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Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria

¹ Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA
² Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA
³ Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
⁴ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8103, USA

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.

Keywords: COG4708; DUF988; noncoding RNA; pre-queuosine₁ ; queuosine; riboswitch

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