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Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds.

Van Der Voort M, Meijer HJ, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM - Front Microbiol (2015)

Bottom Line: 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.SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands.

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.

No MeSH data available.


Related in: MedlinePlus

Antagonistic activity of Pseudomonas sp. SH-C52. Wild-type (WT) and the thanamycin mutant strains (ThaB, ThaC2) were tested in dual culture assays for activity against fungal plant pathogens (upper panel) and oomycete plant pathogens (lower panel).
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Figure 3: Antagonistic activity of Pseudomonas sp. SH-C52. Wild-type (WT) and the thanamycin mutant strains (ThaB, ThaC2) were tested in dual culture assays for activity against fungal plant pathogens (upper panel) and oomycete plant pathogens (lower panel).

Mentions: Based on mutant analysis, the thanamycin gene cluster was shown to be important for the growth-inhibitory activity of strain SH-C52 against Rhizoctonia solani (Mendes et al., 2011). The thanamycin gene cluster shows similarity to a fragmented NRPS gene cluster in P. corrugata CFBP5454 (Figure 2), but the incomplete and scattered P. corrugata sequences complicate a clear comparison between the thanamycin and cormycin gene clusters. Alignments of the thanamycin NRPSs and the annotated parts of cormycin NRPSs show 85–97% protein identity. To test the antimicrobial activity-spectrum of thanamycin, wild type SH-C52 and two thanamycin biosynthesis mutants (Mendes et al., 2011) were tested for activity against fungi, oomycetes and bacteria. Here, we show that the activity spectrum of thanamycin is not exclusive for R. solani, but extends to an array of other fungi (Figure 3) and the Gram-positive bacterium Bacillus megaterium (data not shown). Also cormycin has been shown to be active against B. megaterium and the yeast Rhodotorula pilimanae (Scaloni et al., 2004). In contrast, thanamycin has little activity against oomycete pathogens (Figure 3) and the Gram-negative bacteria Pseudomonas syringae and Pectobacterium atrosepticum (data not shown).


Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds.

Van Der Voort M, Meijer HJ, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM - Front Microbiol (2015)

Antagonistic activity of Pseudomonas sp. SH-C52. Wild-type (WT) and the thanamycin mutant strains (ThaB, ThaC2) were tested in dual culture assays for activity against fungal plant pathogens (upper panel) and oomycete plant pathogens (lower panel).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493835&req=5

Figure 3: Antagonistic activity of Pseudomonas sp. SH-C52. Wild-type (WT) and the thanamycin mutant strains (ThaB, ThaC2) were tested in dual culture assays for activity against fungal plant pathogens (upper panel) and oomycete plant pathogens (lower panel).
Mentions: Based on mutant analysis, the thanamycin gene cluster was shown to be important for the growth-inhibitory activity of strain SH-C52 against Rhizoctonia solani (Mendes et al., 2011). The thanamycin gene cluster shows similarity to a fragmented NRPS gene cluster in P. corrugata CFBP5454 (Figure 2), but the incomplete and scattered P. corrugata sequences complicate a clear comparison between the thanamycin and cormycin gene clusters. Alignments of the thanamycin NRPSs and the annotated parts of cormycin NRPSs show 85–97% protein identity. To test the antimicrobial activity-spectrum of thanamycin, wild type SH-C52 and two thanamycin biosynthesis mutants (Mendes et al., 2011) were tested for activity against fungi, oomycetes and bacteria. Here, we show that the activity spectrum of thanamycin is not exclusive for R. solani, but extends to an array of other fungi (Figure 3) and the Gram-positive bacterium Bacillus megaterium (data not shown). Also cormycin has been shown to be active against B. megaterium and the yeast Rhodotorula pilimanae (Scaloni et al., 2004). In contrast, thanamycin has little activity against oomycete pathogens (Figure 3) and the Gram-negative bacteria Pseudomonas syringae and Pectobacterium atrosepticum (data not shown).

Bottom Line: 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.SH-C52, with at least three structurally diverse lipopeptides, each with a different antimicrobial activity spectrum.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Phytopathology, Wageningen University Wageningen, Netherlands.

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.

No MeSH data available.


Related in: MedlinePlus