Genomics-driven discovery of a biosynthetic gene cluster required for the synthesis of BII-Rafflesfungin from the fungus Phoma sp. F3723

Swati Sinha,Falicia Goh,Siew Bee Ng,Mohammad Alfatah,Alexander Lezhava,Swaine L Chen,Sharon Crasta,Yoganathan Kanagasundaram,Kia-Ngee Low,Choy-Eng Nge,Frank Eisenhaber,Huibin Zhang,Veronica Ng,Prakash Arumugam,Birgit Eisenhaber,Chung Yan Leong

doi:10.1186/s12864-019-5762-6

Abstract

BackgroundPhomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. We combed publicly available Phoma genomes but failed to find any putative biosynthetic gene cluster that could account for its biosynthesis.ResultsTherefore, we sequenced the genome of one of our Phoma strains (F3723) previously identified as having antifungal activity in a high-throughput screen. We found a biosynthetic gene cluster that was predicted to synthesize a cyclic lipodepsipeptide that differs in the amino acid composition compared to Phomafungin. Antifungal activity guided isolation yielded a new compound, BII-Rafflesfungin, the structure of which was determined.ConclusionsWe describe the NRPS-t1PKS cluster ‘BIIRfg’ compatible with the synthesis of the cyclic lipodepsipeptide BII-Rafflesfungin [HMHDA-L-Ala-L-Glu-L-Asn-L-Ser-L-Ser-D-Ser-D-allo-Thr-Gly]. We report new Stachelhaus codes for Ala, Glu, Asn, Ser, Thr, and Gly. We propose a mechanism for BII-Rafflesfungin biosynthesis, which involves the formation of the lipid part by BIIRfg_PKS followed by activation and transfer of the lipid chain by a predicted AMP-ligase on to the first PCP domain of the BIIRfg_NRPS gene.

Highlights

Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown
No nonribosomal peptide synthetases (NRPSs)/polyketide synthases (PKSs) was detected that could be speculated as the correct gene cluster for the synthesis of Phomafungin
Because we did not have access to the original Phoma strain from which Phomafungin was isolated, we tested extracts derived from Phoma strains in a large strain collection [5] for antifungal activity and found that the extract of one strain, F3723, had growth inhibitory activity against Candida albicans

Summary

Introduction

Phomafungin is a recently reported broad spectrum antifungal compound but its biosynthetic pathway is unknown. Nonribosomal peptides and polyketides represent a large class of natural products Despite their immense structural and functional diversity, they are synthesized by strikingly similar multimodular enzymes called nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), respectively [7,8,9]. The sequences of both types of enzymes, NRPSs and PKSs, consist of modules where each module is thought to be responsible for catalyzing the attachment of a specific substrate on-to the growing chain in an assembly-line like manner [7, 8]. Amino acids (NRPS) or simple carboxylic acids (PKS) are the

Methods

Results

Discussion

Conclusion