Abstract
The base composition at three different codon positions in relation to codon usagebias and gene expressivity was studied in a sample of twenty five essential genes from Haemophilus influenzae. ENC, CBI and Fop were used to quantify the variation in codon usage bias for the cds. CAI is used to estimate the level of gene expression of the cds selected in the present study. To find out the relationship between the extent of codon bias and nucleotide composition the values of A, T, G, C and GC they were compared with the A3, T3, G3, C3 and GC3 values, respectively. The results showed relatively weak codon usage bias among the coding sequences (cds) of Haemophilus influenzae. This in turn, implies that the essential genes prefer to use a set of restricted codons. However, the base compositional analysis of essential genes in Haemophilus influenzae revealed preference of AT to GC bases within their coding sequences and this preference might affect gene expression as indicated by the relatively high CAI values ofthe coding sequences.
Highlights
The genetic information from mRNA is passed to protein with the help of translational machinery, a fundamental process occurring within all living cells
Models cds was computed by using the software acua available for effective number of codons (ENC), codon bias index (CBI) and frequency of optimal codon (Fop) were used to quantify the variation in non-commercial purposes
Our results revealed that the overall codon usage bias among different genes of Haemophilus influenzae is low, slightly biased and mainly affected by base composition
Summary
The genetic information from mRNA is passed to protein with the help of translational machinery, a fundamental process occurring within all living cells. The genetic code uses sixty-four codons to encode the proteins. Many codons are redundant i.e. two or more codons code for a single amino acid, with the exception of methionine (AUG). Such codons are described as being synonymous, and mostly differ by one nucleotide at the third codon position. Codon usage bias (CUB) refers to the nonrandom usage of synonymous codons for encoding the same amino acid in a protein (Lu et al, 2005). Synonymous codons are used in unequal frequencies between genomes, genes from the same genome and within a single gene (Hooper and Berg, 2000; Lavner and Kotler, 2005; Supek and Vlahovicek, 2005). The least frequently used codons are non optimal or minor codons and lead to the premature termination during elongation stage of translation. The understanding of the extent of codon bias with compositional dynamics provides an insight into the prediction of the level of gene expression and genome characterization
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