Expanding the genetic tool kit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum

We elucidated the global regulatory network of sigma E in Fusobacterium nucleatum. For this, we developed new genetic tools for the anaerobic bacterium. This uncovered a conserved regulon of the sigma factor including a noncoding arm of the sRNA FoxI. In this process, FoxI serves as a negative regulator of sigma E to downregulate several outer membrane proteins as well as the putative galactose transporter mglBAC. Overall design: Samples were treated with anhydrotetracycline (100ng/ml) or left untreated for 20min (FoxI) or 30min (rpoE) at mid-exponential phase. Samples marked with "shock" were either treated with polymyxin B or exposed to atmospheric oxygen for 20min at mid-exponential phase. Isolated RNA was used for cDNA library generation following the RNA-seq protocol.