The proteomic response to mutants of the Escherichia coli RNA degradosome

Li Zhou, Ang B. Zhang, Rong Wang, Edward M. Marcotte, Christine Vogel

Research output: Contribution to journalArticle

Abstract

The Escherichia coli RNA degradosome recognizes and degrades RNA through the coordination of four main protein components, the endonuclease RNase E, the exonuclease PNPase, the RhlB helicase and the metabolic enzyme enolase. To help our understanding of the functions of the RNA degradosome, we quantified expression changes of >2300 proteins using mass spectrometry based shotgun proteomics in E. coli strains deficient in rhlB, eno, pnp (which displays temperature sensitive growth), or rne(1-602) which encodes a C-terminal truncation mutant of RNase E and is deficient in degradosome assembly. Global protein expression changes are most similar between the pnp and rhlB mutants, confirming the functional relationship between the genes. We observe down-regulation of protein chaperones including GroEL and DnaK (which associate with the degradosome), a decrease in translation related proteins in Δpnp, ΔrhlB and rne(1-602) cells, and a significant increase in the abundance of aminoacyl-tRNA synthetases. Analysis of the observed proteomic changes points to a shared motif, CGCTGG, that may be associated with RNA degradosome targets. Further, our data provide information on the expression modulation of known degradosome-associated proteins, such as DeaD and RNase G, as well as other RNA helicases and RNases-suggesting or confirming functional complementarity in some cases. Taken together, our results emphasize the role of the RNA degradosome in the modulation of the bacterial proteome and provide the first large-scale proteomic description of the response to perturbation of this major pathway of RNA degradation.

Original languageEnglish (US)
Pages (from-to)750-757
Number of pages8
JournalMolecular BioSystems
Volume9
Issue number4
DOIs
StatePublished - Apr 2013

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Proteomics
Escherichia coli
Ribonucleases
Proteins
RNA Helicases
Amino Acyl-tRNA Synthetases
Exonucleases
Phosphopyruvate Hydratase
Endonucleases
RNA Stability
Firearms
Protein Biosynthesis
Proteome
degradosome
Mass Spectrometry
Down-Regulation
RNA
Temperature
Enzymes
Growth

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology

Cite this

The proteomic response to mutants of the Escherichia coli RNA degradosome. / Zhou, Li; Zhang, Ang B.; Wang, Rong; Marcotte, Edward M.; Vogel, Christine.

In: Molecular BioSystems, Vol. 9, No. 4, 04.2013, p. 750-757.

Research output: Contribution to journalArticle

Zhou, Li ; Zhang, Ang B. ; Wang, Rong ; Marcotte, Edward M. ; Vogel, Christine. / The proteomic response to mutants of the Escherichia coli RNA degradosome. In: Molecular BioSystems. 2013 ; Vol. 9, No. 4. pp. 750-757.
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