Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch

Montange, R.K.; Mondragón, Estefanía; Tyne, Daria Van; Garst, Andrew D.; Ceres, Pablo; Batey, Robert T.

doi:10.1016/j.jmb.2009.12.007

Cited by 71 publications

(97 citation statements)

References 49 publications

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“…2A), which is conserved in SAM-I and SAM-I/IV but is a G-C pair in SAM-IV. Mutation of this A-U pair to G-C in the TteSAM-I and Bacillus subtilis yitJ SAM-I aptamer domains results in a moderate loss in affinity (10,20). Despite the identical SAM-binding cores (within the coordinate error of the known structures), the crystal structure of env87 (ΔU92) reveals a completely novel peripheral architecture surrounding the core in the SAM-I/IV aptamer.…”

Section: Rna Crystallization and Structure Determinationmentioning

confidence: 95%

Structural basis for diversity in the SAM clan of riboswitches

Trausch¹,

Xu²,

Edwards³

et al. 2014

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

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In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-L-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAMbinding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor.RNA structure | X-ray crystallography | chemical probing | isothermal titration calorimetry | gene regulation R iboswitches are noncoding RNA elements generally found in the leader of bacterial mRNAs that regulate expression via direct binding of a specific cellular metabolite (reviewed in refs.

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Section: Rna Crystallization and Structure Determinationmentioning

confidence: 95%

Structural basis for diversity in the SAM clan of riboswitches

Trausch¹,

Xu²,

Edwards³

et al. 2014

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

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“…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%

“…A study has reported the existence of SAH-sensing riboswitches, 37 indicating that SAM/SAH riboswitches exploit chemical differences between closelyrelated metabolites to prevent cellular misregulation, which is consistent with recently obtained crystal structures. 38 SAM riboswitches have also been found in tandem arrangement with a coenzyme B 12 riboswitch, where both riboswitches function as a two-input Boolean NOR logic gate. 39 Figure 1.…”

Section: S-adenosylmethionine (Sam) Riboswitchesmentioning

confidence: 99%

Folding of the SAM-I riboswitch

et al. 2012

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“…The crystal structures of the SAM-I riboswitch in Thermoanearobacter tencongensis upstream of the metF-H2 gene and in B. subtilis upstream of the yitJ gene revealed that SAM binds to a pocket formed by four coaxially stacked helices (P1, P2, P3, P4) joined by junctions J1/2, J2/3, and J3/4 ( Fig. 1; Montange and Batey 2006;Lu et al 2010;Montange et al 2010). Mutational analysis and biophysical studies show that a kink-turn-mediated pseudoknot formation assists the global folding of the riboswitch cooperatively with Mg 2+ present (Winkler et al 2001;McDaniel et al 2005;Heppell and Lafontaine 2008;Lu et al 2010).…”

Section: Introductionmentioning

confidence: 99%

Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch

Boyapati¹,

Huang²,

Spedale³

et al. 2012

RNA

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Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the Bacillus subtilis yitJ SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming ''hybrid'' structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.

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Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch

Cited by 71 publications

References 49 publications

Structural basis for diversity in the SAM clan of riboswitches

Structural basis for diversity in the SAM clan of riboswitches

Folding of the SAM-I riboswitch

Basis for ligand discrimination between ON and OFF state riboswitch conformations: The case of the SAM-I riboswitch

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