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Yu J, Zhang Y, Zhang L, Shi J, Wang K, Yuan W, Lin Z, Ning S, Wang B, Wang X, Qiu Y, Hsiang T, Zhang L, Liu X, Zhu G. New N-acylated aminoalkanoic acids from tea roots derived biocontrol agent Clonostachys rosea 15020. Synth Syst Biotechnol 2024; 9:684-693. [PMID: 38846337 PMCID: PMC11153888 DOI: 10.1016/j.synbio.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 06/09/2024] Open
Abstract
Four new N-acylated aminoalkanoic acids, namely clonoroseins E-H (1-4), together with three previously identified analogs, clonoroseins A, B, and D (5-7), were identified from the endophytic fungus Clonostachys rosea strain 15020 (CR15020), using Feature-based Molecular Networking (FBMN). The elucidation of their chemical structures, including their absolute configurations, was achieved through spectroscopic analysis combined with quantum chemical calculations. Bioinformatics analyses suggested that an iterative type I HR-PKS (CrsE) generates the polyketide side chain of these clonoroseins. Furthermore, a downstream adenylate-forming enzyme of the PKS (CrsD) was suspected to function as an amide synthetase. CrsD potentially facilitates the transformation of the polyketide moiety into an acyl-AMP intermediate, followed by nucleophilic substitution with either β-alanine or γ-aminobutyric acid to produce amide derivatives. These findings significantly expand our understanding of PKS-related products originating from C. rosea and also underscore the powerful application of FBMN analytical methods in characterization of new compounds.
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Affiliation(s)
- Jiaming Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yue Zhang
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Li Zhang
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Jie Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Kun Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weize Yuan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zexu Lin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shangqian Ning
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bohao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuyang Qiu
- School of Insurance, Shandong University of Finance and Economics, Jinan, 250014, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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2
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Konkel Z, Kubatko L, Slot JC. CLOCI: unveiling cryptic fungal gene clusters with generalized detection. Nucleic Acids Res 2024:gkae625. [PMID: 39016185 DOI: 10.1093/nar/gkae625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
Gene clusters are genomic loci that contain multiple genes that are functionally and genetically linked. Gene clusters collectively encode diverse functions, including small molecule biosynthesis, nutrient assimilation, metabolite degradation, and production of proteins essential for growth and development. Identifying gene clusters is a powerful tool for small molecule discovery and provides insight into the ecology and evolution of organisms. Current detection algorithms focus on canonical 'core' biosynthetic functions many gene clusters encode, while overlooking uncommon or unknown cluster classes. These overlooked clusters are a potential source of novel natural products and comprise an untold portion of overall gene cluster repertoires. Unbiased, function-agnostic detection algorithms therefore provide an opportunity to reveal novel classes of gene clusters and more precisely define genome organization. We present CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier), an algorithm that identifies gene clusters using multiple proxies of selection for coordinated gene evolution. Our approach generalizes gene cluster detection and gene cluster family circumscription, improves detection of multiple known functional classes, and unveils non-canonical gene clusters. CLOCI is suitable for genome-enabled small molecule mining, and presents an easily tunable approach for delineating gene cluster families and homologous loci.
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Affiliation(s)
- Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Laura Kubatko
- Department of Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
- Department of Statistics, The Ohio State University, Columbus, OH 43210, USA
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
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Xu Y, Chen C, Cai J, Lin L, Song W, Yang K, Zhao Y, Wen C, Wei J, Liu Z. Comparative analysis of sipeimine content, metabolome and chloroplast genome in cultivated and wild varieties of Fritillaria taipaiensis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38630097 DOI: 10.1002/jsfa.13548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/22/2024] [Accepted: 04/17/2024] [Indexed: 05/03/2024]
Abstract
BACKGROUND The wild variety Fritillaria taipaiensis E.B (EB) is known for its superior therapeutic effects, but its limited production cannot meet demand. As a result, the cultivated variety F. taipaiensis P. Y. Li (PY) has been widely grown. In this study, we conducted a comprehensive analysis comparing EB and PY in terms of external features, sipeimine content, metabolome and chloroplast genome to differentiate these two varieties. RESULTS Our research revealed that the petals and pods of EB are green, while those of PY have purple markings. The bulbs of EB contain significantly higher levels of sipeimine compared to those of PY. Metabolomic analysis identified 56 differentially expressed metabolites (DMs), with 23 upregulated and 33 downregulated in EB bulbs. Particularly, 3-hydroxycinnamic acid and secoxyloganin may serve as distinctive DMs. These DMs were associated with 17 KEGG pathways, including pyrimidine metabolism, alanine, aspartate and glutamate metabolism, and galactose metabolism. Differences in the length of the chloroplast genome were primarily observed in the large single-copy (LSC) region, with the largest variation in the trnH-GUC-psbA region. The placement of the trnH gene and the rps gene in proximity to the LSC/IRb boundary differs between EB and PY. CONCLUSION The results of this study provide valuable insights for the introduction and comprehensive development of wild F. taipaiensis from a scientific perspective. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Yue Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Cun Chen
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu, China
| | - Jing Cai
- West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Ling Lin
- NeiJiang Academy of Agricultural Sciences, Neijiang, China
| | - Wei Song
- NeiJiang Academy of Agricultural Sciences, Neijiang, China
| | - Kexin Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yiran Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chun Wen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiahong Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhibin Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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4
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Key J, Gispert S, Kandi AR, Heinz D, Hamann A, Osiewacz HD, Meierhofer D, Auburger G. CLPP-Null Eukaryotes with Excess Heme Biosynthesis Show Reduced L-arginine Levels, Probably via CLPX-Mediated OAT Activation. Biomolecules 2024; 14:241. [PMID: 38397478 PMCID: PMC10886707 DOI: 10.3390/biom14020241] [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: 01/18/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The serine peptidase CLPP is conserved among bacteria, chloroplasts, and mitochondria. In humans and mice, its loss causes Perrault syndrome, which presents with growth deficits, infertility, deafness, and ataxia. In the filamentous fungus Podospora anserina, CLPP loss leads to longevity. CLPP substrates are selected by CLPX, an AAA+ unfoldase. CLPX is known to target delta-aminolevulinic acid synthase (ALAS) to promote pyridoxal phosphate (PLP) binding. CLPX may also influence cofactor association with other enzymes. Here, the evaluation of P. anserina metabolomics highlighted a reduction in arginine/histidine levels. In Mus musculus cerebellum, reductions in arginine/histidine and citrulline occurred with a concomitant accumulation of the heme precursor protoporphyrin IX. This suggests that the increased biosynthesis of 5-carbon (C5) chain deltaALA consumes not only C4 succinyl-CoA and C1 glycine but also specific C5 delta amino acids. As enzymes responsible for these effects, the elevated abundance of CLPX and ALAS is paralleled by increased OAT (PLP-dependent, ornithine delta-aminotransferase) levels. Possibly as a consequence of altered C1 metabolism, the proteome profiles of P. anserina CLPP-null cells showed strong accumulation of a methyltransferase and two mitoribosomal large subunit factors. The reduced histidine levels may explain the previously observed metal interaction problems. As the main nitrogen-storing metabolite, a deficiency in arginine would affect the urea cycle and polyamine synthesis. Supplementation of arginine and histidine might rescue the growth deficits of CLPP-mutant patients.
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Affiliation(s)
- Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Experimental Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (J.K.); (S.G.); (A.R.K.)
| | - Suzana Gispert
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Experimental Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (J.K.); (S.G.); (A.R.K.)
| | - Arvind Reddy Kandi
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Experimental Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (J.K.); (S.G.); (A.R.K.)
| | - Daniela Heinz
- Institute of Molecular Biosciences, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (D.H.); (A.H.); (H.D.O.)
| | - Andrea Hamann
- Institute of Molecular Biosciences, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (D.H.); (A.H.); (H.D.O.)
| | - Heinz D. Osiewacz
- Institute of Molecular Biosciences, Faculty of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany; (D.H.); (A.H.); (H.D.O.)
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany;
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Experimental Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (J.K.); (S.G.); (A.R.K.)
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Zhou L, Awakawa T, Ushimaru R, Kanaida M, Abe I. Characterization of Aziridine-Forming α-Ketoglutarate-Dependent Oxygenase in l-Isovaline Biosynthesis. Org Lett 2024; 26:724-727. [PMID: 38227980 DOI: 10.1021/acs.orglett.3c04185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
l-Isovaline biosynthesis by TqaLFM-ti from Tolypocladium inflatum was demonstrated in vitro. The biochemical analysis of the α-ketoglutarate-dependent oxygenase TqaL-ti revealed that it produces (2S,3S)-3-ethyl-3-methylaziridine-2-carboxylic acid from l-isoleucine, thus exhibiting a stereoselectivity different from those of the reported homologues. Remarkably, a single mutation on I295 in TqaL-ti completely exchanged its stereoselectivity to produce the C-3 stereoisomer. TqaFM-ti generates d-isovaline from (2S,3R)-aziridine-2-carboxylic acid, suggesting that the stereochemistry of the TqaL product defines that of isovaline.
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Affiliation(s)
- Lu Zhou
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masahiro Kanaida
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Hopiavuori A, McKinnie SMK. Algal Kainoid Synthases Exhibit Substrate-Dependent Hydroxylation and Cyclization Activities. ACS Chem Biol 2023; 18:2457-2463. [PMID: 38047879 PMCID: PMC10728896 DOI: 10.1021/acschembio.3c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
FeII/α-ketoglutarate-dependent dioxygenases (Fe/αKG) make up a large enzyme family that functionalize C-H bonds on diverse organic substrates. Although Fe/αKG homologues catalyze an array of chemically useful reactions, hydroxylation typically predominates. Microalgal DabC uniquely forms a novel C-C bond to construct the bioactive pyrrolidine ring in domoic acid biosynthesis; however, we have identified that this kainoid synthase exclusively performs a stereospecific hydroxylation reaction on its cis substrate regioisomer. Mechanistic and kinetic analyses with native and alternative substrates identified a 20-fold rate increase in DabC radical cyclization over β-hydroxylation with no observable 1,5-hydrogen atom transfer. Moreover, this dual activity was conserved among macroalgal RadC1 and KabC homologues and provided insight into substrate recognition and reactivity trends. Investigation of this substrate-dependent chemistry improves our understanding of kainoid synthases and their biocatalytic application.
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Affiliation(s)
- Austin
R. Hopiavuori
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Shaun M. K. McKinnie
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
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7
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Rassbach J, Hilsberg N, Haensch VG, Dörner S, Gressler J, Sonnabend R, Semm C, Voigt K, Hertweck C, Gressler M. Non-canonical two-step biosynthesis of anti-oomycete indole alkaloids in Kickxellales. Fungal Biol Biotechnol 2023; 10:19. [PMID: 37670394 PMCID: PMC10478498 DOI: 10.1186/s40694-023-00166-x] [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: 05/30/2023] [Accepted: 08/06/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Fungi are prolific producers of bioactive small molecules of pharmaceutical or agricultural interest. The secondary metabolism of higher fungi (Dikarya) has been well-investigated which led to > 39,000 described compounds. However, natural product researchers scarcely drew attention to early-diverging fungi (Mucoro- and Zoopagomycota) as they are considered to rarely produce secondary metabolites. Indeed, only 15 compounds have as yet been isolated from the entire phylum of the Zoopagomycota. RESULTS Here, we showcase eight species of the order Kickxellales (phylum Zoopagomycota) as potent producers of the indole-3-acetic acid (IAA)-derived compounds lindolins A and B. The compounds are produced both under laboratory conditions and in the natural soil habitat suggesting a specialized ecological function. Indeed, lindolin A is a selective agent against plant-pathogenic oomycetes such as Phytophthora sp. Lindolin biosynthesis was reconstituted in vitro and relies on the activity of two enzymes of dissimilar evolutionary origin: Whilst the IAA-CoA ligase LinA has evolved from fungal 4-coumaryl-CoA synthetases, the subsequently acting IAA-CoA:anthranilate N-indole-3-acetyltransferase LinB is a unique enzyme across all kingdoms of life. CONCLUSIONS This is the first report on bioactive secondary metabolites in the subphylum Kickxellomycotina and the first evidence for a non-clustered, two-step biosynthetic route of secondary metabolites in early-diverging fungi. Thus, the generally accepted "gene cluster hypothesis" for natural products needs to be reconsidered for early diverging fungi.
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Affiliation(s)
- Johannes Rassbach
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Nathalie Hilsberg
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Veit G Haensch
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Sebastian Dörner
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Julia Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Robin Sonnabend
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Caroline Semm
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Kerstin Voigt
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
- Jena Microbial Resource Collection (JMRC), Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
| | - Christian Hertweck
- Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Adolf-Reichwein-Strasse 23, 07745, Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 25, 07743, Jena, Germany
| | - Markus Gressler
- Faculty of Biological Sciences, Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, Winzerlaer Strasse 2, 07745, Jena, Germany.
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8
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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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Zwick CR, Renata H. Overview of Amino Acid Modifications by Iron- and α-Ketoglutarate-Dependent Enzymes. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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10
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Okhovat A, Cruces W, Docampo-Palacios ML, Ray KP, Ramirez GA. Psychoactive Isoxazoles, Muscimol, and Isoxazole Derivatives from the Amanita (Agaricomycetes) Species: Review of New Trends in Synthesis, Dosage, and Biological Properties. Int J Med Mushrooms 2023; 25:1-10. [PMID: 37824402 DOI: 10.1615/intjmedmushrooms.2023049458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Herbal products found in nature can serve as great systems of study for drug design. The Amanita muscaria mushroom is native to many parts of the Northern Hemisphere and has a very distinctive appearance with its red cap and white spotted warts. The mushroom comprises several pharmacologically active alkaloids, including muscazone, muscarine, ibotenic acid, and muscimol, the latter two compounds being potent GABA agonists. Muscimol has served as a backbone in the design of GABA agonists devoid of effects on the GABA-metabolizing enzyme, GABA transaminase, and GABA uptake systems. In this sense, several analogs of muscimol have been synthesized and studied including THIP, THPO, iso-THIP, iso-THAZ and 4-PIOL which all interact with the GABA receptors much differently. The growing pharmacological and toxicological interest based on many conflicting opinions on the use of the neuroprotective role of muscimol analogs against some neurodegenerative diseases, its potent role in the treatment of cerebral ischemia and other socially significant health conditions provided the basis for this review.
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Affiliation(s)
- Alex Okhovat
- Colorado Chromatography Labs, Parker, CO 80134, USA
| | | | | | - Kyle P Ray
- Colorado Chromatography Labs, Parker, CO 80134, USA
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11
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Pardeshi SS, Labhane PK, Disale ST, More DH, Sapkal BM. Regioselective Synthesis of 3, 5‐Disubstituted Isoxazole Catalyzed by Cu
2
O−ZnO Nanocomposite. ChemistrySelect 2022. [DOI: 10.1002/slct.202201818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Prakash K. Labhane
- Department of Chemistry MGSM'S A.S.C. College Chopda Jalgaon 425107 (MS) India
| | - Shamrao T. Disale
- Department of Chemistry Kankavli College, Kankavli Sindhudurg 416602 (MS) India
| | - Dhananjay H. More
- School of Chemical Sciences K. B. C. North Maharashtra University Jalgaon 425001 (MS) India
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12
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He MQ, Wang MQ, Chen ZH, Deng WQ, Li TH, Vizzini A, Jeewon R, Hyde KD, Zhao RL. Potential benefits and harms: a review of poisonous mushrooms in the world. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Lee S, Yu JS, Lee SR, Kim KH. Non-peptide secondary metabolites from poisonous mushrooms: overview of chemistry, bioactivity, and biosynthesis. Nat Prod Rep 2022; 39:512-559. [PMID: 34608478 DOI: 10.1039/d1np00049g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: up to June 2021A wide variety of mushrooms have traditionally been recognized as edible fungi with high nutritional value and low calories, and abundantly produce structurally diverse and bioactive secondary metabolites. However, accidental ingestion of poisonous mushrooms can result in serious illnesses and even death. Chemically, mushroom poisoning is associated with secondary metabolites produced in poisonous mushrooms, causing specific toxicity. However, many poisonous mushrooms have not been fully investigated for their secondary metabolites, and the secondary metabolites of poisonous mushrooms have not been systematically summarized for details such as chemical composition and biosynthetic mechanisms. The isolation and identification of secondary metabolites from poisonous mushrooms have great research value since these compounds could be lethal toxins that contribute to the toxicity of mushrooms or could provide lead compounds with remarkable biological activities that can promote advances in other related disciplines, such as biochemistry and pharmacology. In this review, we summarize the structures and biological activities of secondary metabolites identified from poisonous mushrooms and provide an overview of the current information on these metabolites, focusing on their chemistry, bioactivity, and biosynthesis.
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Affiliation(s)
- Seulah Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea. .,Division of Life Sciences, Korea Polar Research Institute, KIOST, Incheon 21990, Republic of Korea
| | - Jae Sik Yu
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Seoung Rak Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea. .,Department of Chemistry, Princeton University, New Jersey, 08544, USA
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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14
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Bruzgulienė J, Račkauskienė G, Bieliauskas A, Milišiūnaitė V, Dagilienė M, Matulevičiūtė G, Martynaitis V, Krikštolaitytė S, Sløk FA, Šačkus A. Regioselective synthesis of methyl 5-( N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates as new amino acid-like building blocks. Beilstein J Org Chem 2022; 18:102-109. [PMID: 35096179 PMCID: PMC8767561 DOI: 10.3762/bjoc.18.11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 12/23/2022] Open
Abstract
A convenient and efficient synthesis of novel achiral and chiral heterocyclic amino acid-like building blocks was developed. Regioisomeric methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates were prepared by the reaction of β-enamino ketoesters (including azetidine, pyrrolidine or piperidine enamines) with hydroxylamine hydrochloride. Unambiguous structural assignments were based on chiral HPLC analysis, 1H, 13C, and 15N NMR spectroscopy, HRMS, and single-crystal X-ray diffraction data.
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Affiliation(s)
- Jolita Bruzgulienė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, Kaunas LT-51423, Lithuania
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Greta Račkauskienė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, Kaunas LT-51423, Lithuania
| | - Aurimas Bieliauskas
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, Kaunas LT-51423, Lithuania
| | - Vaida Milišiūnaitė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, Kaunas LT-51423, Lithuania
| | - Miglė Dagilienė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, Kaunas LT-51423, Lithuania
| | - Gita Matulevičiūtė
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, Kaunas LT-51423, Lithuania
| | - Vytas Martynaitis
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Sonata Krikštolaitytė
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
| | - Frank A Sløk
- Vipergen ApS, Gammel Kongevej 23A, DK-1610 Copenhagen V, Denmark
| | - Algirdas Šačkus
- Institute of Synthetic Chemistry, Kaunas University of Technology, K. Baršausko g. 59, Kaunas LT-51423, Lithuania
- Department of Organic Chemistry, Kaunas University of Technology, Radvilėnų pl. 19, Kaunas LT-50254, Lithuania
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15
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Post translational modifications of Trifolitoxin: a blue fluorescent peptide antibiotic. J Antibiot (Tokyo) 2022; 75:125-135. [PMID: 35022574 PMCID: PMC8816728 DOI: 10.1038/s41429-021-00497-0] [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: 08/11/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 11/09/2022]
Abstract
Trifolitoxin (TFX, C41H63N15O15S) is a selective, ribosomally-synthesized, post-translationally modified, peptide antibiotic, produced by Rhizobium leguminosarum bv. trifolii T24. TFX specifically inhibits α-proteobacteria, including the plant symbiont Rhizobium spp., the plant pathogen Agrobacterium spp. and the animal pathogen Brucella abortus. TFX-producing strains prevent legume root nodulation by TFX-sensitive rhizobia. TFX has been isolated as a pair of geometric isomers, TFX1 and TFX2, which are derived from the biologically inactive primary amino acid sequence: Asp-Ile-Gly-Gly-Ser-Arg-Gln-Gly-Cys-Val-Ala. Gly-Cys is present as a thiazoline ring and the Arg-Gln-Gly sequence is extensively modified to a UV absorbing, blue fluorescent chromophore. The chromophore consists of a conjugated, 5-membered heterocyclic ring and side chain of modified glutamine.
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16
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Popoff A, Hug JJ, Walesch S, Garcia R, Keller L, Müller R. Structure and Biosynthesis of Myxofacyclines: Unique Myxobacterial Polyketides Featuring Varing and Rare Heterocycles [] *. Chemistry 2021; 27:16654-16661. [PMID: 34617331 PMCID: PMC9298251 DOI: 10.1002/chem.202103095] [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: 08/25/2021] [Indexed: 11/06/2022]
Abstract
A metabolome-guided screening approach in the novel myxobacterium Corallococcus sp. MCy9072 resulted in the isolation of the unprecedented natural product myxofacycline A, which features a rare isoxazole substructure. Identification and genomic investigation of additional producers alongside targeted gene inactivation experiments and heterologous expression of the corresponding biosynthetic gene cluster in the host Myxococcus xanthus DK1622 confirmed a noncanonical megaenzyme complex as the biosynthetic origin of myxofacycline A. Induced expression of the respective genes led to significantly increased production titers enabling the identification of six further members of the myxofacycline natural product family. Whereas myxofacyclines A-D display an isoxazole substructure, intriguingly myxofacyclines E and F were found to contain 4-pyrimidinole, a heterocycle unprecedented in natural products. Lastly, myxofacycline G features another rare 1,2-dihydropyrol-3-one moiety. In addition to a full structure elucidation, we report the underlying biosynthetic machinery and present a rationale for the formation of all myxofacyclines. Unexpectedly, an extraordinary polyketide synthase-nonribosomal peptide synthetase hybrid was found to produce all three types of heterocycle in these natural products.
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Affiliation(s)
- Alexander Popoff
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig (Germany)
| | - Joachim J Hug
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig (Germany)
| | - Sebastian Walesch
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig (Germany)
| | - Ronald Garcia
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig (Germany)
| | - Lena Keller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig (Germany)
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123, Saarbrücken, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig (Germany)
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17
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Das S, Chanda K. An overview of metal-free synthetic routes to isoxazoles: the privileged scaffold. RSC Adv 2021; 11:32680-32705. [PMID: 35493554 PMCID: PMC9042182 DOI: 10.1039/d1ra04624a] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/11/2021] [Indexed: 12/19/2022] Open
Abstract
In the field of drug discovery, isoxazole is a five-membered heterocyclic moiety commonly found in many commercially available drugs. In view of their enormous significance, it is always imperative to unleash new eco-friendly synthetic strategies. Among various novel synthetic techniques in use for isoxazole synthesis, most synthetic methods employ Cu(i) or Ru(ii) as catalysts for (3 + 2) cycloaddition reaction. The particular disadvantages associated with metal-catalyzed reactions are high costs, low abundance, toxicity, a significant generation of waste, and difficulty to separate from the reaction mixtures. In view of these drawbacks, it is always imperative to develop alternate metal-free synthetic routes. This review article highlights a comprehensive overview on the potential application of metal-free synthetic routes for the synthesis of isoxazoles with significant biological interests.
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Affiliation(s)
- Soumyadip Das
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore-632014 India
| | - Kaushik Chanda
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology Vellore-632014 India
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18
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Li Y, Zhuo L, Li X, Zhu Y, Wu S, Shen T, Hu W, Li YZ, Wu C. Myxadazoles, Myxobacterium-Derived Isoxazole-Benzimidazole Hybrids with Cardiovascular Activities. Angew Chem Int Ed Engl 2021; 60:21679-21684. [PMID: 34314077 DOI: 10.1002/anie.202106275] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/05/2021] [Indexed: 12/14/2022]
Abstract
There is a continuous need for novel microbial natural products to fill the drying-up drug development pipeline. Herein, we report myxadazoles from Myxococcus sp. SDU36, a family of novel chimeric small molecules that consist of N-ribityl 5,6-dimethylbenzimidazole and a linear fatty acid chain endowed with an isoxazole ring. The experiments of genome sequencing, gene insertion mutation, isotope labelling, and precursor feeding demonstrated that the fatty acid chain was encoded by a non-canonical PKS/NRPS gene cluster, whereas the origin of N-ribityl 5,6-dimethylbenzimidazole was related to the vitamin B12 metabolism. The convergence of these two distinct biosynthetic pathways through a C-N coupling led to the unique chemical framework of myxadazoles, which is an unprecedented hybridization mode in the paradigm of natural products. Myxadazoles exhibited potent vasculogenesis promotion effect and moderate antithrombotic activity, underscoring their potential usage for the treatment of cardiovascular diseases.
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Affiliation(s)
- Yuelan Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Xiaobin Li
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), No. 28789 Jingshi Dong Road, Jinan, 250103, P. R. China
| | - Yongqiang Zhu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), No. 28789 Jingshi Dong Road, Jinan, 250103, P. R. China
| | - Shuge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Tao Shen
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Shandong University, No. 44 West Wenhua Road, Jinan, 250012, P. R. China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72 Binhai Avenue, Qingdao, 266237, P. R. China
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19
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Li Y, Zhuo L, Li X, Zhu Y, Wu S, Shen T, Hu W, Li Y, Wu C. Myxadazoles, Myxobacterium‐Derived Isoxazole–Benzimidazole Hybrids with Cardiovascular Activities. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuelan Li
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Li Zhuo
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Xiaobin Li
- Biology Institute Qilu University of Technology (Shandong Academy of Sciences) No. 28789 Jingshi Dong Road Jinan 250103 P. R. China
| | - Yongqiang Zhu
- Biology Institute Qilu University of Technology (Shandong Academy of Sciences) No. 28789 Jingshi Dong Road Jinan 250103 P. R. China
| | - Shuge Wu
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Tao Shen
- Key Lab of Chemical Biology (MOE) School of Pharmaceutical Sciences Shandong University No. 44 West Wenhua Road Jinan 250012 P. R. China
| | - Wei Hu
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Yue‐Zhong Li
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
| | - Changsheng Wu
- State Key Laboratory of Microbial Technology Institute of Microbial Technology Shandong University No. 72 Binhai Avenue Qingdao 266237 P. R. China
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20
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Medema MH, de Rond T, Moore BS. Mining genomes to illuminate the specialized chemistry of life. Nat Rev Genet 2021; 22:553-571. [PMID: 34083778 PMCID: PMC8364890 DOI: 10.1038/s41576-021-00363-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.
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Affiliation(s)
- Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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21
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Obermaier S, Müller M. Das Gift des Fliegenpilzes. CHEM UNSERER ZEIT 2021. [DOI: 10.1002/ciuz.202000085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Enzymatic Synthesis of l- threo-β-Hydroxy-α-Amino Acids via Asymmetric Hydroxylation Using 2-Oxoglutarate-Dependent Hydroxylase from Sulfobacillus thermotolerans Y0017. Appl Environ Microbiol 2021; 87:e0133521. [PMID: 34347519 DOI: 10.1128/aem.01335-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
β-Hydroxy-α-amino acids are useful compounds for pharmaceutical development. Enzymatic synthesis of β-hydroxy-α-amino acids has attracted considerable interest as a selective, sustainable, and environmentally benign process. In this study, we identified a novel amino acid hydroxylase, AEP14369, from Sulfobacillus thermotolerans Y0017, which is included in a previously constructed CAS-like superfamily protein library, to widen the variety of amino acid hydroxylases. The detailed structures determined by nuclear magnetic resonance and X-ray crystallography analysis of the enzymatically produced compounds revealed that AEP14369 catalyzed threo-β-selective hydroxylation of l-His and l-Gln in a 2-oxoglutarate-dependent manner. Furthermore, the production of l-threo-β-hydroxy-His and l-threo-β-hydroxy-Gln was achieved using Escherichia coli expressing the gene encoding AEP14369 as a whole-cell biocatalyst. Under optimized reaction conditions, 137 mM (23.4 g L-1) l-threo-β-hydroxy-His and 150 mM l-threo-β-hydroxy-Gln (24.3 g L-1) were obtained, indicating that the enzyme is applicable for preparative-scale production. AEP14369, an l-His/l-Gln threo-β-hydroxylase, increases the availability of 2-oxoglutarate-dependent hydroxylase and opens the way for the practical production of β-hydroxy-α-amino acids in the future. The amino acids produced in this study would also contribute to the structural diversification of pharmaceuticals that affect important bioactivities. Importance Owing to an increasing concern for sustainability, enzymatic approaches for producing industrially useful compounds have attracted considerable attention as a powerful complement to chemical synthesis for environment-friendly synthesis. In this study, we developed a bioproduction method for β-hydroxy-α-amino acid synthesis using a newly discovered enzyme. AEP14369 from the moderate thermophilic bacterium Sulfobacillus thermotolerans Y0017 catalyzed the hydroxylation of l-His and l-Gln in a regioselective and stereoselective fashion. Furthermore, we biotechnologically synthesized both l-threo-β-hydroxy-His and l-threo-β-hydroxy-Gln with a titer of over 20 g L-1 through whole-cell bioconversion using recombinant Escherichia coli cells. As β-hydroxy-α-amino acids are important compounds for pharmaceutical development, this achievement would facilitate future sustainable and economical industrial applications.
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23
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Jamieson CS, Misa J, Tang Y, Billingsley JM. Biosynthesis and synthetic biology of psychoactive natural products. Chem Soc Rev 2021; 50:6950-7008. [PMID: 33908526 PMCID: PMC8217322 DOI: 10.1039/d1cs00065a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Psychoactive natural products play an integral role in the modern world. The tremendous structural complexity displayed by such molecules confers diverse biological activities of significant medicinal value and sociocultural impact. Accordingly, in the last two centuries, immense effort has been devoted towards establishing how plants, animals, and fungi synthesize complex natural products from simple metabolic precursors. The recent explosion of genomics data and molecular biology tools has enabled the identification of genes encoding proteins that catalyze individual biosynthetic steps. Once fully elucidated, the "biosynthetic pathways" are often comparable to organic syntheses in elegance and yield. Additionally, the discovery of biosynthetic enzymes provides powerful catalysts which may be repurposed for synthetic biology applications, or implemented with chemoenzymatic synthetic approaches. In this review, we discuss the progress that has been made toward biosynthetic pathway elucidation amongst four classes of psychoactive natural products: hallucinogens, stimulants, cannabinoids, and opioids. Compounds of diverse biosynthetic origin - terpene, amino acid, polyketide - are identified, and notable mechanisms of key scaffold transforming steps are highlighted. We also provide a description of subsequent applications of the biosynthetic machinery, with an emphasis placed on the synthetic biology and metabolic engineering strategies enabling heterologous production.
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Affiliation(s)
- Cooper S Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. and Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA. and Invizyne Technologies, Inc., Monrovia, CA, USA
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24
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Regiodivergent Biocatalytic Hydroxylation of L-Glutamine Facilitated by Characterization of Non-Heme Dioxygenases from Non-Ribosomal Peptide Biosyntheses. Tetrahedron 2021; 90. [PMID: 34366493 DOI: 10.1016/j.tet.2021.132190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We report the functional characterization of two iron- and α-ketoglutarate-dependent dioxygenases that are capable of hydroxylating free-standing glutamine at its C3 and C4 position respectively. In particular, the C4 hydroxylase, Q4Ox, catalyzes the reaction with approximately 4,300 total turnover numbers, facilitating synthesis of a solid-phase compatible building block and stereochemical elucidation at the C4 position of the hydroxylated product. This work will enable the development of novel synthetic strategies to prepare useful glutamine derivatives and stimulate further discoveries of new amino acid hydroxylases with distinct substrate specificities.
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25
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Gressler M, Löhr NA, Schäfer T, Lawrinowitz S, Seibold PS, Hoffmeister D. Mind the mushroom: natural product biosynthetic genes and enzymes of Basidiomycota. Nat Prod Rep 2021; 38:702-722. [PMID: 33404035 DOI: 10.1039/d0np00077a] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to September 2020 Mushroom-forming fungi of the division Basidiomycota have traditionally been recognised as prolific producers of structurally diverse and often bioactive secondary metabolites, using the methods of chemistry for research. Over the past decade, -omics technologies were applied on these fungi, and sophisticated heterologous gene expression platforms emerged, which have boosted research into the genetic and biochemical basis of the biosyntheses. This review provides an overview on experimentally confirmed natural product biosyntheses of basidiomycete polyketides, amino acid-derived products, terpenoids, and volatiles. We also present challenges and solutions particular to natural product research with these fungi. 222 references are cited.
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Affiliation(s)
- Markus Gressler
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Nikolai A Löhr
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Tim Schäfer
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Stefanie Lawrinowitz
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Paula Sophie Seibold
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
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Echinocandins: structural diversity, biosynthesis, and development of antimycotics. Appl Microbiol Biotechnol 2020; 105:55-66. [PMID: 33270153 PMCID: PMC7778625 DOI: 10.1007/s00253-020-11022-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 02/04/2023]
Abstract
Abstract Echinocandins are a clinically important class of non-ribosomal antifungal lipopeptides produced by filamentous fungi. Due to their complex structure, which is characterized by numerous hydroxylated non-proteinogenic amino acids, echinocandin antifungal agents are manufactured semisynthetically. The development of optimized echinocandin structures is therefore closely connected to their biosynthesis. Enormous efforts in industrial research and development including fermentation, classical mutagenesis, isotope labeling, and chemical synthesis eventually led to the development of the active ingredients caspofungin, micafungin, and anidulafungin, which are now used as first-line treatments against invasive mycosis. In the last years, echinocandin biosynthetic gene clusters have been identified, which allowed for the elucidation but also engineering of echinocandin biosynthesis on the molecular level. After a short description of the history of echinocandin research, this review provides an overview of the current knowledge of echinocandin biosynthesis with a special focus of the diverse structural elements, their biosynthetic background, and structure−activity relationships. Key points • Complex and highly oxidized lipopeptides produced by fungi. • Crucial in the design of drugs: side chain, solubility, and hydrolytic stability. • Genetic methods for engineering biosynthesis have recently become available. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-020-11022-y.
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Genomics-directed activation of cryptic natural product pathways deciphers codes for biosynthesis and molecular function. J Nat Med 2020; 75:261-274. [PMID: 33274411 PMCID: PMC7902601 DOI: 10.1007/s11418-020-01466-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/06/2020] [Indexed: 12/22/2022]
Abstract
Natural products, which can be isolated from living organisms worldwide, have played a pivotal role in drug discovery since ancient times. However, it has become more challenging to identify a structurally novel molecule with promising biological activity for pharmaceutical development, mainly due to the limited methodologies for their acquisition. In this review, we summarize our recent studies that activate the biosynthetic potential of filamentous fungi by genetic engineering to harness the metabolic flow for the efficient production of unprecedented natural products. The recent revolution in genome sequencing technology enables the accumulation of vast amounts of information on biosynthetic genes, the blueprint of the molecular construction. Utilizing the established heterologous expression system, activation of the pathway-specific transcription factor coupled with a knockout strategy, and manipulating the global regulatory gene, the biosynthetic genes were exploited to activate biosynthetic pathways and decipher the encoded enzyme functions. We show that this methodology was beneficial for acquiring fungal treasures for drug discovery. These studies also enabled the investigation of the molecular function of natural products in fungal development.
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