Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation.
Genomic and proteomic analyses of the fungus Arthrobotrys oligospora provide insights into nematode-trap formation.
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少孢节孢菌的基因组和蛋白质组分析为线虫诱捕器的形成提供了见解
DOI：
10.1371/journal.ppat.1002179
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发表时间：
2011-09
期刊：
影响因子：
6.7
通讯作者：
Zhang KQ
中科院分区：
文献类型：
--
作者：
Yang J;Wang L;Ji X;Feng Y;Li X;Zou C;Xu J;Ren Y;Mi Q;Wu J;Liu S;Liu Y;Huang X;Wang H;Niu X;Li J;Liang L;Luo Y;Ji K;Zhou W;Yu Z;Li G;Liu Y;Li L;Qiao M;Feng L;Zhang KQ
捕食线虫的真菌是“肉食性的”，使用专门的捕食设备攻击它们的宿主。这些圈闭的形态发育是它们从腐生生活方式转变为捕食生活方式的关键指标。这里是捕食线虫的真菌少孢节丛孢菌的基因组。(ATCC24927)。该基因组包含40.07Mb的组装序列，包含11,479个预测基因。比较分析表明，寡孢链霉菌与致病真菌的基因同源性远高于与非致病真菌的同源性。具体地说，与几种已测序的子囊菌相比，少孢曲霉基因组在枯草杆菌酶、纤维素酶、纤维二糖水解酶和果胶酯酶基因家族中拥有更多与致病相关的基因。通过对病原菌-寄主互作基因数据库的检索，在其他真菌中发现了398个与致病相关的同源基因。对重复序列的分析为寡孢链霉菌的重复诱导点突变提供了证据。蛋白质组学和定量聚合酶链式反应(QPCR)分析表明，90个基因在线虫提取物诱捕早期显著上调，其中大部分基因参与翻译、氨基酸代谢、碳水化合物代谢、细胞壁和膜生物发生。基于基因组学、蛋白质组学和定量聚合酶链式反应的综合数据，提出了该真菌中线虫捕捉器的形成模型。在这个模型中，多条真菌信号转导通路被其捕食的线虫激活，以进一步调节与不同细胞过程相关的下游基因，如能量代谢、细胞壁和黏附蛋白的生物合成、细胞分裂、甘油积累和过氧化酶体的生物发生。这项研究将有助于鉴定致病相关基因，并为了解真菌-线虫相互作用的分子和进化机制提供广泛的基础。少孢节丛孢菌有多种生活方式。它不仅是一种线虫病原菌，还是一种腐生植物，是其他真菌的病原菌，也是植物根的定殖者。少孢链霉菌作为一种线虫病原体，形成粘附性网络捕捉线虫，是了解这些真菌与寄主线虫相互作用的模式生物。本研究报道了少孢链霉菌的全基因组序列。我们对线虫提取物处理细胞10h和48h后细胞内蛋白的蛋白质组图谱进行了分析，发现了一组参与陷阱形成的关键基因。定量聚合酶链式反应进一步证实了一些TRAP形成相关基因的蛋白质水平的变化。基因组和蛋白质组相结合的分析确定了与少孢链霉菌陷阱形成有关的主要遗传和代谢途径。我们的结果首次让我们得以一窥这群令人着迷的食肉真菌的基因组和蛋白质组。这些数据将为进一步研究捕食线虫的真菌与其宿主线虫之间的相互作用提供路线图，为病原线虫的生物防治研究提供广泛的基础。
Nematode-trapping fungi are “carnivorous” and attack their hosts using specialized trapping devices. The morphological development of these traps is the key indicator of their switch from saprophytic to predacious lifestyles. Here, the genome of the nematode-trapping fungus Arthrobotrys oligospora Fres. (ATCC24927) was reported. The genome contains 40.07 Mb assembled sequence with 11,479 predicted genes. Comparative analysis showed that A. oligospora shared many more genes with pathogenic fungi than with non-pathogenic fungi. Specifically, compared to several sequenced ascomycete fungi, the A. oligospora genome has a larger number of pathogenicity-related genes in the subtilisin, cellulase, cellobiohydrolase, and pectinesterase gene families. Searching against the pathogen-host interaction gene database identified 398 homologous genes involved in pathogenicity in other fungi. The analysis of repetitive sequences provided evidence for repeat-induced point mutations in A. oligospora. Proteomic and quantitative PCR (qPCR) analyses revealed that 90 genes were significantly up-regulated at the early stage of trap-formation by nematode extracts and most of these genes were involved in translation, amino acid metabolism, carbohydrate metabolism, cell wall and membrane biogenesis. Based on the combined genomic, proteomic and qPCR data, a model for the formation of nematode trapping device in this fungus was proposed. In this model, multiple fungal signal transduction pathways are activated by its nematode prey to further regulate downstream genes associated with diverse cellular processes such as energy metabolism, biosynthesis of the cell wall and adhesive proteins, cell division, glycerol accumulation and peroxisome biogenesis. This study will facilitate the identification of pathogenicity-related genes and provide a broad foundation for understanding the molecular and evolutionary mechanisms underlying fungi-nematodes interactions. The fungus Arthrobotrys oligospora has multiple lifestyles. It's not only a nematode pathogen, but also a saprophyte, a pathogen of other fungi, and a colonizer of plant roots. As a nematode pathogen, A. oligospora forms adhesive networks to capture nematodes and is a model organism for understanding the interaction between these fungi and their host nematodes. In this study, the whole genome sequence of A. oligospora was reported. Our analyses of the proteome profiles of intracellular proteins from cells treated with nematode extracts for 10 h and 48 h revealed a key set of genes involved in trap formation. The changes in protein levels for some trap formation related genes were further confirmed by qPCR. The combined genome and proteome analysis identified the major genetic and metabolic pathways involved in trap formation in A. oligospora. Our results provide the first glimpse into the genome and proteome of this fascinating group of carnivorous fungi. The data should serve as a roadmap for further investigations into the interaction between nematode-trapping fungi and their host nematodes, providing broad foundations for research on the biocontrol of pathogenic nematodes.
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