Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

Bailor, Maximillian H.; Sun, Xiao; Al‐Hashimi, Hashim M.

doi:10.1126/science.1181085

Cited by 176 publications

(266 citation statements)

References 29 publications

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“…It is widely appreciated that the topology of local secondary structure motifs can significantly limit the types of spatial configurations possible at helical junctions (Lilley 1998;Batey et al 1999;Tinoco and Bustamante 1999;Lescoute and Westhof 2006;Bailor et al 2010). These geometric constraints often determine the shape and size of small RNA molecules.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, because long RNAs allow for a large number of intramolecular base-pairing combinations having the same energy (Yoffe et al 2008), they are best represented by an ensemble of many thermally accessible secondary structures. Because the topological constraints for tertiary (overall) structures originate from secondary structure (Lilley 1998;Tinoco and Bustamante 1999;Lescoute and Westhof 2006;Bailor et al 2010), the lack of a distinctly preferred secondary structure implies that no two molecules of the same sequence are likely to have the same 3D conformations. This diversity of spatial conformations implies that a long RNA molecule in solution behaves as a statistical object whose properties are derived from an ensemble of possible structures.…”

Section: Introductionmentioning

confidence: 99%

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Visualizing large RNA molecules in solution

Gopal¹,

Zhou²,

Knobler³

et al. 2011

RNA

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Single-stranded RNAs (ssRNAs) longer than a few hundred nucleotides do not have a unique structure in solution. Their equilibrium properties therefore reflect the average of an ensemble of structures. We use cryo-electron microscopy to image projections of individual long ssRNA molecules and characterize the anisotropy of their ensembles in solution. A flattened prolate volume is found to best represent the shapes of these ensembles. The measured sizes and anisotropies are in good agreement with complementary determinations using small-angle X-ray scattering and coarse-grained molecular dynamics simulations. A long viral ssRNA is compared with shorter noncoding transcripts to demonstrate that prolate geometry and flatness are generic properties independent of sequence length and origin. The anisotropy persists under physiological as well as low-ionic-strength conditions, revealing a direct correlation between secondary structure asymmetry and 3D shape and size. We discuss the physical origin of the generic anisotropy and its biological implications.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Visualizing large RNA molecules in solution

Gopal¹,

Zhou²,

Knobler³

et al. 2011

RNA

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“…A critical wobble G-U pair, forming only two of three hydrogen bonds of Watson-Crick G-C, accounts for the deafness of sopD2 to SgrS. This unprecedented discrimination by a single hydrogen bond seems to be independent of base topology, which can allow noncanonical base pairs to impact the formation and strength of RNA duplexes (45). First, flipping the G-C pair in the SgrS-sopD duplex (SI Appendix, Fig.…”

Section: Discussionmentioning

confidence: 99%

The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair

Papenfort

Podkaminski²,

Hinton³

et al. 2012

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

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SgrS RNA is a model for the large class of Hfq-associated small RNAs that act to posttranscriptionally regulate bacterial mRNAs. The function of SgrS is well-characterized in nonpathogenic Escherichia coli , where it was originally shown to counteract glucose-phosphate stress by acting as a repressor of the ptsG mRNA, which encodes the major glucose transporter. We have discovered additional SgrS targets in Salmonella Typhimurium, a pathogen related to E. coli that recently acquired one-quarter of all genes by horizontal gene transfer. We show that the conserved short seed region of SgrS that recognizes ptsG was recruited to target the Salmonella -specific sopD mRNA of a secreted virulence protein. The SgrS– sopD interaction is exceptionally selective; we find that sopD2 mRNA, whose gene arose from sopD duplication during Salmonella evolution, is deaf to SgrS because of a nonproductive G-U pair in the potential SgrS- sopD2 RNA duplex vs. G-C in SgrS- sopD . In other words, SgrS discriminates the two virulence factor mRNAs at the level of a single hydrogen bond. Our study suggests that bacterial pathogens use their large suites of conserved Hfq-associated regulators to integrate horizontally acquired genes into existing posttranscriptional networks, just as conserved transcription factors are recruited to tame foreign genes at the DNA level. The results graphically illustrate the importance of the seed regions of bacterial small RNAs to select new targets with high fidelity and suggest that target predictions must consider all or none decisions by individual seed nucleotides.

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“…For example, junctions (linkers) limit the conformations of unfolded states (52)(53)(54) and can be rigidified by Mg 2þ . In support of this, the [Mg 2þ ]-dependent decrease in the entropic cost of TL-R docking is much more pronounced in the A 7 vs. U 7 constructs (Tables 1 and 2)-suggesting that [Mg 2þ ]-dependent rigidification of the linker is of large entropic benefit to the docking process.…”

Section: Discussionmentioning

confidence: 99%

Entropic origin of Mg ²⁺ -facilitated RNA folding

Fiore

Holmstrom

Nesbitt

2012

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

158

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Mg 2þ is essential for the proper folding and function of RNA, though the effect of Mg 2þ concentration on the free energy, enthalpy, and entropy landscapes of RNA folding is unknown. This work exploits temperature-controlled single-molecule FRET methods to address the thermodynamics of RNA folding pathways by probing the intramolecular docking/undocking kinetics of the ubiquitous GAAA tetraloop−receptor tertiary interaction as a function of [Mg 2þ ]. These measurements yield the barrier and standard state enthalpies, entropies, and free energies for an RNA tertiary transition, in particular, revealing the thermodynamic origin of [Mg 2þ ]-facilitated folding. Surprisingly, these studies reveal that increasing [Mg 2þ ] promotes tetraloop-receptor interaction by reducing the entropic barrier (−T ΔS ‡ dock ) and the overall entropic penalty (−T ΔS°d ock ) for docking, with essentially negligible effects on both the activation enthalpy (ΔH ‡ dock ) and overall exothermicity (ΔH°d ock ). These observations contrast with the conventional notion that increasing [Mg 2þ ] facilitates folding by minimizing electrostatic repulsion of opposing RNA helices, which would incorrectly predict a decrease in ΔH ‡ dock and ΔH°d ock with [Mg 2þ ]. Instead we propose that higher [Mg 2þ ] can aid RNA folding by decreasing the entropic penalty of counterion uptake and by reducing disorder of the unfolded conformational ensemble.T he folding of RNA proceeds hierarchically, whereby secondary structure is formed rapidly and subsequent slow helical packing is mediated by tertiary interactions (1, 2). RNA secondary structure prediction from the known thermodynamics is quite reliable (3), though correspondingly accurate prediction of tertiary structure remains a major challenge (1). Static tertiary structure data alone are also not enough to predict RNA functionality, as time-dependent conformational dynamics occur during biochemical processes (4, 5). As a result, one needs the full free energy, enthalpy, and entropy landscapes for folding. A major road block in achieving a predictive understanding of RNA folding landscapes is that they are often "rugged,", i.e., with alternative conformations acting as kinetic traps (6, 7). Moreover, the electrostatic challenge of folding a charged biopolymer highlights the particularly critical role of Mg 2þ and other counterions in the folding process.Characterization of folding transition states-and the role of Mg 2þ in stabilizing transition states-remains a crucial bottleneck for reconciling the kinetics and thermodynamics of RNA folding (8-13). Some insight into the free energy landscapes for RNA folding can be obtained from temperature-dependent stopped-flow kinetic studies, which offer the ability to deconstruct free energy barriers (ΔG ‡ ) into enthalpic (ΔH ‡ ) and entropic (−TΔS ‡ ) components. However, with such methods, only the net rate constant (i.e., k total ¼ k fold þ k unfold ) for approach to equilibrium can be observed, which requires strong assumptions (e.g., that k fold ≫ k unfol...

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Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

Cited by 176 publications

References 29 publications

Visualizing large RNA molecules in solution

Visualizing large RNA molecules in solution

The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair

Entropic origin of Mg ²⁺ -facilitated RNA folding

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Topology Links RNA Secondary Structure with Global Conformation, Dynamics, and Adaptation

Cited by 176 publications

References 29 publications

Visualizing large RNA molecules in solution

Visualizing large RNA molecules in solution

The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair

Entropic origin of Mg 2+ -facilitated RNA folding

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Entropic origin of Mg ²⁺ -facilitated RNA folding