The ykkC-yxkD RNA motif is a conserved regulatory element found upstream of the ykkC and yxkD genes in Bacillus subtilis and related genes in other bacteria. The ykkCD operon encodes a multidrug resistance efflux pump with a broad specificity, whereas the yxkD gene function is unknown. Genetic reporter assays suggeste the ykkC RNA motif functions as a gene control element [21317561]. Testing of a large collection of metabolites for binding to a ykkC RNA representative from B. subtilis (including putrescine, agmatine, spermidine, uric acid etc.) did not reveal a molecular effector of the ykkC regulatory RNA [21317561]. more

Additional conserved RNA structures, including mini-ykkC, have been identified associated with many of the same genes as the ykkC RNA. The mini-ykkC RNA motif is structurally distinct from the ykkC RNA. Nevertheless, both mini-ykkC and ykkC RNA motifs were hypothesized to respond to the same biological condition or effectors.