Targeting of HIV-1 Nef to the centrosome: implications for antigen processing.

To gain a better understanding of the intracellular sites of antigen processing we have looked at the localization of human immunodeficiency virus (HIV)-1 Nef protein by confocal microscopic and biochemical means. We found that ubiquitin (Ub)-Nef fusion proteins were localized to the centrosome in transfected COS-7 cells, and that the colocalization was inhibited by the microtubule-disrupting agent, nocodazole. Interestingly, we found that Ub-Nef trafficking to the centrosome was not dependent upon the metabolic stability of Ub-Nef nor on the inhibition of proteasome activity. We also analyzed the MHC class I antigen processing of a reporter epitope linked to the Ub-Nef fusion proteins and found that Ub-Nef was processed in COS-7 cells. In addition, we show that this processing was inhibited by nocodazole. We suggest that the centrosome may serve as a site of antigen processing in vivo.

Herpes simplex virus inhibitor ICP47 destabilizes the transporter associated with antigen processing (TAP) heterodimer.

Chemical cross-linking of the transporter associated with antigen processing (TAP) heterodimer was used to determine whether the herpes simplex virus inhibitor of TAP, ICP47, induces a conformational change in TAP. Cross-linking of TAP in cellular membranes produced a major species of approximately 220 kDa which was comprised solely of TAP.1 and TAP.2 and most likely represents the TAP heterodimer. Interestingly, prior treatment of TAP-containing membranes with TAP peptide substrates stimulated the formation of the cross-linked TAP heterodimer, whereas pretreatment of membranes with ICP47 completely blocked the formation of the cross-linked heterodimer. These data suggest that suitable substrates for TAP stabilize the TAP heterodimer, whereas ICP47 destabilizes the heterodimer. The results indicate that subtle conformational changes occur in the TAP heterodimer upon the binding of peptides and the inhibitor ICP47 and that ICP47 has a deleterious effect on TAP heterodimer structure, in addition to its role as a potent blocker of substrate binding to TAP.

Binding and transport of melanoma-specific antigenic peptides by the transporter associated with antigen processing.

To gain insight into how tumor antigens are generated and presented, a panel of peptides corresponding to melanoma-specific T cell epitopes were tested for their transport capacity by the transporter associated with antigen processing (TAP). The melanoma epitopes exhibited differential capacities to be transported by TAP in streptolysin O-permeabilized cells, as well as differential competition for peptide binding to TAP. The data indicate that some melanoma-specific epitopes are good substrates for TAP, while others are poor substrates for TAP. One of the epitopes, derived from tyrosinase, was transported into the endoplasmic reticulum (ER), in spite of being a poor competitor for reporter peptide transport and for peptide binding. These results suggest that the melanoma antigens follow distinct pathways for presentation, along the MHC class I pathway.

Use of microsatellite loci to classify individuals by relatedness.

This study investigates the use of microsatellite loci for estimating relatedness between individuals in wild, outbred, vertebrate populations. We measured allele frequencies at 20 unlinked, dinucleotide-repeat microsatellite loci in a population of wild mice (Mus musculus), and used these observed frequencies to generate the expected distributions of pairwise relatedness among full sib, half sib, and unrelated pairs of individuals, as would be estimated from the microsatellite data. In this population one should be able to discriminate between unrelated and full-sib dyads with at least 97% accuracy, and to discriminate half-sib pairs from unrelated pairs or from full-sib pairs with better than 80% accuracy. If one uses the criterion that parent-offspring pairs must share at least one allele per locus, then only 15% of full-sib pairs, 2% of half-sib pairs, and 0% of unrelated pairs in this population would qualify as potential parent-offspring pairs. We verified that the simulation results (which assume a random mating population in Hardy-Weinberg and linkage equilibrium) accurately predict results one would obtain from this population in real life by scoring laboratory-bred full- and half-sib families whose parents were wild-caught mice from the study population. We also investigated the effects of using different numbers of loci, or loci of different average heterozygosities (He), on misclassification frequencies. Both variables have strong effects on misclassification rate. For example, it requires almost twice as many loci of He = 0.62 to achieve the same accuracy as a given number of loci He = 0.75. Finally, we tested the ability of UPGMA clustering to identify family groups in our population. Clustering of allele matching scores among the offspring of four sets of independent maternal half sibships (four females, each mated to two different males) perfectly recovered the true family relationships.