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Salamzade R, Tran PQ, Martin C, Manson AL, Gilmore MS, Earl AM, Anantharaman K, Kalan LR. zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.07.544063. [PMID: 37333121 PMCID: PMC10274777 DOI: 10.1101/2023.06.07.544063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of ortholog groups for individual protein-encoding genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of evolutionary statistics for each inferred ortholog group. Importantly, in comparison to tools for visual exploration of homologous relationships between gene clusters, zol can scale to thousands of gene cluster instances and produce detailed reports that are easy to digest. To showcase fai and zol, we apply them for: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-level genetic insights of two common BGCs in the fungal species Aspergillus flavus, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.
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Affiliation(s)
- Rauf Salamzade
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Patricia Q. Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Freshwater and Marine Science Doctoral Program, University of Wisconsin-Madison, WI, USA
| | - Cody Martin
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Abigail L. Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Gilmore
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Ophthalmology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School and Mass Eye and Ear, Boston, Massachusetts, USA
| | - Ashlee M. Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, Division of Infectious Disease, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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2
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Sato M. Structural diversity of decalin forming Diels-Alderase. Biosci Biotechnol Biochem 2024; 88:719-726. [PMID: 38758077 DOI: 10.1093/bbb/zbae040] [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: 02/09/2024] [Accepted: 03/22/2024] [Indexed: 05/18/2024]
Abstract
The Diels-Alder (DA) reaction, specifically referring to the [4 + 2] cycloaddition reaction in pericyclic reactions, is a process that forms two carbon-carbon covalent bonds in a single step via an electron ring transition state. Among the secondary metabolites produced by microorganisms, numerous compounds are biosynthesized through DA reactions, most of which are enzymatic. Our research group has discovered an enzyme named Diels-Alderase (DAase) that catalyzes the DA reaction in filamentous fungi, and we have been investigating its catalytic mechanism. This review describes the reported microbial DAase enzymes, with a particular focus on those involved in the construction of the decalin ring.
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Affiliation(s)
- Michio Sato
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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3
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Karahoda B, Pfannenstiel BT, Sarikaya-Bayram Ö, Dong Z, Ho Wong K, Fleming AB, Keller NP, Bayram Ö. The KdmB-EcoA-RpdA-SntB (KERS) chromatin regulatory complex controls development, secondary metabolism and pathogenicity in Aspergillus flavus. Fungal Genet Biol 2023; 169:103836. [PMID: 37666447 PMCID: PMC10841535 DOI: 10.1016/j.fgb.2023.103836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/28/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
The filamentous fungus Aspergillus flavus is a plant and human pathogen predominantly found in the soil as spores or sclerotia and is capable of producing various secondary metabolites (SM) such as the carcinogenic mycotoxin aflatoxin. Recently, we have discovered a novel nuclear chromatin binding complex (KERS) that contains the JARID1-type histone demethylase KdmB, a putative cohesion acetyl transferase EcoA, a class I type histone deacetylase RpdA and the PHD ring finger reader protein SntB in the model filamentous fungus Aspergillus nidulans. Here, we show the presence of the KERS complex in A. flavus by immunoprecipitation-coupled mass spectrometry and constructed kdmBΔ and rpdAΔ strains to study their roles in fungal development, SM production and histone post-translational modifications (HPTMs). We found that KdmB and RpdA couple the regulation of SM gene clusters with fungal light-responses and HPTMs. KdmB and RpdA have opposing roles in light-induced asexual conidiation, while both factors are positive regulators of sclerotia development through the nsdC and nsdD pathway. KdmB and RpdA are essential for the productions of aflatoxin (similar to findings for SntB) as well as cyclopiazonic acid, ditryptophenaline and leporin B through controlling the respective SM biosynthetic gene clusters. We further show that both KdmB and RpdA regulate H3K4me3 and H3K9me3 levels, while RpdA also acts on H3K14ac levels in nuclear extracts. Therefore, the chromatin modifiers KdmB and RpdA of the KERS complex are key regulators for fungal development and SM metabolism in A. flavus.
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Affiliation(s)
- Betim Karahoda
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Brandon T Pfannenstiel
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA
| | | | - Zhiqiang Dong
- Faculty of Health Sciences, University of Macau, Macau
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau; Institute of Translational Medicine, University of Macau, Macau; Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau
| | - Alastair B Fleming
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, USA
| | - Özgür Bayram
- Biology Department, Maynooth University, Maynooth, Co. Kildare, Ireland.
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4
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Liu X, Li RQ, Zeng QX, Li YQ, Chen XA. A Novel Zn 2Cys 6 Transcription Factor, TopC, Positively Regulates Trichodin A and Asperpyridone A Biosynthesis in Tolypocladium ophioglossoides. Microorganisms 2023; 11:2578. [PMID: 37894236 PMCID: PMC10609478 DOI: 10.3390/microorganisms11102578] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Asperpyridone A represents an unusual class of pyridone alkaloids with demonstrated potential for hypoglycemic activity, primarily by promoting glucose consumption in HepG2 cells. Trichodin A, initially isolated from the marine fungus Trichoderma sp. strain MF106, exhibits notable antibiotic activities against Staphylococcus epidermidis. Despite their pharmacological significance, the regulatory mechanisms governing their biosynthesis have remained elusive. In this investigation, we initiated the activation of a latent gene cluster, denoted as "top", through the overexpression of the Zn2Cys6 transcription factor TopC in Tolypocladium ophioglossoides. The activation of the top cluster led to the biosynthesis of asperpyridone A, pyridoxatin, and trichodin A. Our study also elucidated that the regulator TopC exerts precise control over the biosynthesis of asperpyridone A and trichodin A through the detection of protein-nucleic acid interactions. Moreover, by complementing these findings with gene deletions involving topA and topH, we proposed a comprehensive biosynthesis pathway for asperpyridone A and trichodin A in T. ophioglossoides.
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Affiliation(s)
- Xiang Liu
- School of Medicine and the Children’s Hospital, Zhejiang University, Hangzhou 310058, China; (X.L.); (R.-Q.L.)
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Rui-Qi Li
- School of Medicine and the Children’s Hospital, Zhejiang University, Hangzhou 310058, China; (X.L.); (R.-Q.L.)
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Qing-Xin Zeng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China;
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Xin-Ai Chen
- School of Medicine and the Children’s Hospital, Zhejiang University, Hangzhou 310058, China; (X.L.); (R.-Q.L.)
- Institute of Pharmaceutical Biotechnology, Zhejiang University, Hangzhou 310058, China;
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5
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Janzen DJ, Zhou J, Li SM. Biosynthesis of p-Terphenyls in Aspergillus ustus Implies Enzymatic Reductive Dehydration and Spontaneous Dibenzofuran Formation. Org Lett 2023; 25:6311-6316. [PMID: 37607357 DOI: 10.1021/acs.orglett.3c02234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
p-Terphenyls contain a central benzene ring substituted with two phenyl residues at its para positions. Heterologous expression of a biosynthetic gene cluster from Aspergillus ustus led to the formation of four new p-terphenyl derivatives. Gene deletion experiments proved the formation and reductive dehydration of the terphenylquinone atromentin, followed by O-methylation and prenylation. Spontaneous dibenzofuran formation led to the final products. These results provide new insights into the biosynthesis of p-terphenyls in fungi and dibenzofuran formation in the biosynthesis of numerous natural products.
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Affiliation(s)
- Daniel J Janzen
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Jing Zhou
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
- School of Life Sciences, Hainan University, Haikou, Hainan 570228, People's Republic of China
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Fachbereich Pharmazie, Philipps-Universität Marburg, Robert-Koch-Straße 4, 35037 Marburg, Germany
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6
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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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7
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Li D, Wang W, Xu K, Li J, Long B, Li Z, Tan G, Yu X. Elucidation of a Dearomatization Route in the Biosynthesis of Oxysporidinone Involving a TenA-like Cytochrome P450 Enzyme. Angew Chem Int Ed Engl 2023; 62:e202301976. [PMID: 37086399 DOI: 10.1002/anie.202301976] [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: 02/08/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 04/23/2023]
Abstract
Oxidative dearomatization of phenols is an important transformation for synthesis of complex molecules. Oxysporidinone and related 2-pyridones feature a hydroxy-substituted cyclohexanone ring, which has been proposed to form by phenol dearomatization, although the details of the biochemical process are still unknown. In this study, we identified the oxysporidinone biosynthetic gene cluster in Fusarium oxysporum by regulator activation and gene knockout studies. Through in vivo and in vitro studies, we confirmed that the phenol dearomatization process involves two enzymes. OsdM, a TenA-like cytochrome P450 with expected ring-expansion activity, converts the phenol ring and the 4-hydroxy-2-pyridone core into an unexpected fused [6-5-6] ring system. OsdN, on the other hand, catalyzes two successive ene reduction reactions, followed by hydroxylation by OsdM. This new route enriches current knowledge on enzymatic phenol dearomatization and the mechanism of TenA-like P450s.
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Affiliation(s)
- Dan Li
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410013, P. R. China
| | - Wenxuan Wang
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410013, P. R. China
| | - Kangping Xu
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410013, P. R. China
| | - Jing Li
- Department of Pharmacy, Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Bi Long
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410013, P. R. China
| | - Zhansheng Li
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410013, P. R. China
| | - Guishan Tan
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410013, P. R. China
- Department of Pharmacy, Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, 410008, P. R. China
| | - Xia Yu
- Xiangya School of Pharmaceutical Sciences, Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha, Hunan, 410013, P. R. China
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8
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Toppo P, Kagatay LL, Gurung A, Singla P, Chakraborty R, Roy S, Mathur P. Endophytic fungi mediates production of bioactive secondary metabolites via modulation of genes involved in key metabolic pathways and their contribution in different biotechnological sector. 3 Biotech 2023; 13:191. [PMID: 37197561 PMCID: PMC10183385 DOI: 10.1007/s13205-023-03605-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
Endophytic fungi stimulate the production of an enormous number of bioactive metabolites in medicinal plants and affect the different steps of biosynthetic pathways of these secondary metabolites. Endophytic fungi possess a number of biosynthetic gene clusters that possess genes for various enzymes, transcription factors, etc., in their genome responsible for the production of secondary metabolites. Additionally, endophytic fungi also modulate the expression of various genes responsible for the synthesis of key enzymes involved in metabolic pathways of such as HMGR, DXR, etc. involved in the production of a large number of phenolic compounds as well as regulate the expression of genes involved in the production of alkaloids and terpenoids in different plants. This review aims to provide a comprehensive overview of gene expression related to endophytes and their impact on metabolic pathways. Additionally, this review will emphasize the studies done to isolate these secondary metabolites from endophytic fungi in large quantities and assess their bioactivity. Due to ease in synthesis of secondary metabolites and their huge application in the medical industry, these bioactive metabolites are now being extracted from strains of these endophytic fungi commercially. Apart from their application in the pharmaceutical industry, most of these metabolites extracted from endophytic fungi also possess plant growth-promoting ability, bioremediation potential, novel bio control agents, sources of anti-oxidants, etc. The review will comprehensively shed a light on the biotechnological application of these fungal metabolites at the industrial level.
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Affiliation(s)
- Prabha Toppo
- Microbiology Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
| | - Lahasang Lamu Kagatay
- Microbiology Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
| | - Ankita Gurung
- Microbiology Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
| | - Priyanka Singla
- Department of Botany, Mount Carmel College, Bengaluru, Karnataka India
| | - Rakhi Chakraborty
- Department of Botany, Acharya Prafulla Chandra Roy Government College, Dist. Darjeeling, Siliguri, West Bengal India
| | - Swarnendu Roy
- Plant Biochemistry Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
| | - Piyush Mathur
- Microbiology Laboratory, Department of Botany, University of North Bengal, Rajarammohunpur, Dist. Darjeeling, Siliguri, West Bengal India
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9
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Chiang CY, Ohashi M, Tang Y. Deciphering chemical logic of fungal natural product biosynthesis through heterologous expression and genome mining. Nat Prod Rep 2023; 40:89-127. [PMID: 36125308 PMCID: PMC9906657 DOI: 10.1039/d2np00050d] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Covering: 2010 to 2022Heterologous expression of natural product biosynthetic gene clusters (BGCs) has become a widely used tool for genome mining of cryptic pathways, bottom-up investigation of biosynthetic enzymes, and engineered biosynthesis of new natural product variants. In the field of fungal natural products, heterologous expression of a complete pathway was first demonstrated in the biosynthesis of tenellin in Aspergillus oryzae in 2010. Since then, advances in genome sequencing, DNA synthesis, synthetic biology, etc. have led to mining, assignment, and characterization of many fungal BGCs using various heterologous hosts. In this review, we will highlight key examples in the last decade in integrating heterologous expression into genome mining and biosynthetic investigations. The review will cover the choice of heterologous hosts, prioritization of BGCs for structural novelty, and how shunt products from heterologous expression can reveal important insights into the chemical logic of biosynthesis. The review is not meant to be exhaustive but is rather a collection of examples from researchers in the field, including ours, that demonstrates the usefulness and pitfalls of heterologous biosynthesis in fungal natural product discovery.
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Affiliation(s)
- Chen-Yu Chiang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Masao Ohashi
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Yi Tang
- Dept. of Chemical and Biomolecular Engineering, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA.
- Dept. of Chemistry and Biochemistry, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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10
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Hatmaker EA, Rangel-Grimaldo M, Raja HA, Pourhadi H, Knowles SL, Fuller K, Adams EM, Lightfoot JD, Bastos RW, Goldman GH, Oberlies NH, Rokas A. Genomic and Phenotypic Trait Variation of the Opportunistic Human Pathogen Aspergillus flavus and Its Close Relatives. Microbiol Spectr 2022; 10:e0306922. [PMID: 36318036 PMCID: PMC9769809 DOI: 10.1128/spectrum.03069-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Fungal diseases affect millions of humans annually, yet fungal pathogens remain understudied. The mold Aspergillus flavus can cause both aspergillosis and fungal keratitis infections, but closely related species are not considered clinically relevant. To study the evolution of A. flavus pathogenicity, we examined genomic and phenotypic traits of two strains of A. flavus and three closely related species, Aspergillus arachidicola (two strains), Aspergillus parasiticus (two strains), and Aspergillus nomiae (one strain). We identified >3,000 orthologous proteins unique to A. flavus, including seven biosynthetic gene clusters present in A. flavus strains and absent in the three nonpathogens. We characterized secondary metabolite production for all seven strains under two clinically relevant conditions, temperature and salt concentration. Temperature impacted metabolite production in all species, whereas salinity did not affect production of any species. Strains of the same species produced different metabolites. Growth under stress conditions revealed additional heterogeneity within species. Using the invertebrate fungal disease model Galleria mellonella, we found virulence of strains of the same species varied widely; A. flavus strains were not more virulent than strains of the nonpathogens. In a murine model of fungal keratitis, we observed significantly lower disease severity and corneal thickness for A. arachidicola compared to other species at 48 h postinfection, but not at 72 h. Our work identifies variations in key phenotypic, chemical, and genomic attributes between A. flavus and its nonpathogenic relatives and reveals extensive strain heterogeneity in virulence that does not correspond to the currently established clinical relevance of these species. IMPORTANCE Aspergillus flavus is a filamentous fungus that causes opportunistic human infections, such as aspergillosis and fungal keratitis, but its close relatives are considered nonpathogenic. To begin understanding how this difference in pathogenicity evolved, we characterized variation in infection-relevant genomic, chemical, and phenotypic traits between strains of A. flavus and its relatives. We found extensive variation (or strain heterogeneity) within the pathogenic A. flavus as well as within its close relatives, suggesting that strain-level differences may play a major role in the ability of these fungi to cause disease. Surprisingly, we also found that the virulence of strains from species not considered to be pathogens was similar to that of A. flavus in both invertebrate and murine models of disease. These results contrast with previous studies on Aspergillus fumigatus, another major pathogen in the genus, for which significant differences in infection-relevant chemical and phenotypic traits are observed between closely related pathogenic and nonpathogenic species.
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Affiliation(s)
- E. Anne Hatmaker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
| | - Manuel Rangel-Grimaldo
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Huzefa A. Raja
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Hadi Pourhadi
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Sonja L. Knowles
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Kevin Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Emily M. Adams
- Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Jorge D. Lightfoot
- Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, USA
| | - Rafael W. Bastos
- Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Nicholas H. Oberlies
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, Tennessee, USA
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11
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Chiang YM, Lin TS, Wang CCC. Total Heterologous Biosynthesis of Fungal Natural Products in Aspergillus nidulans. JOURNAL OF NATURAL PRODUCTS 2022; 85:2484-2518. [PMID: 36173392 PMCID: PMC9621686 DOI: 10.1021/acs.jnatprod.2c00487] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fungal natural products comprise a wide range of bioactive compounds including important drugs and agrochemicals. Intriguingly, bioinformatic analyses of fungal genomes have revealed that fungi have the potential to produce significantly more natural products than what have been discovered so far. It has thus become widely accepted that most biosynthesis pathways of fungal natural products are silent or expressed at very low levels under laboratory cultivation conditions. To tap into this vast chemical reservoir, the reconstitution of entire biosynthetic pathways in genetically tractable fungal hosts (total heterologous biosynthesis) has become increasingly employed in recent years. This review summarizes total heterologous biosynthesis of fungal natural products accomplished before 2020 using Aspergillus nidulans as heterologous hosts. We review here Aspergillus transformation, A. nidulans hosts, shuttle vectors for episomal expression, and chromosomal integration expression. These tools, collectively, not only facilitate the discovery of cryptic natural products but can also be used to generate high-yield strains with clean metabolite backgrounds. In comparison with total synthesis, total heterologous biosynthesis offers a simplified strategy to construct complex molecules and holds potential for commercial application.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Tzu-Shyang Lin
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
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12
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Becchimanzi A, Nicoletti R. Aspergillus-bees: A dynamic symbiotic association. Front Microbiol 2022; 13:968963. [PMID: 36160228 PMCID: PMC9489833 DOI: 10.3389/fmicb.2022.968963] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/22/2022] [Indexed: 11/24/2022] Open
Abstract
Besides representing one of the most relevant threats of fungal origin to human and animal health, the genus Aspergillus includes opportunistic pathogens which may infect bees (Hymenoptera, Apoidea) in all developmental stages. At least 30 different species of Aspergillus have been isolated from managed and wild bees. Some efficient behavioral responses (e.g., diseased brood removal) exerted by bees negatively affect the chance to diagnose the pathology, and may contribute to the underestimation of aspergillosis importance in beekeeping. On the other hand, bee immune responses may be affected by biotic and abiotic stresses and suffer from the loose co-evolutionary relationships with Aspergillus pathogenic strains. However, if not pathogenic, these hive mycobiota components can prove to be beneficial to bees, by affecting the interaction with other pathogens and parasites and by detoxifying xenobiotics. The pathogenic aptitude of Aspergillus spp. likely derives from the combined action of toxins and hydrolytic enzymes, whose effects on bees have been largely overlooked until recently. Variation in the production of these virulence factors has been observed among strains, even belonging to the same species. Toxigenic and non-toxigenic strains/species may co-exist in a homeostatic equilibrium which is susceptible to be perturbed by several external factors, leading to mutualistic/antagonistic switch in the relationships between Aspergillus and bees.
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Affiliation(s)
- Andrea Becchimanzi
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Rosario Nicoletti
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Council for Agricultural Research and Economics, Research Centre for Olive, Fruit and Citrus Crops, Caserta, Italy
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13
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Toopaang W, Bunnak W, Srisuksam C, Wattananukit W, Tanticharoen M, Yang YL, Amnuaykanjanasin A. Microbial polyketides and their roles in insect virulence: from genomics to biological functions. Nat Prod Rep 2022; 39:2008-2029. [PMID: 35822627 DOI: 10.1039/d1np00058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: May 1966 up to January 2022Entomopathogenic microorganisms have potential for biological control of insect pests. Their main secondary metabolites include polyketides, nonribosomal peptides, and polyketide-nonribosomal peptide (PK-NRP) hybrids. Among these secondary metabolites, polyketides have mainly been studied for structural identification, pathway engineering, and for their contributions to medicine. However, little is known about the function of polyketides in insect virulence. This review focuses on the role of bacterial and fungal polyketides, as well as PK-NRP hybrids in insect infection and killing. We also discuss gene distribution and evolutional relationships among different microbial species. Further, the role of microbial polyketides and the hybrids in modulating insect-microbial symbiosis is also explored. Understanding the mechanisms of polyketides in insect pathogenesis, how compounds moderate the host-fungus interaction, and the distribution of PKS genes across different fungi and bacteria will facilitate the discovery and development of novel polyketide-derived bio-insecticides.
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Affiliation(s)
- Wachiraporn Toopaang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand. .,Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Warapon Bunnak
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Chettida Srisuksam
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Wilawan Wattananukit
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
| | - Morakot Tanticharoen
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok 10140, Thailand
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan. .,Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan
| | - Alongkorn Amnuaykanjanasin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand.
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14
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Yang K, Tian J, Keller NP. Post-translational modifications drive secondary metabolite biosynthesis in Aspergillus: a review. Environ Microbiol 2022; 24:2857-2881. [PMID: 35645150 PMCID: PMC9545273 DOI: 10.1111/1462-2920.16034] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 12/26/2022]
Abstract
Post‐translational modifications (PTMs) are important for protein function and regulate multiple cellular processes and secondary metabolites (SMs) in fungi. Aspergillus species belong to a genus renown for an abundance of bioactive secondary metabolites, many important as toxins, pharmaceuticals and in industrial production. The genes required for secondary metabolites are typically co‐localized in biosynthetic gene clusters (BGCs), which often localize in heterochromatic regions of genome and are ‘turned off’ under laboratory condition. Efforts have been made to ‘turn on’ these BGCs by genetic manipulation of histone modifications, which could convert the heterochromatic structure to euchromatin. Additionally, non‐histone PTMs also play critical roles in the regulation of secondary metabolism. In this review, we collate the known roles of epigenetic and PTMs on Aspergillus SM production. We also summarize the proteomics approaches and bioinformatics tools for PTM identification and prediction and provide future perspectives on the emerging roles of PTM on regulation of SM biosynthesis in Aspergillus and other fungi.
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Affiliation(s)
- Kunlong Yang
- School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China.,Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, 53705, USA
| | - Jun Tian
- School of Life Science, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, People's Republic of China
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, Wisconsin, 53705, USA
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15
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Skellam E. Biosynthesis of fungal polyketides by collaborating and trans-acting enzymes. Nat Prod Rep 2022; 39:754-783. [PMID: 34842268 DOI: 10.1039/d1np00056j] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Covering: 1999 up to 2021Fungal polyketides encompass a range of structurally diverse molecules with a wide variety of biological activities. The giant multifunctional enzymes that synthesize polyketide backbones remain enigmatic, as do many of the tailoring enzymes involved in functional modifications. Recent advances in elucidating biosynthetic gene clusters (BGCs) have revealed numerous examples of fungal polyketide synthases that require the action of collaborating enzymes to synthesize the carbon backbone. This review will discuss collaborating and trans-acting enzymes involved in loading, extending, and releasing polyketide intermediates from fungal polyketide synthases, and additional modifications introduced by trans-acting enzymes demonstrating the complexity encountered when investigating natural product biosynthesis in fungi.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA.
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16
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Okamoto T, Kishimoto S, Watanabe K. Isolation of Natural Prodrug-Like Metabolite by Simulating Human Prodrug Activation in Filamentous Fungus. Chem Pharm Bull (Tokyo) 2022; 70:304-308. [DOI: 10.1248/cpb.c21-01099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takumi Okamoto
- Department of Pharmaceutical Sciences, University of Shizuoka
| | | | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka
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17
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Kalaitzakis D, Bosveli A, Montagnon T, Vassilikogiannakis G. Sequential Visible Light‐Induced Reactions Using Different Photocatalysts: Transformation of Furans into 2‐Pyridones via γ‐Lactams Using a New Ring Expansion Reaction. Chemistry 2022; 28:e202200322. [DOI: 10.1002/chem.202200322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Indexed: 12/11/2022]
Affiliation(s)
- Dimitris Kalaitzakis
- Department of Chemistry University of Crete Vasilika Vouton 71003 Iraklion, Crete Greece
| | - Artemis Bosveli
- Department of Chemistry University of Crete Vasilika Vouton 71003 Iraklion, Crete Greece
| | - Tamsyn Montagnon
- Department of Chemistry University of Crete Vasilika Vouton 71003 Iraklion, Crete Greece
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18
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Guo Y, Contesini FJ, Wang X, Ghidinelli S, Tornby DS, Andersen TE, Mortensen UH, Larsen TO. Biosynthesis of Calipyridone A Represents a Fungal 2-Pyridone Formation without Ring Expansion in Aspergillus californicus. Org Lett 2022; 24:804-808. [PMID: 35045257 DOI: 10.1021/acs.orglett.1c03792] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A chemical investigation of the filamentous fungus Aspergillus californicus led to the isolation of a polyketide-nonribosomal peptide hybrid, calipyridone A (1). A putative biosynthetic gene cluster cpd for production of 1 was next identified by genome mining. The role of the cpd cluster in the production of 1 was confirmed by multiple gene deletion experiments in the host strain as well as by heterologous expression of the hybrid gene cpdA inAspergillus oryzae. Moreover, chemical analyses of the mutant strains allowed the biosynthesis of 1 to be elucidated. The results indicate that the generation of the 2-pyridone moiety of 1 via nucleophilic attack of the iminol nitrogen to the carbonyl carbon is different from the biosynthesis of other fungal 2-pyridone products through P450-catalyzed tetramic acid ring expansions. In addition, two biogenetic intermediates, calipyridones B and C, showed modest inhibition effects on the plaque-forming ability of SARS-CoV-2.
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Affiliation(s)
- Yaojie Guo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark.,Department of Microbiology, Zhejiang University School of Medicine, Yuhangtang Road 866, Hangzhou 310058, China
| | - Fabiano J Contesini
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Xinhui Wang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Simone Ghidinelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Ditte S Tornby
- Department of Clinical Research, University of Southern Denmark, Winløwsparken 21, 2. sal, 5000 Odense, Denmark
| | - Thomas E Andersen
- Department of Clinical Research, University of Southern Denmark, Winløwsparken 21, 2. sal, 5000 Odense, Denmark
| | - Uffe H Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark
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19
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Gao Y, Xie M, Yu C, Zhang M, Huang J, Li Q, Zhang H, Li L. Heterologous Expression of Macrollins from Phytopathogenic Macrophomina phaseolina Revealed a Cytochrome P450 Mono-oxygenase in the Biosynthesis of β-Hydroxyl Tetramic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15175-15183. [PMID: 34881573 DOI: 10.1021/acs.jafc.1c05304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Macrophomina phaseolina (M. phaseolina) is a crucial pathogenic fungus that can cause severe charcoal rot in economic crops and other plants. In this study, four new natural products, macrollins A-D, were discovered from M. phaseolina by the strategy of heterologous expression. To our knowledge, macrollins are the first reported polyketide-amino acid hybrids from the plant pathogen. Heterologous expression and in vitro reactions revealed a cytochrome P450 mono-oxygenase (MacC) catalyzing the hydroxylation at the β-carbon of tetramic acid molecules, which is different from P450s leading to the ring expansion in the biosynthesis of fungal 2-pyridones. Phylogenetic analysis of P450s involved in the fungal polyketide-amino acid hybrids showed that MacC was not classified in any known clades. The putative oxidative mechanisms of the P450s and the biosynthetic pathway of macrollins were also proposed.
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Affiliation(s)
- Yangle Gao
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Mengsi Xie
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Cui Yu
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Mingliang Zhang
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Qin Li
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Huaidong Zhang
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Li Li
- Engineering Research Center of Industrial Microbiology, Fujian Normal University, Fuzhou, Fujian 350117, China
- College of Life Sciences, Fujian Normal University, Fuzhou, Fujian 350117, China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen, Fujian 361021, China
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20
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Inductive Production of the Iron-Chelating 2-Pyridones Benefits the Producing Fungus To Compete for Diverse Niches. mBio 2021; 12:e0327921. [PMID: 34903054 PMCID: PMC8669486 DOI: 10.1128/mbio.03279-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Diverse 2-pyridone alkaloids have been identified with an array of biological and pharmaceutical activities, including the development of drugs. However, the biosynthetic regulation and chemical ecology of 2-pyridones remain largely elusive. Here, we report the inductive activation of the silent polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) (tenS) gene cluster for the biosynthesis of the tenellin-type 2-pyridones in the insect-pathogenic fungus Beauveria bassiana when cocultured with its natural competitor fungus Metarhizium robertsii. A pathway-specific transcription factor, tenR, was identified, and the overexpression of tenR well expanded the biosynthetic mechanism of 15-hydroxytenellin (15-HT) and its derivatives. In particular, a tandemly linked glycosyltransferase-methyltransferase gene pair located outside the tenS gene cluster was verified to mediate the rare and site-specific methylglucosylation of 15-HT at its N-OH residue. It was evident that both tenellin and 15-HT can chelate iron, which could benefit B. bassiana to outcompete M. robertsii in cocultures and to adapt to iron-replete and -depleted conditions. Relative to the wild-type strain, the deletion of tenS had no obvious negative effect on fungal virulence, but the overexpression of tenR could substantially increase fungal pathogenicity toward insect hosts. The results of this study well advance the understanding of the biosynthetic machinery and chemical ecology of 2-pyridones.
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21
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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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22
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Vignolle GA, Schaffer D, Zehetner L, Mach RL, Mach-Aigner AR, Derntl C. FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution. PLoS Comput Biol 2021; 17:e1009372. [PMID: 34570757 PMCID: PMC8476034 DOI: 10.1371/journal.pcbi.1009372] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs. The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.
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Affiliation(s)
- Gabriel A. Vignolle
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Denise Schaffer
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Leopold Zehetner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Robert L. Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Astrid R. Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Christian Derntl
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
- * E-mail:
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23
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Abstract
It has been proposed that biosyntheses of many natural products involve pericyclic reactions, including Diels-Alder (DA) reaction. However, only a small set of enzymes have been proposed to catalyze pericyclic reactions. Most surprisingly, there has been no formal identification of natural enzymes that can be defined to catalyze DA reactions (DAases), despite the wide application of the reaction in chemical syntheses of complex organic compounds. However, recent studies began to accumulate a growing body of evidence that supports the notion that enzymes that formally catalyze DA reactions, in fact exist. In this review, I will begin by describing a short history behind the discovery and characterization of macrophomate synthase, one of the earliest enzymes that was proposed to catalyze an intermolecular DA reaction during the biosynthesis of a substituted benzoic acid in a phytopathogenic fungus Macrophoma commelinae. Then, I will discuss representative enzymes that have been chemically authenticated to catalyze DA reactions, with emphasis on more recent discoveries of DAases involved mainly in fungal secondary metabolite biosynthesis except for one example from a marine streptomycete. The current success in identification of a series of DAases and enzymes that catalyze other pericyclic reactions owes to the combined efforts from both the experimental and theoretical approaches in discovering natural products. Such efforts typically involve identifying the chemical features derived from cycloaddition reactions, isolating the biosynthetic genes that encode enzymes that generate such chemical features and deciphering the reaction mechanisms for the enzyme-catalyzed pericyclic reactions.
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Affiliation(s)
- Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
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24
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Microevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungi. Proc Natl Acad Sci U S A 2021; 118:2021683118. [PMID: 34016748 DOI: 10.1073/pnas.2021683118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fungi produce a wealth of pharmacologically bioactive secondary metabolites (SMs) from biosynthetic gene clusters (BGCs). It is common practice for drug discovery efforts to treat species' secondary metabolomes as being well represented by a single or a small number of representative genomes. However, this approach misses the possibility that intraspecific population dynamics, such as adaptation to environmental conditions or local microbiomes, may harbor novel BGCs that contribute to the overall niche breadth of species. Using 94 isolates of Aspergillus flavus, a cosmopolitan model fungus, sampled from seven states in the United States, we dereplicate 7,821 BGCs into 92 unique BGCs. We find that more than 25% of pangenomic BGCs show population-specific patterns of presence/absence or protein divergence. Population-specific BGCs make up most of the accessory-genome BGCs, suggesting that different ecological forces that maintain accessory genomes may be partially mediated by population-specific differences in secondary metabolism. We use ultra-high-performance high-resolution mass spectrometry to confirm that these genetic differences in BGCs also result in chemotypic differences in SM production in different populations, which could mediate ecological interactions and be acted on by selection. Thus, our results suggest a paradigm shift that previously unrealized population-level reservoirs of SM diversity may be of significant evolutionary, ecological, and pharmacological importance. Last, we find that several population-specific BGCs from A. flavus are present in Aspergillus parasiticus and Aspergillus minisclerotigenes and discuss how the microevolutionary patterns we uncover inform macroevolutionary inferences and help to align fungal secondary metabolism with existing evolutionary theory.
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25
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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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26
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Abdallah MF, Audenaert K, Saeger SD, Houbraken J. Revisiting an Aspergillus flavus Strain Isolated from an Egyptian Sugarcane Field in 1930. Microorganisms 2020; 8:E1633. [PMID: 33105779 PMCID: PMC7690594 DOI: 10.3390/microorganisms8111633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 11/17/2022] Open
Abstract
The aflatoxin type B and G producer Aspergillus novoparasiticus was described in 2012 and was firstly reported from sputum, hospital air (Brazil), and soil (Colombia). Later, several survey studies reported the occurrence of this species in different foods and other agricultural commodities from several countries worldwide. This short communication reports on an old fungal strain (CBS 108.30), isolated from Pseudococcus sacchari (grey sugarcane mealybug) from an Egyptian sugarcane field in (or before) 1930. This strain was initially identified as Aspergillus flavus; however, using the latest taxonomy schemes, the strain is, in fact, A. novoparasiticus. These data and previous reports indicate that A. novoparasiticus is strongly associated with sugarcane, and pre-harvest biocontrol approaches with non-toxigenic A. novoparasiticus strains are likely to be more successful than those using non-toxigenic A. flavus strains. Further studies on the association between A. novoparasiticus and Pseudococcus sacchari might shed light on the distribution (and aflatoxin contamination) of this species in sugarcane. Additionally, the interaction between A. novoparasiticus, Pseudococcus sacchari, and sugarcane crop under different scenarios of climate change will be critical in order to get more insight into the host-pathogen interaction and host resistance and propose appropriate prevention strategies to decrease mycotoxin contamination and crop loss due to A. novoparasiticus attack.
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Affiliation(s)
- Mohamed F. Abdallah
- Centre of Excellence in Mycotoxicology and Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, B-9000 Ghent, Belgium;
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium;
- Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, Assiut University, Assiut 71515, Egypt
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium;
| | - Sarah De Saeger
- Centre of Excellence in Mycotoxicology and Public Health, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, B-9000 Ghent, Belgium;
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands;
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27
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Dubrulle G, Picot A, Madec S, Corre E, Pawtowski A, Baroncelli R, Zivy M, Balliau T, Le Floch G, Pensec F. Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis. Microorganisms 2020; 8:microorganisms8101621. [PMID: 33096724 PMCID: PMC7589765 DOI: 10.3390/microorganisms8101621] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/07/2023] Open
Abstract
The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection.
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Affiliation(s)
- Guillaume Dubrulle
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
| | - Adeline Picot
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
| | - Stéphanie Madec
- CNRS, IRD, Ifremer, LEMAR, Université de Brest, F-29280 Plouzané, France;
| | - Erwan Corre
- Station Biologique de Roscoff, FR2424 CNRS Sorbonne Université, Place Georges Teissier, 29680 Roscoff, France;
| | - Audrey Pawtowski
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
| | - Riccardo Baroncelli
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca, Calle del Duero 12, 37185 Villamayor (Salamanca), Spain;
| | - Michel Zivy
- INRAE le Moulon, Plateforme PAPPSO, ferme du Moulon, 91190 Gif-sur-Yvette, France; (M.Z.); (T.B.)
| | - Thierry Balliau
- INRAE le Moulon, Plateforme PAPPSO, ferme du Moulon, 91190 Gif-sur-Yvette, France; (M.Z.); (T.B.)
| | - Gaétan Le Floch
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
| | - Flora Pensec
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
- Correspondence: ; Tel.: +33-(0)298-017-200
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28
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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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29
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Liao L, Zhou Y, Peng T, Guo Y, Zhao Y, Zeng Z. Crystal structure of a S-adenosyl-L-methionine-dependent O-methyltransferase-like enzyme from Aspergillus flavus. Proteins 2020; 89:185-192. [PMID: 32875607 DOI: 10.1002/prot.26004] [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: 12/11/2019] [Revised: 08/05/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
S-adenosyl-L-methionine (SAM)-dependent methyltransferases (MTases) are widely distributed among almost all organisms and often characterized with conserved Rossmann fold, TIM barrel, and D×G×G×G motif. However, some MTases show no methyltransferase activity. In the present study, the crystal structure of LepI, one MTase-like enzyme isolated from A. flavus that catalyzes pericyclic reactions, was investigated to determine its structure-function relationship. The overall structure of LepI in complex with the SAM mimic S-adenosyl-L-homocysteine (SAH) (PDB ID: 6IV7) indicated that LepI is a tetramer in solution. The residues His133, Arg197, Arg295, and Asp296 located near the active site can form hydrogen bonds with the substrate, thus participating in catalytic reactions. The binding of SAH in LepI is almost identical to that in other resolved MTases; however, the location of catalytic residues differs significantly. Phylogenetic trials suggest that LepI proteins share a common ancestor in plants and algae, which may explain the conserved SAM-binding site. However, the accelerated evolution of A. flavus has introduced both functional and structural changes in LepI. More importantly, the residue Arg295, which is unique to LepI, might be a key determinant for the altered enzymatic behavior. Collectively, the differences in the composition of catalytic residues, as well as the unique tetrameric form of LepI, define its unique enzymatic behavior. The present work provides an additional understanding of the structure-function relationship of MTases and MTase-like enzymes.
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Affiliation(s)
- Lijing Liao
- Shandong Provincial Key Laboratory of Microbial Engineering, College of Bioengineering, Qilu University of Technology, Jinan, China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yuanze Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Ting Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yan Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, P. R. China
| | - Zhixiong Zeng
- Shandong Provincial Key Laboratory of Microbial Engineering, College of Bioengineering, Qilu University of Technology, Jinan, China
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30
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Minami A, Ugai T, Ozaki T, Oikawa H. Predicting the chemical space of fungal polyketides by phylogeny-based bioinformatics analysis of polyketide synthase-nonribosomal peptide synthetase and its modification enzymes. Sci Rep 2020; 10:13556. [PMID: 32782278 PMCID: PMC7421883 DOI: 10.1038/s41598-020-70177-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/24/2020] [Indexed: 11/10/2022] Open
Abstract
Fungal polyketide synthase (PKS)–nonribosomal peptide synthetase (NRPS) hybrids are key enzymes for synthesizing structurally diverse hybrid natural products (NPs) with characteristic biological activities. Predicting their chemical space is of particular importance in the field of natural product chemistry. However, the unexplored programming rule of the PKS module has prevented prediction of its chemical structure based on amino acid sequences. Here, we conducted a phylogenetic analysis of 884 PKS–NRPS hybrids and a modification enzyme analysis of the corresponding biosynthetic gene cluster, revealing a hidden relationship between its genealogy and core structures. This unexpected result allowed us to predict 18 biosynthetic gene cluster (BGC) groups producing known carbon skeletons (number of BGCs; 489) and 11 uncharacterized BGC groups (171). The limited number of carbon skeletons suggests that fungi tend to select PK skeletons for survival during their evolution. The possible involvement of a horizontal gene transfer event leading to the diverse distribution of PKS–NRPS genes among fungal species is also proposed. This study provides insight into the chemical space of fungal PKs and the distribution of their biosynthetic gene clusters.
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Affiliation(s)
- Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Takahiro Ugai
- 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
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
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31
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Frawley D, Greco C, Oakley B, Alhussain MM, Fleming AB, Keller NP, Bayram Ö. The tetrameric pheromone module SteC-MkkB-MpkB-SteD regulates asexual sporulation, sclerotia formation and aflatoxin production in Aspergillus flavus. Cell Microbiol 2020; 22:e13192. [PMID: 32068947 PMCID: PMC7202998 DOI: 10.1111/cmi.13192] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/07/2020] [Accepted: 01/26/2020] [Indexed: 11/29/2022]
Abstract
For eukaryotes like fungi to regulate biological responses to environmental stimuli, various signalling cascades are utilized, like the highly conserved mitogen‐activated protein kinase (MAPK) pathways. In the model fungus Aspergillus nidulans, a MAPK pathway known as the pheromone module regulates development and the production of secondary metabolites (SMs). This pathway consists five proteins, the three kinases SteC, MkkB and MpkB, the adaptor SteD and the scaffold HamE. In this study, homologs of these five pheromone module proteins have been identified in the plant and human pathogenic fungus Aspergillus flavus. We have shown that a tetrameric complex consisting of the three kinases and the SteD adaptor is assembled in this species. It was observed that this complex assembles in the cytoplasm and that MpkB translocates into the nucleus. Deletion of steC, mkkB, mpkB or steD results in abolishment of both asexual sporulation and sclerotia production. This complex is required for the positive regulation of aflatoxin production and negative regulation of various SMs, including leporin B and cyclopiazonic acid (CPA), likely via MpkB interactions in the nucleus. These data highlight the conservation of the pheromone module in Aspergillus species, signifying the importance of this pathway in regulating fungal development and secondary metabolism.
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Affiliation(s)
- Dean Frawley
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Claudio Greco
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Berl Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, USA
| | - Mohamed M Alhussain
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Alastair B Fleming
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Özgür Bayram
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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32
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Jamieson CS, Ohashi M, Liu F, Tang Y, Houk KN. The expanding world of biosynthetic pericyclases: cooperation of experiment and theory for discovery. Nat Prod Rep 2019; 36:698-713. [PMID: 30311924 DOI: 10.1039/c8np00075a] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: 2000 to 2018 Pericyclic reactions are a distinct class of reactions that have wide synthetic utility. Before the recent discoveries described in this review, enzyme-catalyzed pericyclic reactions were not widely known to be involved in biosynthesis. This situation is changing rapidly. We define the scope of pericyclic reactions, give a historical account of their discoveries as biosynthetic reactions, and provide evidence that there are many enzymes in nature that catalyze pericyclic reactions. These enzymes, the "pericyclases," are the subject of this review.
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Affiliation(s)
- Cooper S Jamieson
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles 90095, USA.
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33
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Lin X, Yuan S, Chen S, Chen B, Xu H, Liu L, Li H, Gao Z. Heterologous Expression of Ilicicolin H Biosynthetic Gene Cluster and Production of a New Potent Antifungal Reagent, Ilicicolin J. Molecules 2019; 24:molecules24122267. [PMID: 31216742 PMCID: PMC6631495 DOI: 10.3390/molecules24122267] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 11/16/2022] Open
Abstract
Ilicicolin H is a broad-spectrum antifungal agent targeting mitochondrial cytochrome bc1 reductase. Unfortunately, ilicicolin H shows reduced activities in vivo. Here, we report our effort on the identification of ilicicolin H biosynthetic gene cluster (BGC) by genomic sequencing a producing strain, Neonectria sp. DH2, and its heterologous production in Aspergillus nidulans. In addition, a shunt product with similar antifungal activities, ilicicolin J, was uncovered. This effort would provide a base for future combinatorial biosynthesis of ilicicolin H analogues. Bioinformatics analysis suggests that the backbone of ilicicolin H is assembled by a polyketide-nonribosomal peptide synthethase (IliA), and then offloaded with a tetramic acid moiety. Similar to tenellin biosynthesis, the tetramic acid is then converted to pyridone by a putative P450, IliC. The decalin portion is most possibly constructed by a S-adenosyl-l-methionine (SAM)-dependent Diels-Alderase (IliD).
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Affiliation(s)
- Xiaojing Lin
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China.
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Siwen Yuan
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Senhua Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Bin Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Hui Xu
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou 510006, China.
| | - Lan Liu
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
| | - Huixian Li
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 510006, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
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34
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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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Sun Q, Hu Y, Gu Y, Huang J, He J, Luo L, Yang Y, Yin S, Dou C, Wang T, Fu X, He L, Qi S, Zhu X, Yang S, Wei X, Cheng W. Deciphering the regulatory and catalytic mechanisms of an unusual SAM-dependent enzyme. Signal Transduct Target Ther 2019; 4:17. [PMID: 31149354 PMCID: PMC6533283 DOI: 10.1038/s41392-019-0052-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 04/28/2019] [Accepted: 05/07/2019] [Indexed: 02/05/2023] Open
Abstract
S-adenosyl-1-methionine (SAM)-dependent enzymes regulate various disease-related behaviors in all organisms. Recently, the leporin biosynthesis enzyme LepI, a SAM-dependent enzyme, was reported to catalyze pericyclic reactions in leporin biosynthesis; however, the mechanisms underlying LepI activation and catalysis remain unclear. This study aimed to investigate the molecular mechanisms of LepI. Here, we reported crystal structures of LepI bound to SAM/5'-deoxy-5'-(methylthio) adenosine (MTA), S-adenosyl-homocysteine (SAH), and SAM/substrate states. Structural and biochemical analysis revealed that MTA or SAH inhibited the enzyme activities, whereas SAM activated the enzyme. The analysis of the substrate-bound structure of LepI demonstrated that this enzymatic retro-Claisen rearrangement was primarily driven by three critical polar residues His133, Arg197, Arg295 around the active site and assisted by SAM with unclear mechanism. The present studies indicate that the unique mechanisms underlying regulatory and catalysis of the unusual SAM-dependent enzyme LepI, not only strengthening current understanding of the fundamentally biochemical catalysis, but also providing novel insights into the design of SAM-dependent enzyme-specific small molecules.
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Affiliation(s)
- Qiu Sun
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yuehong Hu
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Yijun Gu
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Zhangheng Road 239, Pudong District, Shanghai, 201203 China
| | - Jiangkun Huang
- Department of Medicinal Chemistry, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041 China
| | - Jun He
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Lan Luo
- Department of Medicinal Chemistry, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041 China
| | - Yi Yang
- West China School of Public Health, Sichuan University, Chengdu, 610041 China
| | - Shuo Yin
- West China School of Public Health, Sichuan University, Chengdu, 610041 China
| | - Chao Dou
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Tianqi Wang
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Xianghui Fu
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Ling He
- Department of Medicinal Chemistry, Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, 610041 China
| | - Shiqian Qi
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Xiaofeng Zhu
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Shengyong Yang
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Xiawei Wei
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Center of Infectious Diseases, National Clinical Research Center for Geriatrics and State Key Laboratory of Biotherapy, West China Hospital of Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041 China
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Chang M, Zhou Y, Wang H, Liu Z, Zhang Y, Feng Y. Crystal structure of the multifunctional SAM-dependent enzyme LepI provides insights into its catalytic mechanism. Biochem Biophys Res Commun 2019; 515:255-260. [PMID: 31101338 DOI: 10.1016/j.bbrc.2019.05.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 05/03/2019] [Indexed: 01/13/2023]
Abstract
Pericyclic reactions are among the most powerful synthetic transformations widely applied in the synthesis of multiple regioselective and stereoselective carbon-carbon bonds. LepI is a recently identified S-adenosyl-l-methionine (SAM)-dependent enzyme, which could catalyze dehydration, Diels-Alder reaction, and the retro-Claisen rearrangement reactions. However, the mechanism underlying these reactions by LepI remains elusive. Here we report the structure of LepI in complex with SAM as its co-factor, which adopts a typical class I methyltransferase fold. Docking studies are performed to investigate the binding modes of various substrates/products and provide insights into the catalytic mechanism of the multiple reactions catalyzed by LepI. Our study suggests that the dehydration reaction may start from the deprotonation of the hydroxyl group on the pyridone ring of the substrate by LepIH133, during which R295 and D296 play important roles in substrate binding and stabilizing the reaction intermediate. The stereoselective dehydration is accomplished through the trans-conformer of the leaving alcohol group which is trapped by nearby residues. The pericyclic reactions following dehydration are facilitated by the hydrophobic and hydrophilic interactions in the binding pocket. H133 and R295, two residues not conserved in other methyltransferases, might account for the unique activity of LepI among the SAM-dependent methyltransferase family. Together, this study provides important structural insights into the unique reactions catalyzed by LepI and will shed light on the knowledge of mechanisms of pericyclic reactions.
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Affiliation(s)
- Min Chang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yu Zhou
- National Institute of Biological Sciences, Beijing, No. 7 Science Park Road, Zhongguancun Life Science Park, Beijing, 102206, PR China
| | - Hao Wang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Zihe Liu
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yi Zhang
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China
| | - Yue Feng
- Beijing Key Lab of Bioprocess, Beijing University of Chemical Technology, Beijing, 100029, PR China.
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Uka V, Moore GG, Arroyo-Manzanares N, Nebija D, De Saeger S, Diana Di Mavungu J. Secondary Metabolite Dereplication and Phylogenetic Analysis Identify Various Emerging Mycotoxins and Reveal the High Intra-Species Diversity in Aspergillus flavus. Front Microbiol 2019; 10:667. [PMID: 31024476 PMCID: PMC6461017 DOI: 10.3389/fmicb.2019.00667] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Aspergillus flavus is one of the most important mycotoxigenic species from the genus Aspergillus, due to its ability to synthesize the potent hepatocarcinogen, aflatoxin B1. Moreover, this fungus is capable of producing several other toxic metabolites from the class of indole-tetramates, non-ribosomal peptides, and indole-diterpenoids. Populations of A. flavus are characterized by considerable diversity in terms of morphological, functional and genetic features. Although for many years A. flavus was considered an asexual fungus, researchers have shown evidence that at best these fungi can exhibit a predominantly asexual existence. We now know that A. flavus contains functional genes for mating, uncovering sexuality as potential contributor for its diversification. Based on our results, we reconfirm that A. flavus is a predominant producer of B-type aflatoxins. Moreover, this fungus can decisively produce AFM1 and AFM2. We did not observe any clear relationship between mating-type genes and particular class of metabolites, probably other parameters such as sexual/asexual ratio should be investigated. A dynamic secondary metabolism was found also in strains intended to be used as biocontrol agents. In addition we succeeded to provide mass spectrometry fragmentation spectra for the most important classes of A. flavus metabolites, which will serve as identification cards for future studies. Both, metabolic and phylogenetic analysis proved a high intra-species diversity for A. flavus. These findings contribute to our understanding about the diversity of Aspergillus section Flavi species, raising the necessity for polyphasic approaches (morphological, metabolic, genetic, etc.) when dealing with this type of complex group of species.
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Affiliation(s)
- Valdet Uka
- Center of Excellence in Mycotoxicology and Public Health, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.,Department of Pharmacy, Faculty of Medicine, University of Prishtina, Prishtina, Kosovo†
| | - Geromy G Moore
- Southern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, New Orleans, LA, United States
| | - Natalia Arroyo-Manzanares
- Department of Analytical Chemistry, Faculty of Chemistry, Regional Campus of International Excellence "Campus Mare-Nostrum", University of Murcia, Murcia, Spain
| | - Dashnor Nebija
- Department of Pharmacy, Faculty of Medicine, University of Prishtina, Prishtina, Kosovo†
| | - 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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Frisvad JC, Møller LLH, Larsen TO, Kumar R, Arnau J. Safety of the fungal workhorses of industrial biotechnology: update on the mycotoxin and secondary metabolite potential of Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei. Appl Microbiol Biotechnol 2018; 102:9481-9515. [PMID: 30293194 PMCID: PMC6208954 DOI: 10.1007/s00253-018-9354-1] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 12/11/2022]
Abstract
This review presents an update on the current knowledge of the secondary metabolite potential of the major fungal species used in industrial biotechnology, i.e., Aspergillus niger, Aspergillus oryzae, and Trichoderma reesei. These species have a long history of safe use for enzyme production. Like most microorganisms that exist in a challenging environment in nature, these fungi can produce a large variety and number of secondary metabolites. Many of these compounds present several properties that make them attractive for different industrial and medical applications. A description of all known secondary metabolites produced by these species is presented here. Mycotoxins are a very limited group of secondary metabolites that can be produced by fungi and that pose health hazards in humans and other vertebrates when ingested in small amounts. Some mycotoxins are species-specific. Here, we present scientific basis for (1) the definition of mycotoxins including an update on their toxicity and (2) the clarity on misclassification of species and their mycotoxin potential reported in literature, e.g., A. oryzae has been wrongly reported as an aflatoxin producer, due to misclassification of Aspergillus flavus strains. It is therefore of paramount importance to accurately describe the mycotoxins that can potentially be produced by a fungal species that is to be used as a production organism and to ensure that production strains are not capable of producing mycotoxins during enzyme production. This review is intended as a reference paper for authorities, companies, and researchers dealing with secondary metabolite assessment, risk evaluation for food or feed enzyme production, or considerations on the use of these species as production hosts.
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Affiliation(s)
- Jens C Frisvad
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Søltofts Plads, B. 221, 2800, Kongens Lyngby, Denmark.
| | - Lars L H Møller
- Department of Product Safety, Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Søltofts Plads, B. 221, 2800, Kongens Lyngby, Denmark
| | - Ravi Kumar
- Department of Genomics and Bioinformatics, Novozymes Inc., 1445 Drew Ave., Davis, CA, 95618, USA
| | - José Arnau
- Department of Fungal Strain Technology and Strain Approval Support, Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark
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Pfannenstiel BT, Greco C, Sukowaty AT, Keller NP. The epigenetic reader SntB regulates secondary metabolism, development and global histone modifications in Aspergillus flavus. Fungal Genet Biol 2018; 120:9-18. [PMID: 30130575 PMCID: PMC6215504 DOI: 10.1016/j.fgb.2018.08.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 12/22/2022]
Abstract
Due to the role, both beneficial and harmful, that fungal secondary metabolites play in society, the study of their regulation is of great importance. Genes for any one secondary metabolite are contiguously arranged in a biosynthetic gene cluster (BGC) and subject to regulation through the remodeling of chromatin. Histone modifying enzymes can place or remove post translational modifications (PTM) on histone tails which influences how tight or relaxed the chromatin is, impacting transcription of BGCs. In a recent forward genetic screen, the epigenetic reader SntB was identified as a transcriptional regulator of the sterigmatocystin BGC in A. nidulans, and regulated the related metabolite aflatoxin in A. flavus. In this study we investigate the role of SntB in the plant pathogen A. flavus by analyzing both ΔsntB and overexpression sntB genetic mutants. Deletion of sntB increased global levels of H3K9K14 acetylation and impaired several developmental processes including sclerotia formation, heterokaryon compatibility, secondary metabolite synthesis, and ability to colonize host seeds; in contrast the overexpression strain displayed fewer phenotypes. ΔsntB developmental phenotypes were linked with SntB regulation of NosA, a transcription factor regulating the A. flavus cell fusion cascade.
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Affiliation(s)
| | - Claudio Greco
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrew T Sukowaty
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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Lebar MD, Cary JW, Majumdar R, Carter-Wientjes CH, Mack BM, Wei Q, Uka V, De Saeger S, Diana Di Mavungu J. Identification and functional analysis of the aspergillic acid gene cluster in Aspergillus flavus. Fungal Genet Biol 2018; 116:14-23. [PMID: 29674152 DOI: 10.1016/j.fgb.2018.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 04/04/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
Abstract
Aspergillus flavus can colonize important food staples and produce aflatoxins, a group of toxic and carcinogenic secondary metabolites. Previous in silico analysis of the A. flavus genome revealed 56 gene clusters predicted to be involved in the biosynthesis of secondary metabolites. A. flavus secondary metabolites produced during infection of maize seed are of particular interest, especially with respect to their roles in the biology of the fungus. A predicted nonribosomal peptide synthetase-like (NRPS-like) gene, designated asaC (AFLA_023020), present in the uncharacterized A. flavus secondary metabolite gene cluster 11 was previously shown to be expressed during the earliest stages of maize kernel infection. Cluster 11 is composed of six additional genes encoding a number of putative decorating enzymes as well as a transporter and transcription factor. We generated knock-out mutants of the seven predicted cluster 11 genes. LC-MS analysis of extracts from knockout mutants of these genes showed that they were responsible for the synthesis of the previously characterized antimicrobial mycotoxin aspergillic acid. Extracts of the asaC mutant showed no production of aspergillic acid or its precursors. Knockout of the cluster 11 P450 oxidoreductase afforded a pyrazinone metabolite, the aspergillic acid precursor deoxyaspergillic acid. The formation of hydroxyaspergillic acid was abolished in a desaturase/hydroxylase mutant. The hydroxamic acid functional group in aspergillic acid allows the molecule to bind to iron resulting in the production of a red pigment in A. flavus identified previously as ferriaspergillin. A reduction of aflatoxin B1 and cyclopiazonic acid that correlated with reduced fungal growth was observed in maize kernel infection assays when aspergillic acid biosynthesis in A. flavus is halted.
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Affiliation(s)
- Matthew D Lebar
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA.
| | - Jeffrey W Cary
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA
| | | | | | - Brian M Mack
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA
| | - Qijian Wei
- Southern Regional Research Center, USDA-ARS, New Orleans, LA, USA
| | - Valdet Uka
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sarah De Saeger
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - José Diana Di Mavungu
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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Aspergillus flavus Secondary Metabolites: More than Just Aflatoxins. Food Saf (Tokyo) 2018; 6:7-32. [PMID: 32231944 DOI: 10.14252/foodsafetyfscj.2017024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/09/2018] [Indexed: 11/21/2022] Open
Abstract
Aspergillus flavus is best known for producing the family of potent carcinogenic secondary metabolites known as aflatoxins. However, this opportunistic plant and animal pathogen also produces numerous other secondary metabolites, many of which have also been shown to be toxic. While about forty of these secondary metabolites have been identified from A. flavus cultures, analysis of the genome has predicted the existence of at least 56 secondary metabolite gene clusters. Many of these gene clusters are not expressed during growth of the fungus on standard laboratory media. This presents researchers with a major challenge of devising novel strategies to manipulate the fungus and its genome so as to activate secondary metabolite gene expression and allow identification of associated cluster metabolites. In this review, we discuss the genetic, biochemical and bioinformatic methods that are being used to identify previously uncharacterized secondary metabolite gene clusters and their associated metabolites. It is important to identify as many of these compounds as possible to determine their bioactivity with respect to fungal development, survival, virulence and especially with respect to any potential synergistic toxic effects with aflatoxin.
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Bhatnagar D, Rajasekaran K, Gilbert M, Cary J, Magan N. Advances in molecular and genomic research to safeguard food and feed supply from aflatoxin contamination. WORLD MYCOTOXIN J 2018. [DOI: 10.3920/wmj2017.2283] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Worldwide recognition that aflatoxin contamination of agricultural commodities by the fungus Aspergillus flavus is a global problem has significantly benefitted from global collaboration for understanding the contaminating fungus, as well as for developing and implementing solutions against the contamination. The effort to address this serious food and feed safety issue has led to a detailed understanding of the taxonomy, ecology, physiology, genomics and evolution of A. flavus, as well as strategies to reduce or control pre-harvest aflatoxin contamination, including (1) biological control, using atoxigenic aspergilli, (2) proteomic and genomic analyses for identifying resistance factors in maize as potential breeding markers to enable development of resistant maize lines, and (3) enhancing host-resistance by bioengineering of susceptible crops, such as cotton, maize, peanut and tree nuts. A post-harvest measure to prevent the occurrence of aflatoxin contamination in storage is also an important component for reducing exposure of populations worldwide to aflatoxins in food and feed supplies. The effect of environmental changes on aflatoxin contamination levels has recently become an important aspect for study to anticipate future contamination levels. The ability of A. flavus to produce dozens of secondary metabolites, in addition to aflatoxins, has created a new avenue of research for understanding the role these metabolites play in the survival and biodiversity of this fungus. The understanding of A. flavus, the aflatoxin contamination problem, and control measures to prevent the contamination has become a unique example for an integrated approach to safeguard global food and feed safety.
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Affiliation(s)
- D. Bhatnagar
- US Department of Agriculture, Agricultural Research Service, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - K. Rajasekaran
- US Department of Agriculture, Agricultural Research Service, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - M. Gilbert
- US Department of Agriculture, Agricultural Research Service, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - J.W. Cary
- US Department of Agriculture, Agricultural Research Service, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, USA
| | - N. Magan
- Applied Mycology Group, Cranfield University, MK45 4DT, Cranfield, United Kingdom
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Glöckle A, Gulder TAM. Eine pericyclische Reaktionskaskade in der Leporin-Biosynthese. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anna Glöckle
- Biosystemchemie, Department Chemie und Center for Integrated Protein Science Munich (CiPSM); Technische Universität München (TUM); Lichtenbergstraße 4 85748 Garching Deutschland
| | - Tobias A. M. Gulder
- Biosystemchemie, Department Chemie und Center for Integrated Protein Science Munich (CiPSM); Technische Universität München (TUM); Lichtenbergstraße 4 85748 Garching Deutschland
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Glöckle A, Gulder TAM. A Pericyclic Reaction Cascade in Leporin Biosynthesis. Angew Chem Int Ed Engl 2018; 57:2754-2756. [DOI: 10.1002/anie.201800629] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Anna Glöckle
- Biosystems Chemistry, Department of Chemistry and Center for Integrated Protein Science Munich (CiPSM); Technical University of Munich (TUM); Lichtenbergstraße 4 85748 Garching Germany
| | - Tobias A. M. Gulder
- Biosystems Chemistry, Department of Chemistry and Center for Integrated Protein Science Munich (CiPSM); Technical University of Munich (TUM); Lichtenbergstraße 4 85748 Garching Germany
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Griffiths S, Mesarich CH, Overdijk EJR, Saccomanno B, de Wit PJGM, Collemare J. Down-regulation of cladofulvin biosynthesis is required for biotrophic growth of Cladosporium fulvum on tomato. MOLECULAR PLANT PATHOLOGY 2018; 19:369-380. [PMID: 27997759 PMCID: PMC6638085 DOI: 10.1111/mpp.12527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/01/2016] [Accepted: 12/09/2016] [Indexed: 05/19/2023]
Abstract
Fungal biotrophy is associated with a reduced capacity to produce potentially toxic secondary metabolites (SMs). Yet, the genome of the biotrophic plant pathogen Cladosporium fulvum contains many SM biosynthetic gene clusters, with several related to toxin production. These gene clusters are, however, poorly expressed during the colonization of tomato. The sole detectable SM produced by C. fulvum during in vitro growth is the anthraquinone cladofulvin. Although this pigment is not detected in infected leaves, cladofulvin biosynthetic genes are expressed throughout the pre-penetration phase and during conidiation at the end of the infection cycle, but are repressed during the biotrophic phase of tomato colonization. It has been suggested that the tight regulation of SM gene clusters is required for C. fulvum to behave as a biotrophic pathogen, whilst retaining potential fitness determinants for growth and survival outside its host. To address this hypothesis, we analysed the disease symptoms caused by mutant C. fulvum strains that do not produce or over-produce cladofulvin during the biotrophic growth phase. Non-producers infected tomato in a similar manner to the wild-type, suggesting that cladofulvin is not a virulence factor. In contrast, the cladofulvin over-producers caused strong necrosis and desiccation of tomato leaves, which, in turn, arrested conidiation. Consistent with the role of pigments in survival against abiotic stresses, cladofulvin protects conidia against UV light and low-temperature stress. Overall, this study demonstrates that the repression of cladofulvin production is required for C. fulvum to sustain its biotrophic lifestyle in tomato, whereas its production is important for survival outside its host.
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Affiliation(s)
- Scott Griffiths
- Laboratory of PhytopathologyWageningen UniversityWageningen6708 PBthe Netherlands
| | - Carl H. Mesarich
- Laboratory of PhytopathologyWageningen UniversityWageningen6708 PBthe Netherlands
- Present address:
Laboratory of Molecular Plant PathologyInstitute of Agriculture and Environment, Massey University, Private Bag 11222Palmerston North4442New Zealand
| | - Elysa J. R. Overdijk
- Laboratory of PhytopathologyWageningen UniversityWageningen6708 PBthe Netherlands
- Laboratory of Cell BiologyWageningen UniversityWageningen6708 PBthe Netherlands
| | - Benedetta Saccomanno
- Laboratory of PhytopathologyWageningen UniversityWageningen6708 PBthe Netherlands
| | | | - Jérôme Collemare
- Laboratory of PhytopathologyWageningen UniversityWageningen6708 PBthe Netherlands
- UMR1345 Institut de Recherche en Horticulture et Semences (IRHS)‐INRA, ACO, Université d'AngersBeaucouzé Cedex49071France
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Majumdar R, Lebar M, Mack B, Minocha R, Minocha S, Carter-Wientjes C, Sickler C, Rajasekaran K, Cary JW. The Aspergillus flavus Spermidine Synthase ( spds) Gene, Is Required for Normal Development, Aflatoxin Production, and Pathogenesis During Infection of Maize Kernels. FRONTIERS IN PLANT SCIENCE 2018; 9:317. [PMID: 29616053 PMCID: PMC5870473 DOI: 10.3389/fpls.2018.00317] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/27/2018] [Indexed: 05/10/2023]
Abstract
Aspergillus flavus is a soil-borne saprophyte and an opportunistic pathogen of both humans and plants. This fungus not only causes disease in important food and feed crops such as maize, peanut, cottonseed, and tree nuts but also produces the toxic and carcinogenic secondary metabolites (SMs) known as aflatoxins. Polyamines (PAs) are ubiquitous polycations that influence normal growth, development, and stress responses in living organisms and have been shown to play a significant role in fungal pathogenesis. Biosynthesis of spermidine (Spd) is critical for cell growth as it is required for hypusination-mediated activation of eukaryotic translation initiation factor 5A (eIF5A), and other biochemical functions. The tri-amine Spd is synthesized from the diamine putrescine (Put) by the enzyme spermidine synthase (Spds). Inactivation of spds resulted in a total loss of growth and sporulation in vitro which could be partially restored by addition of exogenous Spd. Complementation of the Δspds mutant with a wild type (WT) A. flavus spds gene restored the WT phenotype. In WT A. flavus, exogenous supply of Spd (in vitro) significantly increased the production of sclerotia and SMs. Infection of maize kernels with the Δspds mutant resulted in a significant reduction in fungal growth, sporulation, and aflatoxin production compared to controls. Quantitative PCR of Δspds mutant infected seeds showed down-regulation of aflatoxin biosynthetic genes in the mutant compared to WT A. flavus infected seeds. Expression analyses of PA metabolism/transport genes during A. flavus-maize interaction showed significant increase in the expression of arginine decarboxylase (Adc) and S-adenosylmethionine decarboxylase (Samdc) genes in the maize host and PA uptake transporters in the fungus. The results presented here demonstrate that Spd biosynthesis is critical for normal development and pathogenesis of A. flavus and pre-treatment of a Δspds mutant with Spd or Spd uptake from the host plant, are insufficient to restore WT levels of pathogenesis and aflatoxin production during seed infection. The data presented here suggest that future studies targeting spermidine biosynthesis in A. flavus, using RNA interference-based host-induced gene silencing approaches, may be an effective strategy to reduce aflatoxin contamination in maize and possibly in other susceptible crops.
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Affiliation(s)
- Rajtilak Majumdar
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Matt Lebar
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Brian Mack
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Rakesh Minocha
- United States Department of Agriculture Forest Service, Northern Research Station, Durham, NH, United States
| | - Subhash Minocha
- Department of Biological Sciences, University of New Hampshire, Durham, NH, United States
| | - Carol Carter-Wientjes
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Christine Sickler
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Jeffrey W. Cary
- Food and Feed Safety Research Unit, United States Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
- *Correspondence: Jeffrey W. Cary,
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Gilbert MK, Medina A, Mack BM, Lebar MD, Rodríguez A, Bhatnagar D, Magan N, Obrian G, Payne G. Carbon Dioxide Mediates the Response to Temperature and Water Activity Levels in Aspergillus flavus during Infection of Maize Kernels. Toxins (Basel) 2017; 10:E5. [PMID: 29271897 PMCID: PMC5793092 DOI: 10.3390/toxins10010005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/17/2017] [Accepted: 12/14/2017] [Indexed: 12/20/2022] Open
Abstract
Aspergillus flavus is a saprophytic fungus that may colonize several important crops, including cotton, maize, peanuts and tree nuts. Concomitant with A. flavus colonization is its potential to secrete mycotoxins, of which the most prominent is aflatoxin. Temperature, water activity (aw) and carbon dioxide (CO₂) are three environmental factors shown to influence the fungus-plant interaction, which are predicted to undergo significant changes in the next century. In this study, we used RNA sequencing to better understand the transcriptomic response of the fungus to aw, temperature, and elevated CO₂ levels. We demonstrate that aflatoxin (AFB₁) production on maize grain was altered by water availability, temperature and CO₂. RNA-Sequencing data indicated that several genes, and in particular those involved in the biosynthesis of secondary metabolites, exhibit different responses to water availability or temperature stress depending on the atmospheric CO₂ content. Other gene categories affected by CO₂ levels alone (350 ppm vs. 1000 ppm at 30 °C/0.99 aw), included amino acid metabolism and folate biosynthesis. Finally, we identified two gene networks significantly influenced by changes in CO₂ levels that contain several genes related to cellular replication and transcription. These results demonstrate that changes in atmospheric CO₂ under climate change scenarios greatly influences the response of A. flavus to water and temperature when colonizing maize grain.
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Affiliation(s)
- Matthew K Gilbert
- USDA/Agricultural Research Service, 1100 Robert E Lee Blvd., New Orleans, LA 70124, USA.
| | - Angel Medina
- Applied Mycology Group, Biotechnology Centre, Cranfield University, Silsoe, Bedford MK45 4DT, UK.
| | - Brian M Mack
- USDA/Agricultural Research Service, 1100 Robert E Lee Blvd., New Orleans, LA 70124, USA.
| | - Matthew D Lebar
- USDA/Agricultural Research Service, 1100 Robert E Lee Blvd., New Orleans, LA 70124, USA.
| | - Alicia Rodríguez
- Food Hygiene and Safety, Meat and Meat products Research Institute, University of Extremadura, 10003 Caceres, Spain.
| | - Deepak Bhatnagar
- USDA/Agricultural Research Service, 1100 Robert E Lee Blvd., New Orleans, LA 70124, USA.
| | - Naresh Magan
- Applied Mycology Group, Biotechnology Centre, Cranfield University, Silsoe, Bedford MK45 4DT, UK.
| | - Gregory Obrian
- Department of Entomology and Plant Pathology, 223 Partners III, P.O. Box 7567, North Carolina State University, Raleigh, NC 27695, USA.
| | - Gary Payne
- Department of Entomology and Plant Pathology, 223 Partners III, P.O. Box 7567, North Carolina State University, Raleigh, NC 27695, USA.
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Majumdar R, Rajasekaran K, Sickler C, Lebar M, Musungu BM, Fakhoury AM, Payne GA, Geisler M, Carter-Wientjes C, Wei Q, Bhatnagar D, Cary JW. The Pathogenesis-Related Maize Seed ( PRms) Gene Plays a Role in Resistance to Aspergillus flavus Infection and Aflatoxin Contamination. FRONTIERS IN PLANT SCIENCE 2017; 8:1758. [PMID: 29089952 PMCID: PMC5651032 DOI: 10.3389/fpls.2017.01758] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/25/2017] [Indexed: 05/26/2023]
Abstract
Aspergillus flavus is an opportunistic plant pathogen that colonizes and produces the toxic and carcinogenic secondary metabolites, aflatoxins, in oil-rich crops such as maize (Zea mays ssp. mays L.). Pathogenesis-related (PR) proteins serve as an important defense mechanism against invading pathogens by conferring systemic acquired resistance in plants. Among these, production of the PR maize seed protein, ZmPRms (AC205274.3_FG001), has been speculated to be involved in resistance to infection by A. flavus and other pathogens. To better understand the relative contribution of ZmPRms to A. flavus resistance and aflatoxin production, a seed-specific RNA interference (RNAi)-based gene silencing approach was used to develop transgenic maize lines expressing hairpin RNAs to target ZmPRms. Downregulation of ZmPRms in transgenic kernels resulted in a ∼250-350% increase in A. flavus infection accompanied by a ∼4.5-7.5-fold higher accumulation of aflatoxins than control plants. Gene co-expression network analysis of RNA-seq data during the A. flavus-maize interaction identified ZmPRms as a network hub possibly responsible for regulating several downstream candidate genes associated with disease resistance and other biochemical functions. Expression analysis of these candidate genes in the ZmPRms-RNAi lines demonstrated downregulation (vs. control) of a majority of these ZmPRms-regulated genes during A. flavus infection. These results are consistent with a key role of ZmPRms in resistance to A. flavus infection and aflatoxin accumulation in maize kernels.
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Affiliation(s)
- Rajtilak Majumdar
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Christine Sickler
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Matthew Lebar
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Bryan M. Musungu
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
- Warm Water Aquaculture Unit, United States Department of Agriculture – Agricultural Research Service, Stoneville, MS, United States
| | - Ahmad M. Fakhoury
- Department of Plant, Soil and Agriculture Systems, Southern Illinois University, Carbondale, IL, United States
| | - Gary A. Payne
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Matt Geisler
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
| | - Carol Carter-Wientjes
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Qijian Wei
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Deepak Bhatnagar
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
| | - Jeffrey W. Cary
- Food and Feed Safety Research Unit, United States Department of Agriculture – Agricultural Research Service, Southern Regional Research Center, New Orleans, LA, United States
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SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis. Nature 2017; 549:502-506. [PMID: 28902839 PMCID: PMC5679075 DOI: 10.1038/nature23882] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/18/2017] [Indexed: 12/19/2022]
Abstract
Pericyclic reactions are among the most powerful synthetic transformations to make multiple regioselective and stereoselective carbon-carbon bonds1. These reactions have been widely applied for the synthesis of biologically active complex natural products containing contiguous stereogenic carbon centers2–6. Despite the prominence of pericyclic reactions in total synthesis, only three naturally existing enzymatic examples, intramolecular Diels-Alder (IMDA) reaction7, Cope8 and Claisen rearrangements9, have been characterized. Here, we report the discovery of a S-adenosyl-L-methionine (SAM) dependent enzyme LepI that can catalyse stereoselective dehydration, bifurcating IMDA/hetero-DA (HDA) reactions via an ambimodal transition state, and a [3,3]-sigmatropic retro-Claisen rearrangement leading to the formation of dihydopyran core in the fungal natural product leporin10. Combined in vitro enzymatic characterization and computational studies provide evidence and mechanistic insight about how the O-methyltransferase-like protein LepI regulates the bifurcating biosynthetic reaction pathways (“direct” HDA and “byproduct recycle” IMDA/retro-Claisen reaction pathways) by utilizing SAM as the cofactor in order to converge to the desired biosynthetic end product. This work highlights that LepI is the first example of an enzyme catalysing a (SAM-dependent) retro-Claisen rearrangement. We suggest that more pericyclic biosynthetic enzymatic transformations are yet to be discovered in the intriguing enzyme toolboxes in Nature11, and propose an ever expanding role of the versatile cofactor SAM in enzyme catalysis.
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Abstract
Oxidative cyclizations are important transformations that occur widely during natural product biosynthesis. The transformations from acyclic precursors to cyclized products can afford morphed scaffolds, structural rigidity, and biological activities. Some of the most dramatic structural alterations in natural product biosynthesis occur through oxidative cyclization. In this Review, we examine the different strategies used by nature to create new intra(inter)molecular bonds via redox chemistry. This Review will cover both oxidation- and reduction-enabled cyclization mechanisms, with an emphasis on the former. Radical cyclizations catalyzed by P450, nonheme iron, α-KG-dependent oxygenases, and radical SAM enzymes are discussed to illustrate the use of molecular oxygen and S-adenosylmethionine to forge new bonds at unactivated sites via one-electron manifolds. Nonradical cyclizations catalyzed by flavin-dependent monooxygenases and NAD(P)H-dependent reductases are covered to show the use of two-electron manifolds in initiating cyclization reactions. The oxidative installations of epoxides and halogens into acyclic scaffolds to drive subsequent cyclizations are separately discussed as examples of "disappearing" reactive handles. Last, oxidative rearrangement of rings systems, including contractions and expansions, will be covered.
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Affiliation(s)
- Man-Cheng Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Yi Zou
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christopher T. Walsh
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, 443 Via Ortega, Stanford, CA 94305
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, 420 Westwood Plaza, Los Angeles, CA 90095, USA
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