豆科植物IPI基因密码子偏好性

异戊烯基焦磷酸异构酶（isopentenyl diphosphate isomerases,IPI）作为2-C-甲基-D-赤藓糖醇-4-磷酸（2-C-methyl-D-erythritol-4-phosphate,MEP）和甲羟戊酸（mevalonate,MVA）途径的关键酶,参与植物萜类化合物的生物合成。豆科植物含多种萜类物质,研究豆科植物IPI基因密码子偏好性对促进豆科植物IPI基因表达、增加萜类物质产率具有重要意义。运用Codon W、EMBOSS等程序分析32个IPI基因的碱基组成、相对密码子使用度（RSCU）、有效密码子数（ENc）、密码子适应指数（CAI）等参数,并结合ENC-GC3s与PR2-plot方法确定豆科植物IPI基因的密码子偏好性。结果表明,豆科植物IPI基因偏好性较强（RSCU>1）的密码子有7个,最优密码子是GGU,第3位碱基的GC含量（GC3s）[落花生2 (Arachis hypogaea 2)除外]与同义密码子GC含量（GC）<0.5,密码子偏好以A/U结尾。ENc为46.69~55.00,CAI为0.23~0.27,IPI基因表达水平偏低。ENc-GC3s与PR2-plot分析结果表明,自然选择是形成豆科植物IPI基因密码子偏好性的主要原因。相较于RSCU聚类树,基于编码序列的系统进化树更能反映物种真实的系统发育关系。大肠埃希菌、烟草与拟南芥可以作为豆科植物IPI基因外源表达的宿主,研究结果将为开展IPI基因的密码子改造与遗传工程操作奠定基础。

Codon bias of IPI gene in leguminous plants

Isopentenyl diphosphate isomerases (IPI), as a key enzyme in 2-C-methyl-D-erythritol 4-phosphate (MEP) and Mevalonate (MVA) pathways, takes part in the biosynthesis of terpenoids. Since leguminous species contain a variety of terpenoids, the codon bias of IPI genes from leguminous species will provide significant basis to increase those expressing levels and thus the terpenoids contents in leguminous species. In this study, Codon W, EMBOSS, ENc-GC3s and PR2-plot were used to calculate the base composition, relative synonymous codon usage (RSCU), effective number of codons (ENc), codon adaptation index (CAI), and etc. As a result, 7 codons showed strong preference (RSCU >1), in which GGU was the most optimal codon. That the low contents (<0.5) of both GC (GC content) and GC3s (GC content of the third base) indicated that A/U was preferable terminal codon. The low expressing level of IPI genes was probably due to the Enc values ranging from 46.69 to 55 and the CAI values ranging from 0.23 to 0.27. The results of ENc-GC3s and PR2-plot supported that the formation of codon bias was mainly contributed from natural selection. Compared with RSCU clustering, the phylogenetic tree based on CDS was closer to the result of classification based on morphology. Finally, Escherichia coli, Nicotiana tabacum and Arabidopsis thaliana were proposed to be suitable hosts for IPI genes from leguminous species. Therefore, the result of this paper laid foundation for transformation of codons and genetic engineering of IPI genes.