From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions
Abstract 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 pr...
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| Format: | Article |
| Language: | English |
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Springer Nature
2021-05-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.20209536 |
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| author | Matteo Mori Zhongge Zhang Amir Banaei‐Esfahani Jean‐Benoît Lalanne Hiroyuki Okano Ben C Collins Alexander Schmidt Olga T Schubert Deok‐Sun Lee Gene‐Wei Li Ruedi Aebersold Terence Hwa Christina Ludwig |
| author_facet | Matteo Mori Zhongge Zhang Amir Banaei‐Esfahani Jean‐Benoît Lalanne Hiroyuki Okano Ben C Collins Alexander Schmidt Olga T Schubert Deok‐Sun Lee Gene‐Wei Li Ruedi Aebersold Terence Hwa Christina Ludwig |
| author_sort | Matteo Mori |
| collection | DOAJ |
| description | Abstract 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 Escherichiacoli 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. |
| format | Article |
| id | doaj-art-6aa5a86f417842f5b356db6414fccb62 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2021-05-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-6aa5a86f417842f5b356db6414fccb622024-12-15T12:13:49ZengSpringer NatureMolecular Systems Biology1744-42922021-05-0117512310.15252/msb.20209536From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditionsMatteo Mori0Zhongge Zhang1Amir Banaei‐Esfahani2Jean‐Benoît Lalanne3Hiroyuki Okano4Ben C Collins5Alexander Schmidt6Olga T Schubert7Deok‐Sun Lee8Gene‐Wei Li9Ruedi Aebersold10Terence Hwa11Christina Ludwig12Department of Physics, University of California at San DiegoSection of Molecular Biology, Division of Biological Sciences, University of California at San DiegoDepartment of Biology, Institute of Molecular Systems Biology, ETH ZurichDepartment of Biology, Massachusetts Institute of TechnologyDepartment of Physics, University of California at San DiegoDepartment of Biology, Institute of Molecular Systems Biology, ETH ZurichBiozentrum, University of BaselDepartment of Human Genetics, University of California, Los AngelesSchool of Computational Sciences, Korea Institute for Advanced StudyDepartment of Biology, Massachusetts Institute of TechnologyDepartment of Biology, Institute of Molecular Systems Biology, ETH ZurichDepartment of Physics, University of California at San DiegoBavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM)Abstract 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 Escherichiacoli 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.https://doi.org/10.15252/msb.20209536absolute quantificationEscherichia colimass spectrometryprotein inferencequantitative proteomics |
| spellingShingle | Matteo Mori Zhongge Zhang Amir Banaei‐Esfahani Jean‐Benoît Lalanne Hiroyuki Okano Ben C Collins Alexander Schmidt Olga T Schubert Deok‐Sun Lee Gene‐Wei Li Ruedi Aebersold Terence Hwa Christina Ludwig From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions Molecular Systems Biology absolute quantification Escherichia coli mass spectrometry protein inference quantitative proteomics |
| 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 |
| topic | absolute quantification Escherichia coli mass spectrometry protein inference quantitative proteomics |
| url | https://doi.org/10.15252/msb.20209536 |
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