口蹄疫病毒密码子使用偏性的位点差异(英文)

doi:10.3969/j.issn.1000-7091.2013.02.006

摘要/Abstract

摘要： 分析了FMDV各血清型病毒基因编码起始区与终止区的密码子使用偏性。结果表明,FMDV各血清型中的稀有密码子倾向出现于编码起始区,而终止区附近稀有密码子出现的倾向较弱。这一有趣的现象,可利用"稀有密码子调控假说"来解释为FMDV起始编码区的稀有密码子的使用对其编码区表达具有负调控作用。而终止区附近的这种较弱的倾向性表明,终止区密码子的使用对编码区基因表达的影响可能没有起始区那样强烈。同时说明,"稀有密码子调控假说"不仅适用于细菌,而且也适用于一些病毒基因组。

关键词: FMDV, 血清型, 密码子, 调控

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

中图分类号:

马晓霞, 冯玉萍, 赵永清, 陈莉, 刘俊林, 郭鹏辉, 陈红, 杨具田, 卢建雄, 陈世恩, 马忠仁. 口蹄疫病毒密码子使用偏性的位点差异(英文)[J]. 华北农学报, 2013, 28(2): 32-37. doi: 10.3969/j.issn.1000-7091.2013.02.006.

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.

http://www.hbnxb.net/CN/Y2013/V28/I2/32

参考文献

[1] Sauna Z E,Kimchi-Sarfaty C,Ambudkar S V,et al. The sounds of silence:synonymous mutations affect function
[J]. Pharmacogenomics,2007,8:527-532.
[2] Gu W,Zhou T,Ma J,et al. Analysis of synonymous codon usage in SARS coronavirus and other viruses in the Nidovirales[J]. Virus Research,2004,101 (2):155-161.
[3] Francino H P,Ochman H. Isochores result from mutation not selection[J]. Nature,1999,400(6739):30-31.
[4] Ma J,Zhou T,Gu W,et al. Cluster analysis of the codon use frequency of MHCgenes from different species[J]. Biosystems,2002,65(2):199-207.
[5] Hooper S D,Berg Og.gradients in nucleotide and codon usage along Escherichia cloigenes[J]. Nucleic Acids Re-search,2000,28(18):3517-3523.
[6] Ohno H,Sakai H,Washio T,et al. Preferential usage of some minor codons in bacteria[J].gene,2001,276:107-115.
[7] Belshamg J. Distinctive features of foot-and-mouth dis-ease virus,a member of the picornavirus family;aspects of virus protein synthesis,protein processing and structure
[J]. Prog Biophys Mol Biol,1993,60:241-60.
[8] Sharp P M,Touhy T,Mosurski K. Codon usage in yeast cluster analysis clearly differentiates highly and lowly ex-pressedgenes[J]. Nucleic Acids Research,1986,14 (13):5125-5143.
[9] Li W. Position dependence of synonymous codon usage
[J]. Acta Biophysica Sinica,2001,17(3):529-534.
[10] Zhou T,Gu W J,Ma J M,et al. Site discrepancy of syn-onymous codon usage in SARS Coronavirus and other vi-ruses in Coronaviridae[J]. Journal of Southeasr Univer-sity,2005,21:203-206.
[11] Cheng T,Inouye M. Suppression of the negative effect of minor arginine codons ongene expression;preferential usage of minor codons within the first 25 codons of the Escherichia Coligenes[J]. Nucleic Acids Research,1990,18,1465-1437.
[12] Gouy M,Gautier C. Codon usage in bacteria:correlation withgene expressivity[J]. Nucleic Acids Res,1982,10: 7055-7074.
[13] Sharp P M,Li W H. An evolutionary perspective on syn-onymous codon usage in unicellular organisms[J]. J Mol Evol,1986,24:28-38.
[14] Sharp P M,Li W H. The codon Adaptation Index-a measure of directional synonymous codon usage bias,and its potential applications[J]. Nuclei Acids Res,1987,15:1281-1295.
[15] Bains W. Codon distribution in vertebrategenes may be used to predictgene length[J]. J Mol Biol,1987,197: 397-388.
[16] Eyre-Walker A. Synonymous codon bias is related togene length in Escherichia coli:selection for translation-al accuracy[J]. Mol Biol Evol,1996,13:864-872.
[17] Ma J,Campbell A,Karlin S. Correlations between Shine-Dalarno sequences andgene features[J]. J Bacteriol,2002,184:5733-7545.
[18] Lobry J R,Gautier C. Hydrophbicity,expressivity and ar-omaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encodedgenes[J]. Nu-cleic Acids Res,1994,22:3174-3180.
[19] D' Onofriog,Ghosh T C,Bernardig. The base composition of thegenes is correlated with the secondary structures of the rncoded proteins[J].gene,2002,300:179-187.
[20] Xie T,Ding D,Tax X,et al. The relationship between synonymous codon usage and protein structure[J]. FEBS Lett,1998,434:93-96.
[21] Bulmer M. Coevolution of codon usage and transfer RNA abundance[J]. Nature,1987,325:728-730.
[22] Sueoka N. Direcional mutation pressure,selective con-straints,andgenetic equilibria[J]. J Mol Evol,1999,34:95-114.
[23] Sueoka N. Two aspects of DNA base composition:G + C content and translation-coupled deviation from intras-trand rule of A = T andg = C[J]. J Mol Evol,1999,49: 49-62.
[24] Karlin S,Mrazek J. What drives codon choice in humangenes? [J]. J Mol Miol,1996,262:459-472.

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