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Nielsen MR, Sørensen T, Pedersen TB, Westphal KR, Díaz Fernández De Quincoces L, Sondergaard TE, Wimmer R, Brown DW, Sørensen JL. Final piece to the Fusarium pigmentation puzzle - Unraveling of the phenalenone biosynthetic pathway responsible for perithecial pigmentation in the Fusarium solani species complex. Fungal Genet Biol 2024; 174:103912. [PMID: 39004163 DOI: 10.1016/j.fgb.2024.103912] [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: 04/18/2024] [Revised: 06/29/2024] [Accepted: 07/04/2024] [Indexed: 07/16/2024]
Abstract
The Fusarium solani species complex (FSSC) is comprised of important pathogens of plants and humans. A distinctive feature of FSSC species is perithecial pigmentation. While the dark perithecial pigments of other Fusarium species are derived from fusarubins synthesized by polyketide synthase 3 (PKS3), the perithecial pigments of FSSC are derived from an unknown metabolite synthesized by PKS35. Here, we confirm in FSSC species Fusarium vanettenii that PKS35 (fsnI) is required for perithecial pigment synthesis by deletion analysis and that fsnI is closely related to phnA from Penicillium herquei, as well as duxI from Talaromyces stipentatus, which produce prephenalenone as an early intermediate in herqueinone and duclauxin synthesis respectively. The production of prephenalenone by expression of fsnI in Saccharomyces cerevisiae indicates that it is also an early intermediate in perithecial pigment synthesis. We next identified a conserved cluster of 10 genes flanking fsnI in F. vanettenii that when expressed in F. graminearum led to the production of a novel corymbiferan lactone F as a likely end product of the phenalenone biosynthetic pathway in FSSC.
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Affiliation(s)
- Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8A, 6700 Esbjerg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Tobias Bruun Pedersen
- Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8A, 6700 Esbjerg, Denmark
| | - Klaus Ringsborg Westphal
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | | | - Teis Esben Sondergaard
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Daren W Brown
- National Center for Agricultural Utilization Research, U.S. Department of Agriculture, 1815 N University St. Peoria IL 61604, United States of America
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8A, 6700 Esbjerg, Denmark.
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Severinsen MM, Westphal KR, Terp M, Sørensen T, Olsen A, Bachleitner S, Studt-Reinhold L, Wimmer R, Sondergaard TE, Sørensen JL. Filling out the gaps - identification of fugralins as products of the PKS2 cluster in Fusarium graminearum. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1264366. [PMID: 38025899 PMCID: PMC10667903 DOI: 10.3389/ffunb.2023.1264366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023]
Abstract
As one of the grain crop pathogenic fungi with the greatest impacts on agricultural economical as well as human health, an elaborate understanding of the life cycle and subsequent metabolome of Fusarium graminearum is of great interest. Throughout the lifetime of the fungus, it is known to produce a wide array of secondary metabolites, including polyketides. One of the F. graminearum polyketides which has remained a mystery until now has been elucidated in this work. Previously, it was suggested that the biosynthetic product of the PKS2 gene cluster was involved in active mycelial growth, the exact mechanism, however, remained unclear. In our work, disruption and overexpression of the PKS2 gene in F. graminearum enabled structural elucidation of a linear and a cyclic tetraketide with a double methyl group, named fugralin A and B, respectively. Further functional characterization showed that the compounds are not produced during infection, and that deletion and overexpression did not affect pathogenicity or visual growth. The compounds were shown to be volatile, which could point to possible functions that can be investigated further in future studies.
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Affiliation(s)
- Manja Mølgaard Severinsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Mikael Terp
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anders Olsen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simone Bachleitner
- Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Lena Studt-Reinhold
- Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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3
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Bao Y, Lin Z, Yao W, Akbar S, Lin W, Powell CA, Xu J, Zhang M. Integration of Transcriptomic and Metabolomic Profiles Provides Insights into the Influence of Nitrogen on Secondary Metabolism in Fusarium sacchari. Int J Mol Sci 2023; 24:10832. [PMID: 37446015 DOI: 10.3390/ijms241310832] [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: 04/11/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Nitrogen availability might play an essential role in plant diseases by enhancing fungal cell growth and influencing the expression of genes required for successful pathogenesis. Nitrogen availability could modulate secondary metabolic pathways as evidenced by the significant differential expression of several core genes involved in mycotoxin biosynthesis and genes encoding polyketide synthase/nonribosomal peptide synthetases, cytochrome P450 and carbohydrate-active enzymes in Fusarium sacchari, grown on different nitrogen sources. A combined analysis was carried out on the transcript and metabolite profiles of regulatory metabolic processes and the virulence of Fusarium sacchari grown on various nitrogen sources. The nitrogen regulation of the gibberellin gene cluster included the metabolic flux and multiple steps of gibberellin synthesis. UHPLC-MS/MS-based metabolome analysis revealed the coordination of these related transcripts and the accumulation of gibberellin metabolites. This integrated analysis allowed us to uncover additional information for a more comprehensive understanding of biological events relevant to fungal secondary metabolic regulation in response to nitrogen availability.
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Affiliation(s)
- Yixue Bao
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology & Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning 530004, China
| | - Zhenyue Lin
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology & Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning 530004, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology & Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning 530004, China
| | - Sehrish Akbar
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology & Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning 530004, China
| | - Wenfeng Lin
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology & Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning 530004, China
| | - Charles A Powell
- IFAS Indian River Research and Education Center, University of Florida, Fort Pierce, FL 34945, USA
| | - Jianlong Xu
- Hainan Yazhou Bay Seed Laboratory, National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572025, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Muqing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agric-Biological Resources & Guangxi Key Lab for Sugarcane Biology & Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning 530004, China
- IFAS Indian River Research and Education Center, University of Florida, Fort Pierce, FL 34945, USA
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4
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Tammam MA, Gamal El-Din MI, Abood A, El-Demerdash A. Recent advances in the discovery, biosynthesis, and therapeutic potential of isocoumarins derived from fungi: a comprehensive update. RSC Adv 2023; 13:8049-8089. [PMID: 36909763 PMCID: PMC9999372 DOI: 10.1039/d2ra08245d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/26/2023] [Indexed: 03/12/2023] Open
Abstract
Microorganisms still remain the main hotspots in the global drug discovery avenue. In particular, fungi are highly prolific producers of vast structurally diverse specialized secondary metabolites, which have displayed a myriad of biomedical potentials. Intriguingly, isocoumarins is one distinctive class of fungal natural products polyketides, which demonstrated numerous remarkable biological and pharmacological activities. This review article provides a comprehensive state-of-the-art over the period 2000-2022 about the discovery, isolation, classifications, and therapeutic potentials of isocoumarins exclusively reported from fungi. Indeed, a comprehensive list of 351 structurally diverse isocoumarins were documented and classified according to their fungal sources [16 order/28 family/55 genera] where they have been originally discovered along with their reported pharmacological activities wherever applicable. Also, recent insights around their proposed and experimentally proven biosynthetic pathways are also briefly discussed.
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Affiliation(s)
- Mohamed A Tammam
- Department of Biochemistry, Faculty of Agriculture, Fayoum University Fayoum 63514 Egypt
| | - Mariam I Gamal El-Din
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Cairo 11566 Egypt
| | - Amira Abood
- Chemistry of Natural and Microbial Products Department, National Research Center Dokki Cairo Egypt
- School of Bioscience, University of Kent Canterbury UK
| | - Amr El-Demerdash
- Organic Chemistry Division, Department of Chemistry, Faculty of Sciences, Mansoura University Mansoura 35516 Egypt
- Department of Biochemistry and Metabolism, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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Zhang J, Zhu W, Goodwin PH, Lin Q, Xia M, Xu W, Sun R, Liang J, Wu C, Li H, Wang Q, Yang L. Response of Fusarium pseudograminearum to Biocontrol Agent Bacillus velezensis YB-185 by Phenotypic and Transcriptome Analysis. J Fungi (Basel) 2022; 8:jof8080763. [PMID: 35893131 PMCID: PMC9331925 DOI: 10.3390/jof8080763] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
The use of biological control agents (BCAs) is a promising alternative control measure for Fusarium crown rot (FCR) of wheat caused by Fusarium pseudograminearum. A bacterial strain, YB-185, was isolated from the soil of wheat plants with FCR and identified as Bacillus velezensis. YB-185 exhibited strong inhibition of F. pseudograminearum mycelial growth and conidial germination in culture. Seed treatment with YB-185 in greenhouse and field resulted in reductions in disease by 66.1% and 57.6%, respectively, along with increased grain yield. Microscopy of infected root tissues confirmed that YB-185 reduced root invasion by F. pseudograminearum. RNA-seq of F. pseudograminearum during co-cultivation with B. velezensis YB-185 revealed 5086 differentially expressed genes (DEGs) compared to the control. Down-regulated DEGs included genes for glucan synthesis, fatty acid synthesis, mechanosensitive ion channels, superoxide dismutase, peroxiredoxin, thioredoxin, and plant-cell-wall-degrading enzymes, whereas up-regulated DEGs included genes for chitin synthesis, ergosterol synthesis, glutathione S-transferase, catalase, and ABC transporters. In addition, fungal cell apoptosis increased significantly, as indicated by TUNEL staining, and the scavenging rate of 2,2′-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt radical cation (ABTS·+) in the fungus significantly decreased. Thus, F. pseudograminearum may be trying to maintain normal cell functions by increasing cell wall and membrane synthesis, antioxidant and anti-stress responses, detoxification of bacterial antimicrobial compounds, and transportation of damaging compounds from its cells. However, cell death and free radical accumulation still occurred, indicating that the responses were insufficient to prevent cell damage. Bacillus velezensis YB-185 is a promising BCA against FCR that acts by directly damaging F. pseudograminearum, thus reducing its ability to colonize roots and produce symptoms.
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Affiliation(s)
- Jie Zhang
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
| | - Wenqian Zhu
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
| | - Paul H. Goodwin
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Qitong Lin
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
| | - Mingcong Xia
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
| | - Wen Xu
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
| | - Runhong Sun
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
| | - Juan Liang
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
| | - Chao Wu
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China;
| | - Qi Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
| | - Lirong Yang
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Henan Biopesticide Engineering Research Center, Henan Agricultural Microbiology Innovation Center, Zhengzhou 450002, China; (J.Z.); (W.Z.); (Q.L.); (M.X.); (W.X.); (R.S.); (J.L.); (C.W.)
- Correspondence: ; Tel.: +86-371-6585-2150
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6
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Nielsen MR, Kaniki SEK, Sørensen JL. Targeted Genetic Engineering via Agrobacterium-Mediated Transformation in Fusarium solani. Methods Mol Biol 2022; 2489:93-114. [PMID: 35524047 DOI: 10.1007/978-1-0716-2273-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Members of the Fusarium solani species complex are filamentous fungi that can act as pathogens to many crops and animals. Although relevant, a robust molecular toolbox is missing for the investigation of gene function and metabolism. In this chapter, we describe how Agrobacterium-mediated transformation can be used to facilitate gene targeting. A flexible vector system, based on in vivo recombination in Saccharomyces cerevisiae, is utilized to achieve overexpression and gene deletion of targeted biosynthetic genes in F. solani f. sp. pisi.
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Affiliation(s)
- Mikkel Rank Nielsen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Esbjerg, Denmark.
| | | | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Esbjerg, Denmark
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7
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Genetic Relationships in the Toxin-Producing Fungal Endophyte, Alternaria oxytropis Using Polyketide Synthase and Non-Ribosomal Peptide Synthase Genes. J Fungi (Basel) 2021; 7:jof7070538. [PMID: 34356917 PMCID: PMC8306250 DOI: 10.3390/jof7070538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/16/2023] Open
Abstract
The legume Oxytropis sericea hosts a fungal endophyte, Alternaria oxytropis, which produces secondary metabolites (SM), including the toxin swainsonine. Polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) enzymes are associated with biosynthesis of fungal SM. To better understand the origins of the SM, an unannotated genome of A. oxytropis was assessed for protein sequences similar to known PKS and NRPS enzymes of fungi. Contigs exhibiting identity with known genes were analyzed at nucleotide and protein levels using available databases. Software were used to identify PKS and NRPS domains and predict identity and function. Confirmation of sequence for selected gene sequences was accomplished using PCR. Thirteen PKS, 5 NRPS, and 4 PKS-NRPS hybrids were identified and characterized with functions including swainsonine and melanin biosynthesis. Phylogenetic relationships among closest amino acid matches with Alternaria spp. were identified for seven highly conserved PKS and NRPS, including melanin synthesis. Three PKS and NRPS were most closely related to other fungi within the Pleosporaceae family, while five PKS and PKS-NRPS were closely related to fungi in the Pleosporales order. However, seven PKS and PKS-NRPS showed no identity with fungi in the Pleosporales or the class Dothideomycetes, suggesting a different evolutionary origin for those genes.
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8
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Shenouda ML, Cox RJ. Molecular methods unravel the biosynthetic potential of Trichoderma species. RSC Adv 2021; 11:3622-3635. [PMID: 35424278 PMCID: PMC8694227 DOI: 10.1039/d0ra09627j] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022] Open
Abstract
Members of the genus Trichoderma are a well-established and studied group of fungi, mainly due to their efficient protein production capabilities and their biocontrol activities. Despite the immense interest in the use of different members of this species as biopesticides and biofertilizers, the study of their active metabolites and their biosynthetic gene clusters has not gained significant attention until recently. Here we review the challenges and opportunities in exploiting the full potential of Trichoderma spp. for the production of natural products and new metabolic engineering strategies used to overcome some of these challenges.
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Affiliation(s)
- Mary L Shenouda
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University 21521 Egypt
| | - Russell J Cox
- OCI, BMWZ, Leibniz University of Hannover Schneiderberg 38 30167 Hannover Germany
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Fu FF, Hao Z, Wang P, Lu Y, Xue LJ, Wei G, Tian Y, Hu B, Xu H, Shi J, Cheng T, Wang G, Yi Y, Chen J. Genome Sequence and Comparative Analysis of Colletotrichum gloeosporioides Isolated from Liriodendron Leaves. PHYTOPATHOLOGY 2020; 110:1260-1269. [PMID: 32202483 DOI: 10.1094/phyto-12-19-0452-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Colletotrichum gloeosporioides is a hemibiotrophic pathogen causing significant losses to economically important crops and forest trees, including Liriodendron. To explore the interaction between C. gloeosporioides and Liriodendron and to identify the candidate genes determining the pathogenesis, we sequenced and assembled the whole genome of C. gloeosporioides Lc1 (CgLc1) using PacBio and Illumina next generation sequencing and performed a comparative genomic analysis between CgLc1 and Cg01, the latter being a described endophytic species of the C. gloeosporioides complex. Gene structure prediction identified 15,744 protein-coding genes and 837 noncoding RNAs. Species-specific genes were characterized using an ortholog analysis followed by a pathway enrichment analysis, which showed that genes specific to CgLc1 were enriched for the arginine biosynthetic process. Furthermore, genome synteny analysis revealed that most of the protein-coding genes fell into collinear blocks. However, two clusters of polyketide synthase genes were identified to be specific for CgLc1, suggesting that they might have an important role in virulence control. Transcriptional regulators coexpressed with polyketide synthase genes were detected through a Weighted Correlation Network Analysis. Taken together, this work provides new insight into the virulence- and pathogenesis-associated genes present in C. gloeosporioides and its possible lifestyle.
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Affiliation(s)
- Fang-Fang Fu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Pengkai Wang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ye Lu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liang-Jiao Xue
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Guoyu Wei
- Shanghai Municipal Agricultural and Rural Affairs Commission, Shanghai, China
| | - Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Haibin Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Guibin Wang
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yin Yi
- State Forestry Administration Key Laboratory of Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, China
- Guizhou Provincial Key Laboratory of Plant Physiology and Developmental Regulation, Guizhou Normal University, Guiyang, China
| | - Jinhui Chen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
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10
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Fusarium Secondary Metabolism Biosynthetic Pathways: So Close but So Far Away. REFERENCE SERIES IN PHYTOCHEMISTRY 2020. [DOI: 10.1007/978-3-319-96397-6_28] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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11
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Nielsen MR, Holzwarth AKR, Brew E, Chrapkova N, Kaniki SEK, Kastaniegaard K, Sørensen T, Westphal KR, Wimmer R, Sondergaard TE, Sørensen JL. A new vector system for targeted integration and overexpression of genes in the crop pathogen Fusarium solani. Fungal Biol Biotechnol 2019; 6:25. [PMID: 31890232 PMCID: PMC6905090 DOI: 10.1186/s40694-019-0089-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Besides their ability to produce several interesting bioactive secondary metabolites, members of the Fusarium solani species complex comprise important pathogens of plants and humans. One of the major obstacles in understanding the biology of this species complex is the lack of efficient molecular tools for genetic manipulation. Results To remove this obstacle we here report the development of a reliable system where the vectors are generated through yeast recombinational cloning and inserted into a specific site in F. solani through Agrobacterium tumefaciens-mediated transformation. As proof-of-concept, the enhanced yellow fluorescent protein (eYFP) was inserted in a non-coding genomic position of F. solani and subsequent analyses showed that the resulting transformants were fluorescent on all tested media. In addition, we cloned and overexpressed the Zn(II)2Cys6 transcriptional factor fsr6 controlling mycelial pigmentation. A transformant displayed deep red/purple pigmentation stemming from bostrycoidin and javanicin. Conclusion By creating streamlined plasmid construction and fungal transformation systems, we are now able to express genes in the crop pathogen F. solani in a reliable and fast manner. As a case study, we targeted and activated the fusarubin (PKS3: fsr) gene cluster, which is the first case study of secondary metabolites being directly associated with the responsible gene cluster in F. solani via targeted activation. The system provides an approach that in the future can be used by the community to understand the biochemistry and genetics of the Fusarium solani species complex, and is obtainable from Addgene catalog #133094. Graphic abstract
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Affiliation(s)
- Mikkel Rank Nielsen
- 1Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark
| | | | - Emmett Brew
- 1Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark
| | - Natalia Chrapkova
- 1Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark
| | | | - Kenneth Kastaniegaard
- 2Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Trine Sørensen
- 2Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Klaus Ringsborg Westphal
- 2Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Reinhard Wimmer
- 2Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Teis Esben Sondergaard
- 2Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Jens Laurids Sørensen
- 1Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark
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12
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Lebeau J, Petit T, Dufossé L, Caro Y. Putative metabolic pathway for the bioproduction of bikaverin and intermediates thereof in the wild Fusarium oxysporum LCP531 strain. AMB Express 2019; 9:186. [PMID: 31748828 PMCID: PMC6868082 DOI: 10.1186/s13568-019-0912-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 12/03/2022] Open
Abstract
Fungal naphthoquinones, like red bikaverin, are of interest due to their growing applications in designing pharmaceutical products. Though considerable work has been done on the elucidation of bikaverin biosynthesis pathway in Fusarium fujikuroi, very few reports are available regarding its bioproduction in F. oxysporum. We are hereby proposing a putative metabolic pathway for bikaverin bioproduction in a wild F. oxysporum strain by cross-linking the pigment profiles we obtained under two different fermentation conditions with literature. Naphthoquinone pigments were extracted with a pressurized liquid extraction method, and characterized by HPLC–DAD and UHPLC-HRMS. The results led to the conclusions that the F. oxysporum LCP531 strain was able to produce bikaverin and its various intermediates, e.g., pre-bikaverin, oxo-pre-bikaverin, dinor-bikaverin, me-oxo-pre-bikaverin, and nor-bikaverin, in submerged cultures in various proportions. To our knowledge, this is the first report of the isolation of these five bikaverin intermediates from F. oxysporum cultures, providing us with steady clues for confirming a bikaverin metabolic pathway as well as some of its regulatory patterns in the F. oxysporum LCP531 strain, based on the previously reported model in F. fujikuroi. Interestingly, norbikaverin accumulated along with bikaverin in mycelial cells when the strain grew on simple carbon and nitrogen sources and additional cofactors. Along bikaverin production, we were able to describe the excretion of the toxin beauvericin as main extrolite exclusively in liquid medium containing complex nitrogen and carbon sources, as well as the isolation of ergosterol derivate in mycelial extracts, which have potential for pharmaceutical uses. Therefore, culture conditions were also concluded to trigger some specific biosynthetic route favoring various metabolites of interest. Such observation is of great significance for selective production of pigments and/or prevention of occurrence of others (aka mycotoxins).
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13
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Nielsen MR, Sondergaard TE, Giese H, Sørensen JL. Advances in linking polyketides and non-ribosomal peptides to their biosynthetic gene clusters in Fusarium. Curr Genet 2019; 65:1263-1280. [DOI: 10.1007/s00294-019-00998-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 11/24/2022]
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14
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Westphal KR, Nielsen KAH, Wollenberg RD, Møllehøj MB, Bachleitner S, Studt L, Lysøe E, Giese H, Wimmer R, Sørensen JL, Sondergaard TE. Fusaoctaxin A, an Example of a Two-Step Mechanism for Non-Ribosomal Peptide Assembly and Maturation in Fungi. Toxins (Basel) 2019; 11:E277. [PMID: 31100892 PMCID: PMC6563249 DOI: 10.3390/toxins11050277] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/23/2022] Open
Abstract
Fungal non-ribosomal peptide synthetase (NRPS) clusters are spread across the chromosomes, where several modifying enzyme-encoding genes typically flank one NRPS. However, a recent study showed that the octapeptide fusaoctaxin A is tandemly synthesized by two NRPSs in Fusarium graminearum. Here, we illuminate parts of the biosynthetic route of fusaoctaxin A, which is cleaved into the tripeptide fusatrixin A and the pentapeptide fusapentaxin A during transport by a cluster-specific ABC transporter with peptidase activity. Further, we deleted the histone H3K27 methyltransferase kmt6, which induced the production of fusaoctaxin A.
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Affiliation(s)
| | | | | | | | - Simone Bachleitner
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Straße 24, Tulln an der Donau 3430, Austria.
| | - Lena Studt
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Straße 24, Tulln an der Donau 3430, Austria.
| | - Erik Lysøe
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, 1433 Ås, Norway.
| | - Henriette Giese
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark.
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15
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Lebeau J, Petit T, Clerc P, Dufossé L, Caro Y. Isolation of two novel purple naphthoquinone pigments concomitant with the bioactive red bikaverin and derivates thereof produced by Fusarium oxysporum. Biotechnol Prog 2018; 35:e2738. [DOI: 10.1002/btpr.2738] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 09/14/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Juliana Lebeau
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments; Université de La Réunion; Saint-Denis France
| | - Thomas Petit
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments; Université de La Réunion; Saint-Denis France
- Département Hygiène Sécurité Environnement (HSE); IUT La Réunion, Université de La Réunion; Saint-Pierre France
| | - Patricia Clerc
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments; Université de La Réunion; Saint-Denis France
| | - Laurent Dufossé
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments; Université de La Réunion; Saint-Denis France
| | - Yanis Caro
- Laboratoire de Chimie des Substances Naturelles et des Sciences des Aliments; Université de La Réunion; Saint-Denis France
- Département Hygiène Sécurité Environnement (HSE); IUT La Réunion, Université de La Réunion; Saint-Pierre France
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16
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Westphal KR, Muurmann AT, Paulsen IE, Nørgaard KTH, Overgaard ML, Dall SM, Aalborg T, Wimmer R, Sørensen JL, Sondergaard TE. Who Needs Neighbors? PKS8 Is a Stand-Alone Gene in Fusarium graminearum Responsible for Production of Gibepyrones and Prolipyrone B. Molecules 2018; 23:E2232. [PMID: 30200525 PMCID: PMC6225250 DOI: 10.3390/molecules23092232] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/28/2018] [Accepted: 09/01/2018] [Indexed: 01/13/2023] Open
Abstract
Genome sequencing of the genus Fusarium has revealed a great capacity for discovery of new natural products of potential economical and therapeutic importance. Several of these are unknown. In this study, we investigated the product of the PKS8 gene in Fusarium graminearum, which was recently linked to gibepyrones in F. fujikuroi. Genomic analyses showed that PKS8 constitutes a stand-alone gene in F. graminearum and related species. Overexpression of PKS8 resulted in production of gibepyrones A, B, D, G and prolipyrone B, which could not be detected in the wild type strain. Our results suggest that PKS8 produces the entry compound gibepyrone A, which is subsequently oxidized by one or several non-clustering cytochrome P450 monooxygenases ending with prolipyrone B.
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Affiliation(s)
| | | | - Iben Engell Paulsen
- Department of Chemistry and Bioscience, Aalborg University, 9100 Aalborg, Denmark.
| | | | - Marie Lund Overgaard
- Department of Chemistry and Bioscience, Aalborg University, 9100 Aalborg, Denmark.
| | | | - Trine Aalborg
- Department of Chemistry and Bioscience, Aalborg University, 9100 Aalborg, Denmark.
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University, 9100 Aalborg, Denmark.
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Wang G, Sun P, Gong Z, Gu L, Lou Y, Fang W, Zhang L, Su L, Yang T, Wang B, Zhou J, Xu JR, Wang Z, Zheng W. Srk1 kinase, a SR protein-specific kinase, is important for sexual reproduction, plant infection and pre-mRNA processing in Fusarium graminearum. Environ Microbiol 2018; 20:3261-3277. [DOI: 10.1111/1462-2920.14299] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 05/24/2018] [Accepted: 05/26/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Guanghui Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
- Institute of Oceanography; Minjiang University; Fuzhou China
| | - Peng Sun
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Ziwen Gong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Center (BFPC), Haixia Institute of Science and Technology; Fujian Agriculture and Forestry University; Fuzhou China
| | - Yi Lou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Wenqin Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Lianhu Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Li Su
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Tao Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Baohua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
| | - Jie Zhou
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins; College of Life Sciences, Fujian Agriculture and Forestry University; Fuzhou China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas; College of Plant Protection, Northwest A&F University; Yangling Shaanxi China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
- Institute of Oceanography; Minjiang University; Fuzhou China
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; College of Plant Protection, Fujian Agriculture and Forestry University; Fuzhou China
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18
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Hoogendoorn K, Barra L, Waalwijk C, Dickschat JS, van der Lee TAJ, Medema MH. Evolution and Diversity of Biosynthetic Gene Clusters in Fusarium. Front Microbiol 2018; 9:1158. [PMID: 29922257 PMCID: PMC5996196 DOI: 10.3389/fmicb.2018.01158] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 05/14/2018] [Indexed: 11/13/2022] Open
Abstract
Plant pathogenic fungi in the Fusarium genus cause severe damage to crops, resulting in great financial losses and health hazards. Specialized metabolites synthesized by these fungi are known to play key roles in the infection process, and to provide survival advantages inside and outside the host. However, systematic studies of the evolution of specialized metabolite-coding potential across Fusarium have been scarce. Here, we apply a combination of bioinformatic approaches to identify biosynthetic gene clusters (BGCs) across publicly available genomes from Fusarium, to group them into annotated families and to study gain/loss events of BGC families throughout the history of the genus. Comparison with MIBiG reference BGCs allowed assignment of 29 gene cluster families (GCFs) to pathways responsible for the production of known compounds, while for 57 GCFs, the molecular products remain unknown. Comparative analysis of BGC repertoires using ancestral state reconstruction raised several new hypotheses on how BGCs contribute to Fusarium pathogenicity or host specificity, sometimes surprisingly so: for example, a gene cluster for the biosynthesis of hexadehydro-astechrome was identified in the genome of the biocontrol strain Fusarium oxysporum Fo47, while being absent in that of the tomato pathogen F. oxysporum f.sp. lycopersici. Several BGCs were also identified on supernumerary chromosomes; heterologous expression of genes for three terpene synthases encoded on the Fusarium poae supernumerary chromosome and subsequent GC/MS analysis showed that these genes are functional and encode enzymes that each are able to synthesize koraiol; this observed functional redundancy supports the hypothesis that localization of copies of BGCs on supernumerary chromosomes provides freedom for evolutionary innovations to occur, while the original function remains conserved. Altogether, this systematic overview of biosynthetic diversity in Fusarium paves the way for targeted natural product discovery based on automated identification of species-specific pathways as well as for connecting species ecology to the taxonomic distributions of BGCs.
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Affiliation(s)
- Koen Hoogendoorn
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands.,Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Lena Barra
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Cees Waalwijk
- Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Jeroen S Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Theo A J van der Lee
- Biointeractions and Plant Health, Plant Research International, Wageningen University and Research, Wageningen, Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, Netherlands
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19
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Efficient genome editing in Fusarium oxysporum based on CRISPR/Cas9 ribonucleoprotein complexes. Fungal Genet Biol 2018; 117:21-29. [PMID: 29763675 DOI: 10.1016/j.fgb.2018.05.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 01/25/2023]
Abstract
The Fusarium oxysporum species complex (FOSC) is an economically important group of pathogenic filamentous fungi that are able to infect both animals and plants. Reverse genetic techniques, including gene disruption/deletion methods, to study these fungi are available although limitations exist resulting in decreased efficiency. Herein we describe a gene editing system developed using a F. oxysporum-optimized Cas9 ribonucleoprotein (RNP) and protoplast transformation method. The Cas9 protein and sgRNA were assembled to form a stable RNP in vitro and this complex was transferred into fungal protoplasts for gene editing with PEG-mediated transformation. In order to determine if the Cas9 RNP system is functional in the FOSC protoplasts and assess the efficacy of the system, two genes, URA5 and URA3, were selected for targeted disruption generating uracil auxotroph mutants that are resistant to 5-fluoroorotic acid, 5-FOA. In addition, a gene in a secondary metabolite biosynthetic cluster, the ortholog of BIK1, was mutated using this system and the maximum efficiency of this gene disruption was about 50%. Further analysis of the bik1 mutant confirmed that this polyketide synthase was involved in the synthesis of the red pigment, bikaverin. The mutants generated in this study displayed the strong expected phenotypes, demonstrating this F. oxysporum-optimized CRISPR/Cas9 system is stable and can efficiently disrupt the genes of interest.
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20
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Atanasova-Penichon V, Legoahec L, Bernillon S, Deborde C, Maucourt M, Verdal-Bonnin MN, Pinson-Gadais L, Ponts N, Moing A, Richard-Forget F. Mycotoxin Biosynthesis and Central Metabolism Are Two Interlinked Pathways in Fusarium graminearum, as Demonstrated by the Extensive Metabolic Changes Induced by Caffeic Acid Exposure. Appl Environ Microbiol 2018; 84:e01705-17. [PMID: 29427428 PMCID: PMC5881057 DOI: 10.1128/aem.01705-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/30/2018] [Indexed: 12/22/2022] Open
Abstract
Fusarium graminearum is a major plant pathogen that causes devastating diseases of cereals and produces type B trichothecene (TCTB) mycotoxins in infected grains. A comprehensive understanding of the molecular and biochemical mechanisms underlying the regulation of TCTB biosynthesis is required for improving strategies to control the TCTB contamination of crops and ensuring that these strategies do not favor the production of other toxic metabolites by F. graminearum Elucidation of the association of TCTB biosynthesis with other central and specialized processes was the focus of this study. Combined 1H nuclear magnetic resonance (1H NMR) and liquid chromatography-quadrupole time of flight-mass spectrometry (LC-QTOF-MS) analyses were used to compare the exo- and endometabolomes of F. graminearum grown under toxin-inducing and -repressing caffeic acid conditions. Ninety-five metabolites were putatively or unambiguously identified, including 26 primary and 69 specialized metabolites. Our data demonstrated that the inhibition of TCTB production induced by caffeic acid exposure was associated with significant changes in the secondary and primary metabolism of F. graminearum, although the fungal growth was not affected. The main metabolic changes were an increase in the accumulation of several polyketides, including toxic ones, alterations in the tricarboxylic organic acid cycle, and modifications in the metabolism of several amino acids and sugars. While these findings provide insights into the mechanisms that govern the inhibition of TCTB production by caffeic acid, they also demonstrate the interdependence between the biosynthetic pathway of TCTB and several primary and specialized metabolic pathways. These results provide further evidence of the multifaceted role of TCTB in the life cycle of F. graminearumIMPORTANCEFusarium graminearum is a major plant pathogen that causes devastating diseases of cereal crops and produces type B trichothecene (TCTB) mycotoxins in infected grains. The best way to restrict consumer exposure to TCTB is to limit their production before harvest, which requires increasing the knowledge on the mechanisms that regulate their biosynthesis. Using a metabolomics approach, we investigated the interconnection between the TCTB production pathway and several fungal metabolic pathways. We demonstrated that alteration in the TCTB biosynthetic pathway can have a significant impact on other metabolic pathways, including the biosynthesis of toxic polyketides, and vice versa. These findings open new avenues for identifying fungal targets for the design of molecules with antimycotoxin properties and therefore improving sustainable strategies to fight against diseases caused by F. graminearum Our data further demonstrate that analyses should consider all fungal toxic metabolites rather than the targeted family of mycotoxins when assessing the efficacy of control strategies.
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Affiliation(s)
| | - Laurie Legoahec
- UR1264 MycSA, INRA, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
| | - Stéphane Bernillon
- UMR1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
| | - Catherine Deborde
- UMR1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
| | - Mickaël Maucourt
- UMR1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
| | | | - Laetitia Pinson-Gadais
- UR1264 MycSA, INRA, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
| | - Nadia Ponts
- UR1264 MycSA, INRA, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
| | - Annick Moing
- UMR1332 Biologie du Fruit et Pathologie, INRA, Université de Bordeaux, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
- Metabolome Facility of Bordeaux Functional Genomics Center, MetaboHUB, IBVM, Centre INRA de Nouvelle Aquitaine-Bordeaux, Villenave d'Ornon, France
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21
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Niehaus EM, Studt L, von Bargen KW, Kummer W, Humpf HU, Reuter G, Tudzynski B. Sound of silence: the beauvericin cluster in Fusarium fujikuroi is controlled by cluster-specific and global regulators mediated by H3K27 modification. Environ Microbiol 2017; 18:4282-4302. [PMID: 27750383 DOI: 10.1111/1462-2920.13576] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 10/11/2016] [Indexed: 01/25/2023]
Abstract
In this study, we compared the secondary metabolite profile of Fusarium fujikuroi and the histone deacetylase mutant ΔHDA1. We identified a novel peak in ΔHDA1, which was identified as beauvericin (BEA). Going in line with a 1000-fold increased BEA production, the respective non-ribosomal peptide synthetase (NRPS)-encoding gene (BEA1), as well as two adjacent genes (BEA2-BEA3), were significantly up-regulated in ΔHDA1 compared to the wild type. A special role was revealed for the ABC transporter Bea3: deletion of the encoding gene resulted in significant up-regulation of BEA1 and BEA2 and drastically elevated product yields. Furthermore, mutation of a conserved sequence motif in the promoter of BEA1 released BEA repression and resulted in elevated product levels. Candidate transcription factors (TFs) that could bind to this motif are the cluster-specific TF Bea4 as well as a homolog of the global mammalian Kruppel-like TF Yin Yang 1 (Yy1), both acting as repressors of BEA biosynthesis. In addition to Hda1, BEA biosynthesis is repressed by the activity of the H3K27 methyltransferase Kmt6. Consistently, Western blot analyses revealed a genome-wide enrichment of H3K27 acetylation (H3K27ac) in the ΔHDA1 and KMT6 knock-down mutants. Subsequent chromatin immunoprecipitation (ChIP) experiments showed elevated H3K27ac modification levels at the BEA cluster.
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Affiliation(s)
- Eva-Maria Niehaus
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, Münster, D-48143
| | - Lena Studt
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, Münster, D-48143
| | - Katharina W von Bargen
- Institut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 45, Münster, D-48149
| | - Wiebke Kummer
- Institut für Genetik, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, Halle (Saale), D-06120
| | - Hans-Ulrich Humpf
- Institut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstr. 45, Münster, D-48149
| | - Gunter Reuter
- Institut für Genetik, Martin Luther Universität Halle-Wittenberg, Weinbergweg 10, Halle (Saale), D-06120
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 8, Münster, D-48143
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22
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Wollenberg RD, Saei W, Westphal KR, Klitgaard CS, Nielsen KL, Lysøe E, Gardiner DM, Wimmer R, Sondergaard TE, Sørensen JL. Chrysogine Biosynthesis Is Mediated by a Two-Module Nonribosomal Peptide Synthetase. JOURNAL OF NATURAL PRODUCTS 2017; 80:2131-2135. [PMID: 28708398 DOI: 10.1021/acs.jnatprod.6b00822] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Production of chrysogine has been reported from several fungal genera including Penicillium, Aspergillus, and Fusarium. Anthranilic acid and pyruvic acid, which are expected precursors of chrysogine, enhance production of this compound. A possible route for the biosynthesis using these substrates is via a nonribosomal peptide synthetase (NRPS). Through comparative analysis of the NRPSs from genome-sequenced producers of chrysogine we identified a candidate NRPS cluster comprising five additional genes named chry2-6. Deletion of the two-module NRPS (NRPS14 = chry1) abolished chrysogine production in Fusarium graminearum, indicating that the gene cluster is responsible for chrysogine biosynthesis. Overexpression of NRPS14 enhanced chrysogine production, suggesting that the NRPS is the bottleneck in the biosynthetic pathway.
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Affiliation(s)
- Rasmus Dam Wollenberg
- Department of Chemistry and Bioscience, Aalborg University , Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Wagma Saei
- Department of Chemistry and Bioscience, Aalborg University , Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Klaus Ringsborg Westphal
- Department of Chemistry and Bioscience, Aalborg University , Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Carina Sloth Klitgaard
- Department of Chemistry and Bioscience, Aalborg University , Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Kåre Lehmann Nielsen
- Department of Chemistry and Bioscience, Aalborg University , Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Erik Lysøe
- Department of Biotechnology and Plant Health, NIBIO-Norwegian Institute of Bioeconomy Research , Høgskoleveien 7, 1430 Ås, Norway
| | - Donald Max Gardiner
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture and Food, Queensland Bioscience Precinct , Brisbane, Australia
| | - Reinhard Wimmer
- Department of Chemistry and Bioscience, Aalborg University , Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Teis Esben Sondergaard
- Department of Chemistry and Bioscience, Aalborg University , Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University , Fredrik Bajers Vej 7H, 9220 Aalborg Ø, Denmark
- Department of Chemistry and Bioscience, Aalborg University , Niels Bohrs Vej 8, 6700 Esbjerg, Denmark
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Studt L, Janevska S, Arndt B, Boedi S, Sulyok M, Humpf HU, Tudzynski B, Strauss J. Lack of the COMPASS Component Ccl1 Reduces H3K4 Trimethylation Levels and Affects Transcription of Secondary Metabolite Genes in Two Plant-Pathogenic Fusarium Species. Front Microbiol 2017; 7:2144. [PMID: 28119673 PMCID: PMC5220078 DOI: 10.3389/fmicb.2016.02144] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/20/2016] [Indexed: 01/07/2023] Open
Abstract
In the two fungal pathogens Fusarium fujikuroi and Fusarium graminearum, secondary metabolites (SMs) are fitness and virulence factors and there is compelling evidence that the coordination of SM gene expression is under epigenetic control. Here, we characterized Ccl1, a subunit of the COMPASS complex responsible for methylating lysine 4 of histone H3 (H3K4me). We show that Ccl1 is not essential for viability but a regulator of genome-wide trimethylation of H3K4 (H3K4me3). Although, recent work in Fusarium and Aspergillus spp. detected only sporadic H3K4 methylation at the majority of the SM gene clusters, we show here that SM profiles in CCL1 deletion mutants are strongly deviating from the wild type. Cross-complementation experiments indicate high functional conservation of Ccl1 as phenotypes of the respective △ccl1 were rescued in both fungi. Strikingly, biosynthesis of the species-specific virulence factors gibberellic acid and deoxynivalenol produced by F. fujikuroi and F. graminearum, respectively, was reduced in axenic cultures but virulence was not attenuated in these mutants, a phenotype which goes in line with restored virulence factor production levels in planta. This suggests that yet unknown plant-derived signals are able to compensate for Ccl1 function during pathogenesis.
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Affiliation(s)
- Lena Studt
- Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life SciencesVienna, Tulln an der Donau, Austria,Institute for Plant Biology and Biotechnology, Westfälische Wilhelms UniversityMünster, Germany,*Correspondence: Lena Studt, Joseph Strauss,
| | - Slavica Janevska
- Institute for Plant Biology and Biotechnology, Westfälische Wilhelms UniversityMünster, Germany
| | - Birgit Arndt
- Institute of Food Chemistry, Westfälische Wilhelms UniversityMünster, Germany
| | - Stefan Boedi
- Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life SciencesVienna, Tulln an der Donau, Austria
| | - Michael Sulyok
- Center for Analytical Chemistry, Department IFA-Tulln, BOKU-University of Natural Resources and Life SciencesVienna, Tulln an der Donau, Austria
| | - Hans-Ulrich Humpf
- Institute of Food Chemistry, Westfälische Wilhelms UniversityMünster, Germany
| | - Bettina Tudzynski
- Institute for Plant Biology and Biotechnology, Westfälische Wilhelms UniversityMünster, Germany
| | - Joseph Strauss
- Division of Microbial Genetics and Pathogen Interactions, Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life SciencesVienna, Tulln an der Donau, Austria,*Correspondence: Lena Studt, Joseph Strauss,
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24
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Fungal Innate Immunity Induced by Bacterial Microbe-Associated Molecular Patterns (MAMPs). G3-GENES GENOMES GENETICS 2016; 6:1585-95. [PMID: 27172188 PMCID: PMC4889655 DOI: 10.1534/g3.116.027987] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Plants and animals detect bacterial presence through Microbe-Associated Molecular Patterns (MAMPs) which induce an innate immune response. The field of fungal-bacterial interaction at the molecular level is still in its infancy and little is known about MAMPs and their detection by fungi. Exposing Fusarium graminearum to bacterial MAMPs led to increased fungal membrane hyperpolarization, a putative defense response, and a range of transcriptional responses. The fungus reacted with a different transcript profile to each of the three tested MAMPs, although a core set of genes related to energy generation, transport, amino acid production, secondary metabolism, and especially iron uptake were detected for all three. Half of the genes related to iron uptake were predicted MirA type transporters that potentially take up bacterial siderophores. These quick responses can be viewed as a preparation for further interactions with beneficial or pathogenic bacteria, and constitute a fungal innate immune response with similarities to those of plants and animals.
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25
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Alvin A, Kalaitzis J, Sasia B, Neilan B. Combined genetic and bioactivity‐based prioritization leads to the isolation of an endophyte‐derived antimycobacterial compound. J Appl Microbiol 2016; 120:1229-39. [DOI: 10.1111/jam.13062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/14/2015] [Accepted: 01/12/2016] [Indexed: 01/09/2023]
Affiliation(s)
- A. Alvin
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW Australia
| | - J.A. Kalaitzis
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW Australia
| | - B. Sasia
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW Australia
| | - B.A. Neilan
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW Australia
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26
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Identification of the non-ribosomal peptide synthetase responsible for biosynthesis of the potential anti-cancer drug sansalvamide in Fusarium solani. Curr Genet 2016; 62:799-807. [PMID: 26936154 DOI: 10.1007/s00294-016-0584-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 02/16/2016] [Accepted: 02/18/2016] [Indexed: 12/24/2022]
Abstract
Sansalvamide is a cyclic pentadepsipeptide produced by Fusarium solani and has shown promising results as potential anti-cancer drug. The biosynthetic pathway has until now remained unidentified, but here we used an Agrobacterium tumefaciens-mediated transformation (ATMT) approach to generate knockout mutants of two candidate non-ribosomal peptide synthetases (NRPS29 and NRPS30). Comparative studies of secondary metabolites in the two deletion mutants and wild type confirmed the absence of sansalvamide in the NRPS30 deletion mutant, implicating this synthetase in the biosynthetic pathway for sansalvamide. Sansalvamide is structurally related to the cyclic hexadepsipeptide destruxin, which both contain an α-hydroxyisocaproic acid (HICA) unit. A gene cluster responsible for destruxin production has previously been identified in Metarhizium robertsii together with a hypothetical biosynthetic pathway. Using comparative bioinformatic analyses of the catalytic domains in the destruxin and sansalvamide NRPSs, we were able to propose a model for sansalvamide biosynthesis. Orthologues of the gene clusters were also identified in species from several other genera including Acremonium chrysogenum and Trichoderma virens, which suggests that the ability to produce compounds related to destruxin and sansalvamide is widespread.
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27
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Hofstad AN, Nussbaumer T, Akhunov E, Shin S, Kugler KG, Kistler HC, Mayer KFX, Muehlbauer GJ. Examining the Transcriptional Response in Wheat Near-Isogenic Lines to Infection and Deoxynivalenol Treatment. THE PLANT GENOME 2016; 9. [PMID: 27898755 DOI: 10.3835/plantgenome2015.05.0032] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
head blight (FHB) is a disease caused predominantly by the fungal pathogen that affects wheat and other small-grain cereals and can lead to severe yield loss and reduction in grain quality. Trichothecene mycotoxins, such as deoxynivalenol (DON), accumulate during infection and increase pathogen virulence and decrease grain quality. The locus on wheat chromosome 3BS confers Type II resistance to FHB and resistance to the spread of infection on the spike and has been associated with resistance to DON accumulation. To gain a better genetic understanding of the functional role of and resistance or susceptibility to FHB, we examined DON and ergosterol accumulation, FHB resistance, and the whole-genome transcriptomic response using RNA-seq in a near-isogenic line (NIL) pair carrying the resistant and susceptible alleles for during infection and DON treatment. Our results provide a gene expression atlas for the resistant and susceptible wheat- interaction. The DON concentration and transcriptomic results show that the rachis is a key location for conferring Type II resistance. In addition, the wheat transcriptome analysis revealed a set of -responsive genes that may play a role in resistance and a set of DON-responsive genes that may play a role in trichothecene resistance. Transcriptomic results from the pathogen show that the genome responds differently to the host level of resistance. The results of this study extend our understanding of host and pathogen responses in the wheat- interaction.
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28
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Coleman JJ. The Fusarium solani species complex: ubiquitous pathogens of agricultural importance. MOLECULAR PLANT PATHOLOGY 2016; 17:146-58. [PMID: 26531837 PMCID: PMC6638333 DOI: 10.1111/mpp.12289] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
UNLABELLED Members of the Fusarium solani species complex (FSSC) are capable of causing disease in many agriculturally important crops. The genomes of some of these fungi include supernumerary chromosomes that are dispensable and encode host-specific virulence factors. In addition to genomics, this review summarizes the known molecular mechanisms utilized by members of the FSSC in establishing disease. TAXONOMY Kingdom Fungi; Phylum Ascomycota; Class Sordariomycetes; Order Hypocreales; Family Nectriaceae; Genus Fusarium. HOST RANGE Members of the FSSC collectively have a very broad host range, and have been subdivided previously into formae speciales. Recent phylogenetic analysis has revealed that formae speciales correspond to biologically and phylogenetically distinct species. DISEASE SYMPTOMS Typically, FSSC causes foot and/or root rot of the infected host plant, and the degree of necrosis correlates with the severity of the disease. Symptoms on above-ground portions of the plant can vary greatly depending on the specific FSSC pathogen and host plant, and the disease may manifest as wilting, stunting and chlorosis or lesions on the stem and/or leaves. CONTROL Implementation of agricultural management practices, such as crop rotation and timing of planting, can reduce the risk of crop loss caused by FSSC. If available, the use of resistant varieties is another means to control disease in the field. USEFUL WEBSITES http://genome.jgi-psf.org/Necha2/Necha2.home.html.
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Affiliation(s)
- Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
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29
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Insights into natural products biosynthesis from analysis of 490 polyketide synthases from Fusarium. Fungal Genet Biol 2016; 89:37-51. [PMID: 26826610 DOI: 10.1016/j.fgb.2016.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 01/02/2023]
Abstract
Species of the fungus Fusarium collectively cause disease on almost all crop plants and produce numerous natural products (NPs), including some of the mycotoxins of greatest concern to agriculture. Many Fusarium NPs are derived from polyketide synthases (PKSs), large multi-domain enzymes that catalyze sequential condensation of simple carboxylic acids to form polyketides. To gain insight into the biosynthesis of polyketide-derived NPs in Fusarium, we retrieved 488 PKS gene sequences from genome sequences of 31 species of the fungus. In addition to these apparently functional PKS genes, the genomes collectively included 81 pseudogenized PKS genes. Phylogenetic analysis resolved the PKS genes into 67 clades, and based on multiple lines of evidence, we propose that homologs in each clade are responsible for synthesis of a polyketide that is distinct from those synthesized by PKSs in other clades. The presence and absence of PKS genes among the species examined indicated marked differences in distribution of PKS homologs. Comparisons of Fusarium PKS genes and genes flanking them to those from other Ascomycetes provided evidence that Fusarium has the genetic potential to synthesize multiple NPs that are the same or similar to those reported in other fungi, but that have not yet been reported in Fusarium. The results also highlight ways in which such analyses can help guide identification of novel Fusarium NPs and differences in NP biosynthetic capabilities that exist among fungi.
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30
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Lysøe E, Frandsen RJN, Divon HH, Terzi V, Orrù L, Lamontanara A, Kolseth AK, Nielsen KF, Thrane U. Draft genome sequence and chemical profiling of Fusarium langsethiae, an emerging producer of type A trichothecenes. Int J Food Microbiol 2016; 221:29-36. [PMID: 26803271 DOI: 10.1016/j.ijfoodmicro.2016.01.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/27/2015] [Accepted: 01/11/2016] [Indexed: 12/27/2022]
Abstract
Fusarium langsethiae is a widespread pathogen of small grain cereals, causing problems with T-2 and HT-2 toxin contamination in grains every year. In an effort to better understand the biology of this fungus, we present a draft genome sequence of F. langsethiae Fl201059 isolated from oats in Norway. The assembly was fragmented, but reveals a genome of approximately 37.5 Mb, with a GC content around 48%, and 12,232 predicted protein-coding genes. Focusing on secondary metabolism we identified candidate genes for 12 polyketide synthases, 13 non-ribosomal peptide synthetases, and 22 genes for terpene/isoprenoid biosynthesis. Some of these were found to be unique compared to sequence databases. The identified putative Tri5 cluster was highly syntenic to the cluster reported in F. sporotrichioides. Fusarium langsethiae Fl201059 produces a high number of secondary metabolites on Yeast Extract Sucrose (YES) agar medium, dominated by type A trichothecenes. Interestingly we found production of glucosylated HT-2 toxin (Glu-HT-2), previously suggested to be formed by the host plant and not by the fungus itself. In greenhouse inoculations of F. langsethiae Fl201059 on barley and oats, we detected the type A trichothecenes: neosolaniol, HT-2 toxin, T-2 toxin, Glu-HT-2 and numerous derivatives of these.
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Affiliation(s)
- Erik Lysøe
- Department of Plant Health and Biotechnology, NIBIO - Norwegian Institute of Bioeconomy Research, Høgskoleveien 7, 1430 Ås, Norway.
| | - Rasmus J N Frandsen
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Hege H Divon
- Section of Mycology, Norwegian Veterinary Institute, PO Box 750, Sentrum 0106, Oslo, Norway
| | - Valeria Terzi
- Genomics Research Centre, Council for Agricultural Research and Economics, via S. Protaso, 302, I-29017 Fiorenzuola d'Arda PC, Italy
| | - Luigi Orrù
- Genomics Research Centre, Council for Agricultural Research and Economics, via S. Protaso, 302, I-29017 Fiorenzuola d'Arda PC, Italy
| | - Antonella Lamontanara
- Genomics Research Centre, Council for Agricultural Research and Economics, via S. Protaso, 302, I-29017 Fiorenzuola d'Arda PC, Italy
| | - Anna-Karin Kolseth
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, PO Box 7043, 75007 Uppsala, Sweden
| | - Kristian F Nielsen
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Ulf Thrane
- Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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31
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Harris LJ, Balcerzak M, Johnston A, Schneiderman D, Ouellet T. Host-preferential Fusarium graminearum gene expression during infection of wheat, barley, and maize. Fungal Biol 2015; 120:111-23. [PMID: 26693688 DOI: 10.1016/j.funbio.2015.10.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/22/2015] [Accepted: 10/19/2015] [Indexed: 11/25/2022]
Abstract
Fusarium graminearum is a broad host pathogen threatening cereal crops in temperate regions around the world. To better understand how F. graminearum adapts to different hosts, we have performed a comparison of the transcriptome of a single strain of F. graminearum during early infection (up to 4 d post-inoculation) of barley, maize, and wheat using custom oligomer microarrays. Our results showed high similarity between F. graminearum transcriptomes in infected wheat and barley spike tissues. Quantitative RT-PCR was used to validate the gene expression profiles of 24 genes. Host-specific expression of genes was observed in each of the three hosts. This included expression of distinct sets of genes associated with transport and secondary metabolism in each of the three crops, as well as host-specific patterns for particular gene categories such as sugar transporters, integral membrane protein PTH11-like proteins, and chitinases. This study identified 69 F. graminearum genes as preferentially expressed in developing maize kernels relative to wheat and barley spikes. These host-specific differences showcase the genomic flexibility of F. graminearum to adapt to a range of hosts.
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Affiliation(s)
- Linda J Harris
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
| | - Anne Johnston
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
| | - Danielle Schneiderman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada.
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32
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Zhou K, Salamov A, Kuo A, Aerts AL, Kong X, Grigoriev IV. Alternative splicing acting as a bridge in evolution. Stem Cell Investig 2015; 2:19. [PMID: 27358887 DOI: 10.3978/j.issn.2306-9759.2015.10.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND Alternative splicing (AS) regulates diverse cellular and developmental functions through alternative protein structures of different isoforms. Alternative exons dominate AS in vertebrates; however, very little is known about the extent and function of AS in lower eukaryotes. To understand the role of introns in gene evolution, we examined AS from a green algal and five fungal genomes using a novel EST-based gene-modeling algorithm (COMBEST). METHODS AS from each genome was classified with COMBEST that maps EST sequences to genomes to build gene models. Various aspects of AS were analyzed through statistical methods. The interplay of intron 3n length, phase, coding property, and intron retention (RI) were examined with Chi-square testing. RESULTS With 3 to 834 times EST coverage, we identified up to 73% of AS in intron-containing genes and found preponderance of RI among 11 types of AS. The number of exons, expression level, and maximum intron length correlated with number of AS per gene (NAG), and intron-rich genes suppressed AS. Genes with AS were more ancient, and AS was conserved among fungal genomes. Among stopless introns, non-retained introns (NRI) avoided, but major RI preferred 3n length. In contrast, stop-containing introns showed uniform distribution among 3n, 3n+1, and 3n+2 lengths. We found a clue to the intron phase enigma: it was the coding function of introns involved in AS that dictates the intron phase bias. CONCLUSIONS Majority of AS is non-functional, and the extent of AS is suppressed for intron-rich genes. RI through 3n length, stop codon, and phase bias bridges the transition from functionless to functional alternative isoforms.
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Affiliation(s)
- Kemin Zhou
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Asaf Salamov
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Alan Kuo
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Andrea L Aerts
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Xiangyang Kong
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
| | - Igor V Grigoriev
- 1 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA ; 2 Roche Molecular Diagnostics, 4300 Hacienda Drive, Pleasanton, CA 94588, USA ; 3 Department of Clinical Medicine, Kunming University of Science and Technology, Kunming 650031, China
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33
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Lee TV, Johnson RD, Arcus VL, Lott JS. Prediction of the substrate for nonribosomal peptide synthetase (NRPS) adenylation domains by virtual screening. Proteins 2015; 83:2052-66. [PMID: 26358936 DOI: 10.1002/prot.24922] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/19/2015] [Accepted: 08/28/2015] [Indexed: 12/28/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) synthesize a diverse array of bioactive small peptides, many of which are used in medicine. There is considerable interest in predicting NRPS substrate specificity in order to facilitate investigation of the many "cryptic" NRPS genes that have not been linked to any known product. However, the current sequence similarity-based methods are unable to produce reliable predictions when there is a lack of prior specificity data, which is a particular problem for fungal NRPSs. We conducted virtual screening on the specificity-determining domain of NRPSs, the adenylation domain, and found that virtual screening using experimentally determined structures results in good enrichment of the cognate substrate. Our results indicate that the conformation of the adenylation domain and in particular the conformation of a key conserved aromatic residue is important in determining the success of the virtual screening. When homology models of NRPS adenylation domains of known specificity, rather than experimentally determined structures, were built and used for virtual screening, good enrichment of the cognate substrate was also achieved in many cases. However, the accuracy of the models was key to the reliability of the predictions and there was a large variation in the results when different models of the same domain were used. This virtual screening approach is promising and is able to produce enrichment of the cognate substrates in many cases, but improvements in building and assessing homology models are required before the approach can be reliably applied to these models.
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Affiliation(s)
- T Verne Lee
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard D Johnson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Vickery L Arcus
- Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - J Shaun Lott
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, University of Auckland, Auckland, New Zealand
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34
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Hegge A, Lønborg R, Nielsen DM, Sørensen JL. Factors Influencing Production of Fusaristatin A in Fusarium graminearum. Metabolites 2015; 5:184-91. [PMID: 25838075 PMCID: PMC4495368 DOI: 10.3390/metabo5020184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 02/27/2015] [Accepted: 03/16/2015] [Indexed: 01/11/2023] Open
Abstract
Fusarium graminearum is a ubiquitous plant pathogen, which is able to produce several bioactive secondary metabolites. Recently, the cyclic lipopeptide fusaristatin A was isolated from this species and the biosynthetic gene cluster identified. Fusaristatin A consists of a C24 reduced polyketide and the three amino acids dehydroalanine, β-aminoisobutyric acid and glutamine and is biosynthesized by a collaboration of a polyketide synthase and a nonribosomal peptide synthetase. To gain insight into the environmental factors, which controls the production of fusaristatin A, we cultivated F. graminearum under various conditions. We developed an LC-MS/MS method to quantify fusaristatin A in F. graminearum extracts. The results showed that yeast extract sucrose (YES) medium was the best medium for fusaristatin A production and that the optimal pH was 7.5 and temperature 25–30 °C. Furthermore, production of fusaristatin A was more than four times higher in stationary cultures than in agitated cultures when F. graminearum was grown in liquid YES medium. The results also showed that fusaristatin A was only present in the mycelium and not in the liquid, which suggests that fusaristatin A is stored intracellulally and not exported to the extracellular environment.
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Affiliation(s)
- Anne Hegge
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark.
| | - Rikke Lønborg
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark.
| | - Ditte Møller Nielsen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark.
| | - Jens Laurids Sørensen
- Department of Chemistry and Bioscience, Aalborg University Esbjerg, Niels Bohrs Vej 8, 6700 Esbjerg, Denmark.
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35
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An update to polyketide synthase and non-ribosomal synthetase genes and nomenclature in Fusarium. Fungal Genet Biol 2015; 75:20-9. [DOI: 10.1016/j.fgb.2014.12.004] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 12/21/2022]
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36
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Oide S, Berthiller F, Wiesenberger G, Adam G, Turgeon BG. Individual and combined roles of malonichrome, ferricrocin, and TAFC siderophores in Fusarium graminearum pathogenic and sexual development. Front Microbiol 2015; 5:759. [PMID: 25628608 PMCID: PMC4290682 DOI: 10.3389/fmicb.2014.00759] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/12/2014] [Indexed: 11/15/2022] Open
Abstract
Intra- and extracellular iron-chelating siderophores produced by fungal non-ribosomal peptide synthetases have been shown to be involved in reproductive and pathogenic developmental processes and in iron and oxidative stress management. Here we report individual and combined contributions of three of these metabolites to developmental success of the destructive cereal pathogen Fusarium graminearum. In previous work, we determined that deletion of the NPS2 gene, responsible for intracellular siderophore biosynthesis, results in inability to produce sexual spores when mutants of this homothallic ascomycete are selfed. Deletion of the NPS6 gene, required for extracellular siderophore biosynthesis, does not affect sexual reproduction but results in sensitivity to iron starvation and oxidative stress and leads to reduced virulence to the host. Building on this, we report that double mutants lacking both NPS2 and NPS6 are augmented in all collective phenotypes of single deletion strains (i.e., abnormal sexual and pathogenic development, hypersensitivity to oxidative and iron-depletion stress), which suggests overlap of function. Using comparative biochemical analysis of wild-type and mutant strains, we show that NPS1, a third gene associated with siderophore biosynthesis, is responsible for biosynthesis of a second extracellular siderophore, malonichrome. nps1 mutants fail to produce this metabolite. Phenotypic characterization reveals that, although single nps1 mutants are like wild-type with respect to sexual development, hypersensitivity to ROS and iron-depletion stress, and virulence to the host, triple nps1nps2nps6 deletion strains, lacking all three siderophores, are even more impaired in these attributes than double nps2nps6 strains. Thus, combinatorial mutants lacking key iron-associated genes uncovered malonichrome function. The intimate connection between presence/absence of siderophores and resistance/sensitivity to ROS is central to sexual and pathogenic development.
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Affiliation(s)
- Shinichi Oide
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA ; The Research Institute of Innovative Technology for the Earth (RITE) Kizugawa-Shi, Japan
| | - Franz Berthiller
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, Austria
| | - Gerlinde Wiesenberger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Austria
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Austria
| | - B Gillian Turgeon
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA
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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. JOURNAL OF NATURAL PRODUCTS 2014; 77:2619-2625. [PMID: 25412204 DOI: 10.1021/np500436r] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [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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Lysøe E, Harris LJ, Walkowiak S, Subramaniam R, Divon HH, Riiser ES, Llorens C, Gabaldón T, Kistler HC, Jonkers W, Kolseth AK, Nielsen KF, Thrane U, Frandsen RJN. The genome of the generalist plant pathogen Fusarium avenaceum is enriched with genes involved in redox, signaling and secondary metabolism. PLoS One 2014; 9:e112703. [PMID: 25409087 PMCID: PMC4237347 DOI: 10.1371/journal.pone.0112703] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 10/13/2014] [Indexed: 12/03/2022] Open
Abstract
Fusarium avenaceum is a fungus commonly isolated from soil and associated with a wide range of host plants. We present here three genome sequences of F. avenaceum, one isolated from barley in Finland and two from spring and winter wheat in Canada. The sizes of the three genomes range from 41.6–43.1 MB, with 13217–13445 predicted protein-coding genes. Whole-genome analysis showed that the three genomes are highly syntenic, and share>95% gene orthologs. Comparative analysis to other sequenced Fusaria shows that F. avenaceum has a very large potential for producing secondary metabolites, with between 75 and 80 key enzymes belonging to the polyketide, non-ribosomal peptide, terpene, alkaloid and indole-diterpene synthase classes. In addition to known metabolites from F. avenaceum, fuscofusarin and JM-47 were detected for the first time in this species. Many protein families are expanded in F. avenaceum, such as transcription factors, and proteins involved in redox reactions and signal transduction, suggesting evolutionary adaptation to a diverse and cosmopolitan ecology. We found that 20% of all predicted proteins were considered to be secreted, supporting a life in the extracellular space during interaction with plant hosts.
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Affiliation(s)
- Erik Lysøe
- Department of Plant Health and Plant Protection, Bioforsk - Norwegian Institute of Agricultural and Environmental Research, Ås, Norway
- * E-mail:
| | - Linda J. Harris
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
| | - Sean Walkowiak
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
- Department of Biology, Carleton University, Ottawa, Canada
| | - Rajagopal Subramaniam
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Canada
- Department of Biology, Carleton University, Ottawa, Canada
| | - Hege H. Divon
- Section of Mycology, Norwegian Veterinary Institute, Oslo, Norway
| | - Even S. Riiser
- Department of Plant Health and Plant Protection, Bioforsk - Norwegian Institute of Agricultural and Environmental Research, Ås, Norway
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - H. Corby Kistler
- ARS-USDA, Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Wilfried Jonkers
- ARS-USDA, Cereal Disease Laboratory, St. Paul, Minnesota, United States of America
| | - Anna-Karin Kolseth
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kristian F. Nielsen
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Ulf Thrane
- Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
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The Fusarium graminearum genome reveals more secondary metabolite gene clusters and hints of horizontal gene transfer. PLoS One 2014; 9:e110311. [PMID: 25333987 PMCID: PMC4198257 DOI: 10.1371/journal.pone.0110311] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/11/2014] [Indexed: 01/07/2023] Open
Abstract
Fungal secondary metabolite biosynthesis genes are of major interest due to the pharmacological properties of their products (like mycotoxins and antibiotics). The genome of the plant pathogenic fungus Fusarium graminearum codes for a large number of candidate enzymes involved in secondary metabolite biosynthesis. However, the chemical nature of most enzymatic products of proteins encoded by putative secondary metabolism biosynthetic genes is largely unknown. Based on our analysis we present 67 gene clusters with significant enrichment of predicted secondary metabolism related enzymatic functions. 20 gene clusters with unknown metabolites exhibit strong gene expression correlation in planta and presumably play a role in virulence. Furthermore, the identification of conserved and over-represented putative transcription factor binding sites serves as additional evidence for cluster co-regulation. Orthologous cluster search provided insight into the evolution of secondary metabolism clusters. Some clusters are characteristic for the Fusarium phylum while others show evidence of horizontal gene transfer as orthologs can be found in representatives of the Botrytis or Cochliobolus lineage. The presented candidate clusters provide valuable targets for experimental examination.
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Fusarium graminearum PKS14 is involved in orsellinic acid and orcinol synthesis. Fungal Genet Biol 2014; 70:24-31. [DOI: 10.1016/j.fgb.2014.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 12/19/2022]
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Schindler D, Nowrousian M. The polyketide synthase gene pks4 is essential for sexual development and regulates fruiting body morphology in Sordaria macrospora. Fungal Genet Biol 2014; 68:48-59. [PMID: 24792494 DOI: 10.1016/j.fgb.2014.04.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 04/02/2014] [Accepted: 04/21/2014] [Indexed: 01/02/2023]
Abstract
Filamentous ascomycetes have long been known as producers of a variety of secondary metabolites, many of which have toxic effects on other organisms. However, the role of these metabolites in the biology of the fungi that produce them remains in most cases enigmatic. A major group of fungal secondary metabolites are polyketides. They are chemically diverse, but have in common that their chemical scaffolds are synthesized by polyketide synthases (PKSs). In a previous study, we analyzed development-dependent expression of pks genes in the filamentous ascomycete Sordaria macrospora. Here, we show that a deletion mutant of the pks4 gene is sterile, producing only protoperithecia but no mature perithecia, whereas overexpression of pks4 leads to enlarged, malformed fruiting bodies. Thus, correct expression levels of pks4 are essential for wild type-like perithecia formation. The predicted PKS4 protein has a domain structure that is similar to homologs in other fungi, but conserved residues of a methyl transferase domain present in other fungi are mutated in PKS4. Expression of several developmental genes is misregulated in the pks4 mutant. Surprisingly, the development-associated app gene is not downregulated in the mutant, in contrast to all other previously studied mutants with a block at the protoperithecial stage. Our data show that the polyketide synthase gene pks4 is essential for sexual development and plays a role in regulating fruiting body morphology.
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Affiliation(s)
- Daniel Schindler
- Lehrstuhl für Allgemeine und Molekulare Botanik, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Fakultät für Biologie und Biotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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Draft Genome Sequence of Phaeomoniella chlamydospora Strain RR-HG1, a Grapevine Trunk Disease (Esca)-Related Member of the Ascomycota. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00098-14. [PMID: 24723699 PMCID: PMC3983288 DOI: 10.1128/genomea.00098-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Ascomycota species Phaeomoniella chlamydospora, in concert with other fungi, is a causal agent for grapevine trunk diseases. Here, we present the first draft of the P. chlamydospora genome sequence, which comprises 355 scaffolds, with a total length of 26.59 Mb and 7,279 predicted protein-coding genes.
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Ma LJ, Geiser DM, Proctor RH, Rooney AP, O'Donnell K, Trail F, Gardiner DM, Manners JM, Kazan K. Fusarium pathogenomics. Annu Rev Microbiol 2014; 67:399-416. [PMID: 24024636 DOI: 10.1146/annurev-micro-092412-155650] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fusarium is a genus of filamentous fungi that contains many agronomically important plant pathogens, mycotoxin producers, and opportunistic human pathogens. Comparative analyses have revealed that the Fusarium genome is compartmentalized into regions responsible for primary metabolism and reproduction (core genome), and pathogen virulence, host specialization, and possibly other functions (adaptive genome). Genes involved in virulence and host specialization are located on pathogenicity chromosomes within strains pathogenic to tomato (Fusarium oxysporum f. sp. lycopersici) and pea (Fusarium 'solani' f. sp. pisi). The experimental transfer of pathogenicity chromosomes from F. oxysporum f. sp. lycopersici into a nonpathogen transformed the latter into a tomato pathogen. Thus, horizontal transfer may explain the polyphyletic origins of host specificity within the genus. Additional genome-scale comparative and functional studies are needed to elucidate the evolution and diversity of pathogenicity mechanisms, which may help inform novel disease management strategies against fusarial pathogens.
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Affiliation(s)
- Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003;
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Zhao C, Waalwijk C, de Wit PJGM, Tang D, van der Lee T. Relocation of genes generates non-conserved chromosomal segments in Fusarium graminearum that show distinct and co-regulated gene expression patterns. BMC Genomics 2014; 15:191. [PMID: 24625133 PMCID: PMC4022177 DOI: 10.1186/1471-2164-15-191] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/07/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genome comparisons between closely related species often show non-conserved regions across chromosomes. Some of them are located in specific regions of chromosomes and some are even confined to one or more entire chromosomes. The origin and biological relevance of these non-conserved regions are still largely unknown. Here we used the genome of Fusarium graminearum to elucidate the significance of non-conserved regions. RESULTS The genome of F. graminearum harbours thirteen non-conserved regions dispersed over all of the four chromosomes. Using RNA-Seq data from the mycelium of F. graminearum, we found weakly expressed regions on all of the four chromosomes that exactly matched with non-conserved regions. Comparison of gene expression between two different developmental stages (conidia and mycelium) showed that the expression of genes in conserved regions is stable, while gene expression in non-conserved regions is much more influenced by developmental stage. In addition, genes involved in the production of secondary metabolites and secreted proteins are enriched in non-conserved regions, suggesting that these regions could also be important for adaptations to new environments, including adaptation to new hosts. Finally, we found evidence that non-conserved regions are generated by sequestration of genes from multiple locations. Gene relocations may lead to clustering of genes with similar expression patterns or similar biological functions, which was clearly exemplified by the PKS2 gene cluster. CONCLUSIONS Our results showed that chromosomes can be functionally divided into conserved and non-conserved regions, and both could have specific and distinct roles in genome evolution and regulation of gene expression.
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Sørensen JL, Knudsen M, Hansen FT, Olesen C, Fuertes PR, Lee TV, Sondergaard TE, Pedersen CNS, Brodersen DE, Giese H. Fungal NRPS-Dependent Siderophores: From Function to Prediction. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1191-2_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Jonkers W, Xayamongkhon H, Haas M, Olivain C, van der Does HC, Broz K, Rep M, Alabouvette C, Steinberg C, Kistler HC. EBR1genomic expansion and its role in virulence ofFusariumspecies. Environ Microbiol 2013; 16:1982-2003. [DOI: 10.1111/1462-2920.12331] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/06/2013] [Indexed: 12/13/2022]
Affiliation(s)
- Wilfried Jonkers
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Henry Xayamongkhon
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Matthew Haas
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
| | - Chantal Olivain
- UMR 1347 Agroécologie; INRA; BP 86510 F-21065 Dijon cedex France
| | - H. Charlotte van der Does
- Plant Pathology; Swammerdam Institute for Life Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Karen Broz
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
| | - Martijn Rep
- Plant Pathology; Swammerdam Institute for Life Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | | | - Christian Steinberg
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
| | - H. Corby Kistler
- Department of Plant Pathology; University of Minnesota; 1991 Upper Buford Circle St. Paul MN 55108 USA
- USDA-ARS; Cereal Disease Laboratory; 1551 Lindig Street St. Paul MN 55108 USA
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Giese H, Sondergaard TE, Sørensen JL. The AreA transcription factor in Fusarium graminearum regulates the use of some nonpreferred nitrogen sources and secondary metabolite production. Fungal Biol 2013; 117:814-21. [DOI: 10.1016/j.funbio.2013.10.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/26/2013] [Accepted: 10/18/2013] [Indexed: 01/06/2023]
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Gueimonde M, Sánchez B, G. de los Reyes-Gavilán C, Margolles A. Antibiotic resistance in probiotic bacteria. Front Microbiol 2013; 4:202. [PMID: 23882264 PMCID: PMC3714544 DOI: 10.3389/fmicb.2013.00202] [Citation(s) in RCA: 320] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/28/2013] [Indexed: 11/17/2022] Open
Abstract
Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. The main probiotic bacteria are strains belonging to the genera Lactobacillus and Bifidobacterium, although other representatives, such as Bacillus or Escherichia coli strains, have also been used. Lactobacillus and Bifidobacterium are two common inhabitants of the human intestinal microbiota. Also, some species are used in food fermentation processes as starters, or as adjunct cultures in the food industry. With some exceptions, antibiotic resistance in these beneficial microbes does not constitute a safety concern in itself, when mutations or intrinsic resistance mechanisms are responsible for the resistance phenotype. In fact, some probiotic strains with intrinsic antibiotic resistance could be useful for restoring the gut microbiota after antibiotic treatment. However, specific antibiotic resistance determinants carried on mobile genetic elements, such as tetracycline resistance genes, are often detected in the typical probiotic genera, and constitute a reservoir of resistance for potential food or gut pathogens, thus representing a serious safety issue.
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Affiliation(s)
| | | | | | - Abelardo Margolles
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones CientíficasVillaviciosa, Spain
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Droce A, Sørensen JL, Giese H, Sondergaard TE. Glass bead cultivation of fungi: combining the best of liquid and agar media. J Microbiol Methods 2013; 94:343-6. [PMID: 23871859 DOI: 10.1016/j.mimet.2013.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/05/2013] [Accepted: 07/07/2013] [Indexed: 10/26/2022]
Abstract
Production of bioactive compounds and enzymes from filamentous fungi is highly dependent on cultivation conditions. Here we present an easy way to cultivate filamentous fungi on glass beads that allow complete control of nutrient supply. Secondary metabolite production in Fusarium graminearum and Fusarium solani cultivated on agar plates, in shaking liquid culture or on glass beads was compared. Agar plate culture and glass bead cultivation yielded comparable results while liquid culture had lower production of secondary metabolites. RNA extraction from glass beads and liquid cultures was easier than from agar plates and the quality was superior. The system allows simple control of nutrient availability throughout fungal cultivation. This combined with the ease of extraction of nucleic acids and metabolites makes the system highly suitable for the study of gene regulation in response to specific nutrient factors.
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Affiliation(s)
- Aida Droce
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, 9000 Aalborg, Denmark.
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