基于转录组和加权基因共表达网络的广叶绣球菌木质纤维素降解特性分析

Characterization of lignocellulose degradation by Sparassis latifolia based on transcriptomics and weighted gene co-expression network analysis

摘要:

【目的】分析广叶绣球菌（Sparassis latifolia）在不同木质纤维素诱导条件下基因表达差异，为广叶绣球菌木质纤维素降解关键基因和分子机制研究提供参考。【方法】以松木、杉木、甘蔗渣和天然堆积发酵后的杉木和发酵后的甘蔗渣为碳源，在液体培养条件下培养诱导广叶绣球菌，对其转录组进行测序研究，并对不同木质纤维素诱导样本进行加权基因共表达网络分析（weighted gene co-expression network analysis，WGCNA）。【结果】杉木培养与松木培养比较组差异表达基因最少（20个），蔗渣培养与松木培养比较组差异表达基因最多（486个）。基因本体（gene ontology，GO）富集分析结果表明，差异表达基因主要涉及氧化还原酶活性、单加氧酶活性和铁离子结合活性等，京都基因和基因组百科全书（Kyoto encyclopedia of genes and genomes，KEGG）通路富集分析结果表明，差异表达基因主要涉及戊糖和葡萄糖醛酸转换、甲烷代谢和乙醛酸盐和二羧酸盐代谢等通路。发酵甘蔗渣为碳源培养时，纤维素和半纤维素降解相关的糖苷水解酶基因表达量总体上较高，而未发酵的松木、杉木和甘蔗渣为碳源培养时木质素降解或修饰相关的碳水化合物辅助酶基因表达量总体上较高。利用WGCNA共鉴定出10个共表达模块，其中green模块与未发酵蔗渣诱导显著正相关，blue模块与发酵甘蔗渣诱导显著正相关，magenta和turquoise模块与发酵杉木诱导显著正相关。GO富集分析结果表明，turquoise模块内基因显著富集到尿素跨膜转运子活性、甲基转移酶活性和单加酶活性等，blue模块基因显著富集到水解酶活性和β-甘露糖苷酶活性。KEGG通路富集分析结果表明，blue模块内基因显著富集的通路有半乳糖代谢、果糖和甘露糖代谢、苯丙氨酸代谢、精氨酸和脯氨酸代谢等。通过构建互作网络图挖掘到12个核心基因，其可能参与了基质降解及相关基因的表达调控。【结论】不同木质纤维素类型显著影响了广叶绣球菌木质纤维素降解基因的差异表达轮廓，这种差异反映了广叶绣球菌对不同木质纤维素特异的降解策略。

Abstract:

[Objective] To explore gene expression profiles of Sparassis latifolia cultivated with different lignocellulose materials and provide a reference for mining the key genes and deciphering the mechanism of lignocellulose degradation by S. latifolia. [Methods] We examined the transcriptomes of S. latifolia cultivated in the liquid medium with pine, spruce, bagasse, fermented spruce, or fermented bagasse as the sole carbon source. Weighted gene co-expression network analysis (WGCNA) was performed on the gene expression of samples cultivated with different lignocellulose materials. [Results] There were only 20 differentially expressed genes (DEGs) between the spruce and pine groups, and 486 DEGs (the highest number) between bagasse and pine groups. Gene ontology (GO) enrichment analysis showed that the DEGs were mainly involved in oxidoreductase activity, monooxygenase activity, and iron ion binding. Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis showed that the DEGs were mainly involved in pentose and glucuronate interconversions, methane metabolism, and glyoxylate and dicarboxylate metabolism. The expression of genes encoding glycoside hydrolases associated with cellulose or hemicellulose degradation was generally higher when the strain was cultured with fermented bagasse as the sole carbon source. The expression of genes encoding carbohydrate-active enzymes for lignin degradation or modification was generally higher when the strain was cultured with pine, spruce, or bagasse as the sole carbon source. A total of 10 co-expression modules were identified by WGCNA. Significant positive correlations existed between the green module and bagasse, between the blue module and fermented bagasse, and between magenta and turquoise modules and fermented spruce. GO enrichment analysis showed that the genes in the turquoise module were enriched in urea transmembrane transporter activity, methyltransferase activity, and monooxygenase activity, while those in the blue module in hydrolase activity and β-mannosidase activity. KEGG pathway enrichment analysis showed that the genes in the blue module were enriched in galactose metabolism, fructose and mannose metabolism, phenylalanine metabolism, arginine and proline metabolism, etc. From the interaction network, 12 hub genes were obtained, which may be involved in lignocellulose degradation or gene expression regulation. [Conclusion] Different lignocellulose materials significantly affected the gene expression profiles ofS. latifolia, which may imply the specific degradation strategies against different lignocellulose materials.