Distribution of single nucleotide polymorphisms and protein domain architecture of toll-like receptor-2 in Pahari cattle (Indian non-descript indigenous breed)

Distribution of polymorphism in TLR2 gene was studied in Pahari (Indian non-descript indigenous breed) cattle of Himachal Pradesh. The complete sequence of TLR2 gene consisted of 136 bp 5'-UTR, 2355 bp CDS and 1316 bp 3'UTR. The phylogenetic analysis revealed clustering of Indian Zebu with Bos taurus as the nearest neighbour. The nucleotide sequences of TLR2 revealed the occurrence of 19 SNPs including 47% non-synonymous and 53% synonymous SNPs within TLR domain among all bovines. The dS/dN ratio (ω) < 1 at polymorphic sites revealed purifying selection and thus, indicating the presence of highly conserved domains. Two SNPs in the extracellular domain of TLR2 were predicted to have damaging effect whereas the rest have benign effect. The amino acid sequence of the coding region corresponds to a protein of 784 amino acids long with predicted molecular weight 104 kDa and 6.97 pI value. The amino acid sequence analysis showed extracellular domain composed of leucine rich repeats (LRR), trans- membrane domain and Toll-IL receptor domain in the protein. The 3D structure of TLR2 is a solenoid-like having active sites buried in the concave side and forming a pocket for ligand binding. The substitution of G with T in nucleotide sequence leads to the replacement of amino acid W ↔ L at position 119 which has not been reported so far. These findings indicate that polymorphism may be associated with PAMPs mediated differential TLR signaling of bovine immunity and could determine the outcome of infection.