Illumination of PRRSV Cytotoxic T Lymphocyte Epitopes by the Three-Dimensional Structure and Peptidome of Swine Lymphocyte Antigen Class I (SLA-I)

Abstract

To investigate CTL epitope applications in swine, SLA-1 * 1502-restricted peptide epitopes matching porcine reproductive and respiratory syndrome virus (PRRSV) strains were explored by crystallography, biochemistry, and the specific pathogen-free (SPF) swine experiments. First, nine predicted PRRSV peptides were tested by assembly of the peptide-SLA-1 * 1502 (pSLA-1 * 1502) complexes, and the crystal structure of the SLA-1 * 1502 complex with one peptide (NSP9-TMP9) was determined. The NSP9-TMP9 peptide conformation presented by pSLA-1 * 1502 is different from that of the peptides presented by the known pSLA-1 * 0401 and pSLA-3 * hs0202 complexes. Two consecutive Pro residues make the turn between P3 and P4 of NSP9-TMP9 much sharper. The D pocket of pSLA-1 * 1502 is unique and is important for peptide binding. Next, the potential SLA-1 * 1502-restricted peptide epitopes matching four typical genetic PRRSV strains were identified based on the peptide-binding motif of SLA-1 * 1502 determined by structural analysis and alanine scanning of the NSP9-TMP9 peptide. The tetrameric complex of SLA-1 * 1502 and NSP9-TMP9 was constructed and examined. Finally, taking NSP9-TMP9 as an example, the CTL immunogenicity of the identified PRRSV peptide epitope was evaluated. The SPF swine expressing the SLA-1 * 1502 alleles were divided into three groups: modified live vaccine (MLV), MLV+NSP9-TMP9, and the blank control group. NSP9-TMP9 was determined as a PRRSV CTL epitope with strong immunogenicity by flow cytometry and IFN-γ expression. Our study developed an integrated approach to identify SLA-I-restricted CTL epitopes from various important viruses and is helpful in designing and applying effective peptide-based vaccines for swine.

Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism

“…The 156 Arg in HLA-B*35:08 was shown to prefer P5 E/D as the secondary anchor residues outside the primary peptide anchor pockets (B and F pocket) (23). In SLA-I molecules, residue 156 also plays a critical role in fixing peptides (30,50,55). The positively charged 156 Arg made the D pocket of SLA-1*04:01 prefer negatively charged P3 residues.…”

The Function of the PRRSV–Host Interactions and Their Effects on Viral Replication and Propagation in Antiviral Strategies

“…The presentation of viral epitopes to CTLs by SLA-1 plays a key role in swine immunity [ 110 ]. The crystal structure of peptide-SLA-1*1502 (pSLA-1*1502) complexes with one peptide (nsp9-TMP9) (PDB code: 5YLX) provides the structural conformation basis of peptide presentation, and the overall structure is very similar to those of pSLA-1*0401 (PDB code: 3QQ3) and pSLA-3*hs0202 (PDB code: 5H94) [ 110 , 111 , 112 ]. The structural information displayed by the D pocket, as shown in Figure 2 , plays a crucial part in determining and fixing the bound peptides, and provides a structural basis for designing effective peptide vaccines [ 111 ].…”

“…The crystal structure of peptide-SLA-1*1502 (pSLA-1*1502) complexes with one peptide (nsp9-TMP9) (PDB code: 5YLX) provides the structural conformation basis of peptide presentation, and the overall structure is very similar to those of pSLA-1*0401 (PDB code: 3QQ3) and pSLA-3*hs0202 (PDB code: 5H94) [ 110 , 111 , 112 ]. The structural information displayed by the D pocket, as shown in Figure 2 , plays a crucial part in determining and fixing the bound peptides, and provides a structural basis for designing effective peptide vaccines [ 111 ]. Study indicated that RdRp has the maximum number of conserved peptides by identifying SLA-1*1502-restricted potential epitopes peptides from whole genomes of different PRRSV strains; thus nsp9/10/11 (especially RdRp) may be the best targets for designing PRRSV vaccines to induce a CTL response to genetically heterologous strains [ 111 ].…”

“…The structural information displayed by the D pocket, as shown in Figure 2 , plays a crucial part in determining and fixing the bound peptides, and provides a structural basis for designing effective peptide vaccines [ 111 ]. Study indicated that RdRp has the maximum number of conserved peptides by identifying SLA-1*1502-restricted potential epitopes peptides from whole genomes of different PRRSV strains; thus nsp9/10/11 (especially RdRp) may be the best targets for designing PRRSV vaccines to induce a CTL response to genetically heterologous strains [ 111 ]. Although the monomer structures of PRRSV nsp10 (PDB code: 6JDU) and nsp11 (PDB code: 5EYI) have been successfully solved, the structure and biological functional mechanisms of nsp9 remain elusive [ 95 , 98 ].…”

PRRSV Non-Structural Proteins Orchestrate Porcine E3 Ubiquitin Ligase RNF122 to Promote PRRSV Proliferation

“…In addition, PRRSV targets host restriction factors such as CH25HC for degradation via ubiquitin proteasomal system [18]. Recent studies have shown that PRRSV utilizes E3 ubiquitin ligase ASB8 to increases the stabilization of nsp1α, which in turn inhibits NF-κB activity by targeting the linear ubiquitin chain assembly complex and also SLA-I for proteasome degradation [19,20]. Currently, how PRRSV interacts with cellular ubiquitin system to promote viral replication has remained poorly understood.…”