ArticleProceedings of the National Academy of Sciences of the United States of America2015
Comprehensive analysis reveals how single nucleotides contribute to noncoding RNA function in bacterial quorum sensing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- An RNA structural switch controlling bacterial toxin translation.Nucleic acids research · 2026Article
- What makes a small RNA work?Nucleic acids research · 2025Review
- The LuxO-OpaR quorum-sensing cascade differentially controls Vibriophage VP882 lysis-lysogeny decision making in liquid and on surfaces.PLoS genetics · 2024Article
- Transcriptome fine-mapping inmBio · 2024Article
- Deep-learning-assisted Sort-Seq enables high-throughput profiling of gene expression characteristics with high precision.Science advances · 2023Article
- Comprehensive insights into the metabolism characteristics of small RNA Qrr4 in Vibrio alginolyticus.Applied microbiology and biotechnology · 2023Article
- Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival ofMicroorganisms · 2021Article
- From Biochemistry to Genetics in a Flash of Light.Genetics · 2020Article
- The intragenus and interspecies quorum-sensing autoinducers exert distinct control over Vibrio cholerae biofilm formation and dispersal.PLoS biology · 2019Article
- Small RNA-Based Regulation of Bacterial Quorum Sensing and Biofilm Formation.Microbiology spectrum · 2018Review
- Contrasting silencing mechanisms of the same target mRNA by two regulatory RNAs in Escherichia coli.Nucleic acids research · 2018Article
- Grad-seq guides the discovery of ProQ as a major small RNA-binding protein.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Article
- The arsenal of pathogens and antivirulence therapeutic strategies for disarming them.Drug design, development and therapy · 2016Review
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Authors and funding
5 authors.
Funding
Abstract
Five homologous noncoding small RNAs (sRNAs), called the Qrr1-5 sRNAs, function in the Vibrio harveyi quorum-sensing cascade to drive its operation. Qrr1-5 use four different regulatory mechanisms to control the expression of ∼ 20 mRNA targets. Little is known about the roles individual nucleotides play in mRNA target selection, in determining regulatory mechanism, or in defining Qrr potency and dynamics of target regulation. To identify the nucleotides vital for Qrr function, we developed a method we call RSort-Seq that combines saturating mutagenesis, fluorescence-activated cell sorting, high-throughput sequencing, and mutual information theory to explore the role that every nucleotide in Qrr4 plays in regulation of two mRNA targets, luxR and luxO. Companion biochemical assays allowed us to assign specific regulatory functions/underlying molecular mechanisms to each important base. This strategy yielded a regional map of nucleotides in Qrr4 vital for stability, Hfq interaction, stem-loop formation, and base pairing to both luxR and luxO, to luxR only, and to luxO only. In terms of nucleotides critical for sRNA function, the RSort-Seq analysis provided strikingly different results from those predicted by commonly used regulatory RNA-folding algorithms. This approach is applicable to any RNA-RNA interaction, including sRNAs in other bacteria and regulatory RNAs in higher organisms.
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