A second riboswitch class for the enzyme cofactor NAD⁺

Abstract

A bacterial noncoding RNA motif almost exclusively associated with <i>pnuC</i> genes was uncovered using comparative sequence analysis. Some PnuC proteins are known to transport nicotinamide riboside (NR), which is a component of the ubiquitous and abundant enzyme cofactor nicotinamide adenine dinucleotide (NAD⁺). Thus, we speculated that the newly found "<i>pnuC</i> motif" RNAs might function as aptamers for a novel class of NAD⁺-sensing riboswitches. RNA constructs that encompass the conserved nucleotides and secondary structure features that define the motif indeed selectively bind NAD⁺, nicotinamide mononucleotide (NMN), and NR. Mutations that disrupt strictly conserved nucleotides of the aptamer also disrupt ligand binding. These bioinformatic and biochemical findings indicate that <i>pnuC</i> motif RNAs are likely members of a second riboswitch class that regulates gene expression in response to NAD⁺ binding.