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

Abstract

BackgroundMicrobe-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.ResultsWe 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.ConclusionsOur 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.

Quantitative Peptidomics Study Reveals That a Wound-Induced Peptide from PR-1 Regulates Immune Signaling in Tomato

“…In Figure 6B, the flg22 highly induced WRKY TRANSCRIPTION FACTOR53 (WRKY53) expression but not PR-1b in tomato. This result was consistent with the public RNA-seq data in the Tomato Functional Genomics Database (Fei et al, 2011), which are based on the experiment "transcriptome sequencing of tomato leaves treated with different bacteria and PAMPs" (Rosli et al, 2013). The RNA-seq data showed that WRKY53 could be induced but PR-1b, Adi3, and ERF5, but could not be significantly induced using 30 min or 6 h treatment of flg22 on the tomato.…”

Comparative study of salt stress-induced physiological and molecular responses in tomato (Solanum lycopersicum L.)

“…For this we exploited RNAseq data for different organs (Tomato Genome Consortium, 2012); treatment with the flg28 elicitor (Rosli et al, 2013); challenge with the fungal pathogen Cladosporium fulvum (Ilyas et al, 2015); and infection with the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (PtoDC3000, Rosli et al, 2013).…”

“…For this we exploited RNAseq data for different organs (Tomato Genome Consortium, 2012); treatment with the flg28 elicitor (Rosli et al, 2013); challenge with the fungal pathogen Cladosporium fulvum (Ilyas et al, 2015); and infection with the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (PtoDC3000, Rosli et al, 2013). As expected for subunits that assemble in stoichiometric complexes, transcript levels of each of the β subunit genes are very similar, with the exception of β2a transcripts, which accumulate 5-10-fold lower when compared to β2b and the other β subunit-encoding transcripts (Fig.29).…”

“…(B) Transcript levels of β subunit-encoding genes in tomato leaves upon treatment with and without flg28. These data were extracted from Rosli et al, (2013). 4-week old tomato plants were infiltrated with and without 1 µM flg28 and RNA was extracted from infected leaves six hours later.…”

“…tomato DC3000. These data were extracted from Rosli et al, (2013). 4-week old tomato plants were infiltrated with and without 5 x 106 bacteria/mL PtoDC3000 and RNA was extracted from infected leaves six hours later.…”