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Related Experiment Video

Updated: May 1, 2026

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How Does Escherichia coli Allocate Proteome?

Chen Liao1,2,3, Priyanka Priyanka1,2, Yi-Hui Lai1,2

  • 1Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.

ACS Synthetic Biology
|August 9, 2024
PubMed
Summary

Microorganisms optimize growth by allocating intracellular resources. This study reveals a mathematical model of guanosine pentaphosphate (ppGpp) regulation in E. coli, uncovering principles of robust and dynamic proteome allocation.

Keywords:
design principlesnegative feedback controlppGppresource allocationultrasensitivity

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Area of Science:

  • Microbial Physiology
  • Systems Biology
  • Biophysics

Background:

  • Microorganisms actively partition intracellular resources for growth optimization.
  • The molecular mechanisms and quantitative principles of this resource allocation remain unclear.

Purpose of the Study:

  • To develop a mathematical framework to uncover design principles of proteome allocation in Escherichia coli.
  • To elucidate the role of guanosine pentaphosphate (ppGpp)-mediated regulation in resource partitioning.

Main Methods:

  • Developed a coarse-grained mathematical framework.
  • Focused on guanosine pentaphosphate (ppGpp)-mediated regulation.
  • Analyzed proteome allocation in Escherichia coli.

Main Results:

  • Identified an ultrasensitive, negative feedback-controlling topology for resource partitioning.
  • Ultrasensitivity arises from zero-order amino acid kinetics and negative feedback from ppGpp-controlled ribosome synthesis.
  • The network topology confers a sliding mode control-like optimization mechanism, robust against variations and efficient for biomass production.

Conclusions:

  • Elucidated the fundamental controlling mechanism of E. coli proteome allocation.
  • Provided insights into quantitative microbial physiology and synthetic gene network design.
  • Demonstrated a robust and efficient resource allocation strategy mimicking nonlinear optimization.