Riboswitches are ligand-binding parts of a transcript and ligand binding changes their structure so that they control the production of the gene product either by controlling transcriptional elongation or translational initiation. Three studies identify bacterial riboswitches. Furukawa et al. used a bioinformatics approach to identify a previously unknown riboswitch sequence that they called the “czc motif” because ~50% of RNAs identified with this motif were upstream of genes encoding proteins involved in the efflux of cobalt, zinc, and cadmium. Analysis for metal-induced changes in structure showed that a representative of this family of riboswitch motifs exhibited high affinity, cooperative binding to Co2+ and Ni2+ but not to Cu2+, Zn2+, Cd2+, or Mn2+; thus, this was designated a NiCo riboswitch. Structural analysis of another member of the NiCo riboswitch from a different bacteria revealed a mechanism for the cooperative binding of four Co2+ ions and also indicated that the structure adopted an antiterminator structure when it bound Co2+, which would enable production of the gene product containing this riboswitch in the presence of Co2+ (or presumably Ni2+). In vitro transcription assays confirmed that full-length transcripts were only produced in the presence of Co2+ or Ni2+ when the untranslated region contained a functional NiCo riboswitch. An NiCo riboswitch motif is present upstream of a putative cation efflux gene in Clostridium scindens and culturing the cells in increasing amounts of Ni2+ increased the abundance of the transcript of the gene.
The second pair of studies identified Mn2+ as the ligand for the widespread orphan yybP-ykoY riboswitch. Dambach et al. investigated the regulation of mntP, encoding a manganese exporter, the expression of which increases in response to Mn2+ and which contains the consensus motif of the yybP-ykoY riboswitch. Using a reporter gene and various portions of the mntP promoter, two distinct regulatory elements were identified—one that stimulated transcription and one that stimulated translation in the presence of Mn2+. Analysis of induction of the reporter controlled by only the transcriptional regulatory element in strains of Escherichia coli lacking various transcription factors supported a model in which the Mn2+-binding transcription factors MntR and Fur displaced the repressor H-NS to stimulate transcription in the presence of Mn2+. Mutating conserved residues in the yybP-ykoY riboswitch region in the context of the reporter controlled by the translational regulatory element abolished the induction of the reporter by Mn2+. In vitro translational assays with the wild-type or mutated yybP-yykoY riboswitch confirmed the importance of this region in Mn2+-regulated translation. In vitro binding assays confirmed that the mntP riboswitch motif bound more Mn2+ than the mutated version. Binding and reporter gene analysis with yybP-yykoY riboswitch motifs in other gene promoters showed Mn2+-dependent induction. However, some of these exhibited a transcriptional, rather than translational, mechanism. Price et al. determined that the Lactococcus lactis yybP-ykoY riboswitch, which is predicted to form a terminator structure that inhibits synthesis of full-length transcripts, conferred Mn2+–dependent induction of full-length transcripts in vitro and exhibited a structural change consistent with the formation of an antiterminator structure in the presence of Mn2+. Crystal structure analysis of an L. lactis yybP-ykoY riboswitch revealed that this bound to one Mn2+ and one Mg2+. The presence of this riboswitch upstream of yoaB, which encodes a putative P-tye ATPase, may function as a Mn2+ efflux pump. Indeed introduction of yoaB controlled by an inducible promoter in Bacillus subtilis mutants that constitutively produce the Mn2+ uptake transporters enabled growth in the presence of Mn2+, consistent with YoaB functioning as a Mn2+ efflux pump. The identification of Mn2+ as the ligand for the yybP-yykoY riboswitch should enable further investigation into the function of genes in which it is present.
K. Furukawa, A. Ramesh, Z. Zhou, Z. Weinberg, T. Vallery, W. C. Winkler, R. R. Breaker, Bacterial riboswitches cooperatively bind Ni2+ or Co2+ ions and control expression of heavy metal transporters. Mol. Cell 57, 1088–1098 (2015). [Online Journal]
M. Dambach, M. Sandoval, T. B. Updegrove, V. Anantharaman, L. Aravind, L. S. Waters, G. Storz, The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element. Mol. Cell 57, 1099–1109 (2015). [PubMed]
I. R. Price, A. Gaballa, F. Ding, J. D. Helmann, A. Ke, Mn2+-sensing mechanisms of yybP-ykoY orphan riboswitches. Mol. Cell 57, 1110–1123 (2015). [PubMed]