Identification of the expressed MHC class II DQB gene of the Asiatic black bear, Ursus thibetanus, in Japan

Abstract

Genetic diversity estimation of the major histocompatibility complex (MHC) gene may be an important tool in the assessment of immune response ability against infectious disease. We were able to identify a near full-length expressed DQB sequence by RACE-PCR method from the Asiatic black bear, Ursus thibetanus in Japan. This is the first such full length expression in the Ursidae. The bear had at least one functional DQB locus. In phylogenetic tree analysis its DQB amino acid sequence formed a monophyletic group with DQB sequences from members of the order Carnivora and had a 90% nucleotide sequence similarity with the DQB allele of the California sea lion, Zalophus californianus. We compared the DQB amino acid composition of U. thibetanus with those of several other mammalian species including Homo sapiens. Amino acid residues known to be functionally important for human MHC genes, tended to be also conserved among other mammalian species while PBRs in the β1 domain were heterogeneous among mammalian species. The DQB sequence obtained from the bear had not only no putative frameshifts or deletions but also no abnormal amino acid mutations such as had been observed in human DQB molecules. This suggests that the bear DQB sequence was an apparently functional DQB allele. As a preliminary study, we sequenced the exon 2 region of DQB alleles from genomic DNA, and succeeded to amplify the exon 2 of DQB loci. Our study will provide useful information for conservation genetics of the U. thibetanus as well as more generally regarding the mammalian MHC region.

MHC class II DQB diversity in the Japanese black bear, Ursus thibetanus japonicus

“…In this ML tree, the DQB sequences formed a clearly separated cluster from the DRB sequences, in agreement with Yasukochi et al [39]. These trees showed that the 31 sequences from the Japanese black bear formed a monophyletic group with the DQBs of the giant panda.…”

“…Thus, in the present study we additionally identified 39 novel variants at the DNA level in 178 samples. The nucleotide sequence of Urth-DQB*0101 was identical to that found in exon 2 of a cDNA sequence derived from mRNA of a bear sample in our previous study [39]. This suggests the amplification of a functional DQB locus in the present study, although there is no evidence of protein translation.…”

“…The tree showed that the DQB sequences of the Japanese black bear formed a monophyletic group with those of the giant panda. In our previous study, we reported that black bear DQB sequences cluster with DQB sequences of various mammalian species [39]. These results suggest that all MHC sequences of black bears are likely to have been derived from the DQB gene.…”

“…An NCBI BLAST search showed that sequence similarities between bear Urth-DQB and panda Aime-DQB variants were 84% to 91% and 93% to 96% similarity at the amino acid and nucleotide levels, respectively [34]. Of all the variants, Urth-DQB*0101 , *0104 , *0401 , *1001 , and *2601 correspond to the Urth-DQB*a to Urth-DQB*e variants detected in our previous study [39], at the DNA level. Thus, in the present study we additionally identified 39 novel variants at the DNA level in 178 samples.…”

“…Because of large variability of MHC, the examination of MHC diversity is also useful for the management of endangered wild-animal populations that show no variation in genetic markers such as microsatellite loci [38]. In our previous study, we reported a functional DQB sequence (1,150 bp) in the Japanese black bear, identified using the rapid amplification of cDNA ends method [39]. Here, we investigated polymorphism in exon 2 of DQB that contains the hypervariable region involved in binding antigens for the Japanese black bear to consider the potential implications for resistance against pathogens and estimate the status of local populations on the basis of their MHC variation.…”