In silico DNA codon optimization of the variant antigen-encoding genes of diverse strains of Nipah virus

Abstract

Due to an increase in human and wildlife interaction, more and more zoonotic diseases are emerging. A prime example of this is the emergence of the Nipah virus (NiV). Due to high rate of mortality specifically in India and Bangladesh, there is an urgent need for accelerated research for NiV involving the development of vaccines or drugs. The genome of NiV consists of six genes (N, P, M, F, G and L) encoding yielding nucleoprotein, phosphoprotein, matrix, fusion, glycoprotein and large RNA polymerase. We have used these six genes for in silico assessment of DNA codon optimization in Escherichia coli. It was observed that the codon adaptation index (CAI) and GC content of the genes in optimized DNA were enhanced significantly as compared to wild-type strain. On an average, CAI and GC content of N gene in optimized DNA was enhanced by 2.3 (135.1%) and 1.2(9.9 %) fold respectively, while in P/V/C it was increased by 2.0 (98.3 %) and 1.1(7.8%) fold respectively. Further, the CAI and GC content in optimized DNA of M gene and F gene was enhanced by 2.0(99.0%) and 1.1(7.2%) fold respectively for gene M and 2.4(142.5 %), 1.2(15.4%) fold respectively for gene F. Gene G showed an increase of 2.1(114.8 %) fold for CAI, 1.1(11.2%) fold for GC content and gene L showed an increase of 2.4(143.7%) fold for CAI, 1.2(17.2%) fold for GC content. Our result demonstrates that the optimized genes could be useful for better expression in host without any truncated proteins and also useful for protein folding and function.