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John E, Verdonk C, Singh KB, Oliver RP, Lenzo L, Morikawa S, Soyer JL, Muria-Gonzalez J, Soo D, Mousley C, Jacques S, Tan KC. Regulatory insight for a Zn2Cys6 transcription factor controlling effector-mediated virulence in a fungal pathogen of wheat. PLoS Pathog 2024; 20:e1012536. [PMID: 39312592 PMCID: PMC11419344 DOI: 10.1371/journal.ppat.1012536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/27/2024] [Indexed: 09/25/2024] Open
Abstract
The regulation of virulence in plant-pathogenic fungi has emerged as a key area of importance underlying host infections. Recent work has highlighted individual transcription factors (TFs) that serve important roles. A prominent example is PnPf2, a member of the Zn2Cys6 family of fungal TFs, which controls the expression of effectors and other virulence-associated genes in Parastagonospora nodorum during infection of wheat. PnPf2 orthologues are similarly important for other major fungal pathogens during infection of their respective host plants, and have also been shown to control polysaccharide metabolism in model saprophytes. In each case, the direct genomic targets and associated regulatory mechanisms were unknown. Significant insight was made here by investigating PnPf2 through chromatin-immunoprecipitation (ChIP) and mutagenesis approaches in P. nodorum. Two distinct binding motifs were characterised as positive regulatory elements and direct PnPf2 targets identified. These encompass known effectors and other components associated with the P. nodorum pathogenic lifestyle, such as carbohydrate-active enzymes and nutrient assimilators. The results support a direct involvement of PnPf2 in coordinating virulence on wheat. Other prominent PnPf2 targets included TF-encoding genes. While novel functions were observed for the TFs PnPro1, PnAda1, PnEbr1 and the carbon-catabolite repressor PnCreA, our investigation upheld PnPf2 as the predominant transcriptional regulator characterised in terms of direct and specific coordination of virulence on wheat, and provides important mechanistic insights that may be conserved for homologous TFs in other fungi.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Callum Verdonk
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Karam B. Singh
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Perth, Australia
| | - Richard P. Oliver
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Leon Lenzo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Shota Morikawa
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Jessica L. Soyer
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Jordi Muria-Gonzalez
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Daniel Soo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Carl Mousley
- Curtin Health Innovation Research Institute, Curtin University, Perth, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
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2
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Morikawa S, Verdonk C, John E, Lenzo L, Sbaraini N, Turo C, Li H, Jiang D, Chooi YH, Tan KC. The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogen Parastagonospora nodorum. BMC Microbiol 2024; 24:299. [PMID: 39127645 PMCID: PMC11316297 DOI: 10.1186/s12866-024-03454-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024] Open
Abstract
The fungus Parastagonospora nodorum causes septoria nodorum blotch on wheat. The role of the fungal Velvet-family transcription factor VeA in P. nodorum development and virulence was investigated here. Deletion of the P. nodorum VeA ortholog, PnVeA, resulted in growth abnormalities including pigmentation, abolished asexual sporulation and highly reduced virulence on wheat. Comparative RNA-Seq and RT-PCR analyses revealed that the deletion of PnVeA also decoupled the expression of major necrotrophic effector genes. In addition, the deletion of PnVeA resulted in an up-regulation of four predicted secondary metabolite (SM) gene clusters. Using liquid-chromatography mass-spectrometry, it was observed that one of the SM gene clusters led to an accumulation of the mycotoxin alternariol. PnVeA is essential for asexual sporulation, full virulence, secondary metabolism and necrotrophic effector regulation.
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Affiliation(s)
- Shota Morikawa
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Callum Verdonk
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Evan John
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115201, Taiwan
| | - Leon Lenzo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Nicolau Sbaraini
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Chala Turo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Hang Li
- School of Molecular Sciences, University of Western Australia, Perth, Australia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - David Jiang
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, Australia.
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3
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Katoch S, Sharma V, Sharma D, Salwan R, Rana SK. Biology and molecular interactions of Parastagonospora nodorum blotch of wheat. PLANTA 2021; 255:21. [PMID: 34914013 DOI: 10.1007/s00425-021-03796-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/14/2021] [Indexed: 06/14/2023]
Abstract
Parastagonospora nodorum is one of the important necrotrophic pathogens of wheat which causes severe economical loss to crop yield. So far, a number of effectors of Parastagonospora nodorum origin and their target interacting genes on the host plant have been characterized. Since targeting effector-sensitive gene carefully can be helpful in breeding for resistance. Therefore, constant efforts are required to further characterize the effectors, their interacting genes, and underlying biochemical pathways. Furthermore, to develop effective counter-strategies against emerging diseases, continuous efforts are required to determine the qualitative resistance that demands to screen of diverse genotypes for host resistance. Stagonospora nodorum blotch also refers to as Stagonospora glume blotch and leaf is caused by Parastagonospora nodorum. The pathogen deploys necrotrophic effectors for the establishment and development on wheat plants. The necrotrophic effectors and their interaction with host receptors lead to the establishment of infection on leaves and extensive lesions formation which either results in host cell death or suppression/activation of host defence mechanisms. The wheat Stagonospora nodorum interaction involves a set of nine host gene-necrotrophic effector interactions. Out of these, Snn1-SnTox1, Tsn1-SnToxA and Snn-SnTox3 are one of the most studied interaction, due to its role in the suppression of reactive oxygen species production, regulating the cytokinin content through ethylene-dependent wayduring initial infection stage. Further, although the molecular basis is not fully unveiled, these effectors regulate the redox state and influence the ethylene biosynthesis in infected wheat plants. Here, we have discussed the biology of the wheat pathogen Parastagonospora nodorum, role of its necrotrophic effectors and their interacting sensitivity genes on the redox state, how they hijack the resistance mechanisms, hormonal regulated immunity and other signalling pathways in susceptible wheat plants. The information generated from effectors and their corresponding sensitivity genes and other biological processes could be utilized effectively for disease management strategies.
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Affiliation(s)
- Shabnam Katoch
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vivek Sharma
- University Centre for Research and Development, Chandigarh University, Gharuan, 140413, Punjab, India.
| | - Devender Sharma
- Crop Improvement Division, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - Richa Salwan
- College of Horticulture and Forestry, Neri, Dr YS Parmar University of Horticulture and Forestry, Solan, Hamirpur, 177 001, India
| | - S K Rana
- Department of Plant Pathology, CSK HPKV Palampur, Palampur, 176062, Himachal Pradesh, India
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4
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Bertazzoni S, Jones DAB, Phan HT, Tan KC, Hane JK. Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome. BMC Genomics 2021; 22:382. [PMID: 34034667 PMCID: PMC8146201 DOI: 10.1186/s12864-021-07699-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/11/2021] [Indexed: 11/19/2022] Open
Abstract
Background The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007. P. nodorum infection is promoted by its production of proteinaceous necrotrophic effectors, three of which are characterised – ToxA, Tox1 and Tox3. Results A chromosome-scale genome assembly of P. nodorum Australian reference isolate Sn15, which combined long read sequencing, optical mapping and manual curation, produced 23 chromosomes with 21 chromosomes possessing both telomeres. New transcriptome data were combined with fungal-specific gene prediction techniques and manual curation to produce a high-quality predicted gene annotation dataset, which comprises 13,869 high confidence genes, and an additional 2534 lower confidence genes retained to assist pathogenicity effector discovery. Comparison to a panel of 31 internationally-sourced isolates identified multiple hotspots within the Sn15 genome for mutation or presence-absence variation, which was used to enhance subsequent effector prediction. Effector prediction resulted in 257 candidates, of which 98 higher-ranked candidates were selected for in-depth analysis and revealed a wealth of functions related to pathogenicity. Additionally, 11 out of the 98 candidates also exhibited orthology conservation patterns that suggested lateral gene transfer with other cereal-pathogenic fungal species. Analysis of the pan-genome indicated the smallest chromosome of 0.4 Mbp length to be an accessory chromosome (AC23). AC23 was notably absent from an avirulent isolate and is predominated by mutation hotspots with an increase in non-synonymous mutations relative to other chromosomes. Surprisingly, AC23 was deficient in effector candidates, but contained several predicted genes with redundant pathogenicity-related functions. Conclusions We present an updated series of genomic resources for P. nodorum Sn15 – an important reference isolate and model necrotroph – with a comprehensive survey of its predicted pathogenicity content. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07699-8.
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Affiliation(s)
| | - Darcy A B Jones
- Centre for Crop & Disease Management, Curtin University, Perth, Australia
| | - Huyen T Phan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, Curtin University, Perth, Australia.
| | - James K Hane
- Centre for Crop & Disease Management, Curtin University, Perth, Australia. .,Curtin Institute for Computation, Curtin University, Perth, Australia.
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5
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El-Demerdash A, Borde C, Genta-Jouve G, Escargueil A, Prado S. Cytotoxic constituents from the wheat plant pathogen Parastagonospora nodorum SN15. Nat Prod Res 2021; 36:1273-1281. [PMID: 33605174 DOI: 10.1080/14786419.2021.1877702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Microbial natural products are continuing to be a promising platform for future drug lead discover. As a part of our ongoing research program on fungal natural product, herein we report metabolites isolated from the fungus Parastagonospora nodorum SN15 a pathogen of wheat and related cereals. Its chemical investigation led to the purification of new isoleucinic acid derivatives (1-2) along with the cis procuramine (4). Their structures were determined based on extensive NMR and the relative configuration by comparison of experimental and predicted NMR chemical shifts. All compounds were evaluated for their cytotoxic activity against a panel of human cell lines and some displayed specific feature towards cancer cells compared to normal immortalised fibroblasts.
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Affiliation(s)
- Amr El-Demerdash
- Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, Muséum National d'Histoire Naturelle, Paris, France.,Organic Chemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Chloé Borde
- INSERM U938, Centre de Recherche Saint-Antoine, Sorbonne Université, Paris, France
| | - Gregory Genta-Jouve
- Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, Muséum National d'Histoire Naturelle, Paris, France.,UMR CNRS 8038, CiTCoM, Université de Paris, Paris, France
| | - Alexandre Escargueil
- INSERM U938, Centre de Recherche Saint-Antoine, Sorbonne Université, Paris, France
| | - Soizic Prado
- Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, Muséum National d'Histoire Naturelle, Paris, France
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6
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Jagadeeswaran G, Veale L, Mort AJ. Do Lytic Polysaccharide Monooxygenases Aid in Plant Pathogenesis and Herbivory? TRENDS IN PLANT SCIENCE 2021; 26:142-155. [PMID: 33097402 DOI: 10.1016/j.tplants.2020.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/07/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), copper-dependent enzymes mainly found in fungi, bacteria, and viruses, are responsible for enabling plant infection and degradation processes. Since their discovery 10 years ago, significant progress has been made in understanding the major role these enzymes play in biomass conversion. The recent discovery of additional LPMO families in fungi and oomycetes (AA16) as well as insects (AA15) strongly suggests that LPMOs might also be involved in biological processes such as overcoming plant defenses. In this review, we aim to give a comprehensive overview of the potential role of different LPMO families from the perspective of plant defense and their multiple implications in devising new strategies for achieving crop protection from plant pathogens and insect pests.
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Affiliation(s)
- Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Lawrie Veale
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Andrew J Mort
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
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7
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Muria-Gonzalez MJ, Yeng Y, Breen S, Mead O, Wang C, Chooi YH, Barrow RA, Solomon PS. Volatile Molecules Secreted by the Wheat Pathogen Parastagonospora nodorum Are Involved in Development and Phytotoxicity. Front Microbiol 2020; 11:466. [PMID: 32269554 PMCID: PMC7111460 DOI: 10.3389/fmicb.2020.00466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/04/2020] [Indexed: 12/01/2022] Open
Abstract
Septoria nodorum blotch is a major disease of wheat caused by the fungus Parastagonospora nodorum. Recent studies have demonstrated that secondary metabolites, including polyketides and non-ribosomal peptides, produced by the pathogen play important roles in disease and development. However, there is currently no knowledge on the composition or biological activity of the volatile organic compounds (VOCs) secreted by P. nodorum. To address this, we undertook a series of growth and phytotoxicity assays and demonstrated that P. nodorum VOCs inhibited bacterial growth, were phytotoxic and suppressed self-growth. Mass spectrometry analysis revealed that 3-methyl-1-butanol, 2-methyl-1-butanol, 2-methyl-1-propanol, and 2-phenylethanol were dominant in the VOC mixture and phenotypic assays using these short chain alcohols confirmed that they were phytotoxic. Further analysis of the VOCs also identified the presence of multiple sesquiterpenes of which four were identified via mass spectrometry and nuclear magnetic resonance as β-elemene, α-cyperone, eudesma-4,11-diene and acora-4,9-diene. Subsequent reverse genetics studies were able to link these molecules to corresponding sesquiterpene synthases in the P. nodorum genome. However, despite extensive testing, these molecules were not involved in either of the growth inhibition or phytotoxicity phenotypes previously observed. Plant assays using mutants of the pathogen lacking the synthetic genes revealed that the identified sesquiterpenes were not required for disease formation on wheat leaves. Collectively, these data have significantly extended our knowledge of the VOCs in fungi and provided the basis for further dissecting the roles of sesquiterpenes in plant disease.
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Affiliation(s)
| | - Yeannie Yeng
- Research School of Biology, ACT, Australian National University, Canberra, ACT, Australia
- Department of Oral Biology and Biomedical Sciences, MAHSA University, Selangor, Malaysia
| | - Susan Breen
- Research School of Biology, ACT, Australian National University, Canberra, ACT, Australia
| | - Oliver Mead
- Research School of Biology, ACT, Australian National University, Canberra, ACT, Australia
| | - Chen Wang
- Research School of Biology, ACT, Australian National University, Canberra, ACT, Australia
| | - Yi-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
| | - Russell A. Barrow
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW, Australia
- Plus 3 Australia Pty Ltd., Hawker, ACT, Australia
| | - Peter S. Solomon
- Research School of Biology, ACT, Australian National University, Canberra, ACT, Australia
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8
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Li H, Wei H, Hu J, Lacey E, Sobolev AN, Stubbs KA, Solomon PS, Chooi YH. Genomics-Driven Discovery of Phytotoxic Cytochalasans Involved in the Virulence of the Wheat Pathogen Parastagonospora nodorum. ACS Chem Biol 2020; 15:226-233. [PMID: 31815421 DOI: 10.1021/acschembio.9b00791] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The etiology of fungal pathogenesis of grains is critical to global food security. The large number of orphan biosynthetic gene clusters uncovered in fungal plant pathogen genome sequencing projects suggests that we have a significant knowledge gap about the secondary metabolite repertoires of these pathogens and their roles in plant pathogenesis. Cytochalasans are a family of natural products of significant interest due to their ability to bind to actin and interfere with cellular processes that involved actin polymerization; however, our understanding of their biosynthesis and biological roles remains incomplete. Here, we identified a putative polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) gene cluster (phm) that was upregulated in the pathogen Parastagonospora nodorum during its infection on wheat. Overexpression of the transcription factor gene phmR encoded in the phm gene cluster resulted in the production of two leucine-derived cytochalasans, phomacins D and E (1 and 2, respectively), and an acetonyl adduct phomacin F. Heterologous expression of the PKS-NRPS gene phmA and the trans-enoyl reductase (ER) gene phmE in Aspergillus nidulans resulted in the production of a novel 2-pyrrolidone precursor prephomacin. Reverse genetics and wheat seedling infection assays showed that ΔphmA mutants exhibited significantly reduced virulence compared to the wild type. We further demonstrated that both 1 and 2 showed potent actin polymerization-inhibitory activities and exhibited potentially monocot-specific antigerminative activities. The findings from this study have advanced our knowledge based on the biosynthesis and biological roles of cytochalasans, the latter of which could have significant implications for our understanding of the molecular mechanisms of fungus-plant interactions.
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Affiliation(s)
| | - Haochen Wei
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | | | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd., Smithfield, New South Wales 2164, Australia
| | | | | | - Peter S. Solomon
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
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9
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A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat. Sci Rep 2019; 9:15884. [PMID: 31685928 PMCID: PMC6828707 DOI: 10.1038/s41598-019-52444-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/17/2019] [Indexed: 12/14/2022] Open
Abstract
The fungus Parastagonospora nodorum infects wheat through the use of necrotrophic effector (NE) proteins that cause host-specific tissue necrosis. The Zn2Cys6 transcription factor PnPf2 positively regulates NE gene expression and is required for virulence on wheat. Little is known about other downstream targets of PnPf2. We compared the transcriptomes of the P. nodorum wildtype and a strain deleted in PnPf2 (pf2-69) during in vitro growth and host infection to further elucidate targets of PnPf2 signalling. Gene ontology enrichment analysis of the differentially expressed (DE) genes revealed that genes associated with plant cell wall degradation and proteolysis were enriched in down-regulated DE gene sets in pf2-69 compared to SN15. In contrast, genes associated with redox control, nutrient and ion transport were up-regulated in the mutant. Further analysis of the DE gene set revealed that PnPf2 positively regulates twelve genes that encode effector-like proteins. Two of these genes encode proteins with homology to previously characterised effectors in other fungal phytopathogens. In addition to modulating effector gene expression, PnPf2 may play a broader role in the establishment of a necrotrophic lifestyle by orchestrating the expression of genes associated with plant cell wall degradation and nutrient assimilation.
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10
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Li H, Hu J, Wei H, Solomon PS, Stubbs KA, Chooi YH. Biosynthesis of a Tricyclo[6.2.2.0 2,7 ]dodecane System by a Berberine Bridge Enzyme-Like Aldolase. Chemistry 2019; 25:15062-15066. [PMID: 31553484 DOI: 10.1002/chem.201904360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Indexed: 11/06/2022]
Abstract
The aldol reaction is one of the most fundamental stereocontrolled carbon-carbon bond-forming reactions and is mainly catalyzed by aldolases in nature. Despite the fact that the aldol reaction has been widely proposed to be involved in fungal secondary metabolite biosynthesis, a dedicated aldolase that catalyzes stereoselective aldol reactions has only rarely been reported in fungi. Herein, we activated a cryptic polyketide biosynthetic gene cluster that was upregulated in the fungal wheat pathogen Parastagonospora nodorum during plant infection; this resulted in the production of the phytotoxic stemphyloxin II (1). Through heterologous reconstruction of the biosynthetic pathway and in vitro assay by using cell-free lysate from Aspergillus nidulans, we demonstrated that a berberine bridge enzyme (BBE)-like protein SthB catalyzes an intramolecular aldol reaction to establish the bridged tricyclo[6.2.2.02,7 ]dodecane skeleton in the post-assembly tailoring step. The characterization of SthB as an aldolase enriches the catalytic toolbox of classic reactions and the functional diversities of the BBE superfamily of enzymes.
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Affiliation(s)
- Hang Li
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jinyu Hu
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Haochen Wei
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Keith A Stubbs
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
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11
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El-Demerdash A, Genta-Jouve G, Bärenstrauch M, Kunz C, Baudouin E, Prado S. Highly oxygenated isoprenylated cyclohexanoids from the fungus Parastagonospora nodorum SN15. PHYTOCHEMISTRY 2019; 166:112056. [PMID: 31302342 DOI: 10.1016/j.phytochem.2019.112056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/13/2019] [Accepted: 06/23/2019] [Indexed: 06/10/2023]
Abstract
The chemical investigation of the wheat plant pathogen Parastagonospora nodorum SN15 led to the purification of seven highly oxygenated acetylenic cyclohexanoids named stagonosporynes A-G. Their structures were determined on the basis of extensive NMR and the relative and absolute configurations by an array of computational methods including simulation of NOESY spectrum and electronic circular dichroism (ECD). All compounds were evaluated for their herbicidal activity and stagonosporyne G displayed the most significant herbicidal activity.
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Affiliation(s)
- Amr El-Demerdash
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, CP 54, 57 Rue Cuvier, 75005, Paris, France; Organic Chemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Grégory Genta-Jouve
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, CP 54, 57 Rue Cuvier, 75005, Paris, France; Université Paris Descartes, Laboratoire de Chimie-Toxicologie Analytique et Cellulaire (C-TAC), UMR CNRS 8638, COMETE, 4 Avenue de l'Observatoire, 75006, Paris, France
| | - Margot Bärenstrauch
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, CP 54, 57 Rue Cuvier, 75005, Paris, France
| | - Caroline Kunz
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, CP 54, 57 Rue Cuvier, 75005, Paris, France; Sorbonne Université, Faculté des Sciences et Ingénierie, UFR 927, F-75005, Paris, France
| | - Emmanuel Baudouin
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine (LBD-IBPS), Paris, F-75005, France
| | - Soizic Prado
- Muséum National d'Histoire Naturelle, Unité Molécules de Communication et Adaptation des Micro-organismes, UMR 7245, CP 54, 57 Rue Cuvier, 75005, Paris, France.
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12
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Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone. Microorganisms 2019; 7:microorganisms7100375. [PMID: 31547186 PMCID: PMC6843230 DOI: 10.3390/microorganisms7100375] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/06/2019] [Accepted: 08/09/2019] [Indexed: 11/20/2022] Open
Abstract
Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal–host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal–plant and fungal–microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant–microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant–microbe interactions.
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Hautbergue T, Jamin EL, Debrauwer L, Puel O, Oswald IP. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. Nat Prod Rep 2019; 35:147-173. [PMID: 29384544 DOI: 10.1039/c7np00032d] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.
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Affiliation(s)
- T Hautbergue
- Toxalim (Research Centre in Food Toxicology) Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027 Toulouse, France.
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14
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Hu J, Sarrami F, Li H, Zhang G, Stubbs KA, Lacey E, Stewart SG, Karton A, Piggott AM, Chooi YH. Heterologous biosynthesis of elsinochrome A sheds light on the formation of the photosensitive perylenequinone system. Chem Sci 2019; 10:1457-1465. [PMID: 30809363 PMCID: PMC6354827 DOI: 10.1039/c8sc02870b] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/21/2018] [Indexed: 12/14/2022] Open
Abstract
Perylenequinones are a class of aromatic polyketides characterised by a highly conjugated pentacyclic core, which confers them with potent light-induced bioactivities and unique photophysical properties. Despite the biosynthetic gene clusters for the perylenequinones elsinochrome A (1), cercosporin (4) and hypocrellin A (6) being recently identified, key biosynthetic aspects remain elusive. Here, we first expressed the intact elc gene cluster encoding 1 from the wheat pathogen Parastagonospora nodorum heterologously in Aspergillus nidulans on a yeast-fungal artificial chromosome (YFAC). This led to the identification of a novel flavin-dependent monooxygenase, ElcH, responsible for oxidative enolate coupling of a perylenequinone intermediate to the hexacyclic dihydrobenzo(ghi)perylenequinone in 1. In the absence of ElcH, the perylenequione intermediate formed a hexacyclic cyclohepta(ghi)perylenequinone system via an intramolecular aldol reaction resulting in 6 and a novel hypocrellin 12 with opposite helicity to 1. Theoretical calculations supported that 6 and 12 resulted from atropisomerisation upon formation of the 7-membered ring. Using a bottom-up pathway reconstruction approach on a tripartite YFAC system developed in this study, we uncovered that both a berberine bridge enzyme-like oxidase ElcE and a laccase-like multicopper oxidase ElcG are involved in the double coupling of two naphthol intermediates to form the perylenequinone core. Gene swapping with the homologs from the biosynthetic pathway of 4 showed that cognate pairing of the two classes of oxidases is required for the formation of the perylenequinone core, suggesting the involvement of protein-protein interactions.
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Affiliation(s)
- Jinyu Hu
- School of Molecular Sciences , University of Western Australia , Perth , WA 6009 , Australia .
| | - Farzaneh Sarrami
- School of Molecular Sciences , University of Western Australia , Perth , WA 6009 , Australia .
| | - Hang Li
- School of Molecular Sciences , University of Western Australia , Perth , WA 6009 , Australia .
| | - Guozhi Zhang
- School of Molecular Sciences , University of Western Australia , Perth , WA 6009 , Australia .
| | - Keith A Stubbs
- School of Molecular Sciences , University of Western Australia , Perth , WA 6009 , Australia .
| | - Ernest Lacey
- Microbial Screening Technologies , Smithfield , NSW 2164 , Australia
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Scott G Stewart
- School of Molecular Sciences , University of Western Australia , Perth , WA 6009 , Australia .
| | - Amir Karton
- School of Molecular Sciences , University of Western Australia , Perth , WA 6009 , Australia .
| | - Andrew M Piggott
- Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences , University of Western Australia , Perth , WA 6009 , Australia .
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15
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Li H, Hu J, Wei H, Solomon PS, Vuong D, Lacey E, Stubbs KA, Piggott AM, Chooi YH. Chemical Ecogenomics-Guided Discovery of Phytotoxic α-Pyrones from the Fungal Wheat Pathogen Parastagonospora nodorum. Org Lett 2018; 20:6148-6152. [DOI: 10.1021/acs.orglett.8b02617] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hang Li
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Jinyu Hu
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Haochen Wei
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Peter S. Solomon
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty Ltd, Smithfield, NSW 2164, Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty Ltd, Smithfield, NSW 2164, Australia
| | - Keith A. Stubbs
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Andrew M. Piggott
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
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Syme RA, Tan KC, Rybak K, Friesen TL, McDonald BA, Oliver RP, Hane JK. Pan-Parastagonospora Comparative Genome Analysis-Effector Prediction and Genome Evolution. Genome Biol Evol 2018; 10:2443-2457. [PMID: 30184068 PMCID: PMC6152946 DOI: 10.1093/gbe/evy192] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2018] [Indexed: 01/01/2023] Open
Abstract
We report a fungal pan-genome study involving Parastagonospora spp., including 21 isolates of the wheat (Triticum aestivum) pathogen Parastagonospora nodorum, 10 of the grass-infecting Parastagonospora avenae, and 2 of a closely related undefined sister species. We observed substantial variation in the distribution of polymorphisms across the pan-genome, including repeat-induced point mutations, diversifying selection and gene gains and losses. We also discovered chromosome-scale inter and intraspecific presence/absence variation of some sequences, suggesting the occurrence of one or more accessory chromosomes or regions that may play a role in host-pathogen interactions. The presence of known pathogenicity effector loci SnToxA, SnTox1, and SnTox3 varied substantially among isolates. Three P. nodorum isolates lacked functional versions for all three loci, whereas three P. avenae isolates carried one or both of the SnTox1 and SnTox3 genes, indicating previously unrecognized potential for discovering additional effectors in the P. nodorum-wheat pathosystem. We utilized the pan-genomic comparative analysis to improve the prediction of pathogenicity effector candidates, recovering the three confirmed effectors among our top-ranked candidates. We propose applying this pan-genomic approach to identify the effector repertoire involved in other host-microbe interactions involving necrotrophic pathogens in the Pezizomycotina.
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Affiliation(s)
- Robert A Syme
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Kasia Rybak
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Timothy L Friesen
- Cereal Crops Research Unit, USDA-ARS Red River Valley Agricultural Research Center, Fargo, North Dakota
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Richard P Oliver
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - James K Hane
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Curtin Institute for Computation, Curtin University, Bentley, Western Australia, Australia
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17
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Duba A, Goriewa-Duba K, Wachowska U. A Review of the Interactions between Wheat and Wheat Pathogens: Zymoseptoria tritici, Fusarium spp. and Parastagonospora nodorum. Int J Mol Sci 2018; 19:E1138. [PMID: 29642627 PMCID: PMC5979484 DOI: 10.3390/ijms19041138] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/24/2018] [Accepted: 04/06/2018] [Indexed: 12/11/2022] Open
Abstract
Zymoseptoria tritici is a hemibiotrophic pathogen which causes Septoria leaf blotch in wheat. The pathogenesis of the disease consists of a biotrophic phase and a necrotrophic phase. The pathogen infects the host plant by suppressing its immune response in the first stage of infection. Hemibiotrophic pathogens of the genus Fusarium cause Fusarium head blight, and the necrotrophic Parastagonosporanodorum is responsible for Septoria nodorum blotch in wheat. Cell wall-degrading enzymes in plants promote infections by necrotrophic and hemibiotrophic pathogens, and trichothecenes, secondary fungal metabolites, facilitate infections caused by fungi of the genus Fusarium. There are no sources of complete resistance to the above pathogens in wheat. Defense mechanisms in wheat are controlled by many genes encoding resistance traits. In the wheat genome, the characteristic features of loci responsible for resistance to pathogenic infections indicate that at least several dozen genes encode resistance to pathogens. The molecular interactions between wheat and Z. tritici, P. nodorum and Fusarium spp. pathogens have been insufficiently investigated. Most studies focus on the mechanisms by which the hemibiotrophic Z. tritici suppresses immune responses in plants and the role of mycotoxins and effector proteins in infections caused by P. nodorum and Fusarium spp. fungi. Trichothecene glycosylation and effector proteins, which are involved in defense responses in wheat, have been described at the molecular level. Recent advances in molecular biology have produced interesting findings which should be further elucidated in studies of molecular interactions between wheat and fungal pathogens. The Clustered Regularly-Interspaced Short Palindromic Repeats/ CRISPR associated (CRISPR/Cas) system can be used to introduce targeted mutations into the wheat genome and confer resistance to selected fungal diseases. Host-induced gene silencing and spray-induced gene silencing are also useful tools for analyzing wheat-pathogens interactions which can be used to develop new strategies for controlling fungal diseases.
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Affiliation(s)
- Adrian Duba
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-719 Olsztyn, Poland.
| | - Klaudia Goriewa-Duba
- Department of Plant Breeding and Seed Production, University of Warmia and Mazury in Olsztyn, pl. Łódzki 3, 10-724 Olsztyn, Poland.
| | - Urszula Wachowska
- Department of Entomology, Phytopathology and Molecular Diagnostics, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 17, 10-719 Olsztyn, Poland.
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18
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Hartmann FE, Sánchez-Vallet A, McDonald BA, Croll D. A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements. THE ISME JOURNAL 2017; 11:1189-1204. [PMID: 28117833 PMCID: PMC5437930 DOI: 10.1038/ismej.2016.196] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/10/2016] [Accepted: 11/25/2016] [Indexed: 11/09/2022]
Abstract
Fungal pathogens can rapidly evolve virulence towards resistant crops in agricultural ecosystems. Gains in virulence are often mediated by the mutation or deletion of a gene encoding a protein recognized by the plant immune system. However, the loci and the mechanisms of genome evolution enabling rapid virulence evolution are poorly understood. We performed genome-wide association mapping on a global collection of 106 strains of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe, to identify polymorphisms linked to virulence on two wheat varieties. We found 25 distinct genomic loci associated with reproductive success of the pathogen. However, no locus was shared between the host genotypes, suggesting host specialization. The main locus associated with virulence encoded a highly expressed, small secreted protein. Population genomic analyses showed that the gain in virulence was explained by a segregating gene deletion polymorphism. The deletion was likely adaptive by preventing detection of the encoded protein. Comparative genomics of closely related species showed that the locus emerged de novo since speciation. A large cluster of transposable elements in direct proximity to the locus generated extensive rearrangements leading to multiple independent gene losses. Our study demonstrates that rapid turnover in the chromosomal structure of a pathogen can drive host specialization.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
| | | | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, Zurich, Switzerland
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19
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Chooi Y, Zhang G, Hu J, Muria‐Gonzalez MJ, Tran PN, Pettitt A, Maier AG, Barrow RA, Solomon PS. Functional genomics‐guided discovery of a light‐activated phytotoxin in the wheat pathogen
Parastagonospora nodorum
via pathway activation. Environ Microbiol 2017; 19:1975-1986. [DOI: 10.1111/1462-2920.13711] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/23/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Yit‐Heng Chooi
- School of Molecular SciencesUniversity of Western AustraliaPerth WA6009 Australia
- Research School of BiologyAustralian National UniversityCanberra ACT2601 Australia
| | - Guozhi Zhang
- Research School of BiologyAustralian National UniversityCanberra ACT2601 Australia
| | - Jinyu Hu
- School of Molecular SciencesUniversity of Western AustraliaPerth WA6009 Australia
| | | | - Phuong N. Tran
- Research School of BiologyAustralian National UniversityCanberra ACT2601 Australia
| | - Amber Pettitt
- School of Molecular SciencesUniversity of Western AustraliaPerth WA6009 Australia
| | - Alexander G. Maier
- Research School of BiologyAustralian National UniversityCanberra ACT2601 Australia
| | - Russell A. Barrow
- Research School of ChemistryAustralian National UniversityCanberra ACT2601 Australia
| | - Peter S. Solomon
- Research School of BiologyAustralian National UniversityCanberra ACT2601 Australia
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20
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Phan HTT, Rybak K, Furuki E, Breen S, Solomon PS, Oliver RP, Tan KC. Differential effector gene expression underpins epistasis in a plant fungal disease. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:343-54. [PMID: 27133896 PMCID: PMC5053286 DOI: 10.1111/tpj.13203] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 04/18/2016] [Accepted: 04/25/2016] [Indexed: 05/18/2023]
Abstract
Fungal effector-host sensitivity gene interactions play a key role in determining the outcome of septoria nodorum blotch disease (SNB) caused by Parastagonospora nodorum on wheat. The pathosystem is complex and mediated by interaction of multiple fungal necrotrophic effector-host sensitivity gene systems. Three effector sensitivity gene systems are well characterized in this pathosystem; SnToxA-Tsn1, SnTox1-Snn1 and SnTox3-Snn3. We tested a wheat mapping population that segregated for Snn1 and Snn3 with SN15, an aggressive P. nodorum isolate that produces SnToxA, SnTox1 and SnTox3, to study the inheritance of sensitivity to SnTox1 and SnTox3 and disease susceptibility. Interval quantitative trait locus (QTL) mapping showed that the SnTox1-Snn1 interaction was paramount in SNB development on both seedlings and adult plants. No effect of the SnTox3-Snn3 interaction was observed under SN15 infection. The SnTox3-Snn3 interaction was however, detected in a strain of SN15 in which SnTox1 had been deleted (tox1-6). Gene expression analysis indicates increased SnTox3 expression in tox1-6 compared with SN15. This indicates that the failure to detect the SnTox3-Snn3 interaction in SN15 is due - at least in part - to suppressed expression of SnTox3 mediated by SnTox1. Furthermore, infection of the mapping population with a strain deleted in SnToxA, SnTox1 and SnTox3 (toxa13) unmasked a significant SNB QTL on 2DS where the SnTox2 effector sensitivity gene, Snn2, is located. This QTL was not observed in SN15 and tox1-6 infections and thus suggesting that SnToxA and/or SnTox3 were epistatic. Additional QTLs responding to SNB and effectors sensitivity were detected on 2AS1 and 3AL.
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Affiliation(s)
- Huyen T T Phan
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, 6102, Australia
| | - Kasia Rybak
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, 6102, Australia
| | - Eiko Furuki
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, 6102, Australia
| | - Susan Breen
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, 6102, Australia.
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, 6102, Australia.
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21
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Syme RA, Tan KC, Hane JK, Dodhia K, Stoll T, Hastie M, Furuki E, Ellwood SR, Williams AH, Tan YF, Testa AC, Gorman JJ, Oliver RP. Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics. PLoS One 2016; 11:e0147221. [PMID: 26840125 PMCID: PMC4739733 DOI: 10.1371/journal.pone.0147221] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/30/2015] [Indexed: 11/29/2022] Open
Abstract
Parastagonospora nodorum, the causal agent of Septoria nodorum blotch (SNB), is an economically important pathogen of wheat (Triticum spp.), and a model for the study of necrotrophic pathology and genome evolution. The reference P. nodorum strain SN15 was the first Dothideomycete with a published genome sequence, and has been used as the basis for comparison within and between species. Here we present an updated reference genome assembly with corrections of SNP and indel errors in the underlying genome assembly from deep resequencing data as well as extensive manual annotation of gene models using transcriptomic and proteomic sources of evidence (https://github.com/robsyme/Parastagonospora_nodorum_SN15). The updated assembly and annotation includes 8,366 genes with modified protein sequence and 866 new genes. This study shows the benefits of using a wide variety of experimental methods allied to expert curation to generate a reliable set of gene models.
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Affiliation(s)
- Robert A. Syme
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - James K. Hane
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
- Curtin Institute for Computation, Curtin University, Bentley, WA, Australia
| | - Kejal Dodhia
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Thomas Stoll
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Marcus Hastie
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Eiko Furuki
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Simon R. Ellwood
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Angela H. Williams
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | | | - Alison C. Testa
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Jeffrey J. Gorman
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, Qld, Australia
| | - Richard P. Oliver
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
- * E-mail:
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22
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SnPKS19 Encodes the Polyketide Synthase for Alternariol Mycotoxin Biosynthesis in the Wheat Pathogen Parastagonospora nodorum. Appl Environ Microbiol 2015; 81:5309-17. [PMID: 26025896 DOI: 10.1128/aem.00278-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/20/2015] [Indexed: 12/12/2022] Open
Abstract
Alternariol (AOH) is an important mycotoxin from the Alternaria fungi. AOH was detected for the first time in the wheat pathogen Parastagonospora nodorum in a recent study. Here, we exploited reverse genetics to demonstrate that SNOG_15829 (SnPKS19), a close homolog of Penicillium aethiopicum norlichexanthone (NLX) synthase gene gsfA, is required for AOH production. We further validate that SnPKS19 is solely responsible for AOH production by heterologous expression in Aspergillus nidulans. The expression profile of SnPKS19 based on previous P. nodorum microarray data correlated with the presence of AOH in vitro and its absence in planta. Subsequent characterization of the ΔSnPKS19 mutants showed that SnPKS19 and AOH are not involved in virulence and oxidative stress tolerance. Identification and characterization of the P. nodorum SnPKS19 cast light on a possible alternative AOH synthase gene in Alternaria alternata and allowed us to survey the distribution of AOH synthase genes in other fungal genomes. We further demonstrate that phylogenetic analysis could be used to differentiate between AOH synthases and the closely related NLX synthases. This study provides the basis for studying the genetic regulation of AOH production and for development of molecular diagnostic methods for detecting AOH-producing fungi in the future.
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23
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Muria-Gonzalez MJ, Chooi YH, Breen S, Solomon PS. The past, present and future of secondary metabolite research in the Dothideomycetes. MOLECULAR PLANT PATHOLOGY 2015; 16:92-107. [PMID: 24889519 PMCID: PMC6638331 DOI: 10.1111/mpp.12162] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The Dothideomycetes represents a large and diverse array of fungi in which prominent plant pathogens are over-represented. Species within the Cochliobolus, Alternaria, Pyrenophora and Mycosphaerella (amongst others) all cause diseases that threaten food security in many parts of the world. Significant progress has been made over the past decade in understanding how some of these pathogens cause disease at a molecular level. It is reasonable to suggest that much of this progress can be attributed to the increased availability of genome sequences. However, together with revealing mechanisms of pathogenicity, these genome sequences have also highlighted the capacity of the Dothideomycetes to produce an extensive array of secondary metabolites, far greater than originally thought. Indeed, it is now clear that we appear to have only scratched the surface to date in terms of the identification of secondary metabolites produced by these fungi. In the first half of this review, we examine the current status of secondary metabolite research in the Dothideomycetes and highlight the diversity of the molecules discovered thus far, in terms of both structure and biological activity. In the second part of this review, we survey the emerging techniques and technologies that will be required to shed light on the vast array of secondary metabolite potential that is encoded within these genomes. Experimental design, analytical chemistry and synthetic biology are all discussed in the context of how they will contribute to this field.
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Affiliation(s)
- Mariano Jordi Muria-Gonzalez
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, 0200, Australia
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24
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Chooi YH, Solomon PS. A chemical ecogenomics approach to understand the roles of secondary metabolites in fungal cereal pathogens. Front Microbiol 2014; 5:640. [PMID: 25477876 PMCID: PMC4237128 DOI: 10.3389/fmicb.2014.00640] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/06/2014] [Indexed: 11/19/2022] Open
Abstract
Secondary metabolites (SMs) are known to play important roles in the virulence and lifestyle of fungal plant pathogens. The increasing availability of fungal pathogen genome sequences and next-generation genomic tools have allowed us to survey the SM gene cluster inventory in individual fungi. Thus, there is immense opportunity for SM discovery in these plant pathogens. Comparative genomics and transcriptomics have been employed to obtain insights on the genetic features that enable fungal pathogens to adapt in individual ecological niches and to adopt the different pathogenic lifestyles. Here, we will discuss how we can use these tools to search for ecologically important SM gene clusters in fungi, using cereal pathogens as models. This ecological genomics approach, combined with genome mining and chemical ecology tools, is likely to advance our understanding of the natural functions of SMs and accelerate bioactive molecule discovery.
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Affiliation(s)
- Yit-Heng Chooi
- Plant Sciences Division, Research School of Biology, The Australian National University Canberra, ACT, Australia
| | - Peter S Solomon
- Plant Sciences Division, Research School of Biology, The Australian National University Canberra, ACT, Australia
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Quantitative trait locus mapping of melanization in the plant pathogenic fungus Zymoseptoria tritici. G3-GENES GENOMES GENETICS 2014; 4:2519-33. [PMID: 25360032 PMCID: PMC4267946 DOI: 10.1534/g3.114.015289] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Melanin plays an important role in virulence and antimicrobial resistance in several fungal pathogens. The wheat pathogen Zymoseptoria tritici is important worldwide, but little is known about the genetic architecture of pathogenicity, including the production of melanin. Because melanin production can exhibit complex inheritance, we used quantitative trait locus (QTL) mapping in two crosses to identify the underlying genes. Restriction site−associated DNA sequencing was used to genotype 263 (cross 1) and 261 (cross 2) progeny at ~8500 single-nucleotide polymorphisms and construct two dense linkage maps. We measured gray values, representing degrees of melanization, for single-spore colonies growing on Petri dishes by using a novel image-processing approach that enabled high-throughput phenotyping. Because melanin production can be affected by stress, each offspring was grown in two stressful environments and one control environment. We detected six significant QTL in cross 1 and nine in cross 2, with three QTL shared between the crosses. Different QTL were identified in different environments and at different colony ages. By obtaining complete genome sequences for the four parents and analyzing sequence variation in the QTL confidence intervals, we identified 16 candidate genes likely to affect melanization. One of these candidates was PKS1, a polyketide synthase gene known to play a role in the synthesis of dihydroxynaphthalene melanin. Three candidate quantitative trait nucleotides were identified in PKS1. Many of the other candidate genes were not previously associated with melanization.
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An in planta-expressed polyketide synthase produces (R)-mellein in the wheat pathogen Parastagonospora nodorum. Appl Environ Microbiol 2014; 81:177-86. [PMID: 25326302 DOI: 10.1128/aem.02745-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Parastagonospora nodorum is a pathogen of wheat that affects yields globally. Previous transcriptional analysis identified a partially reducing polyketide synthase (PR-PKS) gene, SNOG_00477 (SN477), in P. nodorum that is highly upregulated during infection of wheat leaves. Disruption of the corresponding SN477 gene resulted in the loss of production of two compounds, which we identified as (R)-mellein and (R)-O-methylmellein. Using a Saccharomyces cerevisiae yeast heterologous expression system, we successfully demonstrated that SN477 is the only enzyme required for the production of (R)-mellein. This is the first identification of a fungal PKS that is responsible for the synthesis of (R)-mellein. The P. nodorum ΔSN477 mutant did not show any significant difference from the wild-type strain in its virulence against wheat. However, (R)-mellein at 200 μg/ml inhibited the germination of wheat (Triticum aestivum) and barrel medic (Medicago truncatula) seeds. Comparative sequence analysis identified the presence of mellein synthase (MLNS) homologues in several Dothideomycetes and two sodariomycete genera. Phylogenetic analysis suggests that the MLNSs in fungi and bacteria evolved convergently from fungal and bacterial 6-methylsalicylic acid synthases.
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Morgenstern I, Powlowski J, Tsang A. Fungal cellulose degradation by oxidative enzymes: from dysfunctional GH61 family to powerful lytic polysaccharide monooxygenase family. Brief Funct Genomics 2014; 13:471-81. [PMID: 25217478 PMCID: PMC4239789 DOI: 10.1093/bfgp/elu032] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our understanding of fungal cellulose degradation has shifted dramatically in the past few years with the characterization of a new class of secreted enzymes, the lytic polysaccharide monooxygenases (LPMO). After a period of intense research covering structural, biochemical, theoretical and evolutionary aspects, we have a picture of them as wedge-like copper-dependent metalloenzymes that on reduction generate a radical copper-oxyl species, which cleaves mainly crystalline cellulose. The main biological function lies in the synergism of fungal LPMOs with canonical hydrolytic cellulases in achieving efficient cellulose degradation. Their important role in cellulose degradation is highlighted by the wide distribution and often numerous occurrences in the genomes of almost all plant cell-wall degrading fungi. In this review, we provide an overview of the latest achievements in LPMO research and consider the open questions and challenges that undoubtedly will continue to stimulate interest in this new and exciting group of enzymes.
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Winterberg B, Du Fall LA, Song X, Pascovici D, Care N, Molloy M, Ohms S, Solomon PS. The necrotrophic effector protein SnTox3 re-programs metabolism and elicits a strong defence response in susceptible wheat leaves. BMC PLANT BIOLOGY 2014; 14:215. [PMID: 25123935 PMCID: PMC4243954 DOI: 10.1186/s12870-014-0215-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/04/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND The fungus Stagonospora nodorum is a necrotrophic pathogen of wheat. It causes disease by secreting proteinaceous effectors which interact with proteins encoded by dominant susceptibility genes in the host. The outcome of these interactions results in necrosis, allowing the fungus to thrive on dead plant material. The mechanisms of these effectors though are poorly understood. In this study, we undertake a comprehensive transcriptomics, proteomic and metabolomic approach to understand how a susceptible wheat cultivar responds to exposure to the Stagonospora nodorum effector protein SnTox3. RESULTS Microarray and proteomic studies revealed that SnTox3 strongly induced responses consistent with those previously associated with classical host defence pathways including the expression of pathogenicity-related proteins and the induction of cell death. Collapse of the photosynthetic machinery was also apparent at the transcriptional and translational level. SnTox3-infiltrated wheat leaves also showed a strong induction of enzymes involved in primary metabolism consistent with increases in hexoses, amino acids and organic acids as determined by primary metabolite profiling. Methionine and homocysteine metabolism was strongly induced upon exposure to SnTox3. Pathogenicity in the presence of homocysteine was inhibited confirming that the compound has a role in plant defence. Consistent with the strong defence responses observed, secondary metabolite profiling revealed the induction of several compounds associated with plant defence, including the phenylpropanoids chlorogenic acid and feruloylquinic acid, and the cyanogenic glucoside dhurrin. Serotonin did not accumulate subsequent to SnTox3 infiltration. CONCLUSIONS These data support the theory that the SnTox3 effector protein elicits a host cell death response to facilitate the pathogen's necrotrophic infection cycle. Our data also demonstrate that the mechanism of SnTox3 appears distinct from the previously characterised Stagonospora nodorum effector SnToxA. Collectively, this comprehensive analysis has advanced our understanding of necrotrophic effector biology and highlighted the complexity of effector-triggered susceptibility.
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Affiliation(s)
- Britta Winterberg
- />Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT 0200 Australia
| | - Lauren A Du Fall
- />Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT 0200 Australia
| | - Xiaomin Song
- />Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109 Australia
| | - Dana Pascovici
- />Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109 Australia
| | - Natasha Care
- />Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109 Australia
| | - Mark Molloy
- />Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109 Australia
| | - Stephen Ohms
- />Molecular Bioscience Division, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200 Australia
| | - Peter S Solomon
- />Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, ACT 0200 Australia
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Lowe RGT, Cassin A, Grandaubert J, Clark BL, Van de Wouw AP, Rouxel T, Howlett BJ. Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species. PLoS One 2014; 9:e103098. [PMID: 25068644 PMCID: PMC4113356 DOI: 10.1371/journal.pone.0103098] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/26/2014] [Indexed: 11/18/2022] Open
Abstract
Leptosphaeria maculans ‘brassicae’ is a damaging fungal pathogen of canola (Brassica napus), causing lesions on cotyledons and leaves, and cankers on the lower stem. A related species, L. biglobosa ‘canadensis’, colonises cotyledons but causes few stem cankers. We describe the complement of genes encoding carbohydrate-active enzymes (CAZys) and peptidases of these fungi, as well as of four related plant pathogens. We also report dual-organism RNA-seq transcriptomes of these two Leptosphaeria species and B. napus during disease. During the first seven days of infection L. biglobosa ‘canadensis’, a necrotroph, expressed more cell wall degrading genes than L. maculans ‘brassicae’, a hemi-biotroph. L. maculans ‘brassicae’ expressed many genes in the Carbohydrate Binding Module class of CAZy, particularly CBM50 genes, with potential roles in the evasion of basal innate immunity in the host plant. At this time, three avirulence genes were amongst the top 20 most highly upregulated L. maculans ‘brassicae’ genes in planta. The two fungi had a similar number of peptidase genes, and trypsin was transcribed at high levels by both fungi early in infection. L. biglobosa ‘canadensis’ infection activated the jasmonic acid and salicylic acid defence pathways in B. napus, consistent with defence against necrotrophs. L. maculans ‘brassicae’ triggered a high level of expression of isochorismate synthase 1, a reporter for salicylic acid signalling. L. biglobosa ‘canadensis’ infection triggered coordinated shutdown of photosynthesis genes, and a concomitant increase in transcription of cell wall remodelling genes of the host plant. Expression of particular classes of CAZy genes and the triggering of host defence and particular metabolic pathways are consistent with the necrotrophic lifestyle of L. biglobosa ‘canadensis’, and the hemibiotrophic life style of L. maculans ‘brassicae’.
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Affiliation(s)
- Rohan G. T. Lowe
- School of Botany, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Cassin
- ARC Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Bethany L. Clark
- School of Botany, The University of Melbourne, Parkville, Victoria, Australia
| | | | | | - Barbara J. Howlett
- School of Botany, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
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Garnica DP, Upadhyaya NM, Dodds PN, Rathjen JP. Strategies for Wheat Stripe Rust Pathogenicity Identified by Transcriptome Sequencing. PLoS One 2013; 8:e67150. [PMID: 23840606 PMCID: PMC3694141 DOI: 10.1371/journal.pone.0067150] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Accepted: 05/14/2013] [Indexed: 12/31/2022] Open
Abstract
Stripe rust caused by the fungus Puccinia striiformis f.sp. tritici (Pst) is a major constraint to wheat production worldwide. The molecular events that underlie Pst pathogenicity are largely unknown. Like all rusts, Pst creates a specialized cellular structure within host cells called the haustorium to obtain nutrients from wheat, and to secrete pathogenicity factors called effector proteins. We purified Pst haustoria and used next-generation sequencing platforms to assemble the haustorial transcriptome as well as the transcriptome of germinated spores. 12,282 transcripts were assembled from 454-pyrosequencing data and used as reference for digital gene expression analysis to compare the germinated uredinospores and haustoria transcriptomes based on Illumina RNAseq data. More than 400 genes encoding secreted proteins which constitute candidate effectors were identified from the haustorial transcriptome, with two thirds of these up-regulated in this tissue compared to germinated spores. RT-PCR analysis confirmed the expression patterns of 94 effector candidates. The analysis also revealed that spores rely mainly on stored energy reserves for growth and development, while haustoria take up host nutrients for massive energy production for biosynthetic pathways and the ultimate production of spores. Together, these studies substantially increase our knowledge of potential Pst effectors and provide new insights into the pathogenic strategies of this important organism.
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Affiliation(s)
- Diana P. Garnica
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Narayana M. Upadhyaya
- Division of Plant Industry, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Peter N. Dodds
- Division of Plant Industry, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - John P. Rathjen
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery. G3-GENES GENOMES GENETICS 2013; 3:959-69. [PMID: 23589517 PMCID: PMC3689807 DOI: 10.1534/g3.112.004994] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Stagonospora nodorum is an important wheat (Triticum aestivum) pathogen in many parts of the world, causing major yield losses. It was the first species in the large fungal Dothideomycete class to be genome sequenced. The reference genome sequence (SN15) has been instrumental in the discovery of genes encoding necrotrophic effectors that induce disease symptoms in specific host genotypes. Here we present the genome sequence of two further S. nodorum strains (Sn4 and Sn79) that differ in their effector repertoire from the reference. Sn79 is avirulent on wheat and produces no apparent effectors when infiltrated onto many cultivars and mapping population parents. Sn4 is pathogenic on wheat and has virulences not found in SN15. The new strains, sequenced with short-read Illumina chemistry, are compared with SN15 by a combination of mapping and de novo assembly approaches. Each of the genomes contains a large number of strain-specific genes, many of which have no meaningful similarity to any known gene. Large contiguous sections of the reference genome are absent in the two newly sequenced strains. We refer to these differences as “sectional gene absences.” The presence of genes in pathogenic strains and absence in Sn79 is added to computationally predicted properties of known proteins to produce a list of likely effector candidates. Transposon insertion was observed in the mitochondrial genomes of virulent strains where the avirulent strain retained the likely ancestral sequence. The study suggests that short-read enabled comparative genomics is an effective way to both identify new S. nodorum effector candidates and to illuminate evolutionary processes in this species.
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Syme RA, Hane JK, Friesen TL, Oliver RP. Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery. G3 (BETHESDA, MD.) 2013. [PMID: 23589517 DOI: 10.1534/g1533.1112.004994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Stagonospora nodorum is an important wheat (Triticum aestivum) pathogen in many parts of the world, causing major yield losses. It was the first species in the large fungal Dothideomycete class to be genome sequenced. The reference genome sequence (SN15) has been instrumental in the discovery of genes encoding necrotrophic effectors that induce disease symptoms in specific host genotypes. Here we present the genome sequence of two further S. nodorum strains (Sn4 and Sn79) that differ in their effector repertoire from the reference. Sn79 is avirulent on wheat and produces no apparent effectors when infiltrated onto many cultivars and mapping population parents. Sn4 is pathogenic on wheat and has virulences not found in SN15. The new strains, sequenced with short-read Illumina chemistry, are compared with SN15 by a combination of mapping and de novo assembly approaches. Each of the genomes contains a large number of strain-specific genes, many of which have no meaningful similarity to any known gene. Large contiguous sections of the reference genome are absent in the two newly sequenced strains. We refer to these differences as "sectional gene absences." The presence of genes in pathogenic strains and absence in Sn79 is added to computationally predicted properties of known proteins to produce a list of likely effector candidates. Transposon insertion was observed in the mitochondrial genomes of virulent strains where the avirulent strain retained the likely ancestral sequence. The study suggests that short-read enabled comparative genomics is an effective way to both identify new S. nodorum effector candidates and to illuminate evolutionary processes in this species.
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Affiliation(s)
- Robert Andrew Syme
- Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Department of Environment and Agriculture, Bentley WA 6845, Australia
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Oliver R. Genomic tillage and the harvest of fungal phytopathogens. THE NEW PHYTOLOGIST 2012; 196:1015-1023. [PMID: 22998436 DOI: 10.1111/j.1469-8137.2012.04330.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/06/2012] [Indexed: 06/01/2023]
Abstract
Genome sequencing has been carried out on a small selection of major fungal ascomycete pathogens. These studies show that simple models whereby pathogens evolved from phylogenetically related saprobes by the acquisition or modification of a small number of key genes cannot be sustained.The genomes show that pathogens cannot be divided into three clearly delineated classes (biotrophs, hemibiotrophs and necrotrophs) but rather into a complex matrix of categories each with subtly different properties. It is clear that the evolution of pathogenicity is ancient, rapid and ongoing. Fungal pathogens have undergone substantial genomic rearrangements that can be appropriately described as 'genomic tillage'. Genomic tillage underpins the evolution and expression of large families of genes - known as effectors - that manipulate and exploit metabolic and defence processes of plants so as to allow the proliferation of pathogens.
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Affiliation(s)
- Richard Oliver
- Australian Centre for Necrotrophic Fungal Pathogens, Department of Environment and Agriculture, Curtin University, Bentley, WA, 6845, Australia
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Oliver RP, Friesen TL, Faris JD, Solomon PS. Stagonospora nodorum: from pathology to genomics and host resistance. ANNUAL REVIEW OF PHYTOPATHOLOGY 2012; 50:23-43. [PMID: 22559071 DOI: 10.1146/annurev-phyto-081211-173019] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Stagonospora nodorum is a major necrotrophic pathogen of wheat that causes the diseases S. nodorum leaf and glume blotch. A series of tools and resources, including functional genomics, a genome sequence, proteomics and metabolomics, host-mapping populations, and a worldwide collection of isolates, have enabled the dissection of pathogenicity mechanisms. Metabolic and signaling genes required for pathogenicity have been defined. Interaction with the host is dominated by interplay of fungal effectors that induce necrosis on wheat lines carrying specific sensitivity loci. As such, the pathogen has emerged as a model for the Pleosporales group of pathogens.
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Affiliation(s)
- Richard P Oliver
- Australian Center for Necrotrophic Fungal Pathogens, Curtin University, Perth WA 6845, Australia.
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