ArticleBMC genomics2009
Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 68 citations in OpenAlex.
- Phosphoproteomics reveals essential regulatory roles of phosphorylation in marine oligotrophic bacteria.Marine life science & technology · 2026Article
- Whole cell affinity for 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in the marine bacterium Candidatus Pelagibacter st. HTCC7211 explains marine dissolved HMP concentrations.Environmental microbiology reports · 2024Article
- The discovery of novel noncoding RNAs in 50 bacterial genomes.Nucleic acids research · 2024Article
- A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments.Microbiology and molecular biology reviews : MMBR · 2023Review
- Key players in regulatory RNA realm of bacteria.Biochemistry and biophysics reports · 2022Review
- Comprehensive discovery of novel structured noncoding RNAs in 26 bacterial genomes.RNA biology · 2021Article
- Revisiting the Relationships Between Genomic G + C Content, RNA Secondary Structures, and Optimal Growth Temperature.Journal of molecular evolution · 2021Article
- A second riboswitch class for the enzyme cofactor NADRNA (New York, N.Y.) · 2021Article
- Biochemical Validation of a Fourth Guanidine Riboswitch Class in Bacteria.Biochemistry · 2020Article
- Former orphan riboswitches reveal unexplored areas of bacterial metabolism, signaling, and gene control processes.RNA (New York, N.Y.) · 2020Review
- A bacterial riboswitch class for the thiamin precursor HMP-PP employs a terminator-embedded aptamer.eLife · 2019Article
- Genome-wide discovery of structured noncoding RNAs in bacteria.BMC microbiology · 2019Article
- Article
- Structure and ligand binding of the SAM-V riboswitch.Nucleic acids research · 2018Article
- Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei.Scientific reports · 2017Article
- Riboswitch diversity and distribution.RNA (New York, N.Y.) · 2017Article
- Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.Methods (San Diego, Calif.) · 2017Article
- Article
- Secondary structural entropy in RNA switch (Riboswitch) identification.BMC bioinformatics · 2015Article
- An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding.PloS one · 2015Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundMetagenomic sequence data are proving to be a vast resource for the discovery of biological components. Yet analysis of this data to identify functional RNAs lags behind efforts to characterize protein diversity. The genome of 'Candidatus Pelagibacter ubique' HTCC 1062 is the closest match for approximately 20% of marine metagenomic sequence reads. It is also small, contains little non-coding DNA, and has strikingly low GC content.
resultsTo aid the discovery of RNA motifs within the marine metagenome we exploited the genomic properties of 'Cand. P. ubique' by targeting our search to long intergenic regions (IGRs) with relatively high GC content. Analysis of known RNAs (rRNA, tRNA, riboswitches etc.) shows that structured RNAs are significantly enriched in such IGRs. To identify additional candidate structured RNAs, we examined other IGRs with similar characteristics from 'Cand. P. ubique' using comparative genomics approaches in conjunction with marine metagenomic data. Employing this strategy, we discovered four candidate structured RNAs including a new riboswitch class as well as three additional likely cis-regulatory elements that precede genes encoding ribosomal proteins S2 and S12, and the cytoplasmic protein component of the signal recognition particle. We also describe four additional potential RNA motifs with few or no examples occurring outside the metagenomic data.
conclusionThis work begins the process of identifying functional RNA motifs present in the metagenomic data and illustrates how existing completed genomes may be used to aid in this task.
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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.