Analysis of Codon Usage Pattern and Predicted Gene Expression in Neurospora Crassa: A Novel in Silico Approach

Life Sciences-Bioinformatics for health care

Abstract

The codon usage pattern  of genes has a key role in the gene expression and adaptive evolution of an organism. It is very significant in understanding the role of complex genomic structure  in defining cell fates and regulating diverse biological functions. In this paper,  we  discussed that  the  codon  usage index (CAIg) based on  all  protein-coding genes is  a promising alternative to the Codon Adaptation Index (CAI). CAIg  which measures the extent that a gene uses a subset of preferred  codons relies exclusively on sequence  features  and is used as a good indicator of the  strength  of codon  bias. A   critical analysis of predicted highly expressed (PHE) genes in Neurospora crassa has been performed using codon usage index (CAIg) as a numerical estimator of gene expression level.   Analyzing compositional properties and codon usage pattern  of genes in Neurospora crassa, our study indicates that codon composition plays an important role in the regulation of gene expression. We found a systematic strong correlation between  CAIg   and CBI (codon bias index) or other  expression-measures. Here, we show that codon usage index CAIg  correlates well with both protein and mRNA levels; suggesting that codon usage is an important determinant of gene expression.  Our  study highlights  the  relationship  between  gene expression  and compositional  signature  in relation  to  codon usage bias in Neurospora crassa and sets the ground for future investigation in eukaryotic biology.