Benocci Tiziano, Aguilar-Pontes Maria Victoria, Kun Roland Sándor, Lubbers Ronnie J M, Lail Kathleen, Wang Mei, Lipzen Anna, Ng Vivian, Grigoriev Igor V, Seiboth Bernhard, Daly Paul, de Vries Ronald P
1Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
2US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA.
Biotechnol Biofuels. 2019 Apr 9;12:81. doi: 10.1186/s13068-019-1422-y. eCollection 2019.
is one of the major producers of enzymes for the conversion of plant biomass to sustainable fuels and chemicals. Crude plant biomass can induce the production of CAZymes in , but there is limited understanding of how the transcriptional response to crude plant biomass is regulated. In addition, it is unknown whether induction on untreated recalcitrant crude plant biomass (with a large diversity of inducers) can be sustained for longer. We investigated the transcriptomic response of to the two industrial feedstocks, corn stover (CS) and soybean hulls (SBH), over time (4 h, 24 h and 48 h), and its regulatory basis using transcription factor deletion mutants (Δ and Δ). We also investigated whether deletion of a xylulokinase gene (Δ) from the pentose catabolic pathway that converts potential inducers could lead to increased CAZyme gene expression.
By analyzing the transcriptomic responses using clustering as well as differential and cumulative expression of plant biomass degrading CAZymes, we found that corn stover induced a broader range and higher expression of CAZymes in , while SBH induced more pectinolytic and mannanolytic transcripts. XYR1 was the major TF regulating CS utilization, likely due to the significant amount of d-xylose in this substrate. In contrast, ARA1 had a stronger effect on SBH utilization, which correlates with a higher abundance of l-arabinose in SBH that activates ARA1. Blocking pentose catabolism by deletion of led to higher expression of CAZyme encoding genes on both substrates at later time points. Surprisingly, this was also observed for Δ at later time points. Many of these genes were XYR1 regulated, suggesting that inducers for this regulator accumulated over time on both substrates.
Our data demonstrates the complexity of the regulatory system related to plant biomass degradation in and the effect the feedstock composition has on this. Furthermore, this dataset provides leads to improve the efficiency of a enzyme cocktail, such as by the choice of substrate or by deleting to obtain higher production of plant biomass degrading CAZymes.
是将植物生物质转化为可持续燃料和化学品的主要酶生产商之一。粗植物生物质可诱导其产生碳水化合物活性酶（CAZymes），但对于粗植物生物质的转录反应是如何调控的，人们了解有限。此外，对于未经处理的顽固性粗植物生物质（诱导剂种类繁多）的诱导作用能否持续更长时间尚不清楚。我们研究了随时间推移（4小时、24小时和48小时）对两种工业原料玉米秸秆（CS）和大豆壳（SBH）的转录组反应，以及使用转录因子缺失突变体（Δ和Δ）的调控基础。我们还研究了从转化潜在诱导剂的戊糖分解代谢途径中缺失木酮糖激酶基因（Δ）是否会导致CAZyme基因表达增加。
通过使用聚类以及植物生物质降解CAZymes的差异表达和累积表达来分析转录组反应，我们发现玉米秸秆在中诱导了更广泛的CAZymes范围和更高的表达，而SBH诱导了更多的果胶分解和甘露聚糖分解转录本。XYR1是调节CS利用的主要转录因子，可能是由于该底物中大量的D-木糖。相比之下，ARA1对SBH利用有更强的作用，这与SBH中激活ARA1的L-阿拉伯糖的较高丰度相关。通过缺失阻断戊糖分解代谢导致在两个底物上后期时间点CAZyme编码基因的表达更高。令人惊讶的是，在后期时间点的Δ中也观察到了这一点。这些基因中的许多受XYR1调控，表明该调节因子的诱导剂在两个底物上随时间积累。
我们的数据证明了与中植物生物质降解相关的调控系统的复杂性以及原料组成对此的影响。此外，该数据集为提高酶混合物的效率提供了线索，例如通过选择底物或通过缺失以获得更高产量的植物生物质降解CAZymes。
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