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Silva E, Dantas R, Barbosa JC, Berlinck RGS, Fill T. Metabolomics approach to understand molecular mechanisms involved in fungal pathogen-citrus pathosystems. Mol Omics 2024; 20:154-168. [PMID: 38273771 DOI: 10.1039/d3mo00182b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Citrus is a crucial crop with a significant economic impact globally. However, postharvest decay caused by fungal pathogens poses a considerable threat, leading to substantial financial losses. Penicillium digitatum, Penicillium italicum, Geotrichum citri-aurantii and Phyllosticta citricarpa are the main fungal pathogens, causing green mold, blue mold, sour rot and citrus black spot diseases, respectively. The use of chemical fungicides as a control strategy in citrus raises concerns about food and environmental safety. Therefore, understanding the molecular basis of host-pathogen interactions is essential to find safer alternatives. This review highlights the potential of the metabolomics approach in the search for bioactive compounds involved in the pathogen-citrus interaction, and how the integration of metabolomics and genomics contributes to the understanding of secondary metabolites associated with fungal virulence and the fungal infection mechanisms. Our goal is to provide a pipeline combining metabolomics and genomics that can effectively guide researchers to perform studies aiming to contribute to the understanding of the fundamental chemical and biochemical aspects of pathogen-host interactions, in order to effectively develop new alternatives for fungal diseases in citrus cultivation. We intend to inspire the scientific community to question unexplored biological systems, and to employ diverse analytical approaches and metabolomics techniques to address outstanding questions about the non-studied pathosystems from a chemical biology perspective.
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Affiliation(s)
- Evandro Silva
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
- University of São Paulo, Institute of Chemistry, CEP 13566-590, São Carlos, SP, Brazil
| | - Rodolfo Dantas
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
| | - Júlio César Barbosa
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
| | - Roberto G S Berlinck
- University of São Paulo, Institute of Chemistry, CEP 13566-590, São Carlos, SP, Brazil
| | - Taicia Fill
- State University of Campinas, Institute of Chemistry, CEP, 13083-970 Campinas, SP, Brazil.
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2
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Bhardwaj M, Kailoo S, Khan RT, Khan SS, Rasool S. Harnessing fungal endophytes for natural management: a biocontrol perspective. Front Microbiol 2023; 14:1280258. [PMID: 38143866 PMCID: PMC10748429 DOI: 10.3389/fmicb.2023.1280258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023] Open
Abstract
In the ever-evolving realm of agriculture, the convoluted interaction between plants and microorganisms have assumed paramount significance. Fungal endophytes, once perceived as mere bystanders within plant tissues, have now emerged as dynamic defenders of plant health. This comprehensive review delves into the captivating world of fungal endophytes and their multifaceted biocontrol mechanisms. Exploring their unique ability to coexist with their plant hosts, fungal endophytes have unlocked a treasure trove of biological weaponry to fend off pathogens and enhance plant resilience. From the synthesis of bioactive secondary metabolites to intricate signaling pathways these silent allies are masters of biological warfare. The world of fungal endophytes is quite fascinating as they engage in a delicate dance with the plant immune system, orchestrating a symphony of defense that challenges traditional notions of plant-pathogen interactions. The journey through the various mechanisms employed by these enigmatic endophytes to combat diseases, will lead to revelational understanding of sustainable agriculture. The review delves into cutting-edge research and promising prospects, shedding light on how fungal endophytes hold the key to biocontrol and the reduction of chemical inputs in agriculture. Their ecological significance, potential for bioprospecting and avenues for future research are also explored. This exploration of the biocontrol mechanisms of fungal endophytes promise not only to enrich our comprehension of plant-microbe relationships but also, to shape the future of sustainable and ecofriendly agricultural practices. In this intricate web of life, fungal endophytes are indeed the unsung heroes, silently guarding our crops and illuminating a path towards a greener, healthier tomorrow.
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Affiliation(s)
| | | | | | | | - Shafaq Rasool
- Molecular Biology Laboratory, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
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3
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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4
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Pokhrel A, Coleman JJ. Inventory of the Secondary Metabolite Biosynthetic Potential of Members within the Terminal Clade of the Fusarium solani Species Complex. J Fungi (Basel) 2023; 9:799. [PMID: 37623570 PMCID: PMC10455376 DOI: 10.3390/jof9080799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
The Fusarium solani species complex (FSSC) constitutes at least 77 phylogenetically distinct species including several agriculturally important and clinically relevant opportunistic pathogens. As with other Fusaria, they have been well documented to produce many secondary metabolites-compounds that are not required for the fungus to grow or develop but may be beneficial to the organism. An analysis of ten genomes from fungi within the terminal clade (clade 3) of the FSSC revealed each genome encoded 35 (F. cucurbitcola) to 48 (F. tenucristatum) secondary metabolite biosynthetic gene clusters (BGCs). A total of seventy-four different BGCs were identified from the ten FSSC genomes including seven polyketide synthases (PKS), thirteen nonribosomal peptide synthetases (NRPS), two terpene synthase BGCs, and a single dimethylallytryptophan synthase (DMATS) BGC conserved in all the genomes. Some of the clusters that were shared included those responsible for producing naphthoquinones such as fusarubins, a red pigmented compound, squalestatin, and the siderophores malonichrome, ferricrocin, and triacetylfusarinine. Eight novel NRPS and five novel PKS BGCs were identified, while BGCs predicted to produce radicicol, gibberellin, and fusaoctaxin were identified, which have not previously described in members of the FSSC. The diversity of the secondary metabolite repertoire of the FSSC may contribute to the expansive host range of these fungi and their ability to colonize broad habitats.
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Affiliation(s)
- Ambika Pokhrel
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA;
- The Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jeffrey J. Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA;
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5
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He R, Zhang J, Shao Y, Gu S, Song C, Qian L, Yin WB, Li Z. Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements. PLoS Comput Biol 2023; 19:e1011100. [PMID: 37186644 DOI: 10.1371/journal.pcbi.1011100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 05/25/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Non-ribosomal peptide synthetase (NRPS) is a diverse family of biosynthetic enzymes for the assembly of bioactive peptides. Despite advances in microbial sequencing, the lack of a consistent standard for annotating NRPS domains and modules has made data-driven discoveries challenging. To address this, we introduced a standardized architecture for NRPS, by using known conserved motifs to partition typical domains. This motif-and-intermotif standardization allowed for systematic evaluations of sequence properties from a large number of NRPS pathways, resulting in the most comprehensive cross-kingdom C domain subtype classifications to date, as well as the discovery and experimental validation of novel conserved motifs with functional significance. Furthermore, our coevolution analysis revealed important barriers associated with re-engineering NRPSs and uncovered the entanglement between phylogeny and substrate specificity in NRPS sequences. Our findings provide a comprehensive and statistically insightful analysis of NRPS sequences, opening avenues for future data-driven discoveries.
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Affiliation(s)
- Ruolin He
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, PR China
| | - Yuanzhe Shao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shaohua Gu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Long Qian
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, PR China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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6
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Li H, Dai J, Shi Y, Zhu X, Jia L, Yang Z. Molecular Regulatory Mechanism of the Iron-Ion-Promoted Asexual Sporulation of Antrodia cinnamomea in Submerged Fermentation Revealed by Comparative Transcriptomics. J Fungi (Basel) 2023; 9:jof9020235. [PMID: 36836349 PMCID: PMC9959139 DOI: 10.3390/jof9020235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/29/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Antrodia cinnamomea is a precious edible and medicinal fungus with activities of antitumor, antivirus, and immunoregulation. Fe2+ was found to promote the asexual sporulation of A. cinnamomea markedly, but the molecular regulatory mechanism of the effect is unclear. In the present study, comparative transcriptomics analysis using RNA sequencing (RNA-seq) and real time quantitative PCR (RT-qPCR) were conducted on A. cinnamomea mycelia cultured in the presence or absence of Fe2+ to reveal the molecular regulatory mechanisms underlying iron-ion-promoted asexual sporulation. The obtained mechanism is as follows: A. cinnamomea acquires iron ions through reductive iron assimilation (RIA) and siderophore-mediated iron assimilation (SIA). In RIA, ferrous iron ions are directly transported into cells by the high-affinity protein complex formed by a ferroxidase (FetC) and an Fe transporter permease (FtrA). In SIA, siderophores are secreted externally to chelate the iron in the extracellular environment. Then, the chelates are transported into cells through the siderophore channels (Sit1/MirB) on the cell membrane and hydrolyzed by a hydrolase (EstB) in the cell to release iron ions. The O-methyltransferase TpcA and the regulatory protein URBS1 promote the synthesis of siderophores. HapX and SreA respond to and maintain the balance of the intercellular concentration of iron ions. Furthermore, HapX and SreA promote the expression of flbD and abaA, respectively. In addition, iron ions promote the expression of relevant genes in the cell wall integrity signaling pathway, thereby accelerating the cell wall synthesis and maturation of spores. This study contributes to the rational adjustment and control of the sporulation of A. cinnamomea and thereby improves the efficiency of the preparation of inoculum for submerged fermentation.
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Affiliation(s)
- Huaxiang Li
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China
| | - Jianing Dai
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China
| | - Yu Shi
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyan Zhu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, Huaian 223003, China
| | - Luqiang Jia
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China
| | - Zhenquan Yang
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Yamaguchi S, Fujioka T, Yoshimi A, Kumagai T, Umemura M, Abe K, Machida M, Kawai K. Discovery of a gene cluster for the biosynthesis of novel cyclic peptide compound, KK-1, in Curvularia clavata. FRONTIERS IN FUNGAL BIOLOGY 2023; 3:1081179. [PMID: 37746209 PMCID: PMC10512319 DOI: 10.3389/ffunb.2022.1081179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/15/2022] [Indexed: 09/26/2023]
Abstract
KK-1, a cyclic depsipeptide with 10 residues produced by a filamentous fungus Curvularia clavata BAUA-2787, is a promising pesticide active compound with high activity against many plant pathogens, especially Botrytis cinerea. As a first step toward the future mass production of KK-1 through synthetic biological approaches, we aimed to identify the genes responsible for the KK-1 biosynthesis. To achieve this, we conducted whole genome sequencing and transcriptome analysis of C. clavata BAUA-2787 to predict the KK-1 biosynthetic gene cluster. We then generated the overexpression and deletion mutants for each cluster gene using our originally developed transformation system for this fungus, and analyzed the KK-1 production and the cluster gene expression levels to confirm their involvement in KK-1 biosynthesis. As a result of these, a region of approximately 71 kb was found, containing 10 open reading frames, which were co-induced during KK-1 production, as a biosynthetic gene cluster. These include kk1B, which encodes nonribosomal peptide synthetase with a domain structure that is consistent with the structural features of KK-1, and kk1F, which encodes a transcription factor. The overexpression of kk1F increased the expression of the entire cluster genes and, consequently, improved KK-1 production, whereas its deletion decreased the expression of the entire cluster genes and almost eliminated KK-1 production, demonstrating that the protein encoded by kk1F regulates the expressions of the other nine cluster genes cooperatively as the pathway-specific transcription factor. Furthermore, the deletion of each cluster gene caused a reduction in KK-1 productivity, indicating that each gene is involved in KK-1 production. The genes kk1A, kk1D, kk1H, and kk1I, which showed a significant decrease in KK-1 productivity due to deletion, were presumed to be directly involved in KK-1 structure formation, including the biosynthesis of the constituent residues. kk1C, kk1E, kk1G, and kk1J, which maintained a certain level of KK-1 productivity despite deletion, were possibly involved in promoting or assisting KK-1 production, such as extracellular transportation and the removal of aberrant units incorporated into the peptide chain.
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Affiliation(s)
- Shigenari Yamaguchi
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
| | - Tomonori Fujioka
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
| | - Akira Yoshimi
- ABE-Project, New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
- Laboratory of Terrestrial Microbial Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | | | - Maiko Umemura
- Bio-system Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Keietsu Abe
- ABE-Project, New Industry Creation Hatchery Center, Tohoku University, Sendai, Japan
- Laboratory of Applied Microbiology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Masayuki Machida
- Bio-system Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Graduate School of Engineering, Genome Biotechnology Laboratory, Kanazawa Institute of Technology, Ishikawa, Japan
| | - Kiyoshi Kawai
- Biotechnology Laboratory, Life & Environment Research Center, Life Science Research Institute, Research & Development Division, Kumiai Chemical Industry Co., Ltd., Shizuoka, Japan
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8
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Interconnected Set of Enzymes Provide Lysine Biosynthetic Intermediates and Ornithine Derivatives as Key Precursors for the Biosynthesis of Bioactive Secondary Metabolites. Antibiotics (Basel) 2023; 12:antibiotics12010159. [PMID: 36671360 PMCID: PMC9854754 DOI: 10.3390/antibiotics12010159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Bacteria, filamentous fungi, and plants synthesize thousands of secondary metabolites with important biological and pharmacological activities. The biosynthesis of these metabolites is performed by networks of complex enzymes such as non-ribosomal peptide synthetases, polyketide synthases, and terpenoid biosynthetic enzymes. The efficient production of these metabolites is dependent upon the supply of precursors that arise from primary metabolism. In the last decades, an impressive array of biosynthetic enzymes that provide specific precursors and intermediates leading to secondary metabolites biosynthesis has been reported. Suitable knowledge of the elaborated pathways that synthesize these precursors or intermediates is essential for advancing chemical biology and the production of natural or semisynthetic biological products. Two of the more prolific routes that provide key precursors in the biosynthesis of antitumor, immunosuppressant, antifungal, or antibacterial compounds are the lysine and ornithine pathways, which are involved in the biosynthesis of β-lactams and other non-ribosomal peptides, and bacterial and fungal siderophores. Detailed analysis of the molecular genetics and biochemistry of the enzyme system shows that they are formed by closely related components. Particularly the focus of this study is on molecular genetics and the enzymatic steps that lead to the formation of intermediates of the lysine pathway, such as α-aminoadipic acid, saccharopine, pipecolic acid, and related compounds, and of ornithine-derived molecules, such as N5-Acetyl-N5-Hydroxyornithine and N5-anhydromevalonyl-N5-hydroxyornithine, which are precursors of siderophores. We provide evidence that shows interesting functional relationships between the genes encoding the enzymes that synthesize these products. This information will contribute to a better understanding of the possibilities of advancing the industrial applications of synthetic biology.
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Hoh DZ, Lee HH, Wada N, Liu WA, Lu MR, Lai CK, Ke HM, Sun PF, Tang SL, Chung WH, Chen YL, Chung CL, Tsai IJ. Comparative genomic and transcriptomic analyses of trans-kingdom pathogen Fusarium solani species complex reveal degrees of compartmentalization. BMC Biol 2022; 20:236. [PMID: 36266645 PMCID: PMC9583462 DOI: 10.1186/s12915-022-01436-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Background The Fusarium solani species complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced, assembled and annotated six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins. We established a pathosystem and investigated the expression data of F. falciforme and F. keratoplasticum in Chinese softshell turtle (Pelodiscus sinensis) host. Results Comparative analyses between the FSSC genomes revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). LS chromosomes contribute to variations in genomes size, with up to 42.2% of variations between F. vanettenii strains. Each chromosome compartment varied in structural architectures, with FC and LS chromosomes contain higher proportions of repetitive elements with genes enriched in functions related to pathogenicity and niche expansion. We identified differences in both selection in the coding sequences and DNA methylation levels between genome features and chromosome compartments which suggest a multi-speed evolution that can be traced back to the last common ancestor of Fusarium. We further demonstrated that F. falciforme and F. keratoplasticum are opportunistic pathogens by inoculating P. sinensis eggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. Conclusions The high-quality genome assemblies provided new insights into the evolution of FSSC chromosomes, which also serve as a resource for studies of fungal genome evolution and pathogenesis. This study also establishes an animal model for fungal pathogens of trans-kingdom hosts. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01436-7.
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Affiliation(s)
- Daphne Z Hoh
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Naohisa Wada
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Wei-An Liu
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Min R Lu
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Cheng-Kuo Lai
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan
| | - Pei-Feng Sun
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, 116 Wenshan, Taipei, Taiwan
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan.,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Wen-Hsin Chung
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Ying-Lien Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan
| | - Isheng Jason Tsai
- Biodiversity Research Center, Academia Sinica, 115 Nangang, Taipei, Taiwan. .,Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan. .,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
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10
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Shokrollahi N, Ho CL, Zainudin NAIM, Wahab MABA, Wong MY. Identification of non-ribosomal peptide synthetase in Ganoderma boninense Pat. that was expressed during the interaction with oil palm. Sci Rep 2021; 11:16330. [PMID: 34381084 PMCID: PMC8358039 DOI: 10.1038/s41598-021-95549-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene.
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Affiliation(s)
- Neda Shokrollahi
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Chai-Ling Ho
- grid.11142.370000 0001 2231 800XDepartment of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Nur Ain Izzati Mohd Zainudin
- grid.11142.370000 0001 2231 800XDepartment of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mohd As’wad Bin Abul Wahab
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Mui-Yun Wong
- grid.11142.370000 0001 2231 800XDepartment of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia ,grid.11142.370000 0001 2231 800XInstitute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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11
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Genetic Relationships in the Toxin-Producing Fungal Endophyte, Alternaria oxytropis Using Polyketide Synthase and Non-Ribosomal Peptide Synthase Genes. J Fungi (Basel) 2021; 7:jof7070538. [PMID: 34356917 PMCID: PMC8306250 DOI: 10.3390/jof7070538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/16/2023] Open
Abstract
The legume Oxytropis sericea hosts a fungal endophyte, Alternaria oxytropis, which produces secondary metabolites (SM), including the toxin swainsonine. Polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) enzymes are associated with biosynthesis of fungal SM. To better understand the origins of the SM, an unannotated genome of A. oxytropis was assessed for protein sequences similar to known PKS and NRPS enzymes of fungi. Contigs exhibiting identity with known genes were analyzed at nucleotide and protein levels using available databases. Software were used to identify PKS and NRPS domains and predict identity and function. Confirmation of sequence for selected gene sequences was accomplished using PCR. Thirteen PKS, 5 NRPS, and 4 PKS-NRPS hybrids were identified and characterized with functions including swainsonine and melanin biosynthesis. Phylogenetic relationships among closest amino acid matches with Alternaria spp. were identified for seven highly conserved PKS and NRPS, including melanin synthesis. Three PKS and NRPS were most closely related to other fungi within the Pleosporaceae family, while five PKS and PKS-NRPS were closely related to fungi in the Pleosporales order. However, seven PKS and PKS-NRPS showed no identity with fungi in the Pleosporales or the class Dothideomycetes, suggesting a different evolutionary origin for those genes.
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Ashraf S, Dhusia K, Verma S. Siderophores Mediated Iron Acquisition and Virulence of Brown Rot Disease in Stone Fruits Caused by Monilinia fructicola in Jammu and Kashmir. Fungal Biol 2021. [DOI: 10.1007/978-3-030-53077-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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13
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Fungal Siderophores: Prospects and Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-53077-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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14
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Iqbal M, Broberg M, Haarith D, Broberg A, Bushley KE, Brandström Durling M, Viketoft M, Funck Jensen D, Dubey M, Karlsson M. Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping. Evol Appl 2020; 13:2264-2283. [PMID: 33005223 PMCID: PMC7513725 DOI: 10.1111/eva.13001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/09/2020] [Accepted: 05/13/2020] [Indexed: 01/28/2023] Open
Abstract
Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large-scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome-wide association study (GWAS) for in vitro antagonism against the root lesion nematode Pratylenchus penetrans in 53 previously genome re-sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p < .001) between strains, indicating a polygenic inheritance. Twenty-one strains produced culture filtrates with higher (p ≤ .05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p ≤ .05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10-10) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes nps4 and nps5 were generated and showed increased (p ≤ .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p < .001) nematicidal activity and reduced (p ≤ .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.
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Affiliation(s)
- Mudassir Iqbal
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Martin Broberg
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Deepak Haarith
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Anders Broberg
- Department of Molecular Sciences Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Kathryn E Bushley
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
| | - Mikael Brandström Durling
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Maria Viketoft
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology Uppsala BioCenter Swedish University of Agricultural Sciences Uppsala Sweden
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Gu X, Yang S, Yang X, Yao L, Gao X, Zhang M, Liu W, Zhao H, Wang Q, Li Z, Li Z, Ding J. Comparative transcriptome analysis of two Cercospora sojina strains reveals differences in virulence under nitrogen starvation stress. BMC Microbiol 2020; 20:166. [PMID: 32546122 PMCID: PMC7298872 DOI: 10.1186/s12866-020-01853-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cercospora sojina is a fungal pathogen that causes frogeye leaf spot in soybean-producing regions, leading to severe yield losses worldwide. It exhibits variations in virulence due to race differentiation between strains. However, the candidate virulence-related genes are unknown because the infection process is slow, making it difficult to collect transcriptome samples. RESULTS In this study, virulence-related differentially expressed genes (DEGs) were obtained from the highly virulent Race 15 strain and mildly virulent Race1 strain under nitrogen starvation stress, which mimics the physiology of the pathogen during infection. Weighted gene co-expression network analysis (WGCNA) was then used to find co-expressed gene modules and assess the relationship between gene networks and phenotypes. Upon comparison of the transcriptomic differences in virulence between the strains, a total of 378 and 124 DEGs were upregulated, while 294 and 220 were downregulated in Race 1 and Race 15, respectively. Annotation of these DEGs revealed that many were associated with virulence differences, including scytalone dehydratase, 1,3,8-trihydroxynaphthalene reductase, and β-1,3-glucanase. In addition, two modules highly correlated with the highly virulent strain Race 15 and 36 virulence-related DEGs were found to contain mostly β-1,4-glucanase, β-1,4-xylanas, and cellobiose dehydrogenase. CONCLUSIONS These important nitrogen starvation-responsive DEGs are frequently involved in the synthesis of melanin, polyphosphate storage in the vacuole, lignocellulose degradation, and cellulose degradation during fungal development and differentiation. Transcriptome analysis indicated unique gene expression patterns, providing further insight into pathogenesis.
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Affiliation(s)
- Xin Gu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Shuai Yang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaohe Yang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Liangliang Yao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Xuedong Gao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Maoming Zhang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Wei Liu
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Haihong Zhao
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Qingsheng Wang
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Zengjie Li
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Zhimin Li
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China
| | - Junjie Ding
- Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, Jiamusi, China.
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16
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Ribeiro THC, Fernandes-Brum CN, de Souza CR, Dias FAN, Almeida-Junior OD, Regina MDA, de Oliveira KKP, Dos Reis GL, Oliveira LM, Fernandes FDP, Torregrosa L, de Souza JT, Chalfun-Junior A. Transcriptome analyses suggest that changes in fungal endophyte lifestyle could be involved in grapevine bud necrosis. Sci Rep 2020; 10:9514. [PMID: 32528037 PMCID: PMC7290027 DOI: 10.1038/s41598-020-66500-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 05/11/2020] [Indexed: 12/04/2022] Open
Abstract
Bud necrosis (BN) is a common disorder that affects Vitis vinifera L. and reduces its potential yield. To minimize the losses caused by BN, the double pruning management was applied in Brazilian Southeast vineyards. In this management strategy plants are pruned at the winter to promote a vegetative cycle and then, at summer, to promote the reproductive cycle at optimal environmental conditions. To investigate the relationship of BN and the double pruning management RNA-seq libraries were sequenced from healthy and necrotic tissues at four different stages of the year. The comparison of differentially expressed genes in necrotic and non-necrotic tissues showed an enhanced expression of genes related to cell death possibly induced by endophytic microorganisms in the necrotic tissues. The de novo assembly, characterization and quantification of transcripts within the RNA-seq libraries showed that genes from the endophytic fungus Alternaria alternata, responsible for the production of toxic compounds were highly expressed under BN. Here we propose a model in which unfavorable conditions and reduced carbohydrate levels in buds can promote the switch from a biotrophic lifestyle to a necrotrophic lifestyle in the endophytic fungi, which seems to be involved in the development of BN.
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Affiliation(s)
| | | | - Claudia Rita de Souza
- Technological Center of Grape and Wine Research, Agronomical Research Institute of Minas Gerais, Caldas, Brazil
| | | | | | | | | | - Gabriel Lasmar Dos Reis
- Laboratory of Molecular Plant Physiology, Department of Biology, Federal University of Lavras, Lavras, Brazil
| | | | - Fernanda de Paula Fernandes
- Technological Center of Grape and Wine Research, Agronomical Research Institute of Minas Gerais, Caldas, Brazil
| | | | | | - Antonio Chalfun-Junior
- Laboratory of Molecular Plant Physiology, Department of Biology, Federal University of Lavras, Lavras, Brazil.
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17
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The siderophore repressor SreA maintains growth, hydrogen peroxide resistance, and cell wall integrity in the phytopathogenic fungus Alternaria alternata. Fungal Genet Biol 2020; 139:103384. [PMID: 32278718 DOI: 10.1016/j.fgb.2020.103384] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 01/18/2023]
Abstract
The siderophore-mediated iron uptake machinery is required by the tangerine pathotype of Alternaria alternata to colonize host plants. The present study reports the functions of the GATA-type transcription regulator SreA by analyzing loss- and gain-of-function mutants. The expression of sreA is transiently upregulated by excess iron. The sreA deficiency mutant (ΔsreA) shows severe growth defect but produces ACT toxin and incites necrotic lesions on citrus leaves as efficiently as wild type. SreA suppresses the expression of genes encoding polypeptides required for siderophore biosynthesis and transport under iron-replete conditions. Under iron-replete conditions, SreA impacts the expression of the genes encoding the NADPH oxidase complex involved in H2O2 production. SreA negatively impacts H2O2 resistance as ΔsreA increases resistance to H2O2. However, sreA deficiency has no effects on the expression of genes encoding several key factors (Yap1, Hog1, and Skn7) involved in oxidative stress resistance. ΔsreA increases resistance to calcofluor white and Congo red, which may suggest a role of SreA in the maintenance of cell wall integrity. Those are novel phenotypes associated with fungal sreA. Overall, our results indicate that SreA is required to protect fungal cells from cytotoxicity caused by excess iron. The results also highlight the regulatory functions of SreA and provide insights into the critical role of siderophore-mediated iron homeostasis in resistance to oxidative stress in A. alternata.
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18
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Human MP, Berger DK, Crampton BG. Time-Course RNAseq Reveals Exserohilum turcicum Effectors and Pathogenicity Determinants. Front Microbiol 2020; 11:360. [PMID: 32265851 PMCID: PMC7099616 DOI: 10.3389/fmicb.2020.00360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/18/2020] [Indexed: 11/16/2022] Open
Abstract
Exserohilum turcicum (sexual stage Setosphaeria turcica) is the hemibiotrophic causal agent of northern leaf blight of maize and sorghum. This study aimed to identify the genes involved in host colonization during the biotrophic and necrotrophic phases of infection. It also aimed to identify race-specific differences in gene expression. RNAseq of maize seedlings inoculated with a race 13N or 23N E. turcicum isolate was conducted before inoculation and at 2, 5, 7, and 13 days post-inoculation (dpi). Biological replicates were pooled per time point for each race and sequenced. A bioinformatics pipeline was used to identify candidate effectors, and expression was validated for selected candidates. Fungal biomass was positively correlated with the percentages of E. turcicum reads mapped, which were low at early time points (2-7 dpi) with a significant increase at 13 dpi, indicating a lifestyle switch from biotrophy to necrotrophy between 7 and 13 dpi. AVRHt1 is the putative E. turcicum effector recognized by the maize resistance gene Ht1. Consistent with this, AVRHt1 was expressed in planta by race 23N, but transcripts were absent in race 13N. In addition, specific transposable elements were expressed in 23N only. Genes encoding the virulence-associated peptidases leupeptin-inhibiting protein 1 and fungalysin were expressed in planta. Transcriptional profiles of genes involved in secondary metabolite synthesis or cell wall degradation revealed the importance of these genes during late stages of infection (13 dpi). A total of 346 expressed candidate effectors were identified, including Ecp6 and proteins similar to the secreted in xylem (SIX) effectors common to formae speciales of Fusarium oxysporum, SIX13 and SIX5. Expression profiling of Ecp6 and SIX13-like indicated a peak in expression at 5 and 7 dpi compared to 2 and 13 dpi. Sequencing of SIX13-like from diverse isolates of E. turcicum revealed host-specific polymorphisms that were mostly non-synonymous, resulting in two groups of SIX13-like proteins that corresponded to the maize or sorghum origin of each isolate. This study suggests putative mechanisms whereby E. turcicum causes disease. Identification of the candidate effector SIX13-like is consistent with the infection mode of E. turcicum through the xylem of susceptible hosts.
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Affiliation(s)
| | | | - Bridget Genevieve Crampton
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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19
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Mesnage R, Oestreicher N, Poirier F, Nicolas V, Boursier C, Vélot C. Transcriptome profiling of the fungus Aspergillus nidulans exposed to a commercial glyphosate-based herbicide under conditions of apparent herbicide tolerance. ENVIRONMENTAL RESEARCH 2020; 182:109116. [PMID: 32069763 DOI: 10.1016/j.envres.2020.109116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/18/2019] [Accepted: 01/02/2020] [Indexed: 05/20/2023]
Abstract
Glyphosate-based herbicides, such as Roundup®, are the most widely used non-selective, broad-spectrum herbicides. The release of these compounds in large amounts into the environment is susceptible to affect soil quality and health, especially because of the non-target effects on a large range of organisms including soil microorganisms. The soil filamentous fungus Aspergillus nidulans, a well-characterized experimental model organism that can be used as a bio-indicator for agricultural soil health, has been previously shown to be highly affected by Roundup GT Plus (R450: 450 g/L of glyphosate) at concentrations far below recommended agricultural application rate, including at a dose that does not cause any macroscopic effect. In this study, we determined alterations in the transcriptome of A. nidulans when exposed to R450 at a dose corresponding to the no-observed-adverse-effect level (NOAEL) for macroscopic parameters. A total of 1816 distinct genes had their expression altered. The most affected biological functions were protein synthesis, amino acids and secondary metabolisms, stress response, as well as detoxification pathways through cytochromes P450, glutathione-S-transferases, and ABC transporters. These results partly explain the molecular mechanisms underlying alterations in growth parameters detected at higher concentrations for this ascomycete fungus. In conclusion, our results highlight molecular disturbances in a soil fungus under conditions of apparent tolerance to the herbicide, and thus confirm the need to question the principle of "substantial equivalence" when applied to plants made tolerant to herbicides.
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Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London, SE1 9RT, United Kingdom; CRIIGEN, 42 Rue de Lisbonne, 75008, Paris, France.
| | - Nathalie Oestreicher
- Equipe VEAC, Université Paris-Sud, Faculté des Sciences, Bât. 350, Avenue Jean Perrin, 91405, Orsay, France; Pôle Risques MRSH-CNRS, EA2608, Université de Caen, Esplanade de la Paix, 14032, Caen, France.
| | - Florence Poirier
- Université Paris 13, UFR SMBH, Plateforme PPUP13, 1 Rue de Chablis, 93017, Bobigny Cedex, France.
| | - Valérie Nicolas
- UMS-IPSIT, US31 Inserm-UMS3679 CNRS, Plateformes Trans-Prot et d'Imagerie Cellulaire, Université Paris-Sud, Faculté de Pharmacie, Tour E1, 5 Rue Jean-Baptiste Clément, 92296, Châtenay-Malabry, France.
| | - Céline Boursier
- UMS-IPSIT, US31 Inserm-UMS3679 CNRS, Plateformes Trans-Prot et d'Imagerie Cellulaire, Université Paris-Sud, Faculté de Pharmacie, Tour E1, 5 Rue Jean-Baptiste Clément, 92296, Châtenay-Malabry, France.
| | - Christian Vélot
- CRIIGEN, 42 Rue de Lisbonne, 75008, Paris, France; Equipe VEAC, Université Paris-Sud, Faculté des Sciences, Bât. 350, Avenue Jean Perrin, 91405, Orsay, France; Pôle Risques MRSH-CNRS, EA2608, Université de Caen, Esplanade de la Paix, 14032, Caen, France.
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20
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Zhang Y, Zhang Y, Yu D, Peng Y, Min H, Lai Z. Copper Ions are Required for Cochliobolus heterostrophus in Appressorium Formation and Virulence on Maize. PHYTOPATHOLOGY 2020; 110:494-504. [PMID: 31464158 DOI: 10.1094/phyto-07-19-0254-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cochliobolus heterostrophus is the causal agent of southern corn leaf blight, a destructive disease on maize worldwide. However, how it regulates virulence on maize is still largely unknown. Here, we report that two copper transporter genes, ChCTR1 and ChCTR4, are required for its virulence. chctr1 and chctr4 mutants showed attenuated virulence on maize compared with the wild-type strain TM17 but development phenotypes of those mutants on media with or without infection-related stress agents were the same as the wild-type strain. Moreover, ChCTR1 and ChCTR4 play critical roles in appressorium formation and mutation of ChCTR1 or ChCTR4 suppresses the appressorium formation. Furthermore, copper-chelating agent ammonium tetrathiomolybdate suppressed the appressorium formation and virulence of C. heterostrophus on maize, whereas copper ions enhanced the appressorium formation and virulence on maize. The results indicate that copper ions are required for appressorium formation and virulence of C. heterostrophus on maize and are acquired from the environment by two copper transporters: ChCTR1 and ChCTR4.
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Affiliation(s)
- Yu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yan Zhang
- Ecology College, Lishui University, Lishui, China
| | - Dandan Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yujiao Peng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Haoxuan Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhibing Lai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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21
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Iqbal M, Dubey M, Broberg A, Viketoft M, Jensen DF, Karlsson M. Deletion of the Nonribosomal Peptide Synthetase Gene nps1 in the Fungus Clonostachys rosea Attenuates Antagonism and Biocontrol of Plant Pathogenic Fusarium and Nematodes. PHYTOPATHOLOGY 2019; 109:1698-1709. [PMID: 31120795 DOI: 10.1094/phyto-02-19-0042-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Secondary metabolites produced by biological control agents may influence the outcome of their interactions with plant pathogenic microorganisms and plants. In the present study, we investigated the role of the nonribosomal peptide synthetase gene nps1 expressed by the biocontrol fungus Clonostachys rosea. A gene expression analysis showed that nps1 was induced during confrontations with the plant pathogenic fungus Botrytis cinerea. Gene deletion strains of nps1 displayed increased growth rates and conidiation. However, the nematicidal activity of culture filtrates from C. rosea Δnps1 strains was significantly weaker than that from wild-type filtrates (P ≤ 0.001); after 24 h of incubation with culture filtrates from nps1 deletion strains, only 13 to 33% of a mixed community of nematodes were dead compared with 42% of nematodes incubated with wild-type culture filtrates. The Δnps1 strains also showed reduced biocontrol efficacy during pot experiments, thus failing to protect wheat seedlings from foot rot disease caused by the plant pathogenic fungus Fusarium graminearum. Furthermore, C. rosea Δnps1 strains were not able to reduce populations of plant-parasitic nematodes in soil or in roots of wheat as efficiently as the wild-type strain. Both C. rosea wild-type and Δnps1 strains increased the dry shoot weight and shoot length of wheat by 20 and 13%, respectively. We showed that NPS1, a putative nonribosomal peptide synthetase encoded by nps1, is a biocontrol factor, presumably by producing a hitherto unknown nonribosomal peptide compound with antifungal and nematicidal properties that contributes to the biocontrol properties of C. rosea.
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Affiliation(s)
- Mudassir Iqbal
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Anders Broberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Viketoft
- Department of Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Dan Funck Jensen
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
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22
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Expression of Fusarium pseudograminearum FpNPS9 in wheat plant and its function in pathogenicity. Curr Genet 2019; 66:229-243. [PMID: 31312935 DOI: 10.1007/s00294-019-01017-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 01/05/2023]
Abstract
Fusarium pseudograminearum-induced crown rot causes significant reduction to wheat production worldwide. To date, efforts to develop effective resistance to this disease have been hampered by the quantitative nature of resistance trait and a lack of understanding of the molecular pathogenesis. Non-ribosomal peptides have important roles in development, pathogenicity, and toxins in many plant pathogens, while less is known in F. pseudograminearum. In this work, we studied the expression and function of a nonribosomal peptide gene FpNPS9 in F. pseudograminearum. We determined the expression of FpNPS9 which was significantly up regulated during the infection of wheat. A deletion mutant Δfpnps9 produced in this study displayed a normal growth and conidiation phenotype, however, hyphae polar growth was obviously affected. Deoxynivalenol production in this mutant was significantly reduced and the infection of wheat coleoptiles and wheat spikelet was attenuated. The Δfpnps9 showed serious defects on the extension of infectious hyphae in plant and inhibition of roots elongation compared with the wild type. The complementation assay using a FpNPS9-GFP fusion construct fully restored the defects of the mutant. GFP signal was detected in the germinating conidia and infectious hyphae in coleoptiles of the infected plants. Interestingly, the signal was not observed when it was grown on culture medium, suggesting that the expression of FpNPS9 was regulated by an unknown host factor. This observation was supported by the result of qRT-PCR. In summary, we provided new knowledge on FpNPS9 expression in F. pseudograminearum and its function in F. pseudograminearum pathogenicity in wheat.
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Distribution and Evolution of Nonribosomal Peptide Synthetase Gene Clusters in the Ceratocystidaceae. Genes (Basel) 2019; 10:genes10050328. [PMID: 31052158 PMCID: PMC6563098 DOI: 10.3390/genes10050328] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 01/07/2023] Open
Abstract
In filamentous fungi, genes in secondary metabolite biosynthetic pathways are generally clustered. In the case of those pathways involved in nonribosomal peptide production, a nonribosomal peptide synthetase (NRPS) gene is commonly found as a main element of the cluster. Large multifunctional enzymes are encoded by members of this gene family that produce a broad spectrum of bioactive compounds. In this research, we applied genome-based identification of nonribosomal peptide biosynthetic gene clusters in the family Ceratocystidaceae. For this purpose, we used the whole genome sequences of species from the genera Ceratocystis,Davidsoniella,Thielaviopsis, Endoconidiophora,Bretziella, Huntiella, and Ambrosiella. To identify and characterize the clusters, different bioinformatics and phylogenetic approaches, as well as PCR-based methods were used. In all genomes studied, two highly conserved NRPS genes (one monomodular and one multimodular) were identified and their potential products were predicted to be siderophores. Expression analysis of two Huntiella species (H. moniliformis and H. omanensis) confirmed the accuracy of the annotations and proved that the genes in both clusters are expressed. Furthermore, a phylogenetic analysis showed that both NRPS genes of the Ceratocystidaceae formed distinct and well supported clades in their respective phylograms, where they grouped with other known NRPSs involved in siderophore production. Overall, these findings improve our understanding of the diversity and evolution of NRPS biosynthetic pathways in the family Ceratocystidaceae.
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Genetic analyses of reddish-brown polyoxin-resistant mutants of Bipolaris maydis. MYCOSCIENCE 2018. [DOI: 10.1016/j.myc.2017.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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A Highly Conserved Basidiomycete Peptide Synthetase Produces a Trimeric Hydroxamate Siderophore. Appl Environ Microbiol 2017; 83:AEM.01478-17. [PMID: 28842536 DOI: 10.1128/aem.01478-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/17/2017] [Indexed: 11/20/2022] Open
Abstract
The model white-rot basidiomycete, Ceriporiopsis (Gelatoporia) subvermispora B, encodes putative natural product biosynthesis genes. Among them is the gene for the seven-domain nonribosomal peptide synthetase CsNPS2. It is a member of the as-yet-uncharacterized fungal type VI siderophore synthetase family, which is highly conserved and widely distributed among the basidiomycetes. These enzymes include only one adenylation (A) domain, i.e., one complete peptide synthetase module, and two thiolation/condensation (T-C) didomain partial modules which together constitute an AT1C1T2C2T3C3 domain setup. The full-length CsNPS2 enzyme (274.5 kDa) was heterologously produced as a polyhistidine fusion in Aspergillus niger as a soluble and active protein. N 5-acetyl-N 5-hydroxy-l-ornithine (l-AHO) and N 5-cis-anhydromevalonyl-N 5 -hydroxy-l-ornithine (l-AMHO) were accepted as the substrates, based on results of an in vitro substrate-dependent [32P]ATP-pyrophosphate radioisotope exchange assay. Full-length holo-CsNPS2 catalyzed amide bond formation between three l-AHO molecules to release the linear l-AHO trimer, called basidioferrin, as the product in vitro, which was verified by liquid chromatography-high-resolution electrospray ionization-mass spectrometry analysis. Phylogenetic analyses suggested that type VI family siderophore synthetases are widespread in mushrooms and evolved in a common ancestor of basidiomycetes.IMPORTANCE The basidiomycete nonribosomal peptide synthetase CsNPS2 represents a member of a widely distributed but previously uninvestigated class (type VI) of fungal siderophore synthetases. Genes orthologous to CsNPS2 are highly conserved across various phylogenetic clades of the basidiomycetes. Hence, our work serves as a broadly applicable model for siderophore biosynthesis and iron metabolism in higher fungi. Also, our results on the amino acid substrate preference of CsNPS2 support a further understanding of the substrate selectivity of fungal adenylation domains. Methodologically, this report highlights the Aspergillus niger/SM-Xpress-based system as a suitable platform to heterologously express multimodular basidiomycete biosynthesis enzymes in the >250-kDa range in soluble and active form.
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Aylward J, Steenkamp ET, Dreyer LL, Roets F, Wingfield BD, Wingfield MJ. A plant pathology perspective of fungal genome sequencing. IMA Fungus 2017; 8:1-15. [PMID: 28824836 PMCID: PMC5493528 DOI: 10.5598/imafungus.2017.08.01.01] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/19/2017] [Indexed: 10/26/2022] Open
Abstract
The majority of plant pathogens are fungi and many of these adversely affect food security. This mini-review aims to provide an analysis of the plant pathogenic fungi for which genome sequences are publically available, to assess their general genome characteristics, and to consider how genomics has impacted plant pathology. A list of sequenced fungal species was assembled, the taxonomy of all species verified, and the potential reason for sequencing each of the species considered. The genomes of 1090 fungal species are currently (October 2016) in the public domain and this number is rapidly rising. Pathogenic species comprised the largest category (35.5 %) and, amongst these, plant pathogens are predominant. Of the 191 plant pathogenic fungal species with available genomes, 61.3 % cause diseases on food crops, more than half of which are staple crops. The genomes of plant pathogens are slightly larger than those of other fungal species sequenced to date and they contain fewer coding sequences in relation to their genome size. Both of these factors can be attributed to the expansion of repeat elements. Sequenced genomes of plant pathogens provide blueprints from which potential virulence factors were identified and from which genes associated with different pathogenic strategies could be predicted. Genome sequences have also made it possible to evaluate adaptability of pathogen genomes and genomic regions that experience selection pressures. Some genomic patterns, however, remain poorly understood and plant pathogen genomes alone are not sufficient to unravel complex pathogen-host interactions. Genomes, therefore, cannot replace experimental studies that can be complex and tedious. Ultimately, the most promising application lies in using fungal plant pathogen genomics to inform disease management and risk assessment strategies. This will ultimately minimize the risks of future disease outbreaks and assist in preparation for emerging pathogen outbreaks.
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Affiliation(s)
- Janneke Aylward
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria 0002, South Africa
| | - Léanne L. Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Francois Roets
- Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | | | - Michael J. Wingfield
- Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria 0002, South Africa
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Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae. Microorganisms 2017; 5:microorganisms5010003. [PMID: 28106722 PMCID: PMC5374380 DOI: 10.3390/microorganisms5010003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/04/2017] [Accepted: 01/07/2017] [Indexed: 11/17/2022] Open
Abstract
Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world's population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs), hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae.
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Mishra VK, Passari AK, Leo VV, Singh BP. Molecular Diversity and Detection of Endophytic Fungi Based on Their Antimicrobial Biosynthetic Genes. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Macheleidt J, Mattern DJ, Fischer J, Netzker T, Weber J, Schroeckh V, Valiante V, Brakhage AA. Regulation and Role of Fungal Secondary Metabolites. Annu Rev Genet 2016; 50:371-392. [DOI: 10.1146/annurev-genet-120215-035203] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Juliane Macheleidt
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
| | - Derek J. Mattern
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Juliane Fischer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Jakob Weber
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
| | - Vito Valiante
- Research Group Biobricks of Microbial Natural Product Syntheses, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745 Jena, Germany;
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), 07745 Jena, Germany; , , , , , ,
- Institute for Microbiology, Friedrich Schiller University Jena, 07737 Jena, Germany
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Penselin D, Münsterkötter M, Kirsten S, Felder M, Taudien S, Platzer M, Ashelford K, Paskiewicz KH, Harrison RJ, Hughes DJ, Wolf T, Shelest E, Graap J, Hoffmann J, Wenzel C, Wöltje N, King KM, Fitt BDL, Güldener U, Avrova A, Knogge W. Comparative genomics to explore phylogenetic relationship, cryptic sexual potential and host specificity of Rhynchosporium species on grasses. BMC Genomics 2016; 17:953. [PMID: 27875982 PMCID: PMC5118889 DOI: 10.1186/s12864-016-3299-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/15/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts. RESULTS The genomes of the different Rhynchosporium species were sequenced, assembled and annotated using ab initio gene predictors trained on several fungal genomes as well as on Rhynchosporium expressed sequence tags. Structures of the rDNA regions and genome-wide single nucleotide polymorphisms provided a hypothesis for intra-genus evolution. Homology screening detected core meiotic genes along with most genes crucial for sexual recombination in ascomycete fungi. In addition, a large number of cell wall-degrading enzymes that is characteristic for hemibiotrophic and necrotrophic fungi infecting monocotyledonous hosts were found. Furthermore, the Rhynchosporium genomes carry a repertoire of genes coding for polyketide synthases and non-ribosomal peptide synthetases. Several of these genes are missing from the genome of the closest sequenced relative, the poplar pathogen Marssonina brunnea, and are possibly involved in adaptation to the grass hosts. Most importantly, six species-specific genes coding for protein effectors were identified in R. commune. Their deletion yielded mutants that grew more vigorously in planta than the wild type. CONCLUSION Both cryptic sexuality and secondary metabolites may have contributed to host adaptation. Most importantly, however, the growth-retarding activity of the species-specific effectors suggests that host adaptation of R. commune aims at extending the biotrophic stage at the expense of the necrotrophic stage of pathogenesis. Like other apoplastic fungi Rhynchosporium colonizes the intercellular matrix of host leaves relatively slowly without causing symptoms, reminiscent of the development of endophytic fungi. Rhynchosporium may therefore become an object for studying the mutualism-parasitism transition.
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Affiliation(s)
- Daniel Penselin
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Susanne Kirsten
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Marius Felder
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Stefan Taudien
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Matthias Platzer
- Genomic Analysis, Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Kevin Ashelford
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | | | | | - David J. Hughes
- Applied Bioinformatics, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Thomas Wolf
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Ekaterina Shelest
- Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Jenny Graap
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Jan Hoffmann
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Claudia Wenzel
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany ,Present address: Food Quality and Nutrition, Agroscope, Bern, Switzerland
| | - Nadine Wöltje
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
| | - Kevin M. King
- Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire UK
| | - Bruce D. L. Fitt
- Biological and Environmental Sciences, University of Hertfordshire, Hatfield, Hertfordshire UK
| | - Ulrich Güldener
- Department of Genome-Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany
| | - Anna Avrova
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Wolfgang Knogge
- Department of Stress and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle/Saale, Germany
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Li YH, Han WJ, Gui XW, Wei T, Tang SY, Jin JM. Putative Nonribosomal Peptide Synthetase and Cytochrome P450 Genes Responsible for Tentoxin Biosynthesis in Alternaria alternata ZJ33. Toxins (Basel) 2016; 8:toxins8080234. [PMID: 27490569 PMCID: PMC4999850 DOI: 10.3390/toxins8080234] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/03/2016] [Accepted: 07/27/2016] [Indexed: 12/16/2022] Open
Abstract
Tentoxin, a cyclic tetrapeptide produced by several Alternaria species, inhibits the F1-ATPase activity of chloroplasts, resulting in chlorosis in sensitive plants. In this study, we report two clustered genes, encoding a putative non-ribosome peptide synthetase (NRPS) TES and a cytochrome P450 protein TES1, that are required for tentoxin biosynthesis in Alternaria alternata strain ZJ33, which was isolated from blighted leaves of Eupatorium adenophorum. Using a pair of primers designed according to the consensus sequences of the adenylation domain of NRPSs, two fragments containing putative adenylation domains were amplified from A. alternata ZJ33, and subsequent PCR analyses demonstrated that these fragments belonged to the same NRPS coding sequence. With no introns, TES consists of a single 15,486 base pair open reading frame encoding a predicted 5161 amino acid protein. Meanwhile, the TES1 gene is predicted to contain five introns and encode a 506 amino acid protein. The TES protein is predicted to be comprised of four peptide synthase modules with two additional N-methylation domains, and the number and arrangement of the modules in TES were consistent with the number and arrangement of the amino acid residues of tentoxin, respectively. Notably, both TES and TES1 null mutants generated via homologous recombination failed to produce tentoxin. This study provides the first evidence concerning the biosynthesis of tentoxin in A. alternata.
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Affiliation(s)
- You-Hai Li
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China.
- Key Laboratory of Ethnic Medicine Resource Chemistry, State Ethnic Affairs Commission & Ministry of Education, Yunnan Minzu University, Kunming 650500, China.
| | - Wen-Jin Han
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China.
| | - Xi-Wu Gui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tao Wei
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China.
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China.
- Key Laboratory of Ethnic Medicine Resource Chemistry, State Ethnic Affairs Commission & Ministry of Education, Yunnan Minzu University, Kunming 650500, China.
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De Bruyne L, Van Poucke C, Di Mavungu DJ, Zainudin NAIM, Vanhaecke L, De Vleesschauwer D, Turgeon BG, De Saeger S, Höfte M. Comparative chemical screening and genetic analysis reveal tentoxin as a new virulence factor in Cochliobolus miyabeanus, the causal agent of brown spot disease on rice. MOLECULAR PLANT PATHOLOGY 2016; 17:805-17. [PMID: 26456797 PMCID: PMC6638388 DOI: 10.1111/mpp.12329] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Brown spot disease, caused by Cochliobolus miyabeanus, is currently considered to be one of the most important yield reducers of rice (Oryza sativa L.). Despite its agricultural importance, little is known about the virulence mechanisms deployed by the fungus. Therefore, we set out to identify novel virulence factors with a role in disease development. This article reports, for the first time, the production of tentoxin by C. miyabeanus as a virulence factor during brown spot disease and the identification of the non-ribosomal protein synthetase (NRPS) CmNps3, responsible for tentoxin biosynthesis. We compared the chemical compounds produced by C. miyabeanus strains differing in virulence ability using ultra-high-performance liquid chromatography (UHPLC) coupled to high-resolution Orbitrap mass spectrometry (HRMS). The production of tentoxin by a highly virulent strain was revealed by principal component analysis of the detected ions and confirmed by UHPLC coupled to tandem-quadrupole mass spectrometry (MS/MS). The corresponding NRPS was identified by in silico genome analysis and confirmed by gene deletion. Infection tests with wild-type and Cmnps3 mutants showed that tentoxin acts as a virulence factor and is correlated with chlorosis development during the second phase of infection. Although rice has previously been classified as a tentoxin-insensitive plant species, our data demonstrate that tentoxin production by C. miyabeanus affects symptom development.
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Affiliation(s)
- Lieselotte De Bruyne
- Department of Crop Protection, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, BE-9000, Ghent, Belgium
| | - Christof Van Poucke
- Department of Bio-analysis, Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, BE-9000, Ghent, Belgium
| | - Diana Jose Di Mavungu
- Department of Bio-analysis, Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, BE-9000, Ghent, Belgium
| | - Nur Ain Izzati Mohd Zainudin
- Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, 14850, Ithaca, NY, USA
- Department of Biology, Faculty of Science, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Lynn Vanhaecke
- Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Faculty of Veterinary Medicine, Ghent University, BE-9000, Ghent, Belgium
| | - David De Vleesschauwer
- Department of Crop Protection, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, BE-9000, Ghent, Belgium
| | - B Gillian Turgeon
- Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, 14850, Ithaca, NY, USA
| | - Sarah De Saeger
- Department of Bio-analysis, Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, BE-9000, Ghent, Belgium
| | - Monica Höfte
- Department of Crop Protection, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, BE-9000, Ghent, Belgium
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Castell-Miller CV, Gutierrez-Gonzalez JJ, Tu ZJ, Bushley KE, Hainaut M, Henrissat B, Samac DA. Genome Assembly of the Fungus Cochliobolus miyabeanus, and Transcriptome Analysis during Early Stages of Infection on American Wildrice (Zizania palustris L.). PLoS One 2016; 11:e0154122. [PMID: 27253872 PMCID: PMC4890743 DOI: 10.1371/journal.pone.0154122] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/08/2016] [Indexed: 12/11/2022] Open
Abstract
The fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice (Oryza sativa) and two North American specialty crops, American wildrice (Zizania palustris) and switchgrass (Panicum virgatum). Despite the importance of C. miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C. miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C. miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs) and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS) present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta. A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses including hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. This work will facilitate future research on C. miyabeanus pathogen-associated molecular patterns and effectors, and in the identification of their corresponding wildrice defense mechanisms.
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Affiliation(s)
- Claudia V. Castell-Miller
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Juan J. Gutierrez-Gonzalez
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, United States of America
- USDA-ARS-Plant Science Research Unit, Saint Paul, Minnesota, United States of America
| | - Zheng Jin Tu
- Mayo Clinic, Division of Biomedical Statistics and Informatics, Rochester, Minnesota, United States of America
| | - Kathryn E. Bushley
- Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Matthieu Hainaut
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Deborah A. Samac
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
- USDA-ARS-Plant Science Research Unit, Saint Paul, Minnesota, United States of America
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Zainudin NAIM, Condon B, De Bruyne L, Van Poucke C, Bi Q, Li W, Höfte M, Turgeon BG. Virulence, Host-Selective Toxin Production, and Development of Three Cochliobolus Phytopathogens Lacking the Sfp-Type 4'-Phosphopantetheinyl Transferase Ppt1. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1130-1141. [PMID: 26168137 DOI: 10.1094/mpmi-03-15-0068-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The Sfp-type 4'-phosphopantetheinyl transferase Ppt1 is required for activation of nonribosomal peptide synthetases, including α-aminoadipate reductase (AAR) for lysine biosynthesis and polyketide synthases, enzymes that biosynthesize peptide and polyketide secondary metabolites, respectively. Deletion of the PPT1 gene, from the maize pathogen Cochliobolus heterostrophus and the rice pathogen Cochliobolus miyabeanus, yielded strains that were significantly reduced in virulence to their hosts. In addition, ppt1 mutants of C. heterostrophus race T and Cochliobolus victoriae were unable to biosynthesize the host-selective toxins (HST) T-toxin and victorin, respectively, as judged by bioassays. Interestingly, ppt1 mutants of C. miyabeanus were shown to produce tenfold higher levels of the sesterterpene-type non-HST ophiobolin A, as compared with the wild-type strain. The ppt1 strains of all species were also reduced in tolerance to oxidative stress and iron depletion; both phenotypes are associated with inability to produce extracellular siderophores biosynthesized by the nonribosomal peptide synthetase Nps6. Colony surfaces were hydrophilic, a trait previously associated with absence of C. heterostrophus Nps4. Mutants were decreased in asexual sporulation and C. heterostrophus strains were female-sterile in sexual crosses; the latter phenotype was observed previously with mutants lacking Nps2, which produces an intracellular siderophore. As expected, mutants were albino, since they cannot produce the polyketide melanin and were auxotrophic for lysine because they lack an AAR.
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Affiliation(s)
- Nur Ain Izzati Mohd Zainudin
- 1 Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- 2 Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Bradford Condon
- 1 Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Lieselotte De Bruyne
- 3 Department of Crop Protection, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Christof Van Poucke
- 4 Department of Bioanalysis, Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University; and
| | - Qing Bi
- 1 Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Wei Li
- 1 Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- 5 Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, P.R. China
| | - Monica Höfte
- 3 Department of Crop Protection, Laboratory of Phytopathology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - B Gillian Turgeon
- 1 Section of Plant Pathology & Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
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Oide S, Berthiller F, Wiesenberger G, Adam G, Turgeon BG. Individual and combined roles of malonichrome, ferricrocin, and TAFC siderophores in Fusarium graminearum pathogenic and sexual development. Front Microbiol 2015; 5:759. [PMID: 25628608 PMCID: PMC4290682 DOI: 10.3389/fmicb.2014.00759] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/12/2014] [Indexed: 11/15/2022] Open
Abstract
Intra- and extracellular iron-chelating siderophores produced by fungal non-ribosomal peptide synthetases have been shown to be involved in reproductive and pathogenic developmental processes and in iron and oxidative stress management. Here we report individual and combined contributions of three of these metabolites to developmental success of the destructive cereal pathogen Fusarium graminearum. In previous work, we determined that deletion of the NPS2 gene, responsible for intracellular siderophore biosynthesis, results in inability to produce sexual spores when mutants of this homothallic ascomycete are selfed. Deletion of the NPS6 gene, required for extracellular siderophore biosynthesis, does not affect sexual reproduction but results in sensitivity to iron starvation and oxidative stress and leads to reduced virulence to the host. Building on this, we report that double mutants lacking both NPS2 and NPS6 are augmented in all collective phenotypes of single deletion strains (i.e., abnormal sexual and pathogenic development, hypersensitivity to oxidative and iron-depletion stress), which suggests overlap of function. Using comparative biochemical analysis of wild-type and mutant strains, we show that NPS1, a third gene associated with siderophore biosynthesis, is responsible for biosynthesis of a second extracellular siderophore, malonichrome. nps1 mutants fail to produce this metabolite. Phenotypic characterization reveals that, although single nps1 mutants are like wild-type with respect to sexual development, hypersensitivity to ROS and iron-depletion stress, and virulence to the host, triple nps1nps2nps6 deletion strains, lacking all three siderophores, are even more impaired in these attributes than double nps2nps6 strains. Thus, combinatorial mutants lacking key iron-associated genes uncovered malonichrome function. The intimate connection between presence/absence of siderophores and resistance/sensitivity to ROS is central to sexual and pathogenic development.
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Affiliation(s)
- Shinichi Oide
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA ; The Research Institute of Innovative Technology for the Earth (RITE) Kizugawa-Shi, Japan
| | - Franz Berthiller
- Department of Agrobiotechnology (IFA-Tulln), Center for Analytical Chemistry, University of Natural Resources and Life Sciences Vienna, Austria
| | - Gerlinde Wiesenberger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Austria
| | - Gerhard Adam
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Austria
| | - B Gillian Turgeon
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA
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Jirakkakul J, Cheevadhanarak S, Punya J, Chutrakul C, Senachak J, Buajarern T, Tanticharoen M, Amnuaykanjanasin A. Tenellin acts as an iron chelator to prevent iron-generated reactive oxygen species toxicity in the entomopathogenic fungus Beauveria bassiana. FEMS Microbiol Lett 2014; 362:1-8. [PMID: 25670702 DOI: 10.1093/femsle/fnu032] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Iron is an essential element for life. However, the iron overload can be toxic. Here, we investigated the significant increase of tenellin and iron-tenellin complex production in ferricrocin-deficient mutants of Beauveria bassiana. Our chemical analysis indicated that the ferricrocin-deficient mutants T1, T3 and T5 nearly abolished ferricrocin production. In turn, these mutants had significant accumulation of iron-tenellin complex in their mycelia at 247-289 mg g(-1) cell dry weight under iron-replete condition. Both tenellin and iron-tenellin complex were not detected in the wild-type under such condition. Mass analysis of the mutants' crude extracts demonstrated that tenellin formed a 3:1 complex with iron in the absence of ferricrocin. The unexpected link between ferricrocin and tenellin biosynthesis in ferricrocin-deficient mutants could be a survival strategy during iron-mediated oxidative stress.
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Affiliation(s)
- Jiraporn Jirakkakul
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Supapon Cheevadhanarak
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Juntira Punya
- Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Chanikul Chutrakul
- Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Jittisak Senachak
- Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Taridaporn Buajarern
- Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Morakot Tanticharoen
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok 10140, Thailand
| | - Alongkorn Amnuaykanjanasin
- Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
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Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z. New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep 2014; 31:1348-75. [PMID: 25156669 DOI: 10.1039/c4np00046c] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are a primary modality for fungal peptidic natural product assembly and are responsible for some of the best known, most useful, and most destructive fungal metabolites. Through genome sequencing and computer-assisted recognition of modular motifs of catalytic domains, one can now confidently identify most NRPS biosynthetic genes of a fungal strain. The biosynthetic gene clusters responsible for two of the most important classes of NRP fungal derived drugs, cyclosporine and the echinocandins, have been recently characterized by genomic sequencing and annotation. Complete biosynthetic gene clusters for the pneumocandins and echinocandins have been mapped at the genetic level and functionally characterized to some extent. Genomic sequencing of representative strains of most of the variants in the echinocandin family, including the wild-type of the three fungal strains employed for industrial-scale production of caspofungin, micafungin and anidulofungin, has enabled characterization of the basic architecture of the echinocandin NRPS pathways. A comparative analysis of how pathway genes cause variations in lipoinitiation, biosynthesis of the non-proteinogenic amino acids, amino acid substitutions, and hydroxylations and sulfonations of the core peptide and contribute to the molecular diversity of the family is presented. We also review new information on the natural functions of NRPs, the differences between fungal and bacterial NRPSs, and functional characterization of selected NRPS gene clusters. Continuing discovery of the new fungal nonribosomal peptides has contributed new structural diversity and potential insights into their biological functions among other natural peptides and peptaibiotics. We therefore provide an update on new peptides, depsipeptides and peptaibols discovered in the Fungi since 2009.
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Affiliation(s)
- Gerald Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Centre at Houston, Houston, Texas 77054, USA.
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Condon BJ, Oide S, Gibson DM, Krasnoff SB, Turgeon BG. Reductive iron assimilation and intracellular siderophores assist extracellular siderophore-driven iron homeostasis and virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:793-808. [PMID: 24762221 DOI: 10.1094/mpmi-11-13-0328-r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Iron is an essential nutrient and prudent iron acquisition and management are key traits of a successful pathogen. Fungi use nonribosomally synthesized secreted iron chelators (siderophores) or reductive iron assimilation (RIA) mechanisms to acquire iron in a high affinity manner. Previous studies with the maize pathogen Cochliobolus heterostrophus identified two genes, NPS2 and NPS6, encoding different nonribosomal peptide synthetases responsible for biosynthesis of intra- and extracellular siderophores, respectively. Deletion of NPS6 results in loss of extracellular siderophore biosynthesis, attenuated virulence, hypersensitivity to oxidative and iron-depletion stress, and reduced asexual sporulation, while nps2 mutants are phenotypically wild type in all of these traits but defective in sexual spore development when NPS2 is missing from both mating partners. Here, it is reported that nps2nps6 mutants have more severe phenotypes than both nps2 and nps6 single mutants. In contrast, mutants lacking the FTR1 or FET3 genes encoding the permease and ferroxidase components, respectively, of the alternate RIA system, are like wild type in all of the above phenotypes. However, without supplemental iron, combinatorial nps6ftr1 and nps2nps6ftr1 mutants are less virulent, are reduced in growth, and are less able to combat oxidative stress and to sporulate asexually, compared with nps6 mutants alone. These findings demonstrate that, while the role of RIA in metabolism and virulence is overshadowed by that of extracellular siderophores as a high-affinity iron acquisition mechanism in C. heterostrophus, it functions as a critical backup for the fungus.
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Rodríguez-Decuadro S, Silva P, Bentancur O, Gamba F, Pritsch C. Histochemical characterization of early response to Cochliobolus sativus infection in selected barley genotypes. PHYTOPATHOLOGY 2014; 104:715-23. [PMID: 24521486 DOI: 10.1094/phyto-05-13-0133-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Much effort is being made to breed barley with durable resistance to leaf spot blotch incited by Bipolaris sorokiniana (teleomorph: Cochliobolus sativus). We hypothesized that susceptibility and resistance traits in 11 diverse barley genotypes inoculated with a single C. sativus isolate might specify a range of distinct host cell responses. Quantitative descriptions of interaction microphenotypes exhibited by different barley genotype seedlings after infection with C. sativus are provided. Early oxidative responses occurring in epidermis and mesophyll leaf tissue were monitored by histochemical analysis of H2O2 accumulation at 8, 24, and 48 h after inoculation. Cell wall apposition (CWA) in epidermal cells and hypersensitive reaction (HR) of epidermal or mesophyll tissue were early defenses in both resistant and susceptible genotypes. There were differences in level, duration, and frequency of occurrence for CWA and HR for the different barley genotypes. Occurrence of HR in epidermal cells at post-penetration stages was indicative of compatibility. Patterns of cell responses were microphenotypically diverse between different resistant and susceptible genotypes. This suggests that timing and level of response are key features of microphenotypic diversity that distinguish different functional mechanisms of resistance and susceptibility present in barley.
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Albarouki E, Schafferer L, Ye F, von Wirén N, Haas H, Deising HB. Biotrophy-specific downregulation of siderophore biosynthesis in Colletotrichum graminicola is required for modulation of immune responses of maize. Mol Microbiol 2014; 92:338-55. [PMID: 24674132 PMCID: PMC4235341 DOI: 10.1111/mmi.12561] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2014] [Indexed: 12/01/2022]
Abstract
The hemibiotrophic maize pathogen Colletotrichum graminicola synthesizes one intracellular and three secreted siderophores. eGFP fusions with the key siderophore biosynthesis gene, SID1, encoding l-ornithine-N(5) -monooxygenase, suggested that siderophore biosynthesis is rigorously downregulated specifically during biotrophic development. In order to investigate the role of siderophores during vegetative development and pathogenesis, SID1, which is required for synthesis of all siderophores, and the non-ribosomal peptide synthetase gene NPS6, synthesizing secreted siderophores, were deleted. Mutant analyses revealed that siderophores are required for vegetative growth under iron-limiting conditions, conidiation, ROS tolerance, and cell wall integrity. Δsid1 and Δnps6 mutants were hampered in formation of melanized appressoria and impaired in virulence. In agreement with biotrophy-specific downregulation of siderophore biosynthesis, Δsid1 and Δnps6 strains were not affected in biotrophic development, but spread of necrotrophic hyphae was reduced. To address the question why siderophore biosynthesis is specifically downregulated in biotrophic hyphae, maize leaves were infiltrated with siderophores. Siderophore infiltration alone did not induce defence responses, but formation of biotrophic hyphae in siderophore-infiltrated leaves caused dramatically increased ROS formation and transcriptional activation of genes encoding defence-related peroxidases and PR proteins. These data suggest that fungal siderophores modulate the plant immune system.
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Affiliation(s)
- Emad Albarouki
- Martin-Luther-Universität Halle-Wittenberg, Interdisziplinäres Zentrum für Nutzpflanzenforschung (IZN), Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany; Martin-Luther-Universität Halle-Wittenberg, Institut für Agrar- und Ernährungswissenschaften, Phytopathologie und Pflanzenschutz, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
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41
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Geng Z, Zhu W, Su H, Zhao Y, Zhang KQ, Yang J. Recent advances in genes involved in secondary metabolite synthesis, hyphal development, energy metabolism and pathogenicity in Fusarium graminearum (teleomorph Gibberella zeae). Biotechnol Adv 2014; 32:390-402. [DOI: 10.1016/j.biotechadv.2013.12.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 11/11/2013] [Accepted: 12/16/2013] [Indexed: 01/01/2023]
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Chen LH, Yang SL, Chung KR. Resistance to oxidative stress via regulating siderophore-mediated iron acquisition by the citrus fungal pathogen Alternaria alternata. MICROBIOLOGY-SGM 2014; 160:970-979. [PMID: 24586035 DOI: 10.1099/mic.0.076182-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability of the necrotrophic fungus Alternaria alternata to detoxify reactive oxygen species (ROS) is crucial for pathogenesis to citrus. We report regulation of siderophore-mediated iron acquisition and ROS resistance by the NADPH oxidase (NOX), the redox activating yes-associated protein 1 (YAP1) regulator, and the high-osmolarity glycerol 1 (HOG1) mitogen-activated protein kinase (MAPK). The A. alternata nonribosomal peptide synthetase (NPS6) is essential for the biosynthesis of siderophores, contributing to iron uptake under low-iron conditions. Fungal strains impaired for NOX, YAP1, HOG1 or NPS6 all display increased sensitivity to ROS. Exogenous addition of iron at least partially rescues ROS sensitivity seen for NPS6, YAP1, HOG1, and NOX mutants. Importantly, expression of the NPS6 gene and biosynthesis of siderophores are regulated by NOX, YAP1 and HOG1, supporting a functional link among these regulatory pathways. Although iron fully rescues H2O2 sensitivity seen in mutants impaired for the response regulator SKN7, neither expression of NPS6 nor biosynthesis of siderophores is controlled by SKN7. Our results indicate that the acquisition of environmental iron has profound effects on ROS detoxification.
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Affiliation(s)
- Li-Hung Chen
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
| | - Siwy Ling Yang
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL 32611, USA.,Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
| | - Kuang-Ren Chung
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, FL 32611, USA.,Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS), University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
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Sørensen JL, Knudsen M, Hansen FT, Olesen C, Fuertes PR, Lee TV, Sondergaard TE, Pedersen CNS, Brodersen DE, Giese H. Fungal NRPS-Dependent Siderophores: From Function to Prediction. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1191-2_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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44
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Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE, Owensby CA, Knaus BJ, Elser J, Miller D, Di Y, McPhail KL, Spatafora JW. The genome of tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PLoS Genet 2013; 9:e1003496. [PMID: 23818858 PMCID: PMC3688495 DOI: 10.1371/journal.pgen.1003496] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 03/20/2013] [Indexed: 01/07/2023] Open
Abstract
The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role of secondary metabolite gene clusters and their metabolites in fungal biology.
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Affiliation(s)
- Kathryn E. Bushley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Rajani Raja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Jason S. Cumbie
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Mariko Nonogaki
- College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Alexander E. Boyd
- Center for Genome Research & Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - C. Alisha Owensby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Brian J. Knaus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Daniel Miller
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Yanming Di
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
| | - Kerry L. McPhail
- College of Pharmacy, Oregon State University, Corvallis, Oregon, United States of America
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
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Chen LH, Lin CH, Chung KR. A nonribosomal peptide synthetase mediates siderophore production and virulence in the citrus fungal pathogen Alternaria alternata. MOLECULAR PLANT PATHOLOGY 2013; 14:497-505. [PMID: 23438010 PMCID: PMC6638914 DOI: 10.1111/mpp.12021] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Alternaria species produce and excrete dimethyl coprogen siderophores to acquire iron. The Alternaria alternata gene AaNPS6, encoding a polypeptide analogous to fungal nonribosomal peptide synthetases, was found to be required for the production of siderophores and virulence on citrus. Siderophores purified from culture filtrates of the wild-type strain did not induce any phytotoxicity on the leaves of citrus. Fungal strains lacking AaNPS6 produced little or no detectable extracellular siderophores and displayed an increased sensitivity to H₂O₂, superoxide-generating compounds (KO₂ and menadione) and iron depletion. Δnps6 mutants were also defective for the production of melanin and conidia. The introduction of a wild-type AaNPS6 under the control of its endogenous promoter to a Δnps6 null mutant at least partially restored siderophore production and virulence to citrus, demonstrating a functional link between iron uptake and fungal pathogenesis. Elevated sensitivity to H₂O₂, seen for the Δnps6 null strain could be relieved by exogenous application of ferric iron. The expression of the AaNPS6 gene was highly up-regulated under low-iron conditions and apparently controlled by the redox-responsive yeast transcriptional regulator YAP1. Hence, the maintenance of iron homeostasis via siderophore-mediated iron uptake also plays an important role in resistance to toxic reactive oxygen species (ROS). Our results demonstrate further the critical role of ROS detoxification for the pathogenicity of A. alternata in citrus.
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Affiliation(s)
- Li-Hung Chen
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences-IFAS, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
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Johnson LJ, Koulman A, Christensen M, Lane GA, Fraser K, Forester N, Johnson RD, Bryan GT, Rasmussen S. An extracellular siderophore is required to maintain the mutualistic interaction of Epichloë festucae with Lolium perenne. PLoS Pathog 2013; 9:e1003332. [PMID: 23658520 PMCID: PMC3642064 DOI: 10.1371/journal.ppat.1003332] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 03/15/2013] [Indexed: 11/19/2022] Open
Abstract
We have identified from the mutualistic grass endophyte Epichloë festucae a non-ribosomal peptide synthetase gene (sidN) encoding a siderophore synthetase. The enzymatic product of SidN is shown to be a novel extracellular siderophore designated as epichloënin A, related to ferrirubin from the ferrichrome family. Targeted gene disruption of sidN eliminated biosynthesis of epichloënin A in vitro and in planta. During iron-depleted axenic growth, ΔsidN mutants accumulated the pathway intermediate N(5)-trans-anhydromevalonyl-N(5)-hydroxyornithine (trans-AMHO), displayed sensitivity to oxidative stress and showed deficiencies in both polarized hyphal growth and sporulation. Infection of Lolium perenne (perennial ryegrass) with ΔsidN mutants resulted in perturbations of the endophyte-grass symbioses. Deviations from the characteristic tightly regulated synchronous growth of the fungus with its plant partner were observed and infected plants were stunted. Analysis of these plants by light and transmission electron microscopy revealed abnormalities in the distribution and localization of ΔsidN mutant hyphae as well as deformities in hyphal ultrastructure. We hypothesize that lack of epichloënin A alters iron homeostasis of the symbiotum, changing it from mutually beneficial to antagonistic. Iron itself or epichloënin A may serve as an important molecular/cellular signal for controlling fungal growth and hence the symbiotic interaction.
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Affiliation(s)
- Linda J Johnson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
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FcStuA from Fusarium culmorum controls wheat foot and root rot in a toxin dispensable manner. PLoS One 2013; 8:e57429. [PMID: 23451228 PMCID: PMC3579838 DOI: 10.1371/journal.pone.0057429] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 01/22/2013] [Indexed: 11/19/2022] Open
Abstract
Fusarium culmorum is one of the most harmful pathogens of durum wheat and is the causal agent of foot and root rot (FRR) disease. F. culmorum produces the mycotoxin deoxynivalenol (DON) that is involved in the pathogenic process. The role of the gene FcStuA, a StuA ortholog protein with an APSES domain sharing 98.5% homology to the FgStuA protein (FGSG10129), was determined by functional characterisation of deletion mutants obtained from two F. culmorum wild-type strains, FcUk99 (a highly pathogenic DON producer) and Fc233B (unable to produce toxin and with a mild pathogenic behavior). The ΔFcStuA mutants originating from both strains showed common phenotypic characters including stunted vegetative growth, loss of hydrophobicity of the mycelium, altered pigmentation, decreased activity of polygalacturonic enzymes and catalases, altered and reduced conidiation, delayed conidial germination patterns and complete loss of pathogenicity towards wheat stem base/root tissue. Glycolytic process efficiency [measured as growth on glucose as sole carbon (C) source] was strongly impaired and growth was partially restored on glutamic acid. Growth on pectin-like sources ranked in between glucose and glutamic acid with the following order (the lowest to the highest growth): beechwood xylan, sugarbeet arabinan, polygalacturonic acid, citrus pectin, apple pectin, potato azogalactan. DON production in the mutants originating from FcUK99 strain was significantly decreased (−95%) in vitro. Moreover, both sets of mutants were unable to colonise non-cereal plant tissues, i.e. apple and tomato fruits and potato tubers. No differences between mutants, ectopic and wild-type strains were observed concerning the level of resistance towards four fungicides belonging to three classes, the demethylase inhibitors epoxiconazole and tebuconzole, the succinate dehydrogenase inhibitor isopyrazam and the cytochrome bc1 inhibitor trifloxystrobin. StuA, given its multiple functions in cell regulation and pathogenicity control, is proposed as a potential target for novel disease management strategies.
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Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet 2013; 9:e1003233. [PMID: 23357949 PMCID: PMC3554632 DOI: 10.1371/journal.pgen.1003233] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/14/2012] [Indexed: 11/17/2022] Open
Abstract
The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
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Affiliation(s)
- Bradford J. Condon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Dongliang Wu
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Kathryn E. Bushley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Robin A. Ohm
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Robert Otillar
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Joel Martin
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - NurAinIzzati MohdZainudin
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Chunsheng Xue
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Rui Wang
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Viola A. Manning
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Braham Dhillon
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Zheng Jin Tu
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Asaf Salamov
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Hui Sun
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Steve Lowry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Kurt LaButti
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - James Han
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Alex Copeland
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Erika Lindquist
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Kerrie Barry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Jeremy Schmutz
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Scott E. Baker
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Lynda M. Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Igor V. Grigoriev
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - B. Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
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Munawar A, Marshall JW, Cox RJ, Bailey AM, Lazarus CM. Isolation and characterisation of a ferrirhodin synthetase gene from the sugarcane pathogen Fusarium sacchari. Chembiochem 2013; 14:388-94. [PMID: 23307607 DOI: 10.1002/cbic.201200587] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Indexed: 01/31/2023]
Abstract
FSN1, a gene isolated from the sugar-cane pathogen Fusarium sacchari, encodes a 4707-residue nonribosomal peptide synthetase consisting of three complete adenylation, thiolation and condensation modules followed by two additional thiolation and condensation domain repeats. This structure is similar to that of ferricrocin synthetase, which makes a siderophore that is involved in intracellular iron storage in other filamentous fungi. Heterologous expression of FSN1 in Aspergillus oryzae resulted in the accumulation of a secreted metabolite that was identified as ferrirhodin. This siderophore was found to be present in both mycelium and culture filtrates of F. sacchari, whereas ferricrocin is found only in the mycelium, thus suggesting that ferricrocin is an intracellular storage siderophore in F. sacchari, whereas ferrirhodin is used for iron acquisition. To our knowledge, this is the first report to characterise a ferrirhodin synthetase gene functionally.
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Affiliation(s)
- Asifa Munawar
- School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
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50
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Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (BETHESDA, MD.) 2013; 3:41-63. [PMID: 23316438 PMCID: PMC3538342 DOI: 10.1534/g3.112.004044] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/02/2012] [Indexed: 12/31/2022]
Abstract
Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.
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Affiliation(s)
- Viola A. Manning
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Iovanna Pandelova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Braham Dhillon
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Larry J. Wilhelm
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Carbone/Ferguson Laboratories, Division of Neuroscience, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon 97006
| | - Stephen B. Goodwin
- USDA–Agricultural Research Service, Purdue University, West Lafayette, Indiana 47907
| | | | - Melania Figueroa
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- USDA-Agricultural Research Service, Forage Seed and Cereal Research Unit, Oregon State University, Corvallis, Oregon 97331
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - James K. Hane
- Commonwealth Scientific and Industrial Research Organization−Plant Industry, Centre for Environment and Life Sciences, Floreat, Western Australia 6014, Australia
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique, 13288 Marseille cedex 9, France
| | - Wade H. Holman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Chinnappa D. Kodira
- The Broad Institute, Cambridge, Massachusetts 02142
- Roche 454, Branford, Connecticut 06405
| | - Joel Martin
- US DOE Joint Genome Institute, Walnut Creek, California 94598
| | - Richard P. Oliver
- Australian Centre for Necrotrophic Fungal Pathogens, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6845, Australia
| | - Barbara Robbertse
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique, 13288 Marseille cedex 9, France
| | | | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - B. Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14850
| | | | - Sarah Young
- The Broad Institute, Cambridge, Massachusetts 02142
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | | | | | - Li-Jun Ma
- The Broad Institute, Cambridge, Massachusetts 02142
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Lynda M. Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
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