ArticleGenome biology2010
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.
Article in Genome biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers.
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Who cites it
244 citing papers in PubMed, 390 citations in OpenAlex.
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- Ancient Species Diversity and Niche Adaptation in Tannerella and Porphyromonas Revealed Through Pangenomics.Genome biology and evolution · 2026Article
- Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.Nucleic acids research · 2026Article
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- High-throughput functional profiling and evolutionary covariation analysis of entire riboswitch sequences.bioRxiv : the preprint server for biology · 2025Article
- A Cyanobacteria-Derived RNA Aptamer Resensitizes Prostate Cancer to Hormone Therapy.Cancer research · 2025Article
- Comprehensive datasets for RNA design, machine learning, and beyond.Scientific reports · 2025Article
- Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.Nucleic acids research · 2025Article
- SMDesigner: a program to design sequence mutations to assess RNA structure.RNA (New York, N.Y.) · 2025Article
- The Role of Bacteriophage-Derived Small RNA Molecules in Bacterial and Phage Interactions.Viruses · 2025Review
- Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.bioRxiv : the preprint server for biology · 2025Article
- CHiTA: A scarless high-throughput pipeline for characterization of ribozymes.Methods (San Diego, Calif.) · 2025Article
- Identification of Small RNAs inInternational journal of molecular sciences · 2024Article
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- The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch.Nucleic acids research · 2024Article
- Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances.Applied and environmental microbiology · 2024Review
- Structural basis for promiscuity in ligand recognition by yjdF riboswitch.Cell discovery · 2024Article
- Compiling a versatile toolbox for inducible gene expression inmicroLife · 2024Article
184 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundStructured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure.
resultsBy applying a comparative genomics-based approach to genome and metagenome sequences from bacteria and archaea, we identified 104 candidate structured RNAs and inferred putative functions for many of these. Twelve candidate metabolite-binding RNAs were identified, three of which were validated, including one reported herein that binds the coenzyme S-adenosylmethionine. Newly identified cis-regulatory RNAs are implicated in photosynthesis or nitrogen regulation in cyanobacteria, purine and one-carbon metabolism, stomach infection by Helicobacter, and many other physiological processes. A candidate riboswitch termed crcB is represented in both bacteria and archaea. Another RNA motif may control gene expression from 3'-untranslated regions of mRNAs, which is unusual for bacteria. Many noncoding RNAs that likely act in trans are also revealed, and several of the noncoding RNA candidates are found mostly or exclusively in metagenome DNA sequences.
conclusionsThis work greatly expands the variety of highly structured noncoding RNAs known to exist in bacteria and archaea and provides a starting point for biochemical and genetic studies needed to validate their biologic functions. Given the sustained rate of RNA discovery over several similar projects, we expect that far more structured RNAs remain to be discovered from bacterial and archaeal organisms.
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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.