Article

Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi

University of California Riverside, United States of America
PLoS ONE (Impact Factor: 3.23). 01/2012; 7(1):e29847. DOI: 10.1371/journal.pone.0029847
Source: PubMed

ABSTRACT

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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    • "tritici, the flax rust Melampsora lini and the coffee rust Hemileia vastatrix (Cantu et al., 2011, 2013; Duplessis et al., 2011a; Zheng et al., 2013; Cristancho et al., 2014; Nemri et al., 2014). Secretomes of rust fungi have been determined based on the presence of predicted N-terminal signal peptides in proteins (Cantu et al., 2011, 2013; Duplessis et al., 2011a; Fernandez et al., 2012; Hacquard et al., 2012; Saunders et al., 2012; Bruce et al., 2013; Garnica et al., 2013; Zheng et al., 2013; Link et al., 2014; Nemri et al., 2014). Signal peptides can be defined using predictors available online (Emanuelsson et al., 2007). "
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    ABSTRACT: The poplar leaf rust fungus, Melampsora larici-populina has been established as a tree-microbe interaction model. Understanding the molecular mechanisms controlling infection by pathogens appears essential for durable management of tree plantations. In biotrophic plant-parasites, effectors are known to condition host cell colonization. Thus, investigation of candidate secreted effector proteins (CSEPs) is a major goal in the poplar–poplar rust interaction. Unlike oomycetes, fungal effectors do not share conserved motifs and candidate prediction relies on a set of a priori criteria established from reported bona fide effectors. Secretome prediction, genome-wide analysis of gene families and transcriptomics of M. larici-populina have led to catalogs of more than a thousand secreted proteins. Automatized effector-mining pipelines hold great promise for rapid and systematic identification and prioritization of CSEPs for functional characterization. In this review, we report on and discuss the current status of the poplar rust fungus secretome and prediction of candidate effectors from this species.
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    • "In contrast, no RCPs could be identified among the 1852 secreted proteins predicted from the proteome of P. graminis f. sp. tritici (Saunders et al., 2012). As such, RCP effectors are expected to play an important role in promoting the colonization of some, but not all, plant-associated organisms. "
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    Full-text · Article · Oct 2015 · Frontiers in Plant Science
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    • "n the secretome of fungal pathogens ( Saunders et al . , 2012 ; Guyon et al . , 2014 ) . Typical effector properties include the presence of a N - terminal secretion signal , small protein size , high Cys content , the absence of characterized protein domains , high rate of non - synonymous over synonymous substitutions ( Hacquard et al . , 2012 ; Saunders et al . , 2012 ; Persoons et al . , 2014 ; Sperschneider et al . , 2014 ) . However , validated virulence factors do not all comply with these properties , such as Verticillium dahlia isochorismatase VdIsc1 harboring an isochorismatase domain but no conventional secretion signal ( Liu et al . , 2014 ) or Melampsora lini AvrM that lacks any Cys ( Catan"
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