Issue 4, 2013
From the journal:

Molecular BioSystems

The proteomic response to mutants of the Escherichia coli RNA degradosome†

Li Zhou,‡ab   Ang B. Zhang,‡c   Rong Wang,ad   Edward M. Marcottea  and  Christine Vogel*ac  

* Corresponding authors

a University of Texas at Austin, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Austin, TX, USA
E-mail: cvogel@nyu.edu

b Department of Molecular Biology, Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA

c New York University, Department of Biology, Center for Genomics and Systems Biology, New York, NY, USA

d National Heart Lung and Blood Institute, NIH, Bethesda, Maryland, USA

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.

Graphical abstract: The proteomic response to mutants of the Escherichia coli RNA degradosome

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Article information

DOI
https://doi.org/10.1039/C3MB25513A
Article type
Paper
Submitted
10 Nov 2012
Accepted
23 Jan 2013
First published
24 Jan 2013

Mol. BioSyst., 2013,9, 750-757

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The proteomic response to mutants of the Escherichia coli RNA degradosome

L. Zhou, A. B. Zhang, R. Wang, E. M. Marcotte and C. Vogel, Mol. BioSyst., 2013, 9, 750 DOI: 10.1039/C3MB25513A

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