Analysis of synonymous codon usage inShigella flexneri2a strain 301 and otherShigellaandEscherichia colistrains

Abstract

In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli. Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.

Genome‐wide analysis of synonymous codon usage in Huaiyangshan virus and other bunyaviruses

“…In this study, we found that, roughly similar to other RNA viruses, such as Ebolavirus (mean ENC = 57.23) , Bovine viral diarrhea virus (mean ENC = 51.43) , West Nile virus (mean ENC = 53.81) , the ENC values for HYSV were high (mean ENC = 51.11 > 40), indicating that the overall extent of codon usage bias in HYSV genomes is low. In fact, the previous results published by Jenkins et al had shown that the overall extent of codon usage bias in RNA viruses was low.…”

“…To further establish mutational bias or translational selection in HYSV can explain their codon usage, first, the G þ C content at the first and second codon positions (GC 12 ) were compared with that at synonymous third codon positions (GC 3 ). It was found that GC 12 and GC 3 were significantly correlated (r ¼ À0.404, p < 0.01). This suggests that they are most likely the result of mutational bias, as natural selection would be selected to act differently on different codon positions.…”

“…The interplay of codon usage among viruses and their hosts is expected to affect viral survival, fitness, evasion from host's immune system and evolution . Therefore, the study of codon usage patterns in viruses can reveal important information about molecular evolution, regulation of viral gene expression, and aid in vaccine design, where the efficient expression of viral proteins may be required to generate immunity . Here, we performed comprehensive analyses of the codon usage of 120 available HYSV genomes, investigated the possible key determinants, and compared it with other bunyaviruses in synonymous codon usage patterns.…”

“…The interplay of codon usage among viruses and their hosts is expected to affect viral survival, fitness, evasion from host's immune system and evolution [12,15]. Therefore, the study of codon usage patterns in viruses can reveal important information about molecular evolution, regulation of viral gene expression, and aid in vaccine design, where the efficient expression of viral proteins may be required to generate immunity [12,13].…”

Synonymous codon usage patterns in different parasitic platyhelminth mitochondrial genomes

“…The mitochondrial genome often accumulates nucleotide substitutions at faster rates than does the nuclear genome, especially for mammalian mitochondrial DNA (Brown et al, 1979;Martin et al, 1992;Ramirez et al, 1993). Various studies have analyzed different organisms, such as viruses (Zhang et al, 2011), bacteria (Luo et al, 2011), yeast (Whittle et al, 2011), plants , and animals (Musto et al, 2001;Fadiel et al, 2002). However, codon usage in platyhelminth mitochondrial genomes has only rarely been studied.…”