Structural analysis of H-2Kf and H-2Kfm1 by using H-2K locus-specific sequences

The H-2Kf allele and the spontaneous mutant Kfm1 have been cloned using locus-specific sequences. The mutation consists of a cluster of four nucleotide changes, resulting in amino acid substitutions at positions 95 (Leu----Ile) and 97 (Val----Arg). This finding has structural, genetic, and technical implications. The amino acid substitutions are located on the beta-strands of the antigen recognition site. Their influence on the allogeneic properties of the Kf glycoprotein is consistent with the hypothesis that alloreactivity results from alterations in the spectrum of peptides presented to T cells. These substitutions would not, however, be predicted to be directly accessible for binding to antibodies. Nonetheless, the fm1 mutant binds anti Kf alloantisera and mAb much less strongly than the parent molecule, suggesting some indirect effect of these residues on serologic phenotype. The mutant is also interesting genetically because the sequence of the mutated region is identical to the sequence of the Df gene. This implies that there is a gene conversion-like mutational mechanism operating in the H-2f haplotype. Finally, the strategy used to obtain these K-locus cDNA should prove generally useful for isolating other MHC alleles.     

Structural diversity of the classical H-2 genes: K, D, and L.

Twenty-three class I DNA sequences, representing alleles of the H-2K, D, and L loci, were analyzed to assess patterns of nucleotide and amino acid diversity. Comparisons of the allelic and nonallelic sequences revealed locus specificity in regions encoding the leader peptides and the carboxyl-terminal segments of the Ag presenting molecules. Analyses focusing on the sequences that determine the Ag binding domains revealed weak or insignificant allelic associations, a finding that is in sharp contrast to previously observed relationships among the homologous human sequences. The amino acid positions exhibiting high diversity in the encoded glycoproteins in both mice and humans are localized primarily to the Ag binding site. In the mouse, diverse amino acids were positioned similarly in the K and D/L glycoproteins, although in humans, the A and B glycoproteins exhibit distinctive differences in their locations within the Ag binding site. The absence of locus specificity among the sequences that determine the Ag binding domains of the mouse is consistent with the hypothesis that ectopic gene conversion leads to interlocus exchange of class I sequences. Comparable interlocus exchanges among human class I genes have not played a similar role in shaping human A and B sequences. The basis of this difference between mice and humans is not clear. The nature of amino acid substitutions distinguishing class I loci in mice and humans are comparable, and the role of natural selection in determining diversity appears to be similar in the two species.     

Stability of surface H-2K(b), H-2D(b), and peptide-receptive H-2K(b) on splenocytes.

We have used flow cytometry to study the stability and peptide-binding capability of MHC class I (MHC-I) on the surface of normal C57BL/6 mouse T lymphoblasts. The MHC-I molecules on each cell are nearly evenly divided into two populations with mean half-life values of approximately 1 and 20 h. Our observations suggest that members of the later contain peptide bound with medium to high affinity. Cell surface MHC-I molecules capable of binding exogenous peptide (thus, "peptide-receptive") belong almost entirely to the less stable population. Before exogenous peptide can bind, MHC-I must undergo a change, probably loss of a very low affinity peptide. For MHC-I-K(b), we found that the maximum rate for binding of exogenous peptide corresponds to a t(1/2) value of 12 min. To maintain the 50:50 steady-state distribution of long- vs short-lived MHC-I molecules on the cell surface, approximately 20 short-lived molecules must be exported to the cell surface for each long-lived molecule.     

H-2-associated specificity of virus-immune cytotoxic T cells fromH-2 mutant and wild-type mice: M523 (H-2K ka ) and M505(H-2K bd ) do,M504 (H-2D da ) and M506(H-2K fa ) do not crossreact with wild-typeH-2K orH-2D

B10.A(3R) (H-2K ^b ) mice infected with lymphocytic choriomeningitis virus (LCMV) or vaccinia virus generate cytotoxic T cells capable of specifically lysing virus-infected macrophage target cells fromH-2K ^b mutant mice M505 (H-2K ^bd ), and vice versa. Similarly, virus-immune B10.A(4R) (H-2K ^k ) T cells specifically lyse infected targets from M523 (H-2K ^ka ), and vice versa. In contrast, virus-specific cytotoxic T cells from neither M504 (H-2D ^da ) and B10.A(5R) (H-2D ^d ) nor M506 (H-2K ^fa ) and B10.M(11R) (H-2K ^f ) mutually crossreact at the cytotoxic effector-cell level. As far as tested, the crossreactivity patterns between wild-type and mutantK orD specificities are identical for LCMV- and vaccinia virus-immune spleen cells. Although this finding is no proof for either the altered self nor the dual recognition concept of T-cell recognition, it may be compatible with the latter model.     

Negatively selected H-2bml and H-2b cells stimulated with vaccinia virus completely discriminate between mutant and wild-type H-2K alleles

Lymphocyte populations from B6, C-H-2bml (KbmlDb) mutant mice cannot, after both in vivo and in vitro negative selection for alloreactivity, be induced to recognize vaccinia virus presented in the context of H-2Kb. This finding may mean that the T cell receptor(s) expresses a component that is very specific for a particular "active site" on the self-H-2 molecule. Alternatively, (if recognition is directed at a virus-H-2 complex) the more similar 2 H-2 molecules are, the more likely it may be that precursor thymocytes in the mutant with the capacity to bind H-2Kb + vaccinia virus may be deleted during ontogeny as a result of cross-reaction with H-2Kbml + endogenous antigen.     

Differential allo-response of murine thymocytes to H- 2 K region different recombinants and to H-2Kb mutants

Thymocytes used as responding cells in a mixed leukocyte culture with x-irradiated splenic stimulating cells generate highly significant proliferative and cytotoxic responses when responding and stimulating cells differ by the entire H-2 complex. On the other hand, when the genetic difference between responding and stimulating cells is only a K region, very little, if any, proliferative response is detectable and no cytotoxic response is found. In contrast, when responding and stimulating cell donors differ by a spontaneous mutation in the K region of the H-2 complex, as found in B6.C-H-2ba, B6-H-2bd and B6.C-H-2bf, highly significant proliferative and cytotoxic responses can be obtained. These results, thus, argue that the H-2 mutants cannot, with regard to their relationship to the parental strain, be readily equated with a K region difference as defined in the recombinant inbred strains.     

Structural definition of the H-2Kd peptide-binding motif

Classic major histocompatibility complex (MHC) proteins associate with antigen- and self-derived peptides in an allele-specific manner. Herein we present the crystal structure of the MHC class I protein H-2K(d) (K(d)) expressed by BALB/c mice in complex with an antigenic peptide derived from influenza A/PR/8/34 nucleoprotein (Flu, residues 147-155, TYQRTRALV). Analysis of our structure in conjunction with the sequences of naturally processed epitopes provides a comprehensive understanding of the dominant K(d) peptide-binding motif. We find that Flu residues Tyr(P2), Thr(P5), and Val(P9) are sequestered into the B, C, and F pockets of the K(d) groove, respectively. The shape and chemistry of the polymorphic B pocket make it an optimal binding site for the side chain of Tyr(P2) as the dominant anchoring residue of nonameric peptides. The non-polar F pocket limits the amino acid repertoire at P9 to hydrophobic residues such as Ile, Leu, or Val, whereas the C pocket restricts the size of the P5-anchoring side chain. We also show that Flu is accommodated in the complex through an unfavorable kink in the otherwise extended peptide backbone due to the presence of a prominent ridge in the K(d) groove. Surprisingly, this backbone conformation is strikingly similar to D(b)-presented peptides despite the fact that these proteins employ distinct motif-anchoring strategies. The results presented in this study provide a solid foundation for the understanding of K(d)-restricted antigen presentation and recognition events.     

Serological analysis of H-2 mutants

Serological absorption experiments showed that mutant B6.M505 (H-2 ^bd ) lacks an H-2K end specificity present in the parental B6 strain. It has a molecular weight of 45,000 dalton, indicating it is an H-2 antigen. It is a private specificity ofK ^b strains, and has been designated H-2.62.     

A novel H-2K splice form: predictions for other alternative H-2 splicing events

A large number of H-2K and H-2D cDNA clones from a C3HfB/HeN spleen cDNA library were extensively characterized. All H-2D^k cDNAs were shown to exhibit the short form of exon 8, consistent with the presence of a single lariat branchpoint site within intron 7. Twenty-five H-2K^km2 cDNAs were found to bear a short exon 8, whereas only two clones were shown to carry the longer form of this exon. In one of the H-2K^km2 cDNAs, a novel pattern of H-2 splicing was identified, in which an extra 15 nucleotides, derived from the 3′ end of intron 5, were inserted between the intact and unaltered exon 5 and exon 6 sequences. Resulting from the apparent use of a cryptic splice acceptor site in place of the canonical intron 5 site, this insertion is predicted to generate an in-frame insertion of five nonpolar amino acid residues within a highly polar region of the intracytoplasmic domain of the H-2K polypeptide. The features of this novel splice form served as the basis for predicting additional rare, alternative H-2 pre-mRNA splicing events that might produce functionally relevant microheterogeneity in the encoded H-2 gene products.     

The nucleotide sequence and comparative analysis of the H-2Dp class I H-2 gene

We present the complete nucleotide sequence and the deduced amino acid sequence of the H-2Dp class I gene. This gene, which was cloned from a B10.P genomic DNA library, encodes and intact, functional H-2Dp molecule. Comparative analysis of the Dp sequence with other class I sequences reveals both similarities and differences. This analysis also shows that these genes exhibit D region-specific, locus-specific, as well as allele-specific sequences. The H-2Dp nucleotide sequence is greater than 90% homologous to the H-2Ld and H-2Db genes and only approximately 85% homologous to the H-2Dd gene. The K region and Qa region genes are less homologous. The 3' noncoding sequences appear to be region-specific. All of the previously described D region genes, Db, Ld, and Dd, possess the B2-SINE Alu-like repetitive sequence, as does Dp. Thus, this B2 repeat is a region-specific marker present in all D region genes studied so far. The additional polyadenylation site found in the H-2Dp gene starting at nucleotide 4671, which is homologous to non-D region sequences, as well as unique protein Dp coding sequences, make this gene an interesting model for studying the evolution of polymorphism and structure/function relationships in the class I gene family.