Short autoinhibitory sequences control phase separation of an essential bacterial transcription termination factor

Within cells, across diverse organisms, macromolecular condensation enables spatial and temporal organization of biochemical reactions by organizing proteins and nucleic acids into compositionally distinct membraneless biomolecular condensates. In the gut bacterium Bacteroides thetaiotaomicron, condensate formation by the transcription termination factor Rho (BtRho) increases its termination activity and promotes B. thetaiotaomicron fitness in the mammalian gut. Here, we elucidate the molecular mechanism governing carbon starvation-induced BtRho phase separation. We establish that short, specific amino acid sequences within BtRho's intrinsically disordered region (IDR) control BtRho condensation via complex coacervation. The identified sequences participate in RNA and intra-IDR regulatory interactions that drive condensate formation in vitro and in vivo. We also report that the signaling molecule ppGpp is essential for BtRho phase separation in vivo, binds to purified BtRho in an IDR-dependent manner, and promotes RNA-dependent BtRho condensation in vitro. Our findings demonstrate how specific short sequences within an IDR dictate phase separation in response to nutritional cues.