Sequence and functional variability of Toll-like receptor 9 gene in equines

Significant structural differences in the extracellular domain of toll-like receptor 9 (TLR9) account for species-specific recognition of its ligand CpG-ODN sequences. TLR9 is extensively studied in human, mice and some domestic animals. The recognition ability appears to be utilized differently by various species and breeds, but so far no comprehensive study exists about the equine TLR9 gene. We characterized TLR9 sequences of Marwari and Zanskari breeds of horses and Poitu donkey. We sequenced and identified the protein coding regions of equine TLR9 and compared with other animals and human beings. Furthermore, we also analyzed the amino acid substitutions and their likely implications on functions. The analysis revealed 14% evolutionary divergence between equine and human TLR9, while it was 1% between the Equus caballus and Equus asinus and less than 1% within Equus caballus. In phylogenetic analysis of predicted amino acids, the indigenous equines grouped with thoroughbred Equus caballus, while human, cattle, dog, sheep, mice, and buffalo formed separate clades. Furthermore, we also analyzed the amino acid substitutions and their likely implications on functions by sorting intolerant from tolerant (SIFT) analysis and predicted two substitutions of amino acids (D80N and S822P) in Marwari horses in leucine rich repeat 1 (LRR1) without any functional effects. The substitutions (V214A and Y579C) in LRR 3 and LRR11 in Zanskari horses were predicted to have functional consequences. Out of overall 8 substitutions, three substitutions (I420V, S970R and R1001C) were found in Equus asinus in LRR7, LRR 13, and toll interleukin receptor (TIR) domains, while the substitution G649S is observed in Poitu donkey only. We report for the first time that despite the conserved residues, the striking effect of substitutions, found within the TLR9 genes of different equine breeds/species may have possible implications.