Molecular Requirements for T Cell Recognition of N-Myristoylated Peptides Derived from the Simian Immunodeficiency Virus Nef Protein

Abstract

We have recently isolated a rhesus macaque cytotoxic T cell line, 2N5.1, that specifically recognizes an N-myristoylated 5-mer peptide (C 14 -Gly-Gly-Ala-Ile-Ser [C14nef5]) derived from the simian immunodeficiency virus (SIV) Nef protein. Such C14nef5-specific T cells expand in the circulation of SIV-infected monkeys, underscoring the capacity of T cells to recognize viral lipopeptides; however, the molecular basis for the lipopeptide antigen presentation remains to be elucidated. Here, functional studies indicated that the putative antigen-presenting molecule for 2N5.1 was likely to have two separate antigen-binding sites, one for interaction with a C 14 -saturated acyl chain and the other for anchorage of the C-terminal serine residue. Mutants with alanine substitutions for the second glycine residue and the fourth isoleucine residue were not recognized by 2N5.1 but interfered with the presentation of C14nef5 to 2N5.1, indicating that these structural analogues retained the ability to interact with the antigenpresenting molecules. In contrast to the highly specific recognition of C14nef5 by 2N5.1, an additional cytotoxic T cell line, SN45, established independently from a C14nef5-stimulated T cell culture, showed superb reactivity to both C14nef5 and an N-myristoylated Nef 4-mer peptide, and therefore, the C-terminal serine residue was dispensable for the recognition of lipopeptides by the SN45 T cells. Furthermore, the mutants with alanine substitutions were indeed recognized by the SN45 T cells. Given that N-myristoylation of the Nef protein occurs in the conserved motifs and is critical for viral pathogenesis, these observations predict that the lipopeptide-specific T cell response is difficult for viruses to avoid by simply introducing amino acid mutations.

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

“…21 In these experiments, recognition of epitopes was driven by consensus tetrapeptides within the immunogenic peptides, and tetrapeptides within cross-reacting T-cell receptor epitopes were necessary and sufficient to drive T-cell proliferation, findings that are consistent with evidence that this polypeptide length can drive recognition by T-cell receptors. 22 Tetrapeptides are used to model genome phylogeny because they occur relatively infrequently in proteins and typically reflect function. 23 …”

Tracking the Emergence of Host-Specific Simian Immunodeficiency Virus env and nef Populations Reveals nef Early Adaptation and Convergent Evolution in Brain of Naturally Progressing Rhesus Macaques

“…Cytotoxic T cells are capable of sensing N-myristoylation of the Nef protein (58)(59)(60), which perhaps accounts for the selection observed in the region. Other positively selected codons, consistent among all infected animals, clustered around the C-terminal loop and the polyproline motif required for SH3 binding (61,62).…”

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

“…21 In these experiments, recognition of epitopes was driven by consensus tetrapeptides within the immunogenic peptides, and tetrapeptides within crossreacting T-cell receptor epitopes were necessary and sufficient to drive T-cell proliferation, findings that are consistent with evidence that this polypeptide length can drive recognition by T-cell receptors. 22 Tetrapeptides are used to model genome phylogeny because they occur relatively infrequently in proteins and typically reflect function. 23 We used the discovery set to generate a predictive signature from the candidate neoepitopes (see the Methods section in the Supplementary Appendix).…”