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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOLOGY AND MANAGEMENT OF SOILBORNE DISEASES OF HORTICULTURAL CROPS

Location: Horticultural Crops Research

Title: Mining Genomes of Biological Control Strains of Pseudomonas spp.: Unexpected Gems and Tailings

Authors
item Kidarsa, Teresa
item Hassan, K -
item Henkels, Marcella
item Shaffer, Brenda
item Gross, H -
item Allen, A -
item Paulsen, I -
item Loper, Joyce

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: March 25, 2010
Publication Date: June 7, 2010
Citation: Kidarsa, T.A., Hassan, K., Henkels, M.D., Shaffer, B.T., Gross, H., Allen, A., Paulsen, I.T., Loper, J.E. 2010. Mining Genomes of Biological Control Strains of Pseudomonas spp.: Unexpected Gems and Tailings. 12th International Conference on Plant-Pathogenic Bacteria Program Book. p.106.

Technical Abstract: The biocontrol bacterium Pseudomonas fluorescens Pf-5 suppresses numerous soilborne plant diseases and produces an array of structurally-characterized secondary metabolites that are toxic to plant pathogenic bacteria, fungi and Oomycetes. Biosynthetic gene clusters for these metabolites compose nearly 6% of the genome and are located in lineage-specific regions absent from the genomes of other sequenced strains of Pseudomonas spp. (1). Orphan gene clusters coding for the biosynthesis of unknown natural products have also been identified in lineage-specific regions of the Pf-5 genome. Combined bioinformatic, genetic, and chemical analyses were used to identify the products encoded by some of these regions as the novel cyclic lipopeptide orfamide A, which lyses zoospores produced by phytopathogenic Phytophthora spp.; the FitD insect toxin, which contributes to the newly-discovered insecticidal activity of Pf-5; and several analogs of rhizoxin, a macrocyclic lactone with antifungal activity (2). In addition, orphan gene clusters expressed under the control of the global regulators GacA, RpoS and PtsP have been identified via transcriptome analysis of Pf-5, demonstrating the value of global-regulator-based genome mining as an approach to decipher the secondary metabolome of Pseudomonas spp. (3). Through these combined approaches, we have discovered novel secondary metabolites and gained new insights into the biology of Pf-5. Recently, we obtained draft genomic sequences of seven other biocontrol strains of Pseudomonas spp., and are employing comparative genomic analyses to expand our understanding of their secondary metabolomes and interactions with plant pathogens.These approaches are providing a new view of the metabolic activity of this biological control bacterium, its perception of the microhabitat it occupies on seed surfaces, and its interactions with target pathogens.

Last Modified: 4/17/2014
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