title: Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds.
abstract: The plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. Previously, we isolated Pseudomonas sp. SH-C52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen Rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (Mendes et al., 2011). To get more insight into its biosynthetic repertoire, the genome of Pseudomonas sp. SH-C52 was sequenced and subjected to in silico, mutational and functional analyses. The sequencing revealed a genome size of 6.3 Mb and 5579 predicted ORFs. Phylogenetic analysis placed strain SH-C52 within the Pseudomonas corrugata clade. In silico analysis for secondary metabolites revealed a total of six non-ribosomal peptide synthetase (NRPS) gene clusters, including the two previously described NRPS clusters for thanamycin and the 2-amino acid antibacterial lipopeptide brabantamide. Here we show that thanamycin also has activity against an array of other fungi and that brabantamide A exhibits anti-oomycete activity and affects phospholipases of the late blight pathogen Phytophthora infestans. Most notably, mass spectrometry led to the discovery of a third lipopeptide, designated thanapeptin, with a 22-amino-acid peptide moiety. Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans. Of the remaining four NRPS clusters, one was predicted to encode for yet another and unknown lipopeptide with a predicted peptide moiety of 8-amino acids. Collectively, these results show an enormous metabolic potential for Pseudomonas sp. SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.
authors.affiliation: Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands.
authors.forename: Menno
authors.initials: M
authors.lastname: Van Der Voort
authors.affiliation: Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands.
authors.forename: Harold J G
authors.initials: HJ
authors.lastname: Meijer
authors.affiliation: Institute for Pharmaceutical Biology, University of Bonn Bonn, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Schmidt
authors.affiliation: Departments of Pharmacology and Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego San Diego, CA, USA.
authors.forename: Jeramie
authors.initials: J
authors.lastname: Watrous
authors.affiliation: Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands.
authors.forename: Ester
authors.initials: E
authors.lastname: Dekkers
authors.affiliation: Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands ; Brazilian Agricultural Research Corporation, Embrapa Environment Jaguariuna, Brazil.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Mendes
authors.affiliation: Departments of Pharmacology and Chemistry and Biochemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego San Diego, CA, USA.
authors.forename: Pieter C
authors.initials: PC
authors.lastname: Dorrestein
authors.affiliation: Department of Pharmaceutical Biology, Pharmaceutical Institute, University of Tübingen Tübingen, Germany.
authors.forename: Harald
authors.initials: H
authors.lastname: Gross
authors.affiliation: Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands ; Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, Netherlands.
authors.forename: Jos M
authors.initials: JM
authors.lastname: Raaijmakers
keywords: Pseudomonads; antimicrobial peptides; beneficial microbes; biocontrol; genome sequencing; mass spectrometry; rhizosphere bacteria