ArticlePLoS computational biology2016
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- On the conditions for shifts in metabolic strategies.PLoS computational biology · 2026Review
- Polyunsaturated aldehydes induce distinct proteomic responses in two diatom-associated bacterial communities.Frontiers in microbiology · 2026Article
- A mismatch between slow protein synthesis and fast environmental fluctuations determines tradeoffs in bacterial proteome allocation strategies.bioRxiv : the preprint server for biology · 2025Article
- Physics of swimming and its fitness cost determine strategies of bacterial investment in flagellar motility.Nature communications · 2025Article
- Single-cell data reveal heterogeneity of investment in ribosomes across a bacterial population.Nature communications · 2025Article
- Selective enrichment of high-affinity clade II NISME communications · 2025Article
- The energy metabolism ofApplied and environmental microbiology · 2024Article
- Yeast9: a consensus genome-scale metabolic model for S. cerevisiae curated by the community.Molecular systems biology · 2024Article
- Integration of proteomic data with genome-scale metabolic models: A methodological overview.Protein science : a publication of the Protein Society · 2024Review
- Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.Nature communications · 2024Article
- CRISPR interference screens reveal growth-robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions.The Plant cell · 2023Article
- PARROT: Prediction of enzyme abundances using protein-constrained metabolic models.PLoS computational biology · 2023Article
- A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes.Journal of the Royal Society, Interface · 2023Article
- Functional decomposition of metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions.Nature communications · 2023Article
- A self-propagating, barcoded transposon system for the dynamic rewiring of genomic networks.Molecular systems biology · 2023Article
- CRISPRi-Mediated Silencing ofJournal of proteome research · 2023Article
- Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains.eLife · 2023Article
- Complex regulation in a Comamonas platform for diverse aromatic carbon metabolism.Nature chemical biology · 2023Article
- Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.bioRxiv : the preprint server for biology · 2023Article
- A Computational Toolbox to Investigate the Metabolic Potential and Resource Allocation in Fission Yeast.mSystems · 2022Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
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3 authors.
Funding
Abstract
The costs and benefits of protein expression are balanced through evolution. Expression of un-utilized protein (that have no benefits in the current environment) incurs a quantifiable fitness costs on cellular growth rates; however, the magnitude and variability of un-utilized protein expression in natural settings is unknown, largely due to the challenge in determining environment-specific proteome utilization. We address this challenge using absolute and global proteomics data combined with a recently developed genome-scale model of Escherichia coli that computes the environment-specific cost and utility of the proteome on a per gene basis. We show that nearly half of the proteome mass is unused in certain environments and accounting for the cost of this unused protein expression explains >95% of the variance in growth rates of Escherichia coli across 16 distinct environments. Furthermore, reduction in unused protein expression is shown to be a common mechanism to increase cellular growth rates in adaptive evolution experiments. Classification of the unused protein reveals that the unused protein encodes several nutrient- and stress- preparedness functions, which may convey fitness benefits in varying environments. Thus, unused protein expression is the source of large and pervasive fitness costs that may provide the benefit of hedging against environmental change.
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