ArticleRNA (New York, N.Y.)2016
The yjdF riboswitch candidate regulates gene expression by binding diverse azaaromatic compounds.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 60 citations in OpenAlex.
- Structural and functional clues challenge the hypothesis that the yjdF riboswitch is natively regulated through broad recognition of azaaromatic compounds.Nucleic acids research · 2025Article
- Integration of the hammerhead ribozyme into structured RNAs to measure ligand-binding events for riboswitch candidates and aptamers.Acta biochimica et biophysica Sinica · 2025Article
- The current riboswitch landscape inMicrobiology (Reading, England) · 2024Review
- Structural basis for promiscuity in ligand recognition by yjdF riboswitch.Cell discovery · 2024Article
- A spermidine riboswitch class in bacteria exploits a close variant of an aptamer for the enzyme cofactor S-adenosylmethionine.Cell reports · 2023Article
- Full-Length NADBiochemistry · 2023Article
- Selection of allosteric dnazymes that can sense phenylalanine by expression-SELEX.Nucleic acids research · 2023Article
- Genomic insights into the diversity of non-coding RNAs in Bacillus cereus sensu lato.Current genetics · 2022Article
- The bacterial yjdF riboswitch regulates translation through its tRNA-like fold.The Journal of biological chemistry · 2022Article
- The Biochemical Landscape of Riboswitch Ligands.Biochemistry · 2022Article
- Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics.BMC genomics · 2021Article
- Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding.Nucleic acids research · 2020Article
- Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes.RNA (New York, N.Y.) · 2020Review
- Transcriptome Profiling ofFrontiers in molecular biosciences · 2020Article
- Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates.Biochemistry · 2019Article
- Gene regulation by a glycine riboswitch singlet uses a finely tuned energetic landscape for helical switching.RNA (New York, N.Y.) · 2018Article
- Small-Molecule-Binding Riboswitches.Microbiology spectrum · 2018Review
- Affinity maturation of a portable Fab-RNA module for chaperone-assisted RNA crystallography.Nucleic acids research · 2018Article
- Computational Methods for Modeling Aptamers and Designing Riboswitches.International journal of molecular sciences · 2017Review
- Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The yjdF motif RNA is an orphan riboswitch candidate that almost exclusively associates with the yjdF protein-coding gene in many bacteria. The function of the YjdF protein is unknown, which has made speculation regarding the natural ligand for this putative riboswitch unusually challenging. By using a structure-probing assay for ligand binding, we found that a surprisingly broad diversity of nitrogen-containing aromatic heterocycles, or "azaaromatics," trigger near-identical changes in the structures adopted by representative yjdF motif RNAs. Regions of the RNA that undergo ligand-induced structural modulation reside primarily in portions of the putative aptamer region that are highly conserved in nucleotide sequence, as is typical for riboswitches. Some azaaromatic molecules are bound by the RNA with nanomolar dissociation constants, and a subset of these ligands activate riboswitch-mediated gene expression in cells. Furthermore, genetic elements most commonly adjacent to the yjdF motif RNA or to the yjdF protein-coding region are homologous to protein regulators implicated in mitigating the toxic effects of diverse phenolic acids or polycyclic compounds. Although the precise type of natural ligand sensed by yjdF motif RNAs remains unknown, our findings suggest that this riboswitch class might serve as part of a genetic response system to toxic or signaling compounds with chemical structures similar to azaaromatics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.