The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa. Neurospora crassa

Background: Pectin is an abundant component in many fruit and vegetable wastes and could therefore be an excellent resource for biorefinery, but is currently underutilized. Fungal pectinases already play a crucial role for industrial purposes, such as for foodstuff processing. However, the regulation of pectinase gene expression is still poorly understood. For an optimal utilization of plant biomass for biorefinery and biofuel production, a detailed analysis of the underlying regulatory mechanisms is warranted. In this study, we applied the genetic resources of the filamentous ascomycete species Neurospora crassa to screen for transcription factors that play a major role in pectinase induction. Results: The pectin degradation regulator-1 (PDR-1) was identified through a transcription factor mutant screen in N. crassa. The Δpdr-1 mutant exhibited a severe growth defect on pectin and all tested pectin-related poly- and monosaccharides. Biochemical as well as transcriptional analyses of WT and the Δpdr-1 mutant revealed that while PDR-1-mediated gene induction was dependent on the presence of L-rhamnose, it also strongly affected the degradation of the homogalacturonan backbone. The expression of the endo-polygalacturonase gh28-1 was greatly reduced in the Δpdr-1 mutant, while the expression levels of all pectate lyase genes increased. Moreover, a pdr-1 overexpression strain displayed substantially increased pectinase production. Promoter analysis of the PDR-1 regulon allowed refinement of the putative PDR-1 DNA binding motif. Conclusions: PDR-1 is highly conserved in filamentous ascomycete fungi and is present in many pathogenic and industrially important fungi. Our data demonstrate that the function of PDR-1 in N. crassa combines features of two recently described transcription factors in Aspergillus niger (RhaR) and Botrytis cinerea (GaaR). The results presented in this study contribute to a broader understanding of how pectin degradation is orchestrated in filamentous fungi and how it could be manipulated for optimized pectinase production. The data here are associated with the following BioProjects: PRJNA256749, PRJNA349646, PRJNA349647, PRJNA349695, PRJNA349696, PRJNA349697, PRJNA349547, PRJNA349548, PRJNA349549, PRJNA349698, PRJNA349699, PRJNA349700 See the links on GSM entries for access to raw data at SRA. Overall design: Data was gathered from carbon source transfer experiments; N. crassa WT and Δpdr-1 mutant were pre-grown for 16 hrs on sucrose, washed 3 times in media without carbon-source and then transferred to either sucrose (WT only), L-rhamnose, pectin or no carbon source, the samples were induced for additional 4 hrs; all samples were performed in biological triplicates except WT on pectin, which was performed in duplicates; sequencing was perfomed on the Illumina HiSeq2000

背景：果胶是多种果蔬废弃物中的丰富组分，因此可成为生物炼制的优质原料，但目前尚未得到充分利用。真菌果胶酶已在食品加工等工业场景中发挥关键作用，然而果胶酶基因表达的调控机制仍有待阐明。为实现植物生物质在生物炼制与生物燃料生产中的最优利用，深入解析其背后的调控机制十分必要。本研究借助丝状子囊菌物种粗糙脉孢霉（Neurospora crassa）的遗传资源，筛选在果胶酶诱导过程中发挥核心作用的转录因子。
结果：通过在粗糙脉孢霉中开展的转录因子突变体筛选，我们鉴定得到果胶降解调控因子-1（Pectin degradation regulator-1，PDR-1）。Δpdr-1突变体在果胶及所有测试的果胶相关多糖、单糖培养基上均表现出严重的生长缺陷。对野生型（WT）与Δpdr-1突变体的生化及转录分析显示，PDR-1介导的基因诱导依赖于L-鼠李糖的存在，同时该因子可显著影响同聚半乳糖醛酸主链的降解。Δpdr-1突变体中内切多聚半乳糖醛酸酶gh28-1的表达量大幅下调，而所有果胶酸裂解酶基因的表达水平均出现上调。此外，pdr-1过表达菌株的果胶酶产量显著提升。通过对PDR-1调控子的启动子分析，我们进一步明确了推定的PDR-1 DNA结合基序。
结论：PDR-1在丝状子囊菌中高度保守，广泛存在于多种致病真菌及工业重要真菌中。本研究数据表明，粗糙脉孢霉中PDR-1的功能兼具黑曲霉（Aspergillus niger）中RhaR与灰葡萄孢（Botrytis cinerea）中GaaR两种新近报道的转录因子的特征。本研究结果有助于更全面地理解丝状真菌中果胶降解的调控过程，以及如何通过人为调控实现果胶酶的高产生产。本研究相关数据关联于以下生物项目：PRJNA256749、PRJNA349646、PRJNA349647、PRJNA349695、PRJNA349696、PRJNA349697、PRJNA349547、PRJNA349548、PRJNA349549、PRJNA349698、PRJNA349699、PRJNA349700。可通过序列读取档案（Sequence Read Archive，SRA）中GSM条目对应的链接获取原始数据。
整体实验设计：本研究数据采集自碳源转移实验：将粗糙脉孢霉野生型与Δpdr-1突变体在蔗糖培养基中预培养16小时，随后用无碳源培养基洗涤3次，再分别转移至蔗糖（仅野生型）、L-鼠李糖、果胶或无碳源的培养基中，诱导培养4小时；除野生型果胶组设置2次生物学重复外，其余所有样本均设置3次生物学重复；测序采用Illumina HiSeq2000平台完成。