刺盘孢菌的蛋白互作预测及侵染早期共表达模块分析

刺盘孢菌是一类重要的植物病原真菌,在全球范围内危害众多单双子叶植物。有许多研究对病菌的侵染模式进行了探索,但仍未阐明其确切的分子机制。本研究在预测病菌蛋白互作的基础上,结合表达谱数据对病菌在活体生存环境下的共表达模块进行挖掘和分析,以期为分子机制的研究提供新的线索。通过同源映射法和结构域法,预测得到刺盘孢菌的4 288个蛋白之间存在41 700个潜在互作,其中39 776个互作发生于异源蛋白之间,1 924个互作发生于同一蛋白内。将蛋白互作数据分别与4个表达谱数据进行整合,构建得到离体I、离体II、活体I和活体II 4个共表达互作组。对离体和活体互作组的共有基因的表达水平进行比较分析,结果表明,与离体互作组相比,活体互作组中与翻译、蛋白代谢等有关的基因表达水平下降,与离子转运、糖物质转运等有关的基因表达水平上升,暗示了物质转运在刺盘孢菌侵染早期的重要作用。进一步对活体互作组进行模块化分析,结果表明,活体I和活体II的特异模块分别与胁迫响应、肌动蛋白纤维长度调控有关,其中胁迫响应子网是以热激蛋白Hsp70为核心的互作簇,可能参与病菌对寄主的识别与对抗;肌动蛋白纤维长度调控子网则可能与病菌菌丝在寄主细胞间的延伸有关。

Prediction of protein-protein interactome in Colletotrichum sp. and analysis of co-expression modules at the early stage of infection

Colletotrichum sp. is an important phytopathogenic fungus that causes serious disease on various monocot and dicot crops worldwide. Although the infection strategies of the pathogen have been explored extensively, the detailed molecular mechanisms remain unclear. In this study, the co-expression modules of Colletotrichum sp. grown in living plants were explored and analyzed by integrating the predicted protein-protein interaction and expression profile data, to provide a new clue for molecular mechanism study on pathogen infection. By means of interologs-based and domain-based approaches, 41 700 protein-protein interactions (PPIs) were predicted among 4 288 proteins, including 39 766 interactions in hetero-complex and 1 924 interactions in homo-complex. By integrating the PPIs result and different gene expression profile data, four co-expression protein interactome (coPIN) with two in vitro state (IV1- and IV2- coPIN) and another two in vivo state (IP1- and IP2- coPIN) were constructed. The expression levels of shared genes between IV-coPIN and IP-coPIN were compared. The result showed that the expression levels of genes involved in translation and protein metabolism process were reduced and those of genes involved in ion transport and sugar transport were significantly increased in IP-coPIN as compared with IV-coPIN, indicating that ion and sugar transport play a key role in the early infection of Colletotrichum sp. Further modular analysis on IP-coPIN revealed that the specific modules in IP1-coPIN and IP2-coPIN were respectively related to stress response and regulation of actin filament length. The ‘response to stress’ subnet in IP1-coPIN was an interaction cluster with Hsp70 as hub protein, which may play an important role in providing pathogen counter-defense against host, while the ‘regulation of actin filament length’ subnet probably participated in the growth of mycelium in host tissues.