Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species

Irene De Bruijn, Maarten J D de Kock, Meng Yang, Pieter de Waard, Teris A van Beek, Jos M Raaijmakers

Research output: Contribution to journalArticle

134 Citations (Scopus)

Abstract

Analysis of microbial genome sequences have revealed numerous genes involved in antibiotic biosynthesis. In Pseudomonads, several gene clusters encoding non-ribosomal peptide synthetases (NRPSs) were predicted to be involved in the synthesis of cyclic lipopeptide (CLP) antibiotics. Most of these predictions, however, are untested and the association between genome sequence and biological function of the predicted metabolite is lacking. Here we report the genome-based identification of previously unknown CLP gene clusters in plant pathogenic Pseudomonas syringae strains B728a and DC3000 and in plant beneficial Pseudomonas fluorescens Pf0-1 and SBW25. For P. fluorescens SBW25, a model strain in studying bacterial evolution and adaptation, the structure of the CLP with a predicted 9-amino acid peptide moiety was confirmed by chemical analyses. Mutagenesis confirmed that the three identified NRPS genes are essential for CLP synthesis in strain SBW25. CLP production was shown to play a key role in motility, biofilm formation and in activity of SBW25 against zoospores of Phytophthora infestans. This is the first time that an antimicrobial metabolite is identified from strain SBW25. The results indicate that genome mining may enable the discovery of unknown gene clusters and traits that are highly relevant in the lifestyle of plant beneficial and plant pathogenic bacteria.
Original languageEnglish
Pages (from-to)417-428
Number of pages12
JournalMolecular Microbiology
Volume63
Issue number2
Early online date21 Nov 2006
DOIs
Publication statusPublished - 1 Jan 2007

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Lipopeptides
Fourier Analysis
Pseudomonas
Genome
Anti-Bacterial Agents
Multigene Family
Peptide Synthases
Pseudomonas fluorescens
Microbial Genome
Phytophthora infestans
Pseudomonas syringae
Essential Genes
Biofilms
Mutagenesis
Life Style
Bacteria
Amino Acids
Peptides
Genes

Keywords

  • anti-bacterial agents
  • antibiosis
  • bacterial proteins
  • biofilms
  • computational biology
  • gene deletion
  • genome, bacterial
  • molecular structure
  • movement
  • multigene family
  • mutagenesis, insertional
  • peptides, cyclic
  • phytophthora
  • pseudomonas fluorescens
  • pseudomonas syringae
  • sequence analysis

Cite this

Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species. / De Bruijn, Irene; de Kock, Maarten J D; Yang, Meng; de Waard, Pieter; van Beek, Teris A; Raaijmakers, Jos M.

In: Molecular Microbiology, Vol. 63, No. 2, 01.01.2007, p. 417-428.

Research output: Contribution to journalArticle

De Bruijn, Irene ; de Kock, Maarten J D ; Yang, Meng ; de Waard, Pieter ; van Beek, Teris A ; Raaijmakers, Jos M. / Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species. In: Molecular Microbiology. 2007 ; Vol. 63, No. 2. pp. 417-428.
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