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Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii

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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-β-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.

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Abbreviations

aa:

amino acid

BLAST:

basic local alignment search tool

CBD:

cellulose-binding domain

CBP:

cellulose-binding protein

cDNA:

complementary DNA

EST:

expressed sequence tag

HMM:

hidden Markov model

J2:

second stage juvenile

NN:

neural network

nt:

nucleotides

ORF:

open reading frame

SL:

spliced leader

SP:

signal peptide

SPIT:

secreted proteins identified from tags

SPW:

standard pore water

TM:

transmembrane

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Acknowledgments

We thank Claire Murphy and Mike Dante for their role in library generation and technical support. H. schachtii EST sequencing was supported by a US National Science Foundation Plant Genome Award 0077503 to D.B. of North Carolina State University and Sandra Clifton of Washington University. Research at Ghent University was supported by the European Union (NONEMA EC, QLT-CT 1999-01501) and the Fund for Scientific Research-Flanders.

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Authors and Affiliations

  1. Molecular Biotechnology Department, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium

    Bartel Vanholme, Wim Van Criekinge & Godelieve Gheysen

  2. Department of Genetics, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO, 63108, USA

    Makedonka Mitreva & James P. McCarter

  3. DEVGEN NV, Technologiepark 9, 9052, Zwijnaarde-Gent, Belgium

    Marc Logghe

  4. Center for the Biology of Nematode Parasitism, North Carolina State University, Box 7253, Raleigh, NC 27695, USA

    David Bird

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  1. Bartel Vanholme
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  2. Makedonka Mitreva
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  3. Wim Van Criekinge
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  4. Marc Logghe
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  5. David Bird
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  6. James P. McCarter
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  7. Godelieve Gheysen
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Corresponding author

Correspondence to Godelieve Gheysen.

Appendix

Appendix

Description of additional data files

All nucleotide sequence data have been submitted to the Genbank dbEST database. The sequences and programs (Perl script) can be freely downloaded from http://www.MolecularBiotechnology.ugent.be/publications/Vanholme2005B

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Vanholme, B., Mitreva, M., Van Criekinge, W. et al. Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii . Parasitol Res 98, 414–424 (2006). https://doi.org/10.1007/s00436-005-0029-3

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