PPI logo P. s. pv. tomato DC3000 P. s. pv. phaseolicola 1448A
Systems Biology and Gene Expression Modeling

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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):

Stodghill, Paul - Acting Research Leader Swingle, Bryan - Molecular Biologist
Cartinhour, Samuel - Lead Scientist Filiatrault, Melanie - Molecular Biologist
Kochian, Leon - Center Director Chris Myers - Computational Biology Service Unit, Cornell University

Selected Publications:

Filiatrault et al, 2011. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000.. PMID: 22216251

Markel et al, 2011. An ECF sigma factor mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores. PMID: 21840980

Butcher et al, 2011. Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000. PMID: 21784947

Filiatrault et al, 2010. Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity. PMID: 20190049

Associated changes to the Pto DC3000 annotation record:

qualifier change significance
/experiment ="RNA sequencing" denotes loci coinciding with sequenced transcripts
/experiment="peptide sequencing" denotes loci coinciding with sequenced peptides
/inference="ab initio prediction:Easygene 1.2" denotes locus predictions made by Easygene
/note="see PMID:20190049 for expression data"
denotes source publication for inference and experiment data
/product="protein of unknown function" denotes previously hypothetical proteins for which expression has been confirmed
/product="conserved protein of unknown function" denotes previously conserved hypothetical proteins for which expression has been confirmed

Annotation changes affect 3015 CDS features. For further details on these changes and annotation of 29 ncRNA features, see the Pto DC3000 chromosomal annotation updates log

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

 

 

 


Magdalen Lindeberg
PPI Project Coordinator
Dept Plant Pathology
Cornell University
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