Riboswitches: Ancient and Promising Genetic Regulators

Blouin, Simon; Mulhbacher, Jérôme; Penedo, J. Carlos; Lafontaine, Daniel A.

doi:10.1002/cbic.200800593

Cited by 75 publications

(51 citation statements)

References 157 publications

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“…In a manner that is controlled by metabolite concentration, nascent mRNAs containing riboswitch domains can enter one of two mutually exclusive folding pathways to impart regulatory control: the outcomes of these folding pathways correspond to ligand-bound or ligand-free states (3)(4)(5). These aptamer folds trigger structural cues into the adjoining expression platform, which, in turn, transduce a signal for "on" or "off" gene expression (6)(7)(8)(9).…”

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confidence: 99%

Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution

Haller

Altman

Soulière

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

115

156

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Thiamine pyrophosphate (TPP)-sensitive mRNA domains are the most prevalent riboswitches known. Despite intensive investigation, the complex ligand recognition and concomitant folding processes in the TPP riboswitch that culminate in the regulation of gene expression remain elusive. Here, we used single-molecule fluorescence resonance energy transfer imaging to probe the folding landscape of the TPP aptamer domain in the absence and presence of magnesium and TPP. To do so, distinct labeling patterns were used to sense the dynamics of the switch helix (P1) and the two sensor arms (P2/P3 and P4/P5) of the aptamer domain. The latter structural elements make interdomain tertiary contacts (L5/P3) that span a region immediately adjacent to the ligandbinding site. In each instance, conformational dynamics of the TPP riboswitch were influenced by ligand binding. The P1 switch helix, formed by the 5′ and 3′ ends of the aptamer domain, adopts a predominantly folded structure in the presence of Mg 2+ alone. However, even at saturating concentrations of Mg 2+ and TPP, the P1 helix, as well as distal regions surrounding the TPP-binding site, exhibit an unexpected degree of residual dynamics and disperse kinetic behaviors. Such plasticity results in a persistent exchange of the P3/P5 forearms between open and closed configurations that is likely to facilitate entry and exit of the TPP ligand. Correspondingly, we posit that such features of the TPP aptamer domain contribute directly to the mechanism of riboswitchmediated translational regulation.RNA | site-specific labeling | allosteric effect | structural preorganization | ergodicity R iboswitch elements located within noncoding regions of mRNA bind metabolites with high selectivity and specificity to mediate control of transcription, translation, or RNA processing (1, 2). In a manner that is controlled by metabolite concentration, nascent mRNAs containing riboswitch domains can enter one of two mutually exclusive folding pathways to impart regulatory control: the outcomes of these folding pathways correspond to ligand-bound or ligand-free states (3-5). These aptamer folds trigger structural cues into the adjoining expression platform, which, in turn, transduce a signal for "on" or "off" gene expression (6-9).The thiamine pyrophosphate (TPP)-sensing riboswitch is one of the earliest discovered regulatory elements in mRNA that is prevalent among bacteria, archaea, fungi, and plants (10-12). TPP riboswitches, sometimes present in tandem (13,14), control genes that are involved in the transport or synthesis of thiamine and its phosphorylated derivatives. The TPP-bound aptamer adopts a uniquely folded structure in which one sensor helix arm (P2/P3) forms an intercalation pocket for the pyrimidine moiety of TPP, and the other sensor helix arm (P4/P5) offers a water-lined binding pocket for the pyrophosphate moiety of TPP that engages bivalent metal ions (Fig. 1) (15-17). Like most riboswitch domains, structural information pertaining to the ligand-free TPP riboswitch is relatively ...

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confidence: 99%

Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution

Haller

Altman

Soulière

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

115

156

View full text Add to dashboard Cite

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“…In this form of regulation, the target mRNA typically undergoes a structural change in response to metabolite binding (5)(6)(7)(8)(9). These mRNA elements have thus been termed "riboswitches" and generally include both a metabolite-sensitive aptamer subdomain and an expression platform.…”

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confidence: 99%

Tuning a riboswitch response through structural extension of a pseudoknot

Soulière

Altman

Schwarz

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

102

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Structural and dynamic features of RNA folding landscapes represent critical aspects of RNA function in the cell and are particularly central to riboswitch-mediated control of gene expression. Here, using single-molecule fluorescence energy transfer imaging, we explore the folding dynamics of the preQ 1 class II riboswitch, an upstream mRNA element that regulates downstream encoded modification enzymes of queuosine biosynthesis. For reasons that are not presently understood, the classical pseudoknot fold of this system harbors an extra stem-loop structure within its 3′-terminal region immediately upstream of the Shine-Dalgarno sequence that contributes to formation of the ligand-bound state. By imaging ligand-dependent preQ 1 riboswitch folding from multiple structural perspectives, we reveal that the extra stem-loop strongly influences pseudoknot dynamics in a manner that decreases its propensity to spontaneously fold and increases its responsiveness to ligand binding. We conclude that the extra stem-loop sensitizes this RNA to broaden the dynamic range of the ON/OFF regulatory switch.SHAPE | single-molecule FRET | site-specific labeling | metabolite sensing RNAs | ligand recognition A variety of small metabolites have been found to regulate gene expression in bacteria, fungi, and plants via direct interactions with distinct mRNA folds (1-4). In this form of regulation, the target mRNA typically undergoes a structural change in response to metabolite binding (5-9). These mRNA elements have thus been termed "riboswitches" and generally include both a metabolite-sensitive aptamer subdomain and an expression platform. For riboswitches that regulate the process of translation, the expression platform minimally consists of a ribosomal recognition site [Shine-Dalgarno (SD)]. In the simplest form, the SD sequence overlaps with the metabolite-sensitive aptamer domain at its downstream end. Representative examples include the S-adenosylmethionine class II (SAM-II) (10) and the S-adenosylhomocysteine (SAH) riboswitches (11, 12), as well as prequeuosine class I (preQ 1 -I) and II (preQ 1 -II) riboswitches (13,14). The secondary structures of these four short RNA families contain a pseudoknot fold that is central to their gene regulation capacity. Although the SAM-II and preQ 1 -I riboswitches fold into classical pseudoknots (15, 16), the conformations of the SAH (17) and preQ 1 -II counterparts are more complex and include a structural extension that contributes to the pseudoknot architecture (14). Importantly, the impact and evolutionary significance of these "extra" stem-loop elements on the function of the SAH and preQ 1 -II riboswitches remain unclear.PreQ 1 riboswitches interact with the bacterial metabolite 7-aminomethyl-7-deazaguanine (preQ 1 ), a precursor molecule in the biosynthetic pathway of queuosine, a modified base encountered at the wobble position of some transfer RNAs (14). The general biological significance of studying the preQ 1 -II system stems from the fact that this gene-regulatory element is found...

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“…2 While the receptor binding domain is highly conserved among distant bacteria, the genetic response can range from transcription termination in Gram-positive bacteria to translation initiation in Gram-negative bacteria. 2,52 One possible explanation is that Gram-positive bacteria are characterized by larger gene cluster operons which would benefit from premature transcription attenuation. On the other hand, the two distant bacteria have also evolved different RNA-based strategies to regulate similar genes, i.e., involved in tryptophan biosynthesis 53 or in sugar and carbohydrate utilization.…”

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confidence: 99%