Submitted to: European Journal of Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2007
Publication Date: 11/1/2007
Citation: Loper, J.E., Gross, H. 2007. Genomic analysis of antifungal metabolite production by Pseudomonas fluorescens Pf-5. European Journal of Plant Pathology. 119:265-278. Interpretive Summary: The entire genome of Pseudomonas fluorescens Pf-5, a biological control agent that lives on plant roots, was sequenced to completion recently. In this article, we describe regions of the genome that are responsible for the production of antibiotics that are toxic to soil fungi that cause plant diseases. Four of the regions have been described before in Pf-5 or other bacteria, but in this article we describe the DNA surrounding those known regions and point out new genes that are also likely to contribute to antibiotic production. We also describe a new region that we discovered in the genome and explain the process we used to identify a new antibiotic that is synthesized from DNA in that region. This new antibiotic is in a new class of compounds that are toxic to plant pathogens in a group of soil organisms called Oomycetes. This new antibiotic is the first to be identified by mining the genome of Pf-5 and the first novel compound to be identified by mining the genome of any Pseudomonas spp.
Technical Abstract: The complete genomic sequences of several Pseudomonas spp. that inhabit the rhizosphere are now available, providing a new opportunity to advance knowledge of plant-growth promoting rhizobacteria through genomics. Among these is the biological control bacterium Pseudomonas fluorescens Pf-5. Nearly 6% of the 7.07 Mb genome of Pf-5 is devoted to the biosynthesis of secondary metabolites, including four antibiotics toxic to soilborne fungi and Oomycetes that infect plant roots and two siderophores involved in iron acquisition. Three orphan gene clusters, for which the encoded natural product was unknown, also were identified in the genome of Pf-5. The product synthesized from one of the orphan gene clusters was identified using a new 'genomisotopic approach', which employs a combination of genomic sequence analysis and isotope guided fractionation. Application of the genomisotopic approach to one orphan gene cluster in Pf-5 resulted in the discovery of orfamide A, founder of a new group of bioactive cyclic lipopeptides with a putative role in biological control of plant disease