Molecular basis of gene regulation by the THI‐box riboswitch

Ontiveros-Palacios, Nancy; Smith, Amanda M.; Grundy, Frank J.; Soberón, Mário; Henkin, Tina M.; Miranda-Ríos, Juan

doi:10.1111/j.1365-2958.2007.06088.x

Cited by 52 publications

(53 citation statements)

References 45 publications

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“…Although the C48-G67 closing base pair is thermodynamically favored at 1 M salt, our data suggest the 59 G48-C67 closing base pair, seen in the wild type, favors the interaction of magnesium with the RNA at pH 7.5. Consistent with our results, OntiverosPalacios et al (2008) showed that TPP binding is threefold weaker when guanine at position 48 is modified to cytosine (Ontiveros-Palacios et al 2008). Upon lowering the pH to 5.5, magnesium binding to the C48-G67 construct is restored to the level of the RNA WT (Fig.…”

Section: Discussionsupporting

confidence: 81%

“…This study examines the pyrophosphate sensor helix region of the thiC riboswitch RNA derived from Arabidopsis thaliana. Five bases in the pyrophosphate sensor domain are conserved (Thore et al 2006;Ontiveros-Palacios et al 2008). Positions C45, G48, and G64 are conserved bases in the helical stems and positions 65 and 66 are conserved in the 2 3 2 internal bulge (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch

Furniss¹,

Grover²

2011

RNA

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Riboswitches are functional mRNA that control gene expression. Thiamine pyrophosphate (TPP) binds to thi-box riboswitch RNA and allosterically inhibits genes that code for proteins involved in the biosynthesis and transport of thiamine. Thiamine binding to the pyrimidine sensor helix and pyrophosphate binding to the pyrophosphate sensor helix cause changes in RNA conformation that regulate gene expression. Here we examine the thermodynamic properties of the internal loop of the pyrophosphate binding domain by comparing the wild-type construct (RNA WT) with six modified 2 3 2 bulged RNA and one 2 3 2 bulged DNA. The wild-type construct retains five conserved bases of the pyrophosphate sensor domain, two of which are in the 2 3 2 bulge (C65 and G66). The RNA WT construct was among the most stable (DG°3 7 = -7.7 kcal/mol) in 1 M KCl at pH 7.5. Breaking the A d G mismatch of the bulge decreases the stability of the construct~0.5-1 kcal/mol, but does not affect magnesium binding to the RNA WT. Guanine at position 48 is important for RNA-Mg 2+ interactions of the TPP-binding riboswitch at pH 7.5. In the presence of 9.5 mM magnesium at pH 5.5, the bulged RNA constructs gained an average of 1.1 kcal/ mol relative to 1 M salt. Formation of a single A+ d C mismatch base pair contributes about 0.5 kcal/mol at pH 5.5, whereas two tandem A+ d C mismatch base pairs together contribute about 2 kcal/mol.

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Section: Discussionsupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch

Furniss¹,

Grover²

2011

RNA

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“…However, the β-galactosidase activity was decreased in the presence of ligand only when using fusions containing significant portions of the coding region (34), suggesting the presence of regulatory element(s) within the btuB ORF that negatively modulate the mRNA level in the absence of translating ribosomes (34). Together with recent studies (16,17), our data suggest that the thiM riboswitch uses a similar genetic regulating mechanism (SI Appendix, Fig. S3).…”

Section: Discussionmentioning

confidence: 70%

“…1C) is observed generally among riboswitches that control translation when inhibiting translation initiation. To address this question, we used the E. coli thiM thiamin pyrophosphate (TPP) riboswitch that previously was shown to act at the translational level (16,17). Although a strong TPP-dependent decrease in β-galactosidase activity was observed for the translational fusion in the presence of 500 μg/mL TPP, no such decrease was detected when the transcriptional construct was used (SI Appendix, Fig.…”

mentioning

confidence: 99%

Dual-acting riboswitch control of translation initiation and mRNA decay

Caron

Bastet

Lussier

et al. 2012

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

153

150

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Riboswitches are mRNA regulatory elements that control gene expression by altering their structure in response to specific metabolite binding. In bacteria, riboswitches consist of an aptamer that performs ligand recognition and an expression platform that regulates either transcription termination or translation initiation. Here, we describe a dual-acting riboswitch from Escherichia coli that, in addition to modulating translation initiation, also is directly involved in the control of initial mRNA decay. Upon lysine binding, the lysC riboswitch adopts a conformation that not only inhibits translation initiation but also exposes RNase E cleavage sites located in the riboswitch expression platform. However, in the absence of lysine, the riboswitch folds into an alternative conformation that simultaneously allows translation initiation and sequesters RNase E cleavage sites. Both regulatory activities can be individually inhibited, indicating that translation initiation and mRNA decay can be modulated independently using the same conformational switch. Because RNase E cleavage sites are located in the riboswitch sequence, this riboswitch provides a unique means for the riboswitch to modulate RNase E cleavage activity directly as a function of lysine. This dual inhibition is in contrast to other riboswitches, such as the thiamin pyrophosphate-sensing thiM riboswitch, which triggers mRNA decay only as a consequence of translation inhibition. The riboswitch control of RNase E cleavage activity is an example of a mechanism by which metabolite sensing is used to regulate gene expression of single genes or even large polycistronic mRNAs as a function of environmental changes.gene regulation | RNA degradosome | translational control S ince the first demonstration that translation attenuation regulates the expression of the tryptophan operon (1), accumulating evidence has revealed the importance of posttranscriptional regulation in prokaryotes and eukaryotes alike. Posttranscriptional regulators include RNA molecules that operate through several mechanisms to control a wide range of physiological responses (2). Among newly identified RNA regulators are riboswitches, which are located in untranslated regions of several mRNAs and that modulate gene expression at the level of transcription, translation, or splicing (3). Riboswitches are highly structured regulatory domains that directly sense cellular metabolites such as amino acids, carbohydrates, coenzymes, and nucleobases. These genetic switches are composed of two modular domains consisting of an aptamer and an expression platform. The aptamer is involved in the specific recognition of the metabolite, and the expression platform is used to control gene expression by altering the structure of the mRNA. Recent bioinformatic analyses have reported the existence of several new RNA motifs exhibiting unconventional expression platforms (4, 5), suggesting that riboswitches using different regulation mechanisms are still likely to be discovered (6).The lysine riboswitch was first...

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“…Nonetheless, the mechanism by which the SAH riboswitch transduces ligand binding into a regulatory response is similar to other riboswitches (Wickiser et al 2005;Fuchs et al 2006;Ontiveros-Palacios et al 2008). Following transcription of the aptamer domain, the riboswitch reaches a folding branch point, each leading to the formation of one of two mutually exclusive hairpin structures in the downstream expression platform (Fig.…”

Section: Discussionmentioning

confidence: 99%

Structural basis for recognition ofS-adenosylhomocysteine by riboswitches

Edwards¹,

Reyes²,

Héroux³

et al. 2010

RNA

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S-adenosyl-(L)-homocysteine (SAH) riboswitches are regulatory elements found in bacterial mRNAs that up-regulate genes involved in the S-adenosyl-(L)-methionine (SAM) regeneration cycle. To understand the structural basis of SAH-dependent regulation by RNA, we have solved the structure of its metabolite-binding domain in complex with SAH. This structure reveals an unusual pseudoknot topology that creates a shallow groove on the surface of the RNA that binds SAH primarily through interactions with the adenine ring and methionine main chain atoms and discriminates against SAM through a steric mechanism. Chemical probing and calorimetric analysis indicate that the unliganded RNA can access bound-like conformations that are significantly stabilized by SAH to direct folding of the downstream regulatory switch. Strikingly, we find that metabolites bearing an adenine ring, including ATP, bind this aptamer with sufficiently high affinity such that normal intracellular concentrations of these compounds may influence regulation of the riboswitch.

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Molecular basis of gene regulation by the THI‐box riboswitch

Cited by 52 publications

References 45 publications

Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch

Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch

Dual-acting riboswitch control of translation initiation and mRNA decay

Structural basis for recognition ofS-adenosylhomocysteine by riboswitches

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