Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

ABSTRACT: To understand the contribution of mRNA synthesis and degradation rates towards setting protein concentrations, we performed RNA-sequencing based measurements of mRNA abundance and degradation to facilitate comparisons with recently collected proteomic datasets (Mori 2021) in the same E. coli strain.

ORGANISM(S): Escherichia coli K-12

PROVIDER: GSE205717 | GEO | 2022/06/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria.

Project description:Protein concentrations are set by a complex interplay between gene-specific regulatory processes and systemic factors, including cell volume and shared gene expression machineries. Elucidating this interplay is crucial for discerning and designing gene regulatory systems. We quantitatively characterized gene-specific and systemic factors that affect transcription and translation genome-wide for Escherichia coli across many conditions. The results revealed two design principles that make regulation of gene expression insulated from concentrations of shared machineries: RNA polymerase activity is fine-tuned to match translational output, and translational characteristics are similar across most messenger RNAs (mRNAs). Consequently, in bacteria, protein concentration is set primarily at the promoter level. A simple mathematical formula relates promoter activities and protein concentrations across growth conditions, enabling quantitative inference of gene regulation from omics data.

| S-EPMC9804519 | biostudies-literature

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

Project description:Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

| PRJNA847230 | ENA

Sequencing of metabolically labeled transcripts in single cells from RPE1-FUCCI cells and murine intestinal organoids.

Project description:Measurements of metabolically labeled transcripts in single cells for estimation of mRNA synthesis and degradation rates throughout the cell cycle and intestinal organoid differentiation.

2020-03-05 | GSE128365 | GEO

Analysing environmentally induced genome-wide frameshift in S. cerevisiae and bacteria using 5PSeq

Project description:In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation.To explore this process, we utilized HT-5PSeq (Zhang & Pelechano, 2021, PMID:35474692) to measure the ribosome footprint of co-translationally degraded mRNAs in S.cerevisiae under different stresses in YPD and CSM (poor nutrients). To show the mechanism is conserved in bacteria, we performed HT-5PSeq in B.subtilis upon starvation .Our goal with HT-5PSeq is to identify gene- and codon-specific features that contribute to genome-wide frameshifting events.

2025-05-14 | GSE230202 | GEO

First-Principles Model to Evaluate Quantitatively the Long-Life Behavior of Cellulose Acetate Polymers.

Project description:A deep understanding of the degradation of cellulose diacetate (CDA) polymer is crucial in finding the appropriate long-term stability solution. This work presents an investigation of the reaction mechanism of hydrolysis using electronic density functional theory calculations with the B3LYP/6-31++G** level of theory to determine the energetics of the degradation reactions. This information was coupled with the transition-state theory to establish the kinetics of degradation for both the acid-catalyzed and noncatalyzed degradation pathways. In this model, the dependence on water concentration of the polymer as a function of pH and the evaporation of acetic acid from the polymer is explicitly accounted for. For the latter, the dependence of the concentration of acetic acid inside the films with the partial pressure on the surrounding environment was measured by sorption isotherms, where Henry's law constant was measured as a function of temperature. The accuracy of this approach was validated through comparison with experimental results of CDA-accelerated aging experiments. This model provides a step forward for the estimation of CDA degradation dependence on environmental conditions. From a broader perspective, this method can be translated to establish degradation models to predict the aging of other types of polymeric materials from first-principles calculations.

| S-EPMC8014918 | biostudies-literature

Analysing the effect of cellular energy levels on codon-specific ribosome occupancy in vivo

Project description:The aim of this study is to evaluate how cellular energy levels shape codon-specific decoding and affect codon-mediated mRNA degradation. To this end we made use of HT5P-seq (Zhang & Pelechano, 2021, PMID:35474692) in S. cerevisiae to footprint the ribosome of co-translationally degraded mRNAs in vivo upon swift changes in the concentration of intracellular ATP and other energy metabolites.

2024-03-08 | GSE216524 | GEO

A first-principles phase field method for quantitatively predicting multi-composition phase separation without thermodynamic empirical parameter.

Project description:To design tailored materials, it is highly desirable to predict microstructures of alloys without empirical parameter. Phase field models (PFMs) rely on parameters adjusted to match experimental information, while first-principles methods cannot directly treat the typical length scale of 10 μm. Combining density functional theory, cluster expansion theory and potential renormalization theory, we derive the free energy as a function of compositions and construct a parameter-free PFM, which can predict microstructures in high-temperature regions of alloy phase diagrams. Applying this method to Ni-Al alloys at 1027 °C, we succeed in reproducing evolution of microstructures as a function of only compositions without thermodynamic empirical parameter. The resulting patterns including cuboidal shaped precipitations are in excellent agreement with the experimental microstructures in each region of the Ni-Al phase diagram. Our method is in principle applicable to any kind of alloys as a reliable theoretical tool to predict microstructures of new materials.

| S-EPMC6671953 | biostudies-literature

Mori soil bacteria

Project description:Mori soil bacteria Raw sequence reads

| PRJNA562039 | ENA

Synthesis and degradation of FtsZ quantitatively predict the first cell division in starved bacteria.

Project description:In natural environments, microbes are typically non-dividing and gauge when nutrients permit division. Current models are phenomenological and specific to nutrient-rich, exponentially growing cells, thus cannot predict the first division under limiting nutrient availability. To assess this regime, we supplied starving Escherichia coli with glucose pulses at increasing frequencies. Real-time metabolomics and microfluidic single-cell microscopy revealed unexpected, rapid protein, and nucleic acid synthesis already from minuscule glucose pulses in non-dividing cells. Additionally, the lag time to first division shortened as pulsing frequency increased. We pinpointed division timing and dependence on nutrient frequency to the changing abundance of the division protein FtsZ. A dynamic, mechanistic model quantitatively relates lag time to FtsZ synthesis from nutrient pulses and FtsZ protease-dependent degradation. Lag time changed in model-congruent manners, when we experimentally modulated the synthesis or degradation of FtsZ. Thus, limiting abundance of FtsZ can quantitatively predict timing of the first cell division.

| S-EPMC6217170 | biostudies-literature

Bacteria

Project description:PCMX degradation by an aerobic consortium (HHD)

| PRJNA1057881 | ENA