteins

MSystems
Anna SuekiAthanasios Typas

Abstract

The molecular architecture and function of the Gram-negative bacterial cell envelope are dictated by protein composition and localization. Proteins that localize to the inner membranes (IM) and outer membranes (OM) of Gram-negative bacteria play critical and distinct roles in cellular physiology; however, approaches to systematically interrogate their distribution across both membranes and the soluble cell fraction are lacking. Here, we employed multiplexed quantitative mass spectrometry using tandem mass tag (TMT) labeling to assess membrane protein localization in a proteome-wide fashion by separating IM and OM vesicles from exponentially growing Escherichia coli K-12 cells on a sucrose density gradient. The migration patterns for >1,600 proteins were classified in an unbiased manner, accurately recapitulating decades of knowledge in membrane protein localization in E. coli For 559 proteins that are currently annotated as peripherally associated with the IM (G. Orfanoudaki and A. Economou, Mol Cell Proteomics 13:3674-3687, 2014, https://doi.org/10.1074/mcp.O114.041137) and that display potential for dual localization to either the IM or cytoplasm, we could allocate 110 proteins to the IM and 206 proteins to the soluble cell f...Continue Reading

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Citations

Apr 27, 2021·Computational and Structural Biotechnology Journal·Xinjie HuiYejun Wang
Jul 31, 2021·Nature Chemical Biology·Jessica El RayesJean-François Collet

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Datasets Mentioned

BETA
PXD016403

Methods Mentioned

BETA
membrane fractionation
electrophoresis

Software Mentioned

UniProt
IsobarQuant
TATFIND
SignalP
R
BOMP
Mascot
stat
STEPdb
TMBB

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