Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

Abstract

Bioinformatics searches of eubacterial genomes have yielded many riboswitch candidates where the identity of the ligand is not immediately obvious on examination of associated genes. One of these motifs is found exclusively in the family Streptococcaceae within the 5′ untranslated regions (UTRs) of genes encoding the hypothetical membrane protein classified as COG4708 or DUF988. While the function of this protein class is unproven, a riboswitch binding the queuosine biosynthetic intermediate pre-queuosine1 (preQ1) has been identified in the 5′ UTR of homologous genes in many Firmicute species of bacteria outside of Streptococcaceae. Here we show that a representative of the COG4708 RNA motif from Streptococcus pneumoniae R6 also binds preQ1. Furthermore, representatives of this RNA have structural and molecular recognition characteristics that are distinct from those of the previously described preQ1 riboswitch class. PreQ1 is the second metabolite for which two or more distinct classes of natural aptamers exist, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. Additionally, the association of preQ1 binding RNAs with most genes encoding proteins classified as COG4708 strongly suggests that these proteins function as transporters for preQ1 or another queuosine biosynthetic intermediate.