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

Jenkins, Jermaine L.; Krucinska, J.; McCarty, Reid M.; Bandarian, Vahe; Wedekind, Joseph E.

doi:10.1074/jbc.m111.230375

Cited by 119 publications

(267 citation statements)

References 64 publications

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“…Surface Plasmon Resonance-To analyze HIV-1 RT T/P interaction, we utilized a surface plasmon resonance technology that was previously described (26,27). In this study we used a Biacore T200 (Biacore Inc., Piscataway, NJ) and a Series S streptavidin-coated (SA) sensor chip (GE Healthcare).…”

Section: Methodsmentioning

confidence: 99%

Effect of Ribonucleotides Embedded in a DNA Template on HIV-1 Reverse Transcription Kinetics and Fidelity

Daddacha

Noble²,

Nguyen

et al. 2013

Journal of Biological Chemistry

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Background: Under limiting dNTP concentrations, HIV-1 RT incorporates rNTPs during DNA synthesis. Results: HIV-1 RT utilizes dNTP less efficiently around rNMPs, and mismatch extension fidelity is significantly reduced. Conclusion: Presence of an rNMP in DNA template slows HIV-1 RT-mediated DNA synthesis and reduces fidelity. Significance: This study provides insight into how rNMP incorporation during proviral DNA synthesis can affect HIV-1 replication kinetics and fidelity.

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Section: Methodsmentioning

confidence: 99%

Effect of Ribonucleotides Embedded in a DNA Template on HIV-1 Reverse Transcription Kinetics and Fidelity

Daddacha

Noble²,

Nguyen

et al. 2013

Journal of Biological Chemistry

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“…preQ 1 -I riboswitches have among the smallest known minimal aptamers, at 34 nt (26), but preQ 1 -II riboswitch aptamers are much larger, at ∼60 nt (27). High-resolution X-ray crystal and solution NMR structures have revealed that preQ 1 -I aptamers form H-type pseudoknots with two stems and three loops (33)(34)(35)(36). Subsequent studies detailing preQ 1 -I riboswitch dynamics and folding pathway have shown that divalent cations bind loop 1 and stabilize the bound conformation (21, 37).…”

mentioning

confidence: 99%

Structural determinants for ligand capture by a class II preQ ₁ riboswitch

Kang

Eichhorn²,

Feigon

2014

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

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Prequeuosine (preQ 1 ) riboswitches are RNA regulatory elements located in the 5′ UTR of genes involved in the biosynthesis and transport of preQ 1 , a precursor of the modified base queuosine universally found in four tRNAs. The preQ 1 class II (preQ 1 -II) riboswitch regulates preQ 1 biosynthesis at the translational level. We present the solution NMR structure and conformational dynamics of the 59 nucleotide Streptococcus pneumoniae preQ 1 -II riboswitch bound to preQ 1 . Unlike in the preQ 1 class I (preQ 1 -I) riboswitch, divalent cations are required for high-affinity binding. The solution structure is an unusual H-type pseudoknot featuring a P4 hairpin embedded in loop 3, which forms a three-way junction with the other two stems. 13 C relaxation and residual dipolar coupling experiments revealed interhelical flexibility of P4. We found that the P4 helix and flanking adenine residues play crucial and unexpected roles in controlling pseudoknot formation and, in turn, sequestering the Shine-Dalgarno sequence. Aided by divalent cations, P4 is poised to act as a "screw cap" on preQ 1 recognition to block ligand exit and stabilize the binding pocket.Comparison of preQ 1 -I and preQ 1 -II riboswitch structures reveals that whereas both form H-type pseudoknots and recognize preQ 1 using one A, C, or U nucleotide from each of three loops, these nucleotides interact with preQ 1 differently, with preQ 1 inserting into different grooves. Our studies show that the preQ 1 -II riboswitch uses an unusual mechanism to harness exquisite control over queuosine metabolism.R iboswitches are functional noncoding RNA elements often found at the 5′ end of genes that bind to effector molecules, usually metabolites, to attenuate gene expression (1-8). They generally contain two modular elements, an aptamer that binds directly to a cognate ligand, followed by an expression platform that carries out the regulatory function. Ligand binding induces a conformational rearrangement in the aptamer domain, which is transduced to the expression platform, turning gene expression on or off at the transcription or translation level.Structural studies of diverse riboswitches bound to their cognate ligands have revealed that they have evolved various strategies for high-affinity and specific binding between RNA receptors and ligands. In general, the aptamer domain enfolds the ligand, forming a highly complex 3D conformation using a host of tertiary interactions, including base triples, kink turns, ribose zippers, A-minor motifs, loop-loop interactions, and pseudoknots (9-11). Some riboswitches require divalent cations for ligand binding (9, 12-16), whereas in others divalent cations stabilize the bound state (17-21). Some ligands, including S-adenosyl methionine (22), S-adenosyl homocysteine (22, 23), cyclic di-GMP (24, 25), and prequeuosine (preQ 1 ) (26, 27), have more than one class of riboswitch, with each class adopting a different 3D fold to achieve recognition of the same ligand.Two classes of riboswitches that bind preQ 1 , a precursor t...

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“…Correspondingly, the preQ 1 -II riboswitch represents a putative target for antibiotic intervention. Although preQ 1 class I (preQ 1 -I) riboswitches have been extensively investigated (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28), preQ 1 class II (preQ 1 -II) riboswitches have been largely overlooked despite the fact that a different mode of ligand binding has been postulated (14).…”

mentioning

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

Cited by 119 publications

References 64 publications

Effect of Ribonucleotides Embedded in a DNA Template on HIV-1 Reverse Transcription Kinetics and Fidelity

Effect of Ribonucleotides Embedded in a DNA Template on HIV-1 Reverse Transcription Kinetics and Fidelity

Structural determinants for ligand capture by a class II preQ ₁ riboswitch

Tuning a riboswitch response through structural extension of a pseudoknot

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

Cited by 119 publications

References 64 publications

Effect of Ribonucleotides Embedded in a DNA Template on HIV-1 Reverse Transcription Kinetics and Fidelity

Effect of Ribonucleotides Embedded in a DNA Template on HIV-1 Reverse Transcription Kinetics and Fidelity

Structural determinants for ligand capture by a class II preQ 1 riboswitch

Tuning a riboswitch response through structural extension of a pseudoknot

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Structural determinants for ligand capture by a class II preQ ₁ riboswitch