Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon

Morten F Lukacs,Krzysztof P Lubieniecki,Marianne Beetz-Sargent,Ben F Koop,Unni Grimholt,Håvard Harstad,Hege G Bakke,Linda Mckinnel

doi:10.1186/1471-2164-11-154

Morten F Lukacs, Krzysztof P Lubieniecki + Show 6 more

Open Access

https://doi.org/10.1186/1471-2164-11-154

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Abstract

BackgroundWe have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA. A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region.ResultsThe genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs were sequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IA region with 150 kb identifying the location of one Z-lineage locus, ZAA. The IB region was extended with 350 kb including three new Z-lineage loci, ZBA, ZCA and ZDA in addition to a UGA locus. An allelic version of the IB region contained a functional UDA locus in addition to the UCA pseudolocus. Additionally a BAC harbouring two MHC class I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus SAA (previously known as UAA) was placed on LG10. Gene expression studies showed limited expression range for all class I genes with exception of UBA being dominantly expressed in gut, spleen and gills, and ZAA with high expression in blood.ConclusionHere we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages in Atlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IB regions, while three class I genes are found on two separate linkage groups. The gene organization of the two regions indicates that the IB region is evolving at a different pace than the IA region. Expression profiling, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one MHC class Ia gene (UBA), in addition to a multitude of nonclassical MHC class I genes from the U-, S- and Z-lineages.

Highlights

We have previously sequenced more than 500 kb of the duplicated Major histocompatibility complex (MHC) class I regions in Atlantic salmon
Here we describe the genomic organization of MHC class I loci from the U, Z, and S-lineages in Atlantic salmon
Expression profiling, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one MHC class Ia gene (UBA), in addition to a multitude of nonclassical MHC class I genes from the U, S- and Z-lineages

Summary

Introduction

We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region. Major histocompatibility complex (MHC) class I molecules have important roles in presenting antigens to immune cells thereby enabling the organism to discriminate between self and non-self. The MHC genomic region is a gene dense region covering more than 4 Mb and encodes MHC class I and II molecules in addition to numerous other immune related molecules. In humans the MHC class Ia molecules are encoded by the HLA-A, HLA-B and HLA-C loci. An emerging view on the MHC class Ib molecules are their prominent role bridging the innate and acquired immunity [2]

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