Abstract
Its small size and short generation time renders the zebrafish (Brachydanio rerio) an ideal vertebrate for immunological research involving large populations. A prerequisite for this is the identification of the molecules critical for an immune response in this species. In earlier studies, we cloned the zebrafish genes coding for the β chains of the class I and class II major histocompatibility complex (MHc) molecules. Here. we describe the cloning of the zebrafish α chain-encoding class II gene, which represents the first identification of a class II A gene in teleost fishes. The gene, which is less than 3 kilobases (kb) distant from one of the β chain-encoding genes, is approximately 1.2 kb long and consist of four exons interrupted by very short (<200 base pairs) introns. Its organization is similar to that of the mammalian class II A genes, but its sequence differs greatly from the sequence of the latter (36% sequence similarity). Among the most conserved parts is the promoter region, which contains X, Y, and TATA boxes with high sequence similarity to the corresponding mammalian boxes. The observed striking conservation of the promoter region suggests that the regulatory system of the class II genes was established more than 400 million years ago and has, principally, remained the same ever since. Like the DMA, but unlike all other mammalian class II A genes, the zebrafish gene codes for two cysteine residues which might potentially be involved in the formation of a disulfide bond in the α1 domain. The primary transcript of the gene is 1196 nucleotides long and contains 708 bucleotides of coding sequence. The gene is expressed in tissues with a high content of lymphoid/myeloid cells (spleen, pronephros, hepatopancreas, and intestine). The analyzed genomic and cDNA sequences are probably derived from different loci (their overall sequence similarity in the coding region is 73% and their 3′ untranslated regions are highly divergent form each other). The genes are apparently functional. Comparison of genes from different zebrafish populations reveals high exon 2 variability concentrated in positions coding for the putative peptide-binding region. Phylogenetic analysis suggests that the zebrafish class II A genes stem form a different ancestor than the mammalian class II A genes and the recently cloned shark class II gene.
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Adam, D., Maeueler, W., and Schartl, M. Transcriptional activation of the melanoma inducing Xmrk oncogene in Xiphophorus. Oncogene 6: 73–80, 1991
auffray, C., Lillie, J. W., Arnot, D., Grossberger, D., Kappes, D., and Stromigner, J. L. Isotypic and allotypic variation of human class II histocompatibility antigen α-chain genes. Nature 308: 327–333, 1984
Barran, P. A. and McMaster, W. R. DNA sequence analysis of the rat RTI. B alpha gene. Immunogenetics 26: 56–62, 1987
Benoist, C. and Mathis, D. Regulation of major histocompatibility complex class II genes: X, Y, and other letters of the alphabet. Annu Rev Immunol 8: 681–715, 1990
Ber, R. and Daniel, V. Structure and sequence of the growth hormone-encoding gene from Tilapia nilotica. Gene 113: 245–250, 1992
Bernardi, G. and Bernardi, G. Compositional properties of nuclear genes from cold blooded vertebrates. J Mol Evol 33: 57–67, 1991
Bjorkman, P. J. and Parham, P. Structure, function, and diversity of class I major histocompatibility complex molecules. Annu Rev Biochem 59: 253–288, 1990
Breathnach, R. and Chanbon, P. Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem 50: 349–383, 1981
Brown, J. H., Jerdetzky, T., Saper, M. A., Samraoui, B., Bjorkman, P. J., Wiley, D. C. A hypothetical model of the foreign antigen binding site of class II histocompatibility molecules. Nature 332: 845–850, 1988
Carrol, R. L. Vertebrate Paleontology and Evolution, W. H. Freeman, New York, 1988
Carson, S. and Trowsdale, J. Molecular organization of the class II genes of the human and mouse major histocompatibility complexes. Oxford Surv Euk Genes 3: 63–94, 1986
Chang, T., Lin, C. L., Chang, W. C., and Chen, P. H. gamma crystallin genes in carp: cloning and characterisation. Biochin Biophys Acta 1090: 261–264, 1991
Chiou, C. S., Chen, H. T., and Chang, W. C. The complete nucleotide sequence of the growth-hormone gene from the common carp (Cyprinus carpio). Biochim Biophys Acta 1087: 91–94, 1990
Cho, S., Attaya, M., and Monaco, J. New class II-like genes in the murine MHC. Nature 3533: 573–576, 1991
Cogswell, J. P., Zeleznik-Le, N., Ting, J. P.-Y. Transcriptional regulation of the HLA-DRA gene. Crit Rev Immunol 11: 87–112, 1991
Cosson, P. and Bonifacio, J S. Role of transmembrane domain interactions in the assembly of class II MHC molecules. Science 258: 659–662, 1992
Feinberg, A. P. and Vogelstein, B. A. Technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochiem 132: 6–13, 1983
Hashimoto, K., Nakanishi, T., and Kurosawa, Y. Isolation of carp genes encoding major histocompatibility complex antigens. Proc Natl Acad Sci USA 87: 6863–6867, 1990
Hirsch, F., Sachs, D. H., Gustafsson, K., Pratt, K., Germana, S., and LeGuern, C. Class II genes of miniature swine. III. Characterization of an expressed pig class II gene homologous to HLA-DQA. Immunogenetics 31: 52–56, 1990
Hong, Y. and Schartl, M. Structure of the rainbow trout metallothionein A gene. Gene 120: 277–279, 1992
Huang, C. J., Huang, F. L., Wang, Y. C., Chang, Y. S., and Lo, T. B. Organization and nucleotide sequence of carp gonadotropin alpha subunit genes. Biochim Biophys Acta 1129: 239–242, 1992
Hordvik, I., Grimholt, U., Fosse, V. M., Lie, O., and Endresen, C. Cloning and sequence analysis of cDNAs encoding the MHC class II β chain in Atlantic salmon, Salmo salar. Immunogenetics 37: 437–441, 1993
Hughes, A. L. and Nei, M. Pattern of nucleotide sustitutions at major histocompatibility complex class I loci reveals overdominant selection. Nature 355: 167–170, 1988
Hyldig-Nielsen, J. J., Schenning, L., Hämmerling, U., Widmark, E., Heldin, E., Lind, P., Servenius, B., Lund, T., Flavel, R., Lee, D., Peterson, P. A., and Rask, L. The complete nucleotide sequence of the I-E-alpha-d immune response gene. Nucleic Acids Res 11: 5055–5071, 1983
Jonsson, A. K. and Rask, L. Human class IIDNA and DOB genes display low sequence variability. Immunogenetics 29: 411–413, 1989
Jonsson, A. K., Anderson, L., and Rask, L. Complete sequences of DQA and DQB1 cDNA clones corresponding to the DQw4 specificity. Immunogenetics 30: 232–234, 1989
Juul-Madsen, H. R., Glamann, J., Madsen, H. O., and Simonsen, M. MHC class II beta-chain expression in the rainbow trout. Scand J Immunol 35: 687–694, 1992
Kasahara, M., Vasquez, M., Sato, K., McKinney, E. C., and Flajnik, M. F. Evolution of the major histocompatibility complex: isolation of a class II A gene from the cartilaginous fish. Proc Natl Acad Sci USA 89: 6688–6692, 1992
Kelly, A. P., Monaco, J. J., Cho, S., and Trowsdale, J. A new human HLA class II-related locus, DM. Nature 353: 571–573, 1991
Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111–120, 1980
Klein, D., Ono, H., O'hUigin, C., Vincek, V., Goldschmidt, T., and Klein, J. Extensive MHC variability in cichlid fishes of Lake Malawi. Nature 364: 330–334, 1993
Klein, J. Natural History of the Major Histocompatibility Complex. John Wiley, New York, 1986
Kozak, M. Compilation and analysis of sequences upstream from the translational start site in eukaryotic mRNAs. Nucleic Acids Res 12: 857–872, 1984
Laale, H. W. The biology and use of zebrafish, Brachydanio rerio, in fisheries research. A literature review. J Fish Biol 10: 121–173, 1977
Lanzavecchia, A. Receptor-mediated antigen uptake and its effect on antigen presentation to class II-restricted T lymphocytes. Annu Rev Immunol 8: 773–793, 1990
Lawrence, S. K., Das, H. K., Pan, J., and Weisman, S. M. The genomic organisation and nucleotide sequence of the HLA-SB (DP) alpha gene. Nucleic Acids Res 13: 7515–7528, 1985
Lee, J. S., Trowsdale, J., Travers, P. J., Carey, J., Grosveld, F., Jenkins, J., and Bodmer, W. F. Sequence of an HLA-DR α-chain cDNA clone and intron-exon organization of the corresponding gene. Nature 299: 750–752, 1982
Liu, Z., Zhu, Z., Roberg, K., Faras, A., Guise, K., Kapuscinski, A. R., and Hackett, P. B. Isolation and characterization of beta-actin gene of carp (Cyprinus carpio). DNA Seq 1: 125–136, 1990
Muller-Schmid, A., Rinder, H., Lottspeich, F., Gertzen, M. E., and Hoffmann, W. Ependymis from the cerebrospinal fluid of salmonid fish: gene structure and molecular characterization. Gene 118: 189–196, 1992
Nei, M. Molecular Evolutionary Genetics, Columbia University Press, New York, 1987
Ono, H., Klein, D., Vincek, V., Figueroa, F., O'hUigin, C., Tichy, H., and Klein, J, Mhc class II genes of zebrafish. Proc Natl Acad Sci USA 89: 11886–11890, 1992
Ono, H., O;hUigin, C., Tichy, H., and Klein, J. Major histocompatibility complex variation in two species of cichlid fishes from Lake Malawi. Mol Biol Evol, in press, 1993a
Ono, H., O'hUigin, C., Vincek, V., and Klein, J. Exon-intron organization of fish major histocompatibility complex class II B genes. Immunogenetics 38: 223–234, 1993b
Ono, H., Figuerao, F., O'hUigin, C., and Klein, J. Cloning of the β2-microglobulin gene in the zebrafish. Immunogenetics 38: 1–10, 1993c
Ono, H., O'hUigin, C., Vincek, V., Stet, R. J. M., Figuerao, F., and Klein, J. New β chain-encoding Mhc class II genes in the carp. Immunogenetics 38: 146–149, 1993d
Rothbard, J. B. and Gefter, M. L. Interactions between immunogenetic peptides and Mhc proteins. Annu Rev Immunol 9: 527–565, 1991
Saitou, N. and Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425, 1987
Sambrook, J., Fritsch, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 1989
Sanger, F., Nicklen, S., and Coulson, A. R. DNA sequencing with chain-terminating inhibitors. Pros Natl Acad Sci USA 74: 5463–5467, 1997
Schamboeck, A., Korman, A. J., Kamb, A., and Strominger, J. L. Organization of the transcriptional unit of a human class II histocompatibility antigen: HLA-DR heavy chain. Nucleic Acids Res 11: 8663–8675, 1983
Schneider, S., Vincek, V., Tichy, H., Figueroa, F., and Klein, J. MHC class II genes of a marsupial, the red-necked wallaby (Macropus rufogriseus): identification of new gene families. Mol Biol Evol 8: 753–766, 1991
Scott, G. K., Hayes, P. H., Fletcher, G. L., and Davies, P. L. Wolffish antifreeze protein genes are primarily organized as tandem repeats that each contain two genes in inverted orientation. Mol Cell Biol 8: 3670–3675, 1988
Sterrer, S., Koenigstorfer, A., and Hoffmann, W., Biosynthesis and expression of ependymin homologous sequences in zebrafish brain. Neuroscience 37: 277–284, 1990
Sültmann, H. Der Haupthistokompatibilitätskomplex in Fischen. Diplomabeit, Eberhard-Karls-Universität Tübingen, Tübingen, 1991
Villen, B. J., Cogswell, J. P, and Ting, J. P.-Y. Requirement for stereospecific alignment of the X and y elements in MHC class II DRA function. Mol Cell Biol 11: 2406–2415, 1991
Von Heijne, G. Patterns of amino acids near signal-sequence cleavage sites. Eur J Biochem 133: 17–21, 1983
Wiley, E. O., Siegel-Causey, D., Brooks, D. R., and Funk, V. A. The Compleat Cladist. A Primer of Phylogenetic Procedures, University of Kansas Museum of Natural History, Lawrence, Kansas, 1991
Wilson, M. R., Middleton, D., and Warr, G. W. Immunoglobulin V(H) genes of the goldfish, Carassius auratus: a reexamination. Mol Immunol 28: 449–457, 1991
Wu, T. T. and Kabat, E. A. An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J Exp Med 132: 211–250, 1970
Zhu, Z., Vincek, V., Figueroa, F., Schönbach, C., and Klein, J. Mhc-DRB genes of the pigtail macaque (Macaca nemestrina): implications for the evolution of human DRB genes. Mol Biol Evol 8: 563–578, 1991
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Sültmann, H., Mayer, W.E., Figueroa, F. et al. Zebrafish Mhc class II α chain-encoding genes: polymorphism, expression, and function. Immunogenetics 38, 408–420 (1993). https://doi.org/10.1007/BF00184521
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DOI: https://doi.org/10.1007/BF00184521