Background Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production. Results We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds. Conclusion In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.

中文翻译：

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连续的生理阶段标志着真菌黑曲霉对木质纤维素的转录组反应。

背景了解真菌如何降解木质纤维素是改进基于可再生能源的生物技术的基石，特别是水解酶的生产。在研究 CAZyme 表达高峰时间点的真菌降解方面已经取得了相当大的进展。然而，人们对真菌在其一生中在木质纤维素上的生存策略的深入了解却被忽视了。在这里，我们的目的是揭示生物技术主力和酶生产者黑曲霉在其一生中对六种对生物燃料生产重要的底物的生理反应。结果我们分析了黑曲霉对原料芒草的反应，并将其与我们之前对小麦秸秆的研究进行了比较，单独或与水热或离子液体原料预处理相结合。通过全基因组转录组学的多变量分析，结合靶向转录本和蛋白质分析，并映射到代谢模型，确定了保守（与底物无关）的代谢反应以及受预处理和原料影响的代谢反应。最初接触所有底物都会增加脂肪酸β-氧化和脂质代谢转录本。在携带构巢曲霉脂肪酸β-氧化转录调节因子farA直系同源物缺失的菌株中，选定的木质纤维素降解CAZyme编码基因的表达减少，表明β-氧化有助于适应木质纤维素。甘露聚糖降解表达依赖于麦秆原料，并且果胶降解在未处理的基质上较高。在生命的后期阶段，已知的和新颖的次生代谢基因簇被激活，由于它们合成生物活性化合物的潜力而引起高度关注。结论 在这项包括曲霉对芒草的首次转录反应的研究中，我们强调了寿命以及底物组成和结构（通过预处理和原料的变化）影响真菌对木质纤维素的反应。我们还证明，真菌反应包含跨底物保守的生理阶段，并且通常在 CAZyme 高表达条件之外发现，例如以脂质和次级代谢为主的阶段。