Analysis of synonymous codon usage in the outer membrane efflux protein gene of Riemerella anatipestifer

Abstract

The aim was to identify the codon usage bias between the newly identified Riemerella Anatipestifer(RA)outer membrane efflux protein gene(GenBank accession NO. CP003388) and outer membrane efflux protein genes of 17 other reference flavobacteriaceae with bioinformatics software. A comparative analysis of the codon usage bias of the 18 flavobacteriaceae was performed by using the CodonW1.4.2 and CUSP program of EMBOSS. The results showed the differences of the synonymous codon usage bias in the 18 flavobacteriaceae indicated by effective number of codons(Enc), and the value of G+C content at the 3 rd codon position. The Enc-plot revealed that these outer membrane efflux protein genes of flavobacteriaceae are subject to GC compositional constraints. In addition, comparisons of the codon preferences in the outer membrane efflux protein gene of RA with those of Escherichia coli, yeast and humans revealed that there are 29 codons showing distinct usage differences between RA outer membrane efflux protein gene and E.coli and 23 between RA outer membrane efflux protein gene and humans, but only 21 between RA outer membrane efflux protein gene and yeast. Therefore, the E.coli system may be more suitable for the expression of the RA outer membrane efflux protein gene. These results may improve the expression of the gene and our understanding of the functional studies of RA.