Over the past decade the purine riboswitch, and in particular its nucleobase-binding aptamer domain, has emerged as an important model system for exploring various aspects of RNA structure and function. Its relatively small size, structural simplicity and readily observable activity enable application of a wide variety of experimental approaches towards the study of this RNA. These analyses have yielded important insights into small molecule recognition, co-transcriptional folding and secondary structural switching, and conformational dynamics that serve as a paradigm for other RNAs. In this article, the current state of understanding of the purine riboswitch family and how this growing knowledge base is starting to be exploited in the creation of novel RNA devices are examined. This article is part of a Special Issue entitled: Riboswitches.
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http://dx.doi.org/10.1016/j.bbagrm.2014.02.014 | DOI Listing |
Nucleic Acids Res
January 2025
Advanced Analysis Data Center, Korea Institute of Science and Technology, Hwarang-ro 14-5, Seongbuk-gu, Seoul 02792, Republic of Korea.
Riboswitches are RNAs that recognize ligands and regulate gene expression. They are typically located in the untranslated region of bacterial messenger RNA and consist of an aptamer and an expression platform. In this study, we examine the folding pathway of the Vc2 (Vibrio cholerae) riboswitch aptamer domain, which targets the bacterial secondary messenger cyclic-di-GMP.
View Article and Find Full Text PDFMol Microbiol
January 2025
Department of Microbiology and Cell Science, IFAS, University of Florida, Gainesville, Florida, USA.
Queuosine (Q) is a modification of the wobble base in tRNAs that decode NA(C/U) codons. It is ubiquitous in bacteria, including many pathogens. Streptococcus mutans is an early colonizer of dental plaque biofilm and a key player in dental caries.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
December 2024
Department of Biochemistry, Brandeis University, Waltham, MA 02453.
The bacterial pathogen forms multicellular communities known as biofilms in which cells are held together by an extracellular matrix principally composed of repurposed cytoplasmic proteins and extracellular DNA. These biofilms assemble during infections or under laboratory conditions by growth on medium containing glucose, but the intracellular signal for biofilm formation and its downstream targets were unknown. Here, we present evidence that biofilm formation is triggered by a drop in the levels of the second messenger cyclic-di-AMP.
View Article and Find Full Text PDFChem Commun (Camb)
December 2024
Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, Haus F, D-81377 Munich, Germany.
-Adenosyl-L-methionine (SAM) is crucial for methylation and tightly controlled in cells. We examined SAM-III riboswitch response to 17 SAM analogues and used a Spinach/SAM aptasensor to monitor their enzymatic formation . Most SAM analogues were recognized, unless they featured an -substituted benzyl ring, indicating potential regulatory effects SAM riboswitches.
View Article and Find Full Text PDFChem Commun (Camb)
December 2024
University of Oregon Department of Chemistry and Biochemistry, Eugene, USA.
The Class II NAD riboswitch is a bacterial RNA that binds ligands containing nicotinamide. Herein, we report a fluorescence and biolayer interferometry study of riboswitch interactions with β-NMN. The results reveal a shift in the prevalence of a pseudoknot structure in the presence of ligand and Mg.
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