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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.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.

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

Whole genome phylogenetic analysis of Pseudomonas sp. SH-C52. Phylogenetic tree constructed by use of CVtree, and based on the analysis performed previously by Redondo-Nieto et al. (2012), with the addition of strains SH-C52, P. corrugata CFBP5454 and P. mediterranea CFBP5447.
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Figure 1: Whole genome phylogenetic analysis of Pseudomonas sp. SH-C52. Phylogenetic tree constructed by use of CVtree, and based on the analysis performed previously by Redondo-Nieto et al. (2012), with the addition of strains SH-C52, P. corrugata CFBP5454 and P. mediterranea CFBP5447.

Mentions: Sequencing and assembly showed that the genome size of Pseudomonas sp. SH-C52 is ~6.3 Mb with a GC content of 61.0%. The genome was assembled in 596 contigs and 25 scaffolds, with an estimated coverage of 99.2%. For annotation, 384 contigs of at least 100-bp and covering 6.3 MB were used. In total, 5579 ORFs were annotated with 5523 CDSs and 56 tRNAs (Table 1). Previous analysis of the 16S rRNA sequence placed SH-C52 within the P. fluorescens clade (Mendes et al., 2011). At that time, however, no conclusive species designation was obtained. Expanding the former genome-wide phylogenetic analysis on P. fluorescens species (Redondo-Nieto et al., 2012) with the SH-C52 genome and the recent draft genomes of P. corrugata CFBP5454 and P. mediteranea CFBP5447, showed that strain SH-C52 clusters within subgroup I of the P. fluorescens group. Within subgroup I, SH-C52 and the strains of P. corrugata and P. mediterranea form a separate clade (Figure 1).


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)

Whole genome phylogenetic analysis of Pseudomonas sp. SH-C52. Phylogenetic tree constructed by use of CVtree, and based on the analysis performed previously by Redondo-Nieto et al. (2012), with the addition of strains SH-C52, P. corrugata CFBP5454 and P. mediterranea CFBP5447.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Whole genome phylogenetic analysis of Pseudomonas sp. SH-C52. Phylogenetic tree constructed by use of CVtree, and based on the analysis performed previously by Redondo-Nieto et al. (2012), with the addition of strains SH-C52, P. corrugata CFBP5454 and P. mediterranea CFBP5447.
Mentions: Sequencing and assembly showed that the genome size of Pseudomonas sp. SH-C52 is ~6.3 Mb with a GC content of 61.0%. The genome was assembled in 596 contigs and 25 scaffolds, with an estimated coverage of 99.2%. For annotation, 384 contigs of at least 100-bp and covering 6.3 MB were used. In total, 5579 ORFs were annotated with 5523 CDSs and 56 tRNAs (Table 1). Previous analysis of the 16S rRNA sequence placed SH-C52 within the P. fluorescens clade (Mendes et al., 2011). At that time, however, no conclusive species designation was obtained. Expanding the former genome-wide phylogenetic analysis on P. fluorescens species (Redondo-Nieto et al., 2012) with the SH-C52 genome and the recent draft genomes of P. corrugata CFBP5454 and P. mediteranea CFBP5447, showed that strain SH-C52 clusters within subgroup I of the P. fluorescens group. Within subgroup I, SH-C52 and the strains of P. corrugata and P. mediterranea form a separate clade (Figure 1).

Bottom Line: Seven structural variants of thanapeptin were found with varying degrees of activity against P. infestans.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.

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