ArticleScientific reports2018
Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 33 citations in OpenAlex.
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- Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning.PloS one · 2025Article
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- The current riboswitch landscape inMicrobiology (Reading, England) · 2024Review
- 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
- X-Ray Crystallography to Study Conformational Changes in a TPP Riboswitch.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.Nucleic acids research · 2022Article
- Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis.Biology · 2022Article
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- Alternate RNA Structures.Cold Spring Harbor perspectives in biology · 2020Review
- Metabolic Model of themBio · 2019Article
- TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida.PLoS genetics · 2018Article
- Machine Learning to Enhance Biophysical Models for Riboswitch Discovery.Wiley interdisciplinary reviews. RNAReview
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 different classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi where their presence has been experimentally validated in a few instances. We analyzed all the available complete fungal and related genomes and identified TPP riboswitch-based regulation systems in 138 fungi and 15 oomycetes. We find that TPP riboswitches are most abundant in Ascomycota and Basidiomycota where they regulate TPP biosynthesis and/or transporter genes. Many of these transporter genes were found to contain conserved domains consistent with nucleoside, urea and amino acid transporter gene families. The genomic location of TPP riboswitches when correlated with the intron structure of the regulated genes enabled prediction of the precise regulation mechanism employed by each riboswitch. Our comprehensive analysis of TPP riboswitches in fungi provides insights about the phylogenomic distribution, regulatory patterns and functioning mechanisms of TPP riboswitches across diverse fungal species and provides a useful resource that will enhance the understanding of RNA-based gene regulation in eukaryotes.
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