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Li F, Lin Z, Schmidt EW. Molecular basis of pigment structural diversity in echinoderms. iScience 2024; 27:110834. [PMID: 39310768 PMCID: PMC11414698 DOI: 10.1016/j.isci.2024.110834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/29/2024] [Accepted: 08/23/2024] [Indexed: 09/25/2024] Open
Abstract
The varied pigments found in animals play both ecological and physiological roles. Virtually all echinoderms contain putative pigment biosynthetic enzymes, the polyketide synthases (PKSs). Among these, crinoids have complex pigments found both today and in ancient fossils. Here, we characterize a key pigment biosynthetic enzyme, CrPKS from the crinoid Anneissia japonica. We show that CrPKS produces 14-carbon aromatic pigment precursors. Despite making a compound previously found in fungi, the crinoid enzyme operates by different biochemical principles, helping to explain the diverse animal PKSs found throughout the metazoan (animal) kingdom. Unlike SpPks1 from sea urchins that had strict starter unit selectivity, CrPKS also incorporated starter units butyryl- or ethylmalonyl-CoA to synthesize a crinoid pigment precursor with a saturated side chain. By performing biochemical experiments, we show how changes in the echinoderm pigment biosynthetic enzymes unveil the vast variety of colors found in animals today.
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Affiliation(s)
- Feng Li
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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2
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Xie L, Liu Y, Zhang Y, Chen K, Yue Q, Wang C, Dun B, Xu Y, Zhang L. The divergence of DHN-derived melanin pathways in Metarhizium robertsii. World J Microbiol Biotechnol 2024; 40:323. [PMID: 39292329 DOI: 10.1007/s11274-024-04134-4] [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: 08/02/2024] [Accepted: 09/07/2024] [Indexed: 09/19/2024]
Abstract
The important role of dihydroxynaphthalene-(DHN) melanin in enhancing fungal stress resistance and its importance in fungal development and pathogenicity are well-established. This melanin also aids biocontrol fungi in surviving in the environment and effectively infecting insects. However, the biosynthetic origin of melanin in the biocontrol agents, Metarhizium spp., has remained elusive due to the complexity resulting from the divergence of two DHN-like biosynthetic pathways. Through the heterologous expression of biosynthetic enzymes from these two pathways in baker's yeast Saccharomyces cerevisiae, we have confirmed the presence of DHN biosynthesis in M. roberstii, and discovered a novel naphthopyrone intermediate, 8, that can produce a different type of pigment. These two pigment biosynthetic pathways differ in terms of polyketide intermediate structures and subsequent modification steps. Stress resistance studies using recombinant yeast cells have demonstrated that both DHN and its intermediates confer resistance against UV light prior to polymerization; a similar result was observed for its naphthopyrone counterpart. This study contributes to the understanding of the intricate and diverse biosynthetic mechanisms of fungal melanin and has the potential to enhance the application efficiency of biocontrol fungi such as Metarhizium spp. in agriculture.
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Affiliation(s)
- Linan Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Yang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Yujie Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Kang Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Qun Yue
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Chen Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Baoqing Dun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Yuquan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Liwen Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
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3
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Ye R, Biango-Daniels M, Steenwyk JL, Rokas A, Louw NL, Nardella R, Wolfe BE. Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genet Biol 2024; 171:103862. [PMID: 38218228 DOI: 10.1016/j.fgb.2023.103862] [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: 08/30/2023] [Revised: 12/06/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
Although Penicillium molds can have significant impacts on agricultural, industrial, and biomedical systems, the ecological roles of Penicillium species in many microbiomes are not well characterized. Here we utilized a collection of 35 Penicillium strains isolated from cheese rinds to broadly investigate the genomic potential for secondary metabolism in cheese-associated Penicillium species, the impact of Penicillium on bacterial community assembly, and mechanisms of Penicillium-bacteria interactions. Using antiSMASH, we identified 1558 biosynthetic gene clusters, 406 of which were mapped to known pathways, including several mycotoxins and antimicrobial compounds. By measuring bacterial abundance and fungal mRNA expression when culturing representative Penicillium strains with a cheese rind bacterial community, we observed divergent impacts of different Penicillium strains, from strong inhibitors of bacterial growth to those with no impact on bacterial growth or community composition. Through differential mRNA expression analyses, Penicillium strains demonstrated limited differential gene expression in response to the bacterial community. We identified a few shared responses between the eight tested Penicillium strains, primarily upregulation of nutrient metabolic pathways, but we did not identify a conserved fungal response to growth in a multispecies community. These results in tandem suggest high variation among cheese-associated Penicillium species in their ability to shape bacterial community development and highlight important ecological diversity within this iconic genus.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, MA, USA
| | | | - Jacob L Steenwyk
- Department of Molecular and Cellular Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Nicolas L Louw
- Department of Biology, Tufts University, Medford, MA, USA
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4
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Cleere MM, Novodvorska M, Geib E, Whittaker J, Dalton H, Salih N, Hewitt S, Kokolski M, Brock M, Dyer PS. New colours for old in the blue-cheese fungus Penicillium roqueforti. NPJ Sci Food 2024; 8:3. [PMID: 38191473 PMCID: PMC10774375 DOI: 10.1038/s41538-023-00244-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
Penicillium roqueforti is used worldwide in the production of blue-veined cheese. The blue-green colour derives from pigmented spores formed by fungal growth. Using a combination of bioinformatics, targeted gene deletions, and heterologous gene expression we discovered that pigment formation was due to a DHN-melanin biosynthesis pathway. Systematic deletion of pathway genes altered the arising spore colour, yielding white to yellow-green to red-pink-brown phenotypes, demonstrating the potential to generate new coloured strains. There was no consistent impact on mycophenolic acid production as a result of pathway interruption although levels of roquefortine C were altered in some deletants. Importantly, levels of methyl-ketones associated with blue-cheese flavour were not impacted. UV-induced colour mutants, allowed in food production, were then generated. A range of colours were obtained and certain phenotypes were successfully mapped to pathway gene mutations. Selected colour mutants were subsequently used in cheese production and generated expected new colourations with no elevated mycotoxins, offering the exciting prospect of use in future cheese manufacture.
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Affiliation(s)
- Matthew M Cleere
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- PhD Program in Biology, The Graduate Center; Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY10031, USA
| | - Michaela Novodvorska
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Elena Geib
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Jack Whittaker
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Heather Dalton
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Nadhira Salih
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- Department of Biology, College of Education, University of Sulaimani, Sulaymaniyah, Iraq
| | - Sarah Hewitt
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Matthias Brock
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Paul S Dyer
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom.
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5
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Li Y, Lin P, Lu X, Yan H, Wei H, Liu C, Liu X, Yang Y, Molnár I, Bai Z. Plasmid Copy Number Engineering Accelerates Fungal Polyketide Discovery upon Unnatural Polyketide Biosynthesis. ACS Synth Biol 2023; 12:2226-2235. [PMID: 37463503 DOI: 10.1021/acssynbio.3c00178] [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] [Indexed: 07/20/2023]
Abstract
Saccharomyces cerevisiae has been extensively used as a convenient synthetic biology chassis to reconstitute fungal polyketide biosynthetic pathways. Despite progress in refactoring these pathways for expression and optimization of the yeast production host by metabolic engineering, product yields often remain unsatisfactory. Such problems are especially acute when synthetic biological production is used for bioprospecting via genome mining or when chimeric fungal polyketide synthases (PKSs) are employed to produce novel bioactive compounds. In this work, we demonstrate that empirically balancing the expression levels of the two collaborating PKS subunits that afford benzenediol lactone (BDL)-type fungal polyketides is a facile strategy to improve the product yields. This is accomplished by systematically and independently altering the copy numbers of the two plasmids that express these PKS subunits. We applied this plasmid copy number engineering strategy to two orphan PKSs from genome mining where the yields of the presumed BDL products in S. cerevisiae were far too low for product isolation. This optimization resulted in product yield improvements of up to 10-fold, allowing for the successful isolation and structure elucidation of new BDL analogues. Heterocombinations of these PKS subunits from genome mining with those from previously identified BDL pathways led to the combinatorial biosynthesis of several additional novel BDL-type polyketides.
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Affiliation(s)
- Ye Li
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Pingxin Lin
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Xuan Lu
- School of Life Science and Biotechnology, Dalian University, Dalian 116622, China
| | - Hao Yan
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Huan Wei
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Chunli Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - István Molnár
- Southwest Center for Natural Products Research, University of Arizona, Tucson, Arizona 85706, United States
- VTT Technical Research Centre of Finland Ltd., Espoo 02044, Finland
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
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6
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Multifunctional Enzymes in Microbial Secondary Metabolic Processes. Catalysts 2023. [DOI: 10.3390/catal13030581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Microorganisms possess a strong capacity for secondary metabolite synthesis, which is represented by tightly controlled networks. The absence of any enzymes leads to a change in the original metabolic pathway, with a decrease in or even elimination of a synthetic product, which is not permissible under conditions of normal life activities of microorganisms. In order to improve the efficiency of secondary metabolism, organisms have evolved multifunctional enzymes (MFEs) that can catalyze two or more kinds of reactions via multiple active sites. However, instead of interfering, the multifunctional catalytic properties of MFEs facilitate the biosynthetic process. Among the numerous MFEs considered of vital importance in the life activities of living organisms are the synthases involved in assembling the backbone of compounds using different substrates and modifying enzymes that confer the final activity of compounds. In this paper, we review MFEs in terms of both synthetic and post-modifying enzymes involved in secondary metabolic biosynthesis, focusing on polyketides, non-ribosomal peptides, terpenoids, and a wide range of cytochrome P450s(CYP450s), and provide an overview and describe the recent progress in the research on MFEs.
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7
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Tammam MA, Gamal El-Din MI, Abood A, El-Demerdash A. Recent advances in the discovery, biosynthesis, and therapeutic potential of isocoumarins derived from fungi: a comprehensive update. RSC Adv 2023; 13:8049-8089. [PMID: 36909763 PMCID: PMC9999372 DOI: 10.1039/d2ra08245d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/26/2023] [Indexed: 03/12/2023] Open
Abstract
Microorganisms still remain the main hotspots in the global drug discovery avenue. In particular, fungi are highly prolific producers of vast structurally diverse specialized secondary metabolites, which have displayed a myriad of biomedical potentials. Intriguingly, isocoumarins is one distinctive class of fungal natural products polyketides, which demonstrated numerous remarkable biological and pharmacological activities. This review article provides a comprehensive state-of-the-art over the period 2000-2022 about the discovery, isolation, classifications, and therapeutic potentials of isocoumarins exclusively reported from fungi. Indeed, a comprehensive list of 351 structurally diverse isocoumarins were documented and classified according to their fungal sources [16 order/28 family/55 genera] where they have been originally discovered along with their reported pharmacological activities wherever applicable. Also, recent insights around their proposed and experimentally proven biosynthetic pathways are also briefly discussed.
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Affiliation(s)
- Mohamed A Tammam
- Department of Biochemistry, Faculty of Agriculture, Fayoum University Fayoum 63514 Egypt
| | - Mariam I Gamal El-Din
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
| | - Amira Abood
- Chemistry of Natural and Microbial Products Department, National Research Center Dokki Cairo Egypt
- School of Bioscience, University of Kent Canterbury UK
| | - Amr El-Demerdash
- Organic Chemistry Division, Department of Chemistry, Faculty of Sciences, Mansoura University Mansoura 35516 Egypt
- Department of Biochemistry and Metabolism, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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8
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Kishimoto S, Minami A, Aoki Y, Matsubara Y, Watanabe S, Watanabe K. Reactive Azlactone Intermediate Drives Fungal Secondary Metabolite Cross-Pathway Generation. J Am Chem Soc 2023; 145:3221-3228. [PMID: 36706030 DOI: 10.1021/jacs.2c13188] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Pathogenic fungi of Aspergillus section Fumigati are known to produce various secondary metabolites. A reported isolation of a compound with an atypical carbon skeleton called fumimycin from A. fumisynnematus prompted us to examine a related fungus, A. lentulus, for production of similar products. Here we report the isolation of fumimycin and a related new racemic compound we named lentofuranine. Detailed analyses revealed that both compounds were assembled by a nonenzymatic condensation of a polyketide intermediate from the terrein biosynthetic pathway and a highly reactive azlactone intermediate produced by an unrelated nonribosomal peptide synthetase carrying a terminal condensation-like domain. While highly reactive azlactone is commonly used in chemical synthesis, its production by a conventional non-metalloenzyme and employment as a biosynthetic pathway intermediate is unprecedented. The observed unusual carbon skeleton formation is likely due to the reactivity of azlactone. Our finding provides another example of a chemical principle being aptly exploited by a biological system.
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Affiliation(s)
- Shinji Kishimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka422-8526, Japan
| | - Ayumi Minami
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka422-8526, Japan
| | - Yoshimitsu Aoki
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka422-8526, Japan
| | - Yuya Matsubara
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka422-8526, Japan
| | - Shogo Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka422-8526, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka422-8526, Japan
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Palkina KA, Balakireva AV, Belozerova OA, Chepurnykh TV, Markina NM, Kovalchuk SI, Tsarkova AS, Mishin AS, Yampolsky IV, Sarkisyan KS. Domain Truncation in Hispidin Synthase Orthologs from Non-Bioluminescent Fungi Does Not Lead to Hispidin Biosynthesis. Int J Mol Sci 2023; 24:1317. [PMID: 36674833 PMCID: PMC9866795 DOI: 10.3390/ijms24021317] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/22/2022] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Hispidin is a polyketide found in plants and fungi. In bioluminescent fungi, hispidin serves as a precursor of luciferin and is produced by hispidin synthases. Previous studies revealed that hispidin synthases differ in orthologous polyketide synthases from non-bioluminescent fungi by the absence of two domains with predicted ketoreductase and dehydratase activities. Here, we investigated the hypothesis that the loss of these domains in evolution led to the production of hispidin and the emergence of bioluminescence. We cloned three orthologous polyketide synthases from non-bioluminescent fungi, as well as their truncated variants, and assessed their ability to produce hispidin in a bioluminescence assay in yeast. Interestingly, expression of the full-length enzyme hsPKS resulted in dim luminescence, indicating that small amounts of hispidin are likely being produced as side products of the main reaction. Deletion of the ketoreductase and dehydratase domains resulted in no luminescence. Thus, domain truncation by itself does not appear to be a sufficient step for the emergence of efficient hispidin synthases from orthologous polyketide synthases. At the same time, the production of small amounts of hispidin or related compounds by full-length enzymes suggests that ancestral fungal species were well-positioned for the evolution of bioluminescence.
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Affiliation(s)
- Kseniia A. Palkina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
| | - Anastasia V. Balakireva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
| | - Olga A. Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Tatiana V. Chepurnykh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nadezhda M. Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
| | - Sergey I. Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Aleksandra S. Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
| | - Ilia V. Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Karen S. Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Planta LLC., 121205 Moscow, Russia
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
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10
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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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11
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Li C, Gu R, Lin F, Xiao H. Sorbicillinoids hyperproduction without affecting the cellulosic enzyme production in Trichoderma reesei JNTR5. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:85. [PMID: 35996177 PMCID: PMC9394075 DOI: 10.1186/s13068-022-02183-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/29/2022] [Indexed: 11/12/2022]
Abstract
Background Microbial production of bioactive secondary metabolites is challenging as most of the encoding genes are silent; and even if they are activated, the biosynthetic pathways are usually complex. Sorbicillinoids with multifunctional bioactivities are examples of these problems, which if solved can result in a more sustainable, simple supply of these important compounds to the pharmaceutical industry. As an excellent producer of cellulosic enzymes, Trichoderma reesei can secrete various sorbicillinoids. Results Here, we obtained a T. reesei mutant strain JNTR5 from the random mutation during overexpression of gene Tr69957 in T. reesei RUT-C30. JNTR5 exhibited a significant constitutive increase in sorbicillinoids production without affecting the cellulosic enzyme production. Confocal laser scanning microscope (CLSM) results indicated that sorbicillinoids were distributed in both mycelium and spores of JNTR5 with blue and green fluorescence. Compared with RUT-C30, JNTR5 displayed different cell morphology, reduced growth rate, and increased sporulation, but a similar biomass accumulation. Furthermore, transcriptome analysis revealed that all genes belonging to the sorbicillinoid gene cluster were upregulated, while most cellulase-encoding genes were downregulated. The cell wall integrity of JNTR5 was damaged, which might benefit the cellulase secretion and contribute to the almost unchanged cellulase and hemicellulase activity given that the damaged cell wall can enhance the secretion of the enzymes. Conclusions For the first time, we constructed a sorbicillinoids hyperproduction T. reesei platform with comparable cellulosic enzymes production. This outperformance of JNTR5, which is strain-specific, is proposed to be attributed to the overexpression of gene Tr69957, causing the chromosome remodeling and subsequently changing the cell morphology, structure, and the global gene expression as shown by phenotype and the transcriptome analysis of JNTR5. Overall, JNTR5 shows great potential for industrial microbial production of sorbicillinoids from cellulose and serves as an excellent model for investigating the distribution and secretion of yellow pigments in T. reesei. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02183-1.
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12
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Li F, Lin Z, Torres JP, Hill EA, Li D, Townsend CA, Schmidt EW. Sea Urchin Polyketide Synthase SpPks1 Produces the Naphthalene Precursor to Echinoderm Pigments. J Am Chem Soc 2022; 144:9363-9371. [PMID: 35588530 DOI: 10.1021/jacs.2c01416] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly every animal species on Earth contains a unique polyketide synthase (PKS) encoded in its genome, yet no animal-clade PKS has been biochemically characterized, and even the chemical products of these ubiquitous enzymes are known in only a few cases. The earliest animal genome-encoded PKS gene to be identified was SpPks1 from sea urchins. Previous genetic knockdown experiments implicated SpPks1 in synthesis of the sea urchin pigment echinochrome. Here, we express and purify SpPks1, performing biochemical experiments to demonstrate that the sea urchin protein is responsible for the synthesis of 2-acetyl-1,3,6,8-tetrahydroxynaphthalene (ATHN). Since ATHN is a plausible precursor of echinochromes, this result defines a biosynthetic pathway to the ubiquitous echinoderm pigments and rewrites the previous hypothesis for echinochrome biosynthesis. Truncation experiments showed that, unlike other type I iterative PKSs so far characterized, SpPks1 produces the naphthalene core using solely ketoacylsynthase (KS), acyltransferase, and acyl carrier protein domains, delineating a unique class of animal nonreducing aromatic PKSs (aPKSs). A series of amino acids in the KS domain define the family and are likely crucial in cyclization activity. Phylogenetic analyses indicate that SpPks1 and its homologs are widespread in echinoderms and their closest relatives, the acorn worms, reinforcing their fundamental importance to echinoderm biology. While the animal microbiome is known to produce aromatic polyketides, this work provides biochemical evidence that animals themselves also harbor ancient, convergent, dedicated pathways to carbocyclic aromatic polyketides. More fundamentally, biochemical analysis of SpPks1 begins to define the vast and unexplored biosynthetic space of the ubiquitous animal PKS family.
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Affiliation(s)
- Feng Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R. China.,Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Joshua P Torres
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric A Hill
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R. China
| | - Craig A Townsend
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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13
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Skellam E. Biosynthesis of fungal polyketides by collaborating and trans-acting enzymes. Nat Prod Rep 2022; 39:754-783. [PMID: 34842268 DOI: 10.1039/d1np00056j] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Covering: 1999 up to 2021Fungal polyketides encompass a range of structurally diverse molecules with a wide variety of biological activities. The giant multifunctional enzymes that synthesize polyketide backbones remain enigmatic, as do many of the tailoring enzymes involved in functional modifications. Recent advances in elucidating biosynthetic gene clusters (BGCs) have revealed numerous examples of fungal polyketide synthases that require the action of collaborating enzymes to synthesize the carbon backbone. This review will discuss collaborating and trans-acting enzymes involved in loading, extending, and releasing polyketide intermediates from fungal polyketide synthases, and additional modifications introduced by trans-acting enzymes demonstrating the complexity encountered when investigating natural product biosynthesis in fungi.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA.
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14
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Xiang P, Li SM. Formation of 3-Orsellinoxypropanoic Acid in Penicillum crustosum is Catalyzed by a Bifunctional Nonreducing Polyketide Synthase. Org Lett 2022; 24:462-466. [PMID: 34962820 DOI: 10.1021/acs.orglett.1c04189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The heterologous expression of a nonreducing polyketide synthase gene oesA from Penicillium crustosum led to the identification of orsellinoylpropanoic acid (1). Domain deletion and recombination proved that OesA catalyzes not only the formation of orsellinic acid but also its transfer to 3-hydroxypropanoic acid. Both ACP domains contribute independently and complementarily to the product formation. Feeding experiments provided evidence that only the orsellinyl residue is derived from acetate.
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Affiliation(s)
- Pan Xiang
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
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15
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González Y, de los Santos-Villalobos S, Castro-Longoria E. Trichoderma Secondary Metabolites Involved in Microbial Inhibition. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Phasha MM, Wingfield BD, Wingfield MJ, Coetzee MPA, Hammerbacher A, Steenkamp ET. Deciphering the effect of FUB1 disruption on fusaric acid production and pathogenicity in Fusarium circinatum. Fungal Biol 2021; 125:1036-1047. [PMID: 34776231 DOI: 10.1016/j.funbio.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
Fusarium circinatum is an important pathogen of pine trees. However, little is known regarding the molecular processes underlying its pathogenesis. We explored the potential role of the phytotoxin fusaric acid (FA) in the pathogenicity of the fungus. FA is produced by products of the FUB biosynthesis gene cluster, containing FUB1-12. Of these, FUB1 encodes the core polyketide synthase, which we disrupted. We used the resulting mutant strain to investigate whether FUB1 and FA production play a role in the virulence of F. circinatum on pine. Our results showed that FA production was abolished both in vitro and in planta. However, bikaverin production was increased in the knockout mutant. FUB1 disruption also corresponded with downregulation of a F. circinatum homologue of LaeA, a master transcriptional regulator of secondary metabolism. Lesion lengths produced by the FUB1 knockout mutant on inoculated Pinus patula seedlings were significantly smaller than those produced by the wild type strain. Collectively, these results show that FUB1 plays a role in FA production in F. circinatum, and that this gene contributes to the aggressiveness of F. circinatum on P. patula. This study will contribute to the limited knowledge we have about the molecular basis of pathogenicity in this fungus.
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Affiliation(s)
- M M Phasha
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa.
| | - B D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa.
| | - M J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa.
| | - M P A Coetzee
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa.
| | - A Hammerbacher
- Department of Zoology and Entomology, FABI, Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa.
| | - E T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Faculty of Natural and Agricultural Sciences, University of Pretoria, South Africa.
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17
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Fan C, Zhang W, Su X, Ji W, Luo H, Zhang Y, Liu B, Yao B, Huang H, Xu X. CRISPR/Cas9-mediated genome editing directed by a 5S rRNA-tRNA Gly hybrid promoter in the thermophilic filamentous fungus Humicola insolens. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:206. [PMID: 34688310 PMCID: PMC8542335 DOI: 10.1186/s13068-021-02057-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Humicola insolens is a filamentous fungus with high potential of producing neutral and heat- and alkali-resistant cellulase. However, the genetic engineering tools, particularly the genome-editing tool, are scarce, hindering the study of cellulase expression regulation in this organism. RESULTS Herein, a CRISPR/Cas9 genome-editing system was established in H. insolens based on a hybrid 5S rRNA-tRNAGly promoter. This system is superior to the HDV (hepatitis delta virus) system in genome editing, allowing highly efficient single gene destruction in H. insolens with rates of deletion up to 84.1% (37/44). With this system, a putative pigment synthesis gene pks and the transcription factor xyr1 gene were disrupted with high efficiency. Moreover, the extracellular protein concentration and cellulase activity largely decreased when xyr1 was deleted, demonstrating for the first time that Xyr1 plays an important role in cellulase expression regulation. CONCLUSIONS The established CRISPR/Cas9 system is a powerful genetic operation tool for H. insolens, which will accelerate studies on the regulation mechanism of cellulase expression and engineering of H. insolens for higher cellulase production.
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Affiliation(s)
- Chao Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Xiaoyun Su
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China
| | - Wangli Ji
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Huiying Luo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Bo Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China
| | - Huoqing Huang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Haidian District, Beijing, 100193, China.
| | - Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 South Zhongguancun St., Haidian District, Beijing, 100081, China.
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18
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19
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Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
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Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
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20
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Tian F, Li C, Li Y. Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships. Front Microbiol 2021; 12:652324. [PMID: 34276589 PMCID: PMC8281127 DOI: 10.3389/fmicb.2021.652324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
Yuanmo [Sarcomyxa edulis (Y.C. Dai, Niemelä & G.F. Qin) T. Saito, Tonouchi & T. Harada] is an important edible and medicinal mushroom endemic to Northeastern China. Here we report the de novo sequencing and assembly of the S. edulis genome using single-molecule real-time sequencing technology. The whole genome was approximately 35.65 Mb, with a G + C content of 48.31%. Genome assembly generated 41 contigs with an N50 length of 1,772,559 bp. The genome comprised 9,364 annotated protein-coding genes, many of which encoded enzymes involved in the modification, biosynthesis, and degradation of glycoconjugates and carbohydrates or enzymes predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I polyketide, siderophore, and fatty acids, which are responsible for the pharmacodynamic activities of S. edulis. We also identified genes encoding 1,3-β-glucan synthase and endo-1,3(4)-β-glucanase, which are involved in polysaccharide and uridine diphosphate glucose biosynthesis. Phylogenetic and comparative analyses of Basidiomycota fungi based on a single-copy orthologous protein indicated that the Sarcomyxa genus is an independent group that evolved from the Pleurotaceae family. The annotated whole-genome sequence of S. edulis can serve as a reference for investigations of bioactive compounds with medicinal value and the development and commercial production of superior S. edulis varieties.
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Affiliation(s)
- Fenghua Tian
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China.,Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Changtian Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
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21
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Singh S, Nimse SB, Mathew DE, Dhimmar A, Sahastrabudhe H, Gajjar A, Ghadge VA, Kumar P, Shinde PB. Microbial melanin: Recent advances in biosynthesis, extraction, characterization, and applications. Biotechnol Adv 2021; 53:107773. [PMID: 34022328 DOI: 10.1016/j.biotechadv.2021.107773] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 12/19/2022]
Abstract
Melanin is a common name for a group of biopolymers with the dominance of potential applications in medical sciences, cosmeceutical, bioremediation, and bioelectronic applications. The broad distribution of these pigments suggests their role to combat abiotic and biotic stresses in diverse life forms. Biosynthesis of melanin in fungi and bacteria occurs by oxidative polymerization of phenolic compounds predominantly by two pathways, 1,8-dihydroxynaphthalene [DHN] or 3,4-dihydroxyphenylalanine [DOPA], resulting in different kinds of melanin, i.e., eumelanin, pheomelanin, allomelanin, pyomelanin, and neuromelanin. The enzymes responsible for melanin synthesis belong mainly to tyrosinase, laccase, and polyketide synthase families. Studies have shown that manipulating culture parameters, combined with recombinant technology, can increase melanin yield for large-scale production. Despite significant efforts, its low solubility has limited the development of extraction procedures, and heterogeneous structural complexity has impaired structural elucidation, restricting effective exploitation of their biotechnological potential. Innumerable studies have been performed on melanin pigments from different taxa of life in order to advance the knowledge about melanin pigments for their efficient utilization in diverse applications. These studies prompted an urgent need for a comprehensive review on melanin pigments isolated from microorganisms, so that such review encompassing biosynthesis, bioproduction, characterization, and potential applications would help researchers from diverse background to understand the importance of microbial melanins and to utilize the information from the review for planning studies on melanin. With this aim in mind, the present report compares conventional and modern ideas for environment-friendly extraction procedures for melanin. Furthermore, the characteristic parameters to differentiate between eumelanin and pheomelanin are also mentioned, followed by their biotechnological applications forming the basis of industrial utilization. There lies a massive scope of work to circumvent the bottlenecks in their isolation and structural elucidation methodologies.
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Affiliation(s)
- Sanju Singh
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Satish B Nimse
- Institute of Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200702, Republic of Korea
| | - Doniya Elze Mathew
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Applied Phycology and Biotechnology Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India
| | - Asmita Dhimmar
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Harshal Sahastrabudhe
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Apexa Gajjar
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vishal A Ghadge
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pankaj Kumar
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pramod B Shinde
- Natural Products & Green Chemistry Division, CSIR-Central Salt and Marine Chemicals Research Institute (CSIR-CSMCRI), Council of Scientific and Industrial Research (CSIR), Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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22
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Kahlert L, Villanueva M, Cox RJ, Skellam EJ. Biosynthesis of 6-Hydroxymellein Requires a Collaborating Polyketide Synthase-like Enzyme. Angew Chem Int Ed Engl 2021; 60:11423-11429. [PMID: 33661567 PMCID: PMC8251887 DOI: 10.1002/anie.202100969] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Indexed: 12/12/2022]
Abstract
The polyketide synthase (PKS)-like protein TerB, consisting of inactive dehydratase, inactive C-methyltransferase, and functional ketoreductase domains collaborates with the iterative non reducing PKS TerA to produce 6-hydroxymellein, a key pathway intermediate during the biosynthesis of various fungal natural products. The catalytically inactive dehydratase domain of TerB appears to mediate productive interactions with TerA, demonstrating a new mode of trans-interaction between iterative PKS components.
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Affiliation(s)
- Lukas Kahlert
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Miranda Villanueva
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current address: The Molecular Biology InstituteUCLALos AngelesCA90095-1570USA
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
| | - Elizabeth J. Skellam
- Institute for Organic Chemistry and BMWZLeibniz Universität HannoverSchneiderberg 3830167HannoverGermany
- Current address: Department of Chemistry & BioDiscovery InstituteUniversity of North Texas1155 Union Circle 305220DentonTX76203USA
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23
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Kahlert L, Villanueva M, Cox RJ, Skellam EJ. Biosynthesis of 6‐Hydroxymellein Requires a Collaborating Polyketide Synthase‐like Enzyme. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lukas Kahlert
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Miranda Villanueva
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Current address: The Molecular Biology Institute UCLA Los Angeles CA 90095-1570 USA
| | - Russell J. Cox
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
| | - Elizabeth J. Skellam
- Institute for Organic Chemistry and BMWZ Leibniz Universität Hannover Schneiderberg 38 30167 Hannover Germany
- Current address: Department of Chemistry & BioDiscovery Institute University of North Texas 1155 Union Circle 305220 Denton TX 76203 USA
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24
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Adrover-Castellano ML, Schmidt JJ, Sherman DH. Biosynthetic Cyclization Catalysts for the Assembly of Peptide and Polyketide Natural Products. ChemCatChem 2021; 13:2095-2116. [PMID: 34335987 PMCID: PMC8320681 DOI: 10.1002/cctc.202001886] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Many biologically active natural products are synthesized by nonribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and their hybrids. These megasynthetases contain modules possessing distinct catalytic domains that allow for substrate initiation, chain extension, processing and termination. At the end of a module, a terminal domain, usually a thioesterase (TE), is responsible for catalyzing the release of the NRPS or PKS as a linear or cyclized product. In this review, we address the general cyclization mechanism of the TE domain, including oligomerization and the fungal C-C bond forming Claisen-like cyclases (CLCs). Additionally, we include examples of cyclization catalysts acting within or at the end of a module. Furthermore, condensation-like (CT) domains, terminal reductase (R) domains, reductase-like domains that catalyze Dieckmann condensation (RD), thioesterase-like Dieckmann cyclases, trans-acting TEs from the penicillin binding protein (PBP) enzyme family, product template (PT) domains and others will also be reviewed. The studies summarized here highlight the remarkable diversity of NRPS and PKS cyclization catalysts for the production of biologically relevant, complex cyclic natural products and related compounds.
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Affiliation(s)
| | - Jennifer J Schmidt
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216 (USA)
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25
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Belov AA, Witte TE, Overy DP, Smith ML. Transcriptome analysis implicates secondary metabolite production, redox reactions, and programmed cell death during allorecognition in Cryphonectria parasitica. G3-GENES GENOMES GENETICS 2021; 11:6025178. [PMID: 33561228 PMCID: PMC7849911 DOI: 10.1093/g3journal/jkaa021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/16/2020] [Indexed: 02/04/2023]
Abstract
The underlying molecular mechanisms of programmed cell death associated with fungal allorecognition, a form of innate immunity, remain largely unknown. In this study, transcriptome analysis was used to infer mechanisms activated during barrage formation in vic3-incompatible strains of Cryphonectria parasitica, the chestnut blight fungus. Pronounced differential expression occurred in barraging strains of genes involved in mating pheromone (mf2-1, mf2-2), secondary metabolite production, detoxification (including oxidative stress), apoptosis-related, RNA interference, and HET-domain genes. Evidence for secondary metabolite production and reactive oxygen species (ROS) accumulation is supported through UPLC-HRMS analysis and cytological staining, respectively. Differential expression of mating-related genes and HET-domain genes was further examined by RT-qPCR of incompatible interactions involving each of the six vegetative incompatibility (vic) loci in C. parasitica and revealed distinct recognition process networks. We infer that vegetative incompatibility in C. parasitica activates defence reactions that involve secondary metabolism, resulting in increased toxicity of the extra- and intracellular environment. Accumulation of ROS (and other potential toxins) may result in detoxification failure and activation of apoptosis, sporulation, and the expression of associated pheromone genes. The incompatible reaction leaves abundant traces of a process-specific metabolome as conidiation is initiated.
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Affiliation(s)
- Anatoly A Belov
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Thomas E Witte
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - David P Overy
- Agriculture and Agri-Food Canada, Ottawa, ON, K1Y 4X2, Canada
| | - Myron L Smith
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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Lin L, Xu J. Fungal Pigments and Their Roles Associated with Human Health. J Fungi (Basel) 2020; 6:E280. [PMID: 33198121 PMCID: PMC7711509 DOI: 10.3390/jof6040280] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Fungi can produce myriad secondary metabolites, including pigments. Some of these pigments play a positive role in human welfare while others are detrimental. This paper reviews the types and biosynthesis of fungal pigments, their relevance to human health, including their interactions with host immunity, and recent progresses in their structure-activity relationships. Fungal pigments are grouped into carotenoids, melanin, polyketides, and azaphilones, etc. These pigments are phylogenetically broadly distributed. While the biosynthetic pathways for some fungal pigments are known, the majority remain to be elucidated. Understanding the genes and metabolic pathways involved in fungal pigment synthesis is essential to genetically manipulate the production of both the types and quantities of specific pigments. A variety of fungal pigments have shown wide-spectrum biological activities, including promising pharmacophores/lead molecules to be developed into health-promoting drugs to treat cancers, cardiovascular disorders, infectious diseases, Alzheimer's diseases, and so on. In addition, the mechanistic elucidation of the interaction of fungal pigments with the host immune system provides valuable clues for fighting fungal infections. The great potential of fungal pigments have opened the avenues for academia and industries ranging from fundamental biology to pharmaceutical development, shedding light on our endeavors for disease prevention and treatment.
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Affiliation(s)
- Lan Lin
- School of Life Science and Technology, Department of Bioengineering, Key Laboratory of Developmental Genes and Human Diseases (MOE), Southeast University, Nanjing 210096, Jiangsu, China;
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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27
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Teratopyrones A-C, Dimeric Naphtho-γ-Pyrones and Other Metabolites from Teratosphaeria sp. AK1128, a Fungal Endophyte of Equisetum arvense. Molecules 2020; 25:molecules25215058. [PMID: 33143346 PMCID: PMC7662774 DOI: 10.3390/molecules25215058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022] Open
Abstract
Bioassay-guided fractionation of a cytotoxic extract derived from a solid potato dextrose agar (PDA) culture of Teratosphaeria sp. AK1128, a fungal endophyte of Equisetum arvense, afforded three new naphtho-γ-pyrone dimers, teratopyrones A–C (1–3), together with five known naphtho-γ-pyrones, aurasperone B (4), aurasperone C (5), aurasperone F (6), nigerasperone A (7), and fonsecin B (8), and two known diketopiperazines, asperazine (9) and isorugulosuvine (10). The structures of 1–3 were determined on the basis of their spectroscopic data. Cytotoxicity assay revealed that nigerasperone A (7) was moderately active against the cancer cell lines PC-3M (human metastatic prostate cancer), NCI-H460 (human non-small cell lung cancer), SF-268 (human CNS glioma), and MCF-7 (human breast cancer), with IC50s ranging from 2.37 to 4.12 μM while other metabolites exhibited no cytotoxic activity up to a concentration of 5.0 μM.
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Cogan DP, Ly J, Nair SK. Structural Basis for Enzymatic Off-Loading of Hybrid Polyketides by Dieckmann Condensation. ACS Chem Biol 2020; 15:2783-2791. [PMID: 33017142 DOI: 10.1021/acschembio.0c00579] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While several bioactive natural products that contain tetramate or pyridone heterocycles have been described, information on the enzymology underpinning these functionalities has been limited. Here we biochemically characterize an off-loading Dieckmann cyclase, NcmC, that installs the tetramate headgroup in nocamycin, a hybrid polyketide/nonribosomal peptide natural product. Crystal structures of the enzyme (1.6 Å) and its covalent complex with the epoxide cerulenin (1.6 Å) guide additional structure-based mutagenesis and product-profile analyses. Our results offer mechanistic insights into how the conserved thioesterase-like scaffold has been adapted to perform a new chemical reaction, namely, heterocyclization. Additional bioinformatics combined with docking and modeling identifies likely candidates for heterocycle formation in underexplored gene clusters and uncovers a modular basis of substrate recognition by the two subdomains of these Dieckmann cyclases.
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Fäseke VC, Raps FC, Sparr C. Polyketide Cyclizations for the Synthesis of Polyaromatics. Angew Chem Int Ed Engl 2020; 59:6975-6983. [DOI: 10.1002/anie.201911255] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/05/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Vincent C. Fäseke
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Felix C. Raps
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
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Fäseke VC, Raps FC, Sparr C. Polyketide Cyclizations for the Synthesis of Polyaromatics. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911255] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Vincent C. Fäseke
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Felix C. Raps
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
| | - Christof Sparr
- Department of Chemistry University of Basel St. Johanns-Ring 19 4056 Basel Switzerland
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Artificial covalent linkage of bacterial acyl carrier proteins for fatty acid production. Sci Rep 2019; 9:16011. [PMID: 31690733 PMCID: PMC6831569 DOI: 10.1038/s41598-019-52344-w] [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: 03/21/2019] [Accepted: 10/10/2019] [Indexed: 11/23/2022] Open
Abstract
Acyl carrier proteins (ACPs) are essential to the production of fatty acids. In some species of marine bacteria, ACPs are arranged into tandem repeats joined by peptide linkers, an arrangement that results in high fatty acid yields. By contrast, Escherichia coli, a relatively low producer of fatty acids, uses a single-domain ACP. In this work, we have engineered the native E. coli ACP into tandem di- and tri-domain constructs joined by a naturally occurring peptide linker from the PUFA synthase of Photobacterium profundum. The size of these tandem fused ACPs was determined by size exclusion chromatography to be higher (21 kDa, 36 kDa and 141 kDa) than expected based on the amino acid sequence (12 kDa, 24 kDa and 37 kDa, respectively) suggesting the formation of a flexible extended conformation. Structural studies using small-angle X-ray scattering (SAXS), confirmed this conformational flexibility. The thermal stability for the di- and tri-domain constructs was similar to that of the unfused ACP, indicating a lack of interaction between domains. Lastly, E. coli cultures harboring tandem ACPs produced up to 1.6 times more fatty acids than wild-type ACP, demonstrating the viability of ACP fusion as a method to enhance fatty acid yield in bacteria.
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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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Metabolic engineering of Saccharomyces cerevisiae for efficient production of endocrocin and emodin. Metab Eng 2019; 54:212-221. [PMID: 31028901 DOI: 10.1016/j.ymben.2019.04.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/16/2019] [Accepted: 04/20/2019] [Indexed: 11/22/2022]
Abstract
The anthraquinones endocrocin and emodin are synthesized by a special class of type I NR-PKSs and a discrete MβL-TE. In this work, we first reconstituted a biosynthetic pathway of endocrocin and emodin in S. cerevisiae by combining enzymes from different sources. We functionally characterized a TE-less NR-PKS (SlACAS) and a MβL-TE (SlTE) from S. lycopersici as well as four orthologous MβL-TEs. SlACAS was coexpressed with different MβL-TEs in S. cerevisiae. SlACAS generated the highest amount of endocrocin when coupled with HyTE, the yield was 115.6% higher than that with the native SlTE. To accumulate more emodin, seven decarboxylases with high homology to HyDC were identified and introduced into the biosynthetic pathway. Among these orthologs, AfDC exhibited the highest catalytic activity and the conversion rate reached 98.6%. A double-point mutant acetyl-CoA carboxylase, ACC1S659A, S1157A, was further introduced to increase the production of malonyl-CoA as a precursor of these anthraquinones. The production of endocrocin (233.6 ± 20.3 mg/L) and emodin (253.2 ± 21.7 mg/L) then dramatically increased. We also optimized the carbon source in the medium and conducted fed-batch fermentation with the engineered strains. The titers of endocrocin and emodin obtained were 661.2 ± 50.5 mg/L and 528.4 ± 62.7 mg/L, respectively, which are higher than previously reported. In this work, by screening a small library of orthologous biosynthetic bricks, an efficient biosynthetic pathway of endocrocin and emodin was first created in S. cerevisiae. This study provides a novel metabolic engineering approach for optimization of the production of desired molecules.
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Docking analysis of hexanoic acid and quercetin with seven domains of polyketide synthase A provided insight into quercetin-mediated aflatoxin biosynthesis inhibition in Aspergillus flavus. 3 Biotech 2019; 9:149. [PMID: 30944796 DOI: 10.1007/s13205-019-1675-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Studies on phytochemicals as anti-aflatoxigenic agents have gained importance including quercetin. Thus, to understand the molecular mechanism behind inhibition of aflatoxin biosynthesis by quercetin, interaction study with polyketide synthase A (PksA) of Aspergillus flavus was undertaken. The 3D structure of seven domains of PksA was modeled using SWISS-MODEL server and docking studies were performed by Autodock tools-1.5.6. Docking energies of both the ligands (quercetin and hexanoic acid) were compared with each of the domains of PksA enzyme. Binding energy for quercetin was lesser that ranged from - 7.1 to - 5.25 kcal/mol in comparison to hexanoic acid (- 4.74 to - 3.54 kcal/mol). LigPlot analysis showed the formation of 12 H bonds in case of quercetin and 8 H bonds in hexanoic acid. During an interaction with acyltransferase domain, both ligands showed H bond formation at Arg63 position. Also, in product template domain, quercetin creates four H bonds in comparison to one in hexanoic acid. Our quantitative RT-PCR analysis of genes from aflatoxin biosynthesis showed downregulation of pksA, aflD, aflR, aflP and aflS at 24 h time point in comparison to 7 h in quercetin-treated A. flavus. Overall results revealed that quercetin exhibited the highest level of binding potential (more number of H bonds) with PksA domain in comparison to hexanoic acid; thus, quercetin possibly inhibits via competitively binding to the domains of polyketide synthase, a key enzyme of aflatoxin biosynthetic pathway. Further, we propose that key enzymes from aflatoxin biosynthetic pathway in aflatoxin-producing Aspergilli could be explored further using other phytochemicals as inhibitors.
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Genome mining and biosynthesis of a polyketide from a biofertilizer fungus that can facilitate reductive iron assimilation in plant. Proc Natl Acad Sci U S A 2019; 116:5499-5504. [PMID: 30842286 DOI: 10.1073/pnas.1819998116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fungi have the potential to produce a large repertoire of bioactive molecules, many of which can affect the growth and development of plants. Genomic survey of sequenced biofertilizer fungi showed many secondary metabolite gene clusters are anchored by iterative polyketide synthases (IPKSs), which are multidomain enzymes noted for generating diverse small molecules. Focusing on the biofertilizer Trichoderma harzianum t-22, we identified and characterized a cryptic IPKS-containing cluster that synthesizes tricholignan A, a redox-active ortho-hydroquinone. Tricholignan A is shown to reduce Fe(III) and may play a role in promoting plant growth under iron-deficient conditions. The construction of tricholignan by a pair of collaborating IPKSs was investigated using heterologous reconstitution and biochemical studies. A regioselective methylation step is shown to be a key step in formation of the ortho-hydroquinone. The responsible methyltransferase (MT) is fused with an N-terminal pseudo-acyl carrier protein (ψACP), in which the apo state of the ACP is essential for methylation of the growing polyketide chain. The ψACP is proposed to bind to the IPKS and enable the trans MT to access the growing polyketide. Our studies show that a genome-driven approach to discovering bioactive natural products from biofertilizer fungi can lead to unique compounds and biosynthetic knowledge.
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36
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Abstract
Covering: up to mid of 2018 Type I fatty acid synthases (FASs) are giant multienzymes catalyzing all steps of the biosynthesis of fatty acids from acetyl- and malonyl-CoA by iterative precursor extension. Two strikingly different architectures of FAS evolved in yeast (as well as in other fungi and some bacteria) and metazoans. Yeast-type FAS (yFAS) assembles into a barrel-shaped structure of more than 2 MDa molecular weight. Catalytic domains of yFAS are embedded in an extensive scaffolding matrix and arranged around two enclosed reaction chambers. Metazoan FAS (mFAS) is a 540 kDa X-shaped dimer, with lateral reaction clefts, minimal scaffolding and pronounced conformational variability. All naturally occurring yFAS are strictly specialized for the production of saturated fatty acids. The yFAS architecture is not used for the biosynthesis of any other secondary metabolite. On the contrary, mFAS is related at the domain organization level to major classes of polyketide synthases (PKSs). PKSs produce a variety of complex and potent secondary metabolites; they either act iteratively (iPKS), or are linked via directed substrate transfer into modular assembly lines (modPKSs). Here, we review the architectures of yFAS, mFAS, and iPKSs. We rationalize the evolution of the yFAS assembly, and provide examples for re-engineering of yFAS. Recent studies have provided novel insights into the organization of iPKS. A hybrid crystallographic model of a mycocerosic acid synthase-like Pks5 yielded a comprehensive visualization of the organization and dynamics of fully-reducing iPKS. Deconstruction experiments, structural and functional studies of specialized enzymatic domains, such as the product template (PT) and the starter-unit acyltransferase (SAT) domain have revealed functional principles of non-reducing iterative PKS (NR-PKSs). Most recently, a six-domain loading region of an NR-PKS has been visualized at high-resolution together with cryo-EM studies of a trapped loading intermediate. Altogether, these data reveal the related, yet divergent architectures of mFAS, iPKS and also modPKSs. The new insights highlight extensive dynamics, and conformational coupling as key features of mFAS and iPKS and are an important step towards collection of a comprehensive series of snapshots of PKS action.
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Affiliation(s)
- Dominik A Herbst
- Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland.
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37
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Hou XF, Song YJ, Zhang M, Lan W, Meng S, Wang C, Pan HX, Cao C, Tang GL. Enzymology of Anthraquinone-γ-Pyrone Ring Formation in Complex Aromatic Polyketide Biosynthesis. Angew Chem Int Ed Engl 2018; 57:13475-13479. [DOI: 10.1002/anie.201806729] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Xian-Feng Hou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Yu-Jiao Song
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Mei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Song Meng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Hai-Xue Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Gong-Li Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
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38
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Hou XF, Song YJ, Zhang M, Lan W, Meng S, Wang C, Pan HX, Cao C, Tang GL. Enzymology of Anthraquinone-γ-Pyrone Ring Formation in Complex Aromatic Polyketide Biosynthesis. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Xian-Feng Hou
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Yu-Jiao Song
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Mei Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Song Meng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Hai-Xue Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
| | - Gong-Li Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 China
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39
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A comprehensive catalogue of polyketide synthase gene clusters in lichenizing fungi. J Ind Microbiol Biotechnol 2018; 45:1067-1081. [PMID: 30206732 DOI: 10.1007/s10295-018-2080-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/24/2018] [Indexed: 10/28/2022]
Abstract
Lichens are fungi that form symbiotic partnerships with algae. Although lichens produce diverse polyketides, difficulties in establishing and maintaining lichen cultures have prohibited detailed studies of their biosynthetic pathways. Creative, albeit non-definitive, methods have been developed to assign function to biosynthetic gene clusters in lieu of techniques such as gene knockout and heterologous expressions that are commonly applied to easily cultivatable organisms. We review a total of 81 completely sequenced polyketide synthase (PKS) genes from lichenizing fungi, comprising to our best efforts all complete and reported PKS genes in lichenizing fungi to date. This review provides an overview of the approaches used to locate and sequence PKS genes in lichen genomes, current approaches to assign function to lichen PKS gene clusters, and what polyketides are proposed to be biosynthesized by these PKS. We conclude with remarks on prospects for genomics-based natural products discovery in lichens. We hope that this review will serve as a guide to ongoing research efforts on polyketide biosynthesis in lichenizing fungi.
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40
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He Y, Wang B, Chen W, Cox RJ, He J, Chen F. Recent advances in reconstructing microbial secondary metabolites biosynthesis in Aspergillus spp. Biotechnol Adv 2018; 36:739-783. [DOI: 10.1016/j.biotechadv.2018.02.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/30/2018] [Accepted: 02/01/2018] [Indexed: 11/28/2022]
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41
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Herbst DA, Huitt-Roehl CR, Jakob RP, Kravetz JM, Storm PA, Alley JR, Townsend CA, Maier T. The structural organization of substrate loading in iterative polyketide synthases. Nat Chem Biol 2018; 14:474-479. [PMID: 29610486 DOI: 10.1038/s41589-018-0026-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/07/2018] [Indexed: 11/09/2022]
Abstract
Polyketide synthases (PKSs) are microbial multienzymes for the biosynthesis of biologically potent secondary metabolites. Polyketide production is initiated by the loading of a starter unit onto an integral acyl carrier protein (ACP) and its subsequent transfer to the ketosynthase (KS). Initial substrate loading is achieved either by multidomain loading modules or by the integration of designated loading domains, such as starter unit acyltransferases (SAT), whose structural integration into PKS remains unresolved. A crystal structure of the loading/condensing region of the nonreducing PKS CTB1 demonstrates the ordered insertion of a pseudodimeric SAT into the condensing region, which is aided by the SAT-KS linker. Cryo-electron microscopy of the post-loading state trapped by mechanism-based crosslinking of ACP to KS reveals asymmetry across the CTB1 loading/-condensing region, in accord with preferential 1:2 binding stoichiometry. These results are critical for re-engineering the loading step in polyketide biosynthesis and support functional relevance of asymmetric conformations of PKSs.
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Affiliation(s)
- Dominik A Herbst
- Department of Biozentrum, University of Basel, Basel, Switzerland
| | | | - Roman P Jakob
- Department of Biozentrum, University of Basel, Basel, Switzerland
| | - Jacob M Kravetz
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Philip A Storm
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Jamie R Alley
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Craig A Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Timm Maier
- Department of Biozentrum, University of Basel, Basel, Switzerland.
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42
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Liu L, Zhang Z, Shao CL, Wang CY. Analysis of the Sequences, Structures, and Functions of Product-Releasing Enzyme Domains in Fungal Polyketide Synthases. Front Microbiol 2017; 8:1685. [PMID: 28928723 PMCID: PMC5591372 DOI: 10.3389/fmicb.2017.01685] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/21/2017] [Indexed: 11/14/2022] Open
Abstract
Product-releasing enzyme (PRE) domains in fungal non-reducing polyketide synthases (NR-PKSs) play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I–VIII). It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE), reductase (R), and metallo-β-lactamase-type TE (MβL-TE). The widely distributed TE or TE-like domains were involved in NR-PKSs of groups I–IV, VI, and VIII. The R domains appeared in NR-PKSs of groups IV and VII, while the physically discrete MβL-TE domains were employed by most NR-PKSs of group V. The changes of catalytic sites and structural characteristics resulted in PRE functional differentiations. The phylogeny revealed that the evolution of TE domains was accompanied by complex functional divergence. The diverse sequence lengths of TE lid-loops affected substrate specificity with different chain lengths. The volume diversification of TE catalytic pockets contributed to catalytic mechanisms with functional differentiations. The above findings may help to understand the crucial catalysis of fungal aromatic polyketide biosyntheses and govern recombination of NR-PKSs to obtain unnatural target products.
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Affiliation(s)
- Lu Liu
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Zheng Zhang
- State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong UniversityJinan, China
| | - Chang-Lun Shao
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, School of Medicine and Pharmacy, Ocean University of ChinaQingdao, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and TechnologyQingdao, China.,Institute of Evolution and Marine Biodiversity, Ocean University of ChinaQingdao, China
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43
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Jacob S, Grötsch T, Foster AJ, Schüffler A, Rieger PH, Sandjo LP, Liermann JC, Opatz T, Thines E. Unravelling the biosynthesis of pyriculol in the rice blast fungus Magnaporthe oryzae. MICROBIOLOGY-SGM 2017; 163:541-553. [PMID: 27902426 DOI: 10.1099/mic.0.000396] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Pyriculol was isolated from the rice blast fungus Magnaporthe oryzae and found to induce lesion formation on rice leaves. These findings suggest that it could be involved in virulence. The gene MoPKS19 was identified to encode a polyketide synthase essential for the production of the polyketide pyriculol in the rice blast fungus M. oryzae. The transcript abundance of MoPKS19 correlates with the biosynthesis rate of pyriculol in a time-dependent manner. Furthermore, gene inactivation of MoPKS19 resulted in a mutant unable to produce pyriculol, pyriculariol and their dihydro derivatives. Inactivation of a putative oxidase-encoding gene MoC19OXR1, which was found to be located in the genome close to MoPKS19, resulted in a mutant exclusively producing dihydropyriculol and dihydropyriculariol. By contrast, overexpression of MoC19OXR1 resulted in a mutant strain only producing pyriculol. The MoPKS19 cluster, furthermore, comprises two transcription factors MoC19TRF1 and MoC19TRF2, which were both found individually to act as negative regulators repressing gene expression of MoPKS19. Additionally, extracts of ΔMopks19 and ΔMoC19oxr1 made from axenic cultures failed to induce lesions on rice leaves compared to extracts of the wild-type strain. Consequently, pyriculol and its isomer pyriculariol appear to be the only lesion-inducing secondary metabolites produced by M. oryzae wild-type (MoWT) under these culture conditions. Interestingly, the mutants unable to produce pyriculol and pyriculariol were as pathogenic as MoWT, demonstrating that pyriculol is not required for infection.
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Affiliation(s)
- Stefan Jacob
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger Str. 56, D-67663 Kaiserslautern, Germany
| | - Thomas Grötsch
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger Str. 56, D-67663 Kaiserslautern, Germany
| | - Andrew J Foster
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger Str. 56, D-67663 Kaiserslautern, Germany
| | - Anja Schüffler
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger Str. 56, D-67663 Kaiserslautern, Germany
| | - Patrick H Rieger
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger Str. 56, D-67663 Kaiserslautern, Germany
| | - Louis P Sandjo
- Institute of Organic Chemistry, Johannes Gutenberg University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Johannes C Liermann
- Institute of Organic Chemistry, Johannes Gutenberg University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Till Opatz
- Institute of Organic Chemistry, Johannes Gutenberg University of Mainz, Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Eckhard Thines
- Institut für Mikrobiologie und Weinforschung, Johannes Gutenberg University of Mainz, Johann-Joachim-Becherweg 15, D-55128 Mainz, Germany.,Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Erwin-Schrödinger Str. 56, D-67663 Kaiserslautern, Germany
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44
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Chemogenomics driven discovery of endogenous polyketide anti-infective compounds from endosymbiotic Emericella variecolor CLB38 and their RNA secondary structure analysis. PLoS One 2017; 12:e0172848. [PMID: 28245269 PMCID: PMC5330499 DOI: 10.1371/journal.pone.0172848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 02/10/2017] [Indexed: 11/19/2022] Open
Abstract
In the postgenomic era, a new strategy for chemical dereplication of polyketide anti-infective drugs requires novel genomics and chromatographic strategies. An endosymbiotic fungal strain CLB38 was isolated from the root tissue of Combretum latifolium Blume (Combretaceae) which was collected from the Western Ghats of India. The isolate CLB38 was then identified as Emericella variecolor by its characteristic stellate ascospores culture morphology and molecular analysis of ITS nuclear rDNA and intervening 5.8S rRNA gene sequence. ITS2 RNA secondary structure modeling clearly distinguished fungal endosymbiont E. variecolor CLB38 with other lifestyles in the same monophyletic clade. Ethyl acetate fraction of CLB38 explored a broad spectrum of antimicrobial activity against multidrug resistant pathogens. Biosynthetic PKS type-I gene and chromatographic approach afford two polyketide antimicrobial compounds which identified as evariquinone and isoindolones derivative emerimidine A. MIC of purified compounds against test microorganisms ranged between 3.12 μg/ml and 12.5 μg/ml. This research highlights the utility of E. variecolor CLB38 as an anticipate source for anti-infective polyketide metabolites evariquinone and emerimidine A to combat multidrug resistant microorganisms. Here we demonstrates a chemogenomics strategy via the feasibility of PKS type-I gene and chromatographic approach as a proficient method for the rapid prediction and discovery of new polyketides compounds from fungal endosymbionts.
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45
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Chen AJ, Frisvad JC, Sun BD, Varga J, Kocsubé S, Dijksterhuis J, Kim DH, Hong SB, Houbraken J, Samson RA. Aspergillus section Nidulantes (formerly Emericella): Polyphasic taxonomy, chemistry and biology. Stud Mycol 2016; 84:1-118. [PMID: 28050053 PMCID: PMC5198626 DOI: 10.1016/j.simyco.2016.10.001] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Aspergillus section Nidulantes includes species with striking morphological characters, such as biseriate conidiophores with brown-pigmented stipes, and if present, the production of ascomata embedded in masses of Hülle cells with often reddish brown ascospores. The majority of species in this section have a sexual state, which were named Emericella in the dual name nomenclature system. In the present study, strains belonging to subgenus Nidulantes were subjected to multilocus molecular phylogenetic analyses using internal transcribed spacer region (ITS), partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Nine sections are accepted in subgenus Nidulantes including the new section Cavernicolus. A polyphasic approach using morphological characters, extrolites, physiological characters and phylogeny was applied to investigate the taxonomy of section Nidulantes. Based on this approach, section Nidulantes is subdivided in seven clades and 65 species, and 10 species are described here as new. Morphological characters including colour, shape, size, and ornamentation of ascospores, shape and size of conidia and vesicles, growth temperatures are important for identifying species. Many species of section Nidulantes produce the carcinogenic mycotoxin sterigmatocystin. The most important mycotoxins in Aspergillus section Nidulantes are aflatoxins, sterigmatocystin, emestrin, fumitremorgins, asteltoxins, and paxillin while other extrolites are useful drugs or drug lead candidates such as echinocandins, mulundocandins, calbistrins, varitriols, variecolins and terrain. Aflatoxin B1 is produced by four species: A. astellatus, A. miraensis, A. olivicola, and A. venezuelensis.
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Affiliation(s)
- A J Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, PR China; CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - J C Frisvad
- Department of Systems Biology, Søltofts Plads B. 221, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - B D Sun
- China General Microbiological Culture Collection Centre, Institute of Microbiology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - J Varga
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726, Szeged, Hungary
| | - S Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, H-6726, Szeged, Hungary
| | - J Dijksterhuis
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - D H Kim
- Division of Forest Environment Protection, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - S-B Hong
- Korean Agricultural Culture Collection, National Institute of Agricultural Science, 166, Nongsaengmyeong-ro, Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - J Houbraken
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - R A Samson
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
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46
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Enhanced production of polyunsaturated fatty acids by enzyme engineering of tandem acyl carrier proteins. Sci Rep 2016; 6:35441. [PMID: 27752094 PMCID: PMC5067506 DOI: 10.1038/srep35441] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/29/2016] [Indexed: 11/25/2022] Open
Abstract
In some microorganisms, polyunsaturated fatty acids (PUFAs) are biosynthesized by PUFA synthases characterized by tandem acyl carrier proteins (ACPs) in subunit A. These ACPs were previously shown to be important for PUFA productivity. In this study, we examined their function in more detail. PUFA productivities increased depending on the number of ACPs without profile changes in each subunit A of eukaryotic and prokaryotic PUFA synthases. We also constructed derivative enzymes from subunit A with 5 × ACPs. Enzymes possessing one inactive ACP at any position produced ~30% PUFAs compared with the parental enzyme but unexpectedly had ~250% productivity compared with subunit A with 4 × ACPs. Enzymes constructed by replacing the 3rd ACP with an inactive ACP from another subunit A or ACP-unrelated sequences produced ~100% and ~3% PUFAs compared with the parental 3rd ACP-inactive enzyme, respectively. These results suggest that both the structure and number of ACP domains are important for PUFA productivity.
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47
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Implication of PKS type I gene and chromatographic strategy for the biodiscovery of antimicrobial polyketide metabolites from endosymbiotic Nocardiopsis prasina CLA68. Naturwissenschaften 2016; 103:45. [DOI: 10.1007/s00114-016-1370-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 12/21/2022]
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48
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Gao SS, Duan A, Xu W, Yu P, Hang L, Houk KN, Tang Y. Phenalenone Polyketide Cyclization Catalyzed by Fungal Polyketide Synthase and Flavin-Dependent Monooxygenase. J Am Chem Soc 2016; 138:4249-59. [PMID: 26978228 PMCID: PMC4988900 DOI: 10.1021/jacs.6b01528] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Phenalenones are polyketide natural products that display diverse structures and biological activities. The core of phenalenones is a peri-fused tricyclic ring system cyclized from a linear polyketide precursor via an unresolved mechanism. Toward understanding the unusual cyclization steps, the phn biosynthetic gene cluster responsible for herqueinone biosynthesis was identified from the genome of Penicillium herquei. A nonreducing polyketide synthase (NR-PKS) PhnA was shown to synthesize the heptaketide backbone and cyclize it into the angular, hemiketal-containing naphtho-γ-pyrone prephenalenone. The product template (PT) domain of PhnA catalyzes only the C4-C9 aldol condensation, which is unprecedented among known PT domains. The transformation of prephenalenone to phenalenone requires an FAD-dependent monooxygenase (FMO) PhnB, which catalyzes the C2 aromatic hydroxylation of prephenalenone and ring opening of the γ-pyrone ring simultaneously. Density functional theory calculations provide insights into why the hydroxylated intermediate undergoes an aldol-like phenoxide-ketone cyclization to yield the phenalenone core. This study therefore unveiled new routes and biocatalysts for polyketide cyclization.
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Affiliation(s)
- Shu-Shan Gao
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Abing Duan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Wei Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Peiyuan Yu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Leibniz Hang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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49
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Barkal LJ, Theberge AB, Guo CJ, Spraker J, Rappert L, Berthier J, Brakke KA, Wang CCC, Beebe DJ, Keller NP, Berthier E. Microbial metabolomics in open microscale platforms. Nat Commun 2016; 7:10610. [PMID: 26842393 PMCID: PMC4742997 DOI: 10.1038/ncomms10610] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/04/2016] [Indexed: 01/04/2023] Open
Abstract
The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. Traditional methods for microbial culture and subsequent metabolomics are time-consuming and labour-intensive. Here the authors present a microscale culture platform with integrated extraction for efficient, low-volume metabolomics of relevant microenvironments and microbial co-cultures.
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Affiliation(s)
- Layla J Barkal
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.,Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Ashleigh B Theberge
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.,Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.,Department of Urology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Chun-Jun Guo
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles California 90089, USA
| | - Joe Spraker
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Lucas Rappert
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Jean Berthier
- Department of Biotechnology, CEA-University Grenoble-Alpes, 17 Avenue des Martyrs, 38054 Grenoble, France
| | - Kenneth A Brakke
- Department of Mathematics, Susquehanna University, Selinsgrove, Pennsylvania 17870, USA
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles California 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles California 90089, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.,Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | - Erwin Berthier
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA.,Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
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50
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Kashiwa N, Ebizuka Y, Fujii I. Identification and Heterologous Expression of the Topopyrone Nonaketide Synthase Gene from <i>Phoma</i> sp. Chem Pharm Bull (Tokyo) 2016; 64:947-51. [DOI: 10.1248/cpb.c16-00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Nobuyuki Kashiwa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Yutaka Ebizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
| | - Isao Fujii
- School of Pharmacy, Iwate Medical University
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