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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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