A Domain-Centric Analysis of Oomycete Plant Pathogen Genomes Reveals Unique Protein Organization    

Abstract

Oomycetes comprise a diverse group of organisms that morphologically resemble fungi but belong to the stramenopile lineage within the supergroup of chromalveolates. Recent studies have shown that plant pathogenic oomycetes have expanded gene families that are possibly linked to their pathogenic lifestyle. We analyzed the protein domain organization of 67 eukaryotic species including four oomycete and five fungal plant pathogens. We detected 246 expanded domains in fungal and oomycete plant pathogens. The analysis of genes differentially expressed during infection revealed a significant enrichment of genes encoding expanded domains as well as signal peptides linking a substantial part of these genes to pathogenicity. Overrepresentation and clustering of domain abundance profiles revealed domains that might have important roles in hostpathogen interactions but, as yet, have not been linked to pathogenicity. The number of distinct domain combinations (bigrams) in oomycetes was significantly higher than in fungi. We identified 773 oomycete-specific bigrams, with the majority composed of domains common to eukaryotes. The analyses enabled us to link domain content to biological processes such as host-pathogen interaction, nutrient uptake, or suppression and elicitation of plant immune responses. Taken together, this study represents a comprehensive overview of the domain repertoire of fungal and oomycete plant pathogens and points to novel features like domain expansion and species-specific bigram types that could, at least partially, explain why oomycetes are such remarkable plant pathogens.

Characterization of the secretome of Plasmopara viticola by de novo transcriptome analysis

“…Table 4 shows that the relative number of apoplastic effectors identified in the P. viticola secretome is very similar to that predicted in the H. arabidopsidis genome [10]. The most prevalent domains identified were proteins containing glycosyl hydrolase and protease domains ( Table 4) in agreement with previous studies that have shown these two classes of highly abundant enzymes to be linked to pathogenicity in oomycetes [8,65].…”

Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis

“…Several plant-infecting oomycetes have large expansions of NLPs in their genomes (25)(26)(27), suggesting that these proteins play an important role in the pathogen's lifestyle. A clear virulence function was observed for NLP Pcc of the rot bacterium Pectobacterium carotovorum (27).…”

Profiling the Secretome and Extracellular Proteome of the Potato Late Blight Pathogen Phytophthora infestans

“…We could also identify five out of the seven berberine-like proteins encoded in the genome. These proteins that are involved in alkaloid biosynthesis and in the production of hydrogen peroxide through the oxidation of numerous metabolites (63), and they are thought to be important virulence factors induced during plant infection (17,64). Alternatively, these proteins might also protect Phytophthora from plant counter defenses.…”