Chem. Biol. 22, 829–837 (2015)

Structure 23, 1375–1381 (2015)

Nat. Struct. Mol. Biol. doi:10.1038/nsmb.3073

Credit: NSMB

ZMP is an intermediate in purine biosynthesis that, along with its triphosphate analog ZTP, serves as an alarmone for 10-formyl-THF starvation. This 'alarm' is sensed by a riboswitch located in the upstream regions of several genes involved in purine and folate metabolism. Three research groups now report the structural basis for this interaction. All three papers found that the ZMP ligand is bound within a pseudoknot formed by two distal sequences, with nucleotide pairing primarily as predicted from prior work. The ligand forms a variety of intermolecular interactions with the RNA scaffold, including hydrogen bonds to the sugar ring and π-stacking of the ZMP nucleobase with several RNA bases. Trausch et al., in their analysis of an engineered riboswitch from Actinomyces odontolyticus, note that this highly specific pocket explains how the riboswitch discriminates against the more prevalent and larger AMP and IMP bases. Ren et al., working on the riboswitch from Thermosinus carboxydivorans, explore the relative contributions of these interactions by testing truncated ZMP analogs and RNA mutants, confirming the precise molecular recognition of the pair. Unlike these productive interactions, the monophosphate group is pointed out of the binding pocket, explaining why the riboswitch does not discriminate between ZMP and ZTP. All three reports also notice an unusual interaction between the carbonyl amide of the ZMP nucleobase and a coordinated Mg2+ ion. Finally, Jones and Ferré-D'Amaré noted that the length of the linker region between the two distal sequences varies widely; in vitro assays of constructs derived from the riboswitch from Fusobacterium ulcerans confirmed that longer linkers yielded entropic penalties in riboswitch assembly, leading to smaller modulations by ZMP in a transcription assay. These combined studies provided a detailed look at unique interactions in alarmone sensing.