Analysis Of Codon In Environmental Pollutant Nitrile-degrading Microbes

The present work analyzed the optimal codons and relative synonymous codonusage (RSCU) among genes of nitrile-degrading microbes, and explored the similarityand differences of the optimal codons between different nitrlie-degrading organisms.Moreover, this study examined the trends in synonymous codon usage innitrile-degrading microbes by correspondence analysis (CA). All these results laid agood foundation for further obtaining nitrile-degrading organisms with a betternitrile-degrading activity by genetic engineering and for the identification ofnitrile-degrading microbes.3744genes in Agrobacterium radiobacter K84chromosome1，2363genes in Agrobacterium radiobacter K84choromosome2,2765genes in Agrobacterium tumefaciens str. C58circular chromosome，1851genes inAgrobacterium tumefaciens str. C58linear chromosome,4799genes in Comamonastestosteroni CNB-2，4064genes in Chelativorans sp. BNC1，5862genes inPseudomonas fluorescens F113，6108genes in Pseudomonas fluorescens Pf-5，5722genes in Pseudomonas fluorescens Pf0-1，5921genes in Pseudomonas fluorescensSBW25，5250genes in Pseudomonas putida F1，5408genes in Pseudomonas putidaGB-1，5350genes in Pseudomonas putida KT2440，5218genes in Pseudomonasputida S16，5182genes in Pseudomonas putida W619，4512genes in Rhodococcusequi103S，6030genes in Rhodococcus erythropolis PR4，4145genes in Bacillussubtilis BSn5，4297genes in Bacillus subtilis subsp. spizizenii TU-B-10，4062genesin Bacillus subtilis subsp. spizizenii str. W23，4101genes in Bacillus subtilis subsp.subtilis RO-NN-1，4176genes in Bacillus subtilis subsp. subtilis str.168，8317genesin Bradyrhizobium japonicum USDA110were obtained from NCBI (National Centerfor Biotechnology Information). The present study used CodonW to analyze andcalculate the optimal codons and relative synonymous codon usage among genes ofnitrile-degrading microbes. The results showed all nitrile-degrading organismspresented the codon usage bias. Among any a nitrile-degrading organism, in additionto a small number of amino acids, most amino acids had the optimal codons.Correspondence analysis based on relative synonymous usage showed that the codonusage was mainly explained by the axes1and2in nitrile-degrading microbes.