A Novel Glutamine Riboswitch, LRN, Regulates the Expression of a Nucleoside Permease in Bacillus thuringiensis

Knowledge of the regulatory mechanism of riboswitches is vital for understanding how microorganisms cope with changes in both intracellular and extracellular environments and for developing and applying RNA biosensors. To date, two types of glutamine-based riboswitches, which are exclusively distributed in cyanobacteria, have been identified. Here, we found an RNA regulatory element in the 5'UTR of the nucleoside permease gene (nupC) in Bacillus thuringensis BMB171; it was identified as a novel glutamine riboswitch and named LRN (leader RNA of nupC). Unlike the two previously known types of glutamine riboswitches found in cyanobacteria, LRN is a single-domain RNA element representing a novel type III glutamine riboswitch. Binding glutamine leads to rearrangements the LRN RNA structure, which inhibits downstream gene expression at the transcriptional level. Biocomputational searches revealed that LRN is frequently found in the Bacillus cereus group and is located mainly upstream of the coding region of the nupC homologues. Thus, this RNA-based sensing mechanism establishes a regulatory feedback loop that couples intracellular glutamine levels to nucleoside transport, which is shared by the B. cereus group.