黑曲霉木质纤维素降解酶基因的可变剪接分析及验证

黑曲霉Aspergillus niger因能够产生大量的木质纤维素降解酶而在木质纤维素资源利用中发挥重要作用。目前,有关黑曲霉基因组中与木质纤维素降解相关的基因是否存在可变剪接的情况尚不清楚。本研究以黑曲霉CBS513.88菌株为研究对象,采用rMATS和ABLas两种方法对黑曲霉在葡萄糖为唯一碳源(G组)和小麦秸秆为唯一碳源(WS组)下的56个木质纤维素降解酶基因的可变剪接事件进行分析,并通过RT-PCR扩增和内含子特异性扩增对3个典型基因的可变剪接体进行了验证。结果表明,ABLas可变剪接分析算法相较于rMATS分析算法更为准确,ABLas分析算法显示G组和WS组共有21个木质纤维素降解酶基因出现了可变剪接,可变剪接类型以内含子保留(IR)为主,占所有可变剪接事件的82.85%。另外,G组和WS组发生可变剪接的木质纤维素降解酶基因也有所不同：G组发生可变剪接的基因为13个,WS组发生可变剪接的基因为14个,两组都发生可变剪接的基因为6个,这表明黑曲霉木质纤维素降解酶基因的可变剪接在不同生长条件下存在差异,另一方面,黑曲霉中众多可变剪接体的存在也为开发新型的木质纤维素降解酶资源提供基础。

Analysis and verification of the alternative splicing events of the lignocellulose degrading enzyme genes from Aspergillus niger

Aspergillus niger plays an important role in utilizing lignocellulosic biomass because of its ability to produce large amounts of lignocellulose degrading enzymes. Until now it is not clear whether there are alternative splicing events on genes related to lignocellulose degradation in A. niger. In this study, rMATS and ABLas analysis algorithms were used to analyze the alternative splicing events on a total of 56 lignocellulose degrading enzyme genes in A. niger strain CBS513.88 growing on media respectively using glucose (Group G) and wheat straw (Group WS) as the sole carbon source. The alternative splicing events occurred on the three typical genes were further verified by RT-PCR and intron-specific amplification. The results showed that ABLas analysis algorithm was more accurate than rMATS analysis algorithm. Based on ABLas analysis algorithm, a total of 21 lignocellulose degrading enzyme genes in both Group G and Group WS was found to have alternative splicing, and the type of alternative splicing occurred was mainly intron retention (IR) which accounted for 82.85% of all alternative splicing events. In addition, the lignocellulose degrading enzyme genes with alternative splicing in Group G and Group WS were different: 13 genes were found to have alternative splicing in Group G while 14 genes in Group WS, with 6 genes being the same in both groups. Our results indicates that the occurrence of alternative splicing on lignocellulose degrading enzyme genes in A. niger changes with different growth conditions. The existence of a large number of splicing variants in A. niger provides a basis for discovery of novel lignocellulose degrading enzymes.