IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, Rueil-Malmaison, 92852, France.
Laboratoire d'Informatique Gaspard-Monge (LIGM), ESIEE Paris, Université-Gustave Eiffel, Marne-la-Vallée, F-77454, France.
BMC Genomics. 2020 Dec 10;21(1):885. doi: 10.1186/s12864-020-07281-8.
The degradation of cellulose and hemicellulose molecules into simpler sugars such as glucose is part of the second generation biofuel production process. Hydrolysis of lignocellulosic substrates is usually performed by enzymes produced and secreted by the fungus Trichoderma reesei. Studies identifying transcription factors involved in the regulation of cellulase production have been conducted but no overview of the whole regulation network is available. A transcriptomic approach with mixtures of glucose and lactose, used as a substrate for cellulase induction, was used to help us decipher missing parts in the network of T. reesei Rut-C30.
Experimental results on the Rut-C30 hyperproducing strain confirmed the impact of sugar mixtures on the enzymatic cocktail composition. The transcriptomic study shows a temporal regulation of the main transcription factors and a lactose concentration impact on the transcriptional profile. A gene regulatory network built using BRANE Cut software reveals three sub-networks related to i) a positive correlation between lactose concentration and cellulase production, ii) a particular dependence of the lactose onto the β-glucosidase regulation and iii) a negative regulation of the development process and growth.
This work is the first investigating a transcriptomic study regarding the effects of pure and mixed carbon sources in a fed-batch mode. Our study expose a co-orchestration of xyr1, clr2 and ace3 for cellulase and hemicellulase induction and production, a fine regulation of the β-glucosidase and a decrease of growth in favor of cellulase production. These conclusions provide us with potential targets for further genetic engineering leading to better cellulase-producing strains in industry-like conditions.
纤维素和半纤维素分子降解为葡萄糖等简单糖是第二代生物燃料生产过程的一部分。木质纤维素底物的水解通常由真菌里氏木霉产生和分泌的酶来完成。已经进行了研究鉴定参与纤维素酶生产调节的转录因子，但没有可用的整个调节网络概述。使用含有葡萄糖和乳糖的混合物的转录组学方法，用作纤维素酶诱导的底物，用于帮助我们破译里氏木霉 Rut-C30 网络中的缺失部分。
在 Rut-C30 高生产菌株上的实验结果证实了糖混合物对酶混合物组成的影响。转录组学研究显示主要转录因子的时间调节和乳糖浓度对转录谱的影响。使用 BRANE Cut 软件构建的基因调控网络揭示了三个与 i）乳糖浓度与纤维素酶生产之间的正相关，ii）乳糖对β-葡糖苷酶调节的特殊依赖性，以及 iii）发育过程和生长的负调节相关的子网络。
这项工作是首次在分批进料模式下研究纯碳源和混合碳源对转录组的影响。我们的研究揭示了 xyr1、clr2 和 ace3 对纤维素酶和半纤维素酶诱导和生产的协同调控，β-葡糖苷酶的精细调节以及生长的减少有利于纤维素酶的生产。这些结论为我们提供了进一步遗传工程的潜在目标，以在工业条件下获得更好的产纤维素酶菌株。
