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Guanidine‐sensing riboswitches: How do they work and what do they regulate?

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After remaining an orphan for over a decade, the ykkC riboswitch family (ykkC, mini‐ykkC, and ykkC‐III) was recently characterized as guanidine‐specific genetic regulatory elements (guanidine‐I, II, and III). They respond to increased levels of intracellular guanidine by turning on genes involved in guanidine export and breakdown. Their existence suggests that regulation of intracellular guanidine levels could be an important piece of bacterial physiology which was not appreciated previously. Structural biologists moved exceptionally fast to reveal the guanidine‐sensing mechanisms of these riboswitches at the atomic level. The crystal structures of all three guanidine family members have been determined. They appear to represent three independently evolved RNA sensors, with distinct tertiary folds but surprisingly similar guanidine‐binding cores. A few key questions remain to be addressed: It is not known which metabolic pathway(s) may lead to guanidine accumulation and the function of close relatives to the guanidine‐I riboswitch that do not respond to guanidine remains unclear. The continued characterization of these and other orphan cis‐regulatory elements represents an orthogonal approach to reveal new facets of bacterial physiology. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Riboswitches RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry
Guanidine‐I riboswitches. (a) 3D crystal structure of Dickeya dadantii guanidine‐I riboswitch bound to its ligand. Surface model of the structure showing boot shape (inset). (b) Guanidine‐binding pocket of the D. dadantii guanidine‐I riboswitch showing cation–π (G67), hydrogen bonding (black dashes), and electrostatic (gray dashes) interactions. Conserved Hoogsteen edge interaction is made by G85. (c) Schematic of guanidine‐I gene regulatory mechanism. Greater than 90% conserved residues in secondary structure representations are in red
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Guanidine‐I‐, II‐, and III‐binding pockets. (a) Guanidine‐I‐binding pocket with guanidine (cyan). (b) Guanidine‐II‐binding pocket with guanidine (cyan). (c) Guanidine‐III‐binding pocket with guanidine (cyan). Hydrogen bonds are represented by black dashes. Electrostatic interactions are represented by gray dashes
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Guanidine‐III riboswitches. (a) 3D crystal structure of Thermobifida fusca guanidine‐III riboswitch bound to its ligand. (b) Guanidine‐binding pocket of the T. fusca guanidine‐III riboswitch showing cation–π (C6) and hydrogen bonding (black dashes) interactions. (c) Schematic of guanidine‐III regulatory mechanism. Greater than 90% conserved residues in secondary structure representations are in red. (d) Predicted secondary structure of guanidine‐I subtype 2. Circled residues contact guanidine in subtype 1 riboswitches, but have relaxed sequence conservation in subtype 2. Greater than 90% conserved residues are in red. Orange box and question mark indicate some ligands remain to be discovered. Subtype 2a binds ppGpp and subtype 2b binds PRPP. Subtypes 2c and 2d are uncharacterized
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Guanidine‐II riboswitches. (a) 3D crystal structure of Pseudomonas aeruginosa guanidine‐II riboswitch bound to its ligand. (b) Guanidine‐binding pocket of the P. aeruginosa guanidine‐II riboswitch showing cation–π (G6) and hydrogen bonding (black dashes) interactions. Conserved Hoogsteen edge interaction is made by G9. (c) Schematic of guanidine‐II gene regulatory mechanism. Greater than 90% conserved residues in secondary structure representations are in red
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RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry
Regulatory RNAs/RNAi/Riboswitches > Riboswitches

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