ArticleNucleic acids research2020
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- Identification of proteins exhibitingRNA biology · 2026Article
- Cross-species R-DeeP profiling reveals a conserved core of RNA-dependent proteins in yeast.Nucleic acids research · 2026Article
- Small Regulatory RNAs in Prokaryotes: Key Features, Identification, Environmental Roles, and Applications.Microorganisms · 2026Review
- APEX2 proximity labeling of RNA in bacteria.Cell reports methods · 2025Article
- Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts.Genome research · 2025Article
- RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets.Nature communications · 2025Article
- Analysis of stress-induced small proteins inScience signaling · 2025Article
- Analysis of stress-induced small proteins inbioRxiv : the preprint server for biology · 2025Article
- Anti-sense oligonucleotide probing as a structural platform for studying ribonucleoprotein complex assembly.Nature communications · 2025Article
- APEX2 proximity labeling of RNA in bacteria.bioRxiv : the preprint server for biology · 2025Article
- Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs.Nucleic acids research · 2025Article
- Improving prediction of bacterial sRNA regulatory targets with expression data.NAR genomics and bioinformatics · 2025Article
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- Genome-Scale Analysis of the Structure and Function of RNA Pathways and Networks in Pseudomonas aeruginosa.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Directed Screening for sRNA Targets in E. coli Using a Plasmid Library.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Ribosome Protein Composition Mediates Translation during theInternational journal of molecular sciences · 2023Article
- An integrated ion-exchange membrane-based microfluidic device for irreversible dissociation and quantification of miRNA from ribonucleoproteins.Lab on a chip · 2023Article
- Grad-seq analysis ofmicroLife · 2023Article
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Authors and funding
6 authors.
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Abstract
Stable protein complexes, including those formed with RNA, are major building blocks of every living cell. Escherichia coli has been the leading bacterial organism with respect to global protein-protein networks. Yet, there has been no global census of RNA/protein complexes in this model species of microbiology. Here, we performed Grad-seq to establish an RNA/protein complexome, reconstructing sedimentation profiles in a glycerol gradient for ∼85% of all E. coli transcripts and ∼49% of the proteins. These include the majority of small noncoding RNAs (sRNAs) detectable in this bacterium as well as the general sRNA-binding proteins, CsrA, Hfq and ProQ. In presenting use cases for utilization of these RNA and protein maps, we show that a stable association of RyeG with 30S ribosomes gives this seemingly noncoding RNA of prophage origin away as an mRNA of a toxic small protein. Similarly, we show that the broadly conserved uncharacterized protein YggL is a 50S subunit factor in assembled 70S ribosomes. Overall, this study crucially extends our knowledge about the cellular interactome of the primary model bacterium E. coli through providing global RNA/protein complexome information and should facilitate functional discovery in this and related species.
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