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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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.
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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