title: Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000.
abstract: Transcriptional reprogramming is integral to effective plant defense. Pathogen effectors act transcriptionally and posttranscriptionally to suppress defense responses. A major challenge to understanding disease and defense responses is discriminating between transcriptional reprogramming associated with microbial-associated molecular pattern (MAMP)-triggered immunity (MTI) and that orchestrated by effectors. A high-resolution time course of genome-wide expression changes following challenge with Pseudomonas syringae pv tomato DC3000 and the nonpathogenic mutant strain DC3000hrpA- allowed us to establish causal links between the activities of pathogen effectors and suppression of MTI and infer with high confidence a range of processes specifically targeted by effectors. Analysis of this information-rich data set with a range of computational tools provided insights into the earliest transcriptional events triggered by effector delivery, regulatory mechanisms recruited, and biological processes targeted. We show that the majority of genes contributing to disease or defense are induced within 6 h postinfection, significantly before pathogen multiplication. Suppression of chloroplast-associated genes is a rapid MAMP-triggered defense response, and suppression of genes involved in chromatin assembly and induction of ubiquitin-related genes coincide with pathogen-induced abscisic acid accumulation. Specific combinations of promoter motifs are engaged in fine-tuning the MTI response and active transcriptional suppression at specific promoter configurations by P. syringae.
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Laura A
authors.initials: LA
authors.lastname: Lewis
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Krzysztof
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authors.lastname: Polanski
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.
authors.forename: Marta
authors.initials: M
authors.lastname: de Torres-Zabala
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.
authors.forename: Siddharth
authors.identifier: http://orcid.org/0000-0003-1524-2232
authors.initials: S
authors.lastname: Jayaraman
authors.affiliation: School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Laura
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authors.lastname: Bowden
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Jonathan
authors.identifier: http://orcid.org/0000-0002-5486-0407
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authors.lastname: Moore
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Christopher A
authors.identifier: http://orcid.org/0000-0001-5823-4705
authors.initials: CA
authors.lastname: Penfold
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Dafyd J
authors.initials: DJ
authors.lastname: Jenkins
authors.affiliation: School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Claire
authors.initials: C
authors.lastname: Hill
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Laura
authors.initials: L
authors.lastname: Baxter
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.
authors.forename: Satish
authors.identifier: http://orcid.org/0000-0001-6132-8868
authors.initials: S
authors.lastname: Kulasekaran
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.
authors.forename: William
authors.initials: W
authors.lastname: Truman
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.
authors.forename: George
authors.identifier: http://orcid.org/0000-0002-8768-2598
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authors.lastname: Littlejohn
authors.affiliation: School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Justyna
authors.initials: J
authors.lastname: Prusinska
authors.affiliation: School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Andrew
authors.identifier: http://orcid.org/0000-0002-4909-8235
authors.initials: A
authors.lastname: Mead
authors.affiliation: School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Jens
authors.identifier: http://orcid.org/0000-0003-1008-2268
authors.initials: J
authors.lastname: Steinbrenner
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Richard
authors.initials: R
authors.lastname: Hickman
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: David
authors.identifier: http://orcid.org/0000-0002-2217-3274
authors.initials: D
authors.lastname: Rand
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: David L
authors.initials: DL
authors.lastname: Wild
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Sascha
authors.initials: S
authors.lastname: Ott
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Vicky
authors.initials: V
authors.lastname: Buchanan-Wollaston
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom.
authors.forename: Nick
authors.identifier: http://orcid.org/0000-0001-5630-5602
authors.initials: N
authors.lastname: Smirnoff
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Jim
authors.initials: J
authors.lastname: Beynon
authors.affiliation: Warwick Systems Biology Centre, University of Warwick, Warwick CV4 7AL, United Kingdom School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom.
authors.forename: Katherine
authors.identifier: http://orcid.org/0000-0002-7857-6814
authors.initials: K
authors.lastname: Denby
authors.affiliation: Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom m.r.grant@exeter.ac.uk.
authors.forename: Murray
authors.identifier: http://orcid.org/0000-0003-3357-0264
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authors.lastname: Grant
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000276:immunology* / Q000382:microbiology; D001483:Base Sequence; D002843:Chromatin / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D007165:Immunosuppression Therapy; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs / Q000235:genetics; D000069452:Pathogen-Associated Molecular Pattern Molecules / Q000378:metabolism*; D010935:Plant Diseases / Q000235:genetics / Q000276:immunology / Q000382:microbiology; D057865:Plant Immunity / Q000235:genetics*; D018515:Plant Leaves / Q000235:genetics / Q000276:immunology* / Q000382:microbiology; D011401:Promoter Regions, Genetic / Q000235:genetics; D044224:Pseudomonas syringae / Q000254:growth & development / Q000502:physiology*; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D000069452:Pathogen-Associated Molecular Pattern Molecules; D014157:Transcription Factors