Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli.

ABSTRACT: The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in Escherichia coli. We comprehensively predict alternative nitrogen sources, including cytosine and cytidine, which trigger differential activation of Nac using a model-driven workflow. In accordance with the prediction, genome-wide measurements with ChIP-exo and RNA-seq were performed. Integrative data analy

SUBMITTER: Park JY 

PROVIDER: S-EPMC9853098 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature