Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP.

Chunxu Song,Jos M Raaijmakers,Gustav Sundqvist,Erik Malm,Irene De Bruijn,Judith Van De Mortel,Vincent Bulone,Aundy Kumar

doi:10.1186/s12866-015-0367-y

Abstract

BackgroundLipopeptides (LP) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities. In Pseudomonas and other bacterial genera, LP biosynthesis is governed by large multimodular nonribosomal peptide synthetases (NRPS). To date, relatively little is known about the regulatory genetic network of LP biosynthesis.ResultsThis study provides evidence that the chaperone ClpA, together with the serine protease ClpP, regulates the biosynthesis of the LP massetolide in Pseudomonas fluorescens SS101. Whole-genome transcriptome analyses of clpA and clpP mutants showed their involvement in the transcription of the NRPS genes massABC and the transcriptional regulator massAR. In addition, transcription of genes associated with cell wall and membrane biogenesis, energy production and conversion, amino acid transport and metabolism, and pilus assembly were altered by mutations in clpA and clpP. Proteome analysis allowed the identification of additional cellular changes associated to clpA and clpP mutations. The expression of proteins of the citrate cycle and the heat shock proteins DnaK and DnaJ were particularly affected. Combined with previous findings, these results suggest that the ClpAP complex regulates massetolide biosynthesis via the pathway-specific, LuxR-type regulator MassAR, the heat shock proteins DnaK and DnaJ, and proteins of the TCA cycle.ConclusionsCombining transcriptome and proteome analyses provided new insights into the regulation of LP biosynthesis in P. fluorescens and led to the identification of specific missing links in the regulatory pathways.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0367-y) contains supplementary material, which is available to authorized users.

Highlights

Lipopeptides (LP) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities
LP biosynthesis is governed by large multi-modular nonribosomal peptide synthetases (NRPS) via a thiotemplate
Together with the serine protease ClpP, it plays an important role in intracellular refolding and degradation of proteins, an essential process for the viability and growth of cells

Summary

Introduction

Lipopeptides (LP) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities. In Pseudomonas and other bacterial genera, LP biosynthesis is governed by large multimodular nonribosomal peptide synthetases (NRPS). Lipopeptides (LPs) are biosurfactants produced by a variety of bacterial genera, including Pseudomonas and Bacillus [1,2]. To identify the genetic networks underlying regulation of massetolide biosynthesis, P. fluorescens strain SS101 was subjected to random mutagenesis. Library of approximately 7,500 random plasposon mutants resulted in the identification of four new regulatory genes, namely phgdh, dnaK, prtR and clpA [10]. In this recent study, we focused our functional analyses on phgdh, dnaK and prtR, but not on clpA. The aims of the present study were to i) study the role of ClpA in regulation of massetolide biosynthesis, and ii) analyse the ClpA regulon at the transcriptional and proteome level in order to narrow down the role of ClpP in regulating massetolide biosynthesis

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