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Schröder MP, Pfeiffer IPM, Mordhorst S. Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry. Beilstein J Org Chem 2024; 20:1652-1670. [PMID: 39076295 PMCID: PMC11285071 DOI: 10.3762/bjoc.20.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
This review article aims to highlight the role of methyltransferases within the context of ribosomally synthesised and post-translationally modified peptide (RiPP) natural products. Methyltransferases play a pivotal role in the biosynthesis of diverse natural products with unique chemical structures and bioactivities. They are highly chemo-, regio-, and stereoselective allowing methylation at various positions. The different possible acceptor regions in ribosomally synthesised peptides are described in this article. Furthermore, we will discuss the potential application of these methyltransferases as powerful biocatalytic tools in the synthesis of modified peptides and other bioactive compounds. By providing an overview of the various methylation options available, this review is intended to emphasise the biocatalytic potential of RiPP methyltransferases and their impact on the field of natural product chemistry.
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Affiliation(s)
- Maria-Paula Schröder
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Isabel P-M Pfeiffer
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Silja Mordhorst
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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2
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Meena SN, Wajs-Bonikowska A, Girawale S, Imran M, Poduwal P, Kodam KM. High-Throughput Mining of Novel Compounds from Known Microbes: A Boost to Natural Product Screening. Molecules 2024; 29:3237. [PMID: 38999189 PMCID: PMC11243205 DOI: 10.3390/molecules29133237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/02/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
Advanced techniques can accelerate the pace of natural product discovery from microbes, which has been lagging behind the drug discovery era. Therefore, the present review article discusses the various interdisciplinary and cutting-edge techniques to present a concrete strategy that enables the high-throughput screening of novel natural compounds (NCs) from known microbes. Recent bioinformatics methods revealed that the microbial genome contains a huge untapped reservoir of silent biosynthetic gene clusters (BGC). This article describes several methods to identify the microbial strains with hidden mines of silent BGCs. Moreover, antiSMASH 5.0 is a free, accurate, and highly reliable bioinformatics tool discussed in detail to identify silent BGCs in the microbial genome. Further, the latest microbial culture technique, HiTES (high-throughput elicitor screening), has been detailed for the expression of silent BGCs using 500-1000 different growth conditions at a time. Following the expression of silent BGCs, the latest mass spectrometry methods are highlighted to identify the NCs. The recently emerged LAESI-IMS (laser ablation electrospray ionization-imaging mass spectrometry) technique, which enables the rapid identification of novel NCs directly from microtiter plates, is presented in detail. Finally, various trending 'dereplication' strategies are emphasized to increase the effectiveness of NC screening.
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Affiliation(s)
- Surya Nandan Meena
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
| | - Anna Wajs-Bonikowska
- Institute of Natural Products and Cosmetics, Faculty of Biotechnology and Food Sciences, Łódz University of Technology, Stefanowskiego Street 2/22, 90-537 Łódz, Poland
| | - Savita Girawale
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
| | - Md Imran
- Department of Botany, University of Delhi, Delhi 110007, India
| | - Preethi Poduwal
- Department of Biotechnology, Dhempe College of Arts and Science, Miramar, Goa 403001, India;
| | - Kisan M. Kodam
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India; (S.N.M.); (K.M.K.)
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Liang L, Wang X, Lan H, Wei S, Lei Y, Zhang S, Zhai H, Hu Y, Lv Y. Comprehensive analysis of aflatoxin B 1 biosynthesis in Aspergillus flavus via transcriptome-wide m 6A methylome response to cycloleucine. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132677. [PMID: 37797576 DOI: 10.1016/j.jhazmat.2023.132677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
Aspergillus flavus and its toxic aflatoxins secondary metabolites contaminate food and grains, posing a severe threat to human health and leading to liver cancer. Here, we demonstrated that cycloleucine blocked aflatoxin B1 synthesis by inhibiting N6-methyladenosine (m6A) methylation modification of messenger RNA (mRNA). m6A Methylation Immunoprecipitation Sequencing (m6A MeRIP-Seq)-based comprehensive transcriptome-wide m6A profiling identified 102 differentially expressed genes that underwent m6A modification, of which 22 hypermethylated genes were downregulated and 49 hypomethylated genes were upregulated, suggesting a negative correlation between m6A methylation and gene expression. Notably, cycloleucine inhibited aflatoxin B1 production via multiple targets. The m6A sites of several key genes involved in the aflatoxin B1 biosynthesis pathway were significantly enriched in the coding sequence and around the stop codon, resulting in their downregulation. Furthermore, m6A methylation on genes related to the aflatoxin B1 biosynthesis pathway led to reduced mRNA stability. Cycloleucine inhibition of aflatoxin B1 production highlights its potential as an agent for removing mycotoxins in environmental pollution. ENVIRONMENTAL IMPLICATION: Aflatoxins, highly carcinogenic secondary metabolites produced by Aspergillus flavus, frequently contaminate crops such as peanut, corn, wheat and sesame leading to irreversible loss in the quality and yield of agricultural products and posing serious threats to food safety. Aflatoxins has also been linked to developmental delays and liver cancer in humans. In our study, 'monitoring aflatoxin concentrations and its bioaccumulation in organisms' has been conducted. The results demonstrated that aflatoxin production in A. flavus was completely blocked after cycloleucine treatment. Additionally, we demonstrated that inhibition of aflatoxin was linked to N6-methyladenosine methylation of multiple genes in aflatoxin biosynthesis pathway.
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Affiliation(s)
- Liuke Liang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Xiaoyan Wang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Haier Lan
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shan Wei
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yang Lei
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shuaibing Zhang
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Huanchen Zhai
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yuansen Hu
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yangyong Lv
- College of biological engineering, Henan University of Technology, Zhengzhou 450001, China.
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4
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Zhang W, Forester NT, Chettri P, Heilijgers M, Mace WJ, Maes E, Morozova Y, Applegate ER, Johnson RD, Johnson LJ. Characterization of the Biosynthetic Gene Cluster for the Ribosomally Synthesized Cyclic Peptide Epichloëcyclins in Epichloë festucae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13965-13978. [PMID: 37704203 PMCID: PMC10540207 DOI: 10.1021/acs.jafc.3c03073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023]
Abstract
The various grass-induced epichloëcyclins of the Epichloë spp. are ribosomally synthesized and post-translationally modified peptides (RiPPs), produced as small, secreted cyclopeptides from a single gene, gigA. Here, four clustered and coregulated genes (gigA, gigB, gigC, and kexB) with predicted roles in epichloëcyclin production in Epichloë festucae were evaluated through gene disruption. Subsequent chemical analysis indicates that GigB is a DUF3328 domain-containing protein associated with cyclization of epichloëcyclins; GigC is a methyltransferase enzyme responsible for N-methylation of desmethylepichloëcyclins; and KexB is a subtilisin-like enzyme, partly responsible for the propeptide cleavage of epichloëcyclin intermediates. Symbiotic effects on the host phenotype were not observed for gigA, gigC, or kexB mutants, although ΔgigB infection correlated with increased host tiller height and biomass, while only ΔkexB exhibited an effect on endophyte morphology. Disrupting epichloëcyclin biosynthesis showed negligible influence on the biosynthesis of E. festucae-associated alkaloids. Epichloëcyclins may perform other secondary metabolism functions in Epichloë and other fungi.
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Affiliation(s)
- Wei Zhang
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Natasha T. Forester
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Pranav Chettri
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Maurice Heilijgers
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Wade J. Mace
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Evelyne Maes
- Lincoln
Research Centre, AgResearch Limited, Lincoln 7608, New Zealand
| | - Yulia Morozova
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Emma R. Applegate
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Richard D. Johnson
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
| | - Linda J. Johnson
- Grasslands
Research Centre, AgResearch Limited, Palmerston North 4442, New Zealand
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Jones MA, Butler ND, Anderson SR, Wirt SA, Govil I, Lyu X, Fang Y, Kunjapur AM. Discovery of L-threonine transaldolases for enhanced biosynthesis of beta-hydroxylated amino acids. Commun Biol 2023; 6:929. [PMID: 37696954 PMCID: PMC10495429 DOI: 10.1038/s42003-023-05293-0] [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: 03/24/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Beta-hydroxy non-standard amino acids (β-OH-nsAAs) have utility as small molecule drugs, precursors for beta-lactone antibiotics, and building blocks for polypeptides. While the L-threonine transaldolase (TTA), ObiH, is a promising enzyme for β-OH-nsAA biosynthesis, little is known about other natural TTA sequences. We ascertained the specificity of the TTA enzyme class more comprehensively by characterizing 12 candidate TTA gene products across a wide range (20-80%) of sequence identities. We found that addition of a solubility tag substantially enhanced the soluble protein expression level within this difficult-to-express enzyme family. Using an optimized coupled enzyme assay, we identified six TTAs, including one with less than 30% sequence identity to ObiH that exhibits broader substrate scope, two-fold higher L-Threonine (L-Thr) affinity, and five-fold faster initial reaction rates under conditions tested. We harnessed these TTAs for first-time bioproduction of β-OH-nsAAs with handles for bio-orthogonal conjugation from supplemented precursors during aerobic fermentation of engineered Escherichia coli, where we observed that higher affinity of the TTA for L-Thr increased titer. Overall, our work reveals an unexpectedly high level of sequence diversity and broad substrate specificity in an enzyme family whose members play key roles in the biosynthesis of therapeutic natural products that could benefit from chemical diversification.
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Affiliation(s)
- Michaela A Jones
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Neil D Butler
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Shelby R Anderson
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sean A Wirt
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Ishika Govil
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Xinyi Lyu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Yinzhi Fang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Aditya M Kunjapur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA.
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Kempken F. Marine fungi: A treasure trove of novel natural products and for biological discovery. PLoS Pathog 2023; 19:e1011624. [PMID: 37733683 PMCID: PMC10513230 DOI: 10.1371/journal.ppat.1011624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Affiliation(s)
- Frank Kempken
- Abteilung Botanische Genetik und Molekularbiologie, Botanisches Institut und Botanischer Garten, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Kiss A, Hariri Akbari F, Marchev A, Papp V, Mirmazloum I. The Cytotoxic Properties of Extreme Fungi's Bioactive Components-An Updated Metabolic and Omics Overview. Life (Basel) 2023; 13:1623. [PMID: 37629481 PMCID: PMC10455657 DOI: 10.3390/life13081623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/27/2023] Open
Abstract
Fungi are the most diverse living organisms on planet Earth, where their ubiquitous presence in various ecosystems offers vast potential for the research and discovery of new, naturally occurring medicinal products. Concerning human health, cancer remains one of the leading causes of mortality. While extensive research is being conducted on treatments and their efficacy in various stages of cancer, finding cytotoxic drugs that target tumor cells with no/less toxicity toward normal tissue is a significant challenge. In addition, traditional cancer treatments continue to suffer from chemical resistance. Fortunately, the cytotoxic properties of several natural products derived from various microorganisms, including fungi, are now well-established. The current review aims to extract and consolidate the findings of various scientific studies that identified fungi-derived bioactive metabolites with antitumor (anticancer) properties. The antitumor secondary metabolites identified from extremophilic and extremotolerant fungi are grouped according to their biological activity and type. It became evident that the significance of these compounds, with their medicinal properties and their potential application in cancer treatment, is tremendous. Furthermore, the utilization of omics tools, analysis, and genome mining technology to identify the novel metabolites for targeted treatments is discussed. Through this review, we tried to accentuate the invaluable importance of fungi grown in extreme environments and the necessity of innovative research in discovering naturally occurring bioactive compounds for the development of novel cancer treatments.
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Affiliation(s)
- Attila Kiss
- Agro-Food Science Techtransfer and Innovation Centre, Faculty for Agro, Food and Environmental Science, Debrecen University, 4032 Debrecen, Hungary;
| | - Farhad Hariri Akbari
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Andrey Marchev
- Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000 Plovdiv, Bulgaria
| | - Viktor Papp
- Department of Botany, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary;
| | - Iman Mirmazloum
- Department of Plant Physiology and Plant Ecology, Institute of Agronomy, Hungarian University of Agriculture and Life Sciences, 1118 Budapest, Hungary
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Maud L, Boyer F, Durrieu V, Bornot J, Lippi Y, Naylies C, Lorber S, Puel O, Mathieu F, Snini SP. Effect of Streptomyces roseolus Cell-Free Supernatants on the Fungal Development, Transcriptome, and Aflatoxin B1 Production of Aspergillus flavus. Toxins (Basel) 2023; 15:428. [PMID: 37505697 PMCID: PMC10467112 DOI: 10.3390/toxins15070428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023] Open
Abstract
Crop contamination by aflatoxin B1 (AFB1), an Aspergillus-flavus-produced toxin, is frequently observed in tropical and subtropical regions. This phenomenon is emerging in Europe, most likely as a result of climate change. Alternative methods, such as biocontrol agents (BCAs), are currently being developed to reduce the use of chemicals in the prevention of mycotoxin contamination. Actinobacteria are known to produce many bioactive compounds, and some of them can reduce in vitro AFB1 concentration. In this context, the present study aims to analyze the effect of a cell-free supernatant (CFS) from Streptomyces roseolus culture on the development of A. flavus, as well as on its transcriptome profile using microarray assay and its impact on AFB1 concentration. Results demonstrated that in vitro, the S. roseolus CFS reduced the dry weight and conidiation of A. flavus from 77% and 43%, respectively, and was therefore associated with a reduction in AFB1 concentration reduction to levels under the limit of quantification. The transcriptomic data analysis revealed that 5198 genes were differentially expressed in response to the CFS exposure and among them 5169 were downregulated including most of the genes involved in biosynthetic gene clusters. The aflatoxins' gene cluster was the most downregulated. Other gene clusters, such as the aspergillic acid, aspirochlorine, and ustiloxin B gene clusters, were also downregulated and associated with a variation in their concentration, confirmed by LC-HRMS.
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Affiliation(s)
- Louise Maud
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31326 Toulouse, France; (L.M.); (F.B.); (J.B.)
| | - Florian Boyer
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31326 Toulouse, France; (L.M.); (F.B.); (J.B.)
| | - Vanessa Durrieu
- Laboratoire de Chimie Agro-Industrielle (LCA), Université de Toulouse, INRAE, INPT, 4 Allée Emile Monso, 31030 Toulouse, France;
| | - Julie Bornot
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31326 Toulouse, France; (L.M.); (F.B.); (J.B.)
| | - Yannick Lippi
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, UPS, 31062 Toulouse, France; (Y.L.); (C.N.); (S.L.); (O.P.)
| | - Claire Naylies
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, UPS, 31062 Toulouse, France; (Y.L.); (C.N.); (S.L.); (O.P.)
| | - Sophie Lorber
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, UPS, 31062 Toulouse, France; (Y.L.); (C.N.); (S.L.); (O.P.)
| | - Olivier Puel
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, UPS, 31062 Toulouse, France; (Y.L.); (C.N.); (S.L.); (O.P.)
| | - Florence Mathieu
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31326 Toulouse, France; (L.M.); (F.B.); (J.B.)
| | - Selma P. Snini
- Laboratoire de Génie Chimique, Université de Toulouse, CNRS, INPT, UPS, 31326 Toulouse, France; (L.M.); (F.B.); (J.B.)
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Selegato DM, Castro-Gamboa I. Enhancing chemical and biological diversity by co-cultivation. Front Microbiol 2023; 14:1117559. [PMID: 36819067 PMCID: PMC9928954 DOI: 10.3389/fmicb.2023.1117559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Yamaguchi S, Fujioka T, Yoshimi A, Kumagai T, Umemura M, Abe K, Machida M, Kawai K. Discovery of a gene cluster for the biosynthesis of novel cyclic peptide compound, KK-1, in Curvularia clavata. FRONTIERS IN FUNGAL BIOLOGY 2023; 3:1081179. [PMID: 37746209 PMCID: PMC10512319 DOI: 10.3389/ffunb.2022.1081179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 09/26/2023]
Abstract
KK-1, a cyclic depsipeptide with 10 residues produced by a filamentous fungus Curvularia clavata BAUA-2787, is a promising pesticide active compound with high activity against many plant pathogens, especially Botrytis cinerea. As a first step toward the future mass production of KK-1 through synthetic biological approaches, we aimed to identify the genes responsible for the KK-1 biosynthesis. To achieve this, we conducted whole genome sequencing and transcriptome analysis of C. clavata BAUA-2787 to predict the KK-1 biosynthetic gene cluster. We then generated the overexpression and deletion mutants for each cluster gene using our originally developed transformation system for this fungus, and analyzed the KK-1 production and the cluster gene expression levels to confirm their involvement in KK-1 biosynthesis. As a result of these, a region of approximately 71 kb was found, containing 10 open reading frames, which were co-induced during KK-1 production, as a biosynthetic gene cluster. These include kk1B, which encodes nonribosomal peptide synthetase with a domain structure that is consistent with the structural features of KK-1, and kk1F, which encodes a transcription factor. The overexpression of kk1F increased the expression of the entire cluster genes and, consequently, improved KK-1 production, whereas its deletion decreased the expression of the entire cluster genes and almost eliminated KK-1 production, demonstrating that the protein encoded by kk1F regulates the expressions of the other nine cluster genes cooperatively as the pathway-specific transcription factor. Furthermore, the deletion of each cluster gene caused a reduction in KK-1 productivity, indicating that each gene is involved in KK-1 production. The genes kk1A, kk1D, kk1H, and kk1I, which showed a significant decrease in KK-1 productivity due to deletion, were presumed to be directly involved in KK-1 structure formation, including the biosynthesis of the constituent residues. kk1C, kk1E, kk1G, and kk1J, which maintained a certain level of KK-1 productivity despite deletion, were possibly involved in promoting or assisting KK-1 production, such as extracellular transportation and the removal of aberrant units incorporated into the peptide chain.
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Affiliation(s)
- Shigenari Yamaguchi
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
| | - Tomonori Fujioka
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
| | - Akira Yoshimi
- ABE-Project, New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
- Laboratory of Terrestrial Microbial Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Maiko Umemura
- Bio-system Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Keietsu Abe
- ABE-Project, New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
- Laboratory of Applied Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Masayuki Machida
- Bio-system Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Graduate School of Engineering, Genome Biotechnology Laboratory, Kanazawa Institute of Technology, Ishikawa, Japan
| | - Kiyoshi Kawai
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
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11
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Samal I, Bhoi TK, Majhi PK, Murmu S, Pradhan AK, Kumar D, Saini V, Paschapur AU, Raj MN, Ankur, Manik S, Behera PP, Mahanta DK, Komal J, Alam P, Balawi TA. Combatting insects mediated biotic stress through plant associated endophytic entomopathogenic fungi in horticultural crops. FRONTIERS IN PLANT SCIENCE 2023; 13:1098673. [PMID: 36743574 PMCID: PMC9894630 DOI: 10.3389/fpls.2022.1098673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/16/2022] [Indexed: 09/12/2023]
Abstract
Horticultural production is a vital catalyst for economic growth, yet insect infestations reduce horticultural crop yield and quality. Pesticides and other pest control methods are used during planting to eliminate pests that cause direct and indirect losses. In such situations, endophytic entomo-pathogenic fungi (EEPF) can act as a potential tools for biological control. They protect plants by boosting growth, nutrition, morpho-physiology and salt or iron tolerance. Antixenosis, antibiosis and plant tolerance change insect performance and preferences. EEPF- plant colonisation slows herbivore development, food consumption, oviposition and larval survival. EEPF changes plant physio-chemical properties like volatile emission profile and secondary metabolite production to regulate insect pest defences. EEPF produces chitinases, laccases, amylases, and cellulases for plant defence. Recent studies focused on EEPF species' significance, isolation, identification and field application. Realizing their full potential is difficult due to insufficient mass production, storage stability and formulation. Genetic-molecular and bioinformatics can help to build EEPF-based biological control systems. Metagenomics helps study microbial EEPF taxonomy and function. Multi-omics and system biology can decode EEPF interactions with host plants and microorganisms. NGS (Next Generation Sequencing), comparative genomics, proteomics, transcriptomics, metabolomics, metatranscriptomics and microarrays are used to evaluate plant-EEPF relationships. IPM requires understanding the abiotic and biotic elements that influence plant-EEPF interaction and the physiological mechanisms of EEPF colonisation. Due to restricted research, there are hundreds of unexplored EEPFs, providing an urgent need to uncover and analyse them.
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Affiliation(s)
- Ipsita Samal
- Department of Entomology, Sri Sri University, Cuttack, Odisha, India
| | - Tanmaya Kumar Bhoi
- Forest Protection Division, Indian Council of Forestry Research and Education (ICFRE) - Arid Forest Research Institute (AFRI), Jodhpur, Rajasthan, India
| | - Prasanta Kumar Majhi
- Department of Plant Breeding and Genetics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Sneha Murmu
- Division of Agricultural Bio-informatics, Indian Council of Agricultural Research (ICAR)- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Asit Kumar Pradhan
- Division, Social Science Division, Indian Council of Agricultural Research (ICAR)- National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Dilip Kumar
- Division of Computer Application and IT, National Institute for Agricultural Economics and Policy Research (NIAP), New Delhi, National Capital Territory of Delhi, India
| | - Varun Saini
- Department of Entomology, Navsari Agricultural University, Navsari, Gujarat, India
| | - Amit Umesh Paschapur
- Crop Protection Division, Indian Council of Agricultural Research (ICAR) - Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - M Nikhil Raj
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - Ankur
- Division of Entomology, Indian Council of Agricultural Research (ICAR-IARI)- Indian Agricultural Research Institute, New Delhi, India
| | - Suryakant Manik
- Department of Seed Science and Technology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Partha Pratim Behera
- Department of Plant Breeding and Genetics, Assam Agricultural University, Jorhat, Assam, India
| | - Deepak Kumar Mahanta
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, Bihar, India
| | - J. Komal
- Department of Entomology, Navsari Agricultural University, Navsari, Gujarat, India
| | - Pravej Alam
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
| | - Thamer Al Balawi
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al Kharj, Saudi Arabia
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12
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Increasing the production of the bioactive compounds in medicinal mushrooms: an omics perspective. Microb Cell Fact 2023; 22:11. [PMID: 36647087 PMCID: PMC9841694 DOI: 10.1186/s12934-022-02013-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Macroscopic fungi, mainly higher basidiomycetes and some ascomycetes, are considered medicinal mushrooms and have long been used in different areas due to their pharmaceutically/nutritionally valuable bioactive compounds. However, the low production of these bioactive metabolites considerably limits the utilization of medicinal mushrooms both in commerce and clinical trials. As a result, many attempts, ranging from conventional methods to novel approaches, have been made to improve their production. The novel strategies include conducting omics investigations, constructing genome-scale metabolic models, and metabolic engineering. So far, genomics and the combined use of different omics studies are the most utilized omics analyses in medicinal mushroom research (both with 31% contribution), while metabolomics (with 4% contribution) is the least. This article is the first attempt for reviewing omics investigations in medicinal mushrooms with the ultimate aim of bioactive compound overproduction. In this regard, the role of these studies and systems biology in elucidating biosynthetic pathways of bioactive compounds and their contribution to metabolic engineering will be highlighted. Also, limitations of omics investigations and strategies for overcoming them will be provided in order to facilitate the overproduction of valuable bioactive metabolites in these valuable organisms.
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13
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Ozaki T, Minami A, Oikawa H. Recent advances in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides of fungal origin. J Antibiot (Tokyo) 2023; 76:3-13. [PMID: 36424516 DOI: 10.1038/s41429-022-00576-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/25/2022]
Abstract
Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are growing class of natural products with potent biological activities. Although the core scaffolds of RiPPs are composed of proteinogenic amino acids, remarkable structural diversity is generated through posttranslational modifications (PTMs) of precursor peptides. In addition, ribosomal origin of biosynthetic precursors enables supply of its analogs through genetic approach such as site-directed mutagenesis on corresponding genes. As PTM enzymes often exhibit substrate tolerance, RiPP biosynthetic machineries are considered as efficient tools for generation of unique peptide derivatives. RiPP pathways are distributed among all domains of life and those derived from bacteria and plants have been known for decades. In contrast, fungal RiPPs (F-RiPPs) have fewer examples. Amatoxins and omphalotins are F-RiPPs produced by Basidiomycota fungi. In the biosynthesis of these compounds, macrocyclization by prolyl oligopeptidase homologs and N-methylations of back bone amides have been characterized, respectively. Ustiloxins and related compounds are another group of F-RiPPs with characteristic macrocyclic ethers. UstYa family proteins, which are fungi-specific putative oxidases, have been identified as common proteins involved in PTMs of these compounds. Despite a limited number of characterized examples, recent progress in sequencing of fungal genomes indicated that a number of RiPP pathways are hidden in fungal resources, making F-RiPPs as attractive target for genome mining studies while more detailed understandings of key biosynthetic enzymes are still necessary. This review seeks to describe recent advances on the F-RiPP biosynthesis with slight emphasis on the function of UstYa family proteins.
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Affiliation(s)
- Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, Guangdong, China.
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14
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Umemura M, Tamano K. How to improve the production of peptidyl compounds in filamentous fungi. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:1085624. [PMID: 37746201 PMCID: PMC10512285 DOI: 10.3389/ffunb.2022.1085624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/02/2022] [Indexed: 09/26/2023]
Abstract
Peptidyl compounds produced by filamentous fungi, which are nonribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs), are rich sources of bioactive compounds with a wide variety of structures. Some of these peptidyl compounds are useful as pharmaceuticals and pesticides. However, for industrial use, their low production often becomes an obstacle, and various approaches have been challenged to overcome this weakness. In this article, we summarize the successful attempts to increase the production of NRPs and RiPPs in filamentous fungi and present our perspectives on how to improve it further.
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Affiliation(s)
- Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Koichi Tamano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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15
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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16
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Mózsik L, Iacovelli R, Bovenberg RAL, Driessen AJM. Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi. Front Bioeng Biotechnol 2022; 10:901037. [PMID: 35910033 PMCID: PMC9335490 DOI: 10.3389/fbioe.2022.901037] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungi are highly productive cell factories, many of which are industrial producers of enzymes, organic acids, and secondary metabolites. The increasing number of sequenced fungal genomes revealed a vast and unexplored biosynthetic potential in the form of transcriptionally silent secondary metabolite biosynthetic gene clusters (BGCs). Various strategies have been carried out to explore and mine this untapped source of bioactive molecules, and with the advent of synthetic biology, novel applications, and tools have been developed for filamentous fungi. Here we summarize approaches aiming for the expression of endogenous or exogenous natural product BGCs, including synthetic transcription factors, assembly of artificial transcription units, gene cluster refactoring, fungal shuttle vectors, and platform strains.
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Affiliation(s)
- László Mózsik
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, Delft, Netherlands
- Department of Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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17
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Ford RE, Foster GD, Bailey AM. Exploring fungal RiPPs from the perspective of chemical ecology. Fungal Biol Biotechnol 2022; 9:12. [PMID: 35752794 PMCID: PMC9233826 DOI: 10.1186/s40694-022-00144-9] [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: 03/31/2022] [Accepted: 06/05/2022] [Indexed: 12/31/2022] Open
Abstract
Since the initial detection, in 2007, of fungal ribosomally synthesised and post-translationally modified peptides (RiPPs), this group of natural products has undergone rapid expansion, with four separate classes now recognised: amatoxins/phallotoxins, borosins, dikaritins, and epichloëcyclins. Largely due to their historically anthropocentric employment in medicine and agriculture, novel fungal proteins and peptides are seldom investigated in relation to the fungus itself. Therefore, although the benefits these compounds confer to humans are often realised, their evolutionary advantage to the fungus, the reason for their continued production, is often obscure or ignored. This review sets out to summarise current knowledge on how these small peptide-derived products influence their producing species and surrounding biotic environment.
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Affiliation(s)
- R E Ford
- School of Biological Sciences, University of Bristol, Life Sciences Building, 28 Tyndall Ave, Bristol, BS8 1TQ, UK
| | - G D Foster
- School of Biological Sciences, University of Bristol, Life Sciences Building, 28 Tyndall Ave, Bristol, BS8 1TQ, UK
| | - A M Bailey
- School of Biological Sciences, University of Bristol, Life Sciences Building, 28 Tyndall Ave, Bristol, BS8 1TQ, UK.
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18
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Kaari M, Manikkam R, Baskaran A. Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:448-467. [PMID: 35394575 DOI: 10.1007/s10126-022-10118-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Marine microbes genetically evolved to survive varying salinity, temperature, pH, and other stress factors by producing different bioactive metabolites. These microbial secondary metabolites (SMs) are novel, have high potential, and could be used as lead molecule. Genome sequencing of microbes revealed that they have the capability to produce numerous novel bioactive metabolites than observed under standard in vitro culture conditions. Microbial genome has specific regions responsible for SM assembly, termed biosynthetic gene clusters (BGCs), possessing all the necessary genes to encode different enzymes required to generate SM. In order to augment the microbial chemo diversity and to activate these gene clusters, various tools and techniques are developed. Metagenomics with functional gene expression studies aids in classifying novel peptides and enzymes and also in understanding the biosynthetic pathways. Genome shuffling is a high-throughput screening approach to improve the development of SMs by incorporating genomic recombination. Transcriptionally silent or lower level BGCs can be triggered by artificially knocking promoter of target BGC. Additionally, bioinformatic tools like antiSMASH, ClustScan, NAPDOS, and ClusterFinder are effective in identifying BGCs of existing class for annotation in genomes. This review summarizes the significance of BGCs and the different approaches for detecting and elucidating BGCs from marine microbes.
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Affiliation(s)
- Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India.
| | - Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, 600 119, Tamil Nadu, India
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19
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Pellekooren S, Donker M, Reijnders E, Boutalab L, Ostelo R, van Tulder M, Pool-Goudzwaard A. The introduction of advanced practice physiotherapy within Dutch primary care is a quest for possibilities, added value, and mutual trust: a qualitative study amongst advanced practice physiotherapists and general practitioners. BMC Health Serv Res 2022; 22:529. [PMID: 35449100 PMCID: PMC9026935 DOI: 10.1186/s12913-022-07906-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Despite the increased deployment and added value of Advanced Practitioner Physiotherapy (APP) in musculoskeletal care internationally, APP is not yet widely accepted within Dutch primary care. This may be due to specific constraints in the implementation of APP within the Dutch healthcare system. This study aimed to explore the experiences and perceptions of Advanced Practitioner Physiotherapists (APPs) and General Practitioners (GPs) with respect to implementing APP within Dutch primary care. Methods This explorative and interpretive qualitative study included 12 APPs and 3 GPs who were in various stages of implementing an APP care model. Semi-structured interviews were conducted between January and March 2021. The topic list was based on existing literature, the personal input of researchers, and the Constellation Approach framework. Data were analysed using a thematic inductive approach. Results Four main themes emerged from the data; 1) Both GPs’ trust in APP and a clear added value of APP are critical for starting implementation, 2) APPs need continuous support from GPs, 3) APPs believe that their position needs strengthening, and 4) Implementation of the APP model creates tension over ownership. These four themes highlight the perceived difficulties in gaining trust, lack of clarity over the added value of APP, ambiguity over APPs’ professional profile and positioning, a need on behalf of GPs to maintain authority, lack of reimbursement structure, and the struggle APPs face to strike a balance with current care. Conclusion This study demonstrates that implementing an APP model of care is challenging, in part, because the deployment of APP does not sufficiently align with the core values of GPs, while GPs appear reluctant to hand over control of elements of patient care to APPs. APPs do not appear to have ownership over the implementation, given their strong dependence on the practice, values and needs of GPs. Trial registration Ethical approval was obtained from the Medical Ethics Committee of VU University Medical Centre in Amsterdam; reference number 2020.17 . All participants were asked to provide written informed consent prior to participating in the study. Supplementary Information The online version contains supplementary material available at 10.1186/s12913-022-07906-6.
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Affiliation(s)
- Sylvia Pellekooren
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences Research Institute, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands. .,Department of Human Movement Sciences, Faculty of Behavioral & Movement Sciences, Vrije Universiteit, Amsterdam Movement Sciences Research Institute, Amsterdam, The Netherlands.
| | - Marianne Donker
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences Research Institute, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Eddy Reijnders
- Huisartsopleiding VUmc, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
| | - Lamyae Boutalab
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences Research Institute, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands
| | - Raymond Ostelo
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences Research Institute, De Boelelaan 1105, 1081 HV, Amsterdam, The Netherlands.,Department of Epidemiology and Data Science, Amsterdam Movement Sciences Research Institute, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
| | - Maurits van Tulder
- Department of Human Movement Sciences, Faculty of Behavioral & Movement Sciences, Vrije Universiteit, Amsterdam Movement Sciences Research Institute, Amsterdam, The Netherlands
| | - Annelies Pool-Goudzwaard
- Department of Human Movement Sciences, Faculty of Behavioral & Movement Sciences, Vrije Universiteit, Amsterdam Movement Sciences Research Institute, Amsterdam, The Netherlands.,SOMT University of Physiotherapy, Amersfoort, The Netherlands
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20
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Rajput A, Tsunemoto H, Sastry AV, Szubin R, Rychel K, Sugie J, Pogliano J, Palsson BO. Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators. Nucleic Acids Res 2022; 50:3658-3672. [PMID: 35357493 PMCID: PMC9023270 DOI: 10.1093/nar/gkac187] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/28/2022] [Accepted: 03/29/2022] [Indexed: 12/16/2022] Open
Abstract
The transcriptional regulatory network (TRN) of Pseudomonas aeruginosa coordinates cellular processes in response to stimuli. We used 364 transcriptomes (281 publicly available + 83 in-house generated) to reconstruct the TRN of P. aeruginosa using independent component analysis. We identified 104 independently modulated sets of genes (iModulons) among which 81 reflect the effects of known transcriptional regulators. We identified iModulons that (i) play an important role in defining the genomic boundaries of biosynthetic gene clusters (BGCs), (ii) show increased expression of the BGCs and associated secretion systems in nutrient conditions that are important in cystic fibrosis, (iii) show the presence of a novel ribosomally synthesized and post-translationally modified peptide (RiPP) BGC which might have a role in P. aeruginosa virulence, (iv) exhibit interplay of amino acid metabolism regulation and central metabolism across different carbon sources and (v) clustered according to their activity changes to define iron and sulfur stimulons. Finally, we compared the identified iModulons of P. aeruginosa with those previously described in Escherichia coli to observe conserved regulons across two Gram-negative species. This comprehensive TRN framework encompasses the majority of the transcriptional regulatory machinery in P. aeruginosa, and thus should prove foundational for future research into its physiological functions.
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Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Joseph Sugie
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
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21
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Tandem repeats in precursor protein stabilize transcript levels and production levels of the fungal ribosomally synthesized and post-translationally modified peptide ustiloxin B. Fungal Genet Biol 2022; 160:103691. [DOI: 10.1016/j.fgb.2022.103691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 11/22/2022]
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22
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Kessler SC, Chooi YH. Out for a RiPP: challenges and advances in genome mining of ribosomal peptides from fungi. Nat Prod Rep 2022; 39:222-230. [PMID: 34581394 DOI: 10.1039/d1np00048a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Covering up to June 2021Ribosomally synthesized and post-translationally modified peptides (RiPPs) from fungi are an underexplored class of natural products, despite their propensity for diverse bioactivities and unique structural features. Surveys of fungal genomes for biosynthetic gene clusters encoding RiPPs have been limited in their scope due to our incomplete understanding of fungal RiPP biosynthesis. Through recent discoveries, along with earlier research, a clearer picture has been emerging of the biosynthetic principles that underpin fungal RiPP pathways. In this Highlight, we trace the approaches that have been used for discovering currently known fungal RiPPs and show that all of them can be assigned to one of three distinct families based on hallmarks of their biosynthesis, which are in turn imprinted on their corresponding gene clusters. We hope that our systematic exposition of fungal RiPP structural and gene cluster features will facilitate more comprehensive approaches to genome mining efforts in the future.
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Affiliation(s)
- Simon C Kessler
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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23
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Navarro-Muñoz JC, Collemare J. A Bioinformatics Workflow for Investigating Fungal Biosynthetic Gene Clusters. Methods Mol Biol 2022; 2489:1-21. [PMID: 35524042 DOI: 10.1007/978-1-0716-2273-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Predicting secondary metabolite biosynthetic gene clusters is a routine analysis performed for each newly sequenced fungal genome. Yet, the usefulness of such predictions remains restricted as they provide total numbers of biosynthetic pathways with only very limited biological significance. In this chapter, we describe a workflow to predict and analyze biosynthetic gene clusters in fungal genomes. It relies on similarity networking and phylogeny to perform genetic dereplication and to prioritize candidate gene clusters that potentially produce new compounds. This basic workflow includes the generation of high-quality figures for publication.
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24
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Costes LH, Lippi Y, Naylies C, Jamin EL, Genthon C, Bailly S, Oswald IP, Bailly JD, Puel O. The Solvent Dimethyl Sulfoxide Affects Physiology, Transcriptome and Secondary Metabolism of Aspergillus flavus. J Fungi (Basel) 2021; 7:jof7121055. [PMID: 34947037 PMCID: PMC8703953 DOI: 10.3390/jof7121055] [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: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dimethyl sulfoxide (DSMO) is a simple molecule widely used because of its great solvating ability, but this solvent also has little-known biological effects, especially on fungi. Aspergillus flavus is a notorious pathogenic fungus which may contaminate a large variety of crops worldwide by producing aflatoxins, endangering at the same time food safety and international trade. The aim of this study was to characterize the effect of DMSO on A. flavus including developmental parameters such as germination and sporulation, as well as its transcriptome profile using high-throughput RNA-sequencing assay and its impact on secondary metabolism (SM). After DMSO exposure, A. flavus displayed depigmented conidia in a dose-dependent manner. The four-day exposition of cultures to two doses of DMSO, chosen on the basis of depigmentation intensity (35 mM “low” and 282 mM “high”), led to no significant impact on fungal growth, germination or sporulation. However, transcriptomic data analysis showed that 4891 genes were differentially regulated in response to DMSO (46% of studied transcripts). A total of 4650 genes were specifically regulated in response to the highest dose of DMSO, while only 19 genes were modulated upon exposure to the lowest dose. Secondary metabolites clusters genes were widely affected by the DMSO, with 91% of clusters impacted at the highest dose. Among these, aflatoxins, cyclopiazonic acid and ustiloxin B clusters were totally under-expressed. The genes belonging to the AFB1 cluster were the most negatively modulated ones, the two doses leading to 63% and 100% inhibition of the AFB1 production, respectively. The SM analysis also showed the disappearance of ustiloxin B and a 10-fold reduction of cyclopiazonic acid level when A. flavus was treated by the higher DMSO dose. In conclusion, the present study showed that DMSO impacted widely A. flavus’ transcriptome, including secondary metabolism gene clusters with the aflatoxins at the head of down-regulated ones. The solvent also inhibits conidial pigmentation, which could illustrate common regulatory mechanisms between aflatoxins and fungal pigment pathways. Because of its effect on major metabolites synthesis, DMSO should not be used as solvent especially in studies testing anti-aflatoxinogenic compounds.
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Affiliation(s)
- Laura H. Costes
- TOXALIM (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, Toulouse 31027, France; (L.H.C.); (Y.L.); (C.N.); (E.L.J.); (S.B.); (I.P.O.); (O.P.)
| | - Yannick Lippi
- TOXALIM (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, Toulouse 31027, France; (L.H.C.); (Y.L.); (C.N.); (E.L.J.); (S.B.); (I.P.O.); (O.P.)
| | - Claire Naylies
- TOXALIM (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, Toulouse 31027, France; (L.H.C.); (Y.L.); (C.N.); (E.L.J.); (S.B.); (I.P.O.); (O.P.)
| | - Emilien L. Jamin
- TOXALIM (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, Toulouse 31027, France; (L.H.C.); (Y.L.); (C.N.); (E.L.J.); (S.B.); (I.P.O.); (O.P.)
- Metatoul-AXIOM Platform, MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, Toulouse 31000, France
| | - Clémence Genthon
- INRAE, US1426, GeT-PlaGe, Genotoul, 31326 Castanet-Tolosan, France;
| | - Sylviane Bailly
- TOXALIM (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, Toulouse 31027, France; (L.H.C.); (Y.L.); (C.N.); (E.L.J.); (S.B.); (I.P.O.); (O.P.)
| | - Isabelle P. Oswald
- TOXALIM (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, Toulouse 31027, France; (L.H.C.); (Y.L.); (C.N.); (E.L.J.); (S.B.); (I.P.O.); (O.P.)
| | - Jean-Denis Bailly
- TOXALIM (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, Toulouse 31027, France; (L.H.C.); (Y.L.); (C.N.); (E.L.J.); (S.B.); (I.P.O.); (O.P.)
- Correspondence:
| | - Olivier Puel
- TOXALIM (Research Center in Food Toxicology), Université de Toulouse, INRAE, ENVT, EI-Purpan, Toulouse 31027, France; (L.H.C.); (Y.L.); (C.N.); (E.L.J.); (S.B.); (I.P.O.); (O.P.)
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Sogahata K, Ozaki T, Igarashi Y, Naganuma Y, Liu C, Minami A, Oikawa H. Biosynthetic Studies of Phomopsins Unveil Posttranslational Installation of Dehydroamino Acids by UstYa Family Proteins. Angew Chem Int Ed Engl 2021; 60:25729-25734. [PMID: 34608734 DOI: 10.1002/anie.202111076] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 12/29/2022]
Abstract
UstYa family proteins (DUF3328) are widely and specifically distributed in fungi. They are known to be involved in the biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs) and nonribosomal peptides, and possibly catalyze various reactions, including oxidative cyclization and chlorination. In this study, we focused on phomopsin A, a fungal RiPP consisting of unique nonproteinogenic amino acids. Gene knockout experiments demonstrated that three UstYa homologues, phomYc, phomYd, and phomYe, are essential for the desaturation of amino acid moieties, showing unprecedented function among UstYa family proteins. Sequence similarity network analysis indicated that their amino acid sequences are highly diverged and that most remain uncharacterized, paving the way for genome mining of fungal metabolites with unique modifications.
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Affiliation(s)
- Kaho Sogahata
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuya Igarashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yuka Naganuma
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Chengwei Liu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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26
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Sogahata K, Ozaki T, Igarashi Y, Naganuma Y, Liu C, Minami A, Oikawa H. Biosynthetic Studies of Phomopsins Unveil Posttranslational Installation of Dehydroamino Acids by UstYa Family Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kaho Sogahata
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Taro Ozaki
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Yuya Igarashi
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Yuka Naganuma
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Chengwei Liu
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Atsushi Minami
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
| | - Hideaki Oikawa
- Department of Chemistry Faculty of Science Hokkaido University Sapporo 060-0810 Japan
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27
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Caesar LK, Montaser R, Keller NP, Kelleher NL. Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities. Nat Prod Rep 2021; 38:2041-2065. [PMID: 34787623 PMCID: PMC8691422 DOI: 10.1039/d1np00036e] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: 2010 to 2021Organisms in nature have evolved into proficient synthetic chemists, utilizing specialized enzymatic machinery to biosynthesize an inspiring diversity of secondary metabolites. Often serving to boost competitive advantage for their producers, these secondary metabolites have widespread human impacts as antibiotics, anti-inflammatories, and antifungal drugs. The natural products discovery field has begun a shift away from traditional activity-guided approaches and is beginning to take advantage of increasingly available metabolomics and genomics datasets to explore undiscovered chemical space. Major strides have been made and now enable -omics-informed prioritization of chemical structures for discovery, including the prospect of confidently linking metabolites to their biosynthetic pathways. Over the last decade, more integrated strategies now provide researchers with pipelines for simultaneous identification of expressed secondary metabolites and their biosynthetic machinery. However, continuous collaboration by the natural products community will be required to optimize strategies for effective evaluation of natural product biosynthetic gene clusters to accelerate discovery efforts. Here, we provide an evaluative guide to scientific literature as it relates to studying natural product biosynthesis using genomics, metabolomics, and their integrated datasets. Particular emphasis is placed on the unique insights that can be gained from large-scale integrated strategies, and we provide source organism-specific considerations to evaluate the gaps in our current knowledge.
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Affiliation(s)
- Lindsay K Caesar
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Rana Montaser
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology and Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Neil L Kelleher
- Department of Chemistry, Northwestern University, Evanston, IL, USA.
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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28
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Takahashi H, Umemura M, Ninomiya A, Kusuya Y, Shimizu M, Urayama SI, Watanabe A, Kamei K, Yaguchi T, Hagiwara D. Interspecies Genomic Variation and Transcriptional Activeness of Secondary Metabolism-Related Genes in Aspergillus Section Fumigati. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:656751. [PMID: 37744138 PMCID: PMC10512231 DOI: 10.3389/ffunb.2021.656751] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/23/2021] [Indexed: 09/26/2023]
Abstract
Filamentous fungi produce various bioactive compounds that are biosynthesized by sets of proteins encoded in biosynthesis gene clusters (BGCs). For an unknown reason, many BGCs are transcriptionally silent in laboratory conditions, which has hampered the discovery of novel fungal compounds. The transcriptional reactiveness of fungal secondary metabolism is not fully understood. To gain the comprehensive view, we conducted comparative genomic and transcriptomic analyses of nine closely-related species of Aspergillus section Fumigati (A. fumigatus, A. fumigatiaffinis, A. novofumigatus, A. thermomutatus, A. viridinutans, A. pseudoviridinutans, A. lentulus, A. udagawae, and Neosartorya fischeri). For expanding our knowledge, we newly sequenced genomes of A. viridinutans and A. pseudoviridinutans, and reassembled and reannotated the previously released genomes of A. lentulus and A. udagawae. Between 34 and 84 secondary metabolite (SM) backbone genes were identified in the genomes of these nine respective species, with 8.7-51.2% being unique to the species. A total of 247 SM backbone gene types were identified in the nine fungi. Ten BGCs are shared by all nine species. Transcriptomic analysis using A. fumigatus, A. lentulus, A. udagawae, A. viridinutans, and N. fischeri was conducted to compare expression levels of all SM backbone genes in four different culture conditions; 32-83% of SM backbone genes in these species were not expressed in the tested conditions, which reconfirmed that large part of fungal SM genes are hard to be expressed. The species-unique SM genes of the five species were expressed with lower frequency (18.8% in total) than the SM genes that are conserved in all five species (56%). These results suggest that the expression tendency of BGCs is correlated with their interspecies distribution pattern. Our findings increase understanding of the evolutionary processes associated with the regulation of fungal secondary metabolism.
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Affiliation(s)
- Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
- Molecular Chirality Research Center, Chiba University, Chiba, Japan
- Plant Molecular Science Center, Chiba University, Chiba, Japan
| | - Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Akihiro Ninomiya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoko Kusuya
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Masaaki Shimizu
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
| | - Syun-ichi Urayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
| | - Akira Watanabe
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Daisuke Hagiwara
- Medical Mycology Research Center, Chiba University, Chiba, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Microbiology Research Center for Sustainability, University of Tsukuba, Tsukuba, Japan
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29
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Jiang Y, Ozaki T, Liu C, Igarashi Y, Ye Y, Tang S, Ye T, Maruyama JI, Minami A, Oikawa H. Biosynthesis of Cyclochlorotine: Identification of the Genes Involved in Oxidative Transformations and Intramolecular O, N-Transacylation. Org Lett 2021; 23:2616-2620. [PMID: 33736433 DOI: 10.1021/acs.orglett.1c00525] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mycotoxin cyclochlorotine (1) and structurally related astins are cyclic pentapeptides containing unique nonproteinogenic amino acids, such as β-phenylalanine, l-allo-threonine, and 3,4-dichloroproline. Herein, we report the biosynthetic pathway for 1, which involves intriguing tailoring processes mediated by DUF3328 proteins, including stereo- and regiospecific chlorination and hydroxylation and intramolecular O,N-transacylation. Our findings demonstrate that DUF3328 proteins, which are known to be involved in oxidative cyclization of fungal ribosomal peptides, have much higher functional diversity than previously expected.
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Affiliation(s)
- Yulu Jiang
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Chengwei Liu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuya Igarashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ying Ye
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shoubin Tang
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen 518055, China
| | - Tao Ye
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Xili, Nanshan District, Shenzhen 518055, China
| | - Jun-Ichi Maruyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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30
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Asemoloye MD, Marchisio MA, Gupta VK, Pecoraro L. Genome-based engineering of ligninolytic enzymes in fungi. Microb Cell Fact 2021; 20:20. [PMID: 33478513 PMCID: PMC7819241 DOI: 10.1186/s12934-021-01510-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/07/2021] [Indexed: 12/23/2022] Open
Abstract
Background Many fungi grow as saprobic organisms and obtain nutrients from a wide range of dead organic materials. Among saprobes, fungal species that grow on wood or in polluted environments have evolved prolific mechanisms for the production of degrading compounds, such as ligninolytic enzymes. These enzymes include arrays of intense redox-potential oxidoreductase, such as laccase, catalase, and peroxidases. The ability to produce ligninolytic enzymes makes a variety of fungal species suitable for application in many industries, including the production of biofuels and antibiotics, bioremediation, and biomedical application as biosensors. However, fungal ligninolytic enzymes are produced naturally in small quantities that may not meet the industrial or market demands. Over the last decade, combined synthetic biology and computational designs have yielded significant results in enhancing the synthesis of natural compounds in fungi. Main body of the abstract In this review, we gave insights into different protein engineering methods, including rational, semi-rational, and directed evolution approaches that have been employed to enhance the production of some important ligninolytic enzymes in fungi. We described the role of metabolic pathway engineering to optimize the synthesis of chemical compounds of interest in various fields. We highlighted synthetic biology novel techniques for biosynthetic gene cluster (BGC) activation in fungo and heterologous reconstruction of BGC in microbial cells. We also discussed in detail some recombinant ligninolytic enzymes that have been successfully enhanced and expressed in different heterologous hosts. Finally, we described recent advance in CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas (CRISPR associated) protein systems as the most promising biotechnology for large-scale production of ligninolytic enzymes. Short conclusion Aggregation, expression, and regulation of ligninolytic enzymes in fungi require very complex procedures with many interfering factors. Synthetic and computational biology strategies, as explained in this review, are powerful tools that can be combined to solve these puzzles. These integrated strategies can lead to the production of enzymes with special abilities, such as wide substrate specifications, thermo-stability, tolerance to long time storage, and stability in different substrate conditions, such as pH and nutrients.
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Affiliation(s)
- Michael Dare Asemoloye
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China.
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Lorenzo Pecoraro
- School of Pharmaceutical Science and Technology, Tianjin University, Nankai District, 92 Weijin Road, Tianjin, 300072, China.
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31
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 408] [Impact Index Per Article: 136.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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32
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Kloosterman AM, Medema MH, van Wezel GP. Omics-based strategies to discover novel classes of RiPP natural products. Curr Opin Biotechnol 2020; 69:60-67. [PMID: 33383297 DOI: 10.1016/j.copbio.2020.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/25/2020] [Accepted: 12/02/2020] [Indexed: 01/15/2023]
Abstract
Ribosomally synthesized and post-translationally modified peptides (RiPPs) form a highly diverse class of natural products, with various biotechnologically and clinically relevant activities. A recent increase in discoveries of novel RiPP classes suggests that currently known RiPPs constitute just the tip of the iceberg. Genome mining has been a driving force behind these discoveries, but remains challenging due to a lack of universal genetic markers for RiPP detection. In this review, we discuss how various genome mining methodologies contribute towards the discovery of novel RiPP classes. Some methods prioritize novel biosynthetic gene clusters (BGCs) based on shared modifications between RiPP classes. Other methods identify RiPP precursors using machine-learning classifiers. The integration of such methods as well as integration with other types of omics data in more comprehensive pipelines could help these tools reach their potential, and keep pushing the boundaries of the chemical diversity of this important class of molecules.
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Affiliation(s)
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands.
| | - Gilles P van Wezel
- Institute of Biology, Leiden University, Sylviusweg 72, 2333BE Leiden, The Netherlands.
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33
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Gao Y, Du X, Li H, Wang Y. Genome sequence of Aspergillus flavus A7, a marine-derived fungus with antibacterial activity. Genome 2020; 64:719-733. [PMID: 33356862 DOI: 10.1139/gen-2020-0066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Due to the specific properties of the marine environment, marine microorganisms have exclusive physicochemical characteristics that are different from those of terrestrial microorganisms, which can produce various secondary metabolites (SMs) with considerable structural diversity and biological activity. In this study, three strains of coepiphytic Aspergillus with potential antibacterial activities, A7 (Aspergillus flavus), B27 (Aspergillus flavipes), and R12 (Aspergillus sydowii), were isolated from the South China Sea. Via the Illumina MiSeq sequencing platform, the genomes of the three strains were sequenced, and genome comparison showed the highest diversity of the biosynthetic gene clusters (BGCs) in A7. In addition, a comparison of physiological and genomic characteristics between A7 and other A. flavus strains demonstrated the superior environmental adaptability of A7, which is apparently consistent with the genetic richness of BGCs. By assigning reads to known BGCs, putative BGCs were allocated in A7 that corresponded to various SMs, including naphthopyrone, pyranonigrin E, and cyclopiazonic acids. Based on gene homology analysis, we surmise that a region is involved in the biosynthesis of ustiloxin-like RiPPs, a less thoroughly studied SM in fungi. Our results provide genetic information for the investigation of marine Aspergillus spp., which may help to elucidate their chemical diversity and adaptive strategies.
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Affiliation(s)
- Yaru Gao
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, PR China.,School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, PR China
| | - Xinyang Du
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, PR China.,School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, PR China
| | - Huanhuan Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, PR China.,School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, PR China
| | - Ying Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, PR China.,School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, PR China
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34
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Almeida H, Palys S, Tsang A, Diallo AB. TOUCAN: a framework for fungal biosynthetic gene cluster discovery. NAR Genom Bioinform 2020; 2:lqaa098. [PMID: 33575642 PMCID: PMC7694738 DOI: 10.1093/nargab/lqaa098] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/28/2020] [Accepted: 11/05/2020] [Indexed: 12/23/2022] Open
Abstract
Fungal secondary metabolites (SMs) are an important source of numerous bioactive compounds largely applied in the pharmaceutical industry, as in the production of antibiotics and anticancer medications. The discovery of novel fungal SMs can potentially benefit human health. Identifying biosynthetic gene clusters (BGCs) involved in the biosynthesis of SMs can be a costly and complex task, especially due to the genomic diversity of fungal BGCs. Previous studies on fungal BGC discovery present limited scope and can restrict the discovery of new BGCs. In this work, we introduce TOUCAN, a supervised learning framework for fungal BGC discovery. Unlike previous methods, TOUCAN is capable of predicting BGCs on amino acid sequences, facilitating its use on newly sequenced and not yet curated data. It relies on three main pillars: rigorous selection of datasets by BGC experts; combination of functional, evolutionary and compositional features coupled with outperforming classifiers; and robust post-processing methods. TOUCAN best-performing model yields 0.982 F-measure on BGC regions in the Aspergillus niger genome. Overall results show that TOUCAN outperforms previous approaches. TOUCAN focuses on fungal BGCs but can be easily adapted to expand its scope to process other species or include new features.
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Affiliation(s)
- Hayda Almeida
- Departement d'Informatique, UQAM, Montréal, QC, H2X 3Y7, Canada
| | - Sylvester Palys
- Centre for Structural and Functional Genomics, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Adrian Tsang
- Departement d'Informatique, UQAM, Montréal, QC, H2X 3Y7, Canada
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35
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Uka V, Cary JW, Lebar MD, Puel O, De Saeger S, Diana Di Mavungu J. Chemical repertoire and biosynthetic machinery of the Aspergillus flavus secondary metabolome: A review. Compr Rev Food Sci Food Saf 2020; 19:2797-2842. [PMID: 33337039 DOI: 10.1111/1541-4337.12638] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022]
Abstract
Filamentous fungi represent a rich source of extrolites, including secondary metabolites (SMs) comprising a great variety of astonishing structures and interesting bioactivities. State-of-the-art techniques in genome mining, genetic manipulation, and secondary metabolomics have enabled the scientific community to better elucidate and more deeply appreciate the genetic and biosynthetic chemical arsenal of these microorganisms. Aspergillus flavus is best known as a contaminant of food and feed commodities and a producer of the carcinogenic family of SMs, aflatoxins. This fungus produces many SMs including polyketides, ribosomal and nonribosomal peptides, terpenoids, and other hybrid molecules. This review will discuss the chemical diversity, biosynthetic pathways, and biological/ecological role of A. flavus SMs, as well as their significance concerning food safety and security.
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Affiliation(s)
- Valdet Uka
- Center of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.,Division of Pharmacy, Faculty of Medicine, University of Pristina, Pristina, Kosovo
| | - Jeffrey W Cary
- Southern Regional Research Center, USDA-ARS, New Orleans, Louisiana
| | - Matthew D Lebar
- Southern Regional Research Center, USDA-ARS, New Orleans, Louisiana
| | - Olivier Puel
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, INP-Purpan, UPS, Université de Toulouse, Toulouse, France
| | - Sarah De Saeger
- Center of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - José Diana Di Mavungu
- Center of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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36
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Shabani S, White JM, Hutton CA. Total Synthesis of the Putative Structure of Asperipin-2a and Stereochemical Reassignment. Org Lett 2020; 22:7730-7734. [DOI: 10.1021/acs.orglett.0c02884] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sadegh Shabani
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jonathan M. White
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Craig A. Hutton
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
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37
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Victorin, the host-selective cyclic peptide toxin from the oat pathogen Cochliobolus victoriae, is ribosomally encoded. Proc Natl Acad Sci U S A 2020; 117:24243-24250. [PMID: 32929037 DOI: 10.1073/pnas.2010573117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The necrotrophic fungal pathogen Cochliobolus victoriae produces victorin, a host-selective toxin (HST) essential for pathogenicity to certain oat cultivars with resistance against crown rust. Victorin is a mixture of highly modified heterodetic cyclic hexapeptides, previously assumed to be synthesized by a nonribosomal peptide synthetase. Herein, we demonstrate that victorin is a member of the ribosomally synthesized and posttranslationally modified peptide (RiPP) family of natural products. Analysis of a newly generated long-read assembly of the C. victoriae genome revealed three copies of precursor peptide genes (vicA1-3) with variable numbers of "GLKLAF" core peptide repeats corresponding to the victorin peptide backbone. vicA1-3 are located in repeat-rich gene-sparse regions of the genome and are loosely clustered with putative victorin biosynthetic genes, which are supported by the discovery of compact gene clusters harboring corresponding homologs in two distantly related plant-associated Sordariomycete fungi. Deletion of at least one copy of vicA resulted in strongly diminished victorin production. Deletion of a gene encoding a DUF3328 protein (VicYb) abolished the production altogether, supporting its predicted role in oxidative cyclization of the core peptide. In addition, we uncovered a copper amine oxidase (CAO) encoded by vicK, in which its deletion led to the accumulation of new glycine-containing victorin derivatives. The role of VicK in oxidative deamination of the N-terminal glycyl moiety of the hexapeptides to the active glyoxylate forms was confirmed in vitro. This study finally unraveled the genetic and molecular bases for biosynthesis of one of the first discovered HSTs and expanded our understanding of underexplored fungal RiPPs.
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Nguyen TQN, Tooh YW, Sugiyama R, Nguyen TPD, Purushothaman M, Leow LC, Hanif K, Yong RHS, Agatha I, Winnerdy FR, Gugger M, Phan AT, Morinaka BI. Post-translational formation of strained cyclophanes in bacteria. Nat Chem 2020; 12:1042-1053. [DOI: 10.1038/s41557-020-0519-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 07/04/2020] [Indexed: 11/09/2022]
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Umemura M, Kuriiwa K, Tamano K, Kawarabayasi Y. Ustiloxin biosynthetic machinery is not compatible between Aspergillus flavus and Ustilaginoidea virens. Fungal Genet Biol 2020; 143:103434. [PMID: 32679089 DOI: 10.1016/j.fgb.2020.103434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/27/2020] [Accepted: 07/06/2020] [Indexed: 11/15/2022]
Abstract
Ustiloxins are ribosomally synthesized and post-translationally modified peptides (RiPPs) first reported in Ascomycetes. Originally identified as metabolites of the rice pathogenic fungus Ustilaginoidea virens, they were recently identified among the metabolites of the mold Aspergillus flavus, along with their corresponding biosynthetic gene cluster. Ustilaginoidea virens produces ustiloxins A and B, whereas A. flavus produces only ustiloxin B. Correspondingly, in U. virens, the ustiloxin precursor peptide, from which the compound backbone is cleaved and cyclized, contains the core peptides Tyr(Y)-Val(V)-Ile(I)-Gly(G) and Tyr(Y)-Ala(A)-Ile(I)-Gly(G) for ustiloxins A and B, respectively, whereas that of A. flavus contains only the YAIG motif for ustiloxin B. In this study, the gene that encodes the precursor peptide in A. flavus, ustA, was replaced with synthetic genes encoding the core peptides YVIG or FAIG, to investigate their compatibility with the ustiloxin biosynthetic machinery. We also examined the importance of the hydroxyl group on the aromatic ring of Tyr for cyclization of the YAIG core peptide. Against our expectation, the ustA variant possessing YVIG core peptides did not produce a detectable amount of ustiloxin A, even though the ustiloxin biosynthetic gene clusters of A. flavus and U. virens both contain 13 homologous genes. We confirmed that the lack of ustiloxin A production was not due to lack or insufficient expression of the substituted synthetic gene. This result, along with the differences between the primary sequences of UstYa and UstYb in A. flavus and U. virens, suggests that the ustiloxin biosynthetic machinery is optimized for the native core peptide sequences. The synthetic FAIG-encoding ustA did not yield any compounds specific to the FAIG core peptide, suggesting that the hydroxyl group on the aromatic ring of Tyr in the core peptide is indispensable for cyclization of the core peptide, even though it is not structurally involved in the cyclization.
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Affiliation(s)
- Maiko Umemura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Kaoru Kuriiwa
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan; Department of Zoology, National Museum of Nature and Science, Ibaraki 305-0005, Japan
| | - Koichi Tamano
- Bioproduction Research Institute, AIST, 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo, Hokkaido 062-8517, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, 5-20, Building 63, Nishi-waseda Campus, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yutaka Kawarabayasi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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Soldatou S, Eldjarn GH, Huerta-Uribe A, Rogers S, Duncan KR. Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery. FEMS Microbiol Lett 2020; 366:5525086. [PMID: 31252431 PMCID: PMC6697067 DOI: 10.1093/femsle/fnz142] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/19/2019] [Indexed: 12/17/2022] Open
Abstract
Secondary metabolites can be viewed as a chemical language, facilitating communication between microorganisms. From an ecological point of view, this metabolite exchange is in constant flux due to evolutionary and environmental pressures. From a biomedical perspective, the chemistry is unsurpassed for its antibiotic properties. Genome sequencing of microorganisms has revealed a large reservoir of Biosynthetic Gene Clusters (BGCs); however, linking these to the secondary metabolites they encode is currently a major bottleneck to chemical discovery. This linking of genes to metabolites with experimental validation will aid the elicitation of silent or cryptic (not expressed under normal laboratory conditions) BGCs. As a result, this will accelerate chemical dereplication, our understanding of gene transcription and provide a comprehensive resource for synthetic biology. This will ultimately provide an improved understanding of both the biosynthetic and chemical space. In recent years, integrating these complex metabolomic and genomic data sets has been achieved using a spectrum of manual and automated approaches. In this review, we cover examples of these approaches, while addressing current challenges and future directions in linking these data sets.
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Affiliation(s)
- Sylvia Soldatou
- Department of Chemistry, University of Aberdeen, Aberdeen, UK. AB24 3UE
| | | | - Alejandro Huerta-Uribe
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK. G4 0RE
| | - Simon Rogers
- School of Computing Science, University of Glasgow, Glasgow, UK. G12 8RZ
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK. G4 0RE
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Volpe M, Miralto M, Gustincich S, Sanges R. ClusterScan: simple and generalistic identification of genomic clusters. Bioinformatics 2019; 34:3921-3923. [PMID: 29912285 DOI: 10.1093/bioinformatics/bty486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 06/12/2018] [Indexed: 01/01/2023] Open
Abstract
Summary Studies on gene clusters proved to be an excellent source of information to understand genomes evolution and identifying specific metabolic pathways or gene families. Improvements in sequencing methods have resulted in a large increase of sequenced genomes for which cluster annotation could be performed and standardized. Currently available programs are developed to search for specific cluster types and none of them is suitable for a broad range of user-based choices. We have developed ClusterScan which allows identifying clusters of any kind of feature simply based on their genomic coordinates and user-defined categorical annotations. Availability and implementation The tool is written in Python, distributed under the GNU General Public License (GPL) and available on Github at http://bit.ly/ClusterScan or as Docker image at sangeslab/clusterscan: latest. It is supported through a mailing-list on http://bit.ly/ClusterScanSupport. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Massimiliano Volpe
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Marco Miralto
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Stefano Gustincich
- Department of Neuroscience and Brain Technologies, Italian Institute of Technologies (IIT), Genova, Italy.,Department of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Remo Sanges
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.,Department of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
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Kjærbølling I, Mortensen UH, Vesth T, Andersen MR. Strategies to establish the link between biosynthetic gene clusters and secondary metabolites. Fungal Genet Biol 2019; 130:107-121. [DOI: 10.1016/j.fgb.2019.06.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/26/2019] [Accepted: 06/02/2019] [Indexed: 01/01/2023]
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Hautbergue T, Jamin EL, Debrauwer L, Puel O, Oswald IP. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. Nat Prod Rep 2019; 35:147-173. [PMID: 29384544 DOI: 10.1039/c7np00032d] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.
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Affiliation(s)
- T Hautbergue
- Toxalim (Research Centre in Food Toxicology) Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027 Toulouse, France.
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Frisvad J, Hubka V, Ezekiel C, Hong SB, Nováková A, Chen A, Arzanlou M, Larsen T, Sklenář F, Mahakarnchanakul W, Samson R, Houbraken J. Taxonomy of Aspergillus section Flavi and their production of aflatoxins, ochratoxins and other mycotoxins. Stud Mycol 2019; 93:1-63. [PMID: 30108412 PMCID: PMC6080641 DOI: 10.1016/j.simyco.2018.06.001] [Citation(s) in RCA: 270] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aflatoxins and ochratoxins are among the most important mycotoxins of all and producers of both types of mycotoxins are present in Aspergillus section Flavi, albeit never in the same species. Some of the most efficient producers of aflatoxins and ochratoxins have not been described yet. Using a polyphasic approach combining phenotype, physiology, sequence and extrolite data, we describe here eight new species in section Flavi. Phylogenetically, section Flavi is split in eight clades and the section currently contains 33 species. Two species only produce aflatoxin B1 and B2 (A. pseudotamarii and A. togoensis), and 14 species are able to produce aflatoxin B1, B2, G1 and G2: three newly described species A. aflatoxiformans, A. austwickii and A. cerealis in addition to A. arachidicola, A. minisclerotigenes, A. mottae, A. luteovirescens (formerly A. bombycis), A. nomius, A. novoparasiticus, A. parasiticus, A. pseudocaelatus, A. pseudonomius, A. sergii and A. transmontanensis. It is generally accepted that A. flavus is unable to produce type G aflatoxins, but here we report on Korean strains that also produce aflatoxin G1 and G2. One strain of A. bertholletius can produce the immediate aflatoxin precursor 3-O-methylsterigmatocystin, and one strain of Aspergillus sojae and two strains of Aspergillus alliaceus produced versicolorins. Strains of the domesticated forms of A. flavus and A. parasiticus, A. oryzae and A. sojae, respectively, lost their ability to produce aflatoxins, and from the remaining phylogenetically closely related species (belonging to the A. flavus-, A. tamarii-, A. bertholletius- and A. nomius-clades), only A. caelatus, A. subflavus and A. tamarii are unable to produce aflatoxins. With exception of A. togoensis in the A. coremiiformis-clade, all species in the phylogenetically more distant clades (A. alliaceus-, A. coremiiformis-, A. leporis- and A. avenaceus-clade) are unable to produce aflatoxins. Three out of the four species in the A. alliaceus-clade can produce the mycotoxin ochratoxin A: A. alliaceus s. str. and two new species described here as A. neoalliaceus and A. vandermerwei. Eight species produced the mycotoxin tenuazonic acid: A. bertholletius, A. caelatus, A. luteovirescens, A. nomius, A. pseudocaelatus, A. pseudonomius, A. pseudotamarii and A. tamarii while the related mycotoxin cyclopiazonic acid was produced by 13 species: A. aflatoxiformans, A. austwickii, A. bertholletius, A. cerealis, A. flavus, A. minisclerotigenes, A. mottae, A. oryzae, A. pipericola, A. pseudocaelatus, A. pseudotamarii, A. sergii and A. tamarii. Furthermore, A. hancockii produced speradine A, a compound related to cyclopiazonic acid. Selected A. aflatoxiformans, A. austwickii, A. cerealis, A. flavus, A. minisclerotigenes, A. pipericola and A. sergii strains produced small sclerotia containing the mycotoxin aflatrem. Kojic acid has been found in all species in section Flavi, except A. avenaceus and A. coremiiformis. Only six species in the section did not produce any known mycotoxins: A. aspearensis, A. coremiiformis, A. lanosus, A. leporis, A. sojae and A. subflavus. An overview of other small molecule extrolites produced in Aspergillus section Flavi is given.
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Affiliation(s)
- J.C. Frisvad
- Department of Biotechnology and Biomedicine, DTU-Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - C.N. Ezekiel
- Department of Microbiology, Babcock University, Ilishan Rémo, Nigeria
| | - S.-B. Hong
- Korean Agricultural Culture Collection, National Academy of Agricultural Science, RDA, Suwon, South Korea
| | - A. Nováková
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - A.J. Chen
- Institute of Medical Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - M. Arzanlou
- Department of Plant Protection, University of Tabriz, Tabriz, Iran
| | - T.O. Larsen
- Department of Biotechnology and Biomedicine, DTU-Bioengineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - F. Sklenář
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague 2, Czech Republic
- Institute of Microbiology of the CAS, v.v.i., Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - W. Mahakarnchanakul
- Department of Food Science and Technology, Faculty of Agro-Industry, Kasetsart University, Bangkok 10900, Thailand
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
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Quijano MR, Zach C, Miller FS, Lee AR, Imani AS, Künzler M, Freeman MF. Distinct Autocatalytic α-N-Methylating Precursors Expand the Borosin RiPP Family of Peptide Natural Products. J Am Chem Soc 2019; 141:9637-9644. [DOI: 10.1021/jacs.9b03690] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marissa R. Quijano
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Christina Zach
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Fredarla S. Miller
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Aileen R. Lee
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Aman S. Imani
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Michael F. Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics and BioTechnology Institute, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
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Araki Y, Awakawa T, Matsuzaki M, Cho R, Matsuda Y, Hoshino S, Shinohara Y, Yamamoto M, Kido Y, Inaoka DK, Nagamune K, Ito K, Abe I, Kita K. Complete biosynthetic pathways of ascofuranone and ascochlorin in Acremonium egyptiacum. Proc Natl Acad Sci U S A 2019; 116:8269-8274. [PMID: 30952781 PMCID: PMC6486709 DOI: 10.1073/pnas.1819254116] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ascofuranone (AF) and ascochlorin (AC) are meroterpenoids produced by various filamentous fungi, including Acremonium egyptiacum (synonym: Acremonium sclerotigenum), and exhibit diverse physiological activities. In particular, AF is a promising drug candidate against African trypanosomiasis and a potential anticancer lead compound. These compounds are supposedly biosynthesized through farnesylation of orsellinic acid, but the details have not been established. In this study, we present all of the reactions and responsible genes for AF and AC biosyntheses in A. egyptiacum, identified by heterologous expression, in vitro reconstruction, and gene deletion experiments with the aid of a genome-wide differential expression analysis. Both pathways share the common precursor, ilicicolin A epoxide, which is processed by the membrane-bound terpene cyclase (TPC) AscF in AC biosynthesis. AF biosynthesis branches from the precursor by hydroxylation at C-16 by the P450 monooxygenase AscH, followed by cyclization by a membrane-bound TPC AscI. All genes required for AC biosynthesis (ascABCDEFG) and a transcriptional factor (ascR) form a functional gene cluster, whereas those involved in the late steps of AF biosynthesis (ascHIJ) are present in another distantly located cluster. AF is therefore a rare example of fungal secondary metabolites requiring multilocus biosynthetic clusters, which are likely to be controlled by the single regulator, AscR. Finally, we achieved the selective production of AF in A. egyptiacum by genetically blocking the AC biosynthetic pathway; further manipulation of the strain will lead to the cost-effective mass production required for the clinical use of AF.
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Affiliation(s)
- Yasuko Araki
- Research and Development Division, Kikkoman Corporation, Noda City, Chiba 278-0037, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Motomichi Matsuzaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki City, Nagasaki 852-8523, Japan
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Rihe Cho
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yudai Matsuda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yasutomo Shinohara
- Research and Development Division, Kikkoman Corporation, Noda City, Chiba 278-0037, Japan
| | - Masaichi Yamamoto
- Institute of Mitochondrial Science Company, Ltd., Tokyo 176-0025, Japan
| | - Yasutoshi Kido
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Institute of Mitochondrial Science Company, Ltd., Tokyo 176-0025, Japan
- Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
- Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki City, Nagasaki 852-8523, Japan
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Kisaburo Nagamune
- Department of Parasitology, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Kotaro Ito
- Research and Development Division, Kikkoman Corporation, Noda City, Chiba 278-0037, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan;
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki City, Nagasaki 852-8523, Japan
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
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Luo S, Dong SH. Recent Advances in the Discovery and Biosynthetic Study of Eukaryotic RiPP Natural Products. Molecules 2019; 24:molecules24081541. [PMID: 31003555 PMCID: PMC6514808 DOI: 10.3390/molecules24081541] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/22/2022] Open
Abstract
Natural products have played indispensable roles in drug development and biomedical research. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of fast-expanding natural products attribute to genome mining efforts in recent years. Most RiPP natural products were discovered from bacteria, yet many eukaryotic cyclic peptides turned out to be of RiPP origin. This review article presents recent advances in the discovery of eukaryotic RiPP natural products, the elucidation of their biosynthetic pathways, and the molecular basis for their biosynthetic enzyme catalysis.
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Affiliation(s)
- Shangwen Luo
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
| | - Shi-Hui Dong
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China.
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Toyotome T, Hamada S, Yamaguchi S, Takahashi H, Kondoh D, Takino M, Kanesaki Y, Kamei K. Comparative genome analysis of Aspergillus flavus clinically isolated in Japan. DNA Res 2019; 26:95-103. [PMID: 30520983 PMCID: PMC6379028 DOI: 10.1093/dnares/dsy041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 11/01/2018] [Indexed: 01/21/2023] Open
Abstract
Aspergillus flavus is an important zoonotic pathogen and a well-known aflatoxin producer. Aspergillus flavus strains that are prevalent in Japanese environments are reported to be non-aflatoxigenic, although their aflatoxin productivity, especially among clinical isolates, has not been thoroughly investigated to date. In this study, we sequenced the genomes of ten strains of A. flavus isolated in Japan and compared their sequences with each other as well as with those of Aspergillus oryzae RIB40 and A. flavus NRRL3357. The phylogenetic analysis based on identified SNPs indicated that five strains were closer to A. oryzae RIB40 than to A. flavus NRRL3357. In contrast, of those isolates that were closer to A. flavus NRRL3357 than to A. oryzae RIB40, three were found to possess either the entire or partial aflatoxin biosynthesis gene cluster of NRRL3357-type. Furthermore, two of the three actually produced either aflatoxin B1 or an intermediate of the reaction leading to aflatoxin formation. Three of the ten strains we isolated were identified to possess part of the aflatoxin gene cluster, while five others retained the A. oryzae RIB40-type cluster. The genome data thus obtained may be further explored and utilized for comparative analysis of aflatoxin production in environmental and clinical isolates of A. flavus.
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Affiliation(s)
- Takahito Toyotome
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan.,Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan.,Graduate School of Animal Husbandry, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan.,Medical Mycology Research Center, Chiba University, Chiba City, Chiba, Japan
| | - Saho Hamada
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Satoe Yamaguchi
- Graduate School of Animal Husbandry, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba City, Chiba, Japan
| | - Daisuke Kondoh
- Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
| | - Masahiko Takino
- Japan Application Center, Life Sciences and Chemical Analysis, Agilent Technologies Japan, Ltd, 9-1 Takakura-cho, Hachioji, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Suruga-ku, Shizuoka, Japan
| | - Katsuhiko Kamei
- Medical Mycology Research Center, Chiba University, Chiba City, Chiba, Japan
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Shabani S, White JM, Hutton CA. Synthesis of the C-Terminal Macrocycle of Asperipin-2a. Org Lett 2019; 21:1877-1880. [DOI: 10.1021/acs.orglett.9b00488] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sadegh Shabani
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jonathan M. White
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Craig A. Hutton
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
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Biological and chemical diversity go hand in hand: Basidiomycota as source of new pharmaceuticals and agrochemicals. Biotechnol Adv 2019; 37:107344. [PMID: 30738916 DOI: 10.1016/j.biotechadv.2019.01.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/20/2022]
Abstract
The Basidiomycota constitutes the second largest higher taxonomic group of the Fungi after the Ascomycota and comprises over 30.000 species. Mycelial cultures of Basidiomycota have already been studied since the 1950s for production of antibiotics and other beneficial secondary metabolites. Despite the fact that unique and selective compounds like pleuromutilin were obtained early on, it took several decades more until they were subjected to a systematic screening for antimicrobial and anticancer activities. These efforts led to the discovery of the strobilurins and several hundreds of further compounds that mainly constitute terpenoids. In parallel the traditional medicinal mushrooms of Asia were also studied intensively for metabolite production, aimed at finding new therapeutic agents for treatment of various diseases including metabolic disorders and the central nervous system. While the evaluation of this organism group has in general been more tedious as compared to the Ascomycota, the chances to discover new metabolites and to develop them further to candidates for drugs, agrochemicals and other products for the Life Science industry have substantially increased over the past decade. This is owing to the revolutionary developments in -OMICS techniques, bioinformatics, analytical chemistry and biotechnological process technology, which are steadily being developed further. On the other hand, the new developments in polythetic fungal taxonomy now also allow a more concise selection of previously untapped organisms. The current review is dedicated to summarize the state of the art and to give an outlook to further developments.
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