Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates

The ykkC RNA motif
was a long-standing orphan
riboswitch candidate that has recently been proposed to encompass
at least five distinct bacterial riboswitch classes. Most ykkC RNAs belong to the subtype 1 group, which are guanidine-I
riboswitches that regulate the expression of guanidine-specific carboxylase
and transporter proteins. The remaining ykkC RNAs
have been organized into at least four major categories called subtypes
2a–2d. Subtype 2a RNAs are riboswitches that sense the bacterial
alarmone ppGpp and typically regulate amino acid biosynthesis genes.
Subtype 2b riboswitches sense the purine biosynthetic intermediate
PRPP and frequently partner with guanine riboswitches to regulate
purine biosynthesis genes. In this study, we examined ykkC subtype 2c RNAs, which are found upstream of genes encoding hydrolase
enzymes that cleave the phosphoanhydride linkages of nucleotide substrates.
Subtype 2c representatives mostly recognize adenosine and cytidine
5′-diphosphate molecules in either their ribose or deoxyribose
forms (ADP, dADP, CDP, and dCDP). Other nucleotide-containing compounds,
especially nucleoside 5′-triphosphates, are strongly rejected
by some members of this putative riboswitch class. High ligand concentrations in vivo are predicted to turn on expression of hydrolase
enzymes, which presumably function to balance cellular nucleotide
pools. These results further showcase the striking functional diversity
derived from the structural scaffold shared among all ykkC motif RNAs, which has been adapted to sense at least five different
types of natural ligands. Moreover, riboswitches for nucleoside diphosphates
provide additional examples of the numerous partnerships observed
between natural RNA aptamers and nucleotide-derived ligands, including
metabolites, coenzymes, and signaling molecules.