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PMID: 12840044 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Validation Study

EST mining and functional expression assays identify extracellular effector proteins from the plant pathogen Phytophthora.

Genome research ·Vol. 13 ·No. 7 ·2003-07-00 ·Pages 1675-85

Torto TA, Li S, Styer A, Huitema E, Testa A, Gow NA, van West P, Kamoun S

Abstract

Plant pathogenic microbes have the remarkable ability to manipulate biochemical, physiological, and morphological processes in their host plants. These manipulations are achieved through a diverse array of effector molecules that can either promote infection or trigger defense responses. We describe a general functional genomics approach aimed at identifying extracellular effector proteins from plant pathogenic microorganisms by combining data mining of expressed sequence tags (ESTs) with virus-based high-throughput functional expression assays in plants. PexFinder, an algorithm for automated identification of extracellular proteins from EST data sets, was developed and applied to 2147 ESTs from the oomycete plant pathogen Phytophthora infestans. The program identified 261 ESTs (12.2%) corresponding to a set of 142 nonredundant Pex (Phytophthora extracellular protein) cDNAs. Of these, 78 (55%) Pex cDNAs were novel with no significant matches in public databases. Validation of PexFinder was performed using proteomic analysis of secreted protein of P. infestans. To identify which of the Pex cDNAs encode effector proteins that manipulate plant processes, high-throughput functional expression assays in plants were performed on 63 of the identified cDNAs using an Agrobacterium tumefaciens binary vector carrying the potato virus X (PVX) genome. This led to the discovery of two novel necrosis-inducing cDNAs, crn1 and crn2, encoding extracellular proteins that belong to a large and complex protein family in Phytophthora. Further characterization of the crn genes indicated that they are both expressed in P. infestans during colonization of the host plant tomato and that crn2 induced defense-response genes in tomato. Our results indicate that combining data mining using PexFinder with PVX-based functional assays can facilitate the discovery of novel pathogen effector proteins. In principle, this strategy can be applied to a variety of eukaryotic plant pathogens, including oomycetes, fungi, and nematodes.

MeSH Terms
Algal Proteins/biosynthesis,genetics,physiology Algorithms Amino Acid Sequence/genetics Caenorhabditis elegans Proteins DNA, Complementary/biosynthesis,genetics,physiology Endodeoxyribonucleases Expressed Sequence Tags Gene Expression Profiling/methods Lycopersicon esculentum/genetics,microbiology Molecular Sequence Data Multigene Family/genetics Necrosis Phenotype Phytophthora/genetics,growth & development,pathogenicity Plant Diseases/genetics,microbiology Proteomics/methods Software Validation Virulence
Chemicals
Algal Proteins Caenorhabditis elegans Proteins DNA, Complementary CRN-1 protein, C elegans Endodeoxyribonucleases
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Torto Trudy A
Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster, Ohio 44691, USA.
Li Shuang
Styer Allison
Huitema Edgar
Testa Antonino
Gow Neil A R
van West Pieter
Kamoun Sophien
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.910003
Published
2003-07-00
Pages
1675-85
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC403741
Subset
IM
Databases
GENBANK
AF424638, AF424639, AF424640, AF424641, AF424642, AF424643, AF424644, AF424645, AF424646, AF424647, AF424648, AF424649, AF424650, AF424651, AF424652, AF424653, AF424654, AF424655, AF424656, AF424657, AF424658, AF424659, AF424660, AF424661, AF424662, AF424663, AF424664, AF424665, AF424666, AF424667, AF424668, AF424669, AF424670, AF424671, AF424672, AF424673, AF424674, AF424675, AF424676, AF424677, AF424678, AF424679, AF424680, AF424681, AF424682, AF424683, AF424684, AF424685, AF424686, AF424687, AF424688, AF424689, AF424690
External Links
PubMed source DOI: 10.1101/gr.910003 PMC Full Text View journal details
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