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

PLoS One. 2013 Sep 12;8(9):e72572. doi: 10.1371/journal.pone.0072572. eCollection 2013.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Wall / metabolism*
  • Plant Cells / enzymology*
  • Polysaccharides / metabolism*
  • Pythium / enzymology*

Substances

  • Polysaccharides

Grants and funding

Funding for the work was provided by a grant to CRB and NT by the USDA National Research Initiative Cooperative State Research Extension Education Service (grant 2006-55605-16645), USDA National Institute of Food and Agriculture Microbial Genome Sequencing Program (2007-35600-17774 and 2007-35600-18886). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.