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Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli.

Hör, Jens
; 
Di Giorgio, Silvia
; 
Gerovac, Milan
; 
Venturini, Elisa
; 
Förstner, Konrad U
; 
Vogel, Jörg
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2020-08-19
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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.
Citation
Nucleic Acids Res. 2020 Sep 18;48(16):9301-9319. doi: 10.1093/nar/gkaa676.
Affiliation
HIRI, Helmholtz-Institut für RNA-basierte Infektionsforschung, Josef-Shneider Strasse 2, 97080 Würzburg, Germany.
Publisher
Oxford University Press
Journal
Nucleic acids research
URI
http://hdl.handle.net/10033/622517
DOI
10.1093/nar/gkaa676
PubMed ID
32813020
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en
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1362-4962
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Attribution-NonCommercial-ShareAlike 4.0 International
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publications of the department of RNA biology of bacterial infections([HIRI] RABI)