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Periplasmic protein quality control at atomic level in live cells.

Lisandro J González1,2, Francisco J Hita3, Letizia Pontoriero4

  • 1Laboratory of Metalloproteins, Institute of Molecular and Cellular Biology of Rosario, National University of Rosario (IBR-CONICET-UNR), Rosario, Argentina. lgonzalez@ibr-conicet.gov.ar.

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|September 24, 2025
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Researchers used in-cell NMR to reveal how gram-negative bacteria control proteins in the periplasm. They discovered how proteases Prc and DegP work together to degrade the metallo-β-lactamase NDM-1 during zinc starvation.

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Area of Science:

  • Microbiology
  • Molecular Biology
  • Biochemistry

Background:

  • The periplasm is vital for gram-negative bacteria, supporting functions like nutrient uptake, cell wall metabolism, antibiotic resistance, and virulence.
  • Effective protein quality control within the periplasm is essential for bacterial survival and fitness.
  • The periplasm's confined space presents challenges for detailed mechanistic studies of its complex processes.

Purpose of the Study:

  • To investigate the mechanism of periplasmic protein quality control in live bacteria.
  • To elucidate the roles of proteases Prc and DegP in degrading the metallo-β-lactamase NDM-1 under zinc-deficient conditions.

Main Methods:

  • Utilized in-cell NMR spectroscopy to achieve high-resolution analysis within the periplasmic compartment.
  • Studied the destabilization and degradation of NDM-1 under zinc starvation to probe quality control pathways.

Main Results:

  • Demonstrated that zinc starvation destabilizes the native structure of NDM-1, marking it for degradation.
  • Showed that the protease Prc specifically targets membrane-bound NDM-1 at distinct residues and secondary structure elements.
  • Revealed that the protease DegP further processes peptide fragments generated by Prc.

Conclusions:

  • Disclosed the coordinated action of Prc and DegP in periplasmic protein degradation at atomic resolution in living cells.
  • Highlighted the importance of protease concert in maintaining protein homeostasis within the bacterial periplasm.
  • Provided novel insights into bacterial survival mechanisms under nutrient stress through protein quality control.