Differential Communications between Fungi and Host Plants Revealed by Secretome Analysis of Phylogenetically Related Endophytic and Pathogenic Fungi

<div><p>During infection, both phytopathogenic and endophytic fungi form intimate contact with living plant cells, and need to resist or disable host defences and modify host metabolism to adapt to their host. Fungi can achieve these changes by secreting proteins and enzymes. A comprehensive comparison of the secretomes of both endophytic and pathogenic fungi can improve our understanding of the interactions between plants and fungi. Although <i>Magnaporthe oryzae</i>, <i>Gaeumannomyces graminis</i>, and <i>M</i>. <i>poae</i> are economically important fungal pathogens, and the related species <i>Harpophora oryzae</i> is an endophyte, they evolved from a common pathogenic ancestor. We used a pipeline analysis to predict the <i>H</i>. <i>oryzae</i>, <i>M</i>. <i>oryzae</i>, <i>G</i>. <i>graminis</i>, and <i>M</i>. <i>poae</i> secretomes and identified 1142, 1370, 1001, and 974 proteins, respectively. Orthologue gene analyses demonstrated that the <i>M</i>. <i>oryzae</i> secretome evolved more rapidly than those of the other three related species, resulting in many species-specific secreted protein-encoding genes, such as avirulence genes. Functional analyses highlighted the abundance of proteins involved in the breakdown of host plant cell walls and oxidation-reduction processes. We identified three novel motifs in the <i>H</i>. and <i>M</i>. <i>oryzae</i> secretomes, which may play key roles in the interaction between rice and <i>H</i>. <i>oryzae</i>. Furthermore, we found that expression of the <i>H</i>. <i>oryzae</i> secretome involved in plant cell wall degradation was downregulated, but the <i>M</i>. <i>oryzae</i> secretome was upregulated with many more upregulated genes involved in oxidation-reduction processes. The divergent <i>in planta</i> expression patterns of the <i>H</i>. and <i>M</i>. <i>oryzae</i> secretomes reveal differences that are associated with mutualistic and pathogenic interactions, respectively.</p></div

Secreted proteins involved in KEGG metabolic pathways.

<p>Secreted proteins involved in KEGG metabolic pathways.</p

<i>De novo</i> motif searches of the unannotated <i>H</i>. and <i>M</i>. <i>oryzae</i> secretomes.

<p>(a) Sequences of the three motifs. (b) Distribution of the three motifs in the amino acid sequence of each protein. Each circle represents one motif.</p

Summary of <i>H</i>. and <i>M</i>. <i>oryzae</i> secretome expression. Fold-changes of gene expression (DAI6 versus DAI2) are presented.

<p>(a) Annotated secretomes. (b) Unannotated secretomes. DAI2 and DAI6 refer to transcripts expressed by <i>H</i>. or <i>M</i>. <i>oryzae</i> infecting rice roots at 2 and 6 days after inoculation, respectively. Unregulated genes, genes with fold-change ≤ 2 and ≥ 0.5; Upregulated genes, genes with fold change > 2; Downregulated genes, genes with fold change < 0.5.</p

Venn diagram showing orthologues among the <i>H</i>. <i>oryzae</i>, <i>M</i>. <i>oryzae</i>, <i>G</i>. <i>graminis</i>, and <i>M</i>. <i>poae</i> secretomes.

<p>The values indicate the counts of the orthologue groups.</p

The 25 most abundant PFAM domains in the four secretomes.

<p>The 25 most abundant PFAM domains in the four secretomes.</p

Expression patterns of genes encoding secreted proteins in <i>H</i>. and <i>M</i>. <i>oryzae</i>.

<p>(a) <i>H</i>. <i>oryzae</i> genes. (b) <i>M</i>. <i>oryzae</i> genes. Red, decrease in transcript abundance; green, increase in transcript abundance. Heat maps were produced based on expression changes (log2 DAI6/DAI2). 1, proteins with Glyco_hydro domain; 2, peptidase; 3, lipase; 4, tyrosinase; 5, cutinase; 6, cellulase; 7, proteins with CBM domain; 8, proteins with Chitin_bind_1 domain; 9, proteins with LysM domain, 10, proteins with FAD_binding_4 domain; 11, proteins with Cu-oxidase domain; and 12, proteins with GMC_oxred_N domain.</p

The analysis pipeline applied to the <i>H</i>. <i>oryzae</i>, <i>M</i>. <i>oryzae</i>, <i>G</i>. <i>graminis</i>, and <i>M</i>. <i>poae</i> secretomes.

<p>The pipeline can be divided in three main steps: 1) secretome prediction, 2) functional analysis, and 3) expression analysis.</p

Additional file 1: of Genome-wide comparative analysis of putative Pth11-related G protein-coupled receptors in fungi belonging to Pezizomycotina

Chromosomal distribution of putative F. graminearum Pth11-related GPCR genes. Chromosome numbers are shown at the top of the chromosomes. (TIFF 39 kb