Sequence-based structural analysis and evaluation of polymorphism in buffalo Nod-like receptor-1 gene

Area of Science:

• Immunology
• Genomics
• Comparative Biology

Background:

• The nucleotide-binding oligomerization domain 1 (NOD1) gene plays a crucial role in innate immunity.
• Understanding NOD1 gene variations and expression in buffalo is essential for livestock health and disease resistance.

Purpose of the Study:

• To perform sequence characterization, polymorphism analysis, and expression profiling of the buffalo NOD1 gene.
• To investigate phylogenetic relationships and structural features of buffalo NOD1.

Main Methods:

• Full-length gene sequencing and analysis of buffalo NOD1.
• Identification and genotyping of single nucleotide polymorphisms (SNPs) across 12 Indian buffalo breeds.
• Quantitative real-time PCR for gene expression analysis in various tissues.
• Structural and molecular interaction analysis of NOD1 protein.

Main Results:

• Buffalo NOD1 gene is conserved with identified alternate splice variants (exon3 skipping).
• 23 polymorphic sites (16 synonymous, 7 non-synonymous) were found in buffalo NOD1, with variable SNP frequencies across breeds.
• NOD1 expression was highest in peripheral blood mononuclear cells (PBMCs) and lungs.
• Structural analysis revealed conserved LxxLL motifs for ligand binding, with species-specific binding energies between buffalo and cattle NOD1.

Conclusions:

• Buffalo NOD1 exhibits conserved domain structures and unique features for species-specific ligand interactions.
• Genetic diversity and distinct clustering of riverine and swamp buffalo breeds were observed based on NOD1 polymorphisms.
• NOD1 plays a role in buffalo immunity, with significant expression in PBMCs and lungs.