title: Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii.
abstract: The beet cyst nematode Heterodera schachtii is an important pathogen worldwide, but its molecular characterization has been limited to studying individual genes of interest. We undertook a high-throughput genomic approach and drastically increased the number of available sequences for this parasite. A total of 2,662 expressed sequence tags were grouped into 1,212 clusters representing a nonredundant catalog of H. schachtii genes. Implementing a bioinformatic workflow, we identified 50 sequences coding for candidate secreted proteins. All of these contain a putative signal peptide required for entry into the secretory pathway and lack any transmembrane domain. Included are previously postulated cell-wall-degrading enzymes and other parasitism-related genes. Moreover, we provide the first report of an arabinogalactan endo-1,4-beta-galactosidase enzyme (EC 3.2.1.89) in animals. As sequence data increase at a rapid rate, developing high-throughput genomic screening is a necessity. The in silico approach described here is an effective way to identify putative secreted proteins and prioritize candidates for further studies.
authors.affiliation: Molecular Biotechnology Department, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium.
authors.forename: Bartel
authors.initials: B
authors.lastname: Vanholme
authors.forename: Makedonka
authors.initials: M
authors.lastname: Mitreva
authors.forename: Wim
authors.initials: W
authors.lastname: Van Criekinge
authors.forename: Marc
authors.initials: M
authors.lastname: Logghe
authors.forename: David
authors.initials: D
authors.lastname: Bird
authors.forename: James P
authors.initials: JP
authors.lastname: McCarter
authors.forename: Godelieve
authors.initials: G
authors.lastname: Gheysen
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D020451:Contig Mapping; D018509:DNA, Helminth / Q000737:chemistry / Q000235:genetics*; D020224:Expressed Sequence Tags; D015723:Gene Library; D006026:Glycoside Hydrolases / Q000737:chemistry / Q000235:genetics; D015801:Helminth Proteins / Q000235:genetics*; D010944:Plants / Q000469:parasitology*; D021382:Protein Sorting Signals / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D014431:Tylenchoidea / Q000235:genetics*
chemical_list: D018509:DNA, Helminth; D015801:Helminth Proteins; D021382:Protein Sorting Signals; D006026:Glycoside Hydrolases; C094192:arabinogalactan endo-1,4-beta-galactosidase