Orfamide C

Introduction

Orfamide C is a cyclic lipodepsipeptide produced by non-ribosomal peptide synthetases in Pseudomonas species. It belongs to a group of structurally similar CLiPs called the Orfamide group. Orfamide C was first extracted as a minor compound from Pseudomonas protegens Pf-5 which produces the groups’ namesake CLiP, orfamide A. This group also contains orfamide B (Gross, 2007, Ma, 2016), orfamides D – G (Ma, 2016), orfamide H (Ma, 2019), orfamides J – M (De Roo, 2022), poaeamides A and B (Zachow, 2015, Nguyen, 2016) and the PPZPMs (Weisshoff, 2014).

Original publication	Gross, 2007
Original source	Pseudomonas protegens Pf-5 (minor compound)
Other known sources (non-putative)	n.a.
Stereochemistry determined by	n.a.

Chemical properties

CAS	n.a.
Molecular formula	C62H110N10O17
Molecular weight	1267.6 g/mol
Mono-isotopic mass	1266.8050 Da
Solubility	Soluble in methanol, ethanol, DMF, DMSO, acetonitrile
CMC	n.a.
3D conformation	n.a.
NMR data available in literature	DMF-d7 (De Roo, 2022)

Chemical structure

Analysis of the orfamide C structure was initially performed by amino acid analysis and MS/MS analysis. (Gross, 2007) Stereochemistry of orfamide C was performed based on NMR spectral matching (De Roo, 2022), using orfamide A as a reference. The structure of orfamide C is 3R-OH C12:0 – L-Leu1 – D-Glu2 – D-aThr3 – D-aIle4 – D-Leu5 – D-Ser6 – L-Leu7 – L-Leu8 – D-Ser9 – L-Val10 and is cyclized by means of an ester bond between the C-terminal carbonyl and the hydroxyl side chain of Thr3. Orfamide C differs from orfamide A at the fatty acid tail, where it possesses a 3-hydroxy dodecanoic acid (3-OH C12:0) instead of a 3-hydroxy tetradecanoic acid (3-OH C14:0) moiety. 

Biological activity

Orfamide C has antagonistic activity against several plant-pathogenic fungi such as Magnaporthe oryzae, Phytophthora porri, Pythium ultimum and Rhizoctonia solani. (Ma, 2016) It has not been tested for its activity against Gram-positive or Gram-negative bacteria. (Geudens, 2018)

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.

Below, we provide the reference NMR data of orfamide C in various formats. This data is recorded in DMF-d7 at room temperature, and can be used to asses similarities of newly isolated CLiPs to orfamide C. Please note that the peptide portion of orfamide C is identical to that of orfamide A. So, be sure to check the identity (length and saturation) of the fatty acid moiety!

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.

Geudens, et al. “Cyclic lipodepsipeptides from Pseudomonas spp. – Biological Swiss-Army Knives.” Frontiers in Microbiology9, 1867 (2018): https://dx.doi.org/10.3389/fmicb.2018.01867.

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, Z., S. Zhang, J. Liang, K. Sun, and J. Hu. 2019. ‘Isolation and characterization of a new cyclic lipopeptide orfamide H from Pseudomonas protegens CHA0’, Journal of Antibiotics.

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.