In silico comparative analysis of tylenchid nematode pectate lyases

Phytoparasitic nematodes can infect a wide range of crop plants, and cause billions of dollars of agricultural losses each year. These parasites represent the largest source of biotic stress experienced by plants. The order Tylenchida comprises the most important parasitic nematodes, particularly the root-knot and cyst nematodes. These parasitic organisms obtain nutrients to support their development through complex interactions with their hosts. Plant-parasitic nematodes secrete a mixture of cell-wall degrading enzymes to facilitate migration through the plant root. Enzymes are secreted that degrade the principal cell-wall components, cellulose, hemi-cellulose, or pectin. Pectate lyases are important parasitism factors in plant-parasitic nematodes. These enzymes degrade polygalacturonic acid, which is a fundamental constituent of pectin of host cell walls. Thus, pectate lyases permit the penetration and colonization of plant host cells by parasites. Here, we analyzed 22 pectate lyase protein sequences from tylenchid nematode species. Our results revealed great variation in the isoelectric points of pectate lyases, and groups of acidic and alkaline proteins that may have distinct enzymatic activities were identified. Phylogenetic analysis also revealed the presence of two main groups of pectate lyases with distinct chemical properties. Seven conserved motifs were identified, but only five were present in all sequences. Results of the molecular docking analysis revealed differences in the predicted interaction sites in the pectate lyases from the two groups. These results may provide a theoretical basis for future studies of host plant resistance to nematode infection.