Nucleotide sequence of a novel DPB1 allele, DPB1*4701

HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action

BACKGROUND

HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR).

METHODS

For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used.

RESULTS

All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found.

CONCLUSIONS

Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.

Novel HLA-DPB1 alleles detected in the Ethiopian population

The number of identified HLA-DPB1 alleles increased rapidly by application of DNA-based typing techniques. PCR-SSO typing indicated the presence of possible new HLA-DPB1 variants in the Ethiopian population. The use of the SBT technique, which considers polymorphic as well as constant regions in the second exon of HLA genes, allowed direct identification of two new allelic variants. Moreover, a recently identified HLA-DPA1 variant was also present in this population. The newly defined allelic HLA-DPB1 sequences found in five individuals of the Ethiopian population were confirmed by cloning and subsequent sequencing of the cloned DNA. One of the new alleles was shown to segregate in a family and was also present in unrelated individuals. Both new DPB1 alleles represent new combinations of existing polymorphism in the hypervariable regions. In different populations the frequency of these new HLA-DP variants remains to be determined.