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| Analysis of Codon Usage Patterns of MUC4 Gene in 13 Species of Mammals |
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Abstract Abstract Escherichia coli served as an important zoonotic pathogen that cause diarrhea in human and neonatal livestock, and the E. coli with fimbriae of the F4 family are one of the major causes of diarrhea. Previous study showed that the Mucin 4 gene (MUC4) was likely to be the receptor of E. coli F4ab/F4ac. Analysis of codon usage patterns contribute to a better understanding of the molecular mechanism and the evolution of a particular gene. To reveal the codon usage patterns of MUC4 gene, this study performed codon usage bias analysis of the complete coding sequences of the MUC4 gene from 13 different mammals. The indexes of codon usage bias of the MUC4 gene including nucleotide composition, effective number of codon and relative synonymous codon usage were calculated. Meanwhile, the analysis of codon usage bias parameter were performed to investigate the main factors that influence the codon usage bias of the MUC4 gene. The results showed that the codons ending with G or C were preferentially used in the MUC4 gene of all the analyzed species. RSCU analysis showed that all of these species had 6 optimal codons, whose biased strongly codons were CUG, AGG, GCC, AUC, GUG, ACA. Moreover, the codon usage patterns of the MUC4 gene were found to be mainly influenced by GC content at the third position. Clustering analysis by RSCU values demonstrated that Sus scrofa and Felis catus, Homo sapiens and Canis lupus familiaris were clustered respectively, which disagreed with taxonomic relationship. In conclusion, this study systematically provides insights into the codon usage patterns of the MUC4 gene. These results can provide the scientific basis for selecting a suitable recipient animal in animal genetic improvement, enhancing exogenous expression level of the MUC4 gene to improve the resistance to E. coli F4ab/F4ac infection by the methods of gene engineering and codon optimization.
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Received: 27 November 2017
Published: 06 August 2018
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| Fund:The National Natural Science Foundation of China |
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