Escherichia coli REL606
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA269622 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RNA-Seq analysis of E.coli, under multiple growth conditions
| PRJNA368968 | ENA
Project description:The chemically mutagenized Escherichia coli strain AS19 was isolated on the basis of its enhanced sensitivity to different antibiotics, in particular to actinomycin. The strain was later modified to study rRNA modifications that confer antibiotic resistance. Here, we present the genome sequence of the variant E. coli AS19-RrmA.
| S-EPMC5940949 | biostudies-literature
Project description:Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in Escherichia coli cells arrested for DNA replication results in a decrease in the concentration of active RNA polymerases and ribosomes. The resulting sub-linear scaling of total active RNA polymerases and ribosomes with cell size leads to sub-exponential growth, even within physiological cell sizes. Cell growth rate scales proportionally with the total number of active ribosomes in a DNA concentration-dependent manner. Tandem-mass-tag mass spectrometry experiments further revealed that a decrease in DNA-to-cell-volume ratio also incrementally remodels proteome composition with cell size. Altogether, our findings indicate that genome concentration is an important driver of exponential cell growth and a global modulator of proteome composition in E. coli. Comparison with studies on eukaryotic cells suggests DNA concentration-dependent scaling principles of gene expression across domains of life.
2024-09-01 | GSE261497 | GEO
Project description:Microbes exhibit precise control over their composition and geometry in order to adapt and grow in diverse environments. However, the mechanisms that orchestrate this simultaneous regulation, and how they are causally linked, remains poorly understood. In this work, we derive and experimentally test a biophysical model of cell size regulation in Escherichia coli which relates the cellular surface-to-volume ratio to the total macromolecular composition and partitioning of the proteome between cellular compartments. Central to this model is the observation that the macromolecular density of the cytoplasm and the protein density within the cell membranes are maintained at a constant ratio across growth conditions. Using quantitative mass spectrometry, single-cell microscopy, and biochemical assays, we show this model quantitatively predicts a non-linear relationship between the surface-to-volume ratio, proteome localization, and the total ribosome content of the cell. This model holds under perturbations of intracellular ppGpp concentrations–thereby changing the ribosomal content–demonstrating that cellular geometry is not strictly determined by the cellular growth rate. These findings provide a biophysical link between the coregulation of proteome organization and cellular geometry, offering a quantitative framework for understanding bacterial size regulation across conditions.
2025-11-26 | PXD071222 | Pride
Project description:Escherichia coli REL606 Raw sequence reads
| PRJNA336011 | ENA
Project description:Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli
| PRJNA257406 | ENA
Project description:Escherichia coli Long-term Evolution Experiment 500 and 1000 Generation Population Sequencing
| PRJNA262100 | ENA
Project description:Escherichia coli REL606 Genome sequencing
| PRJNA189495 | ENA
Project description:Genome evolution and adaptation in a long-term experiment with Escherichia coli.
| PRJNA294164 | ENA
Project description:Escherichia coli REL606 Raw sequence reads
| PRJNA385021 | ENA