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Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity

Hernan G Rosli12, Yi Zheng1, Marina A Pombo1, Silin Zhong13, Aureliano Bombarely1, Zhangjun Fei1, Alan Collmer45 and Gregory B Martin145*

Author Affiliations

1 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA

2 Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús (IIB-INTECH) UNSAM-CONICET, Chascomús B7130IWA, Buenos Aires, Argentina

3 School of Life Sciences, The Chinese University of Hong Kong, NT, Hong Kong

4 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA

5 Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia

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Genome Biology 2013, 14:R139  doi:10.1186/gb-2013-14-12-r139

Published: 20 December 2013



Microbe-associated molecular patterns, such as those present in bacterial flagellin, are powerful inducers of the innate immune response in plants. Successful pathogens deliver virulence proteins, termed effectors, into the plant cell where they can interfere with the immune response and promote disease. Engineering the plant immune system to enhance disease resistance requires a thorough understanding of its components.


We describe a high-throughput screen, using RNA sequencing and virus-induced gene silencing, to identify tomato genes whose expression is enhanced by the flagellin microbe-associated molecular pattern flgII-28, but reduced by activities of the Pseudomonas syringae pv. tomato (Pst) type III effectors AvrPto and AvrPtoB. Gene ontology terms for this category of Flagellin-induced repressed by effectors (FIRE) genes showed enrichment for genes encoding certain subfamilies of protein kinases and transcription factors. At least 25 of the FIRE genes have been implicated previously in plant immunity. Of the 92 protein kinase-encoding FIRE genes, 33 were subjected to virus-induced gene silencing and their involvement in pattern-triggered immunity was tested with a leaf-based assay. Silencing of one FIRE gene, which encodes the cell wall-associated kinase SlWAK1, compromised the plant immune response resulting in increased growth of Pst and enhanced disease symptoms.


Our transcriptomic approach identifies FIRE genes that represent a pathogen-defined core set of immune-related genes. The analysis of this set of candidate genes led to the discovery of a cell wall-associated kinase that participates in plant defense. The FIRE genes will be useful for further elucidation of the plant immune system.