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Impact of Type III effectors on plant defense responses

Experiment Name: Impact of Type III effectors on plant defense responses
Accession No. & GeneChip: AT13, ATH1-121501
Submitter: Experimenter: Marta de Torres Zabala, submitted by Lishuang Shen
Experiment Type: normal vs. diseased comparison
time course
Experiment Factor: compound
time
Number of Replicates: 4
Quality Control Steps: biological replicates
Quality Control Description: Quality Control Measures Taken: no-plants-pooled 4 leaves/plant; 18 plants/time point.
Publication_id: None
Last Update Time: 2004-06-10 09:37:57
Expression Data
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Description: This experiment submission is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database (http://ssbdjc2.nottingham.ac.uk/narrays/experimentbrowse.pl). The data was generated from NASC's Affymetrix service and offered for public access at BarleyBase.

If you publish with this data, please reference data from NASC/GARNet:

Craigon DJ., James N., Okyere J., Higgins J., Jotham J., May S.
NASCArrays: A repository for Microarray Data generated by NASC's Transcriptomics Service.
Nucleic Acids Research, (2004). volume 32, Database issue D575-D577.

Following is the original experiment description:

About the Experimenter
Name: Dr Marta de Torres Zabala
Head of Lab Name: Dr Murray Grant
Address: Department of Agricultural Sciences, Imperial College at Wye, Wye
Postcode: TN25 5AH
Country: UK
Telephone Number: 02075942883
Fax Number: 02075942640

Experiment Type: gene_overexpression; time_course; normal_diseased;
Experimental Parameters:
Quality Control Measures Taken: no-plants-pooled 4 leaves/plant; 18 plants/time point.

Experiment: Impact of Type III effectors on plant defense responses
Experiment Description:
Our interest lie in how plants respond to bacterial pathogens. Over the past three years we have identified and documented reproducible, landmark biochemical and molecular events following challenge of Arabidopsis with the phytopathogenic enterobacteria P. syringae. Significantly, our studies revealed 60% of cDNA-AFLP differentials not present on the 8,200 feature GeneChips and 20% absent from public EST databases (de Torres in press). We now seek to exploit this background using carefully defined time-points to analyse global changes in the Arabidopsis transcriptome using challenges selected to define gene targets implicated in (i) expression of basal immunity (ii) the establishment of successful parasitism (resistance) by a virulent pathogen (host). The results will provide a rationale for future functional assays of the identified pathways using transgenic knockouts and mutant analyses. Additionally, data will provide underpinning support for comparative proteomics of the defense response currently in progress with GARNet support using the same experimental parameters (BBSRC 32/P14635).

We propose the following treatments:

(i) Mock vs. DC3000hrpA @ 60 min: 60 minutes is subsequent to host immediate-early stress responses and will catalogue the innate responses induced by pathogen associated molecular patterns. The hrpA lesion will ensure no type III effectors influence transcriptional responses. Gene products induced at this time are predicted to potentiate latter host responses (2 treatments X 3 biological replicates = 6 chips).

(ii) Mock vs. DC3000 vs. DC3000hrpA vs. DC3000::avrRpm1 @ 4 hours: A key time point previously defined where no macroscopic symptoms are visible but significant differences exist between compatible and incompatible interactions at the molecular and physiological levels. These treatments will serve to define the earliest genes induced by the complement of DC3000 type III effector and will specifically define genes/pathways suppressed by virulence factors in addition to those implicated in orchestration of the hypersensitive cell death. We will also include an incompatible interaction on a transgenic line expressing an RPM1 interacting protein, which fails to mount an HR but exhibits hyper-resistance. We predict this challenge will separate the resistance response (pathogen restriction) from that associated with hypersensitive cell death (5 treatments X 3 biological replicates = 15 chips).

(iii) Mock vs. DC3000 vs. DC3000hrpA @ 14 hours: At 10 h before phenotypes are apparent in the DC3000 background, Type III effector delivery is well advanced and impact on host transcription maximal (3 treatments X 3 biological replicates = 9 chips).
Providers:
Name: Dr Marta de Torres Zabala
Institution: Department of Agricultural Sciences Imperial College at Wye Wye
Head of Laborotary: Dr Murray Grant
email:
Homepage:

 
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