铁皮石斛咖啡酸-O-甲基转移酶(COMT)密码子偏好模式分析

The Codon Usage Bias of Caffeic Acid-O-Methyltransferase Gene(COMT)in Dendrobium catenatum

咖啡酸-O-甲基转移酶(COMT)是木质素合成过程的关键酶,参与苯丙烷代谢。了解铁皮石斛COMT(Caffeic acid-O-methyltransferase)基因密码子的偏好性可为其功能和分子进化研究提供科学依据。采用Codon W、EMBOSS、SPSS、Origin等分析铁皮石斛COMT的密码子偏好参数,并通过ENC绘图、中性绘图和PR2-plot分析探讨COMT基因密码子偏好性形成的可能因素,同时使用SPSS19.0和MEGA6.0进行聚类分析。结果显示,铁皮石斛COMT基因ENC值、GC含量以及GC3分别为49、0.452和0.396,表明其密码子偏好性较弱,偏好使用A或T结尾的密码子;ENC、中性绘图分析显示突变压力是COMT密码子偏好性形成的主要作用力;铁皮石斛COMT基因和同为兰科植物的香味蝴蝶兰(Phalaenopsis bellina)的亲缘关系最近,两者的GC1s、GC2s、GC3s、GC、CAI和ENC也较为相近,表明物种进化关系上越相近其密码子偏好性也较为相似,但有些物种仍存在一些差异。此外,从密码子使用频率分析得出酵母菌真核表达系统适合铁皮石斛COMT基因的异源表达,模式植物烟草、番茄可以作为其遗传转化受体。本研究为COMT基因功能进一步研究提供参考。

Caffeic acid-O-methyltransferase(COMT), a key enzyme in lignin synthesis, is involved in phenylpropane metabolism. To provide a theoretical basis for further functional and evolutionary analysis of COMT. We used Codon W, EMBOSS, SPSS, Origin to investigate the codon usage bias of COMT and the effective number of codon(ENC) plots, neutral drawing, and PR2-plot were subsequently used for the statistical of possible factors that affect the formation of the bias, the statistical package for the social sciences(SPSS) version 19.0 or MEGA 6.0 was used for cluster analysis of COMT. The results showed that the ENC, GC and GC3 s site were 49, 0.452 and 0.396 respectively for COMT, which suggests that the codon bias level of COMT in D. catenatum research was low and biased towards the synonymous codons with A or U on the 3 rd site. ENC-plot, neutral drawing analysis shows that mutation pressure is the main force in the formation of COMT codon preference. The relationship between COMT gene of D. catenatum and Phalaenopsis bellina is close, and their GC1 s, GC2 s, GC3 s, GC, CAI and ENC are similar, indicating that the closer the species evolutionary relationship is, the more similar their codon preference is. However, some species still have some differences. In addition, the Saccharomyces cerevisiae expression system was more suitable for the heterologous expression of COMT gene of D. catenatum. The model plant Nicotiana tabacum and Solanum lycopersicum could be used as genetic transformation receptors. This study provides a reference for further study of COMT gene function.