Identification of small regulatory RNAs involved in persister formation

Small regulatory RNA (srRNA) is widely distributed in three kingdoms of life and fulfills functions in many aspects of cellular life, but their role in bacterial persistence remains unknown. In this study, we comprehensively interrogated the expression levels of the known srRNAs on three critical time points, stage 1 (S1) where no persisters are formed, stage 2 (S2) where persisters are beginning to appear, and stage 3 (S3) where persister numbers increase significantly. Three upregulated srRNAs (OmrB, an outer member associated srRNA; RdlB, a swarming motility and curli expression regulator; McaS, a flagellar motility and biofilm formation regulator) overlapping in S2/S1 and S3/S1, together with the other four upregulated srRNAs (MicF, a ribosome binding inhibitor; MicL, an outer membrane associated srRNA; RybB, a cell envelope stress regulator; RydB, regulator of a global regulator RpoS) in S2/S1 are of special interest. By constructing deletion mutants and overexpression strains in uropathogenic E. coli strain UTI89, we tested their persister-formation capabilities in log phase and stationary phase cultures exposed to antibiotics (gentamicin, cefotaxime and levofloxacin) and stresses (heat, hyperosmosis, H₂O₂, and acid). The results of the deletion mutant studies showed that all the seven identified sRNAs have varying effects on persister formation with different antibiotics or stresses. Moreover, we found all the deletion mutants of these srRNAs have reduced biofilm formation. Additionally, except the McaS and the RydB overexpression strains, all of the srRNAs overexpression strains demonstrated increased persister-formation in antibiotic and stress persister assays, confirming the role of these srRNAs in persistence. Together, we identified seven srRNAs (OmrB, RdlB, McaS, MicF, MicL, RybB, and RydB) that are involved in type II persister formation for the first time. These findings provide convincing evidence for a new level of rapid persistence regulation via srRNA and furnish novel therapeutic targets for intervention.