草酸乙酰化降解途径酶基因密码子偏好性分析

Codon usage bias for genes involved in oxalate acetylation degradation pathway

【目的】分析100种植物中参与草酸乙酰化降解途径的草酰-CoA合成酶(AAE3)、草酰-CoA脱羧酶(OCD)和甲酸脱氢酶(FDH)基因的密码子偏好性及其影响因素,并分析其适配的异源表达受体,为揭示AAE3、OCD和FDH基因在植物中的遗传修饰和进化规律及提高其异源表达效率提供理论依据。【方法】运用CodonW 1.4.2、CUSP及Python等软件工具,通过PR2-plot分析、ENC-plot分析、相对同义密码子使用量(RSCU)分析、中性绘图分析及密码子使用频率比较分析,深入解析AAE3、OCD和FDH基因编码区(CDS)序列的碱基组成特征、密码子偏好及其主要影响因素、高频密码子、最优密码子及异源表达适配受体。【结果】AAE3、OCD和FDH基因CDS序列在不同位置上GC含量差异较大,但三者均偏好使用以G/C结尾的密码子。AAE3、OCD和FDH基因表达水平较低,且密码子偏好性均较弱,偏好性排序:FDH>AAE3>OCD。在进化过程中AAE3、OCD和FDH基因的密码子偏好性主要受自然选择的影响,突变压力对其影响则较小。RSCU分析结果显示,AAE3、OCD和FDH基因分别有31、26和27个高频密码子,分别有19、14和9个最优密码子,其中AAE3和FDH基因的最优密码子均以G/C结尾,而OCD基因的最优密码子中以G/C结尾的有8个,占最优密码子的57.14%。拟南芥和烟草可作为AAE3、OCD和FDH基因的异源表达适配受体,当选择大肠杆菌和酿酒酵母作为异源表达受体时,则需要优化较多的密码子(17~19个)。【结论】AAE3、OCD和FDH基因在进化过程中表现出较相似的密码子偏好特征,选择异源表达受体时应优先考虑拟南芥和烟草。

【Objective】This study aimed to explore the condon preference of oxalyl-CoA synthase(AAE3),oxalyl-CoA decarboxylase(OCD)and formate dehydrogenase(FDH)genes involved in the oxalate acetylation degradation pathway among 100 plant species,as well as the factors that influenced condon preference,and analyzed their suitable heterologous expression receptors,which could provide scientific basis for understanding the genetic modification and evolution of AAE3,OCD and FDH genes in plants,and for enhancing their heterologous expression efficiency.【Method】Comprehensively used CodonW 1.4.2,CUSP and Python softwares,through PR2-plot analysis,ENC-plot analysis,relative synonymous codon usage(RSCU)analysis,neutral plot analysis and codon frequency comparison analysis,the base composition characteristics,codon preference and its main influencing factors,high-frequency codons,optimal codons and heterologous expression adaptation receptors of AAE3,OCD,and FDH coding sequences(CDS)were deeply elucidated.【Result】The GC content of the CDS sequences of AAE3,OCD and FDH genes varied greatly at different positions,but they all preferred codon ending with G/C.The gene expression levels of AAE3,OCD and FDH genes were low,and the codon preference was weak,with the degree of FDH>AAE3>OCD.During evolution,the codon preference of AAE3,OCD and FDH genes was mainly influenced by natural selection,with mutation pressure having little effect.RSCU analysis showed that AAE3,OCD and FDH genes had 31,26 and 27 high-frequency codons,and 19,14 and 9 optimal codons respectively,among which the optimal codons of AAE3 and FDH genes all ended in G/C,and 8 of the optimal codons of OCD gene ended in G/C,accounting for 57.14%of the optimal codons.Arabidopsis thaliana and Nicotiana tabacum could serve as adaptive receptors for heterologous expression of AAE3,OCD and FDH genes.When Esche-richia coli and Saccharomyces cerevisiae were selected as heterologous expression receptors,more codons(17-19)needed to be modified.【Conclusion】AAE3,OCD and FDH genes exhibit highly similar codon preference characteristics during evolutionary process,and the selection of heterologous expression receptors should prioritize A.thaliana and N.tabacum.