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Dynamic Remodeling of Escherichia coli Interactome in Response to Environmental Perturbations
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  • Ahmed Youssef,
  • Fei Bian,
  • Nicolai Paniikov,
  • Mark Crovella,
  • Andrew Emili
Ahmed Youssef
Boston University
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Fei Bian
Shandong Academy of Agricultural Sciences
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Nicolai Paniikov
Northeastern University - Boston Campus
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Mark Crovella
Boston University
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Andrew Emili
Oregon Health & Science University

Corresponding Author:[email protected]

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Proteins play an essential role in the vital biological processes governing cellular functions. Most proteins function as members of macromolecular machines, with the network of interacting proteins revealing the molecular mechanisms driving the formation of these complexes. Profiling the physiology-driven remodeling of these interactions within different contexts constitutes a crucial component to achieving a comprehensive systems-level understanding of interactome dynamics. Here, we apply co-fractionation mass spectrometry and computational modeling to quantify and profile the interactions of ~2,000 proteins in the bacterium Escherichia coli cultured under ten distinct culture conditions. The resulting quantitative co-elution patterns revealed large-scale condition-dependent interaction remodeling among protein complexes involved in diverse biochemical pathways in response to the unique environmental challenges. Network-level analysis highlighted interactome-wide biophysical properties and structural patterns governing interaction remodeling. Our results provide evidence of the local and global plasticity of the E. coli interactome along with a rigorous generalizable framework to define protein interaction specificity. We provide an accompanying interactive web application to facilitate exploration of these rewired networks.
02 Apr 2023Submitted to PROTEOMICS
03 Apr 2023Submission Checks Completed
03 Apr 2023Assigned to Editor
03 Apr 2023Review(s) Completed, Editorial Evaluation Pending
03 Apr 2023Reviewer(s) Assigned
18 Apr 2023Editorial Decision: Revise Minor
28 Apr 2023Review(s) Completed, Editorial Evaluation Pending
28 Apr 20231st Revision Received
02 May 2023Reviewer(s) Assigned
04 May 2023Editorial Decision: Accept