RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn

Schroeder, Kersten T.; Daldrop, Peter; Lilley, David M.J.

doi:10.1016/j.str.2011.07.003

Cited by 59 publications

(90 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…23 In agreement with this model, it was previously found that the folding of the kink-turn motif located in the P2 helical domain is crucial for the structure and ligand binding activity of the SAM-I aptamer. 46,50 Our study also revealed that SAM binding to the aptamer produces a second folding transition involving the stacking of stems P1 and P4. 23 SAM binding was also previously shown to reorganize regions J1/2 and J3/4, 33,54 consistent with the formation of the native RNA-ligand complex as observed in the crystal structure.…”

Section: S-adenosylmethionine (Sam) Riboswitchessupporting

confidence: 51%

See 1 more Smart Citation

Folding of the SAM-I riboswitch

et al. 2012

View full text Add to dashboard Cite

Section: S-adenosylmethionine (Sam) Riboswitchessupporting

confidence: 51%

“…2B). 27,38,49,50 The binding site is constituted by the minor grooves of helices P1 and P3, in which the SAM adenine moiety interacts with a bulge located in the P3 stem. The methionine group of the ligand is involved in interactions with the J1/2 region.…”

Section: Folding Of the Sam-i Riboswitchmentioning

confidence: 99%

Folding of the SAM-I riboswitch

et al. 2012

View full text Add to dashboard Cite

“…K-turns often mediate long-range interactions in RNAs (Schroeder et al 2011). The increased binding affinity we observed by ITC for VcI-II Kt over VcI-II may reflect promotion of interaptamer ("quaternary") interactions by the Kturn.…”

Section: +mentioning

confidence: 73%

“…The cognate K-turn binding protein YbxF enhances glycine binding to BsI-II Kt K-turns can be stabilized by tertiary structure formation, increased Mg 2+ concentrations, or by K-turn binding proteins (Schroeder et al 2011). To test whether YbxF might improve glycine binding under physiologically relevant Mg 2+ concentrations, we performed ITC as described above with the BsI-II Kt RNA and a 1.5-fold molar excess of B. subtilis YbxF in the sample cell.…”

Section: +mentioning

confidence: 99%

Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches

Baird

Ferré-D′Amaré

2012

RNA

View full text Add to dashboard Cite

Most known glycine riboswitches have two homologous aptamer domains arranged in tandem and separated by a short linker. The two aptamers associate through reciprocal "quaternary" interactions that have been proposed to result in cooperative glycine binding. Recently, the interaptamer linker was found to form helix P0 with a previously unrecognized segment 5′ to the first aptamer domain. P0 was shown to increase glycine affinity, abolish cooperativity, and conform to the K-turn motif consensus. We examine the global thermodynamic and structural role of P0 using isothermal titration calorimetry (ITC) and small-angle X-ray scattering (SAXS), respectively. To evaluate the generality of P0 function, we prepared glycine riboswitch constructs lacking and including P0 from Bacillus subtilis, Fusobacterium nucleatum, and Vibrio cholerae. We find that P0 indeed folds into a K-turn, supports partial pre-folding of all three glycine-free RNAs, and is required for ITC observation of glycine binding under physiologic Mg 2+ concentrations. Except for the unusually small riboswitch from F. nucleatum, the K-turn is needed for maximally compacting the glycine-bound states of the RNAs. Formation of a ribonucleoprotein complex between the B. subtilis or the F. nucleatum RNA constructs and the bacterial K-turn binding protein YbxF promotes additional folding of the free riboswitch, and enhances glycine binding. Consistent with the previously reported loss of cooperativity, P0-containing B. subtilis and V. cholerae tandem aptamers bound no more than one glycine molecule per riboswitch. Our results indicate that the P0 K-turn helps organize the quaternary structure of tandem glycine riboswitches, thereby facilitating ligand binding under physiologic conditions.

show abstract

“…The kink-turn motif is not unprecedented in riboswitches; it has been reported in SAM-I riboswitches connecting to the four-way junction motif (Montange and Batey 2006) as well as in the class II c-di-GMP (Lee et al 2010) and lysine riboswitches (Blouin and Lafontaine 2007). This SAM-I kink-turn motif follows the exact consensus derived from the ribosome kink-turns and is stabilized by RNA tertiary structure (Schroeder et al 2011), different from those stabilized by metal ions (Liu and Lilley 2007) or protein binding (Turner et al 2005;Turner and Lilley 2008). It will be interesting to investigate which strategy is used in the glycine riboswitch to stabilize the kinkturn motif located at the 59 boundary of the regulatory RNA element.…”

Section: Discussionmentioning

confidence: 92%

An energetically beneficial leader–linker interaction abolishes ligand-binding cooperativity in glycine riboswitches

Sherman¹,

Esquiaqui²,

Elsayed³

et al. 2012

RNA

View full text Add to dashboard Cite

Comprised of two aptamers connected by a short nucleotide linker, the glycine riboswitch was the first example of naturally occurring RNA elements reported to bind small organic molecules cooperatively. Earlier works have shown binding of glycine to the second aptamer allows tertiary interactions to be made between the two aptamers, which facilitates binding of a separate glycine molecule to the first aptamer, leading to glycine-binding cooperativity. Prompted by a distinctive protection pattern in the linker region of a minimal glycine riboswitch construct, we have identified a highly conserved (>90%) leader-linker duplex involving leader nucleotides upstream of the previously reported consensus glycine riboswitch sequences. In >50% of the glycine riboswitches, the leader-linker interaction forms a kink-turn motif. Characterization of three glycine ribsowitches showed that the leader-linker interaction improved the glycine-binding affinities by 4.5-to 86-fold. In-line probing and native gel assays with two aptamers in trans suggested synergistic action between glycine-binding and interaptamer interaction during global folding of the glycine riboswitch. Mutational analysis showed that there appeared to be no ligand-binding cooperativity in the glycine riboswitch when the leader-linker interaction is present, and the previously measured cooperativity is simply an artifact of a truncated construct missing the leader sequence.

show abstract

RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn

Cited by 59 publications

References 33 publications

Folding of the SAM-I riboswitch

Folding of the SAM-I riboswitch

Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches

An energetically beneficial leader–linker interaction abolishes ligand-binding cooperativity in glycine riboswitches

Contact Info

Product

Resources

About