Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria

An
intriguing consequence of ongoing riboswitch discovery efforts
is the occasional identification of metabolic or toxicity response
pathways for unusual ligands. Recently, we reported the experimental
validation of three distinct bacterial riboswitch classes that regulate
gene expression in response to the selective binding of a guanidinium
ion. These riboswitch classes, called guanidine-I, -II, and -III,
regulate numerous genes whose protein products include previously
misannotated guanidine exporters and enzymes that degrade guanidine
via an initial carboxylation reaction. Guanidine is now recognized
as the primal substrate of many multidrug efflux pumps that are important
for bacterial resistance to certain antibiotics. Guanidine carboxylase
enzymes had long been annotated as urea carboxylase enzymes but are
now understood to participate in guanidine degradation. Herein, we
report the existence of a fourth riboswitch class for this ligand,
called guanidine-IV. Members of this class use a novel aptamer to
selectively bind guanidine and use an unusual expression platform
arrangement that is predicted to activate gene expression when ligand
is present. The wide distribution of this abundant riboswitch class,
coupled with the striking diversity of other guanidine-sensing RNAs,
demonstrates that many bacterial species maintain sophisticated sensory
and genetic mechanisms to avoid guanidine toxicity. This finding further
highlights the mystery regarding the natural source of this nitrogen-rich
chemical moiety.