Molecular Strategies of Carbohydrates Binding to Intrinsically Disordered Regions in Bacterial Transcription Factors

Intrinsically disordered regions enable transcription factors (TFs) to undergo structural changes upon ligand binding, facilitating the transduction of environmental signals into gene expression. In this study, we combined molecular modeling methods to explore the hypothesis that unstructured inter-domain and subdomain linkers in bacterial TFs can function as sensors for carbohydrate signaling molecules. We combined molecular dy-namics simulations and carbohydrate docking to analyze six repressors with GntR-type DNA-binding domains, including UxuR, GntR and FarR from Escherichia coli, as well as AraR, NagR and YydK from Bacillus subtilis. Protein models obtained from different time points of the dynamic simulations were subjected to the sequential carbohydrates dock-ing. We found that the inter-domain linker of the UxuR monomer binds D-fructuronate, D-galacturonate, D-glucose, and D-glucuronate with affinities lower that its structured FadR-type effector-binding domain. However, in the monomer, these ligands formed mul-timolecular clusters, a feature absent in the dimer, suggesting that protein dimerization may depend on linker occupancy by cellular carbohydrates. Interacting with linkers con-necting subdomains of the LacI/GalR-type E-domains in GntR and AraR, D-glucose was able to form hydrogen bonds connecting distant structural modules of the proteins, while in NagR, FarR and YydK it bridged the inter-domain linkers and a β-sheet within the HutC-type E-domains. Our results establish flexible linkers as pivotal metabolic sensors that directly integrate nutritional cues to alter gene expression in bacteria.