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Project Objectives:

• Identify promoters and ECF sigma factors that control expression of known and suspected virulence factors in Pseudomonas syringae.
• Characterize the subset of the transcriptome related to growth in defined medium, induction of virulence factors, and response to iron bioavailability
• Elucidate mechanisms leading to iron-dependent expression of operons encoding virulence factors and regulators.

This research employs an interdisciplinary approach involving computational biology and laboratory methods for high-throughput functional
genomics and genetics. Expression studies including the use of microarrays and high-throughput reporter screens are being used to
characterize the components and behavior of virulence-related pathways, especially those related to iron homeostasis.

Investigators (Plant-Micobe Interactions Research, USDA-ARS, Ithaca NY):

Schneider, David - Research Leader	Swingle, Bryan - Molecular Biologist	Stodghill, Paul - Physical Scientist
Cartinhour, Samuel - Molecular Biologist	Filiatrault, Melanie - Molecular Biologist	Chris Myers - Computational Biology Service Unit, Cornell University
Kochian, Leon - Center Director	Bronstein, Philip - Molecular Biologist

Research:

Swingle et al, 2008. Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals
regulon members and insights regarding PvdS function in other pseudomonads. PMID: 18363796

Associated resources:

PvdS box models (gff format, readable with Artemis) for pseudomonads with available genome sequences Go to View genomes in Artemis for instructions on viewing sequences of a specified accession number in Artemis
Aligned training sets for models A, B, C	Notes on file format

Organism/Entry	RefSeq Accession	PvdS box model
Pseudomonas syringae pv. tomato DC3000	NC_004578	PvdS_box_model_A_NC_004578
Pseudomonas syringae pv. tomato DC3000	NC_004578	PvdS_box_model_B_NC_004578
Pseudomonas syringae pv. tomato DC3000	NC_004578	PvdS_box_model_C_NC_004578
Pseudomonas syringae pv. tomato str. DC3000 plasmid pDC3000A	NC_004633	PvdS_box_model_B_NC_004633
Pseudomonas syringae pv. tomato str. DC3000 plasmid pDC3000A	NC_004633	PvdS_box_model_C_NC_004633
Pseudomonas syringae pv. tomato str. DC3000 plasmid pDC3000B	NC_004632	PvdS_box_model_A_NC_004632
Pseudomonas syringae pv. tomato str. DC3000 plasmid pDC3000B	NC_004632	PvdS_box_model_B_NC_004632
Pseudomonas syringae pv. tomato str. DC3000 plasmid pDC3000B	NC_004632	PvdS_box_model_C_NC_004632
Pseudomonas syringae pv. phaseolicola 1448A	NC_005773	PvdS_box_model_A_NC_005773
Pseudomonas syringae pv. phaseolicola 1448A	NC_005773	PvdS_box_model_B_NC_005773
Pseudomonas syringae pv. phaseolicola 1448A	NC_005773	PvdS_box_model_C_NC_005773
Pseudomonas syringae pv. phaseolicola 1448A large plasmid	NC_007274	PvdS_box_model_A_NC_007274
Pseudomonas syringae pv. phaseolicola 1448A large plasmid	NC_007274	PvdS_box_model_B_NC_007274
Pseudomonas syringae pv. phaseolicola 1448A large plasmid	NC_007274	PvdS_box_model_C_NC_007274
Pseudomonas syringae pv. phaseolicola 1448A small plasmid	NC_007275	PvdS_box_model_A_NC_007275
Pseudomonas syringae pv. phaseolicola 1448A small plasmid	NC_007275	PvdS_box_model_B_NC_007275
Pseudomonas syringae pv. phaseolicola 1448A small plasmid	NC_007275	PvdS_box_model_C_NC_007275
Pseudomonas syringae pv. syringae B728a	NC_007005	PvdS_box_model_A_NC_007005
Pseudomonas syringae pv. syringae B728a	NC_007005	PvdS_box_model_B_NC_007005
Pseudomonas syringae pv. syringae B728a	NC_007005	PvdS_box_model_C_NC_007005
Pseudomonas aeruginosa PAO1	NC_002516	PvdS_box_model_A_NC_002516
Pseudomonas aeruginosa PAO1	NC_002516	PvdS_box_model_B_NC_002516
Pseudomonas aeruginosa PAO1	NC_002516	PvdS_box_model_C_NC_002516
Pseudomonas aeruginosa UCBPP-PA14	NC_008463	PvdS_box_model_A_NC_008463
Pseudomonas aeruginosa UCBPP-PA14	NC_008463	PvdS_box_model_B_NC_008463
Pseudomonas aeruginosa UCBPP-PA14	NC_008463	PvdS_box_model_C_NC_008463
Pseudomonas aeruginosa PA7	NC_009656	PvdS_box_model_A_NC_009656
Pseudomonas aeruginosa PA7	NC_009656	PvdS_box_model_B_NC_009656
Pseudomonas aeruginosa PA7	NC_009656	PvdS_box_model_C_NC_009656
Pseudomonas fluorescens Pf-5	NC_004129	PvdS_box_model_A_NC_004129
Pseudomonas fluorescens Pf-5	NC_004129	PvdS_box_model_B_NC_004129
Pseudomonas fluorescens Pf-5	NC_004129	PvdS_box_model_C_NC_004129
Pseudomonas fluorescens PfO-1	NC_007492	PvdS_box_model_A_NC_007492
Pseudomonas fluorescens PfO-1	NC_007492	PvdS_box_model_B_NC_007492
Pseudomonas fluorescens PfO-1	NC_007492	PvdS_box_model_C_NC_007492
Pseudomonas putida KT2440	NC_002947	PvdS_box_model_A_NC_002947
Pseudomonas putida KT2440	NC_002947	PvdS_box_model_B_NC_002947
Pseudomonas putida KT2440	NC_002947	PvdS_box_model_C_NC_002947
Pseudomonas putida F1	NC_009512	PvdS_box_model_A_NC_009512
Pseudomonas putida F1	NC_009512	PvdS_box_model_B_NC_009512
Pseudomonas putida F1	NC_009512	PvdS_box_model_C_NC_009512
Pseudomonas entomophila L48	NC_008027	PvdS_box_model_A_NC_008027
Pseudomonas entomophila L48	NC_008027	PvdS_box_model_B_NC_008027
Pseudomonas entomophila L48	NC_008027	PvdS_box_model_C_NC_008027
Pseudomonas mendocina ymp	NC_009439	PvdS_box_model_A_NC_009439
Pseudomonas mendocina ymp	NC_009439	PvdS_box_model_B_NC_009439
Pseudomonas mendocina ymp	NC_009439	PvdS_box_model_C_NC_009439
Pseudomonas stutzeri A1501	NC_009434	PvdS_box_model_A_NC_009434
Pseudomonas stutzeri A1501	NC_009434	PvdS_box_model_B_NC_009434
Pseudomonas stutzeri A1501	NC_009434	PvdS_box_model_C_NC_009434