From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions
Author(s)
Mori, Matteo; Zhang, Zhongge; Banaei‐Esfahani, Amir; Lalanne, Jean‐Benoît; Okano, Hiroyuki; Collins, Ben C; Schmidt, Alexander; Schubert, Olga T; Lee, Deok‐Sun; Li, Gene‐Wei; Aebersold, Ruedi; Hwa, Terence; Ludwig, Christina; ... Show more Show less
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Accurate measurements of cellular protein concentrations are invaluable to quantitative studies of gene expression and physiology in living cells. Here, we developed a versatile mass spectrometric workflow based on data-independent acquisition proteomics (DIA/SWATH) together with a novel protein inference algorithm (xTop). We used this workflow to accurately quantify absolute protein abundances in Escherichia coli for > 2,000 proteins over > 60 growth conditions, including nutrient limitations, non-metabolic stresses, and non-planktonic states. The resulting high-quality dataset of protein mass fractions allowed us to characterize proteome responses from a coarse (groups of related proteins) to a fine (individual) protein level. Hereby, a plethora of novel biological findings could be elucidated, including the generic upregulation of low-abundant proteins under various metabolic limitations, the non-specificity of catabolic enzymes upregulated under carbon limitation, the lack of large-scale proteome reallocation under stress compared to nutrient limitations, as well as surprising strain-dependent effects important for biofilm formation. These results present valuable resources for the systems biology community and can be used for future multi-omics studies of gene regulation and metabolic control in E. coli.
Date issued
2021Department
Massachusetts Institute of Technology. Department of Biology; Massachusetts Institute of Technology. Department of PhysicsJournal
Molecular Systems Biology
Publisher
EMBO