Direct sequencing of a HLA-DRB gene by polymerase chain reaction: sequence variation in DRw8 specificity

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.

Sequence variation in Japanese HLA-DRw8 specificity

There are four DRw8 haplotypes with different DQ alleles in Japanese: DRw8-DQw6 (w1), DRw8-DQw4, DRw8-DQw8(w3), and DRw8-DQw7 (w3). We previously reported the nucleotide sequence of DRB1 gene of DRw8-DQw6(w1) and it was named DRB1*08032. The nucleotide sequences of the other DRw8 DRB1 alleles and their correspondence to internationally recognized DRw8 subspecificities were still unclear. We have cloned these DRB1 genes and determined the nucleotide sequences. The comparison of the sequences with the published sequences revealed that the differences were occurred at two amino acid positions, and these four haplotypes are classified in two groups: (a) DRw8-DQw6(w1) and DRw8-DQw7(w3), and (b) DRw8-DQw4 and DRw8-DQw8(w3). The DRB1 molecules of DRw8-DQw6(w1) and DRw8-DQw7(w3) have Ser57 and Ile67, and those of DRw8-DQw4 and DRw8-DQw8(w3) have Asp57 and Phe67. The former has the same sequence as that of DRB1*08032, and the latter is same as that of DRB1*0802. The classification corresponds to the serologic subtyping, which divides DRw8 into DR8.1 and DR8.2, reported in the 10th Japan HLA Workshop.

HLA class I nucleotide sequences, 1991

The HLA class I sequences included in this compilation are taken from publications listed in the accompanying paper. Nomenclature for factors of the HLA system. 1990 (Bodmer et al. 1991) and Nomenclature for factors of the HLA system, 1989 (Bodmer et al. 1990). Where discrepancies have arisen between reported sequences the original authors have been contacted where possible, and necessary amendments to published sequences have been incorporated into this alignment. Future sequencing may identify errors in this list and we would welcome any evidence that helps to maintain the accuracy of this compilation. In the sequence alignments identity between residues is indicated by a hyphen (-). Unavailable sequence is indicated by a period (.). Gaps in the sequence are inserted to maintain the alignment between different alleles showing variation in amino acid number.