Proteasomal cleavage prediction

Proteasome cleavage overview

The proteasome is a component of the autophagy process. Indeed, the proteasome is responsible for the breakdown of proteins into short peptides. By degrading these proteins into short peptides, proteasomal degradation regulates cell growth and apoptosis. In addition, proteasome degrades denatured or abnormal proteins, such as virally infected cells or cancer cells. The degradation consists in a chemical reaction that breaks peptide bonds by proteolysis and helped by proteases. Peptides resulting have 8-10 amino acids. Peptides are transported into the lumen of the endoplasmic reticulum by a transporter. That allows, then, to load the peptide on the major histocompatibility complexes class I molecules (MHC I). The complex of MHC/peptide leave the endoplasmic reticulum and migrate through the secretory pathway to the cell surface. This complex reaches to meet a T lymphocyte (CTL) and to start an immunological reaction.

Proteasome structure

The proteasome is a large protease cylindrical complex. The core of the proteasome, called 20S proteasome, contains four stacked heptameric rings which form a central pore. This pore is a catalytic chamber allowing the protein degradation. The two outer rings are made of seven α-subunits which allow to maintain a gate through protein enter. α-subunits are controlled by some molecular mechanisms such as molecules which recognize polyubiquitin tags on protein. The inner rings are composed of seven β-subunits which contain several protease active sites on the interior surface of the rings.

Ubiquitin-proteasome system (UPS)

The ubiquitin-proteasome system consists in the degradation of intracellular proteins which are tagged with a small protein, called ubiquitin. Ubiquitin ligases tag abnormal proteins. When one ubiquitin tag attaches a protein, others ubiquitin ligases come to attach additional ubiquitin molecules. The protein tagged has a polyubiquitin chain which is able to bind the proteasome and to begin the degradation process. The proteasome complex degrades protein into peptides of 8 to 10 amino acids which can be presented by major histocompatibility class I molecules.

Proteasomal cleavage prediction databases

A proteasome cleavage process can be simulated by several informatics tools such as Immune Epitope Database and Analysis Resource (IEDB) and NetChop server. Indeed, proteasomal cleavage prediction database allows to predict cleavage sites of a protein and the generation of antigens.

Several methods are used by these tools to the proteasomal cleavage prediction:

NetChop: production of neural network predictions by proteasomal degradation

NetCtl: production of T cell epitopes in protein sequences

NetCtlPan: production of T cell epitopes in protein sequences with restriction to any MHC molecules.

Proteasomal degradation prediction in neoantigen drug discovery

Proteasomal degradation predictions have a huge interest in neoantigen discovery. Indeed, applications of proteasomal cleavage predictions are essentially in immune-oncology, virology, microbial infection researches. Proteasomal cleavage predictions are helpful in neoantigen drug discovery but also in vaccine development.

Proteasomal cleavage prediction is a simple and valuable tool to predict antigens possibly generated by a protein. SB-PEPTIDE can synthesize these antigens through different services (peptide synthesis library or individual peptide synthesis service). Also offer a catalog of antigens.

Peptide synthesis

1- Sijts E J A M and Kloetzel P M. Cell Mol Life Sci. 68(9):1491-502 (2011)

The role of the proteasome in the generation of MHC class I ligands and immune responses

The ubiquitin-proteasome system (UPS) degrades intracellular proteins into peptide fragments that can be presented by major histocompatibility complex (MHC) class I molecules. While the UPS is functional in all mammalian cells, its subunit composition differs depending on cell type and stimuli received. Thus, cells of the hematopoietic lineage and cells exposed to (pro)inflammatory cytokines express three proteasome immunosubunits, which form the catalytic centers of immunoproteasomes, and the proteasome activator PA28. Cortical thymic epithelial cells express a thymus-specific proteasome subunit that induces the assembly of thymoproteasomes. We here review new developments regarding the role of these different proteasome components in MHC class I antigen processing, T cell repertoire selection and CD8 T cell responses. We further discuss recently discovered functions of proteasomes in peptide splicing, lymphocyte survival and the regulation of cytokine production and inflammatory responses.

2- Dikic Ivan. Annu Rev Biochem. 86:193-224 (2017)

Proteasomal and Autophagic Degradation Systems

Autophagy and the ubiquitin-proteasome system are the two major quality control pathways responsible for cellular homeostasis. As such, they provide protection against age-associated changes and a plethora of human diseases. Ubiquitination is utilized as a degradation signal by both systems, albeit in different ways, to mark cargoes for proteasomal and lysosomal degradation. Both systems intersect and communicate at multiple points to coordinate their actions in proteostasis and organelle homeostasis. This review summarizes molecular details of how proteasome and autophagy pathways are functionally interconnected in cells and indicates common principles and nodes of communication that can be therapeutically exploited.

3- Vigneron N et al. Mol Immunol. 113:93-102 (2019)

Production of spliced peptides by the proteasome

CD8+ cytolytic T lymphocytes are essential players of anti-tumor immune responses. On tumors, they recognize peptides of about 8-to-10 amino acids that generally result from the degradation of cellular proteins by the proteasome. Until a decade ago, these peptides were thought to solely correspond to linear fragments of proteins that were liberated after the hydrolysis of the peptide bonds located at their extremities. However, several examples of peptides containing two fragments originally distant in the protein sequence challenged this concept and demonstrated that proteasome could also splice peptides together by creating a new peptide bond between two distant fragments. Unexpectedly, peptide splicing emerges as an essential way to increase the peptide repertoire diversity as these spliced peptides were shown to represent up to 25% of the peptides presented on a cell by MHC class I. Here, we review the different steps that led to the discovery of peptide splicing by the proteasome as well as the lightening offered by the recent progresses of mass spectrometry and bioinformatics in the analysis of the spliced peptide repertoire.

4- Nat Biotechnol. 35(2):97 (2017). doi: 10.1038/nbt.3800.

The problem with neoantigen prediction

Personalized immunotherapy is all the rage, but neoantigen discovery and validation remains a daunting problem.

5- Nature volume 404, 770–774 (2000). doi: 10.1038/35008096

Rapid degradation of a large fraction of newly synthesized proteins by proteasomes.

MHC class I molecules function to present peptides eight to ten residues long to the immune system. These peptides originate primarily from a cytosolic pool of proteins through the actions of proteasomes¹, and are transported into the endoplasmic reticulum, where they assemble with nascent class I molecules². Most peptides are generated from proteins that are apparently metabolically stable. To explain this, we previously proposed that peptides arise from proteasomal degradation of defective ribosomal products (DRiPs). DRiPs are polypeptides that never attain native structure owing to errors in translation or post-translational processes necessary for proper protein folding³. Here we show, first, that DRiPs constitute upwards of 30% of newly synthesized proteins as determined in a variety of cell types; second, that at least some DRiPs represent ubiquitinated proteins; and last, that ubiquitinated DRiPs are formed from human immunodeficiency virus Gag polyprotein, a long-lived viral protein that serves as a source of antigenic peptides.

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