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

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.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Hör J,Di Giorgio S,Gerovac M,Venturini E,Förstner KU,Vogel J

doi

10.1093/nar/gkaa676

subject

Has Abstract

pub_date

2020-09-18 00:00:00

pages

9301-9319

issue

16

eissn

0305-1048

issn

1362-4962

pii

5894416

journal_volume

48

pub_type

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