The ydaO-yuaA RNA motif is a putative regulatory element found upstream of ydaO and ktrAB genes in Bacillus subtilis and related Gram-positive bacteria . Since the KtrAB potassium ion transporter is involved in osmoadaptation of B. subtilis , it was proposed that the ydaO RNA motif may be triggered during osmotic shock. However, transcriptome analysis of osmotically shocked B. subtilis did not reveal an increased level of expression of either ydaO of ktrAB genes . Further work has established that the ydaO element is widespread and is associated with a diverse set of genes which it controls in a sequence and structure-dependent fashion.
In-line probing of the RNA associated with the ydaO gene in B. subtilis confirmed the structural organization of the ydaO element [20511502
]. The genetic experiments also confirmed that the ydaO element is involved in the transcriptional control of downstream genes [20511502
]. In vivo experiments in B. subtilis suggested that the ligand of ydaO riboswitch is present in cells grown a defined media. However, the riboswitch natural ligand has not been yet identified.