Adaptability of the GroEL/GroES chaperonin to proteostatic challenge revealed by directed evolution

The folding of newly synthesized proteins is assisted by an essential network of proteins known as molecular chaperones. In bacteria, the chaperones Trigger Factor (TF), DnaK/DnaJ (Hsp70 system), and GroEL/GroES (chaperonin system) are key players in proteostasis maintenance. Here, we further explore the cooperation and substrate preference within the bacterial chaperone network by performing directed evolution of GroEL/GroES in Escherichia coli lacking both TF and DnaK chaperone pathways. We found that single amino acid substitutions in GroEL were sufficient to significantly improve its chaperone activity in vivo at high temperature in the absence of TF and DnaKJ, with a combination of selected mutations further enhancing functionality. In vitro analysis showed that high-performing GroEL variants have a higher rate of ATP hydrolysis and an increased folding rate for certain substrates at low ATP concentration, thereby compensating for the significant drop in ATP level observed in vivo in cells lacking TF and DnaKJ. Analysis of substrates bound to GroEL in vivo showed that experimentally evolved chaperones likely adapted toward obligate GroEL substrates with low solubility, thus bypassing cooperation with upstream chaperones like TF and DnaKJ.