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Status |
Public on Apr 06, 2021 |
Title |
From coarse to fine: The absolute Escherichia coli proteome under diverse growth conditions |
Organisms |
Escherichia coli; Escherichia coli str. K-12 substr. MG1655 |
Experiment type |
Other
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Summary |
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 E. coli for >2000 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.
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Overall design |
Three ribosome profiling datasets in E. coli (various strains: NCM3722, NQ1390, MG1655).
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Contributor(s) |
Aebersold R, Esfahani AB, Collins B, Hwa T, Lalanne J, Li G, Ludwig C, Mori M, Okano H, Schmidt A, Schubert O, Zhang Z |
Citation(s) |
34032011 |
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Submission date |
Nov 05, 2019 |
Last update date |
Jun 19, 2021 |
Contact name |
Jean-Benoit Lalanne |
E-mail(s) |
lalannej@uw.edu
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Organization name |
University of Washington
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Department |
Genome Sciences
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Lab |
Jay Shendure
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Street address |
3720 15th Ave NE
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
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Platforms (2) |
GPL21117 |
Illumina NextSeq 500 (Escherichia coli str. K-12 substr. MG1655) |
GPL21222 |
Illumina NextSeq 500 (Escherichia coli) |
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Samples (3) |
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Relations |
BioProject |
PRJNA587780 |
SRA |
SRP228611 |
Supplementary file |
Size |
Download |
File type/resource |
GSE139983_RAW.tar |
23.2 Mb |
(http)(custom) |
TAR (of WIG) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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