Miniature NAD + -II riboswitches control bacterial genes for nicotinamide salvage and de novo NAD + biosynthesis

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous enzyme cofactor that serves as a carrier of hydride ions for metabolic oxidation-reduction reactions. NAD is also sometimes used as a source of activated adenosine monophosphate (AMP) for adenylation reactions or as a precursor of ADP-ribose upon removal of nicotinamide. Many bacterial riboswitch classes are known to sense nucleotide-derived enzyme cofactors, but NAD is one of several ancient cofactors that have few or no known riboswitch representatives. Two rare riboswitch classes, named NAD⁺-I and NAD⁺-II, have been reported that regulate genes relevant to NAD biosynthesis and transport. However, these RNAs exhibit unusual functional and structural properties. Here we report that miniature NAD⁺-II riboswitches, named mini-NAD⁺-II, are more abundant and widespread than the longer RNAs that were used to define the original consensus model for this class. The newfound examples are commonly found within lactic acid bacteria, which are notable for varied metabolic fermentation strategies used to maintain sufficient NAD⁺ Furthermore, the simple H-type pseudoknot core of mini-NAD⁺-II aptamers is similar to that of class I preQ₁ riboswitch (preQ₁-I) aptamers. Thus, H-type pseudoknots might serve as a versatile architecture for the natural or synthetic construction of ligand-binding aptamers.