Ann-Sophie Rüttiger (Würzburg / DE), Daniel Ryan (Würzburg / DE), Luisella Spiga (Nashville, TN / US), Vanessa Lamm-Schmidt (Würzburg / DE), Gianluca Prezza (Würzburg / DE), Sarah Reichardt (Würzburg / DE), Lars Barquist (Würzburg / DE), Franziska Faber (Würzburg / DE), Wenhan Zhu (Nashville, TN / US), Alexander J. Westermann (Würzburg / DE)
Paramount to human health, symbiotic bacteria in the gastrointestinal tract rely on the breakdown of complex polysaccharides to thrive in this sugar-deprived environment. Gut Bacteroides, as metabolic generalists, deploy dozens of polysaccharide utilization loci (PULs) to forage diverse dietary and host-derived glycans. The expression of the multi-protein PUL complexes is tightly regulated at the transcriptional level. However, how PULs are orchestrated at translational level in response to fluctuating substrate levels is unknown. Here, we identify the RNA-binding protein RbpB and a family of noncoding RNAs as key players in post-transcriptional PUL regulation. Ablation of RbpB in Bacteroides thetaiotaomicron compromises colonization in the mouse gut, dependent on the host diet. Current dogma holds that individual PULs are regulated by dedicated transcriptional regulators. We demonstrate that RbpB acts as a global RNA binder interacting with several hundred cellular transcripts. This includes a paralogous noncoding RNA family comprised of 14 members, the FopS (family of paralogous sRNAs) cluster. Through a series of in-vitro and in-vivo assays, we reveal that FopS sRNAs repress the translation of a SusC-like glycan transporter when substrates are limited —an effect antagonized by RbpB. Together, this study implicates RNA-coordinated metabolic control as an important, yet overlooked, factor contributing to the in-vivo fitness of Bacteroides in dynamic nutrient landscapes.