Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome concentration limits cell growth and modulates proteome composition in Escherichia coli

ABSTRACT: Genome concentration limits cell growth and modulates proteome composition in Escherichia coli

PROVIDER: PRJNA1087324 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28330970_1.fastq.gz	Fastqsanger.gz
	SRR28330970_2.fastq.gz	Fastqsanger.gz
	SRR28330971_1.fastq.gz	Fastqsanger.gz
	SRR28330971_2.fastq.gz	Fastqsanger.gz
	SRR28330972_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Genome concentration limits cell growth and modulates proteome composition in Escherichia coli

Project description:Cell size proteomics in E. coli. See the manuscript titled - Genome concentration limits cell growth and modulates proteome composition in Escherichia coli - for more information on the project

2024-06-05 | PXD050093 | Pride

Genome concentration limits cell growth and modulates proteome composition in Escherichia coli

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

Cytosolic copper concentration modulates spore germination and secondary metabolism in Streptomyces coelicolor

Project description:Cytosolic copper concentration modulates spore germination and secondary metabolism in Streptomyces coelicolor

| PRJNA435982 | ENA

Proteome-scale movements and compartment connectivity during the eukaryotic cell cycle

Project description:Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ~20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control, while changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level.

2024-02-29 | GSE240513 | GEO

Increasing cell size remodels the proteome and promotes senescence

Project description:Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the proteome changes with cell size. Protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA damage-, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology through remodeling the proteome and provide a rationale for cell size control and polyploidization.

2022-08-01 | GSE208348 | GEO

Threonine concentration effect on L. lactis growth

Project description:L. lactis was grown in steady-state cultures at specific growth rate 0.2 h-1. The concentration of L-threonine in the growth environment was smoothly increased from 1.24mM to 4mM and proteome measurements were carried out to detect proteins involved in threonine metabolism.

2015-03-19 | PXD001602 | Pride

Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells

Project description:Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. Here, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.

2024-06-05 | GSE269091 | GEO

Proteome allocation constraints determine cellular growth rates and demand fitness trade-offs

Project description: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. First, we show that the observed variation in growth rates across environments is largely determined by the expression of protein not utilized for growth in a given environment. We then elucidate the overall transcriptional regulatory logic that underlies the expression of unused protein. We systematically classify the unused proteome into segments devoted to environmental readiness and stress resistance functions. While expression of these proteome segments incurs a fitness cost of decreased growth in a fixed environment, they provide fitness benefits in a changing environment. Thus, the systems biology of the prokaryotic proteome can be quantitatively understood based on resource allocation to growth, environmental readiness, and stress resistance functions.

2018-08-01 | GSE72020 | GEO

The mRNA methyltransferase Mettl3 modulates cytokine mRNA stability and limits functional responses in mast cells

Project description:The mRNA methyltransferase Mettl3 modulates cytokine mRNA stability and limits functional responses in mast cells

| PRJNA950438 | ENA

miR167 limits anther growth to potentiate anther dehiscence

Project description:miR167 limits anther growth to potentiate anther dehiscence

| PRJNA505255 | ENA