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4D Imaging of Protein Aggregation in Live Cells
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Condition-dependent amorphous protein agglomerates control cytoplasmic rheology.

José Losa1, François Simon2, Dmitrii Linnik3

  • 1Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.

Molecular Cell
|April 12, 2026
PubMed
Summary

Bacterial cytoplasm crowding affects molecular diffusion. Amino acid metabolism proteins form clusters, controlling diffusion and elasticity by altering cytoplasmic rheology.

Keywords:
amino acid metabolismcytoplasmintracellular diffusionprotein agglomerationsingle-particle tracking

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Area of Science:

  • Microbiology and Biophysics
  • Investigating molecular dynamics within bacterial cells.

Background:

  • Bacterial cytoplasm exhibits molecular crowding, hindering large molecule diffusion and affecting cellular functions.
  • Existing models do not fully explain the observed variations in cytoplasmic diffusion and rheology.

Purpose of the Study:

  • To investigate the factors influencing cytoplasmic diffusion and rheology in Escherichia coli.
  • To identify the molecular mechanisms behind variations in diffusion under different growth conditions.

Main Methods:

  • Utilized single-particle tracking to monitor the diffusion of a 40-nm particle in Escherichia coli.
  • Employed photoactivated light microscopy and electron microscopy to analyze protein behavior.
  • Assessed the correlation between diffusion coefficients and protein abundance, specifically amino acid metabolism proteins (COG category 'E').

Main Results:

  • Observed a three-fold variation in particle diffusion across exponential growth conditions.
  • Found a significant anticorrelation between diffusion coefficient and the abundance of amino acid metabolism proteins.
  • Demonstrated that lower diffusion correlates with increased cytoplasmic elasticity and identified protein agglomerate formation as a key factor.

Conclusions:

  • Cytoplasmic diffusion and rheology are significantly influenced by the formation of protein agglomerates, particularly from amino acid metabolism proteins.
  • Condition-induced changes in proteome composition directly impact cytoplasmic rheology through protein aggregation.
  • This study reveals a novel mechanism controlling molecular transport and cellular mechanics in bacteria.