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PMID: 15517241 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Open reading frame sequencing and structure-based alignment of polypeptides encoded by RT1-Bb, RT1-Ba, RT1-Db, and RT1-Da alleles.

Immunogenetics ·Vol. 56 ·No. 8 ·2004-11-00 ·Pages 585-96

Ettinger RA, Moustakas AK, Lobaton SD

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-Bbeta, RT1-Balpha, RT1-Dbeta, and RT1-Dalpha 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-Bbeta, RT1-Balpha, RT1-Dbeta, and RT1-Dalpha, respectively. The extent and distribution of amino-acid polymorphism was comparable with mouse and human MHC class II. Structure-based alignment identified the beta65-66 deletion, the beta84a insertion, the alpha9a insertion, and the alpha1a-1c insertion in RT1-B previously described for H2-A. Rat allele-specific deletions were found at RT1-Balpha76 and RT1-Dbeta90-92. The mature RT1-Dbeta 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.

MeSH Terms
Alleles Amino Acid Sequence Animals Gene Deletion Genes, MHC Class II Histocompatibility Antigens/chemistry,genetics Male Molecular Sequence Data Open Reading Frames Polymorphism, Genetic Rats Sequence Alignment
Chemicals
Histocompatibility Antigens histocompatibility antigens RT, rat
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ettinger Ruth A
Robert H. Williams Lab, Department of Immunology, University of Washington, Box 357710, 1959 NE Pacific St, HSB K-165, Seattle, WA 98195-7710, USA. [email protected]
Moustakas Antonis K
Lobaton Suzanne D
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Article Info
Journal
Immunogenetics
Abbr.
Immunogenetics
ISSN
0093-7711
DOI
10.1007/s00251-004-0725-7
Email
[email protected]
Published
2004-11-00
Epub
2004-00-23
Pages
585-96
Language
English
Region
United States
NLM ID
0420404
Subset
IM
Grants
NIAID NIH HHS · P01 AI42380 · United States
Databases
GENBANK
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External Links
PubMed source DOI: 10.1007/s00251-004-0725-7 View journal details
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