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Riboswitch structure in the ligand‐free state

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Molecular investigations of riboswitches bound to small‐molecule effectors have produced a wealth of information on how these molecules achieve high affinity and specificity for a target ligand. X‐ray crystal structures have been determined for the ligand‐free state for representatives of the preQ1‐I, S‐adenosylmethionine I, lysine, and glycine aptamer classes. These structures in conjunction with complimentary techniques, such as in‐line probing, NMR spectroscopy, Förster resonance energy transfer, small‐angle scattering, and computational simulations, have demonstrated that riboswitches adopt multiple conformations in the absence of ligand. Despite a number of investigations that support ligand‐dependent folding, mounting evidence suggests that free‐state riboswitches interact with their effectors in the sub‐populations of largely prefolded states as embodied by the principle of conformational selection, which has been documented extensively for protein‐mediated ligand interactions. Fundamental riboswitch investigations of the bound and free states have advanced our understanding of RNA folding, ligand recognition, and how these factors culminate in communication between an aptamer and its expression platform. An understanding of these topics is essential to comprehend riboswitch gene regulation at the molecular level, which has already provided a basis to understand the mechanism of action of natural antimicrobials. WIREs RNA 2012, 3:369–384. doi: 10.1002/wrna.114.

Figure 1.

Representative mechanisms of action by which riboswitches regulate gene expression. (a) Schematic depiction of transcriptional repression by a bacterial riboswitch. In the ligand‐free state, the aptamer is not stably folded and favors anti‐terminator helix formation, thus allowing transcription. On binding ligand (star), the folded structure predominates and a rho‐independent terminator helix forms, thus attenuating transcription. (b) A schematic depiction of translational regulation by a bacterial riboswitch. In the ligand‐free state, the aptamer is not stably folded and favors an exposed Shine–Dalgarno (SD) sequence favoring translation. On ligand binding, the folded structure predominates and the SD sequence is sequestered, thus attenuating translation. (c) A schematic depiction of splicing regulation by the THIC thiamine pyrophosphate (TPP) riboswitch from Arabidopsis thaliana. When TPP levels are low the aptamer base pairs with a sequence used in 5′‐splice‐site selection. This bypasses splicing and necessitates use of a 3′‐end processing signal (red rectangle) that yields a short 3′‐UTR associated with high protein expression levels. When TPP levels are high the aptamer binds TPP during transcription and exposes the 5′‐splice site. The ligand‐bound aptamer results in splicing whereby the upstream 3′‐end processing site is removed, which necessitates the use of an inferior downstream processing site. This results in a longer, unstable mRNA that produces lower quantities of THIC protein.

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Figure 2.

Cartoon and ball‐and‐stick diagrams of the S‐adenosylmethionine (SAM)‐I riboswitch aptamer domains. (a) Cartoon depiction of the Thermoanaerobacter tengcongensis SAM‐I riboswitch structure in the ligand‐bound state. SAM is depicted as space‐filling surface (green); PK is the abbreviation for pseudoknot. A common color code is used in all figures, which corresponds to the pairing (P) and joining (J) regions. Dashed black lines show putative hydrogen bonds. The coordinates are from PDB entry 2GIS. (b) The SAM ligand‐binding site in the bound state derived from (a). (c) The SAM‐binding site in the ligand‐free state. The coordinates are from PDB entry 3IQP. (d) Cartoon diagram of the tertiary structure of the Bacillus subtilis SAM‐I riboswitch from PDB entry 3NPB.

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Figure 3.

Cartoon and ball‐and‐stick diagrams of the metX S‐adenosylmethionine (SAM)‐II riboswitch from the Sargasso Sea metagenome. (a) Cartoon showing the tertiary structure of the SAM‐II riboswitch in the bound state. The coordinates are from PDB entry 2QWY. (b) Ball‐and‐stick diagram of the structure in (a) showing interactions with SAM; red dashed lines indicate putative electrostatic interactions. (c) Close up view of the interaction between A19 and A47 showing the potential for chemical modification.

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Figure 4.

Cartoon, ball‐and‐stick, and secondary structure diagrams of the S‐adenosylmethionine (SAM)‐III (SMK) riboswitch from Enterococcus faecalis. (a) Cartoon diagram showing the tertiary structure of the SMK riboswitch in the ligand‐bound state. The coordinates are from PDB entry 3E5C. (b) Ball‐and‐stick diagram of the structure in (a) showing interactions between SAM and nucleotides A73 and G26 involved in SAM binding. (c) Additional interactions for the structure in (a) between SAM and nucleotides that stabilize ligand binding. (d) Secondary structure of the E. faecalis SMK riboswitch when SAM is absent. Nucleotides in blue are present in SMK59 and absent in SMK5160; the ribosome‐binding site (RBS) is highlighted in yellow. (e) Secondary structure of the E. faecalis SMK riboswitch when ligand is present. Nucleotides in blue are present in SMK59 and absent in SMK51.60

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Figure 5.

Cartoon, ball‐and‐stick, and secondary structure diagrams of the adenine and guanine riboswitches. (a) Cartoon diagram showing the tertiary structure of the Bacillus subtilis xpt guanine binding riboswitch. The coordinates are from PDB entry 1Y27. (b) Cartoon diagram showing the tertiary structure of the Vibrio vulnificus add adenine riboswitch. The coordinates are from PDB entry 1Y26. (c) Ball‐and‐stick diagram of the structure in (a) showing interactions between guanine and the riboswitch. (d) Ball‐and‐stick diagram of the structure in (b) showing interactions between adenine and the riboswitch. (e) Secondary structure diagram of the pbuE adenine riboswitch in the bound state. Nucleotides that were mutated to disrupt loop–loop interactions are highlighted in green as described in the text and Ref 64.

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Figure 6.

Cartoon and ball‐and‐stick diagrams of the Thermoanaerobacter tengcongensis preQ1‐I riboswitch. (a) Cartoon diagram showing the tertiary structure of the riboswitch. The A‐rich pseudoknotted tail is shown in blue. The coordinates are from PDB entry 3Q50. (b) Ball‐and‐stick diagram of the structure in (a) showing interactions between preQ1and the aptamer. (c) The preQ1‐binding site in the ligand‐free state from PDB entry 3Q51.

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Figure 7.

Cartoon and ball‐and‐stick diagrams of the Thermotoga maritima lysine riboswitch. (a) Cartoon diagram showing the tertiary structure of the lysine riboswitch in the bound state. The coordinates are from PDB entry 3DIL. (b) Ball‐and‐stick diagram of the structure in (a) showing hydrogen bonds with the riboswitch and coordination with a potassium ion; water is shown as a red sphere. The coordinates were derived from PDB entry 3DIL (c) The lysine‐binding site in the ligand‐free state riboswitch. No significant conformational changes are observed compared to the structure in (b). The coordinates were derived from PDB entry 3DIS.

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Figure 8.

Cartoon and ball‐and‐stick diagrams of the Vibrio cholerae VCII glycine riboswitch. (a) Cartoon diagram depicting the tertiary structure of the glycine VCII riboswitch in the ligand‐bound state. The coordinates are from PDB entry 3OWW. (b) Ball‐and‐stick diagram of the structure in (a) showing hydrogen bonds between the riboswitch and glycine. (c) The VCII glycine‐binding site from a ligand‐free crystal structure of the VCII glycine riboswitch. There are no substantial conformational changes relative to the bound structure. The coordinates were derived from PDB entry 3OX0.

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RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions
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