COMPLETE GENOME SEQUENCE OF THE PLANT COMMENSAL PSEUDOMONAS FLUORESCENS PF-5: INSIGHTS INTO THE BIOLOGICAL CONTROL OF PLANT DISEASE.

Authors: PAULSEN, I - INSTITUTE OF GENOMICS; Press, Caroline; RAVEL, J - INSTITUTE OF GENOMICS; KOBAYASHI, D - DEPT OF PLANT-RUTGERS; MYERS, G.S. - INSTITUTE OF GENOMICS; MAVRODI, D - WASHINGTON STATE UNIV.; DEBOY, R - INSTITUTE OF GENOMICS; SESHADRI, R - INSTITUTE OF GENOMICS; REN, Q - INSTITUTE OF GENOMICS; MADUPU, R - INSTITUTE OF GENOMICS; DODSON, R - INSTITUTE OF GENOMICS; DURKIN, A - INSTITUTE OF GENOMICS; BRINKAC, L - INSTITUTE OF GENOMICS; DAUGHERTY, S - INSTITUTE OF GENOMICS; SULLIVAN, S - INSTITUTE OF GENOMICS; ROSOVITZ, M - INSTITUTE OF GENOMICS; GWINN, M - INSTITUTE OF GENOMICS; ZHOU, L - INSTITUTE OF GENOMICS; NELSON, W - INSTITUTE OF GENOMICS; WEIDMAN, J - INSTITUTE OF GENOMICS; WATKINS, K - INSTITUTE OF GENOMICS; TRAN, K - INSTITUTE OF GENOMICS; KHOURI, H - INSTITUTE OF GENOMICS; PIERSON, E - UNIV. OF ARIZONA; PIERSON III, L - UNIV OF ARIZONA; Thomashow, Linda; Loper, Joyce

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2005
Publication Date: 5/20/2005
Citation: Paulsen, I.T., Press, C.M., Ravel, J., Kobayashi, D.Y., Myers, G.A., Mavrodi, D.V., Deboy, R.T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R.J., Durkin, A.S., Brinkac, L.M., Daugherty, S.C., Sullivan, S.A., Rosovitz, M.J., Gwinn, M.L., Zhou, L., Nelson, W.C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E.A., Pierson Iii, L.S., Thomashow, L.S., Loper, J.E. 2005. Complete genome sequence of the plant commensal pseudomonas fluorescens pf-5: insights into the biological control of plant disease. Nature Biotechnology. 23:873:878

Interpretive Summary: Root diseases caused by soilborne pathogens are major yield-limiting factors in the production of food, fiber and ornamental crops. Trends in agriculture toward greater sustainability and less dependence on synthetic fungicides have created a need for more ecologically sound methods of disease control. Biological control, which exploits the natural antagonistic activity of certain root-colonizing bacteria against fungal pathogens, is one such approach. In this study, the DNA sequence of the entire genome of the biocontrol agent Pseudomonas fluorescens Pf-5 was determined. The sequence provides many insights into the lifestyle and biocontrol capabilities of this organism. The Pf-5 genome is larger than genomes of other species of Pseudomonas that have been sequenced. The size is due in part to the presence of large segments of DNA that encode many novel genes for the synthesis of antibiotics and other antifungal factors that contribute to the superior biocontrol activity of the strain. At least some of these DNA segments may have been acquired by gene transfer from other strains or species of bacteria. The study identified numerous genes that contribute to the ability of Pf-5 to colonize plants, as well as genes for the synthesis of previously undetected compounds that may contribute to the ability of Pf-5 to antagonize plant pathogens. The complete genome sequence of Pf-5 provides a framework for future studies to understand the biological basis of biocontrol.

Technical Abstract: Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and its production of a range of antibiotics and secondary metabolites provides the capability to suppress a number of plant diseases caused by soilborne plant pathogens. The complete sequence of the 7.1 Mb genome of this biological control agent was determined. Analysis of repeat sequences in the genome provided a novel approach for identifying genomic islands that together with more traditional approaches, suggested that recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. A number of features were identified which contribute to its commensal lifestyle on plants including broad catabolic and transport capabilities enabling the utilization of plant-derived compounds, the apparent ability to utilize a diversity of iron siderophores, an array of detoxification systems to protect from oxidative stress, and the lack of a Type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by Pf-5, three novel secondary metabolite biosynthesis gene clusters were identified that may contribute to the biocontrol properties of Pf-5, and structural features of the putative compounds were deduced from genomic analysis.