Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation.

Ratna Prabha,Dhananjaya P Singh,Shailendra K Gupta,Samir Farooqi,Anil Rai

doi:10.6026/97320630008622

Abstract

Analysis of synonymous codon usage pattern in the genome of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 using multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation in the organism. This axis is correlated with the GC content at third base of synonymous codons (GC3s) in correspondence analysis taking T. elongatus genes. A negative correlation was observed between effective number of codons i.e. Nc and GC3s. Results suggested a mutational bias as the major factor in shaping codon usage in this cyanobacterium. In comparison to the lowly expressed genes, highly expressed genes of this organism possess significantly higher proportion of pyrimidine-ending codons suggesting that besides, mutational bias, translational selection also influenced codon usage variation in T. elongatus. Correspondence analysis of relative synonymous codon usage (RSCU) with A, T, G, C at third positions (A3s, T3s, G3s, C3s, respectively) also supported this fact and expression levels of genes and gene length also influenced codon usage. A role of translational accuracy was identified in dictating the codon usage variation of this genome. Results indicated that although mutational bias is the major factor in shaping codon usage in T. elongatus, factors like translational selection, translational accuracy and gene expression level also influenced codon usage variation.

Highlights

Most amino acids in the organisms are coded by more than one triplet of nucleotides which are called synonymous codons that usually differ by single nucleotide in the third codon position but for some amino acids, it differs in the second position
codon adaptation index (CAI) showed a positive correlation with C3s (r = 0.605, P
These results suggested that mutational bias is the major factor in shaping codon usage in this organism

Summary

Introduction

Most amino acids in the organisms are coded by more than one triplet of nucleotides which are called synonymous codons that usually differ by single nucleotide in the third codon position but for some amino acids, it differs in the second position . Codon usage is specially a genome strategy in which each genome has a particular codon usage signature that reflects particular evolutionary forces acting within that genome [1]. Different pattern in codon usage in bacterial genomes indicates lateral gene transfer events and the analysis of codon bias helps establish the fact that the horizontal gene transfer is a major evolutionary force [10]. Within the genomes which are the source of valuable biological information [18], codon usage pattern has both practical and theoretical importance in understanding the molecular basics of biology. This strategy can directly be utilized in molecular

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