The global regulator FfSge1 is required for expression of secondary metabolite gene clusters but not for pathogenicity in Fusarium fujikuroi. Fusarium fujikuroi

The phytopathogenic fungus Fusarium fujikuroi is the causal agent of bakanae disease on rice due to its ability to produce gibberellins. Besides these phytohormones, F. fujikuroi is able to produce a wide range of other secondary metabolites (SMs), such as mycotoxins and pigments. Although much progress has been made in the field of secondary metabolism over the last years, the transcriptional regulation of SM biosynthetic genes is complex and far from being fully understood. Environmental conditions (e.g. nitrogen availability and pH), global and pathway-specific regulators as well as chromatin remodeling were shown to play major roles in this regulation. Here, the role of FfSge1, a homolog of the morphological switch regulators Wor1 and Ryp1 in Candida albicans and Histoplasma capsulatum, respectively, is explored with emphasis on secondary metabolism. FfSge1 is not required for conidia formation and pathogenicity, but is involved in vegetative growth. Genome-wide transcriptome analysis of the Δffsge1 deletion mutant compared to the wild type revealed that FfSge1 is a global regulator of secondary metabolism in F. fujikuroi that activates the expression of several SMs. In addition, FfSge1 is also required for expression of a yet uncharacterized SM gene cluster containing a noncanonical non-ribosomal peptide synthetase. Investigation of whole genome gene expression of the Fusarium fujikuroi wild type IMI58289, Δffsge1 mutant under nitrogen starvation and nitrogen sufficient conditions. Overall design: In this study we hybridized in total 8 microarrays using total RNA recovered from a wild-type culture of F. fujikuroi IMI58289 and Δffsge1 mutant culture. All cultures were grown on a 6 mM Gln (10%) and a 60 mM Gln medium (100%). For each combination of culture and medium a biological replicate was created. Each chip measures the expression level of 14,397 genes from F. fujikuroi IMI58289 with eight 60-mer probes. Please note that the wild type samples have been published as part of the GEO accession GSE43745, but re-analyzed with the Δffsge1 mutant samples in the current study.

稻藤镰孢（Fusarium fujikuroi）是引发水稻恶苗病（bakanae disease）的病原真菌，其致病能力依赖于赤霉素（gibberellins）的合成。除上述植物激素外，F. fujikuroi还可产生多种次生代谢物（secondary metabolites, SMs），包括真菌毒素（mycotoxins）与色素等。尽管近年次生代谢研究领域已取得诸多进展，但次生代谢合成基因的转录调控机制复杂，目前尚未完全阐明。研究表明，环境条件（如氮素有效性、培养基pH）、全局及通路特异性调控因子，以及染色质重塑，在该调控过程中发挥核心作用。
本研究针对FfSge1的功能展开探究，该蛋白分别为白色念珠菌（Candida albicans）与荚膜组织胞浆菌（Histoplasma capsulatum）中形态转换调控因子Wor1和Ryp1的同源蛋白，研究重点聚焦于其在次生代谢中的调控功能。实验结果显示，FfSge1并非分生孢子形成与致病性所必需，但参与菌株的营养生长过程。对Δffsge1缺失突变体与野生型菌株开展全基因组转录组分析后发现，FfSge1是F. fujikuroi次生代谢的全局调控因子，可激活多个次生代谢合成基因的表达。此外，FfSge1对于一个尚未被功能注释的次生代谢基因簇的表达同样不可或缺，该基因簇包含一个非典型非核糖体肽合成酶（non-ribosomal peptide synthetase）。
本研究检测了F. fujikuroi野生型菌株IMI58289与Δffsge1突变体在氮饥饿及氮充足条件下的全基因组基因表达谱。整体实验设计：本研究共使用8张微阵列芯片（microarray），实验所用总RNA提取自F. fujikuroi野生型IMI58289与Δffsge1突变体的培养物。所有培养物分别在6 mM谷氨酰胺（Gln，10%氮源浓度）与60 mM谷氨酰胺（Gln，100%氮源浓度）培养基中培养。针对每种培养物与培养基的组合，均设置了生物学重复。每张芯片用于检测F. fujikuroi IMI58289的14397个基因的表达水平，每个基因对应8个60聚体探针。需要说明的是，野生型样本此前已作为GEO登录号"GSE43745"的一部分发表，但本研究将其与Δffsge1突变体样本一同进行了重新分析。