Predicting the Structure of Cyclic Lipopeptides by Bioinformatics: Structure Revision of Arthrofactin

Lange, Anna; Sun, Han; Pilger, Jens; Reinscheid, Uwe M.; Gross, Harald

doi:10.1002/cbic.201200532

Cited by 23 publications

(20 citation statements)

References 30 publications

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“…In most lipopeptide-producing Pseudomonas , promiscuity is observed with respect to chain length of the incorporated saturated 3-hydroxy fatty acids. Relaxed amino acid substrate specificity, as observed here for the terminal module in XtlC giving rise to minor amounts of xantholysin B, is common among Pseudomonas NRPS systems [5], [8], [9], [43].…”

Section: Resultssupporting

confidence: 61%

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The Antimicrobial Compound Xantholysin Defines a New Group of Pseudomonas Cyclic Lipopeptides

Rokni‐Zadeh

Vleeschouwer

et al. 2013

PLoS ONE

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The rhizosphere isolate Pseudomonas putida BW11M1 produces a mixture of cyclic lipopeptide congeners, designated xantholysins. Properties of the major compound xantholysin A, shared with several other Pseudomonas lipopeptides, include antifungal activity and toxicity to Gram-positive bacteria, a supportive role in biofilm formation, and facilitation of surface colonization through swarming. Atypical is the lipopeptide’s capacity to inhibit some Gram-negative bacteria, including several xanthomonads. The lipotetradecadepsipeptides are assembled by XtlA, XtlB and XtlC, three co-linearly operating non-ribosomal peptide synthetases (NRPSs) displaying similarity in modular architecture with the entolysin-producing enzymes of the entomopathogenic Pseudomonas entomophila L48. A shifted serine-incorporating unit in the eight-module enzyme XtlB elongating the central peptide moiety not only generates an amino acid sequence differing at several equivalent positions from entolysin, but also directs xantholysin’s macrocyclization into an octacyclic structure, distinct from the pentacyclic closure in entolysin. Relaxed fatty acid specificity during lipoinitiation by XtlA (acylation with 3-hydroxydodec-5-enoate instead of 3-hydroxydecanoate) and for incorporation of the ultimate amino acid by XtlC (valine instead of isoleucine) account for the production of the minor structural variants xantholysin C and B, respectively. Remarkably, the genetic backbones of the xantholysin and entolysin NRPS systems also bear pronounced phylogenetic similarity to those of the P. putida strains PCL1445 and RW10S2, albeit generating the seemingly structurally unrelated cyclic lipopeptides putisolvin (undecapeptide containing a cyclotetrapeptide) and WLIP (nonapeptide containing a cycloheptapeptide), respectively. This similarity includes the linked genes encoding the cognate LuxR-family regulator and tripartite export system components in addition to individual modules of the NRPS enzymes, and probably reflects a common evolutionary origin. Phylogenetic scrutiny of the modules used for selective amino acid activation by these synthetases indicates that bacteria such as pseudomonads recruit and reshuffle individual biosynthetic units and blocks thereof to engineer reorganized or novel NRPS assembly lines for diversified synthesis of lipopeptides.

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Section: Resultssupporting

confidence: 61%

“…The termination module of XtlC harbors two thioesterase domains (TE1/TE2 tandem) which is similar to most known Pseudomonas lipopeptide biosynthesis systems, except for the syringomycin group [6], [43], [44] (Fig. 2).…”

Section: Resultsmentioning

confidence: 99%

The Antimicrobial Compound Xantholysin Defines a New Group of Pseudomonas Cyclic Lipopeptides

Rokni‐Zadeh

Vleeschouwer

et al. 2013

PLoS ONE

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“…Nowadays, it is possible to predict the cyclization process by bioinformatics because the TE's reveal clades of enzymes that reflect the cyclization step. Bioinformatic analyses with the TE-I of ArfC led to the hypothesis that the ring closure occurred between Asp11 and Thr3 to give structure 6 instead of a lactone ring between Asp11 and the 3-hydroxy group of the fatty decanoic acid side chain as originally suggested 55 …”

Section: Structure Revisionmentioning

confidence: 92%

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

et al. 2019

Self Cite

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Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

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“…Such unsaturations haveonly been observed in a few Pseudomonas cyclic lipopeptides. 42–47 Compared to massetolide A, the bananamides substitute the Glu with an Asp, the first Ser residue with a Gln, and an Ile with a Leu. An equivalent of the second Ser residue is absent.…”

Section: Discovery Of Specialized Metabolitesmentioning

confidence: 99%

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

et al. 2016

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Pseudomonads are cosmopolitan microbes able to produce a wide array of specialized metabolites. These molecules allow Pseudomonas to scavenge nutrients, sense population density, and enhance or inhibit growth of competing microbes. However, these valuable metabolites are typically characterized one-molecule-one-microbe at a time instead of inventoried in large numbers. To index and map the diversity of molecules detected from these organisms, 260 strains of ecologically diverse origins were subjected to mass spectrometry-based molecular networking. Molecular networking not only enables dereplication of molecules, but also sheds light on their structural relationships. Moreover, it accelerates discovery of new molecules. Herein, through indexing the Pseudomonas specialized metabolome, we report the molecular networking-based discovery of four molecules and their evolutionary relationships: a poaeamide analog, and a molecular sub-family of cyclic lipopeptides, the bananamides 1, 2, and 3. Analysis of their biosynthetic gene cluster shows that it constitutes a distinct evolutionary branch of the Pseudomonas cyclic lipopeptides. Through analysis of an additional 370 extracts of wheat-associated Pseudomonas, we demonstrate how the detailed knowledge from our reference index can be efficiently propagated to annotate complex metabolomic data from other studies akin to the way newly generated genomic information can be compared to data from public databases.

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Predicting the Structure of Cyclic Lipopeptides by Bioinformatics: Structure Revision of Arthrofactin

Cited by 23 publications

References 30 publications

The Antimicrobial Compound Xantholysin Defines a New Group of Pseudomonas Cyclic Lipopeptides

The Antimicrobial Compound Xantholysin Defines a New Group of Pseudomonas Cyclic Lipopeptides

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides

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