The interaction network of the proteasome assembly chaperone PSMD9 regulates proteostasis

Abstract

Functional networks in cells are created by physical, genetic, and regulatory interactions. Mapping them and annotating their functions by available methods remains a challenge. We use affinity purification mass spectrometry (AP‐MS) coupled with SLiMFinder to discern such a network involving 26S proteasome non‐ATPase regulatory subunit 9 (PSMD9), a chaperone of proteasome assembly. Approximately 20% of proteins within the PSMD9 interactome carry a short linear motif (SLiM) of the type ‘EXKK’. The binding of purified PSMD9 with the peptide sequence ERKK, proteins heterogeneous nuclear ribonucleoproteins A2/B1 (hnRNPA2B1; containing ERKK), and peroxiredoxin‐6 (PRDX6; containing EAKK) provided proof of principle for this motif‐driven network. The EXKK motif in the peptide primarily interacts with the coiled‐coil N domain of PSMD9, a unique interaction not reported for any coiled‐coil domain. PSMD9 knockout (KO) HEK293 cells experience endoplasmic reticulum (ER) stress and respond by increasing the unfolded protein response (UPR) and reducing the formation of aggresomes and lipid droplets. Trans‐expression of PSMD9 in the KO cells rescues lipid droplet formation. Overexpression of PSMD9 in HEK293 cells results in reduced UPR, and increased lipid droplet and aggresome formation. The outcome argues for the prominent role of PSMD9 in maintaining proteostasis. Probable mechanisms involve the binding of PSMD9 to binding immunoglobulin protein (BIP/GRP78; containing EDKK), an endoplasmic reticulum chaperone and key regulator of the UPR, and fatty acid synthase (FASN; containing ELKK), involved in fatty acid synthesis/lipid biogenesis. We propose that PSMD9 acts as a buffer in the cellular milieu by moderating the UPR and enhancing aggresome formation to reduce stress‐induced proteotoxicity. Akin to waves created in ponds that perpetuate to a distance, perturbing the levels of PSMD9 would cause ripples down the networks, affecting final reactions in the pathway, one of which is altered proteostasis.

The Role of Z Chromosome Localization Gene psmd9 in Spermatogenesis of Cynoglossus semilaevis

“…PSMD9 is a companion to protease assembly. A cell knockout experiment confirmed that psmd9 plays a significant role in maintaining protein balance [ 16 ]. In addition, PSMD9 interacts with several free ribosomes subunits and plays a role in the transport of ribosomal proteins to the nucleolus, which helps to maintain the structure and morphology of the nucleolar membrane-free compartment [ 28 ].…”

“…Proteasome 26S Subunit, Non-ATPase 9 ( psmd9 ) is an active hub gene that links numerous pathways that are important for organelle structure, cell signaling, growth, survival and therapy resistance [ 16 ]. PSMD family members and their interacting molecules participate in the regulation of biological processes, such as the cell cycle, cell invasion and migration.…”