Site Discrepancy of Synonymous Codon Usage in FMDV

doi:10.3969/j.issn.1000-7091.2013.02.006

Abstract

Abstract: The synonymous codon usage in the translational initiation and termination regions ofgenes of seven different serotypes belonging to foot-and-mouth disease virus(FMDV) was particularly analyzed. The results indicate that the pattern of codon usage with low propensity at some sites in the initial region is preferentially existed,and the interesting phenomenon may imply a negative effect ongene expression,which can be explained by the "minor co-don modulator hypothesis". Nevertheless,this interesting phenomenon fails to exist obviously in the terminal region. Obviously,some information about the pattern of codon usage in the initial translation region may indicate that the sites of codon usage with low propensity may have an more obvious effect on FMDVgene transcription or translation than the terminal region. The proposed results imply that the "minor codon modulator hypothesis" may be applied to both bacteria and some RNA viruses(e.g. FMDV).

Key words: Foot-and-mouth disease virus, Serotype, Codon usage, Modulator

CLC Number:

MA Xiao-xia, FENG Yu-ping, ZHAO Yong-qing, CHEN Li, LIU Jun-lin,gUO Peng-hui, CHEN Hong, YANG Ju-tian, LU JIAN-xiong, CHEN Shi-en, MA Zhong-ren. Site Discrepancy of Synonymous Codon Usage in FMDV[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2013, 28(2): 32-37. doi: 10.3969/j.issn.1000-7091.2013.02.006.

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