title: Transcriptomic analysis reveals tomato genes  whose expression is induced specifically during  effector-triggered immunity and identifies the  Epk1 protein kinase which is required for the host  response to three bacterial effector proteins.
abstract: BACKGROUND
  Plants have two related immune systems to defend themselves against pathogen attack. Initially,pattern-triggered immunity is activated upon recognition of microbe-associated molecular patterns by pattern recognition receptors. Pathogenic bacteria deliver effector proteins into the plant cell that interfere with this immune response and promote disease. However, some plants express resistance proteins that detect the presence of specific effectors leading to a robust defense response referred to as effector-triggered immunity. The interaction of tomato with Pseudomonas syringae pv. tomato is an established model system for understanding the molecular basis of these plant immune responses.
  
  
  RESULTS
  We apply high-throughput RNA sequencing to this pathosystem to identify genes whose expression changes specifically during pattern-triggered or effector-triggered immunity. We then develop reporter genes for each of these responses that will enable characterization of the host response to the large collection of P. s. pv. tomato strains that express different combinations of effectors. Virus-induced gene silencing of 30 of the effector-triggered immunity-specific genes identifies Epk1 which encodes a predicted protein kinase from a family previously unknown to be involved in immunity. Knocked-down expression of Epk1 compromises effector-triggered immunity triggered by three bacterial effectors but not by effectors from non-bacterial pathogens. Epistasis experiments indicate that Epk1 acts upstream of effector-triggered immunity-associated MAP kinase signaling.
  
  
  CONCLUSIONS
  Using RNA-seq technology we identify genes involved in specific immune responses. A functional genomics screen led to the discovery of Epk1, a novel predicted protein kinase required for plant defense activation upon recognition of three different bacterial effectors.
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, USA.
authors.forename: Marina A
authors.initials: MA
authors.lastname: Pombo
authors.forename: Yi
authors.initials: Y
authors.lastname: Zheng
authors.forename: Noe
authors.initials: N
authors.lastname: Fernandez-Pozo
authors.forename: Diane M
authors.initials: DM
authors.lastname: Dunham
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Martin
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D054884:Host-Pathogen Interactions / Q000235:genetics / Q000276:immunology; D018551:Solanum lycopersicum / Q000235:genetics* / Q000276:immunology / Q000378:metabolism; D020935:MAP Kinase Signaling System; D057865:Plant Immunity / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D011494:Protein Kinases / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D044224:Pseudomonas syringae / Q000502:physiology; D017423:Sequence Analysis, RNA
chemical_list: D010940:Plant Proteins; D011494:Protein Kinases