A global regulatory atlas of Streptomyces reveals conserved and diversified transcriptional networks across actinomycetes

Abstract

Transcriptional regulatory networks determine how bacteria integrate environmental signals with growth, metabolism and stress adaptation. Actinomycetes encode exceptionally large repertoires of transcription factors (TFs) coordinating morphological development, environmental adaptation and specialized metabolism, yet their regulatory networks remain poorly defined. Here, we apply DNA affinity purification sequencing (DAP-seq) to 789 predicted TFs of Streptomyces coelicolor, generating genome-wide binding maps for 393 regulators and expanding the experimentally supported regulome from [~]8% to [~]50%. Integration with ChIP-seq reveals pleiotropic regulators and hierarchical network architecture linking primary metabolism, development and biosynthetic gene clusters (BGCs). Multiplexed DAP-seq (multiDAP) across 16 additional actinomycetes uncovered deeply conserved regulatory circuits alongside widespread divergence in TF-target interactions. Together, these data establish a regulatory atlas for Streptomyces and related actinomycetes, enabling researchers to explore control of genes, pathways, BGCs and conserved network modules. This provides a foundation for predictive analysis and engineering of complex bacterial phenotypes in biotechnology and medicine.