Submitted to: Pseudomonas
Publication Type: Book / Chapter
Publication Acceptance Date: 10/25/2006
Publication Date: 7/2/2007
Citation: Mavrodi, D.V., Paulsen, I.T., Ren, Q., Loper, J.E. 2007. Genomics of Pseudomonas Fluorescens Pf-5. In: Ramos, J.L., Filloux, A., editors. Pseudomonas, A Model System in Biology. Springer, The Netherlands. p.3-30. Interpretive Summary: This article compares the genome sequences of bacteria in the genus Pseudomonas. We found that only 40% of the genes are shared among the four species of Pseudomonas whose genomes have been sequenced to date. Pseudomonas fluorescens Pf-5 is a biological control agent that suppresses plant diseases. Its genomic sequence was compared to those of two other strains of P. fluorescens, and only 60% of the genes are shared among the three strains. These results are important because they highlight the unique characteristics of strains of Pseudomonas that contribute to biological control of plant diseases. Genes unique to Pf-5, and lacking in other strains or species of Pseudomonas, are clustered in the genome and are responsible for traits such as antibiotic production, which are important in biological control. Genomics is providing new insight into the diversity of environmental microorganisms and the traits important in biological control.
Technical Abstract: Three complete genomic sequences for five species of Pseudomonas and three strains of Pseudomonas fluorescens are now available. Comparisons of the genomic sequences highlight the diversity of the genus, as well as among strains of P. fluorescens. This chapter focuses on Pf-5, a rhizosphere bacterium that suppresses seedling emergence diseases and produces a spectrum of antibiotics toxic to plant pathogenic fungi and Oomycetes. Genes unique to Pf-5, and absent from the genomes of other Pseudomonas spp., are not randomly distributed throughout the genome of Pf-5, but are present in clusters. These clusters of unique genes confer functions such as secondary metabolite biosynthesis and bacteriophages. One cluster contains a 115-kbp mobile genomic island, PFGI-1, which resembles a large self-transmissible plasmid capable of site-specific integration into one of the two tRNALys genes. PFGI-1 is the first large MGE of this kind found in P. fluorescens. As expected for a bacterium with a large genome that lives in a rapidly changing environment, Pf-5 has an extensive collection of regulatory genes, including 32 sigma factors, 27 of which are in the extracytoplasmic factor class of sigma factors. A phylogenetic analysis of these sigma factors indicates that 20 are involved in iron acquisition, being linked to TonB receptors or siderophore biosynthesis genes.