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Genomic, genetic and structural analysis of pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25.

Moon CD, Zhang XX, Matthijs S, Schäfer M, Budzikiewicz H, Rainey PB - BMC Microbiol. (2008)

Bottom Line: The genome of P. fluorescens SBW25 contains an extensively dispersed set of PVD genes in comparison to other sequenced Pseudomonas strains.The PAO1 PVD regulatory model, which involves a branched Fpv signaling pathway, is generally conserved in SBW25, however there is a significant difference in fpvR regulation.SBW25 produces PVD with a partly cyclic seven amino acid residue backbone, and is able to utilize a wide variety of exogenous PVDs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK. christina.moon@agresearch.co.nz

ABSTRACT

Background: Pyoverdines (PVDs) are high affinity siderophores, for which the molecular mechanisms of biosynthesis, uptake and regulation have been extensively studied in Pseudomonas aeruginosa PAO1. However, the extent to which this regulatory model applies to other pseudomonads is unknown. Here, we describe the results of a genomic, genetic and structural analysis of pyoverdine-mediated iron uptake by the plant growth-promoting bacterium P. fluorescens SBW25.

Results: In silico analysis of the complete, but un-annotated, SBW25 genome sequence identified 31 genes putatively involved in PVD biosynthesis, transport or regulation, which are distributed across seven different regions of the genome. PVD gene iron-responsiveness was tested using 'lacZ fusions to five PVD loci, representative of structural and regulatory genes. Transcription of all fusions increased in response to iron starvation. In silico analyses suggested that regulation of fpvR (which is predicted to encode a cytoplasmic membrane-spanning anti-sigma factor) may be unique. Transcriptional assays using gene expression constructs showed that fpvR is positively regulated by FpvI (an extracytoplasmic family (ECF) sigma factor), and not directly by the ferric uptake regulator (Fur) as for PAO1. Deletion of pvdL, encoding a predicted non-ribosomal peptide synthetase (NRPS) involved in PVD chromophore biosynthesis confirmed the necessity of PvdL for PVD production and for normal growth in iron-limited media. Structural analysis of the SBW25 PVD shows a partly cyclic seven residue peptide backbone, identical to that of P. fluorescens ATCC13525. At least 24 putative siderophore receptor genes are present in the SBW25 genome enabling the bacterium to utilize 19 structurally distinct PVDs from 25 different Pseudomonas isolates.

Conclusion: The genome of P. fluorescens SBW25 contains an extensively dispersed set of PVD genes in comparison to other sequenced Pseudomonas strains. The PAO1 PVD regulatory model, which involves a branched Fpv signaling pathway, is generally conserved in SBW25, however there is a significant difference in fpvR regulation. SBW25 produces PVD with a partly cyclic seven amino acid residue backbone, and is able to utilize a wide variety of exogenous PVDs.

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Comparison of the arrangement of PVD genes in P. fluorescens SBW25 and Pseudomonas aeruginosa PAO1. PAO1 PVD genes are annotated according to [23], and gene names, if given, are shown beneath genes, otherwise PA gene numbers are shown above. PVD gene homologues in SBW25 were identified by BLAST searches, and Pflu gene numbers [22] are shown above genes, if names are not given. Yellow and green dots preceding genes represent sequences that are highly consistent with the Fur-box (5'-GATAATGATAATCATTATC-3') [11], and IS-box (5'-TAAAT-N16-CGT-3') [12, 23, 41] consensus sequences, respectively. Gene sizes are not drawn to linear scale, and double vertical lines represent intervening DNA (sizes in kb shown above). Figure adapted from Ravel & Cornelis (2003).
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Figure 1: Comparison of the arrangement of PVD genes in P. fluorescens SBW25 and Pseudomonas aeruginosa PAO1. PAO1 PVD genes are annotated according to [23], and gene names, if given, are shown beneath genes, otherwise PA gene numbers are shown above. PVD gene homologues in SBW25 were identified by BLAST searches, and Pflu gene numbers [22] are shown above genes, if names are not given. Yellow and green dots preceding genes represent sequences that are highly consistent with the Fur-box (5'-GATAATGATAATCATTATC-3') [11], and IS-box (5'-TAAAT-N16-CGT-3') [12, 23, 41] consensus sequences, respectively. Gene sizes are not drawn to linear scale, and double vertical lines represent intervening DNA (sizes in kb shown above). Figure adapted from Ravel & Cornelis (2003).

Mentions: Interrogation of the complete genome sequence of SBW25 using genes known to be involved in PVD-mediated iron acquisition in P. aeruginosa PAO1 [23] revealed 31 homologues with predicted roles in PVD biosynthesis, transport and regulation. The results are summarized in Figure 1 and Additional file 1.


Genomic, genetic and structural analysis of pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25.

Moon CD, Zhang XX, Matthijs S, Schäfer M, Budzikiewicz H, Rainey PB - BMC Microbiol. (2008)

Comparison of the arrangement of PVD genes in P. fluorescens SBW25 and Pseudomonas aeruginosa PAO1. PAO1 PVD genes are annotated according to [23], and gene names, if given, are shown beneath genes, otherwise PA gene numbers are shown above. PVD gene homologues in SBW25 were identified by BLAST searches, and Pflu gene numbers [22] are shown above genes, if names are not given. Yellow and green dots preceding genes represent sequences that are highly consistent with the Fur-box (5'-GATAATGATAATCATTATC-3') [11], and IS-box (5'-TAAAT-N16-CGT-3') [12, 23, 41] consensus sequences, respectively. Gene sizes are not drawn to linear scale, and double vertical lines represent intervening DNA (sizes in kb shown above). Figure adapted from Ravel & Cornelis (2003).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2235872&req=5

Figure 1: Comparison of the arrangement of PVD genes in P. fluorescens SBW25 and Pseudomonas aeruginosa PAO1. PAO1 PVD genes are annotated according to [23], and gene names, if given, are shown beneath genes, otherwise PA gene numbers are shown above. PVD gene homologues in SBW25 were identified by BLAST searches, and Pflu gene numbers [22] are shown above genes, if names are not given. Yellow and green dots preceding genes represent sequences that are highly consistent with the Fur-box (5'-GATAATGATAATCATTATC-3') [11], and IS-box (5'-TAAAT-N16-CGT-3') [12, 23, 41] consensus sequences, respectively. Gene sizes are not drawn to linear scale, and double vertical lines represent intervening DNA (sizes in kb shown above). Figure adapted from Ravel & Cornelis (2003).
Mentions: Interrogation of the complete genome sequence of SBW25 using genes known to be involved in PVD-mediated iron acquisition in P. aeruginosa PAO1 [23] revealed 31 homologues with predicted roles in PVD biosynthesis, transport and regulation. The results are summarized in Figure 1 and Additional file 1.

Bottom Line: The genome of P. fluorescens SBW25 contains an extensively dispersed set of PVD genes in comparison to other sequenced Pseudomonas strains.The PAO1 PVD regulatory model, which involves a branched Fpv signaling pathway, is generally conserved in SBW25, however there is a significant difference in fpvR regulation.SBW25 produces PVD with a partly cyclic seven amino acid residue backbone, and is able to utilize a wide variety of exogenous PVDs.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford OX1 3RB, UK. christina.moon@agresearch.co.nz

ABSTRACT

Background: Pyoverdines (PVDs) are high affinity siderophores, for which the molecular mechanisms of biosynthesis, uptake and regulation have been extensively studied in Pseudomonas aeruginosa PAO1. However, the extent to which this regulatory model applies to other pseudomonads is unknown. Here, we describe the results of a genomic, genetic and structural analysis of pyoverdine-mediated iron uptake by the plant growth-promoting bacterium P. fluorescens SBW25.

Results: In silico analysis of the complete, but un-annotated, SBW25 genome sequence identified 31 genes putatively involved in PVD biosynthesis, transport or regulation, which are distributed across seven different regions of the genome. PVD gene iron-responsiveness was tested using 'lacZ fusions to five PVD loci, representative of structural and regulatory genes. Transcription of all fusions increased in response to iron starvation. In silico analyses suggested that regulation of fpvR (which is predicted to encode a cytoplasmic membrane-spanning anti-sigma factor) may be unique. Transcriptional assays using gene expression constructs showed that fpvR is positively regulated by FpvI (an extracytoplasmic family (ECF) sigma factor), and not directly by the ferric uptake regulator (Fur) as for PAO1. Deletion of pvdL, encoding a predicted non-ribosomal peptide synthetase (NRPS) involved in PVD chromophore biosynthesis confirmed the necessity of PvdL for PVD production and for normal growth in iron-limited media. Structural analysis of the SBW25 PVD shows a partly cyclic seven residue peptide backbone, identical to that of P. fluorescens ATCC13525. At least 24 putative siderophore receptor genes are present in the SBW25 genome enabling the bacterium to utilize 19 structurally distinct PVDs from 25 different Pseudomonas isolates.

Conclusion: The genome of P. fluorescens SBW25 contains an extensively dispersed set of PVD genes in comparison to other sequenced Pseudomonas strains. The PAO1 PVD regulatory model, which involves a branched Fpv signaling pathway, is generally conserved in SBW25, however there is a significant difference in fpvR regulation. SBW25 produces PVD with a partly cyclic seven amino acid residue backbone, and is able to utilize a wide variety of exogenous PVDs.

Show MeSH
Related in: MedlinePlus