Grad-seq shines light on unrecognized RNA and protein complexes in the model bacteriumEscherichia coli
Preprint
- 29 June 2020
- preprint
- Published by Cold Spring Harbor Laboratory
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.Keywords
Other Versions
- Published version: Version Nucleic Acids Research, 48, preprints
This publication has 97 references indexed in Scilit:
- Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coliJournal of Inorganic Biochemistry, 2012
- Cryptic prophages help bacteria cope with adverse environmentsNature Communications, 2010
- Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNAThe EMBO Journal, 2010
- Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron MicroscopyBiological Procedures Online, 2009
- VARNA: Interactive drawing and editing of the RNA secondary structureBioinformatics, 2009
- Jalview Version 2—a multiple sequence alignment editor and analysis workbenchBioinformatics, 2009
- MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantificationNature Biotechnology, 2008
- The RNA chaperone Hfq is essential for the virulence of Salmonella typhimuriumMolecular Microbiology, 2006
- Large-scale identification of protein–protein interaction of Escherichia coli K-12Genome Research, 2006
- Gene Expression Omnibus: NCBI gene expression and hybridization array data repositoryNucleic Acids Research, 2002