ArticleMolecular systems biology2021
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 93 papers.
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Who cites it
93 citing papers in PubMed.
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- Cell geometry and membrane protein crowding constrain Escherichia coli growth rate, overflow metabolism, respiration, and maintenance energy.FEBS letters · 2026Article
- Enzyme kinetics shapes the growth response of metabolic networks.PLoS computational biology · 2026Article
- Selective Reprogramming of Ribosome Assembly and Translational Control during Bacterial Growth Phase Transitions.ACS omega · 2026Article
- Single-cell heterogeneity in ribosome levels and protein synthesis during nutrient starvation is driven by cAMP signaling.Science advances · 2026Article
- On the conditions for shifts in metabolic strategies.PLoS computational biology · 2026Review
- Fitness advantage of sequential metabolic strategies emerges from community interactions in strongly fluctuating environments.PLoS computational biology · 2026Article
- Backbone Thioamidation of a Ribosomal Subunit Protein in Pseudomonadota.Biochemistry · 2026Article
- A proteome optimal allocation model for elucidating effects of temperature on bacterial growth.NPJ systems biology and applications · 2026Article
- LysG-driven transcriptional network rewiring underlies lineage-specific phenotypes in Mycobacterium tuberculosis.Nature communications · 2026Article
- Global analysis of protein degradation reveals instability of diverse regulators inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Heterologous expression ofEngineering microbiology · 2026Article
- The biophysical properties of the bacterial nucleoid are dynamic, heterogeneous, and responsive to perturbations of cellular processes.bioRxiv : the preprint server for biology · 2026Article
- Bacterial iron acquisition byProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Milk Lipids as Bioactive Modulators of the Bacterial Proteome: Mechanisms Linking Dairy Management to Microbial Performance.Animals : an open access journal from MDPI · 2026Review
- Approaches to Study Proteins Encoded by Essential Genes.Proteins · 2026Review
- Stoichiometric analysis of microbial communities links function, structure, and biomass carrying capacity.The ISME journal · 2026Review
33 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
13 authors.
Funding
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 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.
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Registered trials
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