Antigen processing and cell homeostasis: role of the proteasome and other proteins

Nathalie Vigneron

The proteasome is a component of the ubiquitin-proteasome system, which is the major ATP-dependent proteolytic machinery in cells. It is responsible for the bulk of protein degradation and it is therefore crucial to the maintenance of cell homeostasis, cell differentiation, cell-cycle progression or apoptosis. In addition to maintaining protein homeostasis, the proteasome plays a key role in immune surveillance by releasing peptides, which are then transported to the lumen of the endoplasmic reticulum by the TAP transporter for loading onto molecules of the major histocompatibility complex I. A few years ago, the Van den Eynde lab has shown that in addition to standard proteasome (SP) and the immunoproteasome (IP), two other intermediate proteasomes exist, which contain either one (ß1-ß2-ß5i) or two (ß1i-ß2-ß5i) immunosubunits (Guillaume et al., 2010). Because of the nature of their catalytic subunits, these four proteasome subtypes display different catalytic activities and produce a different set of antigenic peptides (Guillaume et al., 2012). We therefore aim to continue our analysis of the processing of a series of human tumor antigens in order to define the peptides with the highest potential as targets of cancer vaccines and adoptive cell therapies.

Intermediate proteasomes represent 30-50% of the proteasome content of human liver, colon, small intestine and kidney. They are also present in human tumor cells and dendritic cells. Apart for their role in establishing the MHC-I antigenic peptide repertoire, the relevance of intermediate proteasomes in cell homeostasis is still unclear.

We therefore investigated the role of the four proteasome subtypes in the degradation of ubiquitinated and oxidized proteins. To do so, we have produced cell lines expressing specifically each of the four proteasome subtypes. These cells were used to show that all four 26S proteasome subtypes degrade ubiquitinated proteins equally well (Abi Habib et al., 2020). On the other hand, we used purified 20S proteasomes corresponding to each proteasome subtype to perform in vitro digestions of oxidized proteins such as calmodulin or hemoglobin, and showed that these oxidized proteins were best degraded by the three β5i-containing 20S proteasomes, whereas their native forms were not degraded at all (Abi Habib et al., 2020). Circular dichroism analyses indicated that ubiquitin-independent recognition of oxidized proteins by 20S proteasomes was triggered by the disruption of their structure. Accordingly, β5i-containing 20S proteasomes degraded unoxidized naturally disordered protein tau, while 26S proteasomes did not. These results suggest that the three β5i-containing 20S proteasomes, namely the immunoproteasome and the two intermediate proteasomes, might help cells eliminate proteins containing disordered domains, including those induced by oxidative stress. Other potential functions of intermediate proteasome in cells still to be explored.

List of publications

Abi Habib, J., E. De Plaen, V. Stroobant, D. Zivkovic, M.P. Bousquet, B. Guillaume, K. Wahni, J. Messens, A. Busse, N. Vigneron, and B.J. Van den Eynde. 2020. Efficiency of the four proteasome subtypes to degrade ubiquitinated or oxidized proteins. Sci Rep 10:15765.

Guillaume, B., J. Chapiro, V. Stroobant, D. Colau, B. Van Holle, G. Parvizi, M.P. Bousquet-Dubouch, I. Theate, N. Parmentier, and B.J. Van den Eynde. 2010. Two abundant proteasome subtypes that uniquely process some antigens presented by HLA class I molecules. Proc Natl Acad Sci U S A 107:18599-18604.

Guillaume, B., V. Stroobant, M.P. Bousquet-Dubouch, D. Colau, J. Chapiro, N. Parmentier, A. Dalet, and B.J. Van den Eynde. 2012. Analysis of the processing of seven human tumor antigens by intermediate proteasomes. J Immunol189:3538-3547.