作 者 :李滢,匡雪君,孙超,陈士林
期 刊 :中国中药杂志 2016年 41卷 11期 页码:2055.
关键词:川贝母 ;转录组 ;密码子使用偏好性 ;
Keywords:Fritillaria cirrhosa , transcriptome , codon usage bias ,
摘 要 :研究川贝母表达基因的密码子的使用模式,探讨其密码子使用偏好性特点,为运用基因工程技术实现贝母碱的异源生物合成提供理论依据。以川贝母转录组9843条全长转录本序列为数据来源,使用CodonW软件对川贝母表达基因的密码子GC含量特点、有效密码子数和同义密码子相对使用频率各项参数进行计算、统计,分析发现,川贝母表达基因密码子偏好程度整体水平不高。该研究确定了15个密码子为川贝母最优密码子UUG,CUU,AUU,GUU,UCA,CCU,CCA,ACU,ACA,GCA,UAU,CAU,AAU,AGA和GGA,最优密码子偏好A/T结尾。计算结果显示26个川贝母生物碱合成相关基因中大肠杆菌和酿酒酵母稀有密码子所占比例较低。根据稀有密码子比例,逐个分析26个关键酶基因在大肠杆菌和酿酒酵母体系中表达时可采用的密码子优化方案。该研究为通过合成生物学手段异源合成川贝母生物碱奠定了前期研究基础。
Abstract:Understanding of codon usage bias of Fritillaria cirrhosa can provide theoretical basis for heterologous biosynthesis of F. cirrhosa alkaloids by genetic engineering technology. A total of 9 843 full length coding sequences (CDS) from the F. cirrhosa transcriptome data were used for the analysis of codon usage bias. The GC and GC3s contents, effective number of codons(ENC) and relative synonymous codon usage (RSCU) were calculated using the CodonW software. The results show that the codon usage bias value is low in the CDS of F. cirrhosa . A total of 15 codons, including UUG, CUU, AUU, GUU, UCA, CCU, CCA, ACU, ACA, GCA, UAU, CAU, AAU, AGA and GGA, were identified as optimal codons in F. cirrhosa . The optimal codons generally end with A/T at the third codon position. By the transcriptome annotation, we found 26 CDSs possibly involved in the biosynthesis of alkaloids in the F. cirrhosa . The proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae are low in these CDSs. We also proposed a method for the codonoptimization in these target genes. Our work lays the foundation for further study on the biosynthesis of alkaloids of the F. cirrhosa in heterologous species.
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