Genome Mining of the Lipopeptide Biosynthesis of Paenibacillus polymyxa E681 in Combination with Mass Spectrometry: Discovery of the Lipoheptapeptide Paenilipoheptin

Abstract

Paenibacillus polymyxa strains are qualified for agro-biotechnological uses such as plant growth promotion and for biocontrol strategies against deleterious phytopathogenic competitors in the soil depending on their attractive arsenal of bioactive compounds. Moreover, they are potent producers of antibiotics for medical applications. To identify new products of such organisms, genome mining strategies in combination with mass spectrometry are the methods of choice. Herein, we performed such studies with the Paenibacillus strain E681. Bioinformatic evaluation of its genome sequence revealed four gene clusters A-D encoding nonribosomal peptide synthetases (NRPSs). Accordingly, four lipopeptide families were detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Clusters A and D codify the well known fusaricidins and polymyxins. A yet-unknown lipoheptapeptide was discovered and structurally characterized by de novo sequencing by using MALDI-LIFT-TOF/TOF MS. It was designated as paenilipoheptin. From structure predictions we infer that the production of this agent is encoded by gene cluster C. Gene cluster B encodes the synthesis of tridecaptins, a family of open-chain lipotridecapeptides. Strain E681 produces new subspecies of such compounds (tridecaptins E) showing variations both in their fatty-acid part as well as in their peptide part.

Chronicle of a Soil Bacterium: Paenibacillus polymyxa E681 as a Tiny Guardian of Plant and Human Health

“…Paenilipoheptin was recently identified by genome mining of P. polymyxa E681. Genome analysis of E681 revealed that the paenilipoheptin BGC is composed of five ORFs encoding the hybrid NRPS- Trans -AT-PKS (Vater et al, 2018). The first two ORFs ( phnAB ) encode Trans -AT-PKS, and the rest ( phnCDE ) encode NRPSs.…”

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“…While the peaks with low intensity exhibited the mass spectrum of nunamycin (m/z 1138.592) [29], putisolvin II (m/z 1436.7) [30], penta-acyl lipid A (m/z 1562.846 and 1693.901) [31] and xantholysin (m/z 1763.976, 1802.856). [32] In IMA5 (Figure 2b), the major peaks revealed the presence of fusaricidins (m/z 883.626, 897.661, 935.629, 954.715, 961.686, 968.733, 982.751 and 999.641), while the peaks with low intensity exhibited the mass spectrum of polymyxins (m/z 1191.871 and 1207.836) [33] and tridecaptins (m/z 1640.024, 1641.985 and 1655.997) [34,35]. In strains IMA4, IMA7 and IMA11 (Figure 2c), no lipopeptides were detected, as reported by [36].…”

Data_Sheet_1.PDF

“…The substrate amino acid of the adenylation domain (AD) of the hybrid PKS/NRPS was predicted to be D-glycine. It should be noted that this amino acid was not previously identified in paenilipoheptin (Vater et al, 2018).…”

“…genomes ( Table 2). The hits of the MIBiG database search were found to be BGC of paenilipoheptin (Vater et al, 2018), but had a low (52.0-82.0% depending on the module) sequence identity. The NaPDoS-based analysis of the ketosynthase (KS) domain of trans-AT PKS/NRPS showed that its sequence similarity with the sequences in the database was ≤59.0%.…”