PPI logo P. s. pv. tomato DC3000 P. s. pv.phaseolicola 1448A
Pto DC3000 - Project Background

DC3000 home

project background

about Pto DC3000

genome properties

tools for genome analysis

Hop database & nomenclature

ongoing annotation

related links

site map

The Pseudomonas-Plant Interaction Project originated with a proposal by a group of investigators, headed by Dr. Alan Collmer at Cornell University, to determine the genome sequence of P. syringae pv tomato DC3000 and begin exploration of the functional genomics of its interaction with the host plant tomato. P. syringae pv tomato DC3000 was chosen because it is the cause of bacterial speck on tomato and Arabidopsis and because is is an important experimental model in molecular plant pathology. Initial funding was provided by the NSF Plant Genome Research Program grant DBI-0077622. (read entire proposal)

Project Objectives:

  • complete sequencing of the DC3000 genome
  • systematic identification of virulence factors
  • cell biological based analyses of DC3000-tomato interactions
  • creation of a Plant-Microbe Interaction Database
  • genomics oriented educational outreach

Achieving these objectives has been greatly aided by collaboration with the USDA-ARS-CAB modelling project at Cornell University


Alan Collmer (PI) Cornell University, Ithaca, NY [website]
James R. Alfano (co-PI)

University of Nebraska, Lincoln, NE [website]

C. Robin Buell (co-PI)
The Institute for Genomic Research, Rockville, MD [website]
Samuel W. Cartinhour (co-PI)
Cornell University, Ithaca, NY [website]
Arun K. Chatterjee (co-PI)
University of Missouri, Columbia, MO [website]
Sondra G. Lazarowitz (co-PI)
Cornell University, Ithaca, NY[website]
Gregory B. Martin (co-PI) Cornell University, Ithaca, NY [website]
Xiaoyan Tang (co-PI)
Kansas State University, Manhattan, KS [website]

Research funded by NSF-PGRP DBI-0077622

Lindeberg, M. et al, 2006. Closing the circle on the discovery of genes encoding Hrp regulon members and type III secretion system effectors in the genomes of three model Pseudomonas syringae strains. MPMI 19:1151-1158.

Schechter, L. M., et al. 2006. Multiple approaches to a complete inventory of Pseudomonas syringae pv tomato DC3000 type III secretion system effector proteins MPMI 19:1180-1192.

Vencato, M., et al., 2006. Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A. MPMI 19:1193-1206.

Ferreira, A. et al.,2006. Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv tomato DC3000 allows de novo reconstruction of the Hrp cis element, and identifies novel co-regulated genes. MPMI 19:1167-1179.

Oh, H. S. and Collmer, A. 2005. Basal resistance against bacteria in Nicotiana benthamiana leaves is accompanied by reduced vascular staining and suppressed by multiple Pseudomonas syringae type III secretion system effector proteins. Plant J. 44:348-59.

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 187:6488-6498.

Guo, M., et al. 2005. Pseudomonas syringae type III chaperones ShcO1, ShcS1, and ShcS2 facilitate translocation of their cognate effectors and can substitute for each other in the secretion of HopO1-1. J Bacteriol 187(12): 4257-69.

Lindeberg, M., et al. 2005. Proposed guidelines for a unified nomenclature and phylogenetic analysis of type III Hop effector proteins in the plant pathogen Pseudomonas syringae. Mol. Plant Microbe Interact. 18: 275-282.

Joardar, et al. 2005. Lineage-specific regions in Pseudomonas syringae pv. tomato DC3000. Mol. Plant Path. 6:53 ( see also supplementary material text, Table S1, Table S2, Table S3, Fig S1)

Petnicki-Ocwieja, T., et al. 2005. The hrpK operon of Pseudomonas syringae pv. tomato DC3000 encodes two proteins secreted by the type III (Hrp) protein secretion system: HopB1 and HrpK, a putative type III translocator. J Bacteriol 187(2): 649-63.

Lin and Martin, 2005. An avrPto/avrPtoB Mutant of Pseudomonas syringae pv. tomato DC3000 does not elicit Pto-mediated resistance and is less virulent on tomato. Mol Plant Microbe Interact. 18:43-51

Espinosa, A. and Alfano, J. R. 2004. Disabling surveillance: bacterial type III secretion system effectors that suppress innate immunity. Cell Microbiol 6(11): 1027-40.

Lopez-Solanilla, et al. 2004. HopPtoN is a Pseudomonas syringae Hrp (type III secretion system) cysteine protease effector that suppresses pathogen-induced necrosis associated with both compatible and incompatible plant interactions. Mol. Microbiol. 54:1365-2958.

Wehling, M. D. et al. 2004. The Pseudomonas syringae HopPtoV Protein Is Secreted in Culture and Translocated into Plant Cells via the Type III Protein Secretion System in a Manner Dependent on the ShcV Type III Chaperone. J. Bacteriol. 186: 3621-3630.

He, P., et al. 2004. Activation of a COI1-dependent pathway in Arabidopsis by Pseudomonas syringae type III effectors and coronatine. Plant J 37(4): 589-602.

Jamir, et al. 2004a. Identification of Pseudomonas syringae type III effectors that can suppress programmed cell death in plants and yeast. Plant J. 37:554-565.

Jamir, et al. 2004b. The genome of Pseudomonas syringae pv. tomato DC3000 and functional genomic studies to better understand plant pathogenesis. Pages 113-138 in.: Pseudomonas, Volume 1: Genomics, LifeStyle and Molecular Architecture. J. L. Ramos, ed. Kluwer/Plenum, London.

Shan, et al. 2004. The HopPtoF locus of Pseudomonas syringae pv. tomato DC3000 encodes a type III chaperone and cognate effector. Mol. Plant-Microbe. Interact. 17:447-455

D'Ascenzo et al. 2004. PeerGAD: a peer-review-based and community-centric web application for viewing and annotating prokaryotic genome sequences. Nucl. Acids. Res. 32:3124-3135.

Schechter, et al. 2004. Pseudomonas syringae Type III secretion system targeting signals and novel effectors studied with a Cya translocation reporter. J. Bacteriol. 186:543-555

Alfano and Collmer, 2004. Type III secretion system effector proteins: Double agents in bacterial disease and plant defense. Ann Rev. Phytopath. 42:385-414

Alfano and Guo, 2003. The Pseudomonas syringae Hrp (type III_ protein secretion system: Advances in the new millenium. Pages 227-258 in: Plant-Microbe Interactions, Vol 6. G. Stacey and N. T. Keen, ed. APS Press, St. Paul.

Chatterjee, et al. 2003. GacA, the response regulator of a two-component system, acts as a master regulator in Pseudomonas syringae pv tomato DC3000 by controlling regulatory RNA, transcriptional activators, and alternate sigma factors. Mol. Plant Microbe Interact. 16:1106-1117.

Buell, et al. 2003. The complete sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci 100:10181-10186. (see also supporting text, supporting Table 2, Table 3, Table 4, Table 5, Table 6, Fig 4, Fig 5, Fig 6)

Badel, et al. 2003. Pseudomonas syringae pv tomato DC3000 HopPtoM (CEL :ORF3) is a major factor in tomato and is secreted and translocated by the Hrp type III secretion system in a chaperone dependent manner. Mol Microbiol. 49:1239-1251.

Espinosa, 2003. The Pseudomonas syringae type III-secreted protein HopPtoD2 possesses protein tyrosine phosphatase activity and suppresses programmed cell death in plants. Mol Microbiol. 49:377-387.

Deng, W. L., et al. 2003. Pseudomonas syringae exchangeable effector loci: sequence diversity in representative pathovars and virulence function in P. syringae pv. syringae B728a. J Bacteriol 185(8): 2592-602.

Abramovitch, 2003. Pseudomonas type III effector AvrPtoB induces plant disease susceptibility by inhibition of host programmed cell death EMBO J. 22:60-69

Collmer, et al. 2002. Genomic mining type III secretion system effectors in Pseudomonas syringae yields new picks for all TTSS prospectors. Trends in Microbiol. 10:462-469

Kim, et al. 2002. Two distinct Pseudomonas effector proteins interact with the Pto kinase and activate plant immunity. Cell 73: 589-598

Petnicki-Ocwieja, 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. 99:7652-7657 (see also supporting Table3, Table4, text)

Fouts, et al. 2002. Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc. Natl. Acad. Sci. 99:2275-2280. (see also supporting info)