Structural Basis for Discriminative Regulation of Gene Expression by Adenine- and Guanine-Sensing mRNAs

Abstract

Metabolite-sensing mRNAs, or "riboswitches," specifically interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, capable of ligand-induced structural changes, and downstream regions, harboring expression-controlling elements. We report the crystal structures of the add A-riboswitch and xpt G-riboswitch aptamer modules that distinguish between bound adenine and guanine with exquisite specificity and modulate expression of two different sets of genes. The riboswitches form tuning fork-like architectures, in which the prongs are held in parallel through hairpin loop interactions, and the internal bubble zippers up to form the purine binding pocket. The bound purines are held by hydrogen bonding interactions involving conserved nucleotides along their entire periphery. Recognition specificity is associated with Watson-Crick pairing of the encapsulated adenine and guanine ligands with uridine and cytosine, respectively.

Towards deciphering the principles underlying an mRNA recognition code

“…Recently, the seminal structure determination of purine-sensing riboswitches [9,10] has been rapidly followed by structures of five more ribosensors: bacterial [11,12] and plant [13] thiamine pyrophosphate (TPP) riboswitches, a Sadenosylmethionine type I (SAM-I) riboswitch [14], a glucosamine-6-phosphate-sensing glmS ribozyme [15,16], a thermosensor [17] and a Mg 2+ ribosensor [18]. Here, we focus on the recent structure of the Mg 2+ ribosensor, since it was not discussed in an earlier review [6].…”

Structural features of metabolite-sensing riboswitches

“…X-ray crystallographic and NMR analyses demonstrate extensive hydrogen bonding interactions between virtually all functional groups within the nucleobase ligand and RNA (Figure 2a and b) [33,34,47]. Specifically, the sugar edge of the purine ligand pairs to the Watson-Crick face of the U51 base.…”

“…Secondary structure patterns of riboswitches that have been established in this manner have generally agreed with threedimensional structural models as determined by X-ray crystallography. Exceptions include regions of extensive non-canonical base interactions and tertiary base contacts that are difficult to predict by sequence analysis alone.Although most helical regions have been successfully predicted by biochemical probing and sequence analyses, recent crystallographic data reveal how they, and their intervening nucleotides, are arranged to form the tertiary conformations adopted for purine-, SAM-, TPP-, and GlcN6P-sensing riboswitches (Figure 2) [28][29][30][31][32][33][34]42]. Similar to published structures of unrelated RNAs, there is extensive co-axial stacking of helices within riboswitches.…”

RNA structural motifs: building blocks of a modular biomolecule

“…3D structures exist for some members of each of these groups that illustrate the binding motifs (Patel & Suri, 2000 ;Adams et al 2004 ;Batey et al 2004 ;Guo et al 2004 ;Serganov et al 2004). Guanine binding by group I intron and riboswitch have been shown to be mediated by a base triple sandwich (stacking) motif (Guo et al 2004 ;Serganov et al 2004). …”