The specificity of proteasomes: impact on MHC class I processing and presentation of antigens

We have studied polypeptide processing by purified protea somes, with regar d to proteolytic specificity and cytotoxic T-lymphocyte (CTL) epitope gener ation. Owing to defined preferences with respect to cleavage sites and frag ment length, proteasomes degrade polypeptide substrates into cohorts of ove rlapping oligopeptides. Many of the proteolytic fragments exhibit structura l features in common with major histocompatibility complex (MHC) class I li gands including fragment size and frequencies of amino acids at fragment bo undaries. Proteasomes frequently generate definitive MHC class I ligands an d/or slightly longer peptides, while substantially larger peptides are rare . Individual CTL epitopes are produced in widely varying amounts, often con sistent with immunohierarchies among CTL epitopes. We further found that po lypeptide processing is remarkably conserved among proteasomes of eukaryoti c origin and that invertebrate proteasomes can efficiently produce known hi gh-copy MHC class I ligands, suggesting evolutionary adaptation of the tran sporter associated with antigen processing and MHC class I to ancient const raints imposed by proteasomal protein degradation.