Miyauchi Shingo, Navarro David, Grisel Sacha, Chevret Didier, Berrin Jean-Guy, Rosso Marie-Noelle
Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.
PAPPSO, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
PLoS One. 2017 Apr 10;12(4):e0175528. doi: 10.1371/journal.pone.0175528. eCollection 2017.
Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO) enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes) and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1) simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases); 2) the key role of lytic polysaccharide monooxygenases (LPMO); 3) the early transcriptional regulation of lignin active peroxidases; 4) the induction of detoxification processes dealing with biomass-derived compounds; and 5) the frequent attachments of the carbohydrate binding module 1 (CBM1) to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various industrial applications.
创新的绿色技术对于将植物废料转化为材料、化学品和能源的可再生资源至关重要。然而,回收农业和林业废料是一项挑战。或许可以在森林中找到解决方案。腐生白腐真菌能够将枯死植物转化为可利用的碳源。可以利用专门的真菌酶来分解坚硬的植物生物聚合物。因此,了解此类真菌的酶作用机制可为我们有效分解植物材料提供线索。以腐生白腐真菌朱红密孔菌作为真菌模型,我们在两个时间点研究了转录组和分泌组对不同类型木质纤维素底物的反应动态。我们的综合组学流程(SHIN+GO)使我们能够将生物信息层压缩成简单的热图,便于直观检查数据。我们鉴定出了共调控基因及其相应的共分泌酶,并通过富集的碳水化合物活性酶(CAZymes)和功能注释推断出其生物学作用。我们观察到真菌对木质纤维素底物降解的早期反应包括:1)CAZy基因的同时表达以及作用于纤维素、半纤维素及其侧链或木质素中不同糖苷键的酶(即水解酶、酯酶和氧化还原酶)的分泌;2)裂解多糖单加氧酶(LPMO)的关键作用;3)木质素活性过氧化物酶的早期转录调控;4)处理生物质衍生化合物的解毒过程的诱导;5)碳水化合物结合模块1(CBM1)频繁附着于木质纤维素反应基因的酶上。我们的组学结合方法及相关生物学发现可能有助于真菌系统生物学知识的积累,并促进针对各种工业应用优化真菌酶混合物。