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Lu Y, Li Y, Dou M, Liu D, Lin W, Fan A. Discovery of a Hybrid Molecule with Phytotoxic Activity by Genome Mining, Heterologous Expression, and OSMAC Strategy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18520-18527. [PMID: 39105744 DOI: 10.1021/acs.jafc.4c04244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Genome mining in association with the OSMAC (one strain, many compounds) approach provides a feasible strategy to extend the chemical diversity and novelty of natural products. In this study, we identified the biosynthetic gene cluster (BGC) of restricticin, a promising antifungal agent featuring a reactive primary amine, from the fungus Aspergillus sclerotiorum LZDX-33-4 by genome mining. Combining heterologous expression and the OSMAC strategy resulted in the production of a new hybrid product (1), along with N-acetyl-restricticin (2) and restricticinol (3). The structure of 1 was determined by spectroscopic data, including optical rotation and electronic circular dichroism (ECD) calculations, for configurational assignment. Compound 1 represents a fusion of restricticin and phytotoxic cichorin. The biosynthetic pathway of 1 was proposed, in which the condensation of a primary amine of restricticin with a precursor of cichorine was postulated. Compound 1 at 5 mM concentration inhibited the growth of the shoots and roots of Lolium perenne, Festuca arundinacea, and Lactuca sativa with inhibitory rates of 71.3 and 88.7% for L. perenne, 79.4 and 73.0% for F. arundinacea, and 58.2 and 52.9% for L. sativa. In addition, compound 1 at 25 μg/mL showed moderate antifungal activity against Fusarium fujikuroi and Trichoderma harzianum with inhibition rates of 22.6 and 31.6%, respectively. These results suggest that heterologous expression in conjunction with the OSMAC approach provides a promising strategy to extend the metabolite novelty due to the incorporation of endogenous metabolites from the host strain with exogenous compounds, leading to the production of more complex compounds and the acquisition of new physiological functions.
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Affiliation(s)
- Yubo Lu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yanpeng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Min Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Institute of Ocean Research, Ningbo Institute of Marine Medicine, Peking University, Ningbo 315832, Zhejiang, China
| | - Aili Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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2
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Son YE, Cho HJ, Park HS. The MYB-like protein MylA contributes to conidiogenesis and conidial germination in Aspergillus nidulans. Commun Biol 2024; 7:768. [PMID: 38918572 PMCID: PMC11199622 DOI: 10.1038/s42003-024-05866-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/26/2024] [Indexed: 06/27/2024] Open
Abstract
Myeloblastosis (MYB)-like proteins are a family of highly conserved transcription factors in animals, plants, and fungi and are involved in the regulation of mRNA expression of genes. In this study, we identified and characterized one MYB-like protein in the model organism Aspergillus nidulans. We screened the mRNA levels of genes encoding MYB-like proteins containing two MYB repeats in conidia and found that the mRNA levels of four genes including flbD, cicD, and two uncharacterized genes, were high in conidia. To investigate the roles of two uncharacterized genes, AN4618 and AN10944, deletion mutants for each gene were generated. Our results revealed that AN4618 was required for fungal development. Therefore, we further investigated the role of AN4618, named as mylA, encoding the MYB-like protein containing two MYB repeats. Functional studies revealed that MylA was essential for normal fungal growth and development. Phenotypic and transcriptomic analyses demonstrated that deletion of mylA affected stress tolerance, cell wall integrity, and long-term viability in A. nidulans conidia. In addition, the germination rate of the mylA deletion mutant conidia was decreased compared with that of the wild-type conidia. Overall, this study suggests that MylA is critical for appropriate development, conidial maturation, dormancy, and germination in A. nidulans.
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Affiliation(s)
- Ye-Eun Son
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - He-Jin Cho
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 41566, Republic of Korea.
- Department of Integrative Biology, Kyungpook National University, Daegu, 41566, Republic of Korea.
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3
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Shama SM, Elissawy AM, Salem MA, Youssef FS, Elnaggar MS, El-Seedi HR, Khalifa SAM, Briki K, Hamdan DI, Singab ANB. Comparative metabolomics study on the secondary metabolites of the red alga, Corallina officinalis and its associated endosymbiotic fungi. RSC Adv 2024; 14:18553-18566. [PMID: 38903055 PMCID: PMC11187739 DOI: 10.1039/d4ra01055h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/20/2024] [Indexed: 06/22/2024] Open
Abstract
Marine endosymbionts have gained remarkable interest in the last three decades in terms of natural products (NPs) isolated thereof, emphasizing the chemical correlations with those isolated from the host marine organism. The current study aimed to conduct comparative metabolic profiling of the marine red algae Corallina officinalis, and three fungal endosymbionts isolated from its inner tissues namely, Aspergillus nidulans, A. flavipes and A. flavus. The ethyl acetate (EtOAc) extracts of the host organism as well as the isolated endosymbionts were analyzed using ultra-high performance liquid chromatography coupled to high resolution tandem mass spectrometry (UHPLC-MS/MS)in both positive and negative ion modes, applying both full scan (FS) and all ion fragmentation (AIF) modes. Extensive interpretation of the LC-MS/MS spectra had led to the identification of 76 metabolites belonging to different phytochemical classes including alkaloids, polyketides, sesquiterpenes, butyrolactones, peptides, fatty acids, isocoumarins, quinones, among others. Metabolites were tentatively identified by comparing the accurate mass and fragmentation pattern with metabolites previously reported in the literature, as well as bioinformatics analysis using GNPS. A relationship between the host C. officinalis and its endophytes (A. flavus, A. nidulans, and A. flavipes) was discovered. C. officinalis shares common metabolites with at least one of the three endosymbiotic fungi. Some metabolites have been identified in endophytes and do not exist in their host. Multivariate analysis (MVA) revealed discrimination of A. flavipes from Corallina officinalis and other associated endophytic Aspergillus fungi (A. flavus and A. nidulans).
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Affiliation(s)
- Sherif M Shama
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University Shibin Elkom 32511 Egypt
| | - Ahmed M Elissawy
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
- Center of Drug Discovery Research and Development, Ain-Shams University Cairo 11566 Egypt
| | - Mohamed A Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University Shibin Elkom 32511 Egypt
| | - Fadia S Youssef
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
| | - Mohamed S Elnaggar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
| | - Hesham R El-Seedi
- Chemistry Department, Faculty of Science, Islamic University of Madinah P. O. Box: 170 Madinah 42351 Saudi Arabia
| | - Shaden A M Khalifa
- International Research Center for Food Nutrition and Safety, Jiangsu University Zhenjiang 212013 China
- Psychiatry and Neurology Department, Capio Saint Göran's Hospital Sankt Göransplan 1 112 19 Stockholm Sweden
| | - Khaled Briki
- Laboratory of Organic Chemistry and Natural Substance, University Ziane Achour Djelfa Algeria
| | - Dalia Ibrahim Hamdan
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University Shibin Elkom 32511 Egypt
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
- Center of Drug Discovery Research and Development, Ain-Shams University Cairo 11566 Egypt
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Christinaki AC, Myridakis AI, Kouvelis VN. Genomic insights into the evolution and adaptation of secondary metabolite gene clusters in fungicolous species Cladobotryum mycophilum ATHUM6906. G3 (BETHESDA, MD.) 2024; 14:jkae006. [PMID: 38214578 PMCID: PMC10989895 DOI: 10.1093/g3journal/jkae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/01/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024]
Abstract
Mycophilic or fungicolous fungi can be found wherever fungi exist since they are able to colonize other fungi, which occupy a diverse range of habitats. Some fungicolous species cause important diseases on Basidiomycetes, and thus, they are the main reason for the destruction of mushroom cultivations. Nonetheless, despite their ecological significance, their genomic data remain limited. Cladobotryum mycophilum is one of the most aggressive species of the genus, destroying the economically important Agaricus bisporus cultivations. The 40.7 Mb whole genome of the Greek isolate ATHUM6906 is assembled in 16 fragments, including the mitochondrial genome and 2 small circular mitochondrial plasmids, in this study. This genome includes a comprehensive set of 12,282 protein coding, 56 rRNA, and 273 tRNA genes. Transposable elements, CAZymes, and pathogenicity related genes were also examined. The genome of C. mycophilum contained a diverse arsenal of genes involved in secondary metabolism, forming 106 biosynthetic gene clusters, which renders this genome as one of the most BGC abundant among fungicolous species. Comparative analyses were performed for genomes of species of the family Hypocreaceae. Some BGCs identified in C. mycophilum genome exhibited similarities to clusters found in the family Hypocreaceae, suggesting vertical heritage. In contrast, certain BGCs showed a scattered distribution among Hypocreaceae species or were solely found in Cladobotryum genomes. This work provides evidence of extensive BGC losses, horizontal gene transfer events, and formation of novel BGCs during evolution, potentially driven by neutral or even positive selection pressures. These events may increase Cladobotryum fitness under various environmental conditions and potentially during host-fungus interaction.
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Affiliation(s)
- Anastasia C Christinaki
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Antonis I Myridakis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Vassili N Kouvelis
- Section of Genetics and Biotechnology, Department of Biology, National and Kapodistrian University of Athens, Athens 15771, Greece
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5
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Lin SY, Oakley CE, Jenkinson CB, Chiang YM, Lee CK, Jones CG, Seidler PM, Nelson HM, Todd RB, Wang CCC, Oakley BR. A heterologous expression platform in Aspergillus nidulans for the elucidation of cryptic secondary metabolism biosynthetic gene clusters: discovery of the Aspergillus fumigatus sartorypyrone biosynthetic pathway. Chem Sci 2023; 14:11022-11032. [PMID: 37860661 PMCID: PMC10583710 DOI: 10.1039/d3sc02226a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/26/2023] [Indexed: 10/21/2023] Open
Abstract
Aspergillus fumigatus is a serious human pathogen causing life-threatening Aspergillosis in immunocompromised patients. Secondary metabolites (SMs) play an important role in pathogenesis, but the products of many SM biosynthetic gene clusters (BGCs) remain unknown. In this study, we have developed a heterologous expression platform in Aspergillus nidulans, using a newly created genetic dereplication strain, to express a previously unknown BGC from A. fumigatus and determine its products. The BGC produces sartorypyrones, and we have named it the spy BGC. Analysis of targeted gene deletions by HRESIMS, NMR, and microcrystal electron diffraction (MicroED) enabled us to identify 12 products from the spy BGC. Seven of the compounds have not been isolated previously. We also individually expressed the polyketide synthase (PKS) gene spyA and demonstrated that it produces the polyketide triacetic acid lactone (TAL), a potentially important biorenewable platform chemical. Our data have allowed us to propose a biosynthetic pathway for sartorypyrones and related natural products. This work highlights the potential of using the A. nidulans heterologous expression platform to uncover cryptic BGCs from A. fumigatus and other species, despite the complexity of their secondary metabolomes.
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Affiliation(s)
- Shu-Yi Lin
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles CA 90089 USA
| | - C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas 1200 Sunnyside Avenue Lawrence KS 66045 USA
| | - Cory B Jenkinson
- Department of Molecular Biosciences, University of Kansas 1200 Sunnyside Avenue Lawrence KS 66045 USA
| | - Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles CA 90089 USA
| | - Ching-Kuo Lee
- School of Pharmacy, College of Pharmacy, Taipei Medical University Taipei 11031 Taiwan
| | - Christopher G Jones
- The Arnold and Mabel Beckman Laboratory of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena California 91125 USA
| | - Paul M Seidler
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles CA 90089 USA
| | - Hosea M Nelson
- The Arnold and Mabel Beckman Laboratory of Chemical Synthesis, Division of Chemistry and Chemical Engineering, California Institute of Technology Pasadena California 91125 USA
| | - Richard B Todd
- Department of Plant Pathology, Kansas State University Manhattan KS 66506 USA
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California Los Angeles CA 90089 USA
- Department of Chemistry, University of Southern California Los Angeles CA 90089 USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas 1200 Sunnyside Avenue Lawrence KS 66045 USA
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An YN, Huang JH, Xu SF, Wang XL, Zhou CH, Xu ZG, Lei J, Chen ZZ. Unexpected Cascade Sequence Forming the C(sp 3)-N/C(sp 2)-C(sp 2) Bond: Direct Access to γ-Lactam-Fused Pyridones with Anticancer Activity. J Org Chem 2023; 88:7998-8009. [PMID: 37279456 DOI: 10.1021/acs.joc.3c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
An unexpected Ugi cascade reaction was developed for the facile construction of γ-lactam-fused pyridone derivatives with high tolerance of substrates. A C(sp3)-N bond and a C(sp2)-C(sp2) bond were formed together, accompanied by a chromone ring-opening in Ugi adducts, under the basic conditions without any metal catalyst for the whole process. Screening data of several difficult-to-inhibit cancer cell lines demonstrated that 7l displayed a high cytotoxicity against HCT116 cells (IC50 = 5.59 ± 0.78 μM). Taken together, our findings revealed new insights into the molecular mechanisms underlying compound 7l and provided potential usage of this scaffold for cancer therapeutics.
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Affiliation(s)
- Ya-Nan An
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, Chongqing University of Arts and Sciences, 319 Honghe Ave., Yongchuan, Chongqing 402160, China
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Jiu-Hong Huang
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, Chongqing University of Arts and Sciences, 319 Honghe Ave., Yongchuan, Chongqing 402160, China
| | - Shi-Fang Xu
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, Chongqing University of Arts and Sciences, 319 Honghe Ave., Yongchuan, Chongqing 402160, China
| | - Xiao-Lin Wang
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, Chongqing University of Arts and Sciences, 319 Honghe Ave., Yongchuan, Chongqing 402160, China
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Applied Chemistry of Chongqing Municipality, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Zhi-Gang Xu
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, Chongqing University of Arts and Sciences, 319 Honghe Ave., Yongchuan, Chongqing 402160, China
| | - Jie Lei
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, Chongqing University of Arts and Sciences, 319 Honghe Ave., Yongchuan, Chongqing 402160, China
| | - Zhong-Zhu Chen
- College of Pharmacy, National & Local Joint Engineering Research Center of Targeted and Innovative Therapeutics, IATTI, Chongqing University of Arts and Sciences, 319 Honghe Ave., Yongchuan, Chongqing 402160, China
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7
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Zhgun AA. Fungal BGCs for Production of Secondary Metabolites: Main Types, Central Roles in Strain Improvement, and Regulation According to the Piano Principle. Int J Mol Sci 2023; 24:11184. [PMID: 37446362 PMCID: PMC10342363 DOI: 10.3390/ijms241311184] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Filamentous fungi are one of the most important producers of secondary metabolites. Some of them can have a toxic effect on the human body, leading to diseases. On the other hand, they are widely used as pharmaceutically significant drugs, such as antibiotics, statins, and immunosuppressants. A single fungus species in response to various signals can produce 100 or more secondary metabolites. Such signaling is possible due to the coordinated regulation of several dozen biosynthetic gene clusters (BGCs), which are mosaically localized in different regions of fungal chromosomes. Their regulation includes several levels, from pathway-specific regulators, whose genes are localized inside BGCs, to global regulators of the cell (taking into account changes in pH, carbon consumption, etc.) and global regulators of secondary metabolism (affecting epigenetic changes driven by velvet family proteins, LaeA, etc.). In addition, various low-molecular-weight substances can have a mediating effect on such regulatory processes. This review is devoted to a critical analysis of the available data on the "turning on" and "off" of the biosynthesis of secondary metabolites in response to signals in filamentous fungi. To describe the ongoing processes, the model of "piano regulation" is proposed, whereby pressing a certain key (signal) leads to the extraction of a certain sound from the "musical instrument of the fungus cell", which is expressed in the production of a specific secondary metabolite.
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Affiliation(s)
- Alexander A Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Leninsky Prosp. 33-2, 119071 Moscow, Russia
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8
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Quantitative characterization of filamentous fungal promoters on a single-cell resolution to discover cryptic natural products. SCIENCE CHINA LIFE SCIENCES 2022; 66:848-860. [PMID: 36287342 DOI: 10.1007/s11427-022-2175-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/15/2022] [Indexed: 11/05/2022]
Abstract
Characterization of filamentous fungal regulatory elements remains challenging because of time-consuming transformation technologies and limited quantitative methods. Here we established a method for quantitative assessment of filamentous fungal promoters based on flow cytometry detection of the superfolder green fluorescent protein at single-cell resolution. Using this quantitative method, we acquired a library of 93 native promoter elements from Aspergillus nidulans in a high-throughput format. The strengths of identified promoters covered a 37-fold range by flow cytometry. PzipA and PsltA were identified as the strongest promoters, which were 2.9- and 1.5-fold higher than that of the commonly used constitutive promoter PgpdA. Thus, we applied PzipA and PsltA to activate the silent nonribosomal peptide synthetase gene Afpes1 from Aspergillus fumigatus in its native host and the heterologous host A. nidulans. The metabolic products of Afpes1 were identified as new cyclic tetrapeptide derivatives, namely, fumiganins A and B. Our method provides an innovative strategy for natural product discovery in fungi.
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Devi A, Seth R, Masand M, Singh G, Holkar A, Sharma S, Singh A, Sharma RK. Spatial Genomic Resource Reveals Molecular Insights into Key Bioactive-Metabolite Biosynthesis in Endangered Angelica glauca Edgew. Int J Mol Sci 2022; 23:ijms231911064. [PMID: 36232367 PMCID: PMC9569870 DOI: 10.3390/ijms231911064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
Angelica glauca Edgew, which is an endangered medicinal and aromatic herb, is a rich source of numerous industrially important bioactive metabolites, including terpenoids, phenolics, and phthalides. Nevertheless, genomic interventions for the sustainable utilization and restoration of its genetic resources are greatly offset due to the scarcity of the genomic resources and key regulators of the underlying specialized metabolism. To unravel the global atlas of the specialized metabolism, the first spatial transcriptome sequencing of the leaf, stem, and root generated 109 million high-quality paired-end reads, assembled de novo into 81,162 unigenes, which exhibit a 61.53% significant homology with the six public protein databases. The organ-specific clustering grouped 1136 differentially expressed unigenes into four subclusters differentially enriched in the leaf, stem, and root tissues. The prediction of the transcriptional-interactome network by integrating enriched gene ontology (GO) and the KEGG metabolic pathways identified the key regulatory unigenes that correspond to terpenoid, flavonoid, and carotenoid biosynthesis in the leaf tissue, followed by the stem and root tissues. Furthermore, the stem and root-specific significant enrichments of phenylalanine ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), and caffeic acid 3-O-methyltransferase (COMT) indicate that phenylalanine mediated the ferulic acid biosynthesis in the stem and root. However, the root-specific expressions of NADPH-dependent alkenal/one oxidoreductase (NADPH-AOR), S-adenosyl-L-methionine-dependent methyltransferases (SDMs), polyketide cyclase (PKC), and CYP72A15 suggest the “root” as the primary site of phthalide biosynthesis. Additionally, the GC-MS and UPLC analyses corresponded to the organ-specific gene expressions, with higher contents of limonene and phthalide compounds in the roots, while there was a higher accumulation of ferulic acid in the stem, followed by in the root and leaf tissues. The first comprehensive genomic resource with an array of candidate genes of the key metabolic pathways can be potentially utilized for the targeted upscaling of aromatic and pharmaceutically important bioactive metabolites. This will also expedite genomic-assisted conservation and breeding strategies for the revival of the endangered A. glauca.
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Affiliation(s)
- Amna Devi
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Mamta Masand
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Gopal Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Ashlesha Holkar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Shikha Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Ashok Singh
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Environmental Technology, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, Himachal Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
- Correspondence: or
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Winkler M, Ling JG. Biocatalytic carboxylate reduction – recent advances and new enzymes. ChemCatChem 2022. [DOI: 10.1002/cctc.202200441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Margit Winkler
- Technische Universitat Graz Austrian Centre of Industrial Biotechnology Petersgasse 14 8010 Graz AUSTRIA
| | - Jonathan Guyang Ling
- Universiti Kebangsaan Malaysia Fakulti Sains dan Teknologi Department of Biological Sciences and Biotechnology 43600 Bangi MALAYSIA
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11
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Liu Q, Zhang D, Xu Y, Gao S, Gong Y, Cai X, Yao M, Yang X. Cloning and Functional Characterization of the Polyketide Synthases Based on Genome Mining of Preussia isomera XL-1326. Front Microbiol 2022; 13:819086. [PMID: 35602042 PMCID: PMC9116485 DOI: 10.3389/fmicb.2022.819086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
Fungal polyketides (PKs) are one of the largest families of structurally diverse bioactive natural products biosynthesized by multidomain megasynthases, in which thioesterase (TE) domains act as nonequivalent decision gates determining both the shape and the yield of the polyketide intermediate. The endophytic fungus Preussia isomera XL-1326 was discovered to have an excellent capacity for secreting diverse bioactive PKs, i.e., the hot enantiomers (±)-preuisolactone A with antibacterial activity, the single-spiro minimoidione B with α-glucosidase inhibition activity, and the uncommon heptaketide setosol with antifungal activity, which drive us to illustrate how the unique PKs are biosynthesized. In this study, we first reported the genome sequence information of P. isomera. Based on genome mining, we discovered nine transcriptionally active genes encoding polyketide synthases (PKSs), Preu1–Preu9, of which those of Preu3, Preu4, and Preu6 were cloned and functionally characterized due to possessing complete sets of synthetic and release domains. Through heterologous expression in Saccharomyces cerevisiae, Preu3 and Preu6 could release high yields of orsellinic acid (OA) derivatives [3-methylorsellinic acid (3-MOA) and lecanoric acid, respectively]. Correspondingly, we found that Preu3 and Preu6 were clustered into OA derivative synthase groups by phylogenetic analysis. Next, with TE domain swapping, we constructed a novel “non-native” PKS, Preu6-TEPreu3, which shared a very low identity with OA synthase, OrsA, from Aspergillus nidulans but could produce a large amount of OA. In addition, with the use of Preu6-TEPreu3, we synthesized methyl 3-methylorsellinate (synthetic oak moss of great economic value) from 3-MOA as the substrate, and interestingly, 3-MOA exhibited remarkable antibacterial activities, while methyl 3-methylorsellinate displayed broad-spectrum antifungal activity. Taken together, we identified two novel PKSs to biosynthesize 3-MOA and lecanoric acid, respectively, with information on such kinds of PKSs rarely reported, and constructed one novel “non-native” PKS to largely biosynthesize OA. This work is our first step to explore the biosynthesis of the PKs in P. isomera, and it also provides a new platform for high-level environment-friendly production of OA derivatives and the development of new antimicrobial agents.
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Affiliation(s)
- Qingpei Liu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Dan Zhang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Yao Xu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Shuaibiao Gao
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Yifu Gong
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Xianhua Cai
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Ming Yao
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
| | - Xiaolong Yang
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan, China
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12
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Ninomiya A, Urayama SI, Hagiwara D. Antibacterial diphenyl ether production induced by co-culture of Aspergillus nidulans and Aspergillus fumigatus. Appl Microbiol Biotechnol 2022; 106:4169-4185. [PMID: 35595930 DOI: 10.1007/s00253-022-11964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/04/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Fungi are a rich source of secondary metabolites with potent biological activities. Co-culturing a fungus with another microorganism has drawn much attention as a practical method for stimulating fungal secondary metabolism. However, in most cases, the molecular mechanisms underlying the activation of secondary metabolite production in co-culture are poorly understood. To elucidate such a mechanism, in this study, we established a model fungal-fungal co-culture system, composed of Aspergillus nidulans and Aspergillus fumigatus. In the co-culture of A. nidulans and A. fumigatus, production of antibacterial diphenyl ethers was enhanced. Transcriptome analysis by RNA-sequencing showed that the co-culture activated expression of siderophore biosynthesis genes in A. fumigatus and two polyketide biosynthetic gene clusters (the ors and cic clusters) in A. nidulans. Gene disruption experiments revealed that the ors cluster is responsible for diphenyl ether production in the co-culture. Interestingly, the ors cluster was previously reported to be upregulated by co-culture of A. nidulans with the bacterium Streptomyces rapamycinicus; orsellinic acid was the main product of the cluster in that co-culture. In other words, the main product of the ors cluster was different in fungal-fungal and bacterial-fungal co-culture. The genes responsible for biosynthesis of the bacterial- and fungal-induced polyketides were deduced using a heterologous expression system in Aspergillus oryzae. The molecular genetic mechanisms that trigger biosynthesis of two different types of compounds in A. nidulans in response to the fungus and the bacterium were demonstrated, which provides an insight into complex secondary metabolic response of fungi to microorganisms. KEY POINTS: • Co-culture of two fungal species triggered antibiotic diphenyl ether production. • The co-culture affected expression levels of several genes for secondary metabolism. • Gene cluster essential for induction of the antibiotics production was determined.
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Affiliation(s)
- Akihiro Ninomiya
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.,Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Syun-Ichi Urayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.,Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Daisuke Hagiwara
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan. .,Microbiology Research Center for Sustainability, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
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13
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Xu K, Li R, Zhu R, Li X, Xu Y, He Q, Xie F, Qiao Y, Luan X, Lou H. Xylarins A-D, Two Pairs of Diastereoisomeric Isoindoline Alkaloids from the Endolichenic Fungus Xylaria sp. Org Lett 2021; 23:7751-7754. [PMID: 34605655 DOI: 10.1021/acs.orglett.1c02730] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two pairs of diastereoisomeric isoindoline alkaloids, xylarins A-D (1-4), were isolated from the endolichenic fungus Xylaria sp. Xylarins A and B (1 and 2) possess a previously undescribed 5/6/5-5/6 polycyclic scaffold, featuring a combination of a novel dihydrobenzofurone unit and an isoindoline unit, while xylarins C and D (3 and 4) contain an additional N,N-dimethylaniline at the C-3' position. Their structures were elucidated by comprehensive spectroscopic analyses combined with single-crystal X-ray diffraction and electronic circular dichroism calculations. The plausible biosynthetic pathways and gene clusters for 1-4 were proposed. Compound 1 exhibited significant antithrombotic activity.
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Affiliation(s)
- Ke Xu
- Department of Natural Product Chemistry, Key Lab of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan 250012, People's Republic of China.,Department of Clinical Pharmacy, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, People's Republic of China
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, People's Republic of China
| | - Rongxiu Zhu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China
| | - Xiaobin Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, People's Republic of China
| | - Yuliang Xu
- Department of Natural Product Chemistry, Key Lab of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan 250012, People's Republic of China
| | - Qiaobian He
- Department of Natural Product Chemistry, Key Lab of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan 250012, People's Republic of China
| | - Fei Xie
- Department of Natural Product Chemistry, Key Lab of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan 250012, People's Republic of China
| | - Yanan Qiao
- Department of Natural Product Chemistry, Key Lab of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan 250012, People's Republic of China
| | - Xiaoyi Luan
- Department of Natural Product Chemistry, Key Lab of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan 250012, People's Republic of China
| | - Hongxiang Lou
- Department of Natural Product Chemistry, Key Lab of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan 250012, People's Republic of China
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14
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Wang W, Yu Y, Keller NP, Wang P. Presence, Mode of Action, and Application of Pathway Specific Transcription Factors in Aspergillus Biosynthetic Gene Clusters. Int J Mol Sci 2021; 22:ijms22168709. [PMID: 34445420 PMCID: PMC8395729 DOI: 10.3390/ijms22168709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 01/21/2023] Open
Abstract
Fungal secondary metabolites are renowned toxins as well as valuable sources of antibiotics, cholesterol-lowering drugs, and immunosuppressants; hence, great efforts were levied to understand how these compounds are genetically regulated. The genes encoding for the enzymes required for synthesizing secondary metabolites are arranged in biosynthetic gene clusters (BGCs). Often, BGCs contain a pathway specific transcription factor (PSTF), a valuable tool in shutting down or turning up production of the BGC product. In this review, we present an in-depth view of PSTFs by examining over 40 characterized BGCs in the well-studied fungal species Aspergillus nidulans and Aspergillus fumigatus. Herein, we find BGC size is a predictor for presence of PSTFs, consider the number and the relative location of PSTF in regard to the cluster(s) regulated, discuss the function and the evolution of PSTFs, and present application strategies for pathway specific activation of cryptic BGCs.
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Affiliation(s)
- Wenjie Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yuchao Yu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Correspondence: (N.P.K.); (P.W.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (W.W.); (Y.Y.)
- Correspondence: (N.P.K.); (P.W.)
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15
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Kim W, Liu R, Woo S, Kang KB, Park H, Yu YH, Ha HH, Oh SY, Yang JH, Kim H, Yun SH, Hur JS. Linking a Gene Cluster to Atranorin, a Major Cortical Substance of Lichens, through Genetic Dereplication and Heterologous Expression. mBio 2021; 12:e0111121. [PMID: 34154413 PMCID: PMC8262933 DOI: 10.1128/mbio.01111-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023] Open
Abstract
The depside and depsidone series compounds of polyketide origin accumulate in the cortical or medullary layers of lichen thalli. Despite the taxonomic and ecological significance of lichen chemistry and its pharmaceutical potentials, there has been no single piece of genetic evidence linking biosynthetic genes to lichen substances. Thus, we systematically analyzed lichen polyketide synthases (PKSs) for categorization and identification of the biosynthetic gene cluster (BGC) involved in depside/depsidone production. Our in-depth analysis of the interspecies PKS diversity in the genus Cladonia and a related Antarctic lichen, Stereocaulon alpinum, identified 45 BGC families, linking lichen PKSs to 15 previously characterized PKSs in nonlichenized fungi. Among these, we identified highly syntenic BGCs found exclusively in lichens producing atranorin (a depside). Heterologous expression of the putative atranorin PKS gene (coined atr1) yielded 4-O-demethylbarbatic acid, found in many lichens as a precursor compound, indicating an intermolecular cross-linking activity of Atr1 for depside formation. Subsequent introductions of tailoring enzymes into the heterologous host yielded atranorin, one of the most common cortical substances of macrolichens. Phylogenetic analysis of fungal PKS revealed that the Atr1 is in a novel PKS clade that included two conserved lichen-specific PKS families likely involved in biosynthesis of depsides and depsidones. Here, we provide a comprehensive catalog of PKS families of the genus Cladonia and functionally characterize a biosynthetic gene cluster from lichens, establishing a cornerstone for studying the genetics and chemical evolution of diverse lichen substances. IMPORTANCE Lichens play significant roles in ecosystem function and comprise about 20% of all known fungi. Polyketide-derived natural products accumulate in the cortical and medullary layers of lichen thalli, some of which play key roles in protection from biotic and abiotic stresses (e.g., herbivore attacks and UV irradiation). To date, however, no single lichen product has been linked to respective biosynthetic genes with genetic evidence. Here, we identified a gene cluster family responsible for biosynthesis of atranorin, a cortical substance found in diverse lichen species, by categorizing lichen polyketide synthase and reconstructing the atranorin biosynthetic pathway in a heterologous host. This study will help elucidate lichen secondary metabolism, harnessing the lichen's chemical diversity, hitherto obscured due to limited genetic information on lichens.
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Affiliation(s)
- Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Rundong Liu
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Sunmin Woo
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Kyo Bin Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, South Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Young Hyun Yu
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Hyung-Ho Ha
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, Changwon, South Korea
| | - Ji Ho Yang
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Hangun Kim
- College of Pharmacy, Sunchon National University, Suncheon, South Korea
- Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon, South Korea
| | - Sung-Hwan Yun
- Department of Medical Sciences, Soonchunhyang University, Asan, South Korea
| | - Jae-Seoun Hur
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
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16
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Guo Y, Ding L, Ghidinelli S, Gotfredsen CH, de la Cruz M, Mackenzie TA, Ramos MC, Sánchez P, Vicente F, Genilloud O, Coriani S, Larsen RW, Frisvad JC, Larsen TO. Taxonomy Driven Discovery of Polyketides from Aspergillus californicus. JOURNAL OF NATURAL PRODUCTS 2021; 84:979-985. [PMID: 33656895 DOI: 10.1021/acs.jnatprod.0c00866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Five new polyketides were isolated from the rare filamentous fungus Aspergillus californicus IBT 16748 including calidiol A (1); three phthalide derivatives califuranones A1, A2, and B (2-4); and a pair of enantiomers (-)-calitetralintriol A (-5) and (+)-calitetralintriol A (+5) together with four known metabolites (6-9). The structures of the new products were established by extensive spectroscopic analyses including HRMS and 1D and 2D NMR. The absolute configurations of two diastereomers 2 and 3 and the enantiomers (-5) and (+5) were assigned by comparing their experimental and calculated ECD data, whereas the absolute configuration of 4 was proposed by analogy. Compound 1 showed moderate activity against methicillin-resistant Staphylococcus aureus.
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Affiliation(s)
- Yaojie Guo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kgs. Lyngby, Denmark
| | - Ling Ding
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kgs. Lyngby, Denmark
| | - Simone Ghidinelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, I-25123 Brescia, Italy
| | - Charlotte H Gotfredsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Mercedes de la Cruz
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Thomas A Mackenzie
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Maria C Ramos
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Pilar Sánchez
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Olga Genilloud
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 34, 18016 Armilla, Granada, Spain
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - René W Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, DK-2800 Kgs. Lyngby, Denmark
| | - Jens C Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kgs. Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, DK-2800 Kgs. Lyngby, Denmark
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17
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Schüller A, Wolansky L, Berger H, Studt L, Gacek-Matthews A, Sulyok M, Strauss J. A novel fungal gene regulation system based on inducible VPR-dCas9 and nucleosome map-guided sgRNA positioning. Appl Microbiol Biotechnol 2020; 104:9801-9822. [PMID: 33006690 PMCID: PMC7595996 DOI: 10.1007/s00253-020-10900-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022]
Abstract
Programmable transcriptional regulation is a powerful tool to study gene functions. Current methods to selectively regulate target genes are mainly based on promoter exchange or on overexpressing transcriptional activators. To expand the discovery toolbox, we designed a dCas9-based RNA-guided synthetic transcription activation system for Aspergillus nidulans that uses enzymatically disabled "dead" Cas9 fused to three consecutive activation domains (VPR-dCas9). The dCas9-encoding gene is under the control of an estrogen-responsive promoter to allow induction timing and to avoid possible negative effects by strong constitutive expression of the highly active VPR domains. Especially in silent genomic regions, facultative heterochromatin and strictly positioned nucleosomes can constitute a relevant obstacle to the transcriptional machinery. To avoid this negative impact and to facilitate optimal positioning of RNA-guided VPR-dCas9 to targeted promoters, we have created a genome-wide nucleosome map from actively growing cells and stationary cultures to identify the cognate nucleosome-free regions (NFRs). Based on these maps, different single-guide RNAs (sgRNAs) were designed and tested for their targeting and activation potential. Our results demonstrate that the system can be used to regulate several genes in parallel and, depending on the VPR-dCas9 positioning, expression can be pushed to very high levels. We have used the system to turn on individual genes within two different biosynthetic gene clusters (BGCs) which are silent under normal growth conditions. This method also opens opportunities to stepwise activate individual genes in a cluster to decipher the correlated biosynthetic pathway. Graphical abstract KEYPOINTS: • An inducible RNA-guided transcriptional regulator based on VPR-dCas9 was established in Aspergillus nidulans. • Genome-wide nucleosome positioning maps were created that facilitate sgRNA positioning. • The system was successfully applied to activate genes within two silent biosynthetic gene clusters.
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Affiliation(s)
- Andreas Schüller
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Lisa Wolansky
- Institute Krems Bioanalytics , IMC FH Krems University of Applied Sciences , Krems, Austria
| | - Harald Berger
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Lena Studt
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
| | - Agnieszka Gacek-Matthews
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria
- Institute of Microbiology, Functional Microbiology Division, University of Veterinary Sciences Vienna, Wien, Austria
| | - Michael Sulyok
- Institute of Bioanalytics and Agrometabolomics, Department of Agrobiotechnology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad-Lorenz-Straße 20, A-3430 Tulln an der Donau, Austria
| | - Joseph Strauss
- Fungal Genetics Lab, Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences Vienna, BOKU-Campus Tulln, Konrad Lorenz Strasse 24, A-3430, Tulln an der Donau, Austria.
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18
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Caesar LK, Kelleher NL, Keller NP. In the fungus where it happens: History and future propelling Aspergillus nidulans as the archetype of natural products research. Fungal Genet Biol 2020; 144:103477. [PMID: 33035657 DOI: 10.1016/j.fgb.2020.103477] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 02/08/2023]
Abstract
In 1990 the first fungal secondary metabolite biosynthetic gene was cloned in Aspergillus nidulans. Thirty years later, >30 biosynthetic gene clusters (BGCs) have been linked to specific natural products in this one fungal species. While impressive, over half of the BGCs in A. nidulans remain uncharacterized and their compounds structurally and functionally unknown. Here, we provide a comprehensive review of past advances that have enabled A. nidulans to rise to its current status as a natural product powerhouse focusing on the discovery and annotation of secondary metabolite clusters. From genome sequencing, heterologous expression, and metabolomics to CRISPR and epigenetic manipulations, we present a guided tour through the evolution of technologies developed and utilized in the last 30 years. These insights provide perspective to future efforts to fully unlock the biosynthetic potential of A. nidulans and, by extension, the potential of other filamentous fungi.
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Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry, Northwestern University, Evanston, IL, United States
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, United States; Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States; Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin- Madison, Madison, WI, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States.
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19
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Ran H, Li SM. Fungal benzene carbaldehydes: occurrence, structural diversity, activities and biosynthesis. Nat Prod Rep 2020; 38:240-263. [PMID: 32779678 DOI: 10.1039/d0np00026d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to April 2020Fungal benzene carbaldehydes with salicylaldehydes as predominant representatives carry usually hydroxyl groups, prenyl moieties and alkyl side chains. They are found in both basidiomycetes and ascomycetes as key intermediates or end products of various biosynthetic pathways and exhibit diverse biological and pharmacological activities. The skeletons of the benzene carbaldehydes are usually derived from polyketide pathways catalysed by iterative fungal polyketide synthases. The aldehyde groups are formed by direct PKS releasing, reduction of benzoic acids or oxidation of benzyl alcohols.
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Affiliation(s)
- Huomiao Ran
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany.
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20
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Abstract
Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.
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Affiliation(s)
- Jason B Hedges
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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21
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Grau MF, Entwistle R, Oakley CE, Wang CCC, Oakley BR. Overexpression of an LaeA-like Methyltransferase Upregulates Secondary Metabolite Production in Aspergillus nidulans. ACS Chem Biol 2019; 14:1643-1651. [PMID: 31265232 DOI: 10.1021/acschembio.9b00380] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Fungal secondary metabolites (SMs) include medically valuable compounds as well as compounds that are toxic, carcinogenic, and/or contributors to fungal pathogenesis. It is consequently important to understand the regulation of fungal secondary metabolism. McrA is a recently discovered transcription factor that negatively regulates fungal secondary metabolism. Deletion of mcrA (mcrAΔ), the gene encoding McrA, results in upregulation of many SMs and alters the expression of more than 1000 genes. One gene strongly upregulated by the deletion of mcrA is llmG, a putative methyl transferase related to LaeA, a major regulator of secondary metabolism. We artificially upregulated llmG by replacing its promoter with strong constitutive promoters in strains carrying either wild-type mcrA or mcrAΔ. Upregulation of llmG on various media resulted in increased production of the important toxin sterigmatocystin and compounds from at least six major SM pathways. llmG is, thus, a master SM regulator. mcrAΔ generally resulted in greater upregulation of SMs than upregulation of llmG, indicating that the full effects of mcrA on secondary metabolism involve genes in addition to llmG. However, the combination of mcrAΔ and upregulation of llmG generally resulted in greater compound production than mcrAΔ alone (in one case more than 460 times greater than the control). This result indicates that deletion of mcrA and/or upregulation of llmG can likely be combined with other strategies for eliciting SM production to greater levels than can be obtained with any single strategy.
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Affiliation(s)
- Michelle F. Grau
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - C. Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Berl R. Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
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Integration of Fungus-Specific CandA-C1 into a Trimeric CandA Complex Allowed Splitting of the Gene for the Conserved Receptor Exchange Factor of CullinA E3 Ubiquitin Ligases in Aspergilli. mBio 2019; 10:mBio.01094-19. [PMID: 31213557 PMCID: PMC6581859 DOI: 10.1128/mbio.01094-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aspergillus species are important for biotechnological applications, like the production of citric acid or antibacterial agents. Aspergilli can cause food contamination or invasive aspergillosis to immunocompromised humans or animals. Specific treatment is difficult due to limited drug targets and emerging resistances. The CandA complex regulates, as a receptor exchange factor, the activity and substrate variability of the ubiquitin labeling machinery for 26S proteasome-mediated protein degradation. Only Aspergillus species encode at least two proteins that form a CandA complex. This study shows that Aspergillus species had to integrate a third component into the CandA receptor exchange factor complex that is unique to aspergilli and required for vegetative growth, sexual reproduction, and activation of the ubiquitin labeling machinery. These features have interesting implications for the evolution of protein complexes and could make CandA-C1 an interesting candidate for target-specific drug design to control fungal growth without affecting the human ubiquitin-proteasome system. E3 cullin-RING ubiquitin ligase (CRL) complexes recognize specific substrates and are activated by covalent modification with ubiquitin-like Nedd8. Deneddylation inactivates CRLs and allows Cand1/A to bind and exchange substrate recognition subunits. Human as well as most fungi possess a single gene for the receptor exchange factor Cand1, which is split and rearranged in aspergilli into two genes for separate proteins. Aspergillus nidulans CandA-N blocks the neddylation site, and CandA-C inhibits the interaction to the adaptor/substrate receptor subunits similar to the respective N-terminal and C-terminal parts of single Cand1. The pathogen Aspergillus fumigatus and related species express a CandA-C with a 190-amino-acid N-terminal extension domain encoded by an additional exon. This extension corresponds in most aspergilli, including A. nidulans, to a gene directly upstream of candA-C encoding a 20-kDa protein without human counterpart. This protein was named CandA-C1, because it is also required for the cellular deneddylation/neddylation cycle and can form a trimeric nuclear complex with CandA-C and CandA-N. CandA-C and CandA-N are required for asexual and sexual development and control a distinct secondary metabolism. CandA-C1 and the corresponding domain of A. fumigatus control spore germination, vegetative growth, and the repression of additional secondary metabolites. This suggests that the dissection of the conserved Cand1-encoding gene within the genome of aspergilli was possible because it allowed the integration of a fungus-specific protein required for growth into the CandA complex in two different gene set versions, which might provide an advantage in evolution.
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Romsdahl J, Wang CCC. Recent advances in the genome mining of Aspergillus secondary metabolites (covering 2012-2018). MEDCHEMCOMM 2019; 10:840-866. [PMID: 31303983 PMCID: PMC6590338 DOI: 10.1039/c9md00054b] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/11/2019] [Indexed: 02/01/2023]
Abstract
Secondary metabolites (SMs) produced by filamentous fungi possess diverse bioactivities that make them excellent drug candidates. Whole genome sequencing has revealed that fungi have the capacity to produce a far greater number of SMs than have been isolated, since many of the genes involved in SM biosynthesis are either silent or expressed at very low levels in standard laboratory conditions. There has been significant effort to activate SM biosynthetic genes and link them to their downstream products, as the SMs produced by these "cryptic" pathways offer a promising source for new drug discovery. Further, an understanding of the genes involved in SM biosynthesis facilitates product yield optimization of first-generation molecules and genetic engineering of second-generation analogs. This review covers advances made in genome mining SMs produced by Aspergillus nidulans, Aspergillus fumigatus, Aspergillus niger, and Aspergillus terreus in the past six years (2012-2018). Genetic identification and molecular characterization of SM biosynthetic gene clusters, along with proposed biosynthetic pathways, will be discussed in depth.
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Affiliation(s)
- Jillian Romsdahl
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Avenue , Los Angeles , CA 90089 , USA . ; Tel: (323) 442 1670
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences , School of Pharmacy , University of Southern California , 1985 Zonal Avenue , Los Angeles , CA 90089 , USA . ; Tel: (323) 442 1670
- Department of Chemistry , Dornsife College of Letters, Arts, and Sciences , University of Southern California , 3551 Trousdale Pkwy , Los Angeles , CA 90089 , USA
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24
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de Marigorta EM, Santos JMDL, Ochoa de Retana AM, Vicario J, Palacios F. Multicomponent reactions (MCRs): a useful access to the synthesis of benzo-fused γ-lactams. Beilstein J Org Chem 2019; 15:1065-1085. [PMID: 31164944 PMCID: PMC6541321 DOI: 10.3762/bjoc.15.104] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/17/2019] [Indexed: 12/17/2022] Open
Abstract
Benzo-fused γ-lactam rings such as isoindolin-2-ones and 2-oxindoles are part of the structure of many pharmaceutically active molecules. They can be often synthesized by means of multicomponent approaches and recent contributions in this field are summarized in this review. Clear advantages of these methods include the efficiency in saving raw materials and working time. However, there is still a need of new catalytic systems to allow the enantioselective preparation of these heterocycles by multicomponent reactions.
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Affiliation(s)
- Edorta Martínez de Marigorta
- Departamento de Química Orgánica I, Facultad de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Jesús M de Los Santos
- Departamento de Química Orgánica I, Facultad de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Ana M Ochoa de Retana
- Departamento de Química Orgánica I, Facultad de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Javier Vicario
- Departamento de Química Orgánica I, Facultad de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
| | - Francisco Palacios
- Departamento de Química Orgánica I, Facultad de Farmacia, University of the Basque Country, UPV/EHU Paseo de la Universidad 7, 01006, Vitoria-Gasteiz, Spain
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25
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Discovery of Three New Phytotoxins from the Fungus Aspergillus nidulans by Pathway Inactivation. Molecules 2019; 24:molecules24030515. [PMID: 30708999 PMCID: PMC6384659 DOI: 10.3390/molecules24030515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/25/2019] [Accepted: 01/27/2019] [Indexed: 11/18/2022] Open
Abstract
Fungi are a source of novel phytotoxic compounds to be explored in the search for effective and environmentally safe herbicides. The genetic inactivation of the biosynthetic pathway of the new phytotoxin cichorine has led to the isolation of three novel phytotoxins from the fungus Aspergillus nidulans: 8-methoxycichorine (4), 8-epi-methoxycichorine (5), and N-(4’-carboxybutyl) cichorine (6). The structure of the new compounds was clearly determined by a combination of nuclear magnetic resonance (NMR) analysis and high-resolution electrospray ionization (HRESIMS). The phytotoxic bioassay was studied on leaves from Zea mays and Medicago polymorpha L. at the concentration of 5 × 10−3 M by using a moist chamber technique. Novel phytotoxins 8-methoxycichorine (4), 8-epi-methoxycichorine (5), and N-(4’-carboxybutyl) cichorine (6) exhibited a better phytotoxic effect than cichorine.
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26
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Pidroni A, Faber B, Brosch G, Bauer I, Graessle S. A Class 1 Histone Deacetylase as Major Regulator of Secondary Metabolite Production in Aspergillus nidulans. Front Microbiol 2018; 9:2212. [PMID: 30283426 PMCID: PMC6156440 DOI: 10.3389/fmicb.2018.02212] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/30/2018] [Indexed: 12/23/2022] Open
Abstract
An outstanding feature of filamentous fungi is their ability to produce a wide variety of small bioactive molecules that contribute to their survival, fitness, and pathogenicity. The vast collection of these so-called secondary metabolites (SMs) includes molecules that play a role in virulence, protect fungi from environmental damage, act as toxins or antibiotics that harm host tissues, or hinder microbial competitors for food sources. Many of these compounds are used in medical treatment; however, biosynthetic genes for the production of these natural products are arranged in compact clusters that are commonly silent under growth conditions routinely used in laboratories. Consequently, a wide arsenal of yet unknown fungal metabolites is waiting to be discovered. Here, we describe the effects of deletion of hosA, one of four classical histone deacetylase (HDAC) genes in Aspergillus nidulans; we show that HosA acts as a major regulator of SMs in Aspergillus with converse regulatory effects depending on the metabolite gene cluster examined. Co-inhibition of all classical enzymes by the pan HDAC inhibitor trichostatin A and the analysis of HDAC double mutants indicate that HosA is able to override known regulatory effects of other HDACs such as the class 2 type enzyme HdaA. Chromatin immunoprecipitation analysis revealed a direct correlation between hosA deletion, the acetylation status of H4 and the regulation of SM cluster genes, whereas H3 hyper-acetylation could not be detected in all the upregulated SM clusters examined. Our data suggest that HosA has inductive effects on SM production in addition to its classical role as a repressor via deacetylation of histones. Moreover, a genome wide transcriptome analysis revealed that in addition to SMs, expression of several other important protein categories such as enzymes of the carbohydrate metabolism or proteins involved in disease, virulence, and defense are significantly affected by the deletion of HosA.
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Affiliation(s)
- Angelo Pidroni
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Birgit Faber
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerald Brosch
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Ingo Bauer
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefan Graessle
- Division of Molecular Biology, Medical University of Innsbruck, Innsbruck, Austria
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27
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Producing Novel Fibrinolytic Isoindolinone Derivatives in Marine Fungus Stachybotrys longispora FG216 by the Rational Supply of Amino Compounds According to Its Biosynthesis Pathway. Mar Drugs 2017; 15:md15070214. [PMID: 28678182 PMCID: PMC5532656 DOI: 10.3390/md15070214] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/26/2017] [Accepted: 07/03/2017] [Indexed: 01/03/2023] Open
Abstract
Many fungi in the Stachybotrys genus can produce various isoindolinone derivatives. These compounds are formed by a spontaneous reaction between a phthalic aldehyde precursor and an ammonium ion or amino compounds. In this study, we suggested the isoindolinone biosynthetic gene cluster in Stachybotrys by genome mining based on three reported core genes. Remarkably, there is an additional nitrate reductase (NR) gene copy in the proposed cluster. NR is the rate-limiting enzyme of nitrate reduction. Accordingly, this cluster was speculated to play a role in the balance of ammonium ion concentration in Stachybotrys. Ammonium ions can be replaced by different amino compounds to create structural diversity in the biosynthetic process of isoindolinone. We tested a rational supply of amino compounds ((±)-3-amino-2-piperidinone, glycine, and l-threonine) in the culture of an isoindolinone high-producing marine fungus, Stachybotrys longispora FG216. As a result, we obtained four new kinds of isoindolinone derivatives (FGFC4–GFC7) by this method. Furthermore, high yields of FGFC4–FGFC7 confirmed the outstanding production capacity of FG216. Among the four new isoindolinone derivatives, FGFC6 and FGFC7 showed promising fibrinolytic activities. The knowledge of biosynthesis pathways may be an important attribute for the discovery of novel bioactive marine natural products.
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28
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Oakley CE, Ahuja M, Sun WW, Entwistle R, Akashi T, Yaegashi J, Guo CJ, Cerqueira GC, Russo Wortman J, Wang CCC, Chiang YM, Oakley BR. Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol 2016; 103:347-365. [PMID: 27775185 DOI: 10.1111/mmi.13562] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2016] [Indexed: 01/17/2023]
Abstract
Fungal secondary metabolites (SMs) are extremely important in medicine and agriculture, but regulation of their biosynthesis is incompletely understood. We have developed a genetic screen in Aspergillus nidulans for negative regulators of fungal SM gene clusters and we have used this screen to isolate mutations that upregulate transcription of the non-ribosomal peptide synthetase gene required for nidulanin A biosynthesis. Several of these mutations are allelic and we have identified the mutant gene by genome sequencing. The gene, which we designate mcrA, is conserved but uncharacterized, and it encodes a putative transcription factor. Metabolite profiles of mcrA deletant, mcrA overexpressing, and parental strains reveal that mcrA regulates at least ten SM gene clusters. Deletion of mcrA stimulates SM production even in strains carrying a deletion of the SM regulator laeA, and deletion of mcrA homologs in Aspergillus terreus and Penicillum canescens alters the secondary metabolite profile of these organisms. Deleting mcrA in a genetic dereplication strain has allowed us to discover two novel compounds as well as an antibiotic not known to be produced by A. nidulans. Deletion of mcrA upregulates transcription of hundreds of genes including many that are involved in secondary metabolism, while downregulating a smaller number of genes.
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Affiliation(s)
- C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Manmeet Ahuja
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Wei-Wen Sun
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
| | - Tomohiro Akashi
- Division of OMICS analysis, Nagoya University Graduate School of Medicine, 65 Tsurumai, Nagoya, Aichi, 466-8550, Japan
| | - Junko Yaegashi
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Chun-Jun Guo
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA
| | - Gustavo C Cerqueira
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Jennifer Russo Wortman
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA.,Department of Chemistry, Dornsife Colleges of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, 90089, USA
| | - Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California, 90089, USA.,Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan City, Taiwan, 71710, Republic of China
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
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29
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Henke MT, Soukup AA, Goering AW, McClure RA, Thomson RJ, Keller NP, Kelleher NL. New Aspercryptins, Lipopeptide Natural Products, Revealed by HDAC Inhibition in Aspergillus nidulans. ACS Chem Biol 2016; 11:2117-23. [PMID: 27310134 PMCID: PMC5119465 DOI: 10.1021/acschembio.6b00398] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Unlocking the biochemical stores of fungi is key for developing future pharmaceuticals. Through reduced expression of a critical histone deacetylase in Aspergillus nidulans, increases of up to 100-fold were observed in the levels of 15 new aspercryptins, recently described lipopeptides with two noncanonical amino acids derived from octanoic and dodecanoic acids. In addition to two NMR-verified structures, MS/MS networking helped uncover an additional 13 aspercryptins. The aspercryptins break the conventional structural orientation of lipopeptides and appear "backward" when compared to known compounds of this class. We have also confirmed the 14-gene aspercryptin biosynthetic gene cluster, which encodes two fatty acid synthases and several enzymes to convert saturated octanoic and dodecanoic acid to α-amino acids.
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Affiliation(s)
- Matthew T. Henke
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Alexandra A. Soukup
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Anthony W. Goering
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Ryan A. McClure
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Regan J. Thomson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Nancy P. Keller
- Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706, United States
- Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, United States
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Neil L. Kelleher
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
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30
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Alves PC, Hartmann DO, Núñez O, Martins I, Gomes TL, Garcia H, Galceran MT, Hampson R, Becker JD, Silva Pereira C. Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans. BMC Genomics 2016; 17:284. [PMID: 27072538 PMCID: PMC4830055 DOI: 10.1186/s12864-016-2577-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/08/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The inherent potential of filamentous fungi, especially of Ascomycota, for producing diverse bioactive metabolites remains largely silent under standard laboratory culture conditions. Innumerable strategies have been described to trigger their production, one of the simplest being manipulation of the growth media composition. Supplementing media with ionic liquids surprisingly enhanced the diversity of extracellular metabolites generated by penicillia. This finding led us to evaluate the impact of ionic liquids' stimuli on the fungal metabolism in Aspergillus nidulans and how it reflects on the biosynthesis of secondary metabolites (SMs). RESULTS Whole transcriptional profiling showed that exposure to 0.7 M cholinium chloride or 1-ethyl-3-methylimidazolium chloride dramatically affected expression of genes encoding both primary and secondary metabolism. Both ionic liquids apparently induced stress responses and detoxification mechanisms but response profiles to each stimulus were unique. Primary metabolism was up-regulated by choline, but down-regulated by 1-ethyl-3-methylimidazolium chloride; both stimulated production of acetyl-CoA (key precursor to numerous SMs) and non proteinogenic amino acids (building blocks of bioactive classes of SMs). In total, twenty one of the sixty six described backbone genes underwent up-regulation. Accordingly, differential analysis of the fungal metabolome showed that supplementing growth media with ionic liquids resulted in ca. 40 differentially accumulated ion masses compared to control conditions. In particular, it stimulated production of monodictyphenone and orsellinic acid, otherwise cryptic. Expression levels of genes encoding corresponding polyketide biosynthetic enzymes (i.e. backbone genes) increased compared to control conditions. The corresponding metabolite extracts showed increased cell polarity modulation potential in an ex vivo whole tissue assay (The lial Live Targeted Epithelia; theLiTE™). CONCLUSIONS Ionic liquids, a diverse class of chemicals composed solely of ions, can provide an unexpected means to further resolve the diversity of natural compounds, guiding discovery of fungal metabolites with clinical potential.
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Affiliation(s)
- Paula C Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Diego O Hartmann
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Oscar Núñez
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028, Barcelona, Spain.,Serra Hunter Fellow, Generalitat de Catalunya, Barcelona, Spain
| | - Isabel Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Teresa L Gomes
- Thelial Technologies S.A., Parque Tecnológico de Cantanhede, Nucleo 04 Lote 3, 3060-197, Cantanhede, Portugal
| | - Helga Garcia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Maria Teresa Galceran
- Department of Analytical Chemistry, University of Barcelona, Diagonal 645, E-08028, Barcelona, Spain
| | - Richard Hampson
- Thelial Technologies S.A., Parque Tecnológico de Cantanhede, Nucleo 04 Lote 3, 3060-197, Cantanhede, Portugal
| | - Jörg D Becker
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Cristina Silva Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CCC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl 2016; 55:1662-5. [PMID: 26563584 PMCID: PMC4724294 DOI: 10.1002/anie.201507097] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/04/2015] [Indexed: 11/07/2022]
Abstract
To reduce the secondary metabolite background in Aspergillus nidulans and minimize the rediscovery of compounds and pathway intermediates, we created a "genetic dereplication" strain in which we deleted eight of the most highly expressed secondary metabolite gene clusters (more than 244,000 base pairs deleted in total). This strain allowed us to discover a novel compound that we designate aspercryptin and to propose a biosynthetic pathway for the compound. Interestingly, aspercryptin is formed from compounds produced by two separate gene clusters, one of which makes the well-known product cichorine. This raises the exciting possibility that fungi use differential regulation of expression of secondary metabolite gene clusters to increase the diversity of metabolites they produce.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan, 71710, Taiwan
| | - Manmeet Ahuja
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
- Industrial Biotechnology Division, Reliance Technology Group, Reliance Industries Limited, Reliance Corporate Park, Thane Belapur Road, Ghansoli, Navi, Mumbai, 400701, India
| | - C Elizabeth Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Ruth Entwistle
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA
| | - Anabanadam Asokan
- Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045, USA
| | - Christoph Zutz
- Institute for Milk Hygiene, University of Veterinary Medicine Vienna, Vienna, 1210, Austria
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66045, USA.
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32
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Donzelli B, Krasnoff S. Molecular Genetics of Secondary Chemistry in Metarhizium Fungi. GENETICS AND MOLECULAR BIOLOGY OF ENTOMOPATHOGENIC FUNGI 2016; 94:365-436. [DOI: 10.1016/bs.adgen.2016.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Chiang YM, Ahuja M, Oakley CE, Entwistle R, Asokan A, Zutz C, Wang CCC, Oakley BR. Development of Genetic Dereplication Strains in Aspergillus nidulans
Results in the Discovery of Aspercryptin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy; University of Southern California; Los Angeles CA 90089 USA
- Department of Pharmacy; Chia Nan University of Pharmacy and Science; Tainan 71710 Taiwan
| | - Manmeet Ahuja
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
- Industrial Biotechnology Division, Reliance Technology Group; Reliance Industries Limited, Reliance Corporate Park; Thane Belapur Road, Ghansoli, Navi Mumbai 400701 India
| | - C. Elizabeth Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| | - Ruth Entwistle
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
| | - Anabanadam Asokan
- Del Shankel Structural Biology Center; University of Kansas; Lawrence KS 66045 USA
| | - Christoph Zutz
- Institute for Milk Hygiene; University of Veterinary Medicine Vienna; Vienna 1210 Austria
| | - Clay C. C. Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy; University of Southern California; Los Angeles CA 90089 USA
- Department of Chemistry; University of Southern California; Los Angeles CA 90089 USA
| | - Berl R. Oakley
- Department of Molecular Biosciences; University of Kansas; Lawrence KS 66045 USA
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Recent advances in natural product discovery. Curr Opin Biotechnol 2014; 30:230-7. [PMID: 25260043 DOI: 10.1016/j.copbio.2014.09.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 09/06/2014] [Accepted: 09/08/2014] [Indexed: 12/11/2022]
Abstract
Natural products have been and continue to be the source and inspiration for a substantial fraction of human therapeutics. Although the pharmaceutical industry has largely turned its back on natural product discovery efforts, such efforts continue to flourish in academia with promising results. Natural products have traditionally been identified from a top-down perspective, but more recently genomics- and bioinformatics-guided bottom-up approaches have provided powerful alternative strategies. Here we review recent advances in natural product discovery from both angles, including diverse sampling and innovative culturing and screening approaches, as well as genomics-driven discovery and genetic manipulation techniques for both native and heterologous expression.
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Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans. J Ind Microbiol Biotechnol 2013; 41:433-42. [PMID: 24342965 DOI: 10.1007/s10295-013-1386-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 11/20/2013] [Indexed: 12/31/2022]
Abstract
Fungi are prolific producers of secondary metabolites (SMs) that show a variety of biological activities. Recent advances in genome sequencing have shown that fungal genomes harbor far more SM gene clusters than are expressed under conventional laboratory conditions. Activation of these "silent" gene clusters is a major challenge, and many approaches have been taken to attempt to activate them and, thus, unlock the vast treasure chest of fungal SMs. This review will cover recent advances in genome mining of SMs in Aspergillus nidulans. We will also discuss current updates in gene annotation of A. nidulans and recent developments in A. nidulans as a molecular genetic system, both of which are essential for rapid and efficient experimental verification of SM gene clusters on a genome-wide scale. Finally, we will describe advances in the use of A. nidulans as a heterologous expression system to aid in the analysis of SM gene clusters from other fungal species that do not have an established molecular genetic system.
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