Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens

ABSTRACT: Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens

PROVIDER: PRJEB23255 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens

Project description:Chickens (Cobb500FF) divergent in residual feed intake were analyzed for muscular (M. pectoralis), duodenal, jejunal and ileal transcriptomic profiles.

2020-03-04 | E-MTAB-6169 | biostudies-arrayexpress

Transcriptional shifts account for divergent resource allocation in feed efficient broiler chickens.

Project description: Not available

| S-EPMC6110741 | biostudies-literature

Growth Rate Dependent and Nutrient-specific Gene Expression Resource Allocation in Fission Yeast

Project description: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 relative protein abundances. Here, we used the simple eukaryote Schizosaccharomyces pombe to determine the importance of growth rate in explaining relative changes in protein and mRNA levels during growth on a series of non-limiting nitrogen sources. Although half of fission yeast genes were significantly correlated with the growth rate, this came alongside widespread nutrient-specific regulation. Proteome and transcriptome often showed coordinated regulation but with notable exceptions, such as metabolic enzymes. Genes positively correlated with growth rate participated in every level of protein production with the notable exception of RNA polymerase II, whereas those negatively correlated mainly belonged to the environmental stress response programme. Critically, metabolic enzymes, which represent ~55-70% of the proteome by mass, showed mainly condition-specific regulation. Specifically, many enzymes involved in glycolysis and NAD-dependent metabolism as well as the fermentative and respiratory pathways were condition-dependent and not consistently correlated with growth. In summary, we provide a rich account of resource allocation to gene expression in a simple eukaryote, advancing our basic understanding of the interplay between growth-rate dependent and nutrient-specific gene expression.

2022-02-24 | PXD027835 | Pride

Proteome resource allocation in bacteria

Project description: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 underlying regulatory network, we find that the proteome partitions into several coarse-grained sectors, with each sector’s total mass abundance exhibiting positive or negative linear relations with the growth rate. The growth-rate dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this model arises from tight coordination between proteome partition and metabolism, suggesting a principle for resource-allocation in proteome economy of the cell. This strategy of global gene regulation should serve as a basis for future studies on gene expression and constructing synthetic biological circuits. Coarse-graining may be an effective approach to derive predictive phenomenological models for other ‘omics’ studies.

2015-02-12 | PXD001467 | Pride

Feed Restriction Reveals Distinct Serum Metabolome Profiles in Chickens Divergent in Feed Efficiency Traits.

Project description: Not available

| S-EPMC6409680 | biostudies-literature

Effect of Feed Restriction on the Behaviour and Welfare of Broiler Chickens.

Project description: Not available

| S-EPMC7278418 | biostudies-literature

Linkage between the intestinal microbiota and residual feed intake in broiler chickens.

Project description: Not available

| S-EPMC7879522 | biostudies-literature

Feed Restriction Modifies Intestinal Microbiota-Host Mucosal Networking in Chickens Divergent in Residual Feed Intake.

Project description: Not available

| S-EPMC6351724 | biostudies-literature

Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency.

Project description: Not available

| S-EPMC5324283 | biostudies-literature

Specific growth rate-dependent proteome resource allocation dynamics in Escherichia coli

Project description:Cells usually respond to changing growth conditions with a change in the specific growth rate (μ) and adjustment of their proteome to adapt and maintain metabolic efficiency. Description of the principles behind proteome resource allocation is thus important for understanding metabolic regulation in responce to changing specific growth rate. We analysed the allocation dynamics of Escherichia coli proteome resources into different metabolic processes in response to changing μ. E. coli was grown on minimal and defined rich media in steady state continuous cultures at different μ and characterised by absolute quantitative LC-MS/MS based proteomics. We detected slowly growing cells investing more proteome resources in energy generation and carbohydrate transport and metabolism whereas for achieving faster growth cells needed to devote most resources to translation and processes closely related to the protein synthesis pipeline. Furthermore, down-regulation of energy generation and carbohydrate metabolism proteins with faster growth displayed very similar expression dynamics with the global transcriptional regulator CRP (cyclic AMP receptor protein), pointing to a dominant protein resource allocating role for this protein. Our data also suggest that acetate overflow may be the result of global proteome resource optimisation as cells saved proteome resources by switching from fully respiratory to respiro-fermentative growth. The presented results give a quantitative overview how E. coli adjusts its proteome to achieve faster growthin response to perturbations in μ. Quantitative understanding of proteome resource allocation could contribute to the design of more efficient cell factories through proteome optimisation towards proteins related to target molecule synthesis.

2015-02-27 | PXD001594 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data