Structural basis for 2′-deoxyguanosine recognition by the 2′-dG-II class of riboswitches

Abstract

A recent bioinformatic analysis of well-characterized classes of riboswitches uncovered subgroups unable to bind to the regulatory molecule of the parental class. Within the guanine/adenine class, seven groups of RNAs were identified that deviate from the consensus sequence at one or more of three positions directly involved purine nucleobase recognition, one of which was validated as a second class of 2′-deoxyguanosine riboswitch (called 2′-dG-II). To understand how 2′-dG-II riboswitches recognize their cognate ligand and how they differ from a previously identified class of 2′-deoxyguanosine binding riboswitches, we have solved the crystal structure of a 2′-dG-II aptamer domain bound to 2′-deoxyguanosine. This structure reveals a global architecture similar to other members of the purine riboswitch family, but contains key differences within the ligand binding core. Defining the 2′-dG-II riboswitches is a two-nucleotide insertion in the three-way junction that promotes novel base-base interactions. Unlike 2′-dG-I riboswitches, the 2′-dG-II class only requires local changes to the ligand binding pocket of the guanine/adenine class to achieve a change in ligand preference. Notably, members of the 2′-dG-II family have variable ability to discriminate between 2′-deoxyguanosine and riboguanosine, suggesting that a subset of 2′-dG-II riboswitches may bind either molecule to regulate gene expression.

Bacterial 2′-Deoxyguanosine Riboswitch Classes as Potential Targets for Antibiotics: A Structure and Dynamics Study

“…Of both 2′-dG riboswitches, the class II predicted binding affinity reproduced the experimental data satisfactorily. The prediction for the rG binding was almost the same as the reported experimental value, approximately −11 kcal/mol [ 12 ], while calculations for dG were not so accurate, and a deviation of almost 6 kcal/mol was observed when compared with the experimental one (−11.6 kcal/mol). When analyzing the ΔG bind decomposition into individual energies in the MM/GBSA method, we noted that the 2′-dG-II riboswitch showed a higher affinity for dG than rG, mainly due to its van der Waals contribution (ΔE vdw ).…”

“…The 2′-dG-I contains a first shell of interacting nucleotides C31, C58, and C80, located approximately <3 Å, similar to equivalent nucleotides U22, C51, and C74 in the 2′-dG-II riboswitch. Cytosine at position 58/51 of the 2′-dG riboswitches classes is critical for establishing selectivity for nucleoside against nucleobasis across the guanine/adenine classes, which has uracil in the same position [ 11 , 12 , 14 ].…”

“…The purine riboswitch family, which regulates aspects of purine biosynthesis and transport in bacteria, recognizes and binds to different ligands like guanine [ 9 ], adenine [ 10 ], or 2′-deoxyguanosine [ 11 , 12 ]. The aptamer domain folding and purine recognition pattern are highly similar within this family of riboswitches.…”

Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding

“…Given the unusual combination of peripheral elements discerned by secondary structure predictions of the B. subtilis cobalamin riboswitch, we considered the possibility that its aptamer domain might exhibit different ligand binding properties as compared to conventional cobalamin riboswitches in a way that is reminiscent of variants of other riboswitch classes, such as purine riboswitches ( 44 , 45 ) and ykkC RNAs ( 46 , 47 ), which utilize different specificity mechanisms but share a common structural scaffold to exhibit altered ligand specificities. Having found an efficient way to incorporate ligand into the riboswitch, we carried out in vitro transcriptions of the same RNA construct with several cobalamin derivatives: adenosylcobalamin, hydroxocobalamin, methylcobalamin, and cyanocobalamin.…”

High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch

“…Discrimination between guanine and adenine is conferred by the pyrimidine residue at position 74 (nucleotide numbering used throughout this work is that of the B. subtilis xpt guanine riboswitch) via the Watson-Crick base pairing with the ligand. Discrimination between nucleobases (guanine and adenine) and nucleosides (2 -deoxyguanosine) is primarily dictated by the identity of the pyrimidine residue at position 51-a uridine (U) for nucleobase recognition and cytidine (C) for nucleoside recognition [18][19][20]. Across a broad spectrum of compounds that bind the guanine riboswitch, the positions of the nucleotides contacting the ligand are fixed (Figure 1B), although a small displacement of cytidine 74 towards the minor groove in relation to the ligand has been observed for a few C6-modified guanine derivatives such as O6-methylguanine and 2-aminopurine [21].…”