Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY.

Proc Natl Acad Sci U S A
Authors
Keywords
Abstract

Global regulators that bind strategic metabolites allow bacteria to adapt rapidly to dynamic environments by coordinating the expression of many genes. We report an approach for determining gene regulation hierarchy using the regulon of the Bacillus subtilis global regulatory protein CodY as proof of principle. In theory, this approach can be used to measure the dynamics of any bacterial transcriptional regulatory network that is affected by interaction with a ligand. In B. subtilis, CodY controls dozens of genes, but the threshold activities of CodY required to regulate each gene are unknown. We hypothesized that targets of CodY are differentially regulated based on varying affinity for the protein's many binding sites. We used RNA sequencing to determine the transcription profiles of B. subtilis strains expressing mutant CodY proteins with different levels of residual activity. In parallel, we quantified intracellular metabolites connected to central metabolism. Strains producing CodY variants F71Y, R61K, and R61H retained varying degrees of partial activity relative to the WT protein, leading to gene-specific, differential alterations in transcript abundance for the 223 identified members of the CodY regulon. Using liquid chromatography coupled to MS, we detected significant increases in branched-chain amino acids and intermediates of arginine, proline, and glutamate metabolism, as well as decreases in pyruvate and glycerate as CodY activity decreased. We conclude that a spectrum of CodY activities leads to programmed regulation of gene expression and an apparent rerouting of carbon and nitrogen metabolism, suggesting that during changes in nutrient availability, CodY prioritizes the expression of specific pathways.

Year of Publication
2014
Journal
Proc Natl Acad Sci U S A
Volume
111
Issue
22
Pages
8227-32
Date Published
2014 Jun 03
ISSN
1091-6490
URL
DOI
10.1073/pnas.1321308111
PubMed ID
24843172
PubMed Central ID
PMC4050614
Links
Grant list
K99 GM099893 / GM / NIGMS NIH HHS / United States
P30 NS047243 / NS / NINDS NIH HHS / United States
R00 GM099893 / GM / NIGMS NIH HHS / United States
R01 GM042219 / GM / NIGMS NIH HHS / United States