11 New Avenues Toward Drug Discovery in Fungi
MICHAL FLAK
1,2
, MARIO K. C. KRESPACH
1,2
, ANNICA J. PSCHIBUL
1,2 , VOLKER SCHROECKH
1 ,
AXEL A. BRAKHAGE
1,2
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
II. Molecular Biology Methods for Fungal Natural
Product Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
A. Manipulation of Regulatory Elements . . . . . . 269
B. Heterologous Expression of Fungal
Biosynthetic Gene Clusters . . . . . . . . . . . . . . . . . 271
C. Molecular Engineering of Biosynthetic
Clusters and Combinatorial Synthetic
Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
D. Novel Techniques for Natural Product
Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
III. Fungal Interactions as a Source of New
Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
A. Induction of Natural Product Formation by
Co-cultivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
B. Discovery of Fungal Natural Products
Inspired by Ecological Interactions . . . . . . . . . 280
IV. Natural Product Discovery in Fungi in the Age
of Omics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
A. Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
B. Transcriptomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
C. Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
D. Metabolomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
E. Integration of Omics Data . . . . . . . . . . . . . . . . . . 285
V. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
I. Introduction
Fungi are a valuable source of medically important natural products (NPs), mostly secondary
metabolites (SMs), low- to medium-molecularmass organic compounds that are not directly
involved in growth, development, or reproduction of the producing organism. Among them,
the antibiotic penicillin, the antifungal griseofulvin, the anti-hypercholesterolemic agent lovastatin, the immunosuppressant cyclosporin,
and the antitumor compound asperlin are
prominent examples (Brakhage 2013).
Classical techniques to discover bioactive
SMs often begin with microbial culture extracts,
followed by iterative rounds of fractionation
and bioassays for activity measurement (Brakhage and Schroeckh 2011). This strategy was
highly successful, yielding a number of “key
access antibiotics” on the WHO Model List of
Essential Medicines (WHO 2017). On the other
hand, metabolites, which are produced in a sufficient amount, facilitating isolation, were preferentially detected. Despite several thousand
SMs having been isolated in this way, with a
growing number of identified compounds
(Hautbergue et al. 2018), re-identification of
known molecules has become a bottleneck of
NP discovery, hindering the discovery of novel
ones (Be ´rdy 2005). The lack of new antibiotics
introduced into the market, combined with the
rise of antibiotic-resistant bacterial and fungal
strains, forms the basis of a phenomenon called
the “antibiotic innovation gap” (Payne et al.
2007). Due to this problematic development,
new strategies to discover novel, unexploited
antibiotics are urgently needed.
1 Department of Molecular and Applied Microbiology, Leibniz
Institute for Natural Product Research and Infection Biology
(HKI), Jena, Germany; e-mail: michal.flak@leibniz-hki.de;
mario.krespach@leibniz-hki.de; annica.pschibul@leibniz-hki.
de; volker.schroeckh@leibniz-hki.de; axel.brakhage@leibnizhki.de
2 Institute of Microbiology, Friedrich Schiller University, Jena,
Germany
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020
MICHAL FLAK
1,2
, MARIO K. C. KRESPACH
1,2
, ANNICA J. PSCHIBUL
1,2 , VOLKER SCHROECKH
1 ,
AXEL A. BRAKHAGE
1,2
CONTENTS
I. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
II. Molecular Biology Methods for Fungal Natural
Product Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269
A. Manipulation of Regulatory Elements . . . . . . 269
B. Heterologous Expression of Fungal
Biosynthetic Gene Clusters . . . . . . . . . . . . . . . . . 271
C. Molecular Engineering of Biosynthetic
Clusters and Combinatorial Synthetic
Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
D. Novel Techniques for Natural Product
Discovery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
III. Fungal Interactions as a Source of New
Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
A. Induction of Natural Product Formation by
Co-cultivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
B. Discovery of Fungal Natural Products
Inspired by Ecological Interactions . . . . . . . . . 280
IV. Natural Product Discovery in Fungi in the Age
of Omics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
A. Genomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
B. Transcriptomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
C. Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
D. Metabolomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
E. Integration of Omics Data . . . . . . . . . . . . . . . . . . 285
V. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
I. Introduction
Fungi are a valuable source of medically important natural products (NPs), mostly secondary
metabolites (SMs), low- to medium-molecularmass organic compounds that are not directly
involved in growth, development, or reproduction of the producing organism. Among them,
the antibiotic penicillin, the antifungal griseofulvin, the anti-hypercholesterolemic agent lovastatin, the immunosuppressant cyclosporin,
and the antitumor compound asperlin are
prominent examples (Brakhage 2013).
Classical techniques to discover bioactive
SMs often begin with microbial culture extracts,
followed by iterative rounds of fractionation
and bioassays for activity measurement (Brakhage and Schroeckh 2011). This strategy was
highly successful, yielding a number of “key
access antibiotics” on the WHO Model List of
Essential Medicines (WHO 2017). On the other
hand, metabolites, which are produced in a sufficient amount, facilitating isolation, were preferentially detected. Despite several thousand
SMs having been isolated in this way, with a
growing number of identified compounds
(Hautbergue et al. 2018), re-identification of
known molecules has become a bottleneck of
NP discovery, hindering the discovery of novel
ones (Be ´rdy 2005). The lack of new antibiotics
introduced into the market, combined with the
rise of antibiotic-resistant bacterial and fungal
strains, forms the basis of a phenomenon called
the “antibiotic innovation gap” (Payne et al.
2007). Due to this problematic development,
new strategies to discover novel, unexploited
antibiotics are urgently needed.
1 Department of Molecular and Applied Microbiology, Leibniz
Institute for Natural Product Research and Infection Biology
(HKI), Jena, Germany; e-mail: michal.flak@leibniz-hki.de;
mario.krespach@leibniz-hki.de; annica.pschibul@leibniz-hki.
de; volker.schroeckh@leibniz-hki.de; axel.brakhage@leibnizhki.de
2 Institute of Microbiology, Friedrich Schiller University, Jena,
Germany
Genetics and Biotechnology, 3 rd Edition
The Mycota II
J.P. Benz, K. Schipper (Eds.)
© Springer Nature Switzerland AG 2020