title: 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.
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.
authors.affiliation: Research Group Microbiology, Department of Bioengineering Sciences, VIB Department of Structural Biology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
authors.forename: Lumeng
authors.initials: L
authors.lastname: Ye
authors.forename: Steven
authors.initials: S
authors.lastname: Ballet
authors.forename: Falk
authors.initials: F
authors.lastname: Hildebrand
authors.forename: Georges
authors.initials: G
authors.lastname: Laus
authors.forename: Karel
authors.initials: K
authors.lastname: Guillemyn
authors.forename: Jeroen
authors.initials: J
authors.lastname: Raes
authors.forename: Sandra
authors.initials: S
authors.lastname: Matthijs
authors.forename: José
authors.initials: J
authors.lastname: Martins
authors.forename: Pierre
authors.initials: P
authors.lastname: Cornelis
mesh_terms: D009842:Oligopeptides / Q000737:chemistry*; D016958:Pseudomonas putida / Q000145:classification / Q000378:metabolism*; D017262:Siderophores / Q000737:chemistry*
chemical_list: D009842:Oligopeptides; D017262:Siderophores; C042453:pyoverdin