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. 2016 Jan;34(1):104-10.
doi: 10.1038/nbt.3418. Epub 2015 Dec 7.

The quantitative and condition-dependent Escherichia coli proteome

Alexander Schmidt  1 , Karl Kochanowski  2 , Silke Vedelaar  3 , Erik Ahrné  1 , Benjamin Volkmer  2 , Luciano Callipo  2 , Kèvin Knoops  4 , Manuel Bauer  1 , Ruedi Aebersold  2   5 , Matthias Heinemann  2   3
Affiliations

The quantitative and condition-dependent Escherichia coli proteome

Alexander Schmidt et al. Nat Biotechnol. 2016 Jan.

Abstract

Measuring precise concentrations of proteins can provide insights into biological processes. Here we use efficient protein extraction and sample fractionation, as well as state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein-abundance map for Escherichia coli. We measure cellular protein concentrations for 55% of predicted E. coli genes (>2,300 proteins) under 22 different experimental conditions and identify methylation and N-terminal protein acetylations previously not known to be prevalent in bacteria. We uncover system-wide proteome allocation, expression regulation and post-translational adaptations. These data provide a valuable resource for the systems biology and broader E. coli research communities.

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Conflict of interest statement

Competing financial interest statement

The authors declare that they have no competing interests as defined by Nature Publishing Group, or other interests that might be perceived to influence the results and/or discussion reported in this paper.

Figures

Figure 1
Figure 1. Workflow of system-wide protein abundance determination.
Figure 2
Figure 2. Fractions of protein mass in different COG processes.
Figure 3
Figure 3. Role of transcriptional regulatory network in determining proteome resource allocation.
Figure 4
Figure 4. Condition-dependent distribution of protein mass in different cellular compartments.
Figure 5
Figure 5. Identification and quantification of post-translational modifications (PTMs).
See this image and copyright information in PMC

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