Phylogenetic Analysis Of CD1Genes In Vertebrates

CD1s (cluster of differentiation1) are the third class of antigen presenting molecules in addition to major histocompatibility complex (MHC) Ⅰ and Ⅱ, and are believed to share a common ancestral gene with MHC Ⅰ or MHC Ⅰ-like genes. Mammalian CD1can present both hydrophobic and amphipathic lipids, thus playing an important role in the adaptive immune system. Although CD1genes have previously only been found in mammals, recent studies demonstrated that the CD1genes are also present in chickens, suggesting that CD1should have emerged earlier than previously thought. However, chicken CD1genes differ from their mammalian counterparts in many aspects:1, There are only two CD1isotypes in chickens albeit five in mammals.2, Although mammalian CD1genes are shown to be located in MHC paralogous regions, in chickens, the CD1genes are directly linked with MHC genes on the same chromosome.3, CD1isotypes are not found to be orthologous between mammals and birds, suggesting an independent diversification of CD1isotypes during the speciation of mammals and birds. Despite these findings, many key issues regarding the CD1genes evolution remain still unclear.Using the chicken CD1sequences as templates, we identified a CD1gene homologous sequence from the green anole lizard (Anolis carolinensis) genome, based on which degenerated primers were designed and employed to obtain full length CD1sequences from the lizard, Chinese alligator (Alligator sinensis), and Thailand crocodile (Crocodylus siamensis) in combination with5’ and3’ RACE PCR. Using these CD1sequences, we carried out a comprehensive genomic survey of CD1genes in mammals, birds and reptiles based on genomic databases. A total of430CD1sequences were identified in74mammals,150from60birds and10from12reptiles. In consistent with previous data, all mammalian CD1genes can be divided into five isotypes (CD1a-e), but the number of CD1genes varies from1-25in different mammalian species. However, our data suggest that there are only four isotypes (CD1.1a, CD1.1b, CD1.1c, CD1.2) in birds, the number of CD1genes varies from2-6. There are only three isotypes found in reptiles.A detailed amino-acid comparsion of CD1moleclues in mammals, birds and reptiles revealed some conserved cysteines and N-linked glycosylation sites in these animals. However, more N-linked glycosylation sites appear to be species-or isotype-specific, which could be generated along with the CD1genes duplication and neofunctionlization. These glycosylation sites may help the interaction of CD1with various antigens. We further made structural prediction of CD1molecules of birds and reptiles based on the solved crystal CD1structures in chickens and mammals. Both the bird and reptile CD1molecules were found to have a small binding groove consisting of one or two pockets, but lack the large binding groove formed by three pockets and a cave in mammals. Syntenic analyses showed that CD1genes in birds and reptiles are either linked with MHC genes, or like in mammals, located in MHC paralogous regions. Unexpectedly, in some species, CD1genes can also be found in regions belonging to neither MHC nor MHC paralogous regions. In summary, this study, for the first time, demonstrates that CD1genes are also present in reptiles. Additional genomic survey, structural predictions, phylogenetic analyses and syntenic gene comparison provide significant clues to our understanding of CD1gene origin and evolution.