From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions
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 inf...
| Main Authors: | , , , , , , , , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
EMBO
2021
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| Online Access: | https://hdl.handle.net/1721.1/135655 |
| _version_ | 1811077998604976128 |
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| author | 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 |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology 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 |
| author_sort | Mori, Matteo |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T10:51:47Z |
| format | Article |
| id | mit-1721.1/135655 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T10:51:47Z |
| publishDate | 2021 |
| publisher | EMBO |
| record_format | dspace |
| spelling | mit-1721.1/1356552023-12-22T21:08:00Z From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions 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 Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Physics 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. 2021-10-27T20:24:29Z 2021-10-27T20:24:29Z 2021 2021-07-21T15:10:00Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/135655 en 10.15252/msb.20209536 Molecular Systems Biology Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf EMBO EMBO Press |
| spellingShingle | 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 From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions |
| title | From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions |
| title_full | From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions |
| title_fullStr | From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions |
| title_full_unstemmed | From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions |
| title_short | From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions |
| title_sort | from coarse to fine the absolute escherichia coli proteome under diverse growth conditions |
| url | https://hdl.handle.net/1721.1/135655 |
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