ArticleBiochemistry2019
Variant Bacterial Riboswitches Associated with Nucleotide Hydrolase Genes Sense Nucleoside Diphosphates.
Article in Biochemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 40 citations in OpenAlex.
- Article
- Article
- The Impact of Second-Shell Nucleotides on Ligand Specificity in Cyclic Dinucleotide Riboswitches.Biochemistry · 2024Article
- Genetic disruption of the bacterialProceedings of the National Academy of Sciences of the United States of America · 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
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- 8-oxoguanine riboswitches in bacteria detect and respond to oxidative DNA damage.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structure and function analysis of a type III preQThe Journal of biological chemistry · 2023Article
- Riboswitches, from cognition to transformation.Synthetic and systems biotechnology · 2023Review
- Discovering riboswitches: the past and the future.Trends in biochemical sciences · 2023Review
- Identification and characterization of RNA binding sites for (p)ppGpp using RNA-DRaCALA.Nucleic acids research · 2023Article
- A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity.RNA biology · 2023Article
- Lithium-sensing riboswitch classes regulate expression of bacterial cation transporter genes.Scientific reports · 2022Article
- Variants of the guanine riboswitch class exhibit altered ligand specificities for xanthine, guanine, or 2'-deoxyguanosine.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- The Biochemical Landscape of Riboswitch Ligands.Biochemistry · 2022Article
- Architectures and complex functions of tandem riboswitches.RNA biology · 2022Article
- Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.RNA biology · 2021Article
- RNA sequence and structure control assembly and function of RNA condensates.RNA (New York, N.Y.) · 2021Article
- Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.Nucleic acids research · 2021Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The ykkC RNA motif was a long-standing orphan riboswitch candidate that has recently been proposed to encompass at least five distinct bacterial riboswitch classes. Most ykkC RNAs belong to the subtype 1 group, which are guanidine-I riboswitches that regulate the expression of guanidine-specific carboxylase and transporter proteins. The remaining ykkC RNAs have been organized into at least four major categories called subtypes 2a-2d. Subtype 2a RNAs are riboswitches that sense the bacterial alarmone ppGpp and typically regulate amino acid biosynthesis genes. Subtype 2b riboswitches sense the purine biosynthetic intermediate PRPP and frequently partner with guanine riboswitches to regulate purine biosynthesis genes. In this study, we examined ykkC subtype 2c RNAs, which are found upstream of genes encoding hydrolase enzymes that cleave the phosphoanhydride linkages of nucleotide substrates. Subtype 2c representatives mostly recognize adenosine and cytidine 5'-diphosphate molecules in either their ribose or deoxyribose forms (ADP, dADP, CDP, and dCDP). Other nucleotide-containing compounds, especially nucleoside 5'-triphosphates, are strongly rejected by some members of this putative riboswitch class. High ligand concentrations in vivo are predicted to turn on expression of hydrolase enzymes, which presumably function to balance cellular nucleotide pools. These results further showcase the striking functional diversity derived from the structural scaffold shared among all ykkC motif RNAs, which has been adapted to sense at least five different types of natural ligands. Moreover, riboswitches for nucleoside diphosphates provide additional examples of the numerous partnerships observed between natural RNA aptamers and nucleotide-derived ligands, including metabolites, coenzymes, and signaling molecules.
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