Modeling Proteasome Assembly Pathways in Bacteria

Abstract

Cells employ various systems to remove unwanted or damaged proteins. The proteasome is one such system, which is a large macromolecular machine that functions in degrading proteins and regulating cellular processes. It consists of a 20S Core Particle (CP) capped by a Regulatory Particle (RP). The CP is comprises of four stacked rings each made up of seven monomers (α and β) stacked in a barrel-shaped architecture. Modulating proteasome function for therapeutic purposes has gained significant interest during the past decade to combat diseases like cancer and drug resistant tuberculosis. Recent findings suggest that Mycobacterium tuberculosis(Mtb) is an attractive target for proteasome inhibitors. The CP of Rhodococcus erythroplisshares about 64% sequence identity to Mtband its assembly has been well-characterized experimentally. In all organisms, CP assembly follows a hierarchical pathway where two Half Proteasomes (HP: α7β7) are formed first and then dimerize to form CP (α7β7β7α7). It is hypothesized that HP formation follows different pathways in archaea, bacteria and eukaryotes, but we currently lack definitive evidence for these hypotheses. In this work, we employed mathematical models to study the CP assembly pathway in R. erythropolis. Specifically, we found that more hierarchical assembly pathways provide the system with greater robustness against kinetic trapping at high concentration. The robustness of these pathways comes at the cost of significantly slower assembly kinetics. Comparison of our simulations with experimental data suggests that the CP in R. erythropolisemploys an assembly pathway that is much less hierarchical than has been previously proposed. Further experimental and theoretical investigation of CP assembly will be crucial to efforts aimed at inhibiting or modulating proteasome function in bacteria and other organisms.