| Computational Models for Gene Control Networks in Pseudomonas syringae |
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Our group uses a variety of laboratory and computational methods to study regulation of gene expression in an important bacterial plant pathogen, Pseudomonas syringae. The primary focus of our work is the DC3000 strain of the tomato pathovar that has the unique property of infecting both tomato and Arabidopsis thaliana, a model plant species with a fully sequenced genome. Since the DC3000 genome is also available [Buell et al, 2003], the DC3000-A. thaliana system is the ideal platform for studying the molecular basis of plant pathogenesis.
Our particular interest is a systems-level approach to molecular pathogenesis from the viewpoint of the pathogen -- how the bacteria senses its environment and responds to those stimuli. The genomic sequence of DC3000 is exploited to design integrated experimental methods and associated analytical techniques that shed light on systems-level behavior. For example, we employ genome-scale microarrays, promoter trapping, transposon reporter screens and shotgun proteomics to detect differential expression coupled with de novo motif identification methods such as Gibbs sampling to infer gene regulation networks and develop specific hypotheses regarding regulatory mechanisms.
Project Personnel
- Staff scientists
- Dave Schneider
- Postdoctoral fellows
- Phil Bronstein
- Bryan Swingle
- Technicians and support staff
- Genevieve DeClerck
- Deepti Thete
- Collaborators
Research projects
- Promoter trapping with overexpression of sigma factors
- Transposon mutagenesis and reporter screens for monitoring environmental responses
- Characterizing mutants and environmental responses using genome-scale proteomics.
Selected publications
Paulsen, I.T., et al (2005). Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5.
Nat Biotechnol. 2005 Jul;23(7):873-8.Joardar, V., et al (2005). Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.
J Bacteriol. 2005 Sep;187(18):6488-98.Buell, C.R., et al (2005). The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000.
Proc Natl Acad Sci U S A. 2003 Sep 2;100(18):10181-6.- Petnicki-Ocwieja, T., et al (2002). Genomewide identification of proteins secreted by the Hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000.
Proc Natl Acad Sci U S A. 2002 May 28;99(11):7652-7. - Fouts, D.E., et al (2002). Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor.
Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2275-80.
Interesting Links
- Biology
- Pseudomonas syringae pv. tomato project (Cornell University)
- Genetics of the Pathogen-Host Interaction in Snap Bean, Tomato and Potato(USDA ARS, Madison WI)
- Ecology and Physiology of Pseudomonas syringae (review article)
- Plant pathogens: Signalling complexities for Pseudomonas(review article)
- Pseudomonas and related bacteria (Todar's Online Textbook of Bacteriology)
- Pathogen profiles (Oxford University)
- Genome resources
- Comprehensive Microbial Resource (TIGR)
- NCBI (National Institutes of Health)
- Center for Biological Sequence Analysis (Technical University of Denmark)
- Biocyc (SRI)
- KEGG (Kyoto University)
- Carbohydrate active enzymes
- MEROPS peptidase database (Sanger Centre)
- SUPERFAMILY
- repairGenes (Centre for Molecular Biology and Neuroscience, Norway)
- Transporter proteins in Pseudomonas syringae pv. tomato DC3000 (TIGR)
- Pseudomonas aeruginosa project
- Oak Ridge National Laboratory (DOE)
- Swiss Institute for Bioinformatics
- Bioinformatics and computational biology
