Abstract
BackgroundPresentation of peptides on Major Histocompatibility Complex (MHC) molecules is the cornerstone in immune system activation and increased knowledge of the characteristics of MHC ligands and their source proteins is highly desirable.Methodology/Principal FindingIn the present large-scale study, we used a large data set of proteins containing experimentally identified MHC class I or II ligands and examined the proteins according to their expression profiles at the mRNA level and their Gene Ontology (GO) classification within the cellular component ontology. Proteins encoded by highly abundant mRNA were found to be much more likely to be the source of MHC ligands. Of the 2.5% most abundant mRNAs as much as 41% of the proteins encoded by these mRNAs contained MHC class I ligands. For proteins containing MHC class II ligands, the corresponding percentage was 11%. Furthermore, we found that most proteins containing MHC class I ligands were localised to the intracellular parts of the cell including the cytoplasm and nucleus. MHC class II ligand donors were, on the other hand, mostly membrane proteins.Conclusions/SignificanceThe results contribute to the ongoing debate concerning the nature of MHC ligand-containing proteins and can be used to extend the existing methods for MHC ligand predictions by including the source protein's localisation and expression profile. Improving the current methods is important in the growing quest for epitopes that can be used for vaccine or diagnostic purposes, especially when it comes to large DNA viruses and cancer.
Highlights
CD8+ T lymphocytes are activated on recognition of Major Histocompatibility Complex (MHC) class I molecules in complex with peptide ligands, whereas CD4+ T lymphocytes are activated by MHC class II molecules in complex with peptide ligands
Using a large data set of proteins containing experimentally identified MHC class I or II ligands obtained from the SYFPEITHI database [16], we examined the proteins according to their Gene Ontology (GO) classification within the cellular component ontology [17] and their concentration at the mRNA level [18]
[16] contains no externally imposed bias with respect to protein cellular location, making it an ideal data set for investigating the presence of biological bias in proteins containing MHC class I or II ligands
Summary
CD8+ T lymphocytes are activated on recognition of MHC class I molecules in complex with peptide ligands, whereas CD4+ T lymphocytes are activated by MHC class II molecules in complex with peptide ligands In both cases, the result is an immune response directed against, e.g., infected or neoplastic cells. The focus of the available methods is, to identify the optimal peptides from provided protein sequences, while little effort has been made towards developing schemes for prioritisation of the optimal protein candidates from a pool of proteins. To this end, increased knowledge about the general characteristics of proteins containing MHC ligands is desirable. Presentation of peptides on Major Histocompatibility Complex (MHC) molecules is the cornerstone in immune system activation and increased knowledge of the characteristics of MHC ligands and their source proteins is highly desirable
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