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Background  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). To date, relatively little is known about the regulatory genetic network of LP biosynthesis.    Results  This 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.    Conclusions  Combining 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 material  The online version of this article (doi:10.1186/s12866-015-0367-y) contains supplementary material, which is available to authorized users.

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