Systems-level transcriptional regulation of Caenorhabditis elegans metabolism.
Mol Syst Biol
; 19(5): e11443, 2023 05 09.
Article
in En
| MEDLINE
| ID: mdl-36942755
ABSTRACT
Metabolism is controlled to ensure organismal development and homeostasis. Several mechanisms regulate metabolism, including allosteric control and transcriptional regulation of metabolic enzymes and transporters. So far, metabolism regulation has mostly been described for individual genes and pathways, and the extent of transcriptional regulation of the entire metabolic network remains largely unknown. Here, we find that three-quarters of all metabolic genes are transcriptionally regulated in the nematode Caenorhabditis elegans. We find that many annotated metabolic pathways are coexpressed, and we use gene expression data and the iCEL1314 metabolic network model to define coregulated subpathways in an unbiased manner. Using a large gene expression compendium, we determine the conditions where subpathways exhibit strong coexpression. Finally, we develop "WormClust," a web application that enables a gene-by-gene query of genes to view their association with metabolic (sub)-pathways. Overall, this study sheds light on the ubiquity of transcriptional regulation of metabolism and provides a blueprint for similar studies in other organisms, including humans.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Caenorhabditis elegans
/
Caenorhabditis elegans Proteins
Limits:
Animals
/
Humans
Language:
En
Journal:
Mol Syst Biol
Journal subject:
BIOLOGIA MOLECULAR
/
BIOTECNOLOGIA
Year:
2023
Document type:
Article
Affiliation country:
United States