Progress 09/15/01 to 09/14/06
Outputs
From the genomic sequence of Pf-5, we discovered three gene clusters encoding for unknown natural products. The genomisotopic approach, which employs a combination of genomic sequence analysis and isotope guided fractionation to identify unknown compounds, was developed to identify the natural product from one of these gene clusters. In collaboration with a team of chemists from Oregon State University and the Scripps Institute of Oceanography, we used the genomisotopic approach to isolate and characterize the natural product Orfamide A, which is the founding member of a new class of cyclic lipopeptides. Orfamide A production by strain Pf-5 was shown to play a key role in motility of the bacterium and lysis of zoospores of a phytopathogenic Phytophthora sp.
Impacts
The genomic sequence of Pseudomonas fluorescens includes gene clusters for the biosynthesis of unknown natural products, which potentially have biological activities useful in agriculture or medicine. These natural products represent an untapped resource that can now be explored through a combination of genomics and natural products chemistry.
Publications
- Loper, J.E., Kobayashi, D.Y., and Paulsen, I.T. 2007. The genomic sequence of Pseudomonas fluorescens Pf-5: Insights into biological control. Phytopathology 97:233-238.
- Gross, H., Stockwell, V.O., Henkels, M.D., Nowak-Thompson, B., Loper, J.E., and Gerwick, W.H. 2007. The Genomisotopic Approach: A Systematic Method to Isolate Products of Orphan Biosynthetic Gene Clusters. Chemistry and Biology 14: 53-64.
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Progress 01/01/05 to 12/31/05
Outputs
Manual annotation of the genomic sequence of the biological control organism Pseudomonas fluorescens Pf-5 was completed. A manuscript describing the genomic sequence was written and published. Three gene clusters encoding for unknown secondary metabolites were discovered in the Pf-5 genome based upon their similarity to known non-ribosomal peptide synthetases or polyketide synthases. One of the three secondary metabolites, whose chemical structure was predicted from the sequence of biosynthetic genes in the Pf-5 genome, was purified and identified as a novel lipopeptide.
Impacts
Pseudomonas fluorescens Pf-5 is the first biological control agent for plant disease whose genomic sequence is published. Knowledge of this genomic sequence will pave the way for future research evaluating how biological control agents suppress plant diseases. Understanding biological control will promote the development of new ways to combat plant diseases without the use of pesticides.
Publications
- Brodhagen, M., Paulsen, I. T., and Loper, J. E. 2005. Reciprocal regulation of pyoluteorin production with membrane transporter gene expression in Pseudomonas fluorescens Pf-5. Appl. Environ. Microbiol. 71:6900-6909.
- Paulsen, I. T., Press, C. M., Ravel, J., Kobayashi, D. Y., Myers, G. S. 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., Schneider, D. J., Cartinhour, S. W., Nelson, W. C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E. A., Pierson, L. S., III, Thomashow, L. S. and Loper, J. E. 2005. Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature Biotechnology 23: 873-878.
- Loper, J.E. 2005. The genomic sequence of Pseudomonas fluorescens Pf-5: Insights into biological control. Phytopathology 95:S144.
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Progress 01/01/04 to 12/31/04
Outputs
The entire genome of the biological control organism Pseudomonas fluorescens Pf-5 was sequenced. The genome of Pf-5 is estimated at 7.1 Megabases, which is larger than genomes of other Pseudomonas spp. that have been sequenced to date. Of the 6147 putative genes in the Pf-5 genome, 681 have no homologs in the genomes of other Pseudomonas whose genome sequences are known (P. syringae, P. putida, and P. aeruginosa). The total lengths of known and putative gene clusters encoding for antibiotic or siderophore biosynthesis is estimated at ca. 400 kb, representing approximately 5.7% of the genome. Genes known to contribute to biological control of Pf-5 are distributed throughout the genome. Numerous genes encoding outer-membrane receptors for siderophores or other iron-uptake systems are found in the genome of Pf-5, suggesting the importance of iron-acquisition in the ecology of this bacterium. Oligonucleotides representing the 6147 genes in the Pf-5 genome were designed
for use in a microarray of the bacterium. Currently, the genome is being annotated manually to assign functions to genes in the genome of Pf-5.
Impacts
This project contributes to efforts to improve agriculture by enhancing biologically-based pest management strategies. Knowledge of the genomic sequence of the biological control agent Pseudomonas fluorescens Pf-5 will pave the way for future research evaluating how biological control agents suppress plant diseases. Understanding biological control will promote the development of new ways to combat plant diseases without the use of pesticides.
Publications
- No publications reported this period
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Progress 01/01/03 to 12/31/03
Outputs
The entire genome of the biological control organism Pseudomonas fluorescens Pf-5 was sequenced. The genome of Pf-5 is estimated at 7.1 Megabases, which is larger than genomes of other Pseudomonas spp. that have been sequenced to date. As expected from the spectrum of antibiotics produced by Pf-5, many biosynthetic gene clusters for secondary metabolite production are present in the genome. Genes known to contribute to biological control of Pf-5 are distributed throughout the genome. Numerous genes encoding outer-membrane receptors for siderophores or other iron-uptake systems are found in the genome of Pf-5, suggesting the importance of iron-acquisition in the ecology of this bacterium. A low density microarray of Pf-5 was established to evaluate factors influencing the expression of genes required for biological control of plant diseases by this bacterium. Currently, the genome is being annotated to assign functions to genes in the genome of Pf-5.
Impacts
This project contributes to efforts to improve agriculture by enhancing biologically-based pest management strategies. Knowledge of the genomic sequence of the biological control agent Pseudomonas fluorescens Pf-5 will pave the way for future research evaluating how biological control agents suppress plant diseases. Understanding biological control will promote the development of new ways to combat plant diseases without the use of pesticides.
Publications
- Loper, J. E., Paulsen, I., Thomashow, L., Pierson, L.S., Kobayashi, D., Pierson, E., Press, C., Mavrodi, D., Reddy, R. 2003. Genomics of Pseudomonas fluorescens Pf-5: insights into biological control. Phytopathology 93:S108
- Press, C. M. Brodhagen, M., and Loper, J.E. 2003. Gene expression profiles of the biocontrol agent Pseudomonas fluorescens Pf-5 assessed using oligonucleotide arrays. Phytopathology 93:S72
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Progress 01/01/02 to 12/31/02
Outputs
A draft sequence (8X) of the genome of Pseudomonas fluorescens strain Pf-5 has been obtained. The current estimate of total genome size is 7.27 Mb, and there are currently 34 physical gaps and 192 sequencing gaps in the assembled sequence data. A workshop was held at The Institute for Genomic Research to train seven collaborators on use of bioinformatics software for annotation and analysis of the genomic sequence. Sequencing efforts are continuing with the goal of closure of the genome.
Impacts
The whole genomic sequence of the biological control agent Pseudomonas fluorescens Pf-5 will be identified. This will pave the way for future research evaluating how biological control agents suppress plant diseases. Understanding biological control will promote the development of new ways to combat plant diseases without the use of pesticides.
Publications
- No publications reported this period
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Progress 09/15/01 to 03/20/02
Outputs
Funds were received on March 19, 2002, and accounts are being established to allow the work to begin
Impacts
The whole genomic sequence of the biological control agent Pseudomonas fluorescens Pf-5 will be identified. This will pave the way for future research evaluating how biological control agents suppress plant diseases. Understanding biological control will promote the development of new ways to combat plant diseases without the use of pesticides.
Publications
- No publications reported this period
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