Structure-based prokaryotic transcription shapes adaptation and host–invader interplay

Prokaryotic gene regulation is governed by the dynamic conformation of the transcription machinery and the nucleoid. To navigate environmental fluctuations, prokaryotes reprogram RNA polymerase (RNAP) via σ factors and transcription factors (TFs) that remodel DNA conformation. Bacteriophages, in turn, exploit these mechanisms to hijack host gene expression. This review dissects recent structural insights into transitions governing transcriptional regulation, highlighting that both TFs and nucleoid-associated proteins act as ‘architects' to remodel DNA structure, thereby blurring the traditional distinction between site-specific regulators and global genome organizers. By linking RNAP and DNA remodeling to broader prokaryotic conflicts, from stress adaptation to arms races between hosts and mobile genetic elements, the authors underscore the profound biological impact of perturbing prokaryotic transcriptional architecture.