ArticleNucleic acids research2023
RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 29 citations in OpenAlex.
- A dual-host regulatory hub integrating biofilm formation and innate immunity resistance.Nature communications · 2026Article
- Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum.Nature communications · 2026Article
- Article
- RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets.Nature communications · 2025Article
- Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.Nucleic acids research · 2025Article
- The type 6 secretion system immunity protein RhsFI has been repurposed for small RNA regulation in pathogenic Escherichia coli.Nucleic acids research · 2025Article
- RNA-binding protein YebC enhances translation of proline-rich amino acid stretches in bacteria.Nature communications · 2025Article
- The RRM domain-containing protein Rbp3 interacts with ribosomes and the 3' ends of mRNAs encoding photosynthesis proteins.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- What makes a small RNA work?Nucleic acids research · 2025Review
- RNA binding proteins (RBPs) on genetic stability and diseases.Global medical genetics · 2025Review
- R-DeeP/TripepSVM identifies the RNA-binding OB-fold-like protein PatR as regulator of heterocyst patterning.Nucleic acids research · 2025Article
- pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data.Life science alliance · 2024Article
- Interrogation of RNA-protein interaction dynamics in bacterial growth.Molecular systems biology · 2024Article
- A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum.Nucleic acids research · 2024Article
- Improved RNA stability estimation through Bayesian modeling reveals mostProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Global Identification of RNA-Binding Proteins in Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Host factorFrontiers in immunology · 2024Article
- Transcriptomic and biochemical analyses revealed antifungal mechanism of trans-anethole on Aspergillus flavus growth.Applied microbiology and biotechnology · 2023Article
- Advantages and limitations of UV cross-linking analysis of protein-RNA interactomes in microbes.Molecular microbiology · 2023Review
- Mixed Messages: Dynamic and Compositional Heterogeneity of Nuclear Messenger Ribonucleoprotein (mRNP) Complexes.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-binding proteins (RPBs) are deeply involved in fundamental cellular processes in bacteria and are vital for their survival. Despite this, few studies have so far been dedicated to direct and global identification of bacterial RBPs. We have adapted the RNA interactome capture (RIC) technique, originally developed for eukaryotic systems, to globally identify RBPs in bacteria. RIC takes advantage of the base pairing potential of poly(A) tails to pull-down RNA-protein complexes. Overexpressing poly(A) polymerase I in Escherichia coli drastically increased transcriptome-wide RNA polyadenylation, enabling pull-down of crosslinked RNA-protein complexes using immobilized oligo(dT) as bait. With this approach, we identified 169 putative RBPs, roughly half of which are already annotated as RNA-binding. We experimentally verified the RNA-binding ability of a number of uncharacterized RBPs, including YhgF, which is exceptionally well conserved not only in bacteria, but also in archaea and eukaryotes. We identified YhgF RNA targets in vivo using CLIP-seq, verified specific binding in vitro, and reveal a putative role for YhgF in regulation of gene expression. Our findings present a simple and robust strategy for RBP identification in bacteria, provide a resource of new bacterial RBPs, and lay the foundation for further studies of the highly conserved RBP YhgF.
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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.