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The quantitative and condition-dependent Escherichia coli proteome

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

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Acknowledgements

Funding is acknowledged from the Netherlands Organisation for Scientific Research (NWO) (VIDI grant 864.11.001 to M.H.), Dupont (Dupont Young Professorship Award to M.H.), the Swiss National Science Foundation (31003A_132428/1 to M.B.) and the Commission of the European Communities through the PROSPECTS consortium (EU FP7 project 201648) (R.A.), the PROMYS consortium (EU H2020 project 613745) (M.H.) and for a Marie Curie Intra-European Fellowship (IEF) grant (330150) (K. Knoops) and the European Research Council (ERC-2008-AdG 233226) (R.A.) Further, the authors would like to thank J. Radzikowski for performing a number of experiments. We also like to thank D. Bumann and S. Marguerat for critical reading of the manuscript.

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Contributions

S.V. and B.V. performed all batch cultivations. K. Kochanowski performed the chemostat cultures and did the transcription factor-based analysis. K. Knoops performed the electron microscopy analyses. L.C. prepared samples for data set 1. A.S. prepared samples for data set 2. A.S. performed all shotgun LC-MS analyses. M.B. carried out all targeted LC-MS analyses. A.S., E.A. and M.B. analyzed MS data. A.S. and M.H. wrote the manuscript with input from K. Kochanowski, E.A. and R.A. A.S., R.A. and M.H. conceived the study.

Corresponding authors

Correspondence to Alexander Schmidt or Matthias Heinemann.

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The authors declare no competing financial interests.

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Schmidt, A., Kochanowski, K., Vedelaar, S. et al. The quantitative and condition-dependent Escherichia coli proteome. Nat Biotechnol 34, 104–110 (2016). https://doi.org/10.1038/nbt.3418

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