Limits...
Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens.

Ye L, Hildebrand F, Dingemans J, Ballet S, Laus G, Matthijs S, Berendsen R, Cornelis P - PLoS ONE (2014)

Bottom Line: Analysis of the draft genome confirmed the presence of putisolvin biosynthesis genes and the corresponding lipopeptides were found to contribute to the antimicrobial activity.P. putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors, conferring a high capacity to utilize pyoverdines from other pseudomonads.One unique feature of W15Oct28 is also the presence of different secretion systems including a full set of genes for type IV secretion, and several genes for type VI secretion and their VgrG effectors.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering Sciences, Research group Microbiology, Vrije Universiteit Brussel and VIB Structural Biology Brussels, Brussels, Belgium.

ABSTRACT
Pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated from a stream in Brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and the plant pathogen Pseudomonas syringae, an unusual characteristic for P. putida. The active compound production only occurred in media with low iron content and without organic nitrogen sources. Transposon mutants which lost their antimicrobial activity had the majority of insertions in genes involved in the biosynthesis of pyoverdine, although purified pyoverdine was not responsible for the antagonism. Separation of compounds present in culture supernatants revealed the presence of two fractions containing highly hydrophobic molecules active against P. aeruginosa. Analysis of the draft genome confirmed the presence of putisolvin biosynthesis genes and the corresponding lipopeptides were found to contribute to the antimicrobial activity. One cluster of ten genes was detected, comprising a NAD-dependent epimerase, an acetylornithine aminotransferase, an acyl CoA dehydrogenase, a short chain dehydrogenase, a fatty acid desaturase and three genes for a RND efflux pump. P. putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors, conferring a high capacity to utilize pyoverdines from other pseudomonads. One unique feature of W15Oct28 is also the presence of different secretion systems including a full set of genes for type IV secretion, and several genes for type VI secretion and their VgrG effectors.

Show MeSH

Related in: MedlinePlus

Phylogeny of TonB-dependent receptors.Neighbor joining tree based on the alignment of amino acid sequences of the 56 TonB dependent receptors (TBDR) detected in the genome of W15oct28 (green font) and a selection of known ferric-pyoverdine receptors from different sequenced Pseudomonas genomes (black font). W15oct28 TBDRs that are regulated through sigma-anti-sigma factors are indicated with a red node. Grey surface indicates part of the tree that contains all ferric-pyoverdine receptors that form a separate cluster.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4219678&req=5

pone-0110038-g002: Phylogeny of TonB-dependent receptors.Neighbor joining tree based on the alignment of amino acid sequences of the 56 TonB dependent receptors (TBDR) detected in the genome of W15oct28 (green font) and a selection of known ferric-pyoverdine receptors from different sequenced Pseudomonas genomes (black font). W15oct28 TBDRs that are regulated through sigma-anti-sigma factors are indicated with a red node. Grey surface indicates part of the tree that contains all ferric-pyoverdine receptors that form a separate cluster.

Mentions: In our previous work, we reported that the only form of pyoverdine produced by P. putida W15Oct28 contains α-keto-glutaric acid as acyl side chain, a dihydropyoverdine chromophore and a 12 amino acid peptide chain [12]. One unique aspect of this pyoverdine is the incorporation of L-homoserine in peptide chain which was only previously reported in the pyoverdine produced by Azotobacter vinelandii DJ [12]. The pyoverdine biosynthesis gene clusters are localized in three regions in the genome. The first pyoverdine genomic region shares high identity (99%) with other P. putida type strains and contains the genes which catalyze the formation of the chromophore precusor (PvdL/G/Y/H) while the last part of the cluster contains genes involved in the transport of ferripyoverdine (fpvC, fpvD, fpvE, fpvF) [29] and in pyoverdine modification (pvdA, pvdQ) [30], [31]. The second cluster of genes shares about 75% identity with other whole genome sequenced P. putida strains and contains the genes pvdM, pvdN, pvdO, pvdP encoding periplasmic enzymes which are involved in the final maturation of the chromophore in the periplasm [32]. The third cluster contains one thioesterase gene, the genes for four non-ribosomal peptide synthetases involved in the peptide chain synthesis (pvdD, pvdI, pvdJ, pvdK) and the fpvA gene corresponding to the TonB-dependent ferri-pyoverdine receptor. These last genes share less than 50% identity with the corresponding genes from other P. putida strains [12]. This third pyoverdine cluster was considered by IslandViewer to correspond to a genomic island (GIs), because of its lower GC content compared to the average. Details about the genes involved in W15Oct28 pyoverdine biosynthesis and uptake have been described in our previous work [12]. Pseudomonas putida W15Oct28 genome contains 56 genes encoding TonB-dependent outer-membrane proteins receptors, 20 of them being probably involved in ferri-pyoverdine uptake, a situation similar to what we observed in P. fluorescens ATCC17400 which has 55 TonB-dependent receptors, including 17 that are involved in the uptake of different ferric pyoverdines [33]. Analysis of these receptors compared to other characterized Pseudomonas TonB-dependent receptors, revealed the presence of homologs of FpvAI, FpvAII, FpvAIII, and FpvU/V/W/X/Y/Z already described in P. protegens Pf-5 [25] (Figure 2). Pyoverdine feeding experiment confirmed the utilization of P. aeruginosa type I, II and III pyoverdines and the pyoverdines produced by P. protegens, and P. fluorescens species (Table 2). Other receptors predicted to recognize siderophores produced by other bacteria were found as well (enterobactin, achromobactin). The W15Oct28 FpvA receptor for its own pyoverdine utilization showed the best blast hit with the FpvA of P. syringae (42% identity), and it clusters with the P. syringae FpvA receptors in the tree presented in Figure 2, confirming the unique structure of the pyoverdine we recently disclosed [12]. The list of TonB-dependent receptors is presented in Table S2 in file S1.


Draft genome sequence analysis of a Pseudomonas putida W15Oct28 strain with antagonistic activity to Gram-positive and Pseudomonas sp. pathogens.

Ye L, Hildebrand F, Dingemans J, Ballet S, Laus G, Matthijs S, Berendsen R, Cornelis P - PLoS ONE (2014)

Phylogeny of TonB-dependent receptors.Neighbor joining tree based on the alignment of amino acid sequences of the 56 TonB dependent receptors (TBDR) detected in the genome of W15oct28 (green font) and a selection of known ferric-pyoverdine receptors from different sequenced Pseudomonas genomes (black font). W15oct28 TBDRs that are regulated through sigma-anti-sigma factors are indicated with a red node. Grey surface indicates part of the tree that contains all ferric-pyoverdine receptors that form a separate cluster.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4219678&req=5

pone-0110038-g002: Phylogeny of TonB-dependent receptors.Neighbor joining tree based on the alignment of amino acid sequences of the 56 TonB dependent receptors (TBDR) detected in the genome of W15oct28 (green font) and a selection of known ferric-pyoverdine receptors from different sequenced Pseudomonas genomes (black font). W15oct28 TBDRs that are regulated through sigma-anti-sigma factors are indicated with a red node. Grey surface indicates part of the tree that contains all ferric-pyoverdine receptors that form a separate cluster.
Mentions: In our previous work, we reported that the only form of pyoverdine produced by P. putida W15Oct28 contains α-keto-glutaric acid as acyl side chain, a dihydropyoverdine chromophore and a 12 amino acid peptide chain [12]. One unique aspect of this pyoverdine is the incorporation of L-homoserine in peptide chain which was only previously reported in the pyoverdine produced by Azotobacter vinelandii DJ [12]. The pyoverdine biosynthesis gene clusters are localized in three regions in the genome. The first pyoverdine genomic region shares high identity (99%) with other P. putida type strains and contains the genes which catalyze the formation of the chromophore precusor (PvdL/G/Y/H) while the last part of the cluster contains genes involved in the transport of ferripyoverdine (fpvC, fpvD, fpvE, fpvF) [29] and in pyoverdine modification (pvdA, pvdQ) [30], [31]. The second cluster of genes shares about 75% identity with other whole genome sequenced P. putida strains and contains the genes pvdM, pvdN, pvdO, pvdP encoding periplasmic enzymes which are involved in the final maturation of the chromophore in the periplasm [32]. The third cluster contains one thioesterase gene, the genes for four non-ribosomal peptide synthetases involved in the peptide chain synthesis (pvdD, pvdI, pvdJ, pvdK) and the fpvA gene corresponding to the TonB-dependent ferri-pyoverdine receptor. These last genes share less than 50% identity with the corresponding genes from other P. putida strains [12]. This third pyoverdine cluster was considered by IslandViewer to correspond to a genomic island (GIs), because of its lower GC content compared to the average. Details about the genes involved in W15Oct28 pyoverdine biosynthesis and uptake have been described in our previous work [12]. Pseudomonas putida W15Oct28 genome contains 56 genes encoding TonB-dependent outer-membrane proteins receptors, 20 of them being probably involved in ferri-pyoverdine uptake, a situation similar to what we observed in P. fluorescens ATCC17400 which has 55 TonB-dependent receptors, including 17 that are involved in the uptake of different ferric pyoverdines [33]. Analysis of these receptors compared to other characterized Pseudomonas TonB-dependent receptors, revealed the presence of homologs of FpvAI, FpvAII, FpvAIII, and FpvU/V/W/X/Y/Z already described in P. protegens Pf-5 [25] (Figure 2). Pyoverdine feeding experiment confirmed the utilization of P. aeruginosa type I, II and III pyoverdines and the pyoverdines produced by P. protegens, and P. fluorescens species (Table 2). Other receptors predicted to recognize siderophores produced by other bacteria were found as well (enterobactin, achromobactin). The W15Oct28 FpvA receptor for its own pyoverdine utilization showed the best blast hit with the FpvA of P. syringae (42% identity), and it clusters with the P. syringae FpvA receptors in the tree presented in Figure 2, confirming the unique structure of the pyoverdine we recently disclosed [12]. The list of TonB-dependent receptors is presented in Table S2 in file S1.

Bottom Line: Analysis of the draft genome confirmed the presence of putisolvin biosynthesis genes and the corresponding lipopeptides were found to contribute to the antimicrobial activity.P. putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors, conferring a high capacity to utilize pyoverdines from other pseudomonads.One unique feature of W15Oct28 is also the presence of different secretion systems including a full set of genes for type IV secretion, and several genes for type VI secretion and their VgrG effectors.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioengineering Sciences, Research group Microbiology, Vrije Universiteit Brussel and VIB Structural Biology Brussels, Brussels, Belgium.

ABSTRACT
Pseudomonas putida is a member of the fluorescent pseudomonads known to produce the yellow-green fluorescent pyoverdine siderophore. P. putida W15Oct28, isolated from a stream in Brussels, was found to produce compound(s) with antimicrobial activity against the opportunistic pathogens Staphylococcus aureus, Pseudomonas aeruginosa, and the plant pathogen Pseudomonas syringae, an unusual characteristic for P. putida. The active compound production only occurred in media with low iron content and without organic nitrogen sources. Transposon mutants which lost their antimicrobial activity had the majority of insertions in genes involved in the biosynthesis of pyoverdine, although purified pyoverdine was not responsible for the antagonism. Separation of compounds present in culture supernatants revealed the presence of two fractions containing highly hydrophobic molecules active against P. aeruginosa. Analysis of the draft genome confirmed the presence of putisolvin biosynthesis genes and the corresponding lipopeptides were found to contribute to the antimicrobial activity. One cluster of ten genes was detected, comprising a NAD-dependent epimerase, an acetylornithine aminotransferase, an acyl CoA dehydrogenase, a short chain dehydrogenase, a fatty acid desaturase and three genes for a RND efflux pump. P. putida W15Oct28 genome also contains 56 genes encoding TonB-dependent receptors, conferring a high capacity to utilize pyoverdines from other pseudomonads. One unique feature of W15Oct28 is also the presence of different secretion systems including a full set of genes for type IV secretion, and several genes for type VI secretion and their VgrG effectors.

Show MeSH
Related in: MedlinePlus