European Journal of Plant Pathology

, Volume 119, Issue 3, pp 265–278 | Cite as

Genomic analysis of antifungal metabolite production by Pseudomonas fluorescens Pf-5

Full Research Paper


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 (PGPR) 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 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 recently 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.


Cyanide Cyclic lipopeptides 2,4-Diacetylphloroglucinol Orphan gene clusters Pyrrolnitrin Pyoluteorin Mcf toxin 



cyclic lipopeptide



GI approach

genomisotopic approach


hydrogen cyanide


non-ribosomal peptide synthetase


Plant growth-promoting rhizobacteria


polyketide synthase


‘makes caterpillars floppy’



The Pf-5 genomic sequencing project was supported by Initiative for Future Agriculture and Food Systems Grant no. 2001-52100-11329 from the U.S. Department of Agriculture Cooperative State Research, Education, and Extension Service. Research in the Loper laboratory is funded by the U.S. Department of Agriculture, Agricultural Research Service CRIS project 5358-12220-002-00D. H.G. thanks the German Research Foundation for a Research Fellowship (GR 2673/1-1).


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Copyright information

© KNPV 2007

Authors and Affiliations

  1. 1.Horticultural Crops Research Laboratory, Agricultural Research ServiceUS Department of AgricultureCorvallisUSA
  2. 2.Institute for Pharmaceutical BiologyUniversity of BonnBonnGermany

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