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Tamano K, Brown DW, Yoshimi A. Editorial: The use of metabolic engineering techniques to increase the productivity of primary and secondary metabolites within filamentous fungi. Front Fungal Biol 2023; 4:1178290. [PMID: 37746119 PMCID: PMC10512314 DOI: 10.3389/ffunb.2023.1178290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/11/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Koichi Tamano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Daren W. Brown
- Mycotoxin Prevention and Applied Microbiology Research (MPM), National Center for Agricultural Utilization Research (NCAUR), Agricultural Research Service, USDA, Peoria, IL, United States
| | - Akira Yoshimi
- Laboratory of Environmental Interface Technology of Filamentous Fungi, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Laboratory of Terrestrial Microbial Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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2
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Lohmar JM, Rhoades NA, Hammond TM, Brown DW. Gene drive by Fusarium SKC1 is dependent on its competing allele. Fungal Genet Biol 2022; 163:103749. [PMID: 36341840 DOI: 10.1016/j.fgb.2022.103749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 01/06/2023]
Abstract
The Fusarium verticillioides SKC1 gene driver is transmitted to offspring in a biased manner through spore killing. The mechanism that allows SKC1 to kill non-SKC1 offspring while sparing others is poorly understood. Here we report that gene drive by SKC1 is dependent on SKC1's competing allele. We propose that SKC1's competing allele influences the ability of a genome defense process to detect SKC1, and we provide evidence that this genome defense process is meiotic silencing by unpaired DNA (MSUD). Our findings suggest that the successful deployment of gene drivers to control pathogenic fungi will require researchers to consider how competing alleles influence the ability of gene drivers to be detected by genome defense processes.
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Affiliation(s)
- Jessica M Lohmar
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, IL 61604, USA
| | - Nicholas A Rhoades
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA.
| | - Daren W Brown
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, IL 61604, USA.
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3
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Cardoza RE, McCormick SP, Izquierdo-Bueno I, Martínez-Reyes N, Lindo L, Brown DW, Collado IG, Proctor RH, Gutiérrez S. Identification of polyketide synthase genes required for aspinolide biosynthesis in Trichoderma arundinaceum. Appl Microbiol Biotechnol 2022; 106:7153-7171. [PMID: 36166052 PMCID: PMC9592644 DOI: 10.1007/s00253-022-12182-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 11/30/2022]
Abstract
The fungus Trichoderma arundinaceum exhibits biological control activity against crop diseases caused by other fungi. Two mechanisms that likely contribute to this activity are upregulation of plant defenses and production of two types of antifungal secondary metabolites: the sesquiterpenoid harzianum A (HA) and the polyketide-derived aspinolides. The goal of the current study was to identify aspinolide biosynthetic genes as part of an effort to understand how these metabolites contribute to the biological control activity of T. arundinaceum. Comparative genomics identified two polyketide synthase genes (asp1 and asp2) that occur in T. arundinaceum and Aspergillus ochraceus, which also produces aspinolides. Gene deletion and biochemical analyses in T. arundinaceum indicated that both genes are required for aspinolide production: asp2 for formation of a 10-member lactone ring and asp1 for formation of a butenoyl subsituent at position 8 of the lactone ring. Gene expression and comparative genomics analyses indicated that asp1 and asp2 are located within a gene cluster that occurs in both T. arundinaceum and A. ochraceus. A survey of genome sequences representing 35 phylogenetically diverse Trichoderma species revealed that intact homologs of the cluster occurred in only two other species, which also produced aspinolides. An asp2 mutant inhibited fungal growth more than the wild type, but an asp1 mutant did not, and the greater inhibition by the asp2 mutant coincided with increased HA production. These findings indicate that asp1 and asp2 are aspinolide biosynthetic genes and that loss of either aspinolide or HA production in T. arundinaceum can be accompanied by increased production of the other metabolite(s). KEY POINTS: • Two polyketide synthase genes are required for aspinolide biosynthesis. • Blocking aspinolide production increases production of the terpenoid harzianum A. • Aspinolides and harzianum A act redundantly in antibiosis of T. arundinaceum.
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Affiliation(s)
- Rosa E Cardoza
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, University of León, 24400, Ponferrada, Spain
| | - Susan P McCormick
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N University St., Peoria, IL, 61604, USA
| | - Inmaculada Izquierdo-Bueno
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Campus Universitario Río San Pedro s/n, Torre Sur, 4ª planta, 11510, Puerto Real, Cádiz, Spain
| | - Natalia Martínez-Reyes
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, University of León, 24400, Ponferrada, Spain
| | - Laura Lindo
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, University of León, 24400, Ponferrada, Spain
| | - Daren W Brown
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N University St., Peoria, IL, 61604, USA
| | - Isidro G Collado
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Cádiz, Campus Universitario Río San Pedro s/n, Torre Sur, 4ª planta, 11510, Puerto Real, Cádiz, Spain
| | - Robert H Proctor
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, 1815 N University St., Peoria, IL, 61604, USA.
| | - Santiago Gutiérrez
- University Group for Research in Engineering and Sustainable Agriculture (GUIIAS), Area of Microbiology, University of León, 24400, Ponferrada, Spain.
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4
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Torres-Cruz TJ, Whitaker BK, Proctor RH, Broders K, Laraba I, Kim HS, Brown DW, O'Donnell K, Estrada-Rodríguez TL, Lee YH, Cheong K, Wallace EC, McGee CT, Kang S, Geiser DM. FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification. Plant Dis 2022; 106:1610-1616. [PMID: 34879732 DOI: 10.1094/pdis-09-21-2105-sr] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID (http://isolate.fusariumdb.org/blast.php) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ∼680-bp 5' portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.
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Affiliation(s)
- Terry J Torres-Cruz
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Briana K Whitaker
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, U.S.A
| | - Robert H Proctor
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, U.S.A
| | - Kirk Broders
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, U.S.A
| | - Imane Laraba
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, U.S.A
| | - Hye-Seon Kim
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, U.S.A
| | - Daren W Brown
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, U.S.A
| | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, U.S.A
| | | | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
| | - Kyeongchae Cheong
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
| | - Emma C Wallace
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Chyanna T McGee
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
| | - David M Geiser
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802, U.S.A
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5
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O'Donnell K, Whitaker BK, Laraba I, Proctor RH, Brown DW, Broders K, Kim HS, McCormick SP, Busman M, Aoki T, Torres-Cruz TJ, Geiser DM. DNA Sequence-Based Identification of Fusarium: A Work in Progress. Plant Dis 2022; 106:1597-1609. [PMID: 34907805 DOI: 10.1094/pdis-09-21-2035-sr] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent's identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise more than 400 phylogenetically distinct species (i.e., phylospecies), with more than 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the nonredundant National Center for Biotechnology Information nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1, and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue (Torres-Cruz et al. 2022), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.
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Affiliation(s)
- Kerry O'Donnell
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Briana K Whitaker
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Imane Laraba
- Oak Ridge Institute for Science and Education Fellow, Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Robert H Proctor
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Daren W Brown
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Kirk Broders
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Hye-Seon Kim
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Susan P McCormick
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Mark Busman
- National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, U.S.A
| | - Takayuki Aoki
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Terry J Torres-Cruz
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - David M Geiser
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
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6
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Brown DW, Kim HS, McGovern A, Probyn C, Proctor RH. Genus-wide analysis of Fusarium polyketide synthases reveals broad chemical potential. Fungal Genet Biol 2022; 160:103696. [DOI: 10.1016/j.fgb.2022.103696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/27/2022]
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7
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Lohmar JM, Rhoades NA, Patel TN, Proctor RH, Hammond TM, Brown DW. A-to-I mRNA editing controls spore death induced by a fungal meiotic drive gene in homologous and heterologous expression systems. Genetics 2022; 221:6528853. [PMID: 35166849 DOI: 10.1093/genetics/iyac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 02/06/2022] [Indexed: 11/13/2022] Open
Abstract
Spore killers are meiotic drive elements that can block development of sexual spores in fungi. In the maize ear rot and mycotoxin-producing fungus Fusarium verticillioides, a spore killer called SkK has been mapped to a 102-kb interval of chromosome V. Here, we show that a gene within this interval, SKC1, is required for SkK-mediated spore killing and meiotic drive. We also demonstrate that SKC1 is associated with at least four transcripts, two sense (sense-SKC1a and sense-SKC1b) and two antisense (antisense-SKC1a and antisense-SKC1b). Both antisense SKC1 transcripts lack obvious protein-coding sequences and thus appear to be non-coding RNAs. In contrast, sense-SKC1a is a protein-coding transcript that undergoes A-to-I editing to sense-SKC1b in sexual tissue. Translation of sense-SKC1a produces a 70 amino acid protein (Skc1a), whereas translation of sense-SKC1b produces an 84 amino acid protein (Skc1b). Heterologous expression analysis of SKC1 transcripts shows that sense-SKC1a also undergoes A-to-I editing to sense-SKC1b during the Neurospora crassa sexual cycle. Site directed mutagenesis studies indicate that Skc1b is responsible for spore killing in F. verticillioides and that it induces most meiotic cells to die in N. crassa. Finally, we report that SKC1 homologs are present in over 20 Fusarium species. Overall, our results demonstrate that fungal meiotic drive elements like SKC1 can influence the outcome of meiosis by hijacking a cell's A-to-I editing machinery and that the involvement of A-to-I editing in a fungal meiotic drive system does not preclude its horizontal transfer to a distantly related species.
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Affiliation(s)
- Jessica M Lohmar
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, Illinois, 61604, USA
| | - Nicholas A Rhoades
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Tejas N Patel
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Robert H Proctor
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, Illinois, 61604, USA
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Daren W Brown
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Unit, 1815 N. University St., Peoria, Illinois, 61604, USA
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8
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Geiser DM, Al-Hatmi AMS, Aoki T, Arie T, Balmas V, Barnes I, Bergstrom GC, Bhattacharyya MK, Blomquist CL, Bowden RL, Brankovics B, Brown DW, Burgess LW, Bushley K, Busman M, Cano-Lira JF, Carrillo JD, Chang HX, Chen CY, Chen W, Chilvers M, Chulze S, Coleman JJ, Cuomo CA, de Beer ZW, de Hoog GS, Del Castillo-Múnera J, Del Ponte EM, Diéguez-Uribeondo J, Di Pietro A, Edel-Hermann V, Elmer WH, Epstein L, Eskalen A, Esposto MC, Everts KL, Fernández-Pavía SP, da Silva GF, Foroud NA, Fourie G, Frandsen RJN, Freeman S, Freitag M, Frenkel O, Fuller KK, Gagkaeva T, Gardiner DM, Glenn AE, Gold SE, Gordon TR, Gregory NF, Gryzenhout M, Guarro J, Gugino BK, Gutierrez S, Hammond-Kosack KE, Harris LJ, Homa M, Hong CF, Hornok L, Huang JW, Ilkit M, Jacobs A, Jacobs K, Jiang C, Jiménez-Gasco MDM, Kang S, Kasson MT, Kazan K, Kennell JC, Kim HS, Kistler HC, Kuldau GA, Kulik T, Kurzai O, Laraba I, Laurence MH, Lee T, Lee YW, Lee YH, Leslie JF, Liew ECY, Lofton LW, Logrieco AF, López-Berges MS, Luque AG, Lysøe E, Ma LJ, Marra RE, Martin FN, May SR, McCormick SP, McGee C, Meis JF, Migheli Q, Mohamed Nor NMI, Monod M, Moretti A, Mostert D, Mulè G, Munaut F, Munkvold GP, Nicholson P, Nucci M, O'Donnell K, Pasquali M, Pfenning LH, Prigitano A, Proctor RH, Ranque S, Rehner SA, Rep M, Rodríguez-Alvarado G, Rose LJ, Roth MG, Ruiz-Roldán C, Saleh AA, Salleh B, Sang H, Scandiani MM, Scauflaire J, Schmale DG, Short DPG, Šišić A, Smith JA, Smyth CW, Son H, Spahr E, Stajich JE, Steenkamp E, Steinberg C, Subramaniam R, Suga H, Summerell BA, Susca A, Swett CL, Toomajian C, Torres-Cruz TJ, Tortorano AM, Urban M, Vaillancourt LJ, Vallad GE, van der Lee TAJ, Vanderpool D, van Diepeningen AD, Vaughan MM, Venter E, Vermeulen M, Verweij PE, Viljoen A, Waalwijk C, Wallace EC, Walther G, Wang J, Ward TJ, Wickes BL, Wiederhold NP, Wingfield MJ, Wood AKM, Xu JR, Yang XB, Yli-Mattila T, Yun SH, Zakaria L, Zhang H, Zhang N, Zhang SX, Zhang X. Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex. Phytopathology 2021; 111:1064-1079. [PMID: 33200960 DOI: 10.1094/phyto-08-20-0330-le] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.
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Affiliation(s)
- David M Geiser
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | | | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Tsutomu Arie
- Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Virgilio Balmas
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Gary C Bergstrom
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
| | | | - Cheryl L Blomquist
- Plant Pest Diagnostics Branch, California Department of Food and Agriculture, Sacramento, CA 95832, U.S.A
| | - Robert L Bowden
- Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), Manhattan, KS 66506, U.S.A
| | - Balázs Brankovics
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Daren W Brown
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Lester W Burgess
- Sydney Institute of Agriculture, Faculty of Science, University of Sydney, Sydney, Australia
| | - Kathryn Bushley
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Mark Busman
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - José F Cano-Lira
- Mycology Unit and IISPV, Universitat Rovira i Virgili Medical School, Reus, Spain
| | - Joseph D Carrillo
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chi-Yu Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, People's Republic of China
| | - Martin Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Sofia Chulze
- Research Institute on Mycology and Mycotoxicology, National Scientific and Technical Research Council, National University of Rio Cuarto, Rio Cuarto, Córdoba, Argentina
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | | | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - G Sybren de Hoog
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | | | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | | | - Wade H Elmer
- Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Akif Eskalen
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | | | - Kathryne L Everts
- Wye Research and Education Center, University of Maryland, Queenstown, MD 21658, U.S.A
| | - Sylvia P Fernández-Pavía
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | | | - Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - Gerda Fourie
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rasmus J N Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Stanley Freeman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Kevin K Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, U.S.A
| | - Tatiana Gagkaeva
- Laboratory of Mycology and Phytopathology, All-Russian Institute of Plant Protection, St. Petersburg-Pushkin, Russia
| | | | - Anthony E Glenn
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Scott E Gold
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Thomas R Gordon
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Nancy F Gregory
- Department of Plant and Soil Sciences, University of Delaware, DE 19716, U.S.A
| | - Marieka Gryzenhout
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Josep Guarro
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Universitat Rovira i Virgili, Reus, Spain
| | - Beth K Gugino
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | | | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Linda J Harris
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Mónika Homa
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences, University of Szeged, Szeged, Hungary
| | - Cheng-Fang Hong
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - László Hornok
- Institute of Plant Protection, Szent István University, Gödöllő, Hungary
| | - Jenn-Wen Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Sarıçam, Adana, Turkey
| | - Adriaana Jacobs
- Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - Karin Jacobs
- Department of Microbiology, Stellenbosch University, Matieland, South Africa
| | - Cong Jiang
- College of Plant Protection, Northwest Agriculture and Forestry University, Xianyang, People's Republic of China
| | - María Del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Matthew T Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, U.S.A
| | - Kemal Kazan
- CSIRO Agriculture and Food, St. Lucia, Australia
| | - John C Kennell
- Biology Department, St. Louis University, St. Louis, MO 63101, U.S.A
| | - Hye-Seon Kim
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - H Corby Kistler
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Gretchen A Kuldau
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Oliver Kurzai
- German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Imane Laraba
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Matthew H Laurence
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Theresa Lee
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - John F Leslie
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Edward C Y Liew
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Lily W Lofton
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Antonio F Logrieco
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Manuel S López-Berges
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Alicia G Luque
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Referencia de Micología, Universidad Nacional de Rosario, Rosario, Argentina
| | - Erik Lysøe
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Høgskoleveien, Ås, Norway
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Robert E Marra
- Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
| | - Frank N Martin
- Crop Improvement and Protection Research Unit, ARS-USDA, Salinas, CA 93905, U.S.A
| | - Sara R May
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Susan P McCormick
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Chyanna McGee
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Jacques F Meis
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Quirico Migheli
- Dipartimento di Agraria and Nucleo Ricerca Desertificazione, Università degli Studi di Sassari, Sassari, Italy
| | - N M I Mohamed Nor
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Michel Monod
- Laboratoire de Mycologie, Service de Dermatologie, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Antonio Moretti
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Diane Mostert
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Giuseppina Mulè
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | | | - Gary P Munkvold
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Marcio Nucci
- Hospital Universitário, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Milan, Italy
| | - Ludwig H Pfenning
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais State, Brazil
| | - Anna Prigitano
- Department of Biomedical Sciences for Health, University of Milano, Milan, Italy
| | - Robert H Proctor
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Stéphane Ranque
- Institut Hospitalier Universitaire Méditerranée Infection, Aix Marseille University, Marseille, France
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A
| | - Martijn Rep
- Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerardo Rodríguez-Alvarado
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Lindy Joy Rose
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Mitchell G Roth
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, U.S.A
| | - Carmen Ruiz-Roldán
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Amgad A Saleh
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Baharuddin Salleh
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - María Mercedes Scandiani
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Referencia de Micología, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jonathan Scauflaire
- Centre de Recherche et de Formation Agronomie, Haute Ecole Louvain en Hainaut, Montignies-sur-Sambre, Belgium
| | - David G Schmale
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, U.S.A
| | | | - Adnan Šišić
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Jason A Smith
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, U.S.A
| | - Christopher W Smyth
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902, U.S.A
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Ellie Spahr
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, U.S.A
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Emma Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Christian Steinberg
- Agroécologie, AgroSup Dijon, INRAE, University of Bourgogne Franche-Comté, Dijon, France
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, Japan
| | - Brett A Summerell
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Antonella Susca
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Cassandra L Swett
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | | | - Terry J Torres-Cruz
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Anna M Tortorano
- Department of Biomedical Sciences for Health, University of Milano, Milan, Italy
| | - Martin Urban
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Lisa J Vaillancourt
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Gary E Vallad
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | - Theo A J van der Lee
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Dan Vanderpool
- Department of Biology, Indiana University, Bloomington, IN 47405, U.S.A
| | - Anne D van Diepeningen
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Martha M Vaughan
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Eduard Venter
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, South Africa
| | - Marcele Vermeulen
- Department of Microbial Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Paul E Verweij
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Altus Viljoen
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Cees Waalwijk
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Emma C Wallace
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Grit Walther
- German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Jie Wang
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94702
| | - Todd J Ward
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Brian L Wickes
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Nathan P Wiederhold
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Ana K M Wood
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Jin-Rong Xu
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Xiao-Bing Yang
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Sung-Hwan Yun
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Republic of Korea
| | - Latiffah Zakaria
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, People's Republic of China
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, U.S.A
| | - Sean X Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, U.S.A
| | - Xue Zhang
- College of Plant Protection, Northwest Agriculture and Forestry University, Xianyang, People's Republic of China
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Kim HS, Lohmar JM, Busman M, Brown DW, Naumann TA, Divon HH, Lysøe E, Uhlig S, Proctor RH. Correction to: Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium. BMC Genomics 2020; 21:712. [PMID: 33059601 PMCID: PMC7558698 DOI: 10.1186/s12864-020-07135-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Hye-Seon Kim
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Jessica M Lohmar
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Mark Busman
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Daren W Brown
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Todd A Naumann
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | | | - Erik Lysøe
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | | | - Robert H Proctor
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA.
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Kim HS, Lohmar JM, Busman M, Brown DW, Naumann TA, Divon HH, Lysøe E, Uhlig S, Proctor RH. Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium. BMC Genomics 2020; 21:510. [PMID: 32703172 PMCID: PMC7376913 DOI: 10.1186/s12864-020-06896-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Sphingolipids are structural components and signaling molecules in eukaryotic membranes, and many organisms produce compounds that inhibit sphingolipid metabolism. Some of the inhibitors are structurally similar to the sphingolipid biosynthetic intermediate sphinganine and are referred to as sphinganine-analog metabolites (SAMs). The mycotoxins fumonisins, which are frequent contaminants in maize, are one family of SAMs. Due to food and feed safety concerns, fumonisin biosynthesis has been investigated extensively, including characterization of the fumonisin biosynthetic gene cluster in the agriculturally important fungi Aspergillus and Fusarium. Production of several other SAMs has also been reported in fungi, but there is almost no information on their biosynthesis. There is also little information on how widely SAM production occurs in fungi or on the extent of structural variation of fungal SAMs. RESULTS Using fumonisin biosynthesis as a model, we predicted that SAM biosynthetic gene clusters in fungi should include a polyketide synthase (PKS), an aminotransferase and a dehydrogenase gene. Surveys of genome sequences identified five putative clusters with this three-gene combination in 92 of 186 Fusarium species examined. Collectively, the putative SAM clusters were distributed widely but discontinuously among the species. We propose that the SAM5 cluster confers production of a previously reported Fusarium SAM, 2-amino-14,16-dimethyloctadecan-3-ol (AOD), based on the occurrence of AOD production only in species with the cluster and on deletion analysis of the SAM5 cluster PKS gene. We also identified SAM clusters in 24 species of other fungal genera, and propose that one of the clusters confers production of sphingofungin, a previously reported Aspergillus SAM. CONCLUSION Our results provide a genomics approach to identify novel SAM biosynthetic gene clusters in fungi, which should in turn contribute to identification of novel SAMs with applications in medicine and other fields. Information about novel SAMs could also provide insights into the role of SAMs in the ecology of fungi. Such insights have potential to contribute to strategies to reduce fumonisin contamination in crops and to control crop diseases caused by SAM-producing fungi.
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Affiliation(s)
- Hye-Seon Kim
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Jessica M Lohmar
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Mark Busman
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Daren W Brown
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | - Todd A Naumann
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA
| | | | - Erik Lysøe
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | | | - Robert H Proctor
- U. S. Department of Agriculture, Agriculture Research Service, National Center for Agricultural Utilization Research, Peoria, IL, USA.
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Villani A, Proctor RH, Kim HS, Brown DW, Logrieco AF, Amatulli MT, Moretti A, Susca A. Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes. BMC Genomics 2019; 20:314. [PMID: 31014248 PMCID: PMC6480918 DOI: 10.1186/s12864-019-5567-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 02/25/2019] [Indexed: 11/29/2022] Open
Abstract
Background The Fusarium incarnatum-equiseti species complex (FIESC) comprises 33 phylogenetically distinct species that have been recovered from diverse biological sources, but have been most often isolated from agricultural plants and soils. Collectively, members of FIESC can produce diverse mycotoxins. However, because the species diversity of FIESC has been recognized only recently, the potential of species to cause mycotoxin contamination of crop plants is unclear. In this study, therefore, we used comparative genomics to investigate the distribution of and variation in genes and gene clusters responsible for the synthesis of mycotoxins and other secondary metabolites (SMs) in FIESC. Results We examined genomes of 13 members of FIESC that were selected based primarily on their phylogenetic diversity and/or occurrence on crops. The presence and absence of SM biosynthetic gene clusters varied markedly among the genomes. For example, the trichothecene mycotoxin as well as the carotenoid and fusarubin pigment clusters were present in all genomes examined, whereas the enniatin, fusarin, and zearalenone mycotoxin clusters were present in only some genomes. Some clusters exhibited discontinuous patterns of distribution in that their presence and absence was not correlated with the phylogenetic relationships of species. We also found evidence that cluster loss and horizontal gene transfer have contributed to such distribution patterns. For example, a combination of multiple phylogenetic analyses suggest that five NRPS and seven PKS genes were introduced into FIESC from other Fusarium lineages. Conclusion Our results suggest that although the portion of the genome devoted to SM biosynthesis has remained similar during the evolutionary diversification of FIESC, the ability to produce SMs could be affected by the different distribution of related functional and complete gene clusters. Electronic supplementary material The online version of this article (10.1186/s12864-019-5567-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alessandra Villani
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Robert H Proctor
- Department of Agriculture Peoria, National Center for Agricultural Utilization Research, U.S., Peoria, IL, USA
| | - Hye-Seon Kim
- Department of Agriculture Peoria, National Center for Agricultural Utilization Research, U.S., Peoria, IL, USA
| | - Daren W Brown
- Department of Agriculture Peoria, National Center for Agricultural Utilization Research, U.S., Peoria, IL, USA
| | - Antonio F Logrieco
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
| | - Maria Teresa Amatulli
- Institute of Sciences of Food Production, National Research Council, Bari, Italy.,Thales Alenia Space Italia, Torino, Italy
| | - Antonio Moretti
- Institute of Sciences of Food Production, National Research Council, Bari, Italy.
| | - Antonia Susca
- Institute of Sciences of Food Production, National Research Council, Bari, Italy
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12
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Vrabka J, Niehaus EM, Münsterkötter M, Proctor RH, Brown DW, Novák O, Pěnčik A, Tarkowská D, Hromadová K, Hradilová M, Oklešt’ková J, Oren-Young L, Idan Y, Sharon A, Maymon M, Elazar M, Freeman S, Güldener U, Tudzynski B, Galuszka P, Bergougnoux V. Production and Role of Hormones During Interaction of Fusarium Species With Maize ( Zea mays L.) Seedlings. Front Plant Sci 2019; 9:1936. [PMID: 30687345 PMCID: PMC6337686 DOI: 10.3389/fpls.2018.01936] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 12/12/2018] [Indexed: 05/22/2023]
Abstract
It has long been known that hormones affect the interaction of a phytopathogen with its host plant. The pathogen can cause changes in plant hormone homeostasis directly by affecting biosynthesis or metabolism in the plant or by synthesizing and secreting the hormone itself. We previously demonstrated that pathogenic fungi of the Fusarium species complex are able to produce three major types of hormones: auxins, cytokinins, and gibberellins. In this work, we explore changes in the levels of these hormones in maize and mango plant tissues infected with Fusarium. The ability to produce individual phytohormones varies significantly across Fusarium species and such differences likely impact host specificity inducing the unique responses noted in planta during infection. For example, the production of gibberellins by F. fujikuroi leads to elongated rice stalks and the suppression of gibberellin biosynthesis in plant tissue. Although all Fusarium species are able to synthesize auxin, sometimes by multiple pathways, the ratio of its free form and conjugates in infected tissue is affected more than the total amount produced. The recently characterized unique pathway for cytokinin de novo synthesis in Fusarium appears silenced or non-functional in all studied species during plant infection. Despite this, a large increase in cytokinin levels was detected in F. mangiferae infected plants, caused likely by the up-regulation of plant genes responsible for their biosynthesis. Thus, the accumulation of active cytokinins may contribute to mango malformation of the reproductive organs upon infection of mango trees. Together, our findings provide insight into the complex role fungal and plant derived hormones play in the fungal-plant interactions.
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Affiliation(s)
- Josef Vrabka
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Eva-Maria Niehaus
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | | | - Robert H. Proctor
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, IL, United States
| | - Daren W. Brown
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, IL, United States
| | - Ondřej Novák
- Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czechia
- Department of Metabolomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Aleš Pěnčik
- Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czechia
- Department of Metabolomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Danuše Tarkowská
- Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czechia
- Department of Metabolomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Kristýna Hromadová
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Michaela Hradilová
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jana Oklešt’ková
- Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czechia
- Department of Metabolomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Liat Oren-Young
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Yifat Idan
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Marcel Maymon
- Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Meirav Elazar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Stanley Freeman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Ulrich Güldener
- Department of Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Petr Galuszka
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Veronique Bergougnoux
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czechia
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13
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Lindo L, McCormick SP, Cardoza RE, Kim HS, Brown DW, Alexander NJ, Proctor RH, Gutiérrez S. Role of Trichoderma arundinaceum tri10 in regulation of terpene biosynthetic genes and in control of metabolic flux. Fungal Genet Biol 2019; 122:31-46. [DOI: 10.1016/j.fgb.2018.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 02/03/2023]
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14
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Lindo L, McCormick SP, Cardoza RE, Brown DW, Kim HS, Alexander NJ, Proctor RH, Gutiérrez S. Effect of deletion of a trichothecene toxin regulatory gene on the secondary metabolism transcriptome of the saprotrophic fungus Trichoderma arundinaceum. Fungal Genet Biol 2018; 119:29-46. [PMID: 30121242 DOI: 10.1016/j.fgb.2018.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 11/16/2022]
Abstract
Trichothecenes are terpenoid toxins produced by multiple fungal species with diverse lifestyles. In these fungi, the trichothecene biosynthetic gene (tri) cluster includes a gene encoding a Cys2His2 Zn-finger protein (TRI6). Analyses of plant pathogenic Fusarium species indicate that tri6 regulates tri gene expression. Here, we analyzed TRI6 function in the saprotrophic fungus Trichoderma arundinaceum, which produces the antimicrobial trichothecene harzianum A (HA). Deletion of the TRI6-encoding gene, tri6, blocked HA production and reduced expression of tri genes, and mevalonate biosynthetic genes required for synthesis of farnesyl diphosphate (FPP), the primary metabolite that feeds into trichothecene biosynthesis. In contrast, tri6 deletion did not affect expression of ergosterol biosynthetic genes required for synthesis of ergosterol from FPP, but did increase ergosterol production, perhaps because increased levels of FPP were available for ergosterol synthesis in the absence of trichothecene production. RNA-seq analyses indicated that genes in 10 of 49 secondary metabolite (SM) biosynthetic gene clusters in T. arundinaceum exhibited increased expression and five exhibited reduced expression in a tri6 deletion mutant (Δtri6). Despite the metabolic and transcriptional changes, Δtri6 mutants were not reduced in their ability to inhibit growth of fungal plant pathogens. Our results indicate that T. arundinaceum TRI6 regulates expression of both tri and mevalonate pathway genes. It remains to be determined whether the effects of tri6 deletion on expression of other SM clusters resulted because TRI6 can bind to promoter regions of cluster genes or because trichothecene production affects other SM pathways.
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Affiliation(s)
- Laura Lindo
- Area of Microbiology, University of León, Campus de Ponferrada, Ponferrada, Spain.
| | - Susan P McCormick
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, IL, United States.
| | - Rosa E Cardoza
- Area of Microbiology, University of León, Campus de Ponferrada, Ponferrada, Spain.
| | - Daren W Brown
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, IL, United States.
| | - Hye-Seon Kim
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, IL, United States.
| | - Nancy J Alexander
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, IL, United States
| | - Robert H Proctor
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, IL, United States.
| | - Santiago Gutiérrez
- Area of Microbiology, University of León, Campus de Ponferrada, Ponferrada, Spain.
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15
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McMillan SD, Oberlie NR, Brown DW, McQuade KL. Exploring the Role of Trehalose‐6‐phosphate Synthase in Oxidative Stress Tolerance of
Fusarium verticillioides. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.538.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sarah D. McMillan
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
| | - Nicole R. Oberlie
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
| | | | - Kristi L. McQuade
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
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16
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Oberlie NR, McMillan SD, Brown DW, McQuade KL. Investigating the Role of Trehalose Metabolism in Resistance to Abiotic Stress in the Filamentous Fungus
Fusarium verticillioides. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.665.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicole Ruth Oberlie
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
| | - Sarah D. McMillan
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
| | | | - Kristi L. McQuade
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
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17
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Pierson PN, Hardtke H, Brown DW, McQuade KL. Effects of cell wall perturbation reagents and plant phenolic compounds on growth, colony morphology, and germination of the corn rot fungus
Fusarium verticillioides. FASEB J 2018. [DOI: 10.1096/fasebj.2018.32.1_supplement.534.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Paige N. Pierson
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
| | - Haley Hardtke
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
| | | | - Kristi L. McQuade
- Mund‐Lagowski Department of Chemistry and BiochemistryBradley UniversityPeoriaIL
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18
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Reynolds HT, Slot JC, Divon HH, Lysøe E, Proctor RH, Brown DW. Differential Retention of Gene Functions in a Secondary Metabolite Cluster. Mol Biol Evol 2017; 34:2002-2015. [DOI: 10.1093/molbev/msx145] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Niehaus EM, Münsterkötter M, Proctor RH, Brown DW, Sharon A, Idan Y, Oren-Young L, Sieber CM, Novák O, Pěnčík A, Tarkowská D, Hromadová K, Freeman S, Maymon M, Elazar M, Youssef SA, El-Shabrawy ESM, Shalaby ABA, Houterman P, Brock NL, Burkhardt I, Tsavkelova EA, Dickschat JS, Galuszka P, Güldener U, Tudzynski B. Comparative "Omics" of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis. Genome Biol Evol 2016; 8:3574-3599. [PMID: 28040774 PMCID: PMC5203792 DOI: 10.1093/gbe/evw259] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2016] [Indexed: 11/14/2022] Open
Abstract
Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae, the cause of mango malformation, and two isolates of F. proliferatum, one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression (in vitro and in planta) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum, the pathogenic versus endophytic life style.
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Affiliation(s)
- Eva-Maria Niehaus
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Robert H Proctor
- United States Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, Illinois
| | - Daren W Brown
- United States Department of Agriculture, National Center for Agricultural Utilization Research, Peoria, Illinois
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Yifat Idan
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Liat Oren-Young
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Christian M Sieber
- Department of Energy Joint Genome Institute, University of California, Walnut Creek, Berkeley, California
| | - Ondřej Novák
- Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University, Olomouc, Czech Republic
| | - Aleš Pěnčík
- Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University, Olomouc, Czech Republic
| | - Danuše Tarkowská
- Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University, Olomouc, Czech Republic
| | - Kristýna Hromadová
- Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University, Olomouc, Czech Republic
| | - Stanley Freeman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), The Volcani Center, Bet-Dagan, Israel
| | - Marcel Maymon
- Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), The Volcani Center, Bet-Dagan, Israel
| | - Meirav Elazar
- Department of Plant Pathology and Weed Research, Agricultural Research Organization (ARO), The Volcani Center, Bet-Dagan, Israel
| | - Sahar A Youssef
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | | | | | - Petra Houterman
- University of Amsterdam, Swammerdam Institute for Life Sciences, Plant Pathology, Amsterdam, The Netherlands
| | - Nelson L Brock
- Rheinische Friedrich-Wilhelms-Universität Bonn, Kekulé-Institut für Organische Chemie und Biochemie, Germany
| | - Immo Burkhardt
- Rheinische Friedrich-Wilhelms-Universität Bonn, Kekulé-Institut für Organische Chemie und Biochemie, Germany
| | - Elena A Tsavkelova
- Department of Microbiology Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Jeroen S Dickschat
- Rheinische Friedrich-Wilhelms-Universität Bonn, Kekulé-Institut für Organische Chemie und Biochemie, Germany
| | - Petr Galuszka
- Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University, Olomouc, Czech Republic
| | - Ulrich Güldener
- Department of Genome-oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, Freising, Germany
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
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20
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Pyle J, Patel T, Merrill B, Nsokoshi C, McCall M, Proctor RH, Brown DW, Hammond TM. A Meiotic Drive Element in the Maize Pathogen Fusarium verticillioides Is Located Within a 102 kb Region of Chromosome V. G3 (Bethesda) 2016; 6:2543-52. [PMID: 27317777 PMCID: PMC4978907 DOI: 10.1534/g3.116.029728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 06/06/2016] [Indexed: 11/24/2022]
Abstract
Fusarium verticillioides is an agriculturally important fungus because of its association with maize and its propensity to contaminate grain with toxic compounds. Some isolates of the fungus harbor a meiotic drive element known as Spore killer (Sk(K)) that causes nearly all surviving meiotic progeny from an Sk(K) × Spore killer-susceptible (Sk(S)) cross to inherit the Sk(K) allele. Sk(K) has been mapped to chromosome V but the genetic element responsible for meiotic drive has yet to be identified. In this study, we used cleaved amplified polymorphic sequence markers to genotype individual progeny from an Sk(K) × Sk(S) mapping population. We also sequenced the genomes of three progeny from the mapping population to determine their single nucleotide polymorphisms. These techniques allowed us to refine the location of Sk(K) to a contiguous 102 kb interval of chromosome V, herein referred to as the Sk region. Relative to Sk(S) genotypes, Sk(K) genotypes have one extra gene within this region for a total of 42 genes. The additional gene in Sk(K) genotypes, herein named SKC1 for Spore Killer Candidate 1, is the most highly expressed gene from the Sk region during early stages of sexual development. The Sk region also has three hyper-variable regions, the longest of which includes SKC1 The possibility that SKC1, or another gene from the Sk region, is an essential component of meiotic drive and spore killing is discussed.
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Affiliation(s)
- Jay Pyle
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Tejas Patel
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Brianna Merrill
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Chabu Nsokoshi
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Morgan McCall
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
| | - Robert H Proctor
- Mycotoxin Prevention and Applied Microbiology, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Agricultural Research Service, Peoria, Illinois 61604
| | - Daren W Brown
- Mycotoxin Prevention and Applied Microbiology, National Center for Agricultural Utilization Research, U.S. Department of Agriculture, Agricultural Research Service, Peoria, Illinois 61604
| | - Thomas M Hammond
- School of Biological Sciences, Illinois State University, Normal, Illinois 61790
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21
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Brown DW, Lee SH, Kim LH, Ryu JG, Lee S, Seo Y, Kim YH, Busman M, Yun SH, Proctor RH, Lee T. Identification of a 12-gene Fusaric Acid Biosynthetic Gene Cluster in Fusarium Species Through Comparative and Functional Genomics. Mol Plant Microbe Interact 2015; 28:319-32. [PMID: 25372119 DOI: 10.1094/mpmi-09-14-0264-r] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In fungi, genes involved in biosynthesis of a secondary metabolite (SM) are often located adjacent to one another in the genome and are coordinately regulated. These SM biosynthetic gene clusters typically encode enzymes, one or more transcription factors, and a transport protein. Fusaric acid is a polyketide-derived SM produced by multiple species of the fungal genus Fusarium. This SM is of concern because it is toxic to animals and, therefore, is considered a mycotoxin and may contribute to plant pathogenesis. Preliminary descriptions of the fusaric acid (FA) biosynthetic gene (FUB) cluster have been reported in two Fusarium species, the maize pathogen F. verticillioides and the rice pathogen F. fujikuroi. The cluster consisted of five genes and did not include a transcription factor or transporter gene. Here, analysis of the FUB region in F. verticillioides, F. fujikuroi, and F. oxysporum, a plant pathogen with multiple hosts, indicates the FUB cluster consists of at least 12 genes (FUB1 to FUB12). Deletion analysis confirmed that nine FUB genes, including two Zn(II)2Cys6 transcription factor genes, are required for production of wild-type levels of FA. Comparisons of FUB cluster homologs across multiple Fusarium isolates and species revealed insertion of non-FUB genes at one or two locations in some homologs. Although the ability to produce FA contributed to the phytotoxicity of F. oxysporum culture extracts, lack of production did not affect virulence of F. oxysporum on cactus or F. verticillioides on maize seedlings. These findings provide new insights into the genetic and biochemical processes required for FA production.
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22
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Brown DW, Busman M, Proctor RH. Fusarium verticillioides SGE1 is required for full virulence and regulates expression of protein effector and secondary metabolite biosynthetic genes. Mol Plant Microbe Interact 2014; 27:809-823. [PMID: 24742071 DOI: 10.1094/mpmi-09-13-0281-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The transition from one lifestyle to another in some fungi is initiated by a single orthologous gene, SGE1, that regulates markedly different genes in different fungi. Despite these differences, many of the regulated genes encode effector proteins or proteins involved in the synthesis of secondary metabolites (SM), both of which can contribute to pathogenicity. Fusarium verticillioides is both an endophyte and a pathogen of maize and can grow as a saprophyte on dead plant material. During growth on live maize plants, the fungus can synthesize a number of toxic SM, including fumonisins, fusarins, and fusaric acid, that can contaminate kernels and kernel-based food and feed. In this study, the role of F. verticillioides SGE1 in pathogenicity and secondary metabolism was examined by gene deletion analysis and transcriptomics. SGE1 is not required for vegetative growth or conidiation but is required for wild-type pathogenicity and affects synthesis of multiple SM, including fumonisins and fusarins. Induced expression of SGE1 enhanced or reduced expression of hundreds of genes, including numerous putative effector genes that could contribute to growth in planta; genes encoding cell surface proteins; gene clusters required for synthesis of fusarins, bikaverin, and an unknown metabolite; as well as the gene encoding the fumonisin cluster transcriptional activator. Together, our results indicate that SGE1 has a role in global regulation of transcription in F. verticillioides that impacts but is not absolutely required for secondary metabolism and pathogenicity on maize.
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23
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Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi. Proc Natl Acad Sci U S A 2014; 111:9923-8. [PMID: 24958869 PMCID: PMC4103376 DOI: 10.1073/pnas.1400592111] [Citation(s) in RCA: 411] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.
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Affiliation(s)
- Robert Riley
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Asaf A Salamov
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Daren W Brown
- US Department of Agriculture (USDA), Peoria, IL 61604
| | - Laszlo G Nagy
- Department of Biology, Clark University, Worcester, MA 01610
| | | | | | - Anthony Levasseur
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1163, Aix-Marseille Université, 13288 Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Aix-Marseille Université, 13288 Marseille, France
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136, Institut National de la Recherche Agronomique-Université de Lorraine, Interactions Arbres/Micro-organismes, 54280 Champenoux, France
| | - Robert Otillar
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Erika A Lindquist
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Hui Sun
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Kurt M LaButti
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598
| | - Jeremy Schmutz
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806
| | - Dina Jabbour
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824
| | - Hong Luo
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Antonio G Pisabarro
- Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Spain; and
| | - Jonathan D Walton
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824
| | | | - Bernard Henrissat
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7257, Aix-Marseille Université, 13288 Marseille, France
| | - Francis Martin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136, Institut National de la Recherche Agronomique-Université de Lorraine, Interactions Arbres/Micro-organismes, 54280 Champenoux, France
| | - Dan Cullen
- USDA Forest Products Laboratory, Madison, WI 53726
| | - David S Hibbett
- Department of Biology, Clark University, Worcester, MA 01610;
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA 94598;
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24
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Wiemann P, Sieber CMK, von Bargen KW, Studt L, Niehaus EM, Espino JJ, Huß K, Michielse CB, Albermann S, Wagner D, Bergner SV, Connolly LR, Fischer A, Reuter G, Kleigrewe K, Bald T, Wingfield BD, Ophir R, Freeman S, Hippler M, Smith KM, Brown DW, Proctor RH, Münsterkötter M, Freitag M, Humpf HU, Güldener U, Tudzynski B. Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog 2013; 9:e1003475. [PMID: 23825955 PMCID: PMC3694855 DOI: 10.1371/journal.ppat.1003475] [Citation(s) in RCA: 320] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 05/18/2013] [Indexed: 12/17/2022] Open
Abstract
The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F. fujikuroi as a rice pathogen.
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Affiliation(s)
- Philipp Wiemann
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Christian M. K. Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Katharina W. von Bargen
- Institute for Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster, Germany
| | - Lena Studt
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
- Institute for Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster, Germany
| | - Eva-Maria Niehaus
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Jose J. Espino
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Kathleen Huß
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Caroline B. Michielse
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Sabine Albermann
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Dominik Wagner
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Sonja V. Bergner
- Institut für Biologie und Biotechnologie der Pflanzen, Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Lanelle R. Connolly
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Andreas Fischer
- Institut of Genetics/Developmental Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Gunter Reuter
- Institut of Genetics/Developmental Genetics, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Karin Kleigrewe
- Institute for Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster, Germany
| | - Till Bald
- Institut für Biologie und Biotechnologie der Pflanzen, Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Brenda D. Wingfield
- Department of Genetics, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Ron Ophir
- Institute of Plant Sciences, Genomics, Agricultural Research Organization (ARO), The Volcani Center, Bet-Dagan, Israel
| | - Stanley Freeman
- Department of Plant Pathology, Agricultural Research Organization (ARO), The Volcani Center, Bet-Dagan, Israel
| | - Michael Hippler
- Institut für Biologie und Biotechnologie der Pflanzen, Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Kristina M. Smith
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Daren W. Brown
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, Illinois, United States of America
| | - Robert H. Proctor
- National Center for Agricultural Utilization Research, United States Department of Agriculture, Peoria, Illinois, United States of America
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Hans-Ulrich Humpf
- Institute for Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster, Germany
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Bettina Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Molecular Biology and Biotechnology of Fungi, Westfälische Wilhelms-Universität Münster, Münster, Germany
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Geiser DM, Aoki T, Bacon CW, Baker SE, Bhattacharyya MK, Brandt ME, Brown DW, Burgess LW, Chulze S, Coleman JJ, Correll JC, Covert SF, Crous PW, Cuomo CA, De Hoog GS, Di Pietro A, Elmer WH, Epstein L, Frandsen RJN, Freeman S, Gagkaeva T, Glenn AE, Gordon TR, Gregory NF, Hammond-Kosack KE, Hanson LE, Jímenez-Gasco MDM, Kang S, Kistler HC, Kuldau GA, Leslie JF, Logrieco A, Lu G, Lysøe E, Ma LJ, McCormick SP, Migheli Q, Moretti A, Munaut F, O'Donnell K, Pfenning L, Ploetz RC, Proctor RH, Rehner SA, Robert VARG, Rooney AP, Bin Salleh B, Scandiani MM, Scauflaire J, Short DPG, Steenkamp E, Suga H, Summerell BA, Sutton DA, Thrane U, Trail F, Van Diepeningen A, Vanetten HD, Viljoen A, Waalwijk C, Ward TJ, Wingfield MJ, Xu JR, Yang XB, Yli-Mattila T, Zhang N. One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology 2013; 103:400-8. [PMID: 23379853 DOI: 10.1094/phyto-07-12-0150-le] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.
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O’Donnell K, Rooney AP, Proctor RH, Brown DW, McCormick SP, Ward TJ, Frandsen RJ, Lysøe E, Rehner SA, Aoki T, Robert VA, Crous PW, Groenewald JZ, Kang S, Geiser DM. Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal Genet Biol 2013; 52:20-31. [DOI: 10.1016/j.fgb.2012.12.004] [Citation(s) in RCA: 284] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 12/14/2012] [Accepted: 12/20/2012] [Indexed: 12/15/2022]
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27
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Clouchoux C, du Plessis AJ, Bouyssi-Kobar M, Tworetzky W, McElhinney DB, Brown DW, Gholipour A, Kudelski D, Warfield SK, McCarter RJ, Robertson RL, Evans AC, Newburger JW, Limperopoulos C. Delayed cortical development in fetuses with complex congenital heart disease. Cereb Cortex 2012; 23:2932-43. [PMID: 22977063 DOI: 10.1093/cercor/bhs281] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Neurologic impairment is a major complication of complex congenital heart disease (CHD). A growing body of evidence suggests that neurologic dysfunction may be present in a significant proportion of this high-risk population in the early newborn period prior to surgical interventions. We recently provided the first evidence that brain growth impairment in fetuses with complex CHD has its origins in utero. Here, we extend these observations by characterizing global and regional brain development in fetuses with hypoplastic left heart syndrome (HLHS), one of the most severe forms of CHD. Using advanced magnetic resonance imaging techniques, we compared in vivo brain growth in 18 fetuses with HLHS and 30 control fetuses from 25.4-37.0 weeks of gestation. Our findings demonstrate a progressive third trimester fall-off in cortical gray and white matter volumes (P < 0.001), and subcortical gray matter (P < 0.05) in fetuses with HLHS. Significant delays in cortical gyrification were also evident in HLHS fetuses (P < 0.001). In the HLHS fetus, local cortical folding delays were detected as early as 25 weeks in the frontal, parietal, calcarine, temporal, and collateral regions and appear to precede volumetric brain growth disturbances, which may be an early marker of elevated risk for third trimester brain growth failure.
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28
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Balderson MJ, Brown DW, Quirk S, Ghasroddashti E, Kirkby C. Poster - Thur Eve - 55: Monte Carlo simulations of variations in planned dose distributions in a prostate patient population. Med Phys 2012; 39:4635. [PMID: 28516705 DOI: 10.1118/1.4740163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Clinical outcome studies with clear and objective endpoints are necessary to make informed radiotherapy treatment decisions. Commonly, clinical outcomes are established after lengthy and costly clinical trials are performed and the data are analyzed and published. One the challenges with obtaining meaningful data from clinical trials is that by the time the information gets to the medical profession the results may be less clinically relevant than when the trial began, An alternative approach is to estimate clinical outcomes through patient population modeling. We are developing a mathematical tool that uses Monte Carlo techniques to simulate variations in planned and delivered dose distributions of prostate patients receiving radiotherapy. Ultimately, our simulation will calculate a distribution of Tumor Control Probabilities (TCPs) for a population of patients treated under a given protocol. Such distributions can serve as a metric for comparing different treatment modalities, planning and setup approaches, and machine parameter settings or tolerances with respect to outcomes on broad patient populations. It may also help researchers understand differences one might expect to find before actually doing the clinical trial. As a first step and for the focus of this abstract we wanted to see if we could answer the question: "Can a population of dose distributions of prostate patients be accurately modeled by a set of randomly generated Gaussian functions?" Our results have demonstrated that using a set of randomly generated Gaussian functions can simulate a distribution of prostate patients.
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Affiliation(s)
- M J Balderson
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada.,Department of Medical Physics, Tom Baker Cancer Centre, Calgary, AB, Canada.,Department of Medical Physics, Jack Ady Cancer Centre, Lethbridge, AB
| | - D W Brown
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada.,Department of Medical Physics, Tom Baker Cancer Centre, Calgary, AB, Canada
| | - S Quirk
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada.,Department of Medical Physics, Tom Baker Cancer Centre, Calgary, AB, Canada
| | - E Ghasroddashti
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada.,Department of Medical Physics, Tom Baker Cancer Centre, Calgary, AB, Canada.,Department of Medical Physics, Jack Ady Cancer Centre, Lethbridge, AB
| | - C Kirkby
- Department of Physics and Astronomy, University of Calgary, Calgary, AB, Canada.,Department of Medical Physics, Tom Baker Cancer Centre, Calgary, AB, Canada.,Department of Medical Physics, Jack Ady Cancer Centre, Lethbridge, AB
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29
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Butchko RAE, Brown DW, Busman M, Tudzynski B, Wiemann P. Lae1 regulates expression of multiple secondary metabolite gene clusters in Fusarium verticillioides. Fungal Genet Biol 2012; 49:602-12. [PMID: 22713715 DOI: 10.1016/j.fgb.2012.06.003] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 06/01/2012] [Accepted: 06/10/2012] [Indexed: 11/18/2022]
Abstract
The filamentous fungus Fusarium verticillioides can cause disease of maize and is capable of producing fumonisins, a family of toxic secondary metabolites linked to esophageal cancer and neural tube defects in humans and lung edema in swine and leukoencephalomalacia in equines. The expression of fumonisin biosynthetic genes is influenced by broad-domain transcription factors (global regulators) and Fum21, a pathway-specific transcription factor. LaeA is a global regulator that in Aspergillus nidulans, affects the expression of multiple secondary metabolite gene clusters by modifying heterochromatin structure. Here, we employed gene deletion analysis to assess the effect of loss of a F. verticillioides laeA orthologue, LAE1, on genome-wide gene expression and secondary metabolite production. Loss of Lae1 resulted in reduced expression of gene clusters responsible for synthesis of the secondary metabolites bikaverin, fumonisins, fusaric acid and fusarins as well as two clusters for which the corresponding secondary metabolite is unknown. Analysis of secondary metabolites revealed that, in contrast to a previously described Fusarium fujikuroi lae1 mutant, bikaverin production is reduced. Fumonisin production is unchanged in the F. verticillioides lae1 mutant. Complementation of the F. verticillioides mutant resulted in increased fumonisin production.
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Affiliation(s)
- Robert A E Butchko
- National Center for Agricultural Utilization Research, Peoria, IL, United States.
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30
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Brown DW, Butchko RAE, Busman M, Proctor RH. Identification of gene clusters associated with fusaric acid, fusarin, and perithecial pigment production in Fusarium verticillioides. Fungal Genet Biol 2012; 49:521-32. [PMID: 22652150 DOI: 10.1016/j.fgb.2012.05.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 05/18/2012] [Accepted: 05/19/2012] [Indexed: 02/05/2023]
Abstract
The genus Fusarium is of concern to agricultural production and food/feed safety because of its ability to cause crop disease and to produce mycotoxins. Understanding the genetic basis for production of mycotoxins and other secondary metabolites (SMs) has the potential to limit crop disease and mycotoxin contamination. In fungi, SM biosynthetic genes are typically located adjacent to one another in clusters of co-expressed genes. Such clusters typically include a core gene, responsible for synthesis of an initial chemical, and several genes responsible for chemical modifications, transport, and/or regulation. Fusarium verticillioides is one of the most common pathogens of maize and produces a variety of SMs of concern. Here, we employed whole genome expression analysis and utilized existing knowledge of polyketide synthase (PKS) genes, a common cluster core gene, to identify three novel clusters of co-expressed genes in F. verticillioides. Functional analysis of the PKS genes linked the clusters to production of three known Fusarium SMs, a violet pigment in sexual fruiting bodies (perithecia) and the mycotoxins fusarin C and fusaric acid. The results indicate that microarray analysis of RNA derived from culture conditions that induce differential gene expression can be an effective tool for identifying SM biosynthetic gene clusters.
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Affiliation(s)
- Daren W Brown
- Bacterial Foodborne Pathogens and Mycology Research, USDA-ARS-NCAUR, 1815 N. University St., Peoria, IL 61604, USA.
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31
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Ma D, Stoica AD, Wang XL, Lu ZP, Clausen B, Brown DW. Elastic moduli inheritance and the weakest link in bulk metallic glasses. Phys Rev Lett 2012; 108:085501. [PMID: 22463541 DOI: 10.1103/physrevlett.108.085501] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Indexed: 05/31/2023]
Abstract
We show that a variety of bulk metallic glasses (BMGs) inherit their Young's modulus and shear modulus from the solvent components. This is attributed to preferential straining of locally solvent-rich configurations among tightly bonded atomic clusters, which constitute the weakest link in an amorphous structure. This aspect of inhomogeneous deformation, also revealed by our in situ neutron diffraction studies of an elastically deformed BMG, suggests a rubberlike viscoelastic behavior due to a hierarchy of atomic bonds in BMGs.
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Affiliation(s)
- D Ma
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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32
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Brown DW, Butchko RAE, Baker SE, Proctor RH. Phylogenomic and functional domain analysis of polyketide synthases in Fusarium. Fungal Biol 2011; 116:318-31. [PMID: 22289777 DOI: 10.1016/j.funbio.2011.12.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/09/2011] [Accepted: 12/10/2011] [Indexed: 12/15/2022]
Abstract
Fusarium species are ubiquitous in nature, cause a range of plant diseases, and produce a variety of chemicals often referred to as secondary metabolites. Although some fungal secondary metabolites affect plant growth or protect plants from other fungi and bacteria, their presence in grain-based food and feed is more often associated with a variety of diseases in plants and in animals. Many of these structurally diverse metabolites are derived from a family of related enzymes called polyketide synthases (PKSs). A search of genomic sequence of Fusarium verticillioides, Fusarium graminearum, Fusarium oxysporum, and Fusarium solani identified a total of 58 PKS genes. To gain insight into how this gene family evolved and to guide future studies, we conducted phylogenomic and functional domain analyses. The resulting geneaology suggested that Fusarium PKSs represent 34 different groups responsible for synthesis of different core metabolites. The analyses indicate that variation in the Fusarium PKS gene family is due to gene duplication and loss events as well as enzyme gain-of-function due to the acquisition of new domains or of loss-of-function due to nucleotide mutations. Transcriptional analysis indicates that the 16 F. verticillioides PKS genes are expressed under a range of conditions, further evidence that they are functional genes that confer the ability to produce secondary metabolites.
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Affiliation(s)
- Daren W Brown
- Bacterial Foodborne Pathogens and Mycology Research, USDA-ARS-NCAUR, Peoria, Illinois 61604, USA.
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33
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Al-Nsour M, Zindah M, Belbeisi A, Hadaddin R, Brown DW, Walke H. Prevalence of Selected Chronic, Noncommunicable Disease Risk Factors in Jordan: Results of the 2007 Jordan Behavioral Risk Factor Surveillance Survey. Prev Chronic Dis 2011. [DOI: 10.5888/pcd9.110077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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34
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Balderson MJ, Spencer DP, Nygren I, Brown DW. Quality assurance using a photodiode array. J Appl Clin Med Phys 2011; 12:3358. [PMID: 21587181 PMCID: PMC5718683 DOI: 10.1120/jacmp.v12i2.3358] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 01/14/2011] [Accepted: 12/02/2010] [Indexed: 11/23/2022] Open
Abstract
Improved treatment techniques in radiation therapy provide incentive to reduce treatment margins, thereby increasing the necessity for more accurate geometrical setup of the linear accelerator and accompanying components. In the present paper, we describe the development of a novel device that enables precise and automated measurement of geometric parameters for the purpose of improving initial setup accuracy, and for standardizing repeated quality control activities. The device consists of a silicon photodiode array, an evaluation board, a data acquisition card, and a laptop. Measurements that demonstrate the utility of the device are also presented. Using the device, we show that the radiation light field congruence for both 6 and 15 MV beams is within 1.3 mm. The maximum measured disagreement between radiation field edges and light field edges was 1.290±0.002 mm, while the smallest disagreement between the light field and radiation field edge was 0.016±0.003 mm. Because measurements are automated, ambiguities resulting from interobserver variability are removed, greatly improving the reproducibility of measurements across observers. We expect the device to find use in consistency measurements on linear accelerators used for stereotactic radiosurgery, during the commissioning of new linear accelerators, or as an alternative to film or other commercially available devices for performing monthly or annual quality control checks. PACS numbers: 87.55.Qr, 87.56.Fc, 87.57.N‐, 87.15mn, 87.15mq
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Affiliation(s)
- M J Balderson
- Department of Physics and Astronomy, University of Calgary, Calgary, Alberta, Canada.
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35
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Larson TM, Kendra DF, Busman M, Brown DW. Fusarium verticillioides chitin synthases CHS5 and CHS7 are required for normal growth and pathogenicity. Curr Genet 2011; 57:177-89. [PMID: 21246198 DOI: 10.1007/s00294-011-0334-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 12/21/2010] [Accepted: 01/03/2011] [Indexed: 12/11/2022]
Abstract
Fusarium verticillioides is both an endophyte and a pathogen of maize and is a health threat in many areas of the world because it can contaminate maize with fumonisins, a toxic secondary metabolite. We identified eight putative chitin synthase (CHS) genes in F. verticillioides genomic sequence, and phylogenetic evidence shows that they group into seven established CHS gene classes. We targeted two CHSs (CHS5 and CHS7) for deletion analysis and found that both are required for normal hyphal growth and maximal disease of maize seedlings and ears. CHS5 and CHS7 encode a putative class V and class VII fungal chitin synthase, respectively; they are located adjacent to each other and are divergently transcribed. Fluorescent microscopy found that both CHS deficient strains produce balloon-shaped hyphae, while growth assays indicated that they were more sensitive to cell wall stressing compounds (e.g., the antifungal compound Nikkomycin Z) than wild type. Pathogenicity assays on maize seedlings and ears indicated that both strains were significantly reduced in their ability to cause disease. Our results demonstrate that both CHS5 and CHS7 are necessary for proper hyphal growth and pathogenicity of F. verticillioides on maize.
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Affiliation(s)
- Troy M Larson
- Bacterial Foodborne Pathogens and Mycology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604-3999, USA.
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37
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Wiemann P, Brown DW, Kleigrewe K, Bok JW, Keller NP, Humpf HU, Tudzynski B. FfVel1 and FfLae1, components of a velvet-like complex in Fusarium fujikuroi, affect differentiation, secondary metabolism and virulence. Mol Microbiol 2010. [PMID: 20572938 DOI: 10.1111/j.1365-2958.2010.07263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Besides industrially produced gibberellins (GAs), Fusarium fujikuroi is able to produce additional secondary metabolites such as the pigments bikaverin and neurosporaxanthin and the mycotoxins fumonisins and fusarin C. The global regulation of these biosynthetic pathways is only poorly understood. Recently, the velvet complex containing VeA and several other regulatory proteins was shown to be involved in global regulation of secondary metabolism and differentiation in Aspergillus nidulans. Here, we report on the characterization of two components of the F. fujikuroi velvet-like complex, FfVel1 and FfLae1. The gene encoding this first reported LaeA orthologue outside the class of Eurotiomycetidae is upregulated in ΔFfvel1 microarray-studies and FfLae1 interacts with FfVel1 in the nucleus. Deletion of Ffvel1 and Fflae1 revealed for the first time that velvet can simultaneously act as positive (GAs, fumonisins and fusarin C) and negative (bikaverin) regulator of secondary metabolism, and that both components affect conidiation and virulence of F. fujikuroi. Furthermore, the velvet-like protein FfVel2 revealed similar functions regarding conidiation, secondary metabolism and virulence as FfVel1. Cross-genus complementation studies of velvet complex component mutants between Fusarium, Aspergillus and Penicillium support an ancient origin for this complex, which has undergone a divergence in specific functions mediating development and secondary metabolism.
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Affiliation(s)
- Philipp Wiemann
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Daren W Brown
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Karin Kleigrewe
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Jin Woo Bok
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Nancy P Keller
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Hans-Ulrich Humpf
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Bettina Tudzynski
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
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Abstract
The homothallic ascomycete Aspergillus nidulans produces two types of pigmented spores: conidia and ascospores. The synthesis and localization of the spore pigments is developmentally regulated and occurs in specialized cell types. On the basis of spectroscopic evidence, we propose that the major ascospore pigment of A. nidulans (ascoquinone A) is a novel dimeric hydroxylated anthraquinone. The structure of ascoquinone A, as well as a comparison to model compounds, suggests that it is the product of a polyketide synthase. Previous studies have revealed that the conidial pigments from A. nidulans and a related Aspergillus species (A. parasiticus) also appear to be produced via polymerization of polyketide precursors (D. W. Brown, F. M. Hauser, R. Tommasi, S. Corlett, and J. J. Salvo, Tetrahedron Lett. 34:419-422, 1993; M. E. Mayorga and W. E. Timberlake, Mol. Gen. Genet. 235:205-212, 1992). The structural similarity between the ascospore pigment and the toxic anthraquinone norsolorinic acid, the first stable intermediate in the aflatoxin pathway, suggests an evolutionary relationship between the respective polyketide synthase systems.
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Affiliation(s)
- D W Brown
- Department of Microbiology, Immunology and Molecular Genetics, Albany Medical College, Albany, New York 12208
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Wiemann P, Brown DW, Kleigrewe K, Bok JW, Keller NP, Humpf HU, Tudzynski B. FfVel1 and FfLae1, components of a velvet-like complex in Fusarium fujikuroi, affect differentiation, secondary metabolism and virulence. Mol Microbiol 2010; 77:972-94. [PMID: 20572938 DOI: 10.1111/j.1365-2958.2010.07263.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Besides industrially produced gibberellins (GAs), Fusarium fujikuroi is able to produce additional secondary metabolites such as the pigments bikaverin and neurosporaxanthin and the mycotoxins fumonisins and fusarin C. The global regulation of these biosynthetic pathways is only poorly understood. Recently, the velvet complex containing VeA and several other regulatory proteins was shown to be involved in global regulation of secondary metabolism and differentiation in Aspergillus nidulans. Here, we report on the characterization of two components of the F. fujikuroi velvet-like complex, FfVel1 and FfLae1. The gene encoding this first reported LaeA orthologue outside the class of Eurotiomycetidae is upregulated in ΔFfvel1 microarray-studies and FfLae1 interacts with FfVel1 in the nucleus. Deletion of Ffvel1 and Fflae1 revealed for the first time that velvet can simultaneously act as positive (GAs, fumonisins and fusarin C) and negative (bikaverin) regulator of secondary metabolism, and that both components affect conidiation and virulence of F. fujikuroi. Furthermore, the velvet-like protein FfVel2 revealed similar functions regarding conidiation, secondary metabolism and virulence as FfVel1. Cross-genus complementation studies of velvet complex component mutants between Fusarium, Aspergillus and Penicillium support an ancient origin for this complex, which has undergone a divergence in specific functions mediating development and secondary metabolism.
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Affiliation(s)
- Philipp Wiemann
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Daren W Brown
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Karin Kleigrewe
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Jin Woo Bok
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Nancy P Keller
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Hans-Ulrich Humpf
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
| | - Bettina Tudzynski
- Institut für Botanik, Westfälische Wilhelms-Universität Münster, Schlossgarten 3, D-48149 Münster, GermanyInstitut für Lebensmittelchemie, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, D-48149 Münster, GermanyBacterial Foodborne Pathogens and Mycology Research, USDA/ARS, 1815 N University St, Peoria, IL 61604, USADepartment of Medical Microbiology and ImmunologyDepartment of Bacteriology, University of Wisconsin, 1550 Linden Dr, Madison, WI 53706-1521, USA
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Woodruff TR, Krishnan VB, Clausen B, Sisneros T, Livescu V, Brown DW, Bourke MAM, Vaidyanathan R. Design, implementation, and testing of a cryogenic loading capability on an engineering neutron diffractometer. Rev Sci Instrum 2010; 81:063903. [PMID: 20590248 DOI: 10.1063/1.3436637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A novel capability was designed, implemented, and tested for in situ neutron diffraction measurements during loading at cryogenic temperatures on the spectrometer for materials research at temperature and stress at Los Alamos National Laboratory. This capability allowed for the application of dynamic compressive forces of up to 250 kN on standard samples controlled at temperatures between 300 and 90 K. The approach comprised of cooling thermally isolated compression platens that in turn conductively cooled the sample in an aluminum vacuum chamber which was nominally transparent to the incident and diffracted neutrons. The cooling/heat rate and final temperature were controlled by regulating the flow of liquid nitrogen in channels inside the platens that were connected through bellows to the mechanical actuator of the load frame and by heaters placed on the platens. Various performance parameters of this system are reported here. The system was used to investigate deformation in Ni-Ti-Fe shape memory alloys at cryogenic temperatures and preliminary results are presented.
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Affiliation(s)
- T R Woodruff
- Department of Mechanical, Materials, and Aerospace Engineering, Advanced Materials Processing and Analysis Center (AMPAC), University of Central Florida, Orlando, Florida 32816, USA
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Ma LJ, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Di Pietro A, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S, Shim WB, Woloshuk C, Xie X, Xu JR, Antoniw J, Baker SE, Bluhm BH, Breakspear A, Brown DW, Butchko RAE, Chapman S, Coulson R, Coutinho PM, Danchin EGJ, Diener A, Gale LR, Gardiner DM, Goff S, Hammond-Kosack KE, Hilburn K, Hua-Van A, Jonkers W, Kazan K, Kodira CD, Koehrsen M, Kumar L, Lee YH, Li L, Manners JM, Miranda-Saavedra D, Mukherjee M, Park G, Park J, Park SY, Proctor RH, Regev A, Ruiz-Roldan MC, Sain D, Sakthikumar S, Sykes S, Schwartz DC, Turgeon BG, Wapinski I, Yoder O, Young S, Zeng Q, Zhou S, Galagan J, Cuomo CA, Kistler HC, Rep M. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 2010; 464:367-73. [PMID: 20237561 PMCID: PMC3048781 DOI: 10.1038/nature08850] [Citation(s) in RCA: 998] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 01/20/2010] [Indexed: 11/09/2022]
Abstract
Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.
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Affiliation(s)
- Li-Jun Ma
- The Broad Institute, Cambridge, Massachusetts 02141, USA
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Ward E, McCartney T, Brown DW, Grant A, Butchart A, Taylor M, Bhoorasingh P, Wong H, Morris C, Deans-Clarke AM, East J, Valentine C, Dundas S, Pinnock C. Results of an exercise to estimate the costs of interpersonal violence in Jamaica. W INDIAN MED J 2009; 58:446-451. [PMID: 20441064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
UNLABELLED This report describes the application of a draft version of the World Health Organization (WHO)/ United States Centers for Disease Control and Prevention (CDC) Manual for estimating the economic costs of injuries due to interpersonal and self-directed violence to measure costs of injuries from interpersonal violence. METHODS Fatal incidence data was obtained from the Jamaica Constabulary Force. The incidence of nonfatal violence-related injuries that required hospitalization was estimated using data obtained from patients treated at and/or admitted to three Type A government hospitals in 2006. RESULTS During 2006, direct medical cost (J$2.1 billion) of injuries due to interpersonal violence accounted for about 12% of Jamaica's total health budget while productivity losses due to violence-related injuries accounted for approximately J$27.5 billion or 160% of Jamaica's total health expenditure and 4% of Jamaica's Gross Domestic Product. CONCLUSIONS The availability of accurate and reliable data of the highest quality from health-related information systems is critical for providing useful data on the burden of violence and injury to decision-makers. As Ministries of Health take a leading role in violence and injury prevention, data collection and information systems must have a central role. This study describes the results of one approach to examining the economic burden of interpersonal violence in developing countries where the burden of violence is heaviest. The WHO-CDC manual also tested in Thailand and Brazil is a first step towards generating a reference point for resource allocation, priority setting and prevention advocacy.
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Affiliation(s)
- E Ward
- Violence Prevention Alliance, Jamaica, The University of the West Indies, Kingston 7, Jamaica, West Indies.
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Cheng S, Stoica AD, Wang XL, Ren Y, Almer J, Horton JA, Liu CT, Clausen B, Brown DW, Liaw PK, Zuo L. Deformation crossover: from nano- to mesoscale. Phys Rev Lett 2009; 103:035502. [PMID: 19659294 DOI: 10.1103/physrevlett.103.035502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2008] [Indexed: 05/28/2023]
Abstract
In situ synchrotron and neutron diffraction were used to study deformation mechanisms in Ni over a broad range of grain sizes. The experimental data show that unlike in coarse-grained metals, where the deformation is dominated by dislocation slip, plastic deformation in nanocrystalline Ni is mediated by grain-boundary activities, as evidenced by the lack of intergranular strain and texture development. For ultrafine-grained Ni, although dislocation slip is an active deformation mechanism, deformation twinning also plays an important role, whose propensity increases with the grain size.
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Affiliation(s)
- S Cheng
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Brown DW, Butchko RAE, Proctor RH. Genomic analysis of Fusarium verticillioides. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2008; 25:1158-1165. [PMID: 19238625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fusarium verticillioides (teleomorph Gibberella moniliformis) can be either an endophyte of maize, causing no visible disease, or a pathogen-causing disease of ears, stalks, roots and seedlings. At any stage, this fungus can synthesize fumonisins, a family of mycotoxins structurally similar to the sphingolipid sphinganine. Ingestion of fumonisin-contaminated maize has been associated with a number of animal diseases, including cancer in rodents, and exposure has been correlated with human oesophageal cancer in some regions of the world, and some evidence suggests that fumonisins are a risk factor for neural tube defects. A primary goal of the authors' laboratory is to eliminate fumonisin contamination of maize and maize products. Understanding how and why these toxins are made and the F. verticillioides-maize disease process will allow one to develop novel strategies to limit tissue destruction (rot) and fumonisin production. To meet this goal, genomic sequence data, expressed sequence tags (ESTs) and microarrays are being used to identify F. verticillioides genes involved in the biosynthesis of toxins and plant pathogenesis. This paper describes the current status of F. verticillioides genomic resources and three approaches being used to mine microarray data from a wild-type strain cultured in liquid fumonisin production medium for 12, 24, 48, 72, 96 and 120h. Taken together, these approaches demonstrate the power of microarray technology to provide information on different biological processes.
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Affiliation(s)
- D W Brown
- Mycotoxin Research Unit, US Department of Agriculture-ARS, Peoria, IL, USA.
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Gladstone BP, Muliyil JP, Jaffar S, Wheeler JG, Le Fevre A, Iturriza-Gomara M, Gray JJ, Bose A, Estes MK, Brown DW, Kang G. Infant morbidity in an Indian slum birth cohort. Arch Dis Child 2008; 93:479-84. [PMID: 17916587 PMCID: PMC2682775 DOI: 10.1136/adc.2006.114546] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To establish incidence rates, clinic referrals, hospitalisations, mortality rates and baseline determinants of morbidity among infants in an Indian slum. DESIGN A community-based birth cohort with twice-weekly surveillance. SETTING Vellore, South India. SUBJECTS 452 newborns recruited over 18 months, followed through infancy. MAIN OUTCOME MEASURES Incidence rates of gastrointestinal illness, respiratory illness, undifferentiated fever, other infections and non-infectious morbidity; rates of community-based diagnoses, clinic visits and hospitalisation; and rate ratios of baseline factors for morbidity. RESULTS Infants experienced 12 episodes (95% confidence interval (CI) 11 to 13) of illness, spending about one fifth of their infancy with an illness. Respiratory and gastrointestinal symptoms were most common with incidence rates (95% CI) of 7.4 (6.9 to 7.9) and 3.6 (3.3 to 3.9) episodes per child-year. Factors independently associated with a higher incidence of respiratory and gastrointestinal illness were age (3-5 months), male sex, cold/wet season and household involved in beedi work. The rate (95% CI) of hospitalisation, mainly for respiratory and gastrointestinal illness, was 0.28 (0.22 to 0.35) per child-year. CONCLUSIONS The morbidity burden due to respiratory and gastrointestinal illness is high in a South Indian urban slum, with children ill for approximately one fifth of infancy, mainly with respiratory and gastrointestinal illnesses. The risk factors identified were younger age, male sex, cold/wet season and household involvement in beedi work.
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Affiliation(s)
- B P Gladstone
- Department of Community Health, Christian Medical College, Vellore, India
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46
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Gnaneshan S, Brown KE, Green J, Brown DW. On-line global/WHO-European regional measles nucleotide surveillance. Euro Surveill 2008; 13:18861. [PMID: 18761979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Affiliation(s)
- S Gnaneshan
- Centre for Infections, Health Protection Agency London, United Kingdom.
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Granerod J, Crowcroft NS, Brown DW, Solomon T. The trials and tribulations of implementing a multi-centre study of encephalitis in England. Clin Med (Lond) 2007; 7:646-7. [PMID: 18193722 PMCID: PMC4954385 DOI: 10.7861/clinmedicine.7-6-646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Proctor RH, Butchko RAE, Brown DW, Moretti A. Functional characterization, sequence comparisons and distribution of a polyketide synthase gene required for perithecial pigmentation in someFusariumspecies. ACTA ACUST UNITED AC 2007; 24:1076-87. [PMID: 17886180 DOI: 10.1080/02652030701546495] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Polyketides are a structurally diverse class of secondary metabolites produced by bacteria, fungi, plants and animals. The fungal genus Fusarium includes agronomically important plant pathogenic and mycotoxin-producing species and produces numerous polyketides. The study further characterized a polyketide synthase-encoding gene (PKS3 = PGL1) that was previously identified in F. graminearum and F. verticillioides. Disruption of the F. verticillioides PGL1 indicated that it is required for the production of the dark pigment in perithecial walls, as previously shown in F. graminearum. A third PGL1 orthologue was identified in the genomic sequence of N. haematococca (anamorph F. solani f. sp. pisi). Analysis of the carboxy-terminal end of the deduced PGL1 protein indicated that it had a functional domain related to dehydrogenases/reductases that is sometimes present in non-ribosomal peptide synthetases. Comparison of the genomic regions flanking PGL1 in F. graminearum, F. verticillioides and N. haematococca revealed that the extent of gene synteny in this region was greater between F. graminearum and F. verticillioides than between either of these species and N. haematococca. Southern blot analysis indicated that PGL1 occurs widely within the genus Fusarium including species with no known sexual stage.
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Affiliation(s)
- R H Proctor
- National Center for Agricultural Utilization Research, US Department of Agriculture, Agricultural Research Service, Peoria, Illinois, USA.
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Abstract
It is well established that rotaviruses of group A are the most important cause of severe diarrhoea in children. The causes of most cases of infectious diarrhoea still remain unidentified, however, and there must be other viruses to be found. 'Novel' rotaviruses have recently been discovered, mainly in animals (serogroups B and C in pigs and humans, D in birds, and one or more further groups in sheep and other mammals). Except for the group B virus which has caused widespread outbreaks of quite severe diarrhoea in adults in China (still not reported from outside China) these novel rotaviruses are rarities in the human and probably represent uncommon zoonotic infections. We speculate that the Chinese virus might have arisen by reassortment of genetic segments of animal group B viruses or perhaps by mutation, and so became infectious for man. The problem of identifying and determining the importance of small round viruses is reviewed. It seems likely that the group of small, round structured viruses, including Norwalk and the viruses of plainly calicivirus morphology, are all representatives of a whole group of enteric caliciviruses. Until they can be more easily cultivated it will be difficult to make diagnostic reagents available to all. Astroviruses and genuine parvoviruses have been found by many people in many countries. Astroviruses are probably more important as pathogens in lambs than in children or calves; parvoviruses can only be established as significant in epidemics. The coronavirus-like particles, first found in Vellore and Bristol, are still enigmatic and their role in diarrhoea is uncertain. Toroviridae, recently discovered as causes of diarrhoea in ungulates, do not seem to be at all important as causes of diarrhoea in humans. Possibly fruitful approaches to future searches are outlined: firstly to make more extensive use of immuno-electron microscopy; and secondly to try to improve existing tissue culture systems to make them more sensitive to enteric viruses.
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Brown DW, Butchko RAE, Busman M, Proctor RH. The Fusarium verticillioides FUM gene cluster encodes a Zn(II)2Cys6 protein that affects FUM gene expression and fumonisin production. Eukaryot Cell 2007; 6:1210-8. [PMID: 17483290 PMCID: PMC1951116 DOI: 10.1128/ec.00400-06] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fumonisins are mycotoxins produced by some Fusarium species and can contaminate maize or maize products. Ingestion of fumonisins is associated with diseases, including cancer and neural tube defects, in humans and animals. In fungi, genes involved in the synthesis of mycotoxins and other secondary metabolites are often located adjacent to each other in gene clusters. Such genes can encode structural enzymes, regulatory proteins, and/or proteins that provide self-protection. The fumonisin biosynthetic gene cluster includes 16 genes, none of which appear to play a role in regulation. In this study, we identified a previously undescribed gene (FUM21) located adjacent to the fumonisin polyketide synthase gene, FUM1. The presence of a Zn(II)2Cys6 DNA-binding domain in the predicted protein suggested that FUM21 was involved in transcriptional regulation. FUM21 deletion (Deltafum21) mutants produce little to no fumonisin in cracked maize cultures but some FUM1 and FUM8 transcripts in a liquid GYAM medium. Complementation of a Deltafum21 mutant with a wild-type copy of the gene restored fumonisin production. Analysis of FUM21 cDNAs identified four alternative splice forms (ASFs), and microarray analysis indicated the ASFs were differentially expressed. Based on these data, we present a model for how FUM21 ASFs may regulate fumonisin biosynthesis.
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Affiliation(s)
- Daren W Brown
- Mycotoxin Research Group, USDA/ARS, 1815 N. University St., Peoria, IL 61604, USA.
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