DnaK functions as a central hub in the E. coli chaperone network

Area of Science:

• Molecular Biology
• Cell Biology
• Biochemistry

Background:

• Cellular chaperone networks maintain proteome integrity by preventing toxic protein aggregation.
• The DnaK system, Trigger factor (TF), and GroEL are key components of these networks.

Purpose of the Study:

• To elucidate the organizational principles of chaperone networks using Escherichia coli as a model.
• To understand the specific roles and cooperation of DnaK, TF, and GroEL in protein homeostasis.

Main Methods:

• Quantitative proteomics was employed to identify DnaK interacting partners.
• Genetic manipulation, including gene deletions (TF, DnaK, GroEL), was used to study chaperone function and cooperation.
• Protein aggregation and proteostasis were assessed under various chaperone-deficient conditions.

Main Results:

• DnaK interacts with approximately 700 cytosolic proteins, including ~180 aggregation-prone proteins, facilitating their folding.
• Loss of TF alters DnaK's substrate specificity, favoring smaller proteins over large multidomain ones.
• DnaK stabilizes proteins for GroEL-mediated folding, acting as a central organizer; its depletion leads to protein accumulation and degradation.
• Combined DnaK and TF deletion results in proteostasis collapse, impaired GroEL function, defective ribosomal biogenesis, and widespread protein aggregation.

Conclusions:

• DnaK is a central organizer of the chaperone network, crucial for substrate triage and subsequent folding steps.
• The interplay between DnaK, TF, and GroEL is essential for maintaining proteome integrity and cellular function.
• Disruption of this chaperone network leads to severe cellular dysfunction and protein aggregation.