16种豆科植物DXS基因密码子偏好性分析

Analysis of codon bias of DXS gene in 16 Leguminous plants

选取16种豆科植物1-脱氧-D-木酮糖-5-磷酸合成酶(1-deoxy-D-xylulose-5-phosphate synthase,DXS)的CDS序列,运用CodonW、CHIPS、CUSP等程序分析序列的碱基组成、有效密码子数(ENc)、相对使用度(RSCU)等参数,并结合ENc-plot和PR2-plot分析,揭示密码子的偏好性。结果显示:豆科植物DXS基因偏好使用的密码子有19个(RSCU>1),最优的是CCA与GGA;GC量和GC3s都小于0.5,表明优先选择A/U为末端的密码子;ENc值为48.66~53.4,表明DXS基因偏好性较弱。ENc-plot和PR2-plot分析显示,突变是影响豆科植物DXS基因密码子偏好性的主要因素。与基于RSCU值聚类结果相比,基于豆科植物DXS的CDS序列聚类结果更适合用于植物系统发育研究。相较大肠杆菌,拟南芥、烟草和酵母是DXS基因的合适宿主。研究结果对通过优化密码子方法提高豆科植物DXS基因在其他宿主中的表达效率,进而提高下游萜类化合物的产量具有一定意义。

The coding sequences(CDS)of 1-deoxy-D-xylulose-5-phosphate synthase(DXS)from 16 Leguminous plants were selected for analysis.CodonW,CHIPS,CUSP and other programs were used to calculate the base composition of the sequences,the effective number of codons(ENc),the relative synonymous codon usage(RSCU)and other related parameters.These sequences were also analyzed by ENc-plot and PR2-plot.The results showed that there were 19 codons(RSCU>1)with strong preference for DXS genes in Leguminosae,in which optimal codons were CCA and GGA;both the GC content and GC3s were less than 0.5,indicating that A/U was preferentially used as the terminal codon.The ENc values ranged from 48.66 to 53.4,indicating weak the codon preference of the DXS genes.The ENc-plot and PR2-plot analysis displayed that the codon usage of DXS gene preference was mainly affected by mutation pressure.The clustering result based on CDS sequence was closer to the evolutionary classification of plants than the result based on RSCU clustering.Compared with Escherichia coli,Saccharomyces cerevisiae,Arabidopsis thaliana and Nicotiana tabacum were suitable hosts for DXS gene.All these results provided important significance to increase the yield of downstream terpenoids,by optimizing codons to improve the expression efficiency of DXS gene in other hosts.