Carbohydrate-active enzymes in pythium and their role in plant cell wall and storage polysaccharide degradation.

Marcelo M Zerillo,Bishwo N Adhikari,C André Lévesque,C Robin Buell,John P Hamilton,Ned Tisserat,Olivier Lespinet

doi:10.1371/journal.pone.0072572

Abstract

Carbohydrate-active enzymes (CAZymes) are involved in the metabolism of glycoconjugates, oligosaccharides, and polysaccharides and, in the case of plant pathogens, in the degradation of the host cell wall and storage compounds. We performed an in silico analysis of CAZymes predicted from the genomes of seven Pythium species (Py. aphanidermatum, Py. arrhenomanes, Py. irregulare, Py. iwayamai, Py. ultimum var. ultimum, Py. ultimum var. sporangiiferum and Py. vexans) using the “CAZymes Analysis Toolkit” and “Database for Automated Carbohydrate-active Enzyme Annotation” and compared them to previously published oomycete genomes. Growth of Pythium spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. The in silico analyses, coupled with our in vitro growth assays, suggest that most of the predicted CAZymes are involved in the metabolism of the oomycete cell wall with starch and sucrose serving as the main carbohydrate sources for growth of these plant pathogens. The genomes of Pythium spp. also encode pectinases and cellulases that facilitate degradation of the plant cell wall and are important in hyphal penetration; however, the species examined in this study lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source. Genes encoding for xylan, xyloglucan, (galacto)(gluco)mannan and cutin degradation were absent or infrequent in Pythium spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among Pythium spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.

Highlights

Oomycetes are part of the Stramenopiles and the supergroup Chromalveolates which likely originated from a biflagellate ancestor containing a red algal symbiont [1,2]
In the companion paper published simultaneously in this issue, we described a comparative analysis of the genomes of seven Pythium spp., Py. aphanidermatum (Pyap), Py. arrhenomanes (Pyar), Py. irregulare (Pyir), Py. iwayamai (Pyiw), Py. ultimum var. ultimum (Pyuu), Py. ultimum var. sporangiiferum (Pyus), and Py. vexans (Pyve), with other plant pathogenic oomycetes and two diatoms in order to understand key genes and mechanisms involved in plant pathogenesis and necrotrophy in Pythium spp. (Adhikari, et al companion paper, PLoS One, this issue)
Pythium species were distributed in two clades: one comprising Pyve which is closely related to Phytophthora, and the other containing two subclades, one of globose sporangial species (Pyus, Pyuu, Pyiw and Pyir), and one with filamentous sporangial species (Pyar and Pyap) (Fig. 1)

Summary

Introduction

Oomycetes (subphylum or class Oomycota) are part of the Stramenopiles and the supergroup Chromalveolates which likely originated from a biflagellate ancestor containing a red algal symbiont [1,2]. The genomes of six phytopathogenic species belonging to the peronosporalean lineage have been sequenced and annotated, including four species of the hemibiotroph Phytophthora Species belonging to clade K fit better in the description of the new genus Phytopythium than Pythium [15,18,19] and further taxonomic revisions within the genus are likely to be necessary [20]. Pythium spp. are biologically diverse and occupy different niches as saprophytes and as parasites of plants, fungi and animals [21,22], including humans [23]. Phytopathogenic Pythium species are primarily necrotrophs that cause seed, root and fruit rots in a diverse range of species [21]

Methods

Results

Conclusion