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Contesini FJ, Frandsen RJN, Damasio A. Editorial: CAZymes in Biorefinery: From Genes to Application. Front Bioeng Biotechnol 2021; 9:622817. [PMID: 33644017 PMCID: PMC7902500 DOI: 10.3389/fbioe.2021.622817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fabiano Jares Contesini
- Synthetic Biology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Rasmus John Normand Frandsen
- Synthetic Biology Section, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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Malik A, Ardalani H, Anam S, McNair LM, Kromphardt KJ, Frandsen RJN, Franzyk H, Staerk D, Kongstad KT. Antidiabetic xanthones with α-glucosidase inhibitory activities from an endophytic Penicillium canescens. Fitoterapia 2020; 142:104522. [DOI: 10.1016/j.fitote.2020.104522] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 10/25/2022]
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Reus E, Nielsen MR, Frandsen RJN. Metabolic and regulatory insights from the experimental horizontal gene transfer of the aurofusarin and bikaverin gene clusters to
Aspergillus nidulans. Mol Microbiol 2019; 112:1684-1700. [DOI: 10.1111/mmi.14376] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Elise Reus
- Department of Biotechnology and Bioengineering Technical University of Denmark Kongens Lyngby Denmark
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Grijseels S, Pohl C, Nielsen JC, Wasil Z, Nygård Y, Nielsen J, Frisvad JC, Nielsen KF, Workman M, Larsen TO, Driessen AJM, Frandsen RJN. Identification of the decumbenone biosynthetic gene cluster in Penicillium decumbens and the importance for production of calbistrin. Fungal Biol Biotechnol 2018; 5:18. [PMID: 30598828 PMCID: PMC6299560 DOI: 10.1186/s40694-018-0063-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Filamentous fungi are important producers of secondary metabolites, low molecular weight molecules that often have bioactive properties. Calbistrin A is a secondary metabolite with an interesting structure that was recently found to have bioactivity against leukemia cells. It consists of two polyketides linked by an ester bond: a bicyclic decalin containing polyketide with structural similarities to lovastatin, and a linear 12 carbon dioic acid structure. Calbistrin A is known to be produced by several uniseriate black Aspergilli, Aspergillus versicolor-related species, and Penicillia. Penicillium decumbens produces calbistrin A and B as well as several putative intermediates of the calbistrin pathway, such as decumbenone A-B and versiol. RESULTS A comparative genomics study focused on the polyketide synthase (PKS) sets found in three full genome sequence calbistrin producing fungal species, P. decumbens, A. aculeatus and A. versicolor, resulted in the identification of a novel, putative 13-membered calbistrin producing gene cluster (calA to calM). Implementation of the CRISPR/Cas9 technology in P. decumbens allowed the targeted deletion of genes encoding a polyketide synthase (calA), a major facilitator pump (calB) and a binuclear zinc cluster transcription factor (calC). Detailed metabolic profiling, using UHPLC-MS, of the ∆calA (PKS) and ∆calC (TF) strains confirmed the suspected involvement in calbistrin productions as neither strains produced calbistrin nor any of the putative intermediates in the pathway. Similarly analysis of the excreted metabolites in the ∆calB (MFC-pump) strain showed that the encoded pump was required for efficient export of calbistrin A and B. CONCLUSION Here we report the discovery of a gene cluster (calA-M) involved in the biosynthesis of the polyketide calbistrin in P. decumbens. Targeted gene deletions proved the involvement of CalA (polyketide synthase) in the biosynthesis of calbistrin, CalB (major facilitator pump) for the export of calbistrin A and B and CalC for the transcriptional regulation of the cal-cluster. This study lays the foundation for further characterization of the calbistrin biosynthetic pathway in multiple species and the development of an efficient calbistrin producing cell factory.
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Affiliation(s)
- Sietske Grijseels
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Carsten Pohl
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jens Christian Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Zahida Wasil
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Yvonne Nygård
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mhairi Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Arnold J. M. Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
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Grijseels S, Nielsen JC, Nielsen J, Larsen TO, Frisvad JC, Nielsen KF, Frandsen RJN, Workman M. Physiological characterization of secondary metabolite producing Penicillium cell factories. Fungal Biol Biotechnol 2017; 4:8. [PMID: 29075506 PMCID: PMC5644182 DOI: 10.1186/s40694-017-0036-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/26/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Penicillium species are important producers of bioactive secondary metabolites. However, the immense diversity of the fungal kingdom is only scarcely represented in industrial bioprocesses and the upscaling of compound production remains a costly and labor intensive challenge. In order to facilitate the development of novel secondary metabolite producing processes, two routes are typically explored: optimization of the native producer or transferring the enzymatic pathway into a heterologous host. Recent genome sequencing of ten Penicillium species showed the vast amount of secondary metabolite gene clusters present in their genomes, and makes them accessible for rational strain improvement. In this study, we aimed to characterize the potential of these ten Penicillium species as native producing cell factories by testing their growth performance and secondary metabolite production in submerged cultivations. RESULTS Cultivation of the fungal species in controlled submerged bioreactors showed that the ten wild type Penicillium species had promising, highly reproducible growth characteristics in two different media. Analysis of the secondary metabolite production using liquid chromatography coupled with high resolution mass spectrometry proved that the species produced a broad range of secondary metabolites, at different stages of the fermentations. Metabolite profiling for identification of the known compounds resulted in identification of 34 metabolites; which included several with bioactive properties such as antibacterial, antifungal and anti-cancer activities. Additionally, several novel species-metabolite relationships were found. CONCLUSIONS This study demonstrates that the fermentation characteristics and the highly reproducible performance in bioreactors of ten recently genome sequenced Penicillium species should be considered as very encouraging for the application of native hosts for production via submerged fermentation. The results are particularly promising for the potential development of the ten analysed Penicillium species for production of novel bioactive compounds via submerged fermentations.
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Affiliation(s)
- Sietske Grijseels
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jens Christian Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jens Christian Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | - Mhairi Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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Andersen-Ranberg J, Kongstad KT, Nafisi M, Staerk D, Okkels FT, Mortensen UH, Lindberg Møller B, Frandsen RJN, Kannangara R. Cover Feature: Synthesis of C-Glucosylated Octaketide Anthraquinones in Nicotiana benthamiana
by Using a Multispecies-Based Biosynthetic Pathway (ChemBioChem 19/2017). Chembiochem 2017. [DOI: 10.1002/cbic.201700482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Johan Andersen-Ranberg
- Plant Biochemistry Laboratory; Department of Plant and Environmental Sciences; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
- Present address: Department of Plant Microbial Biology; University of California Berkeley; 441 Koshland Hall Berkeley CA 94720-3102 USA
| | - Kenneth Thermann Kongstad
- Faculty of Health and Medical Sciences; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Majse Nafisi
- Plant Biochemistry Laboratory; Department of Plant and Environmental Sciences; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
- Chr. Hansen A/S; Bøge Alle 10-12 2970 Hørsholm Denmark
| | - Dan Staerk
- Faculty of Health and Medical Sciences; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Finn Thyge Okkels
- Chr. Hansen A/S; Bøge Alle 10-12 2970 Hørsholm Denmark
- Present address: ActaBio ApS; Kongemarken 11 4000 Roskilde Denmark
| | - Uffe Hasbro Mortensen
- Department of Biotechnology and Biomedicine; Technical University of Denmark; Søltofts Plads Building 221 and 223 2800 Kongens Lyngby Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory; Department of Plant and Environmental Sciences; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
| | - Rasmus John Normand Frandsen
- Department of Biotechnology and Biomedicine; Technical University of Denmark; Søltofts Plads Building 221 and 223 2800 Kongens Lyngby Denmark
| | - Rubini Kannangara
- Plant Biochemistry Laboratory; Department of Plant and Environmental Sciences; University of Copenhagen; Thorvaldsensvej 40 1871 Frederiksberg Denmark
- Chr. Hansen A/S; Bøge Alle 10-12 2970 Hørsholm Denmark
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Andersen-Ranberg J, Kongstad KT, Nafisi M, Staerk D, Okkels FT, Mortensen UH, Lindberg Møller B, Frandsen RJN, Kannangara R. Synthesis of C-Glucosylated Octaketide Anthraquinones in Nicotiana benthamiana by Using a Multispecies-Based Biosynthetic Pathway. Chembiochem 2017; 18:1893-1897. [PMID: 28719729 DOI: 10.1002/cbic.201700331] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/27/2022]
Abstract
Carminic acid is a C-glucosylated octaketide anthraquinone and the main constituent of the natural dye carmine (E120), possessing unique coloring, stability, and solubility properties. Despite being used since ancient times, longstanding efforts to elucidate its route of biosynthesis have been unsuccessful. Herein, a novel combination of enzymes derived from a plant (Aloe arborescens, Aa), a bacterium (Streptomyces sp. R1128, St), and an insect (Dactylopius coccus, Dc) that allows for the biosynthesis of the C-glucosylated anthraquinone, dcII, a precursor for carminic acid, is reported. The pathway, which consists of AaOKS, StZhuI, StZhuJ, and DcUGT2, presents an alternative biosynthetic approach for the production of polyketides by using a type III polyketide synthase (PKS) and tailoring enzymes originating from a type II PKS system. The current study showcases the power of using transient expression in Nicotiana benthamiana for efficient and rapid identification of functional biosynthetic pathways, including both soluble and membrane-bound enzymes.
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Affiliation(s)
- Johan Andersen-Ranberg
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Present address: Department of Plant Microbial Biology, University of California Berkeley, 441 Koshland Hall, Berkeley, CA, 94720-3102, USA
| | - Kenneth Thermann Kongstad
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Majse Nafisi
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Chr. Hansen A/S, Bøge Alle 10-12, 2970, Hørsholm, Denmark
| | - Dan Staerk
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Finn Thyge Okkels
- Chr. Hansen A/S, Bøge Alle 10-12, 2970, Hørsholm, Denmark
- Present address: ActaBio ApS, Kongemarken 11, 4000, Roskilde, Denmark
| | - Uffe Hasbro Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221 and 223, 2800, Kongens Lyngby, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Rasmus John Normand Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221 and 223, 2800, Kongens Lyngby, Denmark
| | - Rubini Kannangara
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
- Chr. Hansen A/S, Bøge Alle 10-12, 2970, Hørsholm, Denmark
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Christodoulides N, Van Dam AR, Peterson DA, Frandsen RJN, Mortensen UH, Petersen B, Rasmussen S, Normark BB, Hardy NB. Gene expression plasticity across hosts of an invasive scale insect species. PLoS One 2017; 12:e0176956. [PMID: 28472112 PMCID: PMC5417585 DOI: 10.1371/journal.pone.0176956] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/19/2017] [Indexed: 12/19/2022] Open
Abstract
For plant-eating insects, we still have only a nascent understanding of the genetic basis of host-use promiscuity. Here, to improve that situation, we investigated host-induced gene expression plasticity in the invasive lobate lac scale insect, Paratachardina pseudolobata (Hemiptera: Keriidae). We were particularly interested in the differential expression of detoxification and effector genes, which are thought to be critical for overcoming a plant's chemical defenses. We collected RNA samples from P. pseudolobata on three different host plant species, assembled transcriptomes de novo, and identified transcripts with significant host-induced gene expression changes. Gene expression plasticity was pervasive, but the expression of most detoxification and effector genes was insensitive to the host environment. Nevertheless, some types of detoxification genes were more differentially expressed than expected by chance. Moreover, we found evidence of a trade-off between expression of genes involved in primary and secondary metabolism; hosts that induced lower expression of genes for detoxification induced higher expression of genes for growth. Our findings are largely consonant with those of several recently published studies of other plant-eating insect species. Thus, across plant-eating insect species, there may be a common set of gene expression changes that enable host-use promiscuity.
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Affiliation(s)
- Nicholas Christodoulides
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
| | - Alex R. Van Dam
- Biosynthetic Pathways Engineering, Department of Bioengineering, Denmark Technical University, Søltofts plads, Lyngby, Denmark
| | - Daniel A. Peterson
- Department of Biology and Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Rasmus John Normand Frandsen
- Biosynthetic Pathways Engineering, Department of Bioengineering, Denmark Technical University, Søltofts plads, Lyngby, Denmark
| | - Uffe Hasbro Mortensen
- Biosynthetic Pathways Engineering, Department of Bioengineering, Denmark Technical University, Søltofts plads, Lyngby, Denmark
| | - Bent Petersen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Simon Rasmussen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
| | - Benjamin B. Normark
- Department of Biology and Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Nate B. Hardy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, United States of America
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Ley A, Coumou HC, Frandsen RJN. Heterologous expression of MlcE in Saccharomyces cerevisiae provides resistance to natural and semi-synthetic statins. Metab Eng Commun 2015; 2:117-123. [PMID: 34150514 PMCID: PMC8193252 DOI: 10.1016/j.meteno.2015.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/19/2015] [Accepted: 09/21/2015] [Indexed: 02/07/2023] Open
Abstract
Statins are inhibitors of 3-hydroxy-3-methylglutaryl coenzyme A reductase, the key enzyme in cholesterol biosynthesis. Their extensive use in treatment and prevention of cardiovascular diseases placed statins among the best selling drugs. Construction of Saccharomyces cerevisiae cell factory for the production of high concentrations of natural statins will require establishment of a non-destructive self-resistance mechanism to overcome the undesirable growth inhibition effects of statins. To establish active export of statins from yeast, and thereby detoxification, we integrated a putative efflux pump-encoding gene mlcE from the mevastatin-producing Penicillium citrinum into the S. cerevisiae genome. The resulting strain showed increased resistance to both natural statins (mevastatin and lovastatin) and semi-synthetic statin (simvastatin) when compared to the wild type strain. Expression of RFP-tagged mlcE showed that MlcE is localized to the yeast plasma and vacuolar membranes. We provide a possible engineering strategy for improvement of future yeast based production of natural and semi-synthetic statins.
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Affiliation(s)
- Ana Ley
- Department of Systems Biology, Technical University of Denmark, Søltofts Plads 223, 2800 Kgs. Lyngby, Denmark
| | - Hilde Cornelijne Coumou
- Department of Systems Biology, Technical University of Denmark, Søltofts Plads 223, 2800 Kgs. Lyngby, Denmark
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Sørensen JL, Sondergaard TE, Covarelli L, Fuertes PR, Hansen FT, Frandsen RJN, Saei W, Lukassen MB, Wimmer R, Nielsen KF, Gardiner DM, Giese H. Identification of the biosynthetic gene clusters for the lipopeptides fusaristatin A and W493 B in Fusarium graminearum and F. pseudograminearum. J Nat Prod 2014; 77:2619-2625. [PMID: 25412204 DOI: 10.1021/np500436r] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The closely related species Fusarium graminearum and Fusarium pseudograminearum differ in that each contains a gene cluster with a polyketide synthase (PKS) and a nonribosomal peptide synthetase (NRPS) that is not present in the other species. To identify their products, we deleted PKS6 and NRPS7 in F. graminearum and NRPS32 in F. pseudograminearum. By comparing the secondary metabolite profiles of the strains we identified the resulting product in F. graminearum as fusaristatin A, and as W493 A and B in F. pseudograminearum. These lipopeptides have previously been isolated from unidentified Fusarium species. On the basis of genes in the putative gene clusters we propose a model for biosynthesis where the polyketide product is shuttled to the NPRS via a CoA ligase and a thioesterase in F. pseudograminearum. In F. graminearum the polyketide is proposed to be directly assimilated by the NRPS.
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Affiliation(s)
- Jens Laurids Sørensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University , DK-9000 Aalborg, Denmark
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Sørensen LQ, Lysøe E, Larsen JE, Khorsand-Jamal P, Nielsen KF, Frandsen RJN. Genetic transformation of Fusarium avenaceum by Agrobacterium tumefaciens mediated transformation and the development of a USER-Brick vector construction system. BMC Mol Biol 2014; 15:15. [PMID: 25048842 PMCID: PMC4133957 DOI: 10.1186/1471-2199-15-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/04/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The plant pathogenic and saprophytic fungus Fusarium avenaceum causes considerable in-field and post-field losses worldwide due to its infections of a wide range of different crops. Despite its significant impact on the profitability of agriculture production and a desire to characterize the infection process at the molecular biological level, no genetic transformation protocol has yet been established for F. avenaceum. In the current study, it is shown that F. avenaceum can be efficiently transformed by Agrobacterium tumefaciens mediated transformation. In addition, an efficient and versatile single step vector construction strategy relying on Uracil Specific Excision Reagent (USER) Fusion cloning, is developed. RESULTS The new vector construction system, termed USER-Brick, is based on a limited number of PCR amplified vector fragments (core USER-Bricks) which are combined with PCR generated fragments from the gene of interest. The system was found to have an assembly efficiency of 97% with up to six DNA fragments, based on the construction of 55 vectors targeting different polyketide synthase (PKS) and PKS associated transcription factor encoding genes in F. avenaceum. Subsequently, the ΔFaPKS3 vector was used for optimizing A. tumefaciens mediated transformation (ATMT) of F. avenaceum with respect to six variables. Acetosyringone concentration, co-culturing time, co-culturing temperature and fungal inoculum were found to significantly impact the transformation frequency. Following optimization, an average of 140 transformants per 106 macroconidia was obtained in experiments aimed at introducing targeted genome modifications. Targeted deletion of FaPKS6 (FA08709.2) in F. avenaceum showed that this gene is essential for biosynthesis of the polyketide/nonribosomal compound fusaristatin A. CONCLUSION The new USER-Brick system is highly versatile by allowing for the reuse of a common set of building blocks to accommodate seven different types of genome modifications. New USER-Bricks with additional functionality can easily be added to the system by future users. The optimized protocol for ATMT of F. avenaceum represents the first reported targeted genome modification by double homologous recombination of this plant pathogen and will allow for future characterization of this fungus. Functional linkage of FaPKS6 to the production of the mycotoxin fusaristatin A serves as a first testimony to this.
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Affiliation(s)
| | | | | | | | | | - Rasmus John Normand Frandsen
- Eukaryotic Molecular Cell Biology Group, Department of Systems Biology, The Technical University of Denmark, Søltofts Plads building 223, DK-2800 Kgs,, Lyngby, Denmark.
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Sørensen JL, Hansen FT, Sondergaard TE, Staerk D, Lee TV, Wimmer R, Klitgaard LG, Purup S, Giese H, Frandsen RJN. Production of novel fusarielins by ectopic activation of the polyketide synthase 9 cluster in Fusarium graminearum. Environ Microbiol 2012; 14:1159-70. [DOI: 10.1111/j.1462-2920.2011.02696.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
Genome sequence data on fungal pathogens provide the opportunity to carry out a reverse genetics approach to uncover gene function. Efficient methods for targeted genome modifications such as knockout and in locus over-expression are in high demand. Here we describe two efficient single-step cloning strategies for construction of vectors for Agrobacterium tumefaciens-mediated transformation (ATMT). Targeted genome modifications require integration by a homologous double crossover event, which is achieved by placing target sequences on either side of a selection marker gene in the vector. Protocols are given for two single-step vector construction techniques. The In-Fusion cloning technique is independent of compatible restriction enzyme sites in the vector and the fragment to be cloned. The method can be directly applied to any vector of choice and it is possible to carry out four fragment cloning without the need for subcloning. The cloning efficiency is not always as high as desired, but it still presents an efficient alternative to restriction enzyme and ligase-based cloning systems. The USER technology offers a higher four fragment cloning efficiency than In-Fusion, but depends on specific structures in the binary vector. The available fungal binary vectors adapted for the USER system are described and protocols are provided for vector design and construction. A general protocol for verification of the resulting gene replacement events in the recipient fungal cells is also given. The cloning systems described above are relevant for all transformation vector constructs, but here we describe their application for ATMT compatible binary vectors. Protocols are provided for ATMT exemplified by Fusarium graminearum. For large-scale reverse genetic projects, the USER technology is recommended combined with ATMT.
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Affiliation(s)
- Rasmus John Normand Frandsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Lyngby, Denmark.
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Frandsen RJN. A guide to binary vectors and strategies for targeted genome modification in fungi using Agrobacterium tumefaciens-mediated transformation. J Microbiol Methods 2011; 87:247-62. [DOI: 10.1016/j.mimet.2011.09.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 01/31/2023]
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