T-box riboswitches constitute a large family of tRNA-binding leader sequences that play a central role in gene regulation in many gram-positive bacteria. Accurate inference of the tRNA binding to T-box riboswitches is critical to predict their cis-regulatory activity. However, there is no central repository of information on the tRNA binding specificities of T-box riboswitches, and de novo prediction of binding specificities requires advanced knowledge of computational tools to annotate riboswitch secondary structure features. Here, we present the T-box Riboswitch Annotation Database (TBDB, https://tbdb.io), an open-access database with a collection of 23,535 T-box riboswitch sequences, spanning the major phyla of 3,632 bacterial species. Among structural predictions, the TBDB also identifies specifier sequences, cognate tRNA binding partners, and downstream regulatory targets. To our knowledge, the TBDB presents the largest collection of feature, sequence, and structural annotations carried out on this important family of regulatory RNA.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7778990 | PMC |
| http://dx.doi.org/10.1093/nar/gkaa721 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Translational T-box riboswitches bind tRNA by modulating conformational flexibility.
Nat Commun
August 2024
Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
T-box riboswitches are noncoding RNA elements involved in genetic regulation of most Gram-positive bacteria. They regulate amino acid metabolism by assessing the aminoacylation status of tRNA, subsequently affecting the transcription or translation of downstream amino acid metabolism-related genes. Here we present single-molecule FRET studies of the Mycobacterium tuberculosis IleS T-box riboswitch, a paradigmatic translational T-box.
View Article and Find Full Text PDFStructural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.
RNA
September 2024
Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
T-box riboswitches are widespread bacterial regulatory noncoding RNAs that directly interact with tRNAs and switch conformations to regulate the transcription or translation of genes related to amino acid metabolism. Recent studies in Bacilli have revealed the core mechanisms of T-boxes that enable multivalent, specific recognition of both the identity and aminoacylation status of the tRNA substrates. However, in-depth knowledge on a vast number of T-boxes in other bacterial species remains scarce, although a remarkable structural diversity, particularly among pathogens, is apparent.
View Article and Find Full Text PDFRNA cis-regulators are important for Streptococcus pneumoniae in vivo success.
PLoS Genet
March 2024
Boston College Department of Biology, Chestnut Hill, Massachusetts, United States of America.
Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4.
View Article and Find Full Text PDFStructural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch.
Nat Commun
November 2023
Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
Article Synopsis
- * The study investigates how these RNA-RNA interactions lead to the correct folding and functionality of the T-box using various advanced techniques like SAXS and single-molecule FRET.
- * Findings show that the presence of magnesium ions enhances the stability and interactions among different RNA segments, facilitating tRNA binding, which is crucial for the riboswitch's activity.
Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble.
Nat Commun
September 2023
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA.
T-box riboswitches are multi-domain noncoding RNAs that surveil individual amino acid availabilities in most Gram-positive bacteria. T-boxes directly bind specific tRNAs, query their aminoacylation status to detect starvation, and feedback control the transcription or translation of downstream amino-acid metabolic genes. Most T-boxes rapidly recruit their cognate tRNA ligands through an intricate three-way stem I-stem II-tRNA interaction, whose establishment is not understood.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!