Distinct modes of folding assistance in cells by protein- and RNA-based chaperones

Abstract

How chaperones mediate protein folding in the crowded cell environment remains poorly understood. To gain insight, we developed CHAP-SEQ, a high-throughput approach for examining how chaperones affect protein folding in cells at amino acid resolution. Performing CHAP-SEQ using three protein-based chaperones and one RNA-based chaperone revealed distinct modes of folding assistance. The protein-based chaperones preferentially act in a partially redundant manner on hydrophobic core residues, whereas the RNA-based chaperone primarily targets structural or dynamic features of the client protein. Furthermore, while the chaperone RNA has little preference for client variants' baseline stability, the protein-based chaperones preferentially assisted clients with greater intrinsic foldability. Together, these findings demonstrated that protein- and RNA-based chaperones promote protein folding through mechanistically distinct modes of action.