Sea bass (Dicentrarchus labrax) invariant chain and class II major histocompatibility complex: Sequencing and structural analysis using 3D homology modelling

The present manuscript reports for the first time the sequencing and characterisation of sea bass (sb) MHCIIα and β chains and Ii chain cDNAs as well as their expression analysis under resting state. 3D homology modelling, using crystal structures from mammalian orthologues, has been used to illustrate and support putative structural homologies of the sea bass counterparts. The sbIi cDNA consists of 96 bp of 5′-UTR, a 843 bp open reading frame (ORF) and 899 bp of 3′-UTR including a canonical polyadenylation signal 16 nucleotides before the polyadenylation tail. The ORF was translated into a 280 amino acid sequence, in which all characteristic domains found in the Ii p41 human form could be identified, including the cytoplasmic N-terminus domain, the transmembrane (TM) region, the CLIP domain, the trimerization domain and the thyroglobulin (Tg) type I domain. The trimerization and Tg domains of sbIi were successfully modelled using the human counterparts as templates. Four different sequences of each class IIα and β MHCII were obtained from a single fish, apparently not derived from a single locus. All the characteristic features of the MHCII chain structure could be identified in the predicted ORF of sea bass α and β sequences, consisting of leader peptide (LP), α1/β1 and α2/β2 domains, connecting peptide and TM and cytoplasmic regions. Furthermore, independently of the HLA-DR crystal structure used as template in homology modelling, a similar predicted 3D structure and trimeric quaternary architecture was obtained for sbMHC, with major deviations occurring only within the sea bass MHCIIα1 domain.