From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions

Mori, Matteo and Zhang, Zhongge and Banaei-Esfahani, Amir and Lalanne, Jean-Benoît and Okano, Hiroyuki and Collins, Ben C. and Schmidt, Alexander and Schubert, Olga T. and Lee, Deok-Sun and Li, Gene-Wei and Aebersold, Ruedi and Hwa, Terence and Ludwig, Christina. (2021) From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Molecular systems biology, 17 (5). e9536.

Full text not available from this repository.

Official URL: https://edoc.unibas.ch/87229/

Downloads: Statistics Overview


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.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Services Biozentrum > Proteomics (Schmidt)
UniBasel Contributors:Schmidt, Alexander
Item Type:Article, refereed
Article Subtype:Research Article
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:22 Jan 2022 13:00
Deposited On:22 Jan 2022 13:00

Repository Staff Only: item control page