title: Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Hernan G
authors.initials: HG
authors.lastname: Rosli
authors.forename: Yi
authors.initials: Y
authors.lastname: Zheng
authors.forename: Marina A
authors.initials: MA
authors.lastname: Pombo
authors.forename: Silin
authors.initials: S
authors.lastname: Zhong
authors.forename: Aureliano
authors.initials: A
authors.lastname: Bombarely
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.forename: Alan
authors.initials: A
authors.lastname: Collmer
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Martin
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D002473:Cell Wall / Q000201:enzymology; D019143:Evolution, Molecular; D005408:Flagellin / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D018551:Solanum lycopersicum / Q000166:cytology / Q000235:genetics / Q000276:immunology* / Q000382:microbiology; D010802:Phylogeny; D010935:Plant Diseases / Q000276:immunology / Q000382:microbiology; D057865:Plant Immunity; D010940:Plant Proteins / Q000235:genetics*; D011494:Protein Kinases / Q000235:genetics*; D011550:Pseudomonas aeruginosa / Q000378:metabolism*; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D001426:Bacterial Proteins; D010940:Plant Proteins; C081695:avrPto protein, Pseudomonas syringae; D005408:Flagellin; D011494:Protein Kinases