ArticleNucleic acids research2020
The conformational landscape of transcription intermediates involved in the regulation of the ZMP-sensing riboswitch from Thermosinus carboxydivorans.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 34 citations in OpenAlex.
- The Role of Chemistry Across Disciplines From Humanities to Life Sciences in Understanding Complexity and Emergence.Angewandte Chemie (International ed. in English) · 2026Review
- Beyond the niche - unlocking the full potential of synthetic riboswitches.Nature communications · 2025Review
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display.Nature communications · 2025Article
- RNA folding kinetics control riboswitch sensitivity in vivo.Nature communications · 2025Article
- Article
- Opportunities for Riboswitch Inhibition by Targeting Co-Transcriptional RNA Folding Events.International journal of molecular sciences · 2024Review
- RNA folding kinetics control riboswitch sensitivity in vivo.bioRxiv : the preprint server for biology · 2024Article
- Tuning strand displacement kinetics enables programmable ZTP riboswitch dynamic range in vivo.Nucleic acids research · 2023Article
- Quantitative Analysis of Transcription Termination via Position-Selective Labeling of RNA (PLOR) Method.International journal of molecular sciences · 2023Article
- Characterization of Structure and Dynamics of the Guanidine-II Riboswitch from Escherichia coli by NMR Spectroscopy and Small-Angle X-ray Scattering (SAXS).Chembiochem : a European journal of chemical biology · 2022Article
- Developments in solution-state NMR yield broader and deeper views of the dynamic ensembles of nucleic acids.Current opinion in structural biology · 2021Review
- Conformational Ensemble ofThe journal of physical chemistry. B · 2021Article
- Parallel Discovery Strategies Provide a Basis for Riboswitch Ligand Design.Cell chemical biology · 2020Article
- Real-time monitoring of single ZTP riboswitches reveals a complex and kinetically controlled decision landscape.Nature communications · 2020Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recently, prokaryotic riboswitches have been identified that regulate transcription in response to change of the concentration of secondary messengers. The ZMP (5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR))-sensing riboswitch from Thermosinus carboxydivorans is a transcriptional ON-switch that is involved in purine and carbon-1 metabolic cycles. Its aptamer domain includes the pfl motif, which features a pseudoknot, impeding rho-independent terminator formation upon stabilization by ZMP interaction. We herein investigate the conformational landscape of transcriptional intermediates including the expression platform of this riboswitch and characterize the formation and unfolding of the important pseudoknot structure in the context of increasing length of RNA transcripts. NMR spectroscopic data show that even surprisingly short pre-terminator stems are able to disrupt ligand binding and thus metabolite sensing. We further show that the pseudoknot structure, a prerequisite for ligand binding, is preformed in transcription intermediates up to a certain length. Our results describe the conformational changes of 13 transcription intermediates of increasing length to delineate the change in structure as mRNA is elongated during transcription. We thus determine the length of the key transcription intermediate to which addition of a single nucleotide leads to a drastic drop in ZMP affinity.
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