Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

Abstract

SUMMARY The guanidyl moiety is a component of fundamental metabolites including the amino acid arginine, the energy carrier creatine, and the nucleobase guanine. Curiously, reports regarding the importance of free guanidine in biology are sparse and no biological receptors that specifically recognize this compound have been previously identified. We report that many members of the ykkC motif RNA, the longest-unresolved riboswitch candidate, naturally sense and respond to guanidine. This RNA is found throughout much of the bacterial domain of life, where it commonly controls the expression of proteins annotated as urea carboxylases and multidrug efflux pumps. Our analyses reveal that these proteins likely function as guanidine carboxylases and guanidine transporters, respectively. Furthermore, we demonstrate that bacteria are capable of endogenously producing guanidine. These and related findings demonstrate that free guanidine is a biologically relevant compound and several gene families exists that can alleviate guanidine toxicity.

Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

“…Furthermore, each discovery links the riboswitch ligand to the protein products of the genes under regulation. Recent riboswitch findings have exposed unique facets of biology, such as the widespread molecular mechanisms that confer fluoride (5) or guanidine (6) resistance, that maintain metal ion homeostasis (7)(8)(9), and that control important bacterial processes such as sporulation, biofilm formation, and chemotaxis (10)(11)(12)(13)(14). Thus, the identification of additional riboswitch classes promises to offer insights into otherwise hidden biological processes and their regulation.…”

“…Three additional ligand specificity changes are suspected. Namely, some molybdenum cofactor riboswitches appear to exploit an altered aptamer structure to selectively recognize tungsten cofactor (20), certain flavin mononucleotide (FMN) riboswitches carry binding site mutations that alter ligand specificity (21,22), and a large number of guanidine-I riboswitches carry mutations in the binding pocket and sense an as-yet-unknown ligand (6).…”

Structural Basis for Ligand Binding to the Guanidine-I Riboswitch

“…They also investigated a transporter (a SugE protein) in Clostridiales controlled by the guanidine-I riboswitch. They found that intrinsic fluorescence of tryptophan residues increases in a guanidine-dependent manner (K d ~1 mM), providing preliminary evidence that this transporter specifically recognizes guanidine (Nelson et al, 2016). …”

“…Ligand identification has proven elusive due to the wide variety of poorly studied genes under its control (Meyer et al, 2011). Nelson et al recently demonstrated that guanidine is the ykkC ligand (Nelson et al, 2016). …”

“…Genes associated with this riboswitch include genes annotated as urea carboxylases, urea carboxylase-associated proteins, and a variety of transporters, including multidrug resistance efflux proteins (Nelson et al, 2016). The guanidine riboswitch exists in the 5’ untranslated region of these genes.…”