Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 Table 2 Comparison of nine conserved residues involved in peptide binding Peptide N terminus Peptide C terminus 7 59 159 171 84 123 143 146 147 Diff. UBA*0301 Y UBA*1001 A ULA - UGA - UDA H UHA1 - UHA2 - ZAA - ZBA - ZCA - SAA R LBA A B-F19 - Trsc-UAA - HLA-A2 - Y - - - - F F - - - F E - - - Y - - - - - - - - - H V - - - Y - - - Q - - F F F L I - - - R - - - - - - - - - H H - - Y F - - L - - - - - - - A - L Y T - - S M - - - - - Y Q - - - K - - - - - - - - - - D - - - W - - - - - - L - - R G - - - 1 0 2 3 1 1 2 1 1 7 9 0 1 2 Comparison of Atlantic Salmon UBA*0301 [Genbank: AAN75116], UBA*1001 [Genbank: AAN75118], ULA [Genbank: ABQ59666], UGA, UDA, UHA1, UHA2, ZAA, ZBA, ZCA, SAA (described in this paper), LBA [Genbank: DY733800 and GO062643], B-F19 (Chicken) [Genbank: M84766], Trsc-UAA*101 (Shark) [Genbank: AF034316] and HLA-A2 [Genbank: AAA76608]. one lineage may bind to UHA, Z-, S- and L -lineage molecules and the other b2 m lineage may bind and sta- bilize the remaining U-lineage molecules that also show a conservation in this region. In humans, there are also at least four class Ib molecules that do not bind b2 m (MICA/B, EPCR, ULBP and ZAG) [2]. Future studies are needed to clarify b2 m binding of salmonid MHC class I molecules. Other features that are shared between the Atlantic salmon class I molecules and nearly all MHC class Ia and Ib molecules of other vertebrates, include 4 con- served cysteine residues located in the a2a3 domains forming disulfide bonds within theses domains and the highly conserved FYP motif at positions 208-210 aa in the a3 domain [28]. Most class I sequences contain an N-linked glycosylation site near the end of the a1 domain. The amino acid residues which correspond to the CD8 binding site of the HLA-A locus are at posi- tions 223-229 in the Atlantic salmon sequences. Both classical and some nonclassical mammalian MHC class I molecules have a well conserved negatively charged CD8 binding site in the a3 domain (ca.218-226). Here the Atlantic salmon classical UBA molecules have an acidic stretch consisting of 4 negatively charged aa (D or E), also found in the ULA, UGA and UDA molecules. The UHA1 and UHA2 molecules consist of 2 and 3 negatively charged aa respectively. The SAA molecule has 1, while the Z molecules has from 2 to 3 negatively charged aa in the this region. Both CD8a and CD8b chains have been described in the Atlantic salmon [31]. Page 12 of 17 The CD8 molecule can be expressed both in a homodi- meric and heterodimeric form, where the latter is most expressed in mammals, preferably in circulating lympho- cytes. The lower acidic content in this region for the UHA, SAA and Z molecules may influence the lympho- cyte interactions in contrast to the higher acidic content for UBA, ULA, UGA and UDA molecules. Having classified the Atlantic salmon class I molecules into functional categories based on traditional criterions, the functional properties of these molecules still remain unclear. Sasa-ULA and Sasa-ZBA exists in a soluble form, while the Sasa-UHA1 locus expresses both mem- brane bound and a soluble variant as a result of alterna- tive splicing, leading to loss of the Tm/Cyt domain by a frame shift. In humans, both MHC class Ia and Ib mole- cules are also known to exist in soluble forms. The clas- sical HLA-A, -B and -C loci express soluble variants that play a role in cell death of activated T cells [32]. Another example is the human non-classical HLA-G molecules that exist in several different isoforms both membrane bound and secreted forms where the soluble variant is caused by alternative splicing where the Tm/ Cyt domains are deleted [33]. The soluble HLA-G is found expressed specifically in placental tissue and is secreted during pregnancy [34] and also thought to be involved in inducing apoptosis in activated maternal CD8+ T cells [35]. The functional relevance of soluble class I molecules remain to be established in fish. Conclusion Here we describe the genomic organization of U-, Z-, and S-lineage MHC class I molecules in Atlantic sal- mon. 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 indi- cates that the IB region is evolving at a different pace than the IA region. The IB region contains 3 chitin synthase genes not present in the IA region. Four gene duplications are seen for both a hypothetical protein as well as for the Z-lineage genes, a phenomenon not found in the IA region. There is also haplotypic UCA/ UDA variation while the UEA and UFA genes residing in the rainbow trout IB region have been lost since Oncorhynchus and Salmo split, which probably was around 15-20 mya. The functional consequence of this evolution remains to be established. Expression profil- ing, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one expressed MHC class Ia gene (UBA), in addition to a multitude of nonclassical loci from the U-, S and Z-lineages. Further studies are needed to verify the functional properties of the MHC class Ib molecules in teleost.