BioMetals

, Volume 26, Issue 4, pp 561–575

A combinatorial approach to the structure elucidation of a pyoverdine siderophore produced by a Pseudomonas putida isolate and the use of pyoverdine as a taxonomic marker for typing P. putida subspecies

  • Lumeng Ye
  • Steven Ballet
  • Falk Hildebrand
  • Georges Laus
  • Karel Guillemyn
  • Jeroen Raes
  • Sandra Matthijs
  • José Martins
  • Pierre Cornelis
Article

DOI: 10.1007/s10534-013-9653-z

Cite this article as:
Ye, L., Ballet, S., Hildebrand, F. et al. Biometals (2013) 26: 561. doi:10.1007/s10534-013-9653-z

Abstract

The structure of a pyoverdine produced by Pseudomonas putida, W15Oct28, was elucidated by combining mass spectrometric methods and bioinformatics by the analysis of non-ribosomal peptide synthetase genes present in the newly sequenced genome. The only form of pyoverdine produced by P. putida W15Oct28 is characterized to contain α-ketoglutaric acid as acyl side chain, a dihydropyoverdine chromophore, and a 12 amino acid peptide chain. The peptide chain is unique among all pyoverdines produced by Pseudomonas subspecies strains. It was characterized as –l-Asp-l-Ala-d-AOHOrn-l-Thr-Gly-c[l-Thr(O-)-l-Hse-d-Hya-l-Ser-l-Orn-l-Hse-l-Ser-O-]. The chemical formula and the detected and calculated molecular weight of this pyoverdine are: C65H93N17O32, detected mass 1624.6404 Da, calculated mass 1624.6245. Additionally, pyoverdine structures from both literature reports and bioinformatics prediction of the genome sequenced P. putida strains are summarized allowing us to propose a scheme based on pyoverdines structures as tool for the phylogeny of P. putida. This study shows the strength of the combination of in silico analysis together with analytical data and literature mining in determining the structure of secondary metabolites such as peptidic siderophores.

Keywords

Pseudomonas putidaPyoverdineStructure elucidationBioinformatic predictionPhylogenetic marker

Supplementary material

10534_2013_9653_MOESM1_ESM.ppt (1.2 mb)
Supplementary Figure 1IEF gel image of pyoverdines produced by P. putida W15Oct28 and P. putida L1. Pyoverdine of P. putida W15Oct28 (left lane) shows white fluorescence under UV light due to the un-matured dihydropyoverdine chromophore, while the pyoverdine L1 shows blue fluorescence and two isoforms. (PPT 1276 kb)
10534_2013_9653_MOESM2_ESM.doc (1.1 mb)
Supplementary Figure 2Amino acid analysis of fully hydrolyzed N-TFA-n-butylester derivates by GC/MS. (DOC 1155 kb)
10534_2013_9653_MOESM3_ESM.ppt (300 kb)
Supplementary Fig. 3Three dimensional structure model of P. putida W15Oct28 pyoverdine–Fe3+ complex based on the hexadentate character. Green: carbons, Red: oxygens, Blue: nitrogen, Brown: Iron ion, non-polar hydrogens not shown. (PPT 302 kb)

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Lumeng Ye
    • 1
  • Steven Ballet
    • 2
  • Falk Hildebrand
    • 1
  • Georges Laus
    • 2
  • Karel Guillemyn
    • 2
  • Jeroen Raes
    • 1
  • Sandra Matthijs
    • 3
  • José Martins
    • 4
  • Pierre Cornelis
    • 1
  1. 1.Research Group Microbiology, Department of Bioengineering Sciences, VIB Department of Structural BiologyVrije Universiteit BrusselBrusselsBelgium
  2. 2.Research Group of Organic Chemistry, Department of ChemistryVrije Universiteit BrusselBrusselsBelgium
  3. 3.Institut de Recherches Microbiologiques—WiameBrusselsBelgium
  4. 4.NMR and Structure Analysis Unit, Department of Organic ChemistryUniversiteit GentGhentBelgium