Predicting input signals of transcription factors in Escherichia coli.

ABSTRACT: The activity of bacterial transcription factors (TFs) is typically modulated through direct interactions with small molecules. However, these input signals remain unknown for most TFs, even in well-studied model bacteria. Identifying these signals typically requires tedious experiments for each TF. Here, we develop a systematic workflow for the identification of TF input signals in bacteria based on metabolomics and transcriptomics data. We inferred the activity of 173 TFs from published transcriptomics data and determined the abundance of 279 metabolites across 40 matched experimental conditions in Escherichia coli. By correlating TF activities with metabolite abundances, we successfully identified previously known TF-metabolite interactions and predicted novel TF effector metabolites for

SUBMITTER: Trouillon J 

PROVIDER: S-EPMC12494820 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature