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

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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 (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.

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Abbreviations

CLP:

cyclic lipopeptide

DAPG:

2,4-diacetylphloroglucinol

GI approach:

genomisotopic approach

HCN:

hydrogen cyanide

NRPS:

non-ribosomal peptide synthetase

PGPR:

Plant growth-promoting rhizobacteria

PKS:

polyketide synthase

Mcf:

‘makes caterpillars floppy’

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Acknowledgements

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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  1. Horticultural Crops Research Laboratory, Agricultural Research Service, US Department of Agriculture, 3420 N.W. Orchard Ave., Corvallis, OR, USA

    Joyce E. Loper

  2. Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany

    Harald Gross

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Correspondence to Joyce E. Loper.

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Loper, J.E., Gross, H. Genomic analysis of antifungal metabolite production by Pseudomonas fluorescens Pf-5. Eur J Plant Pathol 119, 265–278 (2007). https://doi.org/10.1007/s10658-007-9179-8

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  • DOI: https://doi.org/10.1007/s10658-007-9179-8

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