Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi.
Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi.
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DOI：
10.1371/journal.pone.0029847
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Raffaele S
中科院分区：
文献类型：
--
作者：
Saunders DG;Win J;Cano LM;Szabo LJ;Kamoun S;Raffaele S
锈菌是一种专性生物营养病原菌，对农作物造成相当大的危害。小麦锈菌(Puccinia graminis f.sp.)小麦茎锈病病原菌Tritici和杨树叶锈病病原菌Melampsora larici-Peoina分别对小麦和杨树木材生产有较强的危害作用。丝状病原体，如锈菌，会分泌一种称为疾病效应器的分子，作为宿主细胞生理的调节器，可以抑制或触发宿主免疫。目前关于其他丝状植物病原体的效应物的知识可以被用于最近测序的锈菌基因组中的效应物的特征。我们设计了一个完整的电子分析管道，从两个植物病原性锈菌的基因组中鉴定可能的效应谱带。根据观察，丝状病原体的已知效应蛋白至少具有下列性质之一：(I)含有分泌信号，(Ii)由植物诱导基因编码，(Iii)与吸器蛋白相似，(Iv)小且富含半胱氨酸，(V)含有已知的效应基序或核定位信号，(Vi)由具有长基因间隔区的基因编码，(Vii)包含内部重复序列，以及(Viii)不包含PFAM结构域，除非与致病性相关的那些。我们使用马尔可夫聚类法和层次聚类法对锈病病原菌的蛋白质家族进行分类，并根据它们成为效应者的可能性对它们进行排序。使用这种方法，我们确定了八个候选效应器家族，我们认为这些家族对功能表征有很高的价值。这项研究揭示了一组不同的候选效应物，包括吸器表达的分泌蛋白和富含半胱氨酸的小蛋白家族。对这些毁灭性的锈病病原体的候选效应进行全面的分类，是探索植物种质资源寻找新的抗性成分的第一步。
Rust fungi are obligate biotrophic pathogens that cause considerable damage on crop plants. Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust, and Melampsora larici-populina, the poplar leaf rust pathogen, have strong deleterious impacts on wheat and poplar wood production, respectively. Filamentous pathogens such as rust fungi secrete molecules called disease effectors that act as modulators of host cell physiology and can suppress or trigger host immunity. Current knowledge on effectors from other filamentous plant pathogens can be exploited for the characterisation of effectors in the genome of recently sequenced rust fungi. We designed a comprehensive in silico analysis pipeline to identify the putative effector repertoire from the genome of two plant pathogenic rust fungi. The pipeline is based on the observation that known effector proteins from filamentous pathogens have at least one of the following properties: (i) contain a secretion signal, (ii) are encoded by in planta induced genes, (iii) have similarity to haustorial proteins, (iv) are small and cysteine rich, (v) contain a known effector motif or a nuclear localization signal, (vi) are encoded by genes with long intergenic regions, (vii) contain internal repeats, and (viii) do not contain PFAM domains, except those associated with pathogenicity. We used Markov clustering and hierarchical clustering to classify protein families of rust pathogens and rank them according to their likelihood of being effectors. Using this approach, we identified eight families of candidate effectors that we consider of high value for functional characterization. This study revealed a diverse set of candidate effectors, including families of haustorial expressed secreted proteins and small cysteine-rich proteins. This comprehensive classification of candidate effectors from these devastating rust pathogens is an initial step towards probing plant germplasm for novel resistance components.
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