PPZPM

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Introduction

The PPZPMs are a collection of 24 somewhat ill-defined cyclic lipodepsipeptides. They are produced by Pseudomonas sp. JX090307, a strain isolated from the hyphae of the phytopathogenic oomycete Phytophthora alni sp. alni. Since they are composed of 10 amino acids, 8 of which form a macrocycle by means of an ester bond, they structurally belong to the Orfamide group. This group of CLiPs also contains orfamide A (Gross, 2007), orfamide B (Ma, 2016), orfamide C (Gross, 2007), orfamides D – G (Ma, 2016), orfamide H (Ma, 2019), orfamides J – M (De Roo, 2022) and poaeamides A and B (Zachow, 2015, Nguyen, 2016).

Original publicationWeisshoff, 2014
Original sourcePseudomonas sp. JX090307
Other known sources (non-putative)n.a.
Stereochemistry determined byGC-analysis (incomplete) (Weisshoff, 2014)

Chemical properties

CASn.a.
Molecular formulaPPZPM-1a: C61H108N10O17
PPZPM-2a: C60H106N10O17
Molecular weightPPZPM-1a:  1253.6 g/mol
PPZPM-2a: 1239.6 g/mol
Mono-isotopic massPPZPM-1a: 1252.7894 Da
PPZPM-2a: 1238.7737 Da
Solubilityn.a.
CMCn.a.
3D conformationn.a.
NMR data available in literaturePPZPM-1a in acetone-d6 (Weisshoff, 2014)
PPZPM-2a in MeOH-d3 (Only 1H) (Weisshoff, 2014)

Chemical structure

The structures of PPMZP-1a and PPZPM-2a are established using NMR spectroscopy and mass spectrometry. Both CLiPs feature an N-terminal 3-hydroxy decanoic acid moiety (the fatty acid tail) linked to a peptide sequence of 10 amino acids. The peptide is cyclized by the presence of an ester bond between the C-terminal carbonyl and the side chain hydroxyl moiety of Thr3. Consequently, the macrocycle is composed of 8 amino acids. PPZPM-1a and 2a differ from each other by the presence of an isoleucine or a valine at position 4, respectively.

GC analysis revealed the presence of D-glutamic acid, D-allothreonine, D-alloisoleucine and D-serine. Furthermore, both L-leucine and D-leucine were found in a 3 to 1 ratio. Unfortunately, the position of the single D-leucine was not resolved.

Aside from the two main compounds (1a and 2a), several minor compounds were characterized. However, these were not purified from the cell extract, but only analyzed by mass spectrometry on the crude sample. Consequently, they are ill-defined.

Schematic sequences of the PPZPMs, where shapes indicate amino acid configuration (circles = L-AA, squares = D-AA, diamonds = unknown) and colors indicate amino acid polarity (green = hydrophobic, red = polar)

NMR fingerprint data

Recently, it was established that the planar structure and stereochemistry of CLiPs can be assessed by simple comparison to a reference. (De Roo, 2022) More specifically, by matching NMR spectra of a CLiP from a newly isolated bacterial source with those of existing (reference) CLiPs, one can determine whether they are identical or not. A detailed explanation on what NMR fingerprint matching is, and how to use it, can be found here.

Currently, we do not have reference data available for the PPZPMs. However, since tabulated NMR chemical shifts are published for PPZPM-1a (Weisshoff, 2014), these can be used for NMR matching. On the one hand, the data for PPZPM-1a could be used to elucidate the structural similarity with e.g. orfamide A. Indeed, since the peptide portion is identical for both CLiPs (they only differ in the length of the fatty acid), we could match the NMR spectra of PPZPM-1a with those of orfamide A. Since the stereochemistry of the latter is known, the NMR matching could elucidate the stereochemistry of PPZPM-1a (if a match occurs). On the other hand, the data can be used to asses similarities of newly isolated CLiPs to PPZPM-1a.

Below, we provide the tabulated NMR data of PPZPM-1a. This data is recorded in acetone-d6 at room temperature.

ATTENTION: The solvent of choice for NMR reference spectra is DMF-d7. However, since no spectra are available in this solvent, we provide the NMR data as recorded in acetone-d6. If you wish to compare spectra of your own CLiP to the data of PPZPM-1a, please use identical conditions!

References

De Roo, et al. “An nuclear magnetic resonance fingerprint matching approach for the identification and structural re-evaluation of Pseudomonas lipopeptides.” Microbiology Spectrum 0, 0
https://dx.doi.org/doi:10.1128/spectrum.01261-22.

Gross, et al. “The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters.” Chemistry & Biology14, 1 (2007): https://dx.doi.org/10.1016/j.chembiol.2006.11.007.

Ma, et al. “Biosynthesis, chemical structure, and structure-activity relationship of orfamide lipopeptides produced by Pseudomonas protegens and related species.” Frontiers in Microbiology7 (2016): https://dx.doi.org/10.3389/fmicb.2016.00382.

Ma, et al. “Isolation and characterization of a new cyclic lipopeptide orfamide H from Pseudomonas protegens CHA0.” Journal of Antibiotics (2019): https://dx.doi.org/10.1038/s41429-019-0254-0.

Nguyen, et al. “Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides.” Nature Microbiology2 (2016): https://dx.doi.org/10.1038/nmicrobiol.2016.197.

Weisshoff, et al. “PPZPMs – a novel group of cyclic lipodepsipeptides produced by the Phytophtora alni associated strain Pseudomonas sp. JX090307 – the missing link between the viscosin and amphisin group.” Natural Products Communications9, 7 (2014).

Zachow, et al. “The novel lipopeptide poaeamide of the endophyte Pseudomonas poae RE*1-1-14 is involved in pathogen suppression and root colonization.” Molecular Plant-Microbe Interactions28, 7 (2015): https://dx.doi.org/10.1094/MPMI-12-14-0406-R.

Previous Orfamide D – G