Temperate phages enhance host fitness via RNA-guided flagellar remodeling

Bacterial flagella drive motility and chemotaxis while also playing critical roles in host-pathogen interactions, as their oligomeric subunit, flagellin, is specifically recognized by the mammalian immune system and serves as a receptor for flagellotropic phages. Recent work uncovered RNA-guided transcription factors (TldRs) that regulate flagellin expression. However, the biological significance for this regulation, particularly in the context of host fitness, remained unknown. Here, we describe a Flagellin Remodeling prophage (FR phage) from a human clinical Enterobacter isolate that uses an RNA-guided TldR and a phage-encoded flagellin isoform to rewire the host's flagellar composition. This transformation has striking biological consequences, enhancing bacterial motility and mammalian immune evasion, and structural studies by cryo-EM of host- and prophage-encoded filaments reveal distinct architectures underlying these physiological changes. Moreover, we find that FR phage improves colonization in the murine gut, illustrating the beneficial effect of prophage-mediated flagellar remodeling in a host-associated environment. Remarkably, flagellin-regulating TldR homologs emerged multiple times independently, further highlighting the strong selective pressures that drove evolution of RNA-guided flagellin control. Collectively, our results reveal how RNA-guided transcription factors emerged in a parallel evolutionary path to CRISPR-Cas and were co-opted by phages to remodel the flagellar apparatus and enhance host fitness.