Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing.
Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing.
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DOI：
10.1371/journal.pgen.1002875
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
Archer DB
中科院分区：
文献类型：
--
作者：
Delmas S;Pullan ST;Gaddipati S;Kokolski M;Malla S;Blythe MJ;Ibbett R;Campbell M;Liddell S;Aboobaker A;Tucker GA;Archer DB
生产第二代生物燃料的一个关键挑战是将木质纤维底物转化为可发酵的糖。酶，特别是来自真菌的酶，是这一过程的核心部分，许多酶已经被分离和鉴定。然而，关于真菌如何响应木质纤维素并产生分解植物生物质所需的酶的研究相对较少。我们研究了真菌黑曲霉在以麦草为木质纤维模型底物时的生理反应。利用RNA测序表明，在稻草暴露24小时后，已知和推定的植物细胞壁降解酶的基因表达对细胞来说是一笔巨大的投资(约占总mRNA的20%)。我们的结果还发现了新的酯酶和表面相互作用蛋白，它们可能构成植物生物量降解的真菌酶库的一部分。利用转录因子缺失突变体(xlnR和CREA)研究了木质纤维素底物和低碳源浓度的反应，结果表明，饥饿诱导了编码降解酶的基因子集。我们的数据支持这样一个模型，即这个酶的子集在饥饿条件下发挥侦察作用，测试可用的复杂多糖并释放诱导糖，从而触发随后大多数水解酶的诱导。我们还发现了大量的反义转录本，并且它们的表达可以受到生长条件的调节。第二代生物燃料的目标是从非粮食作物和秸秆等农业废弃物中生产燃料。关键的一步是从复杂的植物原料中提取单糖(糖化)，这一步往往是有限的。这通常需要使用真菌酶。许多这样的酶已经被分离和表征，但人们对真菌如何自然地利用它们的一系列酶以及它们在降解植物材料方面采用了哪些其他策略知之甚少。在本研究中，我们发现丝状真菌黑曲霉在以小麦秸秆为碳源时，会产生大量的植物细胞壁降解酶。我们的结果确定了几种可能在这一过程中发挥作用的其他类型的蛋白质，从而为改进目前的糖化过程提供了应用。此外，我们发现小麦秸秆本身最初并没有被真菌检测到，相反，碳饥饿的开始触发了一小部分降解酶的释放。这些酶可能起到侦察作用，感知植物细胞壁的存在，并启动小规模的降解，进而释放糖，使真菌表达其完全降解的武器库。
A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall–degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA). Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA) to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions. The aim of second generation biofuels is to produce fuels from non-food crops and agricultural wastes such as straw. A key, and often limiting, step is the extraction of simple sugars (saccharification) from the complex plant materials. This typically requires the use of fungal enzymes. Many such enzymes have been isolated and characterised, but less is known about how fungi naturally utilise their array of enzymes and what other strategies they employ in degrading plant material. In this study, we show that the filamentous fungus Aspergillus niger deploys a large number of plant cell wall-degrading enzymes when using wheat straw as its carbon source. Our results identify several other types of proteins that may play a role in this process, and thereby offer applications in the improvement of current saccharification processes. In addition, we show that wheat straw itself is not initially detected by the fungus and, instead, the onset of carbon starvation triggers the release of a small subset of degradative enzymes. These enzymes might play a scouting role, to sense the presence of plant cell walls and initiate degradation on a small scale, in turn releasing sugars that cause the fungus to express its full degradative arsenal.
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影响因子：
4.8
作者：
CarleUrioste, JC;EscobarVera, J;ElDorry, H
通讯作者：
ElDorry, H
影响因子：
4.4
作者：
deVries, RP;Michelsen, B;Visser, J
通讯作者：
Visser, J
影响因子：
5.7
作者：
Bourne, Y;Hasper, AA;Marchot, P
通讯作者：
Marchot, P
影响因子：
6.3
作者：
de Souza WR;de Gouvea PF;Savoldi M;Malavazi I;de Souza Bernardes LA;Goldman MHS;de Vries RP;de Castro Oliveira JV;Goldman GH
通讯作者：
Goldman GH
影响因子：
7
作者：
Andersen, Mikael R.;Salazar, Margarita P.;Baker, Scott E.
通讯作者：
Baker, Scott E.