Lukacs et al. BMC Genomics 2010, 11:154 http://www.biomedcentral.com/1471-2164/11/154 was 2-fold more expressed in the heart than in the spleen, but lower in the other tissues. The Z-lineage genes seem ubiquitously expressed in most tissues tested similar to that observed by Miller et al [15]. Little differ- ence in expression patterns for the various tissues was observed for the SAA gene. Both ULA and ZBA lack transmembrane, connecting peptide and cytoplasmic domains and probably are secreted MHC class I molecules. Based on their expres- sion patterns they could have specific functions in the heart. The Z-lineage expression such as ZAA in blood and heart, and ZBA in the heart, suggest interesting functions to be unravelled. During the initial studies we checked the PCR pro- ducts amplified during realtime PCR on agarose gels, and observed that products for UHA1 contained two bands that were equally expressed, with exception in muscle where the smallest band was missing. Sequen- cing of these PCR products showed that the largest frag- ment represented the UHA1*0201 allele with the additional exon, while the smallest PCR product repre- sented the UHA1*0101 allele. We have only investigated un-stimulated tissues, and it is most likely that the expression patterns would be different in stimulated tissues. Based on expression pat- terns and polymorphic content only UBA can be classi- fied as a true classical MHC class I gene, while the others should be classified as nonclassical MHC molecules. Structure and function of Atlantic salmon MHC class I molecules Structure and composition of MHC class I genes are quite variable both within and between vertebrate groups, with the a1a2 domains containing most of the polymorphism. In mammals, the presence of nine evolu- tionary conserved sites within the a1a2 domains have been defined as residues that anchor the peptide [28,29]. These residues are highly conserved in classical as well as in most nonclassical molecules like HLA-E, HLA-F and HLA-G. The set of residues in mammals are YYYYYYTKW, while in non-mammalian vertebrates it has changed slightly to YYYYRFTKW [16,23]. Deduced Atlantic salmon MHC class I amino acid sequences identified in our BACs in addition to a sequence belong- ing to the L-lineage (LBA) [Genbank: DY733800 and GO062643] were aligned with human MHC class I sequences (Figure 5). Presence of conserved peptide anchoring sites for all Atlantic salmon class I sequences including human, chicken and shark are summarized in Table 2. For the MHC class I UBA locus we included two highly divergent alleles, where UBA*0301 contains the non-mammalian motif while UBA*1001 differ in one Page 10 of 17 residue, A7. One or rarely two substitutions of these conserved residues have also been observed in both human and mouse MHC class Ia sequences [28,29]. The ULA locus described as a secretory class I molecule due to a missing transmembrane domain [13], does display the conserved motif for non mammalian vertebrates, and may thus still bind peptides. The two UHA loci have one residue different from the classical UBA locus at F59. A tyrosine/phenylalanine substitution is common amongst non mammalian vertebrates, and may not interfere with binding capacity. The UDA and UGA have two and three residues different from UBA. These are not conservative substitutions (e.g. Y/F), and most likely influence peptide-binding. Overall it seems like all the U-lineage sequences in Atlantic salmon are able to present peptides based on these nine anchor residues. Both SAA and LBA sequences have quite different residues in some or all of these positions when com- pared against the UBA classical class I sequences. Seven of the nine residues are found to differ from the non- mammalian motif in SAA sequences, while all of the nine residues are found to differ in LBA sequences. In mammals, the class Ib molecule CD1, known to bind lipid and glycolipid ligands do not contain this peptide binding motif [2]. Thus it is likely that SAA and LBA binds non-peptide ligands or none at all as the mamma- lian class Ib molecules MIC-A/B and HFE. In rainbow trout, Shum et al concluded that Onmy-SAA (similar to Sasa-SAA) has properties indicative of a particularly divergent class Ib gene [16]. The Z-lineage sequences also follow the non mamma- lian motif with the exception of one common different residue, F171. Three amino acids downstream of F171, all Z-lineage sequences have a tyrosine (Y) residue which might function as the conserved peptide anchor- ing residue. This has also been observed in cyprinid class I ZE sequences which suggests that use of the tyro- sine Y174 might affect and extend the peptide binding groove, leading to binding of somewhat larger peptides [5]. Another possibility is that a substitution of a tyro- sine (Y) residue by a phenylalanine (F) in position Y171 may not have major implications for the ability to bind peptide termini since most non mammalian MHC class Ia sequences have a similar substitution of a tyrosine residue by a phenylalanine residue at position Y123. In humans there is a stretch from aa 231-244 in the class I a3 domain known to interact with b2 m [30]. In this region, the UHA and all Z-, S- and L-lineage sequences have a specific motif, P235, Y241 and R244, which may influence the association with b2 m. Atlantic salmon express up to twelve different b2 m molecules (unpublished data), which group into two lineages, BA1 [Genbank: AF180478] and BA6 [Genbank: AF180484] which may stabilize different MHC class I sequences;