Diversity of Natural Self-Derived Ligands Presented by Different HLA Class I Molecules in Transporter Antigen Processing-Deficient Cells

Elena Lorente,Mercedes Jiménez,Ilan Beer,Arie Admon,Eilon Barnea,Susana Infantes,Fátima Lasala,Noel García-Medel,Daniel López,Alejandro Barriga

doi:10.1371/journal.pone.0059118

Abstract

The transporter associated with antigen processing (TAP) translocates the cytosol-derived proteolytic peptides to the endoplasmic reticulum lumen where they complex with nascent human leukocyte antigen (HLA) class I molecules. Non-functional TAP complexes and viral or tumoral blocking of these transporters leads to reduced HLA class I surface expression and a drastic change in the available peptide repertoire. Using mass spectrometry to analyze complex human leukocyte antigen HLA-bound peptide pools isolated from large numbers of TAP-deficient cells, we identified 334 TAP-independent ligands naturally presented by four different HLA-A, -B, and -C class I molecules with very different TAP dependency from the same cell line. The repertoire of TAP-independent peptides examined favored increased peptide lengths and a lack of strict binding motifs for all four HLA class I molecules studied. The TAP-independent peptidome arose from 182 parental proteins, the majority of which yielded one HLA ligand. In contrast, TAP-independent antigen processing of very few cellular proteins generated multiple HLA ligands. Comparison between TAP-independent peptidome and proteome of several subcellular locations suggests that the secretory vesicle-like organelles could be a relevant source of parental proteins for TAP-independent HLA ligands. Finally, a predominant endoproteolytic peptidase specificity for Arg/Lys or Leu/Phe residues in the P1 position of the scissile bond was found for the TAP-independent ligands. These data draw a new and intricate picture of TAP-independent pathways.

Highlights

Proteolysis, by the proteasome and other cytosolic proteases, of both newly synthesized proteins and the mature cell proteome continuously generates short peptides that are transported into the endoplasmic reticulum (ER) by the transporter associated with antigen processing (TAP) [1]
Approximately 70 human TAP-independent ligands from classical human leukocyte antigen (HLA) class I molecules are known [7,9], and are mostly restricted to HLA-A2 and derived by cleavage of signal sequences generated by the signal peptidase (SPase) complex
The comparison of TAP-independent peptide pools derived from HLA-A2, HLAB27, an allele high TAP-dependent [26], and other HLA class molecules, such as HLA-B51 or -Cw1, with no data about their TAP dependency, could be relevant in the study of alternative antigen processing pathways

Summary

Introduction

Proteolysis, by the proteasome and other cytosolic proteases, of both newly synthesized proteins and the mature cell proteome continuously generates short peptides that are transported into the endoplasmic reticulum (ER) by the transporter associated with antigen processing (TAP) [1] These peptides are assembled with a nascent HLA class I heavy chain and b2-microglobulin to generate stable HLA/peptide complexes that are exported to the cell membrane and subjected to cytotoxic CD8+ T lymphocyte recognition (reviewed in [2]). Patients with an HLA class I deficiency have a reduced functional CD8+ population but may appear asymptomatic for long periods of time with only a limited susceptibility to chronic respiratory bacterial infections Their immune systems must be reasonably efficient, and in addition to different unaltered layered defenses, it remains possible that the reduced cytolytic CD8+ ab T subpopulation that is specific for TAPindependent antigens may contribute to immune defenses that protect against severe infections in these individuals. We identified more than three hundred TAP-independent ligands bound to different HLA-A, -B, and -C class I molecules

Methods

Results

Conclusion