橄榄查尔酮异构酶基因CHI的密码子偏好模式

Codon usage pattern of chalcone isomerase gene(CHI) in Canarium album(Lour.) Raeusch

黄酮类化合物是橄榄[Canarium album(Lour.)Raeusch]的重要活性成分,而查尔酮异构酶(Chalcone isomerase,CHI)是黄酮合成的关键酶类之一,了解橄榄查尔酮异构酶基因CHI的密码子偏好模式可为其功能和分子进化研究提供科学依据.采用Codon W和EMBOSS分析橄榄CHI的密码子偏好性参数,并通过有效密码子数(Effective number of codon,ENc)绘图、中性绘图和偏倚分析探讨单双子叶植物CHI密码子偏好性形成的可能因素,同时分别采用SPSS19.0和MEGA5.2基于密码子偏好性和序列相似性进行聚类分析.结果显示:橄榄CHI ENc值、G和C的含量(GC)以及密码子第3位上G和C含量(GC3s)分别为50.89、0.451和0.465,表明其密码子偏好性较弱,但倾向使用富含A和U,并以A或U结尾的密码子;单子叶植物CHI的密码子偏好性普遍高于双子叶植物,基于密码子偏好性和核酸序列相似性均能将单双子叶植物进行较准确的归类;密码子碱基成分和相关性分析发现,物种间CHI密码子偏好性受编码区长度的影响较小,而与碱基的组成密切相关;此外,橄榄CHI与模式生物拟南芥、烟草、大肠杆菌和酵母菌基因组均存在较大的密码子偏好性差异.本研究表明突变压力是单双子叶植物间CHI严格的密码子偏好规律形成的主要作用力,而橄榄CHI外源表达和遗传转化时需要根据宿主基因组偏好模式进行密码子优化和改造.

Chalcone isomerase （CHI） is one of the key enzymes in the flavonoid synthesis pathway of Canarium album （Lour.） Raeusch. To provide a theoretical basis for further functional and evolutionary analysis of CHI, the codon usage pattern of C. album （Lour.） Raeusch CHI （CaCHI） was analyzed. We used CodonW and EMBOSS to investigate the codon usage bias of CaCHI and the effective number of codon （ENc） plots, neutral drawing, and parity rule 2 plot were subsequently used for the exploration of possible factors that affect the formation of the bias. Moreover, based on codon bias or sequence similarity, the statistical package for the social sciences （SPSS） version 19.0 or MEGA5.2 was used for cluster analysis of CHI in monocotyledon and dicotyledon plants. The results showed that the ENc, GC content （GC）, and GC content of the 3rd site （GC3s） were 50.89, 0.451, and 0.465 respectively for CaCHI, which suggests that the codon bias level of CHI in C. album （Lour.） Raeusch was low and biased toward the synonymous codons with A or U on the 3rd site. It was also identified that the codon bias level of CHI in monocotyledons was generally higher than that in dicotyledons. Notably, according to the codon bias and sequence similarity of CHI, the results of phylogenetic tree analysis accurately classified the 40 investigated plants into monocotyledon and dicotyledon groups. Moreover, the correlation analysis revealed that the base composition but not the coding region length greatly affected the codon bias of plants. Additionally, the codon usage bias of CaCHI was quite different from that of model organisms such as Arabidopsis thaliana, Nicotiana sylvestris, Escherichia coli, and Saccharomyces cerevisiae. Our data confirmed that mutation pressure contributed dominantly to the strict codon usage rules in both monocotyledon and dicotyledon plants. Furthermore, it might be extremely essential to perform codon optimizations and modifications according to the codon bias of the host genome for heterologous expression and genetic transformation analysis of CaCHI.