Genomics-driven discovery of the pneumocandin biosynthetic gene cluster in the fungus Glarea lozoyensis

Li Chen,Zhiqiang An,Xingzhong Liu,Chengshu Wang,Shaojie Li,Meichun Xiang,Yongsheng Che,Francisco Javier Ortiz-López,Gerald F Bills,Xinyu Zhang,Qun Yue

doi:10.1186/1471-2164-14-339

Abstract

BackgroundThe antifungal therapy caspofungin is a semi-synthetic derivative of pneumocandin B0, a lipohexapeptide produced by the fungus Glarea lozoyensis, and was the first member of the echinocandin class approved for human therapy. The nonribosomal peptide synthetase (NRPS)-polyketide synthases (PKS) gene cluster responsible for pneumocandin biosynthesis from G. lozoyensis has not been elucidated to date. In this study, we report the elucidation of the pneumocandin biosynthetic gene cluster by whole genome sequencing of the G. lozoyensis wild-type strain ATCC 20868.ResultsThe pneumocandin biosynthetic gene cluster contains a NRPS (GLNRPS4) and a PKS (GLPKS4) arranged in tandem, two cytochrome P450 monooxygenases, seven other modifying enzymes, and genes for L-homotyrosine biosynthesis, a component of the peptide core. Thus, the pneumocandin biosynthetic gene cluster is significantly more autonomous and organized than that of the recently characterized echinocandin B gene cluster. Disruption mutants of GLNRPS4 and GLPKS4 no longer produced the pneumocandins (A0 and B0), and the Δglnrps4 and Δglpks4 mutants lost antifungal activity against the human pathogenic fungus Candida albicans. In addition to pneumocandins, the G. lozoyensis genome encodes a rich repertoire of natural product-encoding genes including 24 PKSs, six NRPSs, five PKS-NRPS hybrids, two dimethylallyl tryptophan synthases, and 14 terpene synthases.ConclusionsCharacterization of the gene cluster provides a blueprint for engineering new pneumocandin derivatives with improved pharmacological properties. Whole genome estimation of the secondary metabolite-encoding genes from G. lozoyensis provides yet another example of the huge potential for drug discovery from natural products from the fungal kingdom.

Highlights

The antifungal therapy caspofungin is a semi-synthetic derivative of pneumocandin B0, a lipohexapeptide produced by the fungus Glarea lozoyensis, and was the first member of the echinocandin class approved for human therapy
We report the elucidation of the pneumocandin biosynthetic gene cluster by genome sequencing of the G. lozoyensis WT strain American Type Culture Collection (ATCC) 20868
Consistent with previous studies by our group [25,26], a combined phylogenomic and phylogenetic analysis confirmed that G. lozoyensis belonged the same major phylogenetic lineage as the plant pathogenic fungi, Sclerotinia sclerotiorum and Botrytis cinerea [27], and the wood endophytic fungus, Ascocoryne sarcoides, the Helotiales [28] (Figure 3)

Summary

Introduction

The antifungal therapy caspofungin is a semi-synthetic derivative of pneumocandin B0, a lipohexapeptide produced by the fungus Glarea lozoyensis, and was the first member of the echinocandin class approved for human therapy. The nonribosomal peptide synthetase (NRPS)-polyketide synthases (PKS) gene cluster responsible for pneumocandin biosynthesis from G. lozoyensis has not been elucidated to date. We report the elucidation of the pneumocandin biosynthetic gene cluster by whole genome sequencing of the G. lozoyensis wild-type strain ATCC 20868. Fungi frequently cause deadly infections in immunocompromised patients resulting from HIV infection, cancer chemotherapy, and organ transplantation [1]. Until the introduction of caspofungin (CANCIDASTM) in 2001, antifungal therapy was limited to the use of polyenes (amphotericin B), azoles, and flucytosine which have high failure rates during management of fungal infection, (a).

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