A Quantitative Chaperone Interaction Network Reveals the Architecture of Cellular Protein Homeostasis Pathways

Abstract

Chaperones are abundant cellular proteins that promote the folding and function of their substrate proteins (clients). In vivo, chaperones also associate with a large and diverse set of co-factors (co-chaperones) that regulate their specificity and function. However, how these co-chaperones regulate protein folding and whether they have chaperone-independent biological functions is largely unknown. We have combined mass spectrometry and quantitative high-throughput LUMIER assays to systematically characterize the chaperone/co-chaperone/client interaction network in human cells. We uncover hundreds of novel chaperone clients, delineate their participation in specific co-chaperone complexes, and establish a surprisingly distinct network of protein/protein interactions for co-chaperones. As a salient example of the power of such analysis, we establish that NUDC family co-chaperones specifically associate with structurally related but evolutionarily distinct β-propeller folds. We provide a framework for deciphering the proteostasis network, its regulation in development and disease, and expand the use of chaperones as sensors for drug/target engagement.

NudC regulates actin dynamics and ciliogenesis by stabilizing cofilin 1

“…A growing body of evidence implies that NudC functions as a co-chaperone of Hsp90 to stabilize client proteins [16][17][18]. Proteomics data from our laboratory and others indicate that NudC may interact with cofilin 1 [17,18], a key regulator of actin dynamics, yet little is known about the role of NudC in actin cytoskeleton.…”

“…Mass spectrometry data of proteins co-immunoprecipitated with NudC reported by our group and others have indicated that cofilin 1 may interact with NudC [17,18]. The similar roles of NudC and cofilin 1 in actin dynamics prompted us to investigate the biochemical interaction between these two proteins [28][29][30].…”

“…We and other groups have found that NudC plays crucial roles in diverse cellular processes, including cell division and neuronal migration, partially by modulating the dynein complex [13][14][15]. A growing body of evidence implies that NudC functions as a co-chaperone of Hsp90 to stabilize client proteins [16][17][18]. Proteomics data from our laboratory and others indicate that NudC may interact with cofilin 1 [17,18], a key regulator of actin dynamics, yet little is known about the role of NudC in actin cytoskeleton.…”

Too much to handle — how gaining chromosomes destabilizes the genome

“…36,37 Several proteins involved in DNA repair and replication are well-characterized clients of molecular chaperones. 38 Specifically Hsp90 contributes to genomic integrity, as it is an essential factor for telomerase activity. 39 Hsp90 inhibition also sensitizes human cells to UV-induced cytotoxicity due to impaired function of Pol h 40 and leads to accumulation of chromosomal aberrations due to FancA degradation.…”

The ribosome regulates flavodoxin folding

“…They prevent protein aggregation and/or stimulate folding towards the native state. Chaperones often interact with co-chaperones (186). After release of a protein from the ribosome, its folding may also be affected by chaperones.…”