Editors' ChoiceMicrobiology

Guanidine throws the riboswitch

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Science Signaling  31 Jan 2017:
Vol. 10, Issue 464, eaam8636
DOI: 10.1126/scisignal.aam8636

A bacterial riboswitch responds to endogenously produced guanidine.

Riboswitches are regulatory elements in bacterial RNA that respond to diverse metabolites. When bound to its ligand, the riboswitch region associated with a gene changes the conformation of the nascent RNA and either suppresses the gene’s expression by terminating transcription or preventing ribosomal binding, or activates gene expression by allowing alternative splicing or preventing the formation of an intrinsic terminator stem. Nelson et al. found that one widespread riboswitch, the ykkC motif, specifically responds to guanidine. Guanidine is a thermal decomposition product of guanine, but whether this is a commonly formed molecule in nature is unknown. The ykkC motif is a predicted riboswitch present in many bacteria and located upstream of genes that code for diverse metabolic enzymes, transporter proteins, and efflux pumps, suggesting that this riboswitch may respond to toxic compounds. In a screen of ~2000 compounds, only guanidine triggered riboswitch-activated reporter gene expression in Bacillus subtilis. In additional reporter assays, guanidine did not activate expression of genes under the control of other riboswitches or of constructs with mutations in ykkC. Deleting the ykkC motif in B. subtilis reduced the concentration of guanidine required to inhibit bacterial growth. An in-line probing assay of RNA structure confirmed that portions of the ykkC RNA undergo similar structural changes upon exposure to guanidine to other riboswitches in response to their ligands but not in response to guanidine analogs. The ykkC motif is frequently found upstream of genes encoding urea carboxylases but not those encoding ureases, although these two types of enzymes are thought to serve the same function. In vitro, recombinant carboxylase from the bacterium Oleomonas sagaranensis exhibited higher catalytic efficiency with guanidine than with urea, suggesting that guanidine is its preferred substrate. Furthermore, guanidine bound to a small multidrug resistance efflux pump, SugE, which is encoded by a gene that contains a ykkC motif. Escherichia coli cells lacking the TolC outer membrane channel and grown in minimal medium expressed ykkC-controlled reporter genes, whereas wild-type cells did not, suggesting that bacteria produce guanidine, which accumulates in cells with compromised efflux capacity. Indeed, mass spectrometry analysis showed that these TolC-deficient cells cultured in minimal medium contained a compound with properties matching guanidine. The authors speculated that bacteria produce guanidine as a result of metabolism of suboptimal substrates and suggested that many ykkC-associated genes may encode proteins involved in guanidine detoxification and export. Mok and Brynildsen further speculate that guanidine could be synthesized as a result of enzyme promiscuity or generated as a toxin against other bacteria.

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