Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression.
Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression.
复制标题
DOI：
10.1016/j.fgb.2016.04.005
复制
发表时间：
2017-05
期刊：
影响因子：
--
通讯作者：
Archer DB
中科院分区：
文献类型：
--
作者：
Daly P;van Munster JM;Kokolski M;Sang F;Blythe MJ;Malla S;Velasco de Castro Oliveira J;Goldman GH;Archer DB
真菌混合种稻草培养物中的第一个全基因组转录反应。在混合培养物中，rRNA丰度用于预测RNA-seq读数丰度。具有混合培养物的产黄青霉CAZy的亚组增加了丰度模式。由于种间拮抗作用，缺乏总体较高的CAZy转录物/活性。在混合培养物中诱导次级代谢产物产生基因簇。通过真菌单一培养对木质纤维素的反应获得新知识是一种广泛使用的方法，可以为木质纤维素糖化（糖的酶促释放，随后用于制造生物燃料）提供更好的鸡尾酒。然而，在木质纤维素混合培养的反应很少研究在相同的细节，即使在自然界中真菌往往降解木质纤维素作为混合社区。使用双重RNA-seq方法，我们描述了野生型菌株尼日尔，里氏木霉和产黄青霉在两个和三个混合物种摇瓶培养与麦草的转录反应的第一次研究。基于物种特异性rRNA的定量，确定了一组条件，其中可以对混合培养物进行采样，以获得足够的RNA-seq读数用于每个物种的分析。差异表达基因的数量从几千到不到一百不等。碳水化合物活性酶（CAZy）编码转录物的比例在大多数混合培养物中比相应的稻草单一培养物低。一小部分P. chrysogenum CAZy基因在与T. reesei。然而，大量的T. reesei CAZy转录物在混合培养物中显示降低的丰度。混合培养物中的高诱导基因表明真菌拮抗作用是混合培养物的主要组成部分。与此一致，次级代谢产物产生基因簇在混合培养物中以及与T. reesei的作用导致A.尼日尔.仅使用少数混合培养物测得秸秆中显著更高的单糖释放，并且没有总体改善。本研究证明了真菌与混合培养物中的转录物、酶活性和生物量的变化的相互作用，虽然对CAZy转录物和活性有微小的有益影响，但T. reesei和其他真菌是本研究最突出的特点。
First genome-wide transcriptional response in fungal mixed species straw cultures. In mixed cultures, rRNA abundance was used to predict RNA-seq read abundance. Subset of P. chrysogenum CAZy with mixed cultures increased abundance pattern. Lack of overall higher CAZy transcripts/activities due to inter-species antagonism. Induction of secondary metabolite producing gene clusters in mixed cultures. Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw. Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement. This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study.