Genome-mining approaches for the evaluation of Pseudomonas protegens and related strains isolated from the rhizosphere in Japan

Root-colonizing fluorescent pseudomonads, represented by Pseudomonas protegens, produce a number of anti-biotic secondary metabolites and extracellular enzymes that contribute to the suppression of pathogens in the rhizosphere. An antibiotic exoproduct that is commonly produced by P. protegens and related strains is 2,4-diac-etylphloroglucinol (DAPG). We recently screened and characterized DAPG-producing strains among ca. 3000 fluorescent pseudomonads isolated from samples collected in the field in Japan. The genome data obtained will provide insights into the characteristics of novel factor(s) contributing to the antibiotic activities of newly iso-lated strain(s). DAPG-producing strains were subjected to a comparative genomic analysis, and the results ob-tained showed the accumulation of strain-specific genomic repertoires for the biosynthesis of secondary metabolites that prevent soil-borne diseases. Exoproduct expression levels were dependent on the Gac/Rsm signal transduction pathway, indicating the conservation of this mechanism in these strains. We herein propose a number of strategies to control these useful strains by promoting this signal transduction pathway in the rhizosphere.