Structural basis for recognition of<i>S</i>-adenosylhomocysteine by riboswitches

Edwards, Anne; Reyes, F.E.; Héroux, A.; Batey, Robert T.

doi:10.1261/rna.2341610

Cited by 68 publications

(65 citation statements)

References 58 publications

(58 reference statements)

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“…On the other hand, a composite molecule that contains helix P1 made from segments that belong to two riboswitch molecules most likely reflects the near-native conformation of the ligand-bound sensing domain. A similar, though smaller domain swap, has recently been documented in the structure of the S-adenosyl-(L)-homocysteine riboswitch (15). Although the domain swap in the THF riboswitch structure does not represent a natural situation, the structure suggests that helix P1 could be relatively easily melted, thereby emphasizing the fine balance between regulation-relevant alternative conformations of this region.…”

Section: Resultssupporting

confidence: 58%

Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch

Huang

Ishibe-Murakami

Patel

et al. 2011

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

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Tetrahydrofolate (THF), a biologically active form of the vitamin folate (B 9 ), is an essential cofactor in one-carbon transfer reactions. In bacteria, expression of folate-related genes is controlled by feedback modulation in response to specific binding of THF and related compounds to a riboswitch. Here, we present the X-ray structures of the THF-sensing domain from the Eubacterium siraeum riboswitch in the ligand-bound and unbound states. The structure reveals an "inverted" three-way junctional architecture, most unusual for riboswitches, with the junction located far from the regulatory helix P1 and not directly participating in helix P1 formation. Instead, the three-way junction, stabilized by binding to the ligand, aligns the riboswitch stems for long-range tertiary pseudoknot interactions that contribute to the organization of helix P1 and therefore stipulate the regulatory response of the riboswitch. The pterin moiety of the ligand docks in a semiopen pocket adjacent to the junction, where it forms specific hydrogen bonds with two moderately conserved pyrimidines. The aminobenzoate moiety stacks on a guanine base, whereas the glutamate moiety does not appear to make strong interactions with the RNA. In contrast to other riboswitches, these findings demonstrate that the THF riboswitch uses a limited number of available determinants for ligand recognition. Given that modern antibiotics target folate metabolism, the THF riboswitch structure provides insights on mechanistic aspects of riboswitch function and may help in manipulating THF levels in pathogenic bacteria.RNA structure | vitamin B9 | tetrahydrobiopterin | coenzyme T he tetrahydrofolate (THF) compounds, biologically active reduced derivatives of folate (vitamin B 9 ), are essential cofactors in one-carbon transfer reactions involved in the biosynthesis of many critical molecules. Therefore, maintaining an adequate cellular level of THF is of primary importance to all living beings. In bacteria, THF can be generated from folate transported from the environment using a special transport system (1) or synthesized de novo. Expression of folate transport and synthetic genes is controlled by riboswitches that respond to THF and related compounds (2).Structured mRNA segments termed riboswitches act as both direct sensors of cellular metabolites and effectors of the regulatory response in all three kingdoms of life (3, 4). Typically, specific binding of a cognate metabolite stabilizes the metabolite-bound conformation of the sensing domain of the riboswitch and, through formation of the regulatory helix P1, directs the folding of the adjacent expression platform that carries signals for transcriptional or translational machineries. If the metabolite concentration does not reach a threshold, the riboswitch adopts an alternative conformation, resulting in an opposite effect on gene expression. Riboswitches respond to various types of metabolites; however, the most widespread and abundant riboswitches, presently counting nine classes, are selective to protei...

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Section: Resultssupporting

confidence: 58%

Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch

Huang

Ishibe-Murakami

Patel

et al. 2011

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

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“…Here, the extra stem-loop in preQ 1 -II indirectly affords submicromolar ligand affinity and tunes the dynamic features of the riboswitch folding landscape as well as the kinetic features underpinning ligand binding. By contrast, the extra P2/P2b stem-loop in the SAH riboswitch is essential because it directly contributes to ligand recognition and binding (17).…”

Section: Truncation Of P4-l4 Impacts the Dynamics And Stability Of Thementioning

confidence: 99%

“…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.…”

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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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“…Despite this disparity, comparisons of bound and free-state aptamers have provided valuable insight into the means by which metabolite binding transmits chemical binding information in the aptamer to distal expression platform signals that activate or attenuate transcription or translation (7,(11)(12)(13). Toward understanding this problem, we undertook a structural and functional analysis of a preQ 1 riboswitch from Thermoanaerobacter tengcongensis in the metabolitebound and free states.…”

mentioning

confidence: 99%

Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation

Jenkins

Krucinska

McCarty

et al. 2011

Journal of Biological Chemistry

116

242

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Riboswitches are RNA regulatory elements that govern gene expression by recognition of small molecule ligands via a high affinity aptamer domain. Molecular recognition can lead to active or attenuated gene expression states by controlling accessibility to mRNA signals necessary for transcription or translation. Key areas of inquiry focus on how an aptamer attains specificity for its effector, the extent to which the aptamer folds prior to encountering its ligand, and how ligand binding alters expression signal accessibility. Here we present crystal structures of the preQ 1 riboswitch from Thermoanaerobacter tengcongensis in the preQ 1 -bound and free states. Although the mode of preQ 1 recognition is similar to that observed for preQ 0 , surface plasmon resonance revealed an apparent K D of 2.1 ؎ 0.3 nM for preQ 1 but a value of 35.1 ؎ 6.1 nM for preQ 0 . This difference can be accounted for by interactions between the preQ 1 methylamine and base G5 of the aptamer. To explore conformational states in the absence of metabolite, the free-state aptamer structure was determined. A14 from the ceiling of the ligand pocket shifts into the preQ 1 -binding site, resulting in "closed" access to the metabolite while simultaneously increasing exposure of the ribosome-binding site. Solution scattering data suggest that the free-state aptamer is compact, but the "closed" free-state crystal structure is inadequate to describe the solution scattering data. These observations are distinct from transcriptional preQ 1 riboswitches of the same class that exhibit strictly ligand-dependent folding. Implications for gene regulation are discussed.

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Structural basis for recognition ofS-adenosylhomocysteine by riboswitches

Cited by 68 publications

References 58 publications

Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch

Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch

Tuning a riboswitch response through structural extension of a pseudoknot

Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation

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