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ProteomicsResource allocation in the archaeon Methanococcus maripaludis during slow growth
We conducted a systems-level study on the physiology of slow growth in the archaeon Methanococcus maripaludis revealing a strategy for acclimation to slow growth that relies on redistribution of energy for cellular maintenance and changes in catabolic and ribosomal activity rather than gene regulati...
ORGANISM(S): Methanococcus Maripaludis S2 (ncbitaxon:267377) 
2021-02-11 | MSV000086844 | MassIVE
GenomicsRegulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity
Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity
PRJNA749746 | ENA
GenomicsBacterial Fitness Landscapes Stratify Based on Proteome Allocation Associated with Discrete Aero-types
Bacterial Fitness Landscapes Stratify Based on Proteome Allocation Associated with Discrete Aero-types
PRJNA689602 | ENA
TranscriptomicsProteome allocation constraints determine cellular growth rates and demand fitness trade-offs
Protein synthesis is costly and the proteome size is constrained. Using a genome-scale computational model of proteome allocation together with absolute proteomics data sets from many growth environments, we determine how these fundamental limitations constrain growth and fitness in Escherichia coli...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2018-08-01 | GSE72020 | GEO
TranscriptomicsRegulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity
Bacteria regulate their cellular resource allocation to enable their fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth and expression profile of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with 3 copies of the stron...
ORGANISM(S): Escherichia coli 
2022-02-21 | GSE180830 | GEO
ProteomicsProteome resource allocation in bacteria
A central aim of cell biology is to understand the strategy of gene expression in response to the environment. Here we study gene expression response to metabolic challenges in exponentially growing Escherichia coli using mass spectrometry. Despite enormous complexity in the details of the underlyin...
ORGANISM(S): Escherichia coli 
2015-02-12 | PXD001467 | Pride
Escherichia coli Proteome partition Growth physiology 
TranscriptomicsBacterial Fitness Landscapes Stratify Based on Proteome Allocation Associated with Discrete Aero-types
The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism and protein Expression (ME-models) to study the distribution ...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2021-01-05 | GSE164236 | GEO
UnknownOptimal proteome allocation and the temperature dependence of microbial growth laws.
Not available
S-EPMC7940435 | biostudies-literature
UnknownConstrained proteome allocation affects coexistence in models of competitive microbial communities.
Not available
S-EPMC8115080 | biostudies-literature
ProteomicsGrowth Rate Dependent and Nutrient-specific Gene Expression Resource Allocation in Fission Yeast
Cellular resources are limited and their relative allocation to gene expression programmes determines physiological states and global properties such as the growth rate. Quantitative studies using various growth conditions have singled out growth rate as a major physiological variable explaining rel...
ORGANISM(S): Schizosaccharomyces pombe OY26 
2022-02-24 | PXD027835 | Pride
Resource allocation Schizosaccharomyces pombe Fission yeast Gene expression Transcriptomics Proteomics 
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