The small RNA SuhB regulates metabolic functions and stress response in Sphingopyxis granuli TFA

Post-transcriptional regulation by small RNAs (sRNAs) allows bacteria to fine-tune gene expression and rapidly adapt to fluctuating environmental conditions. In the environmental alphaproteobacterium Sphingopyxis granuli TFA, SuhB is the only sRNA characterized to date and was previously shown to control the degradation of the organic solvent tetralin under carbon catabolite repression. Here, we reveal additional regulatory roles of SuhB beyond carbon metabolism that position this sRNA as a global post-transcriptional regulator influencing metabolic adaptation and stress response. Deletion of suhB increases sensitivity to multiple abiotic stresses, including osmotic, oxidative, desiccation, and copper stress. Label-free quantitative proteomic analysis further reveals widespread alterations in the proteome in the absence of SuhB, affecting metabolic pathways and membrane-associated proteins with a notable impact on TonB-dependent receptors. Combining these results with bioinformatic analysis and translational reporter assays, we identified new SuhB targets, including genes involved in polyhydroxybutyrate biosynthesis. In addition, we identify a LysR-type transcriptional regulator that directly binds to the suhB promoter and activates its expression.