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Wang C, Xiao D, Dun B, Yin M, Tsega AS, Xie L, Li W, Yue Q, Wang S, Gao H, Lin M, Zhang L, Molnár I, Xu Y. Chemometrics and genome mining reveal an unprecedented family of sugar acid-containing fungal nonribosomal cyclodepsipeptides. Proc Natl Acad Sci U S A 2022; 119:e2123379119. [PMID: 35914151 PMCID: PMC9371744 DOI: 10.1073/pnas.2123379119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/23/2022] [Indexed: 02/03/2023] Open
Abstract
Xylomyrocins, a unique group of nonribosomal peptide secondary metabolites, were discovered in Paramyrothecium and Colletotrichum spp. fungi by employing a combination of high-resolution tandem mass spectrometry (HRMS/MS)-based chemometrics, comparative genome mining, gene disruption, stable isotope feeding, and chemical complementation techniques. These polyol cyclodepsipeptides all feature an unprecedented d-xylonic acid moiety as part of their macrocyclic scaffold. This biosynthon is derived from d-xylose supplied by xylooligosaccharide catabolic enzymes encoded in the xylomyrocin biosynthetic gene cluster, revealing a novel link between carbohydrate catabolism and nonribosomal peptide biosynthesis. Xylomyrocins from different fungal isolates differ in the number and nature of their amino acid building blocks that are nevertheless incorporated by orthologous nonribosomal peptide synthetase (NRPS) enzymes. Another source of structural diversity is the variable choice of the nucleophile for intramolecular macrocyclic ester formation during xylomyrocin chain termination. This nucleophile is selected from the multiple available alcohol functionalities of the polyol moiety, revealing a surprising polyspecificity for the NRPS terminal condensation domain. Some xylomyrocin congeners also feature N-methylated amino acid residues in positions where the corresponding NRPS modules lack N-methyltransferase (M) domains, providing a rare example of promiscuous methylation in the context of an NRPS with an otherwise canonical, collinear biosynthetic program.
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Affiliation(s)
- Chen Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Dongliang Xiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Baoqing Dun
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Miaomiao Yin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Adigo Setargie Tsega
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Linan Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Wenhua Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Qun Yue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Sibao Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Han Gao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, P.R. China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, Tucson, AZ 85706
- VTT Technical Research Centre of Finland, FI-02044 VTT, Espoo, Finland
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
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Pinneh EC, Mina JG, Stark MJR, Lindell SD, Luemmen P, Knight MR, Steel PG, Denny PW. The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity. Sci Rep 2019; 9:8083. [PMID: 31147620 PMCID: PMC6542793 DOI: 10.1038/s41598-019-44544-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/17/2019] [Indexed: 12/16/2022] Open
Abstract
Resistance to 157 different herbicides and 88% of known sites of action has been observed, with many weeds resistant to two or more modes. Coupled with tighter environmental regulation, this demonstrates the need to identify new modes of action and novel herbicides. The plant sphingolipid biosynthetic enzyme, inositol phosphorylceramide synthase (IPCS), has been identified as a novel, putative herbicide target. The non-mammalian nature of this enzyme offers the potential of discovering plant specific inhibitory compounds with minimal impact on animals and humans, perhaps leading to the development of new non-toxic herbicides. The best characterised and most highly expressed isoform of the enzyme in the model-dicot Arabidopsis, AtIPCS2, was formatted into a yeast-based assay which was then utilized to screen a proprietary library of over 11,000 compounds provided by Bayer AG. Hits from this screen were validated in a secondary in vitro enzyme assay. These studies led to the identification of a potent inhibitor that showed selectivity for AtIPCS2 over the yeast orthologue, and activity against Arabidopsis seedlings. This work highlighted the use of a yeast-based screening assay to discover herbicidal compounds and the status of the plant IPCS as a novel herbicidal target.
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Affiliation(s)
- Elizabeth C Pinneh
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK
| | - John G Mina
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Michael J R Stark
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Stephen D Lindell
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Peter Luemmen
- Bayer AG, Crop Science Division, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Marc R Knight
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Patrick G Steel
- Department of Chemistry, Durham University, Durham, DH1 3LE, UK.
| | - Paul W Denny
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.
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Abstract
To date approximately 100 000 fungal species are known although far more than one million are expected. The variety of species and the diversity of their habitats, some of them less exploited, allow the conclusion that fungi continue to be a rich source of new metabolites. Besides the conventional fungal isolates, an increasing interest in endophytic and in marine-derived fungi has been noticed. In addition new screening strategies based on innovative chemical, biological, and genetic approaches have led to novel fungal metabolites in recent years. The present review focuses on new fungal natural products published from 2009 to 2013 highlighting the originality of the structures and their biological potential. Furthermore synthetic products based on fungal metabolites as well as new developments in the uses or the biological activity of known compounds or new derivatives are discussed.
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Affiliation(s)
- Anja Schueffler
- Institut für Biotechnologie und Wirkstoff-Forschung (Institute of Biotechnology and Drug Research), Erwin-Schroedinger-Str. 56, 67663 Kaiserslautern, Germany.
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Haplofungins, novel inositol phosphorylceramide synthase inhibitors, from Lauriomyces bellulus SANK 26899 III. Absolute structure of haplofungin A. J Antibiot (Tokyo) 2009; 62:559-63. [DOI: 10.1038/ja.2009.74] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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