Abstract
MHC class II genes are major genetic components in rats developing autoimmunity. The majority of rat MHC class II sequencing has focused on exon 2, which forms the first external domain. Sequence of the complete open reading frame for rat MHC class II haplotypes and structure-based alignment is lacking. Herein, the complete open reading frame for RT1-Bβ, RT1-Bα, RT1-Dβ, and RT1-Dα was sequenced from ten different rat strains, covering eight serological haplotypes, namely a, b, c, d, k, l, n, and u. Each serological haplotype was unique at the nucleotide level of the sequenced RT1-B/D region. Within individual genes, the number of alleles identified was seven, seven, six, and three and the degree of amino-acid polymorphism between allotypes for each gene was 22%, 16%, 19%, and 0.4% for RT1-Bβ, RT1-Bα, RT1-Dβ, and RT1-Dα, respectively. The extent and distribution of amino-acid polymorphism was comparable with mouse and human MHC class II. Structure-based alignment identified the β65–66 deletion, the β84a insertion, the α9a insertion, and the α1a–1c insertion in RT1-B previously described for H2-A. Rat allele-specific deletions were found at RT1-Bα76 and RT1-Dβ90–92. The mature RT1-Dβ polypeptide was one amino acid longer than HLA-DRB1 due to the position of the predicted signal peptide cleavage site. These data are important to a comprehensive understanding of MHC class II structure-function and for mechanistic studies of rat models of autoimmunity.
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References
Acha-Orbea H, Scarpellino L (1991) Nonobese diabetic and nonobese nondiabetic mice have unique MHC class II haplotypes. Immunogenetics 34:57–59
Aizawa M, Natori T (1998) Major histocompatibility complex of the rat, Rattus norvegicus: its structure and function. Hokkaido University Medical Library Series, vol 21. Hokkaido University School of Medicine, Sapporo, pp 43–73
Arimura Y, Tang WR, Koda T, Kakinuma M (1995) Structure of novel rat major histocompatibility complex class II genes RT1.Ha and Hb. Immunogenetics 41:320–325
Awata T, Guberski DL, Like AA (1995) Genetics of the BB rat: association of autoimmune disorders (diabetes, insulitis, and thyroiditis) with lymphopenia and major histocompatibility complex class II. Endocrinology 136:5731–5735
Benoist CO, Mathis DJ, Kanter MR, Williams VE II, McDevitt HO (1983) The murine Ia α chains, Eα and Aα, show a surprising degree of sequence homology. Proc Natl Acad Sci USA 80:534–538
Bieg S, Koike G, Jiang J, Klaff L, Pettersson A, MacMurray AJ, Jacob HJ, Lander ES, Lernmark Å (1998) Genetic isolation of iddm1 on chromosome 4 in the BioBreeding (BB) rat. Mamm Genome 9:324–326
Brown JH, Jardetzky TS, Gorga JC, Stern LJ, Urban RG, Strominger JL, Wiley DC (1993) Three-dimensional structure of the human class II histocompatibility antigen HLA-DR1. Nature 364:33–39
Butcher GW, Diamond AG, Clark M, Howard JC (1983) Similarity of RT1Dβ chains from independent rat haplotypes. Transplant Proc 15:1573–1577
Chao NJ, Timmerman L, McDevitt HO, Jacob CO (1989) Molecular characterization of MHC class II antigens (β1 domain) in the BB diabetes-prone and -resistant rat. Immunogenetics 29:231–234
Chu Z-TE, Carswell-Crumpton C, Cole BC, Jones PP (1994) The minimal polymorphism of class II Eα chains is not due to the functional neutrality of mutations. Immunogenetics 40:9–20
Colle E, Guttmann RD, Seemayer T (1981) Spontaneous diabetes mellitus syndrome in the rat. I. Association with the major histocompatibility complex. J Exp Med 154:1237–1242
Corper AL, Stratmann T, Apostolopoulos V, Scott CA, Garcia KC, Kang AS, Wilson IA, Teyton L (2000) A structural framework for deciphering the link between I-Ag7 and autoimmune diabetes. Science 288:505–511
Cramer DV, Davis BK, Shonnard JW, Stark O, Gill TJ III (1978) Phenotypes of the major histocompatibility complex in wild rats of different geographic origins. J Immunol 120:179–187
Diamond AG, Hood LE, Howard JC, Windle M, Winoto A (1989) The class II genes of the rat MHC. J Immunol 142:3268–3274
Easterfield AJ, Bradley JA, Bolton EM (2003) Complementary DNA sequences encoding the rat MHC class II RT1-Bu and RT1-Du α and β chains. Immunogenetics 55:344–350
Estess P, Begovich AB, Koo M, Jones PP, McDevitt HO (1986) Sequence analysis and structure-function correlations of murine q, k, u, s, and f haplotype I-Aβ cDNA clones. Proc Natl Acad Sci USA 83:3594–3598
Fremont DH, Monnaie D, Nelson CA, Hendrickson WA, Unanue ER (1998) Crystal structure of I-Ak in complex with a dominant epitope of lysozyme. Immunity 8:305–317
Fujii H, Kakinuma M, Yoshiki T, Natori T (1991) Polymorphism of the class II gene of rat major histocompatibility complex, RT1: partial sequence comparison of the first domain of the RT1.Bβ 1 alleles. Immunogenetics 33:399–403
Griffiths MM, Encinas JA, Remmers EF, Kuchroo VK, Wilder RL (1999) Mapping autoimmunity genes. Curr Opin Immunol 11:689–700
Günther E, Walter L (2001) The major histocompatibility complex of the rat (Rattus norvegicus). Immunogenetics 53:520–542
Gustafsson K, Wiman K, Emmoth E, Larhammar D, Böhme J, Hyldig-Nielsen JJ, Ronne H, Peterson PA, Rask L (1984) Mutations and selection in the generation of class II histocompatibility antigen polymorphism. EMBO J 3:1655–1661
Hedrich HJ (ed) (1990) Genetic monitoring of inbred strains of rats. Gustav Fischer Verlag, Stuttgart New York, pp 380–384, 500--521
Holmdahl R, Karlsson M, Gustafsson K, Hedrich H (1993) Structural polymorphism of six rat RT1Ba genes. Immunogenetics 38:381
Holowachuk EW, Greer M-K, Martin DR (1987) The complete sequence of the MHC class II chain RT1Dαu of the diabetic BB rat: mRNA levels of RT1.Dα in lymphocytes. Nucleic Acids Res 15:10551–10567
Hurt P, Walter L, Sudbrak R, Klages S, Müller I, Shiina T, Inoko H, Lehrach H, Günther E, Reinhardt R, Himmelbauer H (2004) The genomic sequence and comparative analysis of the rat major histocompatibility complex. Genome Res 14:631–639
International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921
Jackson RA, Buse JB, Rifai R, Pelletier D, Milford EL, Carpenter CB, Eisenbarth GS, Williams RM (1984) Two genes required for diabetes in BB rats. Evidence from cyclical intercrosses and backcrosses. J Exp Med 159:1629–1636
Joe B, Griffiths MM, Remmers EF, Wilder RL (1999) Animal models of rheumatoid arthritis and related inflammation. Cur Rheumatol Rep 1:139–148
Kaufman J, Salomonsen J, Flajnik M (1994) Evolutionary conservation of MHC class I and class II molecules—different yet the same. Semin Immunol 6:411–424
Kawano K, Hirashima T, Mori S, Saitoh Y, Kurosumi M, Natori T (1991) New inbred strain of Long-Evans Tokushima Lean rats with IDDM without lymphopenia. Diabetes 40:1375–1381
Kent WJ (2002) BLAT—The BLAST-like alignment tool. Genome Res 12:656–664
König R, Shen X, Germain RN (1995) Involvement of both major histocompatibility complex class II α and β chains in CD4 function indicates a role for ordered oligomerization in T cell activation. J Exp Med 182:779–787
Krogh A, Larsson B, von Heijne G, Sonnhammer ELL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580
Latek RR, Suri A, Petzold SJ, Nelson CA, Kanagawa O, Unanue ER, Fremont DH (2000) Structural basis of peptide binding and presentation by the type I diabetes-associated MHC class II molecule of NOD mice. Immunity 12:699–710
Lee KH, Wucherpfennig KW, Wiley DC (2001) Structure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes. Nature Immunol 2:501–507
Lenzen S, Tiedge M, Elsner M, Lortz S, Weiss H, Jörns A, Klöppel G, Wedekind D, Prokop C-M, Hedrich HJ (2001) The LEW.1AR1/Ztm-iddm rat: a new model of spontaneous insulin-dependent diabetes mellitus. Diabetologia 44:1189–1196
Male DK, Pryce G, Butcher GW (1987) Serological evidence for a defect in RT1.B (I-A) expression by the BDIX rat strain. J Immunogenetics 14:301–312
Margulies DH, McCluskey J (1985) Exon shuffling: new genes from old. Surv Immunol Res 4:146–159
Martinez NR, Augstein P, Moustakas AK, Papadopoulos GK, Gregori S, Adorini L, Jackson DC, Harrison LC (2003) Disabling an integral CTL epitope allows suppression of autoimmune diabetes by intranasal proinsulin peptide. J Clin Invest 111:1365–1371
Mouse Genome Sequencing Consortium (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420:520–562
Münz C, Hofmann M, Yoshida K, Moustakas AK, Kikutani H, Stevanovic S, Papadopoulos GK, Rammensee H-G (2002) Peptide analysis, stability studies, and structural modeling explain contradictory peptide motifs and unique properties of the NOD mouse MHC class II molecule H2-Ag7. Eur J Immunol 32:2105–2116
Nabavi N, Freeman GJ, Gault A, Godfrey D, Nadler LM, Glimcher LH (1992) Signalling through the MHC class II cytoplasmic domain is required for antigen presentation and induces B7 expression. Nature 360:266–268
Nepom BS, Nepom GT, Coleman M, Kwok WW (1996) Critical contribution of β chain residue 57 in peptide binding ability of both HLA-DR and -DQ molecules. Proc Natl Acad Sci USA 93:7202–7206
Nielsen H, Engelbrecht J, Brunak S, von Heijne G (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10:1–6
Pettersson A, Wilson D, Daniels T, Tobin S, Jacobs HJ, Lander ES, Lernmark Å (1995) Thyroiditis in the BB rat is associated with lymphopenia but occurs independently of diabetes. J Autoimmun 8:493–505
Rat Genome Sequencing Project Consortium (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428:493–521
Reche PA, Reinherz EL (2003) Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms. J Mol Biol 331:623–641
Reinherz EL, Tan K, Tang L, Kern P, Liu J-h, Xiong Y, Hussey RE, Smolyar A, Hare B, Zhang R, Joachimiak A, Chang H-C, Wagner G, Wang J-h (1999) The crystal structure of a T cell receptor in complex with peptide and MHC class II. Science 286:1913–1921
Robinson J, Waller MJ, Parham P, de Groot N, Bontrop R, Kennedy LJ, Stoehr P, Marsh SGE (2003) IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res 31:311–314
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Schøller J, Lernmark Å (1985) Isolation of a rat immune response gene identical to an alleged mouse A class II β-chain pseudogene. Immunogenetics 22:601–608
Shonnard JW, Davis BK, Cramer DV, Radka SF, Gill TJ III (1979) The association of immune responsiveness, mixed lymphocyte responses, and Ia antigens in natural populations of Norway rats. J Immunol 123:778–783
St-Pierre Y, Nabavi N, Ghogawala Z, Glimcher LH, Watts TH (1989) A functional role for signal transduction via the cytoplasmic domains of MHC class II proteins. J Immunol 143:808–812
Stefferl A, Brehm U, Storch M, Lambracht-Washington D, Bourquin C, Wonigeit K, Lassmann H, Linington C (1999) Myelin oligodendrocyte glycoprotein induces experimental autoimmune encephalomyelitis in the “resistant” brown norway rat: disease susceptibility is determined by MHC and MHC-linked effects on the B cell response. J Immunol 163:40–49
Stern LJ, Brown JH, Jardetzky TS, Gorga JC, Urban RG, Strominger JL, Wiley DC (1994) Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 368:215–221
Swofford DL (2000) PAUP*. Phylogenetic analysis using parsimony (* and other methods), version 4. Sinauer, Sunderland
Syha J, Henkes W, Reske K (1989) Complete cDNA sequence coding for the MHC class II RT1.B α chain of the Lewis rat. Nucleic Acids Res 17:3985
Syha-Jedelhauser J, Reske K (1990) Sequence of rat cDNA clone pLRβ112 coding for the RT1.Dβ1 chain. Nucleic Acids Res 18:4598
Syha-Jedelhauser J, Wendling U, Reske K (1991) Complete coding nucleotide sequence of cDNA for the class II RT1.B βl chain of the Lewis rat. Biochim Biophys Acta 1089:414–416
Tacchini-Cottier F, Mayer WE, Begovich AB, Jones PP (1995) Inactivation of Eα and Eβ expression in inbred and wild mice by multiple distinct mutations, some of which predate speciation within Mus species. Int Immunol 7:1459–1471
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, and Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882
Tian L, Wang M, Yu J, Kahan BD, Stepkowski SM (1999) Nucleotide sequences of three distinct complementary DNA clones encoding rat class II major histocompatibility complex RT1.D β-chain proteins. Immunogenetics 49:735–737
Vestberg M, Brunsberg U, Bergsteinsdottir K, Karlsson M, Gustafsson K, Wedekind D, Hedrich H, Holmdahl R (1998) Limited polymorphism in the first domain of the rat MHC class II RT1-D molecule. Immunogenetics 48:344–349
Weissert R, Wallström E, Storch MK, Stefferl A, Lorentzen J, Lassmann H, Linington C, and Olsson T (1998) MHC haplotype-dependent regulation of MOG-induced EAE in rats. J Clin Invest 102:1265–1273
Acknowledgements
This work was supported by an American Diabetes Association Junior Faculty Award to Ruth Ettinger (1-02-JF-06) and in part by the National Institutes of Health (PO1 AI42380). The authors thank Dr Åke Lernmark and Dr George K. Papadopoulos for helpful discussions and for critically reviewing the manuscript. All experiments complied with the current laws of the United States of America.
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Nucleotide sequence data reported are available in the GenBank database under the accession numbers AY626180–AY626189 for all RT1-Bb sequences, AY626190–AY626199 for all RT1-Ba sequences, AY626200-AY626209 for all RT1-Db sequences and AY626210–AY626219 for all RT1-Da sequences.
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Ettinger, R.A., Moustakas, A.K. & Lobaton, S.D. Open reading frame sequencing and structure-based alignment of polypeptides encoded by RT1-Bb, RT1-Ba, RT1-Db, and RT1-Da alleles. Immunogenetics 56, 585–596 (2004). https://doi.org/10.1007/s00251-004-0725-7
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DOI: https://doi.org/10.1007/s00251-004-0725-7