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

Chen L, Yue Q, Zhang X, Xiang M, Wang C, Li S, Che Y, Ortiz-López FJ, Bills GF, Liu X, An Z - BMC Genomics (2013)

Bottom Line: Thus, the pneumocandin biosynthetic gene cluster is significantly more autonomous and organized than that of the recently characterized echinocandin B gene cluster.Characterization 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

ABSTRACT

Background: 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. 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.

Results: The 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.

Conclusions: Characterization 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.

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Schematic representation of the pneumocandins and echinocandin B biosynthetic gene cluster. (a) Pneumocandins biosynthetic gene cluster. (b) Echinocandin B biosynthetic gene clusters (including L-homotyrosine biosynthetic gene cluster) based on [8,24].
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Figure 8: Schematic representation of the pneumocandins and echinocandin B biosynthetic gene cluster. (a) Pneumocandins biosynthetic gene cluster. (b) Echinocandin B biosynthetic gene clusters (including L-homotyrosine biosynthetic gene cluster) based on [8,24].

Mentions: NRPSs include modules that incorporate amino acids into the final peptide product. Each module minimally contains three domains, the adenylation domain (A domain), the thiolation domain (T domain), and the condensation domain (C domain). In addition to its abundant and diverse PKS pathways, the G. lozoyensis genome harbored six NRPS genes. Three NRPSs (GLNRPS2, GLNRPS3, GLNRPS5), contained a single module, encoding products with a single amino acid, the other three NRPSs (GLNRPS1, GLNRPS4, GLNRPS6), were multi-modular, encoding products with more than one amino acids (Figure 7). Gene cluster analysis revealed that GLNRPS1 (with two modules), GLNRPS2 and one NRPS-like genes located in the same cluster flanked by three clavaminate synthases (oxygenases) and MFS general substrate transporter genes (Additional file 1: Figure S1). These data indicated that a hydroxylation tetrapeptide product may be formed and excreted. GLNRPS4, with six modules that encode a hexapeptide product and located in a cluster bordered by various modifying enzymes, was proposed to be responsible for pneumocandin biosynthesis (Figure 7 and Figure 8a). Domain analysis revealed that GLNRPS6 had five modules, and module 1, module 3, module 5 contain one epimerization (E) domain respectively. The glnrps6 was located in a cluster flanked by one MFS general substrate transporter gene, and thus suggested that a pentapeptide with three D-amino acids may be formed and excreted. Thirteen additional NRPS-like genes clusters were identified in G. lozoyensis, and some of them were located in clusters flanked by cytochrome P450, methyltranferase and transporter genes, thus indicating some hydroxylation and methylation products may be formed and excreted (Additional file 1: Figure S1).


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

Chen L, Yue Q, Zhang X, Xiang M, Wang C, Li S, Che Y, Ortiz-López FJ, Bills GF, Liu X, An Z - BMC Genomics (2013)

Schematic representation of the pneumocandins and echinocandin B biosynthetic gene cluster. (a) Pneumocandins biosynthetic gene cluster. (b) Echinocandin B biosynthetic gene clusters (including L-homotyrosine biosynthetic gene cluster) based on [8,24].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3672099&req=5

Figure 8: Schematic representation of the pneumocandins and echinocandin B biosynthetic gene cluster. (a) Pneumocandins biosynthetic gene cluster. (b) Echinocandin B biosynthetic gene clusters (including L-homotyrosine biosynthetic gene cluster) based on [8,24].
Mentions: NRPSs include modules that incorporate amino acids into the final peptide product. Each module minimally contains three domains, the adenylation domain (A domain), the thiolation domain (T domain), and the condensation domain (C domain). In addition to its abundant and diverse PKS pathways, the G. lozoyensis genome harbored six NRPS genes. Three NRPSs (GLNRPS2, GLNRPS3, GLNRPS5), contained a single module, encoding products with a single amino acid, the other three NRPSs (GLNRPS1, GLNRPS4, GLNRPS6), were multi-modular, encoding products with more than one amino acids (Figure 7). Gene cluster analysis revealed that GLNRPS1 (with two modules), GLNRPS2 and one NRPS-like genes located in the same cluster flanked by three clavaminate synthases (oxygenases) and MFS general substrate transporter genes (Additional file 1: Figure S1). These data indicated that a hydroxylation tetrapeptide product may be formed and excreted. GLNRPS4, with six modules that encode a hexapeptide product and located in a cluster bordered by various modifying enzymes, was proposed to be responsible for pneumocandin biosynthesis (Figure 7 and Figure 8a). Domain analysis revealed that GLNRPS6 had five modules, and module 1, module 3, module 5 contain one epimerization (E) domain respectively. The glnrps6 was located in a cluster flanked by one MFS general substrate transporter gene, and thus suggested that a pentapeptide with three D-amino acids may be formed and excreted. Thirteen additional NRPS-like genes clusters were identified in G. lozoyensis, and some of them were located in clusters flanked by cytochrome P450, methyltranferase and transporter genes, thus indicating some hydroxylation and methylation products may be formed and excreted (Additional file 1: Figure S1).

Bottom Line: Thus, the pneumocandin biosynthetic gene cluster is significantly more autonomous and organized than that of the recently characterized echinocandin B gene cluster.Characterization 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

ABSTRACT

Background: 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. 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.

Results: The 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.

Conclusions: Characterization 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.

Show MeSH
Related in: MedlinePlus