title: A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein.
abstract: BACKGROUND
  Effector proteins are translocated into host cells by plant-pathogens to undermine pattern-triggered immunity (PTI), the plant response to microbe-associated molecular patterns that interferes with the infection process. Individual effectors are found in variable repertoires where some constituents target the same pathways. The effector protein AvrPto from Pseudomonas syringae has a core domain (CD) and C-terminal domain (CTD) that each promotes bacterial growth and virulence in tomato. The individual contributions of each domain and whether they act redundantly is unknown.
  
  
  RESULTS
  We use RNA-Seq to elucidate the contribution of the CD and CTD to the suppression of PTI in tomato leaves 6 h after inoculation. Unexpectedly, each domain alters transcript levels of essentially the same genes but to a different degree. This difference, when quantified, reveals that although targeting the same host genes, the two domains act synergistically. AvrPto has a relatively greater effect on genes whose expression is suppressed during PTI, and the effect on these genes appears to be diminished by saturation.
  
  
  CONCLUSIONS
  RNA-Seq profiles can be used to observe relative contributions of effector subdomains to PTI suppression. Our analysis shows the CD and CTD multiplicatively affect the same gene transcript levels with a greater relative impact on genes whose expression is suppressed during PTI. The higher degree of up-regulation versus down-regulation during PTI is plausibly an evolutionary adaptation against effectors that target immune signaling.
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853-1801, USA. jnw29@cornell.edu.
authors.forename: Jay N
authors.identifier: http://orcid.org/0000-0002-5923-1159
authors.initials: JN
authors.lastname: Worley
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853-1801, USA.
authors.forename: Marina A
authors.initials: MA
authors.lastname: Pombo
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853-1801, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853-1801, USA.
authors.forename: Diane M
authors.initials: DM
authors.lastname: Dunham
authors.affiliation: Institute of Biotechnology, Cornell University, Ithaca, NY, 14853-1801, USA.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Myers
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853-1801, USA.
authors.forename: Zhangjun
authors.initials: Z
authors.lastname: Fei
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853-1801, USA. gbm7@cornell.edu.|Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853-1801, USA. gbm7@cornell.edu.
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Martin
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D015536:Down-Regulation; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000235:genetics* / Q000382:microbiology; D010935:Plant Diseases / Q000382:microbiology*; D057865:Plant Immunity / Q000235:genetics*; D044224:Pseudomonas syringae / Q000472:pathogenicity*; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D015854:Up-Regulation
chemical_list: D001426:Bacterial Proteins; C081695:avrPto protein, Pseudomonas syringae
keywords: Pattern-triggered immunity; Plant immunity; Pseudomonas syringae; RNA-Seq; Type III effectors