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

Pseudomonas phylogenetic tree.A phylogenetic tree of different Pseudomonas species based on the comparison of four different housekeeping genes sequences (16s rDNA, gyrB, rpoB, rpoD). The P. putida cluster is highlighted and the strain W15Oct28 is indicated in red. W15Oct28 closest relative is the P. putida type strain NBRC14164T.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110038-g001: Pseudomonas phylogenetic tree.A phylogenetic tree of different Pseudomonas species based on the comparison of four different housekeeping genes sequences (16s rDNA, gyrB, rpoB, rpoD). The P. putida cluster is highlighted and the strain W15Oct28 is indicated in red. W15Oct28 closest relative is the P. putida type strain NBRC14164T.

Mentions: The genome assembly resulted in 138 contigs assembled in 99 scaffolds representing the draft genome (longest scaffold size: 283,647 bp, 22 scaffolds longer that 100 kb, mean scaffold size 4,5726 bp, N50 scaffold size: 105,817 bp); the genome is 6,331,075 bps in length with average GC content of 62.8%. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JENB00000000. The version described in this paper is version JENB01000000, biosample SAMN02644482. The genome contains 5,540 predicted coding sequences (CDS), a total of 116 RNA genes, including 6 rRNA operons (8 copies of 5S rRNAs, 6 copies of 16S rRNAs, and 6 copies of 23S rRNAs). In addition, 71 tRNA genes were identified. The W15Oct28 strain was clearly confirmed to be Pseudomonas putida by analysis of different housekeeping genes sequences (16s rDNA, gyrB, rpoB, rpoD) according to the phylogeny method described by Mulet et al. [10], [26] with 99%, 97%, 98%, and 99% DNA sequence identity, respectively with the type strain of P. putida NBRC14164T (Figure 1). It is interesting to notice that the closest relatives of W15Oct28 are the P. putida type strain NBRC 14164T, and the recently sequenced strain H8234, a clinical isolate [27], confirming that our strain probably belongs to the species P. putida[28]. It appears also from the phylogenetic tree of Figure 1 that the other strains designated as P. putida probably represent other species. As a confirmation of this preliminary taxonomical assignment, Table 1 shows the Average Nucleotide Identity based on BLAST (ANIb) between the genomes of all the P. putida group strains represented in Figure 1. The table confirms that P. putida W15Oct28 shares about 94% of its genome with the recently sequenced NBRC14164T strain and 92% with H8234, totally in line with the previous phylogenetic assignment presented in Figure 1. The percentage of identity with other representatives of the P. putida group is lower, again confirming the previous multi-locus analysis-based taxonomic assignment. P. putida KT2440, BIRD 1, and DOT T1E form another cluster of related strains (Table 1). The circular map of the P. putida W15Oct28 genome is presented in Figure 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)

Pseudomonas phylogenetic tree.A phylogenetic tree of different Pseudomonas species based on the comparison of four different housekeeping genes sequences (16s rDNA, gyrB, rpoB, rpoD). The P. putida cluster is highlighted and the strain W15Oct28 is indicated in red. W15Oct28 closest relative is the P. putida type strain NBRC14164T.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110038-g001: Pseudomonas phylogenetic tree.A phylogenetic tree of different Pseudomonas species based on the comparison of four different housekeeping genes sequences (16s rDNA, gyrB, rpoB, rpoD). The P. putida cluster is highlighted and the strain W15Oct28 is indicated in red. W15Oct28 closest relative is the P. putida type strain NBRC14164T.
Mentions: The genome assembly resulted in 138 contigs assembled in 99 scaffolds representing the draft genome (longest scaffold size: 283,647 bp, 22 scaffolds longer that 100 kb, mean scaffold size 4,5726 bp, N50 scaffold size: 105,817 bp); the genome is 6,331,075 bps in length with average GC content of 62.8%. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JENB00000000. The version described in this paper is version JENB01000000, biosample SAMN02644482. The genome contains 5,540 predicted coding sequences (CDS), a total of 116 RNA genes, including 6 rRNA operons (8 copies of 5S rRNAs, 6 copies of 16S rRNAs, and 6 copies of 23S rRNAs). In addition, 71 tRNA genes were identified. The W15Oct28 strain was clearly confirmed to be Pseudomonas putida by analysis of different housekeeping genes sequences (16s rDNA, gyrB, rpoB, rpoD) according to the phylogeny method described by Mulet et al. [10], [26] with 99%, 97%, 98%, and 99% DNA sequence identity, respectively with the type strain of P. putida NBRC14164T (Figure 1). It is interesting to notice that the closest relatives of W15Oct28 are the P. putida type strain NBRC 14164T, and the recently sequenced strain H8234, a clinical isolate [27], confirming that our strain probably belongs to the species P. putida[28]. It appears also from the phylogenetic tree of Figure 1 that the other strains designated as P. putida probably represent other species. As a confirmation of this preliminary taxonomical assignment, Table 1 shows the Average Nucleotide Identity based on BLAST (ANIb) between the genomes of all the P. putida group strains represented in Figure 1. The table confirms that P. putida W15Oct28 shares about 94% of its genome with the recently sequenced NBRC14164T strain and 92% with H8234, totally in line with the previous phylogenetic assignment presented in Figure 1. The percentage of identity with other representatives of the P. putida group is lower, again confirming the previous multi-locus analysis-based taxonomic assignment. P. putida KT2440, BIRD 1, and DOT T1E form another cluster of related strains (Table 1). The circular map of the P. putida W15Oct28 genome is presented in Figure 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