RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger.
RNA-sequencing reveals the complexities of the transcriptional response to lignocellulosic biofuel substrates in Aspergillus niger.
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DOI：
10.1186/s40694-014-0003-x
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发表时间：
2014
影响因子：
--
通讯作者：
Archer DB
中科院分区：
文献类型：
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作者：
Pullan ST;Daly P;Delmas S;Ibbett R;Kokolski M;Neiteler A;van Munster JM;Wilson R;Blythe MJ;Gaddipati S;Tucker GA;Archer DB
腐生真菌是碳水化合物活性酶 (CAZymes) 的主要工业来源，用于第二代生物燃料生产过程中木质纤维素的糖化。生产更有效的酶混合物是高效生物燃料生产的关键目标。为了实现这一目标，了解真菌对木质纤维素底物的反应至关重要。我们之前的研究使用 RNA-seq 来鉴定黑曲霉中针对生物燃料原料麦秆的诱导基因，并表明诱导基因的范围比以前使用简单诱导剂看到的更大。在这项工作中，我们使用 RNA-seq 来鉴定黑曲霉中诱导的基因，以响应短轮伐期的矮林柳，并将其与我们之前研究中同一时间点的小麦秸秆的响应进行比较。对柳树的反应显示编码 CAZymes 的基因表达大幅增加。在柳树上诱导编码糖化木质纤维素所需的主要活性的基因，例如内切葡聚糖酶、纤维二糖水解酶和木聚糖酶。对柳树的转录组反应与对稻草的反应有许多相似之处，但个别基因的表达水平存在一些显着差异，这些差异与底物组成或其他因素的差异有关。转录水平的差异包括小麦秸秆中编码属于 GH62（一种阿拉伯呋喃糖苷酶）和 CE1（一种阿魏酸酯酶）CAZy 家族成员的酶的基因的转录水平较高，而编码属于 GH5 家族成员的两个内切葡聚糖酶基因在暴露于柳树时具有较高的转录水平。当用柳树或稻草培养时，黑曲霉分泌的酶混合物发生了变化。使用特定酶的测定以及糖化测定来比较混合物的酶活性。麦秆诱导产生一种酶混合物，其糖化麦秆的程度比柳树更大。不编码 CAZymes 的基因也在柳树上被诱导，例如疏水蛋白以及未知功能的基因。一些基因被确定为未来研究的有希望的目标。通过比较真菌对柳树的整体转录反应和对稻草的反应的首次研究，我们发现诱导木质纤维素底物对黑曲霉表达的转录物和酶的范围具有显着影响。工业上使用麦秆或柳树等复杂基质有利于高效生物燃料生产。本文的在线版本 (doi:10.1186/s40694-014-0003-x) 包含补充材料，可供授权用户使用。
Saprobic fungi are the predominant industrial sources of Carbohydrate Active enZymes (CAZymes) used for the saccharification of lignocellulose during the production of second generation biofuels. The production of more effective enzyme cocktails is a key objective for efficient biofuel production. To achieve this objective, it is crucial to understand the response of fungi to lignocellulose substrates. Our previous study used RNA-seq to identify the genes induced in Aspergillus niger in response to wheat straw, a biofuel feedstock, and showed that the range of genes induced was greater than previously seen with simple inducers. In this work we used RNA-seq to identify the genes induced in A. niger in response to short rotation coppice willow and compared this with the response to wheat straw from our previous study, at the same time-point. The response to willow showed a large increase in expression of genes encoding CAZymes. Genes encoding the major activities required to saccharify lignocellulose were induced on willow such as endoglucanases, cellobiohydrolases and xylanases. The transcriptome response to willow had many similarities with the response to straw with some significant differences in the expression levels of individual genes which are discussed in relation to differences in substrate composition or other factors. Differences in transcript levels include higher levels on wheat straw from genes encoding enzymes classified as members of GH62 (an arabinofuranosidase) and CE1 (a feruloyl esterase) CAZy families whereas two genes encoding endoglucanases classified as members of the GH5 family had higher transcript levels when exposed to willow. There were changes in the cocktail of enzymes secreted by A. niger when cultured with willow or straw. Assays for particular enzymes as well as saccharification assays were used to compare the enzyme activities of the cocktails. Wheat straw induced an enzyme cocktail that saccharified wheat straw to a greater extent than willow. Genes not encoding CAZymes were also induced on willow such as hydrophobins as well as genes of unknown function. Several genes were identified as promising targets for future study. By comparing this first study of the global transcriptional response of a fungus to willow with the response to straw, we have shown that the inducing lignocellulosic substrate has a marked effect upon the range of transcripts and enzymes expressed by A. niger. The use by industry of complex substrates such as wheat straw or willow could benefit efficient biofuel production. The online version of this article (doi:10.1186/s40694-014-0003-x) contains supplementary material, which is available to authorized users.