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 Plant, Soil and Nutrition Research: Ithaca, NY
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                        Robert W. Holley Center for Agriculture & Health
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ARS Home Northeast Area Ithaca, New York Robert W. Holley Center for Agriculture & Health Plant, Soil and Nutrition Research Docs





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Computational Models for Gene Control Networks in Pseudomonas syringaeheadline bar 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 scientistsSam CartinhourDave SchneiderPostdoctoral fellowsPhil BronsteinBryan SwingleTechnicians and support staffGenevieve DeClerckDeepti TheteCollaboratorsChris Myers (Theory Center, Cornell University)Alan Collmer (Plant Pathology, Cornell University)Kelvin Lee (Chemical Engineering, Cornell University)Michael Shuler (Chemical Engineering, Cornell University)Matt DeLisa (Chemical Engineering, Cornell University)Jim Alfano (Plant Pathology, Univ. of Nebraska)Joyce Loper (USDA ARS, Corvallis OR)Carol Bender (Entomology and Plant Pathology, Oklahoma State Univ.) Research projects Promoter trapping with overexpression of sigma factorsTransposon mutagenesis and reporter screens for monitoring environmental responsesCharacterizing 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 enzymesMEROPS peptidase database(Sanger Centre)SUPERFAMILYrepairGenes (Centre for Molecular Biology and Neuroscience, Norway)Transporter proteins in Pseudomonas syringae pv. tomato DC3000 (TIGR)*Pseudomonas aeruginosa* projectOak Ridge National Laboratory(DOE)Swiss Institute for BioinformaticsBioinformatics and computational biology EMBOSSNCBI C++ toolkitHMMerWebLogoBioPythonBioSQLSloppyCell


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