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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

Non-ribosomal peptide synthetase gene clusters present in the genome of Pseudomonas sp. SH-C52. (A) The six NRPS gene clusters predicted in the genome of SH-C52. (B) A comparison of the SH-C52 thanamycin-thanapeptin-brabantamide cluster with the putative equivalent cluster of P. corrugata CFBP5454. Thana/corpeptin related NRPS genes are in dark gray, thana/cormycin NRPS genes are in light gray, and brabantamide genes are in near black. The P. corrugata genes are not bordered, as the genome information is scattered over contigs and needs to be confirmed. Dotted lines indicate (expected) sequence conservation. Amino acids are indicated in their standard three-letter annotation. Non-standard amino acids were abbreviated as follows: Hse, homoserine; Ilx, isoleucine or leucine; Dab, 2,4-diaminobutanoic acid; Dhb, 2,3-dehydro- 2-aminobutanoic acid; Dhp, dehydro-2-aminopropanoic acid (dehydroalanine). The asterisk in the thana/cormycin structure indicates chlorination of this amino acid.
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Figure 2: Non-ribosomal peptide synthetase gene clusters present in the genome of Pseudomonas sp. SH-C52. (A) The six NRPS gene clusters predicted in the genome of SH-C52. (B) A comparison of the SH-C52 thanamycin-thanapeptin-brabantamide cluster with the putative equivalent cluster of P. corrugata CFBP5454. Thana/corpeptin related NRPS genes are in dark gray, thana/cormycin NRPS genes are in light gray, and brabantamide genes are in near black. The P. corrugata genes are not bordered, as the genome information is scattered over contigs and needs to be confirmed. Dotted lines indicate (expected) sequence conservation. Amino acids are indicated in their standard three-letter annotation. Non-standard amino acids were abbreviated as follows: Hse, homoserine; Ilx, isoleucine or leucine; Dab, 2,4-diaminobutanoic acid; Dhb, 2,3-dehydro- 2-aminobutanoic acid; Dhp, dehydro-2-aminopropanoic acid (dehydroalanine). The asterisk in the thana/cormycin structure indicates chlorination of this amino acid.

Mentions: The SH-C52 genome contains six NRPS gene clusters, including the putative (orni-) corrugatin gene cluster (Figure 2). The other five clusters include the known NRPS gene clusters for the synthesis of thanamycin (BN844_0670-0673 and BN844_0703-0704, Mendes et al., 2011), and brabantamide (BN844_0705-0707, Schmidt et al., 2014). In close proximity to the thanamycin and brabantamide gene clusters, a third NRPS gene cluster (BN844_0667-0664) was identified (Figure 2). This NRPS is predicted to code for a 22 amino-acid lipopeptide with similarity to corpeptin (Figure 2) produced by P. corrugata. Therefore, in agreement with the naming of cormycin and corpeptin, we designated the predicted 22-amino-acid compound of SH-C52 as thanapeptin. The genome of P. corrugata CFBP5454 contains several NRPS genes with similarity to the 22 amino-acid related gene cluster in SH-C52. However, in P. corrugata this gene cluster is divided over different contigs. Recently, a partial gene cluster containing a partial NRPS gene, encoding two adenylation-domains and two transport genes, were linked to corpeptin production (Strano et al., 2014). Because of the incomplete nature of the draft genome sequence for strain CFBP5454, it remains unclear if the organization of the gene clusters for cormycin and corpeptin of P. corrugata is also similar to that of thanamycin and thanapeptin in SH-C52. However, consistent with the gene organization in SH-C52, a putative brabantamide-like gene cluster was also found in P. corrugata down-stream of the putative cormycin gene cluster (Figure 2). In addition, the biocontrol strain P. fluorescens In5 was recently reported to produce the antagonistic metabolites nunamycin and nunapeptin, also with similarity to cormycin and corpeptin, respectively. Although gene clusters for nunamycin and nunapeptin were presented (Michelsen et al., 2015), the genome information of strain In5 was not provided.


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)

Non-ribosomal peptide synthetase gene clusters present in the genome of Pseudomonas sp. SH-C52. (A) The six NRPS gene clusters predicted in the genome of SH-C52. (B) A comparison of the SH-C52 thanamycin-thanapeptin-brabantamide cluster with the putative equivalent cluster of P. corrugata CFBP5454. Thana/corpeptin related NRPS genes are in dark gray, thana/cormycin NRPS genes are in light gray, and brabantamide genes are in near black. The P. corrugata genes are not bordered, as the genome information is scattered over contigs and needs to be confirmed. Dotted lines indicate (expected) sequence conservation. Amino acids are indicated in their standard three-letter annotation. Non-standard amino acids were abbreviated as follows: Hse, homoserine; Ilx, isoleucine or leucine; Dab, 2,4-diaminobutanoic acid; Dhb, 2,3-dehydro- 2-aminobutanoic acid; Dhp, dehydro-2-aminopropanoic acid (dehydroalanine). The asterisk in the thana/cormycin structure indicates chlorination of this amino acid.
© Copyright Policy
Related In: Results  -  Collection

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Figure 2: Non-ribosomal peptide synthetase gene clusters present in the genome of Pseudomonas sp. SH-C52. (A) The six NRPS gene clusters predicted in the genome of SH-C52. (B) A comparison of the SH-C52 thanamycin-thanapeptin-brabantamide cluster with the putative equivalent cluster of P. corrugata CFBP5454. Thana/corpeptin related NRPS genes are in dark gray, thana/cormycin NRPS genes are in light gray, and brabantamide genes are in near black. The P. corrugata genes are not bordered, as the genome information is scattered over contigs and needs to be confirmed. Dotted lines indicate (expected) sequence conservation. Amino acids are indicated in their standard three-letter annotation. Non-standard amino acids were abbreviated as follows: Hse, homoserine; Ilx, isoleucine or leucine; Dab, 2,4-diaminobutanoic acid; Dhb, 2,3-dehydro- 2-aminobutanoic acid; Dhp, dehydro-2-aminopropanoic acid (dehydroalanine). The asterisk in the thana/cormycin structure indicates chlorination of this amino acid.
Mentions: The SH-C52 genome contains six NRPS gene clusters, including the putative (orni-) corrugatin gene cluster (Figure 2). The other five clusters include the known NRPS gene clusters for the synthesis of thanamycin (BN844_0670-0673 and BN844_0703-0704, Mendes et al., 2011), and brabantamide (BN844_0705-0707, Schmidt et al., 2014). In close proximity to the thanamycin and brabantamide gene clusters, a third NRPS gene cluster (BN844_0667-0664) was identified (Figure 2). This NRPS is predicted to code for a 22 amino-acid lipopeptide with similarity to corpeptin (Figure 2) produced by P. corrugata. Therefore, in agreement with the naming of cormycin and corpeptin, we designated the predicted 22-amino-acid compound of SH-C52 as thanapeptin. The genome of P. corrugata CFBP5454 contains several NRPS genes with similarity to the 22 amino-acid related gene cluster in SH-C52. However, in P. corrugata this gene cluster is divided over different contigs. Recently, a partial gene cluster containing a partial NRPS gene, encoding two adenylation-domains and two transport genes, were linked to corpeptin production (Strano et al., 2014). Because of the incomplete nature of the draft genome sequence for strain CFBP5454, it remains unclear if the organization of the gene clusters for cormycin and corpeptin of P. corrugata is also similar to that of thanamycin and thanapeptin in SH-C52. However, consistent with the gene organization in SH-C52, a putative brabantamide-like gene cluster was also found in P. corrugata down-stream of the putative cormycin gene cluster (Figure 2). In addition, the biocontrol strain P. fluorescens In5 was recently reported to produce the antagonistic metabolites nunamycin and nunapeptin, also with similarity to cormycin and corpeptin, respectively. Although gene clusters for nunamycin and nunapeptin were presented (Michelsen et al., 2015), the genome information of strain In5 was not provided.

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