ArticleNucleic acids research2009
In vivo expression and purification of aptamer-tagged small RNA regulators.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 114 citations in OpenAlex.
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- RNA aptamers as tools for the purification and analysis of in vivo assembled ribonucleoproteins.RNA (New York, N.Y.) · 2025Review
- Exploring the interactome of the Staphylococcus aureus sRNA Srn_9342 identified a complex formation with RNAIII leading to the modulation of δ-hemolysin expression.BMC microbiology · 2025Article
- Advancing RNA phage biology through meta-omics.Nucleic acids research · 2025Review
- Revealing the Arabidopsis AtGRP7 mRNA binding proteome by specific enhanced RNA interactome capture.BMC plant biology · 2024Article
- RNAIII is linked with the pentose phosphate pathway through the activation of RpiRc inmSphere · 2024Article
- A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum.Nucleic acids research · 2024Article
- Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches.Current opinion in microbiology · 2024Review
- Global Identification of RNA-Binding Proteins in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- An Easy-to-Use Plasmid Toolset for Efficient Generation and Benchmarking of Synthetic Small RNAs in Bacteria.ACS synthetic biology · 2022Article
- Directed evolution of orthogonal RNA-RBP pairs through library-vs-library in vitro selection.Nucleic acids research · 2022Article
- Synthetase of the methyl donor S-adenosylmethionine from nitrogen-fixing α-rhizobia can bind functionally diverse RNA species.RNA biology · 2021Article
- Reprograming of sRNA target specificity by the leader peptide peTrpL in response to antibiotic exposure.Nucleic acids research · 2021Article
- Three Ribosomal Operons ofFrontiers in microbiology · 2021Article
- Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control.The EMBO journal · 2020Article
- Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance inFrontiers in bioengineering and biotechnology · 2020Article
- RNA-binding proteins in bacteria.Nature reviews. Microbiology · 2018Review
- Gene network analysis identifies a central post-transcriptional regulator of cellular stress survival.eLife · 2018Article
- A bacterial three-hybrid assay detects Escherichia coli Hfq-sRNA interactions in vivo.Nucleic acids research · 2018Article
- Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World.Frontiers in molecular biosciences · 2018Review
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small non-coding RNAs (sRNAs) are an emerging class of post-transcriptional regulators of bacterial gene expression. To study sRNAs and their potential protein interaction partners, it is desirable to purify sRNAs from cells in their native form. Here, we used RNA-based affinity chromatography to purify sRNAs following their expression as aptamer-tagged variants in vivo. To this end, we developed a family of plasmids to express sRNAs with any of three widely used aptamer sequences (MS2, boxB, eIF4A), and systematically tested how the aptamer tagging impacted on intracellular accumulation and target regulation of the Salmonella GcvB, InvR or RybB sRNAs. In addition, we successfully tagged the chromosomal rybB gene with MS2 to observe that RybB-MS2 is fully functional as an envelope stress-induced repressor of ompN mRNA following induction of sigmaE. We further demonstrate that the common sRNA-binding protein, Hfq, co-purifies with MS2-tagged sRNAs of Salmonella. The presented affinity purification strategy may facilitate the isolation of in vivo assembled sRNA-protein complexes in a wide range of bacteria.
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Registered trials
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.