The Implication of Codon Usage Design and Expression Level in Determining the Nature of Selection and Functionality Amongst the Amino Acid Biosynthetic Pathway Coding Sequences of Arthrobacter sp. FB24

Ayon      Pal; Uttam   Kumar   Mondal; Subhasis      Mukhopadhyay; Arnab      Sen; Asim   Kumar   Bothra

doi:10.2174/15748936113086660012

Abstract

Amino acid biosynthesis is an immensely important life process requiring the participation of nearly hundred gene products, differing in terms of codon usage pattern, expressivity and selection pressure. In this study an attempt was made to categorize the gene products according to their expression level, nature of selection and functionality analyzing the amino acid biosynthetic pathway genes of the soil bacterium Arthrobacter, known for its varied metabolic activities and a key agent for industrial production of amino acids. The relationship between the different parameters like expression level, codon usage and selection pressure was calculated to find out the correlation of biasness, expression level, nature of selection and functionality amongst the genes involved in amino acid biosynthetic pathways. We found that genes coding for enzymes and proteins with large number of functions have higher codon usage bias and are subjected mostly to purifying selection. Gene sequences of proteins and enzymes with low functionality showed less codon usage bias and are under positive selection. The multifunctional genes mostly show high expression level and it is highly correlated with codon usage bias. The results of this study demonstrate that functionality and nature of selective forces acting on the coding sequences can be determined by studying the correlation between the different parameters like effective number of codon, codon adaptation index and nucleotide substitution ratios and careful study of all these parameters is a pretty good indicator for determining the functionality of the genes and this can be extended towards the genes of unknown function(s).

Keywords: Amino acid biosynthetic pathways, Arthrobacter, CAI, Nc, Ka/Ks, synonymous and non-synonymous nucleotide substitution rates, positive selection, purifying selection.