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Prescott TAK, Hill R, Mas-Claret E, Gaya E, Burns E. Fungal Drug Discovery for Chronic Disease: History, New Discoveries and New Approaches. Biomolecules 2023; 13:986. [PMID: 37371566 DOI: 10.3390/biom13060986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Fungal-derived drugs include some of the most important medicines ever discovered, and have proved pivotal in treating chronic diseases. Not only have they saved millions of lives, but they have in some cases changed perceptions of what is medically possible. However, now the low-hanging fruit have been discovered it has become much harder to make the kind of discoveries that have characterised past eras of fungal drug discovery. This may be about to change with new commercial players entering the market aiming to apply novel genomic tools to streamline the discovery process. This review examines the discovery history of approved fungal-derived drugs, and those currently in clinical trials for chronic diseases. For key molecules, we discuss their possible ecological functions in nature and how this relates to their use in human medicine. We show how the conservation of drug receptors between fungi and humans means that metabolites intended to inhibit competitor fungi often interact with human drug receptors, sometimes with unintended benefits. We also plot the distribution of drugs, antimicrobial compounds and psychoactive mushrooms onto a fungal tree and compare their distribution to those of all fungal metabolites. Finally, we examine the phenomenon of self-resistance and how this can be used to help predict metabolite mechanism of action and aid the drug discovery process.
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Affiliation(s)
| | - Rowena Hill
- Earlham Institute, Norwich NR4 7UZ, Norfolk, UK
| | | | - Ester Gaya
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, Surrey, UK
| | - Edie Burns
- Royal Botanic Gardens, Kew, Richmond TW9 3AB, Surrey, UK
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2
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Ammar HA, Ezzat SM, Elshourbagi E, Elshahat H. Titer improvement of mycophenolic acid in the novel producer strain Penicillium arizonense and expression analysis of its biosynthetic genes. BMC Microbiol 2023; 23:135. [PMID: 37198535 DOI: 10.1186/s12866-023-02884-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
Mycophenolic acid (MPA) is the active ingredient in the most important immunosuppressive pharmaceuticals. It has antifungal, antibacterial, antiviral, anti-psoriasis, and antitumor activities. Therefore, its overproduction in addition to gene expression analysis was our main target. Through this study, we isolated a novel potent mycophenolic acid (MPA) producer strain of the genus Penicillium from the refrigerated Mozzarella cheese and it was identified with the molecular marker ITS and benA genes as P. arizonenseHEWt1. Three MPA overproducer mutants were isolated by exposing the wild type to different doses of gamma-rays, and the fermentation conditions for the highest production of MPA were optimized. The results indicated that MPA amounts produced by the mutants MT1, MT2, and MT3 were increased by 2.1, 1.7, and 1.6-fold, respectively, compared with the wild-type. The growth of both mutant and wild-type strains on PD broth, adjusted to pH 6 and incubated at 25 °C for 15 d, were the best conditions for maximum production of MPA. In a silico study, five orthologs genes of MPA biosynthesizing gene clusters in P. brevicompactum were predicted from the genome of P. arizonense. Sequencing and bioinformatic analyses proved the presence of five putative genes namely mpaA, mpaC, mpaF, mpaG, and mpaH in the P. arizonense HEWt1 genome. Gene expression analysis by qRT-PCR indicated an increase in the transcription value of all annotated genes in the three mutants over the wild type. A highly significant increase in the gene expression of mpaC, mpaF, and mpaH was observed in P. arizonense-MT1 compared with wild-type. These results confirmed the positive correlation of these genes in MPA biosynthesis and are the first report regarding the production of MPA by P. arizonense.Kew word.Mycophenolic acid, Penicillium arizonense, mutagenesis, gene expression.
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Affiliation(s)
- Hala A Ammar
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt.
| | - Saeid M Ezzat
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | | | - Hind Elshahat
- Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
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3
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Chávez R, Vaca I, García-Estrada C. Secondary Metabolites Produced by the Blue-Cheese Ripening Mold Penicillium roqueforti; Biosynthesis and Regulation Mechanisms. J Fungi (Basel) 2023; 9:jof9040459. [PMID: 37108913 PMCID: PMC10144355 DOI: 10.3390/jof9040459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/29/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Filamentous fungi are an important source of natural products. The mold Penicillium roqueforti, which is well-known for being responsible for the characteristic texture, blue-green spots, and aroma of the so-called blue-veined cheeses (French Bleu, Roquefort, Gorgonzola, Stilton, Cabrales, and Valdeón, among others), is able to synthesize different secondary metabolites, including andrastins and mycophenolic acid, as well as several mycotoxins, such as Roquefortines C and D, PR-toxin and eremofortins, Isofumigaclavines A and B, festuclavine, and Annullatins D and F. This review provides a detailed description of the biosynthetic gene clusters and pathways of the main secondary metabolites produced by P. roqueforti, as well as an overview of the regulatory mechanisms controlling secondary metabolism in this filamentous fungus.
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Affiliation(s)
- Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), Santiago 9170022, Chile
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Campus de Vegazana, Universidad de León, 24071 León, Spain
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4
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Jenkinson CB, Podgorny AR, Zhong C, Oakley BR. Computer-aided, resistance gene-guided genome mining for proteasome and HMG-CoA reductase inhibitors. J Ind Microbiol Biotechnol 2023; 50:kuad045. [PMID: 38061800 PMCID: PMC10734572 DOI: 10.1093/jimb/kuad045] [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: 06/09/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023]
Abstract
Secondary metabolites (SMs) are biologically active small molecules, many of which are medically valuable. Fungal genomes contain vast numbers of SM biosynthetic gene clusters (BGCs) with unknown products, suggesting that huge numbers of valuable SMs remain to be discovered. It is challenging, however, to identify SM BGCs, among the millions present in fungi, that produce useful compounds. One solution is resistance gene-guided genome mining, which takes advantage of the fact that some BGCs contain a gene encoding a resistant version of the protein targeted by the compound produced by the BGC. The bioinformatic signature of such BGCs is that they contain an allele of an essential gene with no SM biosynthetic function, and there is a second allele elsewhere in the genome. We have developed a computer-assisted approach to resistance gene-guided genome mining that allows users to query large databases for BGCs that putatively make compounds that have targets of therapeutic interest. Working with the MycoCosm genome database, we have applied this approach to look for SM BGCs that target the proteasome β6 subunit, the target of the proteasome inhibitor fellutamide B, or HMG-CoA reductase, the target of cholesterol reducing therapeutics such as lovastatin. Our approach proved effective, finding known fellutamide and lovastatin BGCs as well as fellutamide- and lovastatin-related BGCs with variations in the SM genes that suggest they may produce structural variants of fellutamides and lovastatin. Gratifyingly, we also found BGCs that are not closely related to lovastatin BGCs but putatively produce novel HMG-CoA reductase inhibitors. ONE-SENTENCE SUMMARY A new computer-assisted approach to resistance gene-directed genome mining is reported along with its use to identify fungal biosynthetic gene clusters that putatively produce proteasome and HMG-CoA reductase inhibitors.
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Affiliation(s)
- Cory B Jenkinson
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
| | - Adam R Podgorny
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Cuncong Zhong
- Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS 66045,USA
| | - Berl R Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045,USA
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5
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Hoffmann CV, Nevez G, Moal MC, Quinio D, Le Nan N, Papon N, Bouchara JP, Le Meur Y, Le Gal S. Selection of Pneumocystis jirovecii Inosine 5'-Monophosphate Dehydrogenase Mutants in Solid Organ Transplant Recipients: Implication of Mycophenolic Acid. J Fungi (Basel) 2021; 7:jof7100849. [PMID: 34682270 PMCID: PMC8537117 DOI: 10.3390/jof7100849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Mycophenolic acid (MPA) targets the inosine 5'-monophosphate dehydrogenase (IMPDH) of human lymphocytes. It is widely used as an immunosuppressant to prevent rejection in solid organ transplant (SOT) recipients who, incidentally, are at risk for Pneumocystis pneumonia (PCP). We hypothesized that MPA exerts selective pressure on P. jirovecii microorganisms considering its in vitro antifungal activity on other fungi. Thus, we analysed impdh gene in P. jirovecii isolates from SOT recipients. P. jirovecii specimens from 26 patients diagnosed with PCP from 2010 to 2020 were retrospectively examined: 10 SOT recipients treated with MPA and 16 non-SOT patients without prior exposure to MPA. The P. jirovecii impdh gene was amplified and sequenced. Nucleotide sequences were aligned with the reference sequences retrieved from available P. jirovecii whole genomes. The deduced IMPDH protein sequences were aligned with available IMPDH proteins from Pneumocystis spp. and other fungal species known to be in vitro sensitive or resistant to MPA. A total of nine SNPs was identified. One SNP (G1020A) that results in an Ala261Thr substitution was identified in all SOT recipients and in none of the non-SOT patients. Considering that IMPDHs of other fungi, resistant to MPA, harbour Thr (or Ser) at the analogous position, the Ala261Thr mutation observed in MPA-treated patients was considered to represent the signature of P. jirovecii exposure to MPA. These results suggest that MPA may be involved in the selection of specific P. jirovecii strains that circulate in the SOT recipient population.
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Affiliation(s)
- Claire V. Hoffmann
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Gilles Nevez
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
- Correspondence: (G.N.); (S.L.G.); Tel.: +33-(0)-2-98-14-51-02 (G.N. & S.L.G.); Fax: +33-(0)-2-98-14-51-49 (G.N. & S.L.G.)
| | - Marie-Christine Moal
- Département de Néphrologie, CHU de Brest, 29609 Brest, France; (M.-C.M.); (Y.L.M.)
| | - Dorothée Quinio
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Nathan Le Nan
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
| | - Nicolas Papon
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université de Brest, Université d’Angers, 49035 Angers, France; (N.P.); (J.-P.B.)
| | - Jean-Philippe Bouchara
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université de Brest, Université d’Angers, 49035 Angers, France; (N.P.); (J.-P.B.)
| | - Yannick Le Meur
- Département de Néphrologie, CHU de Brest, 29609 Brest, France; (M.-C.M.); (Y.L.M.)
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, Inserm, Labex IGO, 20609 Brest, France
| | - Solène Le Gal
- Laboratoire de Parasitologie et Mycologie, Hôpital de La Cavale Blanche, CHU de Brest, 29609 Brest, France; (C.V.H.); (D.Q.)
- Groupe d’Etude des Interactions Hôte-Pathogène (GEIHP), Université d’Angers, Université de Brest, 29238 Brest, France;
- Correspondence: (G.N.); (S.L.G.); Tel.: +33-(0)-2-98-14-51-02 (G.N. & S.L.G.); Fax: +33-(0)-2-98-14-51-49 (G.N. & S.L.G.)
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6
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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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7
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David F, Davis AM, Gossing M, Hayes MA, Romero E, Scott LH, Wigglesworth MJ. A Perspective on Synthetic Biology in Drug Discovery and Development-Current Impact and Future Opportunities. SLAS DISCOVERY 2021; 26:581-603. [PMID: 33834873 DOI: 10.1177/24725552211000669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The global impact of synthetic biology has been accelerating, because of the plummeting cost of DNA synthesis, advances in genetic engineering, growing understanding of genome organization, and explosion in data science. However, much of the discipline's application in the pharmaceutical industry remains enigmatic. In this review, we highlight recent examples of the impact of synthetic biology on target validation, assay development, hit finding, lead optimization, and chemical synthesis, through to the development of cellular therapeutics. We also highlight the availability of tools and technologies driving the discipline. Synthetic biology is certainly impacting all stages of drug discovery and development, and the recognition of the discipline's contribution can further enhance the opportunities for the drug discovery and development value chain.
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Affiliation(s)
- Florian David
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew M Davis
- Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Michael Gossing
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Martin A Hayes
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elvira Romero
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Louis H Scott
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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8
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Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. Metabolites 2021; 11:metabo11010048. [PMID: 33445429 PMCID: PMC7827101 DOI: 10.3390/metabo11010048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 01/28/2023] Open
Abstract
The UniProt Knowledgebase UniProtKB is a comprehensive, high-quality, and freely accessible resource of protein sequences and functional annotation that covers genomes and proteomes from tens of thousands of taxa, including a broad range of plants and microorganisms producing natural products of medical, nutritional, and agronomical interest. Here we describe work that enhances the utility of UniProtKB as a support for both the study of natural products and for their discovery. The foundation of this work is an improved representation of natural product metabolism in UniProtKB using Rhea, an expert-curated knowledgebase of biochemical reactions, that is built on the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Knowledge of natural products and precursors is captured in ChEBI, enzyme-catalyzed reactions in Rhea, and enzymes in UniProtKB/Swiss-Prot, thereby linking chemical structure data directly to protein knowledge. We provide a practical demonstration of how users can search UniProtKB for protein knowledge relevant to natural products through interactive or programmatic queries using metabolite names and synonyms, chemical identifiers, chemical classes, and chemical structures and show how to federate UniProtKB with other data and knowledge resources and tools using semantic web technologies such as RDF and SPARQL. All UniProtKB data are freely available for download in a broad range of formats for users to further mine or exploit as an annotation source, to enrich other natural product datasets and databases.
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9
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Freedman R, Yu R, Sarkis AW, Hedstrom L. A structural determinant of mycophenolic acid resistance in eukaryotic inosine 5'-monophosphate dehydrogenases. Protein Sci 2019; 29:686-694. [PMID: 31675145 DOI: 10.1002/pro.3766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 01/21/2023]
Abstract
Mycophenolic acid (MPA) is a potent natural product inhibitor of fungal and other eukaryotic inosine 5'-monophosphate dehydrogenases (IMPDHs) originally isolated from spoiled corn silage. MPA is produced by the filamentous fungi Penicillium brevicompactum, which contains two IMPDHs, PbIMPDHA and PbIMPDHB, both of which are MPA-resistant. The MPA binding sites of these enzymes are identical to MPA-sensitive IMPDHs, so the structural determinants of resistance are unknown. Here we show that a single residue, Ser267, accounts for the MPA resistance of PbIMPDHA. Substitution of Ser267 with Ala, the residue most commonly found in this position in eukaryotic IMPDHs, makes PbIMPDHA sensitive to MPA. Conversely, Aspergillus nidulans IMPDH becomes MPA-resistant when the analogous Ala residue is substituted with Ser. These substitutions have little effect on the catalytic cycles of either enzyme, suggesting the fitness costs are negligible despite the strong conservation of Ala at this position. Intriguingly, while only 1% of fungal IMPDHs contain Ser or Thr at position 267, these residues are found in the IMPDHs from several Aspergillus species that grow at the low temperatures also favored by Penicillium. Perhaps Ser/Thr267 is an evolutionary signature of MPA exposure.
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Affiliation(s)
- Rebecca Freedman
- Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts
| | - Runhan Yu
- Department of Chemistry, Brandeis University, Waltham, Massachusetts
| | - Alexander W Sarkis
- Graduate Program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts
| | - Lizbeth Hedstrom
- Department of Chemistry, Brandeis University, Waltham, Massachusetts.,Department of Biology, Brandeis University, Waltham, Massachusetts
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10
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Chen X, Wang L, Zhang J, Jiang T, Hu C, Li D, Zou Y. Immunosuppressant mycophenolic acid biosynthesis employs a new globin-like enzyme for prenyl side chain cleavage. Acta Pharm Sin B 2019; 9:1253-1258. [PMID: 31867170 PMCID: PMC6900556 DOI: 10.1016/j.apsb.2019.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/16/2023] Open
Abstract
Mycophenolic acid (MPA, 1) and its derivatives are first-line immunosuppressants used in organ transplantation and for treating autoimmune diseases. Despite chemical synthetic achievements, the biosynthetic formation of a seven-carbon carboxylic acid pharmacophore side chain of 1, especially the processes involving the cleavage of the prenyl side chain between DHMP (4) and DMMPA (5), remains unknown. In this work, we identified a membrane-bound prenyltransferase, PgMpaA, that transfers FPP to 4 to yield FDHMP (6). Compound 6 undergoes the first cleavage step via a new globin-like enzyme PgMpaB to form a cryptic intermediate 12. Heterologous expression of PgMpa genes in Aspergillus nidulans demonstrates that the second cleavage step (from 12 to 5) of 1 is a PgMpa cluster-independent process in vivo. Our results, especially the discovery of the broad tolerance of substrates recognized by PgMpaB, set up a strategy for the formation of "pseudo-isopentenyl" natural products using fungal globin-like enzymes.
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11
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Ogawara H. Comparison of Antibiotic Resistance Mechanisms in Antibiotic-Producing and Pathogenic Bacteria. Molecules 2019; 24:E3430. [PMID: 31546630 PMCID: PMC6804068 DOI: 10.3390/molecules24193430] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance poses a tremendous threat to human health. To overcome this problem, it is essential to know the mechanism of antibiotic resistance in antibiotic-producing and pathogenic bacteria. This paper deals with this problem from four points of view. First, the antibiotic resistance genes in producers are discussed related to their biosynthesis. Most resistance genes are present within the biosynthetic gene clusters, but some genes such as paromomycin acetyltransferases are located far outside the gene cluster. Second, when the antibiotic resistance genes in pathogens are compared with those in the producers, resistance mechanisms have dependency on antibiotic classes, and, in addition, new types of resistance mechanisms such as Eis aminoglycoside acetyltransferase and self-sacrifice proteins in enediyne antibiotics emerge in pathogens. Third, the relationships of the resistance genes between producers and pathogens are reevaluated at their amino acid sequence as well as nucleotide sequence levels. Pathogenic bacteria possess other resistance mechanisms than those in antibiotic producers. In addition, resistance mechanisms are little different between early stage of antibiotic use and the present time, e.g., β-lactam resistance in Staphylococcus aureus. Lastly, guanine + cytosine (GC) barrier in gene transfer to pathogenic bacteria is considered. Now, the resistance genes constitute resistome composed of complicated mixture from divergent environments.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, 33-9, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, 522-1, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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12
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Wencewicz TA. Crossroads of Antibiotic Resistance and Biosynthesis. J Mol Biol 2019; 431:3370-3399. [PMID: 31288031 DOI: 10.1016/j.jmb.2019.06.033] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022]
Abstract
The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic producers are an integral part of the growing antibiotic resistance threat. The origins of clinically relevant antibiotic resistance genes found in human pathogens have been traced to ancient microbial producers of antibiotics in natural environments. Widespread and frequent antibiotic use amplifies environmental pools of antibiotic resistance genes and increases the likelihood for the selection of a resistance event in human pathogens. This perspective will provide an overview of the origins of antibiotic resistance to highlight the crossroads of antibiotic biosynthesis and producer self-protection that result in clinically relevant resistance mechanisms. Some case studies of synergistic antibiotic combinations, adjuvants, and hybrid antibiotics will also be presented to show how native antibiotic producers manage the emergence of antibiotic resistance.
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Affiliation(s)
- Timothy A Wencewicz
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, USA.
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13
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Abstract
Mycophenolic acid (MPA) from filamentous fungi is the first natural product antibiotic to be isolated and crystallized, and a first-line immunosuppressive drug for organ transplantations and autoimmune diseases. However, some key biosynthetic mechanisms of such an old and important molecule have remained unclear. Here, we elucidate the MPA biosynthetic pathway that features both compartmentalized enzymatic steps and unique cooperation between biosynthetic and β-oxidation catabolism machineries based on targeted gene inactivation, feeding experiments in heterologous expression hosts, enzyme functional characterization and kinetic analysis, and microscopic observation of protein subcellular localization. Besides identification of the oxygenase MpaB' as the long-sought key enzyme responsible for the oxidative cleavage of the farnesyl side chain, we reveal the intriguing pattern of compartmentalization for the MPA biosynthetic enzymes, including the cytosolic polyketide synthase MpaC' and O-methyltransferase MpaG', the Golgi apparatus-associated prenyltransferase MpaA', the endoplasmic reticulum-bound oxygenase MpaB' and P450-hydrolase fusion enzyme MpaDE', and the peroxisomal acyl-coenzyme A (CoA) hydrolase MpaH'. The whole pathway is elegantly comediated by these compartmentalized enzymes, together with the peroxisomal β-oxidation machinery. Beyond characterizing the remaining outstanding steps of the MPA biosynthetic steps, our study highlights the importance of considering subcellular contexts and the broader cellular metabolism in natural product biosynthesis.
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Resistance Gene-Directed Genome Mining of 50 Aspergillus Species. mSystems 2019; 4:mSystems00085-19. [PMID: 31098395 PMCID: PMC6517689 DOI: 10.1128/msystems.00085-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 04/13/2019] [Indexed: 11/22/2022] Open
Abstract
Species belonging to the Aspergillus genus are known to produce a large number of secondary metabolites; some of these compounds are used as pharmaceuticals, such as penicillin, cyclosporine, and statin. With whole-genome sequencing, it became apparent that the genetic potential for secondary metabolite production is much larger than expected. As an increasing number of species are whole-genome sequenced, thousands of secondary metabolite genes are predicted, and the question of how to selectively identify novel bioactive compounds from this information arises. To address this question, we have created a pipeline to predict genes involved in the production of bioactive compounds based on a resistance gene hypothesis approach. Fungal secondary metabolites are a rich source of valuable natural products, and genome sequencing has revealed a proliferation of predicted biosynthetic gene clusters in the genomes. However, it is currently an unfeasible task to characterize all biosynthetic gene clusters and to identify possible uses of the compounds. Therefore, a rational approach is needed to identify a short list of gene clusters responsible for producing valuable compounds. To this end, several bioactive clusters include a resistance gene, which is a paralog of the target gene inhibited by the compound. This mechanism can be used to identify these clusters. We have developed the FRIGG (fungal resistance gene-directed genome mining) pipeline for identifying this type of biosynthetic gene cluster based on homology patterns of the cluster genes. In this work, the FRIGG pipeline was run using 51 Aspergillus and Penicillium genomes, identifying 72 unique families of putative resistance genes. The pipeline also identified the previously characterized resistance gene inpE from the fellutamide B cluster, thereby validating the approach. We have successfully developed an approach to identify putative valuable bioactive clusters based on a specific resistance mechanism. This approach will be highly useful as an ever-increasing amount of genomic data becomes available; the art of identifying and selecting the right clusters producing novel valuable compounds will only become more crucial. IMPORTANCE Species belonging to the Aspergillus genus are known to produce a large number of secondary metabolites; some of these compounds are used as pharmaceuticals, such as penicillin, cyclosporine, and statin. With whole-genome sequencing, it became apparent that the genetic potential for secondary metabolite production is much larger than expected. As an increasing number of species are whole-genome sequenced, thousands of secondary metabolite genes are predicted, and the question of how to selectively identify novel bioactive compounds from this information arises. To address this question, we have created a pipeline to predict genes involved in the production of bioactive compounds based on a resistance gene hypothesis approach.
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15
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O'Neill EC, Schorn M, Larson CB, Millán-Aguiñaga N. Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining. Crit Rev Microbiol 2019; 45:255-277. [PMID: 30985219 DOI: 10.1080/1040841x.2019.1590307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Intense competition between microbes in the environment has directed the evolution of antibiotic production in bacteria. Humans have harnessed these natural molecules for medicinal purposes, magnifying them from environmental concentrations to industrial scale. This increased exposure to antibiotics has amplified antibiotic resistance across bacteria, spurring a global antimicrobial crisis and a search for antibiotics with new modes of action. Genetic insights into these antibiotic-producing microbes reveal that they have evolved several resistance strategies to avoid self-toxicity, including product modification, substrate transport and binding, and target duplication or modification. Of these mechanisms, target duplication or modification will be highlighted in this review, as it uniquely links an antibiotic to its mode of action. We will further discuss and propose a strategy to mine microbial genomes for these genes and their associated biosynthetic gene clusters to discover novel antibiotics using target directed genome mining.
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Affiliation(s)
- Ellis C O'Neill
- a Department of Plant Sciences, University of Oxford , Oxford , Oxfordshire , UK
| | - Michelle Schorn
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Charles B Larson
- b Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California , San Diego , CA , USA
| | - Natalie Millán-Aguiñaga
- c Universidad Autónoma de Baja California, Facultad de Ciencias Marinas , Ensenada , Baja California , México
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16
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Tran PN, Yen MR, Chiang CY, Lin HC, Chen PY. Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi. Appl Microbiol Biotechnol 2019; 103:3277-3287. [PMID: 30859257 PMCID: PMC6449301 DOI: 10.1007/s00253-019-09708-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/17/2019] [Accepted: 02/18/2019] [Indexed: 11/23/2022]
Abstract
Secondary metabolites (SM) produced by fungi and bacteria have long been of exceptional interest owing to their unique biomedical ramifications. The traditional discovery of new natural products that was mainly driven by bioactivity screening has now experienced a fresh new approach in the form of genome mining. Several bioinformatics tools have been continuously developed to detect potential biosynthetic gene clusters (BGCs) that are responsible for the production of SM. Although the principles underlying the computation of these tools have been discussed, the biological background is left underrated and ambiguous. In this review, we emphasize the biological hypotheses in BGC formation driven from the observations across genomes in bacteria and fungi, and provide a comprehensive list of updated algorithms/tools exclusively for BGC detection. Our review points to a direction that the biological hypotheses should be systematically incorporated into the BGC prediction and assist the prioritization of candidate BGC.
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Affiliation(s)
- Phuong Nguyen Tran
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan
| | - Chen-Yu Chiang
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan
| | - Hsiao-Ching Lin
- Institute of Biological Chemistry, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan.
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan.
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17
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Abstract
One of the exciting movements in microbial sciences has been a refocusing and revitalization of efforts to mine the fungal secondary metabolome. The magnitude of biosynthetic gene clusters (BGCs) in a single filamentous fungal genome combined with the historic number of sequenced genomes suggests that the secondary metabolite wealth of filamentous fungi is largely untapped. Mining algorithms and scalable expression platforms have greatly expanded access to the chemical repertoire of fungal-derived secondary metabolites. In this Review, I discuss new insights into the transcriptional and epigenetic regulation of BGCs and the ecological roles of fungal secondary metabolites in warfare, defence and development. I also explore avenues for the identification of new fungal metabolites and the challenges in harvesting fungal-derived secondary metabolites.
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18
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Tang M, Zou Y, Yee D, Tang Y. Identification of the Pyranonigrin A Biosynthetic Gene Cluster by Genome Mining in Penicillium thymicola IBT 5891. AIChE J 2018; 64:4182-4186. [PMID: 31588145 DOI: 10.1002/aic.16324] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Man‐Cheng Tang
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA 90095
| | - Yi Zou
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA 90095
| | - Danielle Yee
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA 90095
| | - Yi Tang
- Dept. of Chemical and Biomolecular EngineeringUniversity of CaliforniaLos AngelesCA 90095
- Dept. of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesCA 90095
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19
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Ogawara H. Comparison of Strategies to Overcome Drug Resistance: Learning from Various Kingdoms. Molecules 2018; 23:E1476. [PMID: 29912169 PMCID: PMC6100412 DOI: 10.3390/molecules23061476] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 06/15/2018] [Indexed: 11/16/2022] Open
Abstract
Drug resistance, especially antibiotic resistance, is a growing threat to human health. To overcome this problem, it is significant to know precisely the mechanisms of drug resistance and/or self-resistance in various kingdoms, from bacteria through plants to animals, once more. This review compares the molecular mechanisms of the resistance against phycotoxins, toxins from marine and terrestrial animals, plants and fungi, and antibiotics. The results reveal that each kingdom possesses the characteristic features. The main mechanisms in each kingdom are transporters/efflux pumps in phycotoxins, mutation and modification of targets and sequestration in marine and terrestrial animal toxins, ABC transporters and sequestration in plant toxins, transporters in fungal toxins, and various or mixed mechanisms in antibiotics. Antibiotic producers in particular make tremendous efforts for avoiding suicide, and are more flexible and adaptable to the changes of environments. With these features in mind, potential alternative strategies to overcome these resistance problems are discussed. This paper will provide clues for solving the issues of drug resistance.
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Affiliation(s)
- Hiroshi Ogawara
- HO Bio Institute, Yushima-2, Bunkyo-ku, Tokyo 113-0034, Japan.
- Department of Biochemistry, Meiji Pharmaceutical University, Noshio-2, Kiyose, Tokyo 204-8588, Japan.
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20
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Almabruk KH, Dinh LK, Philmus B. Self-Resistance of Natural Product Producers: Past, Present, and Future Focusing on Self-Resistant Protein Variants. ACS Chem Biol 2018; 13:1426-1437. [PMID: 29763292 DOI: 10.1021/acschembio.8b00173] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nature is a prolific producers of bioactive natural products with an array of biological activities and impact on human and animal health. But with great power comes great responsibility, and the organisms that produce a bioactive compound must be resistant to its biological effects to survive during production/accumulation. Microorganisms, particularly bacteria, have developed different strategies to prevent self-toxicity. Here, we review a few of the major mechanisms including the mechanism of resistance with a focus on self-resistant protein variants, target proteins that contain amino acid substitutions to reduce the binding of the bioactive natural product, and therefore its inhibitory effects are highlighted in depth. We also try to identify some future avenues of research and challenges that need to be addressed.
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Affiliation(s)
- Khaled H. Almabruk
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Linh K. Dinh
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
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21
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Yue Q, Li Y, Chen L, Zhang X, Liu X, An Z, Bills GF. Genomics-driven discovery of a novel self-resistance mechanism in the echinocandin-producing fungus Pezicula radicicola. Environ Microbiol 2018. [PMID: 29528534 DOI: 10.1111/1462-2920.14089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The echinocandins are antifungal lipopeptides targeting fungi via noncompetitive inhibition of the β-1,3-d-glucan synthase FKS1 subunit. A novel echinocandin resistance mechanism involving an auxiliary copy of FKS1 in echinocandin-producing fungus Pezicula radicicola NRRL 12192 was discovered. We sequenced the genome of NRRL 12192 and predicted two FKS1-encoding genes (prfks1n and prfks1a), rather than a single FKS1 gene typical of filamentous ascomycetes. The prfks1a gene sits immediately adjacent to an echinocandin (sporiofungin) gene cluster, which was confirmed by disruption of prnrps4 and abolishment of sporiofungin production. Disruption of prfks1a dramatically increased the strain's sensitivity to exogenous echinocandins. In the absence of echinocandins, transcription levels of prfks1a relative to β-tubulin in the wild type and in Δprnrps4 stains were similar. Moreover, prfks1a is consistently transcribed at low levels and is upregulated in the presence of exogenous echinocandin, but not during growth conditions promoting endogenous production of sporiofungin. Therefore, we conclude that prfks1a is primarily responsible for protecting the fungus against extracellular echinocandin toxicity. The presence of unclustered auxiliary copies of FKS1 with high similarity to prfks1a in two other echinocandin-producing strains suggests that this previously unrecognized resistance mechanism may be common in echinocandin-producing fungi of the family Dermataceae of the class Leotiomycetes.
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Affiliation(s)
- Qun Yue
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yan Li
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA.,Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Li Chen
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xiaoling Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhiqiang An
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
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22
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Abstract
Many Fungi have a well-developed secondary metabolism. The diversity of fungal species and the diversification of biosynthetic gene clusters underscores a nearly limitless potential for metabolic variation and an untapped resource for drug discovery and synthetic biology. Much of the ecological success of the filamentous fungi in colonizing the planet is owed to their ability to deploy their secondary metabolites in concert with their penetrative and absorptive mode of life. Fungal secondary metabolites exhibit biological activities that have been developed into life-saving medicines and agrochemicals. Toxic metabolites, known as mycotoxins, contaminate human and livestock food and indoor environments. Secondary metabolites are determinants of fungal diseases of humans, animals, and plants. Secondary metabolites exhibit a staggering variation in chemical structures and biological activities, yet their biosynthetic pathways share a number of key characteristics. The genes encoding cooperative steps of a biosynthetic pathway tend to be located contiguously on the chromosome in coregulated gene clusters. Advances in genome sequencing, computational tools, and analytical chemistry are enabling the rapid connection of gene clusters with their metabolic products. At least three fungal drug precursors, penicillin K and V, mycophenolic acid, and pleuromutilin, have been produced by synthetic reconstruction and expression of respective gene clusters in heterologous hosts. This review summarizes general aspects of fungal secondary metabolism and recent developments in our understanding of how and why fungi make secondary metabolites, how these molecules are produced, and how their biosynthetic genes are distributed across the Fungi. The breadth of fungal secondary metabolite diversity is highlighted by recent information on the biosynthesis of important fungus-derived metabolites that have contributed to human health and agriculture and that have negatively impacted crops, food distribution, and human environments.
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Affiliation(s)
- Gerald F Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77054
| | - James B Gloer
- Department of Chemistry, University of Iowa, Iowa City, IA 52245
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23
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Gillot G, Jany JL, Dominguez-Santos R, Poirier E, Debaets S, Hidalgo PI, Ullán RV, Coton E, Coton M. Genetic basis for mycophenolic acid production and strain-dependent production variability in Penicillium roqueforti. Food Microbiol 2016; 62:239-250. [PMID: 27889155 DOI: 10.1016/j.fm.2016.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 08/29/2016] [Accepted: 10/03/2016] [Indexed: 11/16/2022]
Abstract
Mycophenolic acid (MPA) is a secondary metabolite produced by various Penicillium species including Penicillium roqueforti. The MPA biosynthetic pathway was recently described in Penicillium brevicompactum. In this study, an in silico analysis of the P. roqueforti FM164 genome sequence localized a 23.5-kb putative MPA gene cluster. The cluster contains seven genes putatively coding seven proteins (MpaA, MpaB, MpaC, MpaDE, MpaF, MpaG, MpaH) and is highly similar (i.e. gene synteny, sequence homology) to the P. brevicompactum cluster. To confirm the involvement of this gene cluster in MPA biosynthesis, gene silencing using RNA interference targeting mpaC, encoding a putative polyketide synthase, was performed in a high MPA-producing P. roqueforti strain (F43-1). In the obtained transformants, decreased MPA production (measured by LC-Q-TOF/MS) was correlated to reduced mpaC gene expression by Q-RT-PCR. In parallel, mycotoxin quantification on multiple P. roqueforti strains suggested strain-dependent MPA-production. Thus, the entire MPA cluster was sequenced for P. roqueforti strains with contrasted MPA production and a 174bp deletion in mpaC was observed in low MPA-producers. PCRs directed towards the deleted region among 55 strains showed an excellent correlation with MPA quantification. Our results indicated the clear involvement of mpaC gene as well as surrounding cluster in P. roqueforti MPA biosynthesis.
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Affiliation(s)
- Guillaume Gillot
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Jean-Luc Jany
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Rebeca Dominguez-Santos
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain; Instituto de Biotecnología de León (INBIOTEC), Avenida Real n°1, Parque Científico de León, 24006 León, Spain
| | - Elisabeth Poirier
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Stella Debaets
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Pedro I Hidalgo
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Ricardo V Ullán
- mAbxience, Upstream Production, Parque Tecnológico de León, Julia Morros s/n, Armunia, 24009, León, Spain
| | - Emmanuel Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Monika Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
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24
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Defosse TA, Mélin C, Clastre M, Besseau S, Lanoue A, Glévarec G, Oudin A, Dugé de Bernonville T, Vandeputte P, Linder T, Bouchara JP, Courdavault V, Giglioli-Guivarc'h N, Papon N. An additionalMeyerozyma guilliermondii IMH3gene confers mycophenolic acid resistance in fungal CTG clade species. FEMS Yeast Res 2016; 16:fow078. [DOI: 10.1093/femsyr/fow078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2016] [Indexed: 01/11/2023] Open
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25
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García-Estrada C, Martín JF. Biosynthetic gene clusters for relevant secondary metabolites produced by Penicillium roqueforti in blue cheeses. Appl Microbiol Biotechnol 2016; 100:8303-13. [PMID: 27554495 DOI: 10.1007/s00253-016-7788-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 10/21/2022]
Abstract
Ripening of blue-veined cheeses, such as the French Bleu and Roquefort, the Italian Gorgonzola, the English Stilton, the Danish Danablu or the Spanish Cabrales, Picón Bejes-Tresviso, and Valdeón, requires the growth and enzymatic activity of the mold Penicillium roqueforti, which is responsible for the characteristic texture, blue-green spots, and aroma of these types of cheeses. This filamentous fungus is able to synthesize different secondary metabolites, including andrastins, mycophenolic acid, and several mycotoxins, such as roquefortines C and D, PR-toxin and eremofortins, isofumigaclavines A and B, and festuclavine. This review provides a detailed description of the main secondary metabolites produced by P. roqueforti in blue cheese, giving a special emphasis to roquefortine, PR-toxin and mycophenolic acid, and their biosynthetic gene clusters and pathways. The knowledge of these clusters and secondary metabolism pathways, together with the ability of P. roqueforti to produce beneficial secondary metabolites, is of interest for commercial purposes.
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Affiliation(s)
| | - Juan-Francisco Martín
- Área de Microbiología, Departamento de Biología Molecular, Universidad de León, 24071, León, Spain
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26
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Studt L, Janevska S, Niehaus EM, Burkhardt I, Arndt B, Sieber CMK, Humpf HU, Dickschat JS, Tudzynski B. Two separate key enzymes and two pathway-specific transcription factors are involved in fusaric acid biosynthesis in Fusarium fujikuroi. Environ Microbiol 2016; 18:936-56. [PMID: 26662839 DOI: 10.1111/1462-2920.13150] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/18/2015] [Accepted: 11/23/2015] [Indexed: 01/03/2023]
Abstract
Fusaric acid (FSA) is a mycotoxin produced by several fusaria, including the rice pathogen Fusarium fujikuroi. Genes involved in FSA biosynthesis were previously identified as a cluster containing a polyketide synthase (PKS)-encoding (FUB1) and four additional genes (FUB2-FUB5). However, the biosynthetic steps leading to FSA as well as the origin of the nitrogen atom, which is incorporated into the polyketide backbone, remained unknown. In this study, seven additional cluster genes (FUB6-FUB12) were identified via manipulation of the global regulator FfSge1. The extended FUB gene cluster encodes two Zn(II)2 Cys6 transcription factors: Fub10 positively regulates expression of all FUB genes, whereas Fub12 is involved in the formation of the two FSA derivatives, i.e. dehydrofusaric acid and fusarinolic acid, serving as a detoxification mechanism. The major facilitator superfamily transporter Fub11 functions in the export of FSA out of the cell and is essential when FSA levels become critical. Next to Fub1, a second key enzyme was identified, the non-canonical non-ribosomal peptide synthetase Fub8. Chemical analyses of generated mutant strains allowed for the identification of a triketide as PKS product and the proposition of an FSA biosynthetic pathway, thereby unravelling the unique formation of a hybrid metabolite consisting of this triketide and an amino acid moiety.
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Affiliation(s)
- Lena Studt
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143, Münster, Germany
| | - Slavica Janevska
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143, Münster, Germany
| | - Eva-Maria Niehaus
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143, Münster, Germany
| | - Immo Burkhardt
- Kekulé Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53121, Bonn, Germany
| | - Birgit Arndt
- Institute of Food Chemistry, Westfälische Wilhelms-University, Corrensstr. 45, 48149, Münster, Germany
| | - Christian M K Sieber
- Lawrence Berkeley National Lab, DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms-University, Corrensstr. 45, 48149, Münster, Germany
| | - Jeroen S Dickschat
- Kekulé Institute for Organic Chemistry and Biochemistry, Rheinische Friedrich-Wilhelms-University Bonn, 53121, Bonn, Germany
| | - Bettina Tudzynski
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-University, Schlossplatz 8, 48143, Münster, Germany
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27
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Del-Cid A, Gil-Durán C, Vaca I, Rojas-Aedo JF, García-Rico RO, Levicán G, Chávez R. Identification and Functional Analysis of the Mycophenolic Acid Gene Cluster of Penicillium roqueforti. PLoS One 2016; 11:e0147047. [PMID: 26751579 PMCID: PMC4708987 DOI: 10.1371/journal.pone.0147047] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 12/28/2015] [Indexed: 11/18/2022] Open
Abstract
The filamentous fungus Penicillium roqueforti is widely known as the ripening agent of blue-veined cheeses. Additionally, this fungus is able to produce several secondary metabolites, including the meroterpenoid compound mycophenolic acid (MPA). Cheeses ripened with P. roqueforti are usually contaminated with MPA. On the other hand, MPA is a commercially valuable immunosuppressant. However, to date the molecular basis of the production of MPA by P. roqueforti is still unknown. Using a bioinformatic approach, we have identified a genomic region of approximately 24.4 kbp containing a seven-gene cluster that may be involved in the MPA biosynthesis in P. roqueforti. Gene silencing of each of these seven genes (named mpaA, mpaB, mpaC, mpaDE, mpaF, mpaG and mpaH) resulted in dramatic reductions in MPA production, confirming that all of these genes are involved in the biosynthesis of the compound. Interestingly, the mpaF gene, originally described in P. brevicompactum as a MPA self-resistance gene, also exerts the same function in P. roqueforti, suggesting that this gene has a dual function in MPA metabolism. The knowledge of the biosynthetic pathway of MPA in P. roqueforti will be important for the future control of MPA contamination in cheeses and the improvement of MPA production for commercial purposes.
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Affiliation(s)
- Abdiel Del-Cid
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Carlos Gil-Durán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Inmaculada Vaca
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Juan F. Rojas-Aedo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Ramón O. García-Rico
- GIMBIO Group, Department of Microbiology, Faculty of Basic Sciences, Universidad de Pamplona, Pamplona, Colombia
| | - Gloria Levicán
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Renato Chávez
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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Exploitation of Fungal Biodiversity for Discovery of Novel Antibiotics. Curr Top Microbiol Immunol 2016; 398:303-338. [PMID: 27422786 DOI: 10.1007/82_2016_496] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fungi were among the first sources for antibiotics. The discovery and development of the penicillin-type and cephalosporin-type β-lactams and their synthetic versions were transformative in emergence of the modern pharmaceutical industry. They remain some of the most important antibiotics, even 70 years after their discovery. Meanwhile, thousands of fungal metabolites have been discovered, yet these metabolites have only contributed a few additional compounds that have entered clinical development. Substantial expansion in fungal biodiversity assessment along with the availability of modern "-OMICS" technology and revolutionary developments in fungal biotechnology have been made in the last 15 years subsequent to the exit of most of the big Pharma companies from the field of novel antibiotics discovery. Therefore, the timing seems opportune to revisit these fascinating chemically rich organisms as a reservoir of small-molecule templates for lead discovery. This review will describe ongoing interdisciplinary scenarios in which specialists in fungal biology collaborate with chemists, pharmacologists and biochemical and process engineers in order to reveal and make new antibiotics. The utility of a pre-selection process based on phylogenetic data and distribution of secondary metabolite encoding gene cluster will be highlighted. Examples of novel bioactive metabolites from fungi derived from special ecological groups and new phylogenetic lineages will also be discussed.
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Zhang W, Cao S, Qiu L, Qi F, Li Z, Yang Y, Huang S, Bai F, Liu C, Wan X, Li S. Functional Characterization of MpaG′, the O-Methyltransferase Involved in the Biosynthesis of Mycophenolic Acid. Chembiochem 2015; 16:565-9. [DOI: 10.1002/cbic.201402600] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Indexed: 11/07/2022]
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Séguin V, Gente S, Heutte N, Vérité P, Kientz-Bouchart V, Sage L, Goux D, Garon D. First report of mycophenolic acid production by Eurotium repens isolated from agricultural and indoor environments. WORLD MYCOTOXIN J 2014. [DOI: 10.3920/wmj2013.1619] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mycophenolic acid is considered as an immunosuppressive pharmaceutical drug, but also as a mycotoxin due to its undesirable presence in various feedstuffs. Although Penicillium brevicompactum has been historically identified as the major producer of mycophenolic acid, this study reports for the first time the production of mycophenolic acid by isolates of Eurotium repens collected from agricultural and indoor environments. Fungal identification was achieved by scanning electron microscopy and molecular techniques, and mycophenolic acid production was confirmed by two analytical methods (gas and liquid chromatography coupled to mass spectrometry). These findings suggest that mycophenolic acid production and immunosuppressive properties of other closely related Eurotium should be evaluated in future studies.
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Affiliation(s)
- V. Séguin
- ABTE EA 4651, Equipe ToxEMAC, Université de Caen Basse-Normandie and Centre François Baclesse, Avenue du Général Harris, 14076 Caen Cedex 05, France
| | - S. Gente
- ABTE EA 4651, Equipe ToxEMAC, Université de Caen Basse-Normandie and Centre François Baclesse, Avenue du Général Harris, 14076 Caen Cedex 05, France
| | - N. Heutte
- INSERM U1086, Université de Caen Basse-Normandie and Centre François Baclesse, Avenue du Général Harris, 14076 Caen Cedex 05, France
| | - P. Vérité
- ABTE EA 4651, Equipe ToxEMAC, Université de Rouen, UFR de Médecine-Pharmacie, Boulevard Gambetta, 76000 Rouen, France
| | - V. Kientz-Bouchart
- Laboratoire Frank Duncombe, Conseil Général du Calvados, 14053 Caen Cedex 04, France
| | - L. Sage
- LECA UMR 5553, Université Joseph Fourier, BP 53, Rue de la Piscine, 38041 Grenoble Cedex 9, France
| | - D. Goux
- Centre de Microscopie Appliquée à la Biologie, Université de Caen Basse-Normandie, , Esplanade de la Paix, 14032 Caen Cedex, France
| | - D. Garon
- ABTE EA 4651, Equipe ToxEMAC, Université de Caen Basse-Normandie and Centre François Baclesse, Avenue du Général Harris, 14076 Caen Cedex 05, France
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31
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Bioactive metabolites from macrofungi: ethnopharmacology, biological activities and chemistry. FUNGAL DIVERS 2013. [DOI: 10.1007/s13225-013-0265-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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32
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Paterson RRM, Lima N. Biochemical mutagens affect the preservation of fungi and biodiversity estimations. Appl Microbiol Biotechnol 2012; 97:77-85. [DOI: 10.1007/s00253-012-4554-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 11/25/2022]
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Involvement of a natural fusion of a cytochrome P450 and a hydrolase in mycophenolic acid biosynthesis. Appl Environ Microbiol 2012; 78:4908-13. [PMID: 22544261 DOI: 10.1128/aem.07955-11] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Mycophenolic acid (MPA) is a fungal secondary metabolite and the active component in several immunosuppressive pharmaceuticals. The gene cluster coding for the MPA biosynthetic pathway has recently been discovered in Penicillium brevicompactum, demonstrating that the first step is catalyzed by MpaC, a polyketide synthase producing 5-methylorsellinic acid (5-MOA). However, the biochemical role of the enzymes encoded by the remaining genes in the MPA gene cluster is still unknown. Based on bioinformatic analysis of the MPA gene cluster, we hypothesized that the step following 5-MOA production in the pathway is carried out by a natural fusion enzyme MpaDE, consisting of a cytochrome P450 (MpaD) in the N-terminal region and a hydrolase (MpaE) in the C-terminal region. We verified that the fusion gene is indeed expressed in P. brevicompactum by obtaining full-length sequence of the mpaDE cDNA prepared from the extracted RNA. Heterologous coexpression of mpaC and the fusion gene mpaDE in the MPA-nonproducer Aspergillus nidulans resulted in the production of 5,7-dihydroxy-4-methylphthalide (DHMP), the second intermediate in MPA biosynthesis. Analysis of the strain coexpressing mpaC and the mpaD part of mpaDE shows that the P450 catalyzes hydroxylation of 5-MOA to 4,6-dihydroxy-2-(hydroxymethyl)-3-methylbenzoic acid (DHMB). DHMB is then converted to DHMP, and our results suggest that the hydrolase domain aids this second step by acting as a lactone synthase that catalyzes the ring closure. Overall, the chimeric enzyme MpaDE provides insight into the genetic organization of the MPA biosynthesis pathway.
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Abstract
MPA (mycophenolic acid) is an immunosuppressive drug produced by several fungi in Penicillium subgenus Penicillium. This toxic metabolite is an inhibitor of IMPDH (IMP dehydrogenase). The MPA-biosynthetic cluster of Penicillium brevicompactum contains a gene encoding a B-type IMPDH, IMPDH-B, which confers MPA resistance. Surprisingly, all members of the subgenus Penicillium contain genes encoding IMPDHs of both the A and B types, regardless of their ability to produce MPA. Duplication of the IMPDH gene occurred before and independently of the acquisition of the MPAbiosynthetic cluster. Both P. brevicompactum IMPDHs are MPA-resistant, whereas the IMPDHs from a non-producer are MPA-sensitive. Resistance comes with a catalytic cost: whereas P. brevicompactum IMPDH-B is >1000-fold more resistant to MPA than a typical eukaryotic IMPDH, its kcat/Km value is 0.5% of 'normal'. Curiously, IMPDH-B of Penicillium chrysogenum, which does not produce MPA, is also a very poor enzyme. The MPA-binding site is completely conserved among sensitive and resistant IMPDHs. Mutational analysis shows that the C-terminal segment is a major structural determinant of resistance. These observations suggest that the duplication of the IMPDH gene in the subgenus Penicillium was permissive for MPA production and that MPA production created a selective pressure on IMPDH evolution. Perhaps MPA production rescued IMPDH-B from deleterious genetic drift.
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Sun XE, Hansen BG, Hedstrom L. Kinetically controlled drug resistance: how Penicillium brevicompactum survives mycophenolic acid. J Biol Chem 2011; 286:40595-600. [PMID: 21979957 PMCID: PMC3220510 DOI: 10.1074/jbc.m111.305235] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 10/04/2011] [Indexed: 11/06/2022] Open
Abstract
The filamentous fungus Penicillium brevicompactum produces the immunosuppressive drug mycophenolic acid (MPA), which is a potent inhibitor of eukaryotic IMP dehydrogenases (IMPDHs). IMPDH catalyzes the conversion of IMP to XMP via a covalent enzyme intermediate, E-XMP*; MPA inhibits by trapping E-XMP*. P. brevicompactum (Pb) contains two MPA-resistant IMPDHs, PbIMPDH-A and PbIMPDH-B, which are 17- and 10(3)-fold more resistant to MPA than typically observed. Surprisingly, the active sites of these resistant enzymes are essentially identical to those of MPA-sensitive enzymes, so the mechanistic basis of resistance is not apparent. Here, we show that, unlike MPA-sensitive IMPDHs, formation of E-XMP* is rate-limiting for both PbIMPDH-A and PbIMPDH-B. Therefore, MPA resistance derives from the failure to accumulate the drug-sensitive intermediate.
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Affiliation(s)
- Xin E. Sun
- From the Graduate Program in Biochemistry and
| | - Bjarne Gram Hansen
- the Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Lizbeth Hedstrom
- Departments of Biology and Chemistry, Brandeis University, Waltham, Massachusetts 02453 and
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