Structure of the Guanidine III Riboswitch

Abstract

Riboswitches are structural elements found in mRNA molecules that couple small-molecule binding to regulation of gene expression, usually by controlling transcription or translation. We have determined high-resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot that includes a triple helix that is continuous with a central core of conserved nucleotides. These form a left-handed helical ramp of inter-nucleotide interactions, generating the guanidinium cation binding site. The ligand is hydrogen bonded to the Hoogsteen edges of two guanine bases. The binding pocket has a side opening that can accommodate a small side chain, shown by structures with bound methylguanidine, aminoguanidine, ethylguanidine, and agmatine. Comparison of the new structure with those of the guanidine I and II riboswitches reveals that evolution generated three different structural solutions for guanidine binding and subsequent gene regulation, although with some common elements.

Keywords: RNA structure; X-ray crystallography; gene regulation; riboregulation.

Graphical abstract

Figure 1

The Overall Conformation of the Guanidine III Riboswitch Parallel-eye stereoscopic pairs are shown for the molecular graphics images. (A) Guanidine III riboswitch sequence and secondary structure (adapted from Sherlock et al., 2017). Nucleotides colored red are >97% identical in all species analyzed. Nucleotides are present at the positions shown by circles with 97% (red), 90% (black), 75% (gray), and 50% (open) probability. (B) The Thermobifida fusca ykkC guanidine III riboswitch sequence drawn in the pseudoknot secondary structure, comprising stem-loops P1 and P2. (C) The structure of the guanidinium cation. (D) Schematic illustration of the structure. Nucleotides colored red are >97% identical in all species analyzed. Tertiary hydrogen bonding interactions are indicated by cyan-colored lines. The color scheme shown here is used throughout Figures 2, 3, 4, 5 and 6. (E and F) Two views of the crystal structure, from opposite sides. (G) View of the crystal structure, from the same perspective as (E), in which nucleotides that are conserved with >97% identity are colored red. Note that the sequence of the entire central section of the riboswitch is conserved.

Figure 2

A Parallel-Eye Stereoscopic View of the P1 Helix Plus the Extra Strand Key long-range hydrogen bonds are shown by broken lines.

Figure 3

A Section of the P2 Regular Triple Helix and Two Representative Nucleotide Triplets Note, the regular triple helical section is continuous with the helical ramp shown in Figure 4. (A) A parallel-eye stereoscopic representation of a section of the triplex region. Hydrogen bonds between the third strand (yellow) and the P2 base pairs are highlighted in red. A view down the axis of the triple helix is presented in Figure S4. (B and C) The structures of the nucleotide triplets involving G10 and U11. Sections of the experimental phasing map contoured at 1.2 σ are shown. C39 is 5-bromocytosine (Br) used to phase the diffraction.

Figure 4

The Helical Ramp (A) Scheme of the chain of interactions between ten nucleotides and the guanidine ligand. The Leontis and Westhof (2001) nomenclature has been used to classify the interactions where possible. Broken lines denote hydrogen bonds to the guanidine ligand (g). (B) A parallel eye stereoscopic view of the helical ramp, from A5 to A8. The continuous set of inter-nucleotide interactions form a gentle left-handed helix. In the interest of clarity the ribose-phosphate backbone is not displayed except where the ribose makes a direct interaction. (C–E) Three sections of the ramp shown in greater detail together with their experimental phasing maps contoured at 1.2 σ. Note that the second and third sections depicted are connected via the guanidine bound to G7 and G17 (see Figure 5).

Figure 5

The Guanidine Binding Site of the Guanidine III Riboswitch The experimental phasing maps contoured at 1.2 σ is shown for the guanidine ligand. The guanidine is colored magenta. Hydrogen bonds donated by guanidinium protons are colored red. Note that the guanidinium cation is stacked upon the nucleobase of C6, making a π-cation interaction. (A) A parallel-eye stereoscopic view of the binding pocket. (B) A view down onto the guanidine, simplified to show only nucleotides involved in direct interaction with the ligand. The electron density for a solvent molecule (presumed water) has been included in this image.

Figure 6

Binding of Guanidine Variants of the Guanidine III Riboswitch (A) View into binding pocket showing the side opening. A parallel-eye stereoscopic pair is shown. A transparent surface has been displayed on the riboswitch structure. The guanidine ligand is shown in stick form, colored magenta, and is clearly visible in the cleft in the RNA. (B–F) Alternative ligands bound into the binding pocket of the riboswitch. The experimental phasing maps contoured at 1.2 σ are shown for the ligands. The guanidine variants are colored magenta, and acetate colored green. Ligands: (B) methylguanidine, (C) aminoguanidine, (D) ethylguanidine, (E) agmatine, and (F) acetate bound into the riboswitch crystallized in the absence of added ligand. Further views of the agmatine complex are shown in Figure S5.

Figure 7

Comparison of the Guanidine Binding Sites of the Three Classes of Guanidine Riboswitch Structures The nucleotides have been colored to reflect their function in ligand binding. Guanine bases accepting hydrogen bonds from guanidine at O6 and N7 on the Hoogsteen edge are green (all classes), guanine bases making hydrogen bonds to O6 alone (A guanidine I riboswitch) are blue, nucleotides only making backbone contacts (B guanidine II riboswitch) are gray, and nucleotides making π-cation interaction with the guanidinium cations (all classes) are yellow. The image of the guanidine I riboswitch was prepared using PDB: 5T83 (Reiss et al., 2017), and that of the guanidine II riboswitch (P1 stem-loop) was prepared using PDB: 5NDI (Huang et al., 2017). The guanidine III riboswitch (C) is the present work.