Open AccessFrom coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions
Author(s) -
Mori Matteo,
Zhang Zhongge,
BanaeiEsfahani Amir,
Lalanne JeanBenoît,
Okano Hiroyuki,
Collins Ben C,
Schmidt Alexander,
Schubert Olga T,
Lee DeokSun,
Li GeneWei,
Aebersold Ruedi,
Hwa Terence,
Ludwig Christina
Publication year - 2021
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.15252/msb.20209536
Subject(s) - proteome , biology , proteomics , escherichia coli , systems biology , computational biology , workflow , protein expression , quantitative proteomics , gene , biochemistry , computer science , database
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 .