真菌漆酶基因的密码子偏好性分析

Analysis of Codon Bias of Laccase Genes in Fungi

漆酶是一种含铜的多酚氧化酶,广泛地存在于各种植物和真菌中。研究使用Codon W和CUSP相关程序对18条真菌漆酶基因CDS序列的密码子使用情况进行分析,比较了真菌漆酶基因与枯草芽孢杆菌、大肠杆菌以及毕赤酵母的密码子偏好性。结果表明,真菌漆酶基因偏好使用以G/C结尾的密码子,29种偏好密码子(相对使用度(RSCU)>1)中偏好性较强的密码子有ATC、CTC、CGC、GTC和TAG(RSCU≥1.5);聚类分析发现,AY450404.1和GU480806.1、XM_951846.2和XM_001228805.1及XM_001389488.2和XM_001818019.2聚为一类,与系统分类关系一致,其余都不一致;在密码子的使用频率上,真菌漆酶基因的密码子用法与枯草芽孢杆菌、大肠杆菌和毕赤酵母的基因组密码子用法都有不同程度的偏好差异,其中与大肠杆菌的密码子用法差异最小,故大肠杆菌更适合作为真菌漆酶基因的外源表达宿主。如果要在上述几种表达系统中实现真菌漆酶基因的高效表达则需对真菌漆酶基因的部分密码子进行优化改造。

Laccase is a kind of polyphenol oxidase which contains copper, and widely exists in all kinds of plants and fungi. The coding sequences of 18 laccase genes from fungi were analyzed to identify their codon usage bias by using CodonW and CUSP programs. The codon bias of fungal laccase genes was compared with that of Bacillus subtilis, Escherichia coli and Pichia pastoris. The results showed that most of fungal laccase genes were bias toward the synonymous codons with G and C at the third codon posi- tion. There were twenty- nine biased codons [ relative synonymous codon usage （RSCU） 〉 1.0 ], among them the codons with stronger bias character （RSCU ≥ 1.5） were ATC, CTC, CGC, GTC and TAG. Clustering analysis showed that AY450404.1 and GU480806.1, XM_951846.2 and XM_001228805.1, XM_001389488.2 and XM_001818019.2 were respectively clustered into a group, which agreed with the taxonomic relationships; while the other clustering results were not the same as the taxonomic relation- ships. The difference in codon usage frequency between fungal laccase genes and genome of Escherichia coli was less than that be- tween fungal laccase genes and genome of Bacillus subtilis or Pichia pastoris. Therefore, Escherichia coli expression system might be more suitable for the expression of fungal laccase genes. For realizing the high-efficient expression of fungal laccase genes in the a- bove three expression systems, it is necessary to optimize several codons of fungal laccase genes.