百合甘油-3-磷酸酰基转移酶(GPAT)基因密码子偏性分析及其表达受体选择

Analysis of Codon Bias and Phylogenetic Relationships of the Glycerol- 3-Phosphate Acyltransferase(GPAT) Gene in Lilium L.

本研究运用CodonW和Emboss中的CHIPS、CUSP软件程序对铁炮百合(Lilium longiflorum)、亚洲百合杂种系品种(Lilium‘Excite’)、王百合(Lilium regale)和毛百合(Lilium pensylvanicum)这4种百合GPAT基因(GenBank登录号分别为:JX524738,JX524739,JX524740和JX524741)密码子进行偏好性分析,分别与5种单子叶和6种双子叶植物的GPAT基因密码子偏好性进行比较与系统进化分析,又与4种常用模式生物基因组密码子的偏好性进行比较分析。结果表明,4种百合GPAT基因密码子偏性均较弱,基因表达水平较低,偏好于以A/T结尾的密码子;偏好密码子基本相同。在一定程度上表明,百合的GPAT基因在属间进化中比较保守。并且发现,GPAT密码子偏好性在单、双子叶植物上体现的差异并不显著,从一定程度上表明GPAT基因在进化上的保守性较高。百合GPAT基因密码子偏性与几种双子叶植物的更相近,某些双子叶植物也是该基因的适宜导入受体。在系统进化分析中,基于相对同义密码子使用度(RSCU)的聚类结果与基于CDS构成的聚类结果存在一定的差异,但均可在一定程度上反映物种间的进化关系。与4种模式生物密码子使用频率比较发现,4种百合与受体生物的差异情况比较一致,百合GPAT的密码子偏好性与受体生物酵母和大肠杆菌的基因组密码子偏好性均有较大的不同,表明需要对百合GPAT基因的部分密码子进行优化改造,才能使其在以上受体中高效的表达。百合GPAT与拟南芥基因组密码子使用频率差值较少,表明百合GPAT在拟南芥受体中的表达效率较高;而百合GPAT在烟草受体中的表达效率一般。对于转化植物的选择,拟南芥优于烟草。为准确预测百合GPAT基因的异源表达,为接下来选择其适宜的表达系统以及提高该基因在受体表达系统中的表达效率,进行有效的功能验证提供了有效的参考。

The CUSP and CHIPS programs in Emboss and CodonW were used to analyzed the codon usage bias of GPAT genes （GenBank Accession No.： JX524738, JX524739, JX524740, JX524741） in Lilium longiflorum, Lilium ＇Excite＇, Lilium regale and Lilium pensylvanicum in this paper. In addition, comparison and analysis to the codon usage bias and phylogenetic analysis of the GPAT genes with another five monocotyledonous and six dicot- yledonous plants were carried out. Comparison with four model organism genomes was also done. The results showed a weak existence of the eodon usage bias of GPAT genes and a relatively low-level expression in the four lilies. While the GPAT genes in the four lilies were biased toward the synonymous codons ended with A and T. The preferred codons were basically the same. The GPAT gene of the lily in intergeneric evolution was more conservative. It was found that the distinction of GPAT gene codon usage bias between monocotyledonous and dicotyledonous plants were not significant. Therefore, to some extent, it indicated that GPAT genes in different plants kept a high evolutionary conservation. The codon usage bias of GPAT genes in Lily was closer to several dicotyledonous plants. This gene may also be suitable for its expression in dicotyledonous plants. In the phyl- ogenetic analysis, though the clustering results based on the relative synonymous codon usage （RSCU） showed some differences with the clustering results based on CDS, they both revealed the evolutional relations between species. Compared with the codon usage frequency of four model organism genomes, the differences between each lily and acceptor organisms were basically consistent. There were distinct codon usage differences between GPAT genes of lilies and genome codons of E. eoli and yeast. It indicated that it was necessary to modify and optimize some codons for efficient expression of GPAT gene in this two hosts. The codon usage frequency differences between GPAT genes of lilies and the genes of A rabidopsis thaliana were fewer. The consequence indicated that the GPAT genes could be efficiently expressed in A rabidopsis thaliana, and at the ordinary level while expressed in Nicotiana tabaeum. Considering on the codon bias, the A rabidopsis thaliana expression system may be more suitable for the expression of GPAT genes of lilies than Nieotiana tabaeum. The effective reference was provided to accur- ately predict the heterologous expression of the lily GPAT gene, further carry on effective functional verification, select the appropriate expression system and improve expression of the lily GPAT gene in receptor systems.