Computational analysis of non-synonymous single nucleotide polymorphism in the bovine PKLR geneComputational analysis...

Area of Science:

• Animal Genetics
• Bioinformatics
• Molecular Biology

Background:

• The Pyruvate Kinase (PKLR) gene is a candidate for influencing milk production traits in cattle.
• Understanding genetic variations, specifically non-synonymous single nucleotide polymorphisms (nsSNPs), is crucial for cattle breeding and milk yield improvement.

Purpose of the Study:

• To computationally identify and characterize deleterious nsSNPs within the bovine PKLR gene.
• To assess the impact of these nsSNPs on protein stability, conservation, and functional domains.

Main Methods:

• In silico analysis using SIFT, Polyphen-2, SNAP2, and Panther to predict deleterious nsSNPs.
• Protein stability assessment via I-mutant, MUpro, CUPSTAT, SDM, and Dynamut.
• Evolutionary conservation analysis using ConSurf.
• Domain identification using InterPro.
• 3D modeling with MODELLER and validation.
• Energy minimization and Molecular Dynamics simulations.

Main Results:

• Out of 170 nsSNPs, 18 were predicted as deleterious and evolutionarily conserved.
• Nine nsSNPs were found to reduce PKLR protein stability.
• 12 nsSNPs were located in the Pyruvate Kinase barrel domain and 6 in the C-terminal domain.
• Mutant structures showed reduced stability compared to the native model, confirmed by energy minimization and MD simulations.

Conclusions:

• Several nsSNPs in the bovine PKLR gene negatively impact protein stability and structure.
• These identified functional nsSNPs provide valuable insights into genetic factors affecting milk production in cattle.
• The study highlights specific mutations (rs441424814, rs449326723, rs476805413, rs472263384, rs474320860, rs475521477, rs441633284) as potentially detrimental to PKLR function.