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Rocafort M, Srivastava V, Bowen JK, Díaz-Moreno SM, Guo Y, Bulone V, Plummer KM, Sutherland PW, Anderson MA, Bradshaw RE, Mesarich CH. Cell Wall Carbohydrate Dynamics during the Differentiation of Infection Structures by the Apple Scab Fungus, Venturia inaequalis. Microbiol Spectr 2023; 11:e0421922. [PMID: 37039647 PMCID: PMC10269774 DOI: 10.1128/spectrum.04219-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/15/2023] [Indexed: 04/12/2023] Open
Abstract
Scab, caused by the biotrophic fungal pathogen Venturia inaequalis, is the most economically important disease of apples. During infection, V. inaequalis colonizes the subcuticular host environment, where it develops specialized infection structures called runner hyphae and stromata. These structures are thought to be involved in nutrient acquisition and effector (virulence factor) delivery, but also give rise to conidia that further the infection cycle. Despite their importance, very little is known about how these structures are differentiated. Likewise, nothing is known about how these structures are protected from host defenses or recognition by the host immune system. To better understand these processes, we first performed a glycosidic linkage analysis of sporulating tubular hyphae from V. inaequalis developed in culture. This analysis revealed that the V. inaequalis cell wall is mostly composed of glucans (44%) and mannans (37%), whereas chitin represents a much smaller proportion (4%). Next, we used transcriptomics and confocal laser scanning microscopy to provide insights into the cell wall carbohydrate composition of runner hyphae and stromata. These analyses revealed that, during subcuticular host colonization, genes of V. inaequalis putatively associated with the biosynthesis of immunogenic carbohydrates, such as chitin and β-1,6-glucan, are downregulated relative to growth in culture, while on the surface of runner hyphae and stromata, chitin is deacetylated to the less-immunogenic carbohydrate chitosan. These changes are anticipated to enable the subcuticular differentiation of runner hyphae and stromata by V. inaequalis, as well as to protect these structures from host defenses and recognition by the host immune system. IMPORTANCE Plant-pathogenic fungi are a major threat to food security. Among these are subcuticular pathogens, which often cause latent asymptomatic infections, making them difficult to control. A key feature of these pathogens is their ability to differentiate specialized subcuticular infection structures that, to date, remain largely understudied. This is typified by Venturia inaequalis, which causes scab, the most economically important disease of apples. In this study, we show that, during subcuticular host colonization, V. inaequalis downregulates genes associated with the biosynthesis of two immunogenic cell wall carbohydrates, chitin and β-1,6-glucan, and coats its subcuticular infection structures with a less-immunogenic carbohydrate, chitosan. These changes are anticipated to enable host colonization by V. inaequalis and provide a foundation for understanding subcuticular host colonization by other plant-pathogenic fungi. Such an understanding is important, as it may inform the development of novel control strategies against subcuticular plant-pathogenic fungi.
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Affiliation(s)
- Mercedes Rocafort
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
| | - Joanna K. Bowen
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, New Zealand
| | - Sara M. Díaz-Moreno
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
| | - Yanan Guo
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Vincent Bulone
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, Sweden
- School of Food, Agriculture and Wine, The University of Adelaide, Waite Campus, Adelaide, South Australia, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, Centre for AgriBiosciences, La Trobe University, Bundoora, Melbourne, Victoria, Australia
| | - Paul W. Sutherland
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, New Zealand
| | - Marilyn A. Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, Victoria, Australia
| | - Rosie E. Bradshaw
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
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Rocafort M, Bowen JK, Hassing B, Cox MP, McGreal B, de la Rosa S, Plummer KM, Bradshaw RE, Mesarich CH. The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi. BMC Biol 2022; 20:246. [PMID: 36329441 PMCID: PMC9632046 DOI: 10.1186/s12915-022-01442-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Background Scab, caused by the biotrophic fungus Venturia inaequalis, is the most economically important disease of apples worldwide. During infection, V. inaequalis occupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth by V. inaequalis, as well as in activating, suppressing, or circumventing resistance protein-mediated defences in apple, is required. Results We generated the first comprehensive RNA-seq transcriptome of V. inaequalis during colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid, or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector from Leptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi. Conclusions Our study reveals the transcriptomic profile underpinning subcuticular growth by V. inaequalis and provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01442-9.
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Affiliation(s)
- Mercedes Rocafort
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Joanna K Bowen
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, 1025, New Zealand
| | - Berit Hassing
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Murray P Cox
- Bioprotection Aotearoa, School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Brogan McGreal
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, 1025, New Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, La Trobe University, AgriBio, Centre for AgriBiosciences, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Rosie E Bradshaw
- Bioprotection Aotearoa, School of Natural Sciences, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand.
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Rodriguez Coy L, Plummer KM, Khalifa ME, MacDiarmid RM. Mycovirus-encoded suppressors of RNA silencing: Possible allies or enemies in the use of RNAi to control fungal disease in crops. Front Fungal Biol 2022; 3:965781. [PMID: 37746227 PMCID: PMC10512228 DOI: 10.3389/ffunb.2022.965781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/21/2022] [Indexed: 09/26/2023]
Abstract
Plants, fungi, and many other eukaryotes have evolved an RNA interference (RNAi) mechanism that is key for regulating gene expression and the control of pathogens. RNAi inhibits gene expression, in a sequence-specific manner, by recognizing and deploying cognate double-stranded RNA (dsRNA) either from endogenous sources (e.g. pre-micro RNAs) or exogenous origin (e.g. viruses, dsRNA, or small interfering RNAs, siRNAs). Recent studies have demonstrated that fungal pathogens can transfer siRNAs into plant cells to suppress host immunity and aid infection, in a mechanism termed cross-kingdom RNAi. New technologies, based on RNAi are being developed for crop protection against insect pests, viruses, and more recently against fungal pathogens. One example, is host-induced gene silencing (HIGS), which is a mechanism whereby transgenic plants are modified to produce siRNAs or dsRNAs targeting key transcripts of plants, or their pathogens or pests. An alternative gene regulation strategy that also co-opts the silencing machinery is spray-induced gene silencing (SIGS), in which dsRNAs or single-stranded RNAs (ssRNAs) are applied to target genes within a pathogen or pest. Fungi also use their RNA silencing machinery against mycoviruses (fungal viruses) and mycoviruses can deploy virus-encoded suppressors of RNAi (myco-VSRs) as a counter-defence. We propose that myco-VSRs may impact new dsRNA-based management methods, resulting in unintended outcomes, including suppression of management by HIGS or SIGS. Despite a large diversity of mycoviruses being discovered using high throughput sequencing, their biology is poorly understood. In particular, the prevalence of mycoviruses and the cellular effect of their encoded VSRs are under-appreciated when considering the deployment of HIGS and SIGS strategies. This review focuses on mycoviruses, their VSR activities in fungi, and the implications for control of pathogenic fungi using RNAi.
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Affiliation(s)
- Lorena Rodriguez Coy
- Australian Research Council Research Hub for Sustainable Crop Protection, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Kim M. Plummer
- Australian Research Council Research Hub for Sustainable Crop Protection, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Mahmoud E. Khalifa
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
| | - Robin M. MacDiarmid
- BioProtection, The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Caruana NJ, Strugnell JM, Finn J, Faou P, Plummer KM, Cooke IR. Quantitative Proteomic Analysis of the Slime and Ventral Mantle Glands of the Striped Pyjama Squid ( Sepioloidea lineolata). J Proteome Res 2020; 19:1491-1501. [PMID: 32091901 DOI: 10.1021/acs.jproteome.9b00738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cephalopods are known to produce an extensive range of secretions including ink, mucus, and venom. Sepiadariidae, a family of small, benthic bobtail squids, are notable for the high volume of viscous slime they emit when stressed. One species, Sepioloidea lineolata (striped pyjama squid), is covered with glands along the perimeter of the ventral mantle, and these structures are hypothesized to be the source of its slime. Using label-free quantitative proteomics, we analyzed five tissue types (dorsal and ventral mantle muscle, dorsal and ventral epithelium, and ventral mantle glands) and the slime from four individuals. In doing so, we were able to determine the relationship between the slime and the tissues as well as highlight proteins that were specifically identified within the slime and ventral mantle glands. A total of 28 proteins were identified to be highly enriched in slime, and these were composed of peptidases and protease inhibitors. Seven of these proteins contained predicted signal peptides, indicating classical secretion, with four proteins having no identifiable domains or similarity to any known proteins. The ventral mantle glands also appear to be the tissue with the closest overall proteomic composition to the slime; therefore, it is likely that the slime originates, at least in part, from these glands.
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Affiliation(s)
- Nikeisha J Caruana
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Jan M Strugnell
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland 4811, Australia
| | - Julian Finn
- Sciences, Museums Victoria, Carlton, Victoria 3053, Australia
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ira R Cooke
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland 4811, Australia
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Zia SF, Berkowitz O, Bedon F, Whelan J, Franks AE, Plummer KM. Direct comparison of Arabidopsis gene expression reveals different responses to melatonin versus auxin. BMC Plant Biol 2019; 19:567. [PMID: 31856719 PMCID: PMC6921455 DOI: 10.1186/s12870-019-2158-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/25/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Melatonin (N-acetyl-5-methoxytryptamine) in plants, regulates shoot and root growth and alleviates environmental stresses. Melatonin and the phyto-hormone auxin are tryptophan-derived compounds. However, it largely remains controversial as to whether melatonin and auxin act through similar or overlapping signalling and regulatory pathways. RESULTS Here, we have used a promoter-activation study to demonstrate that, unlike auxin (1-naphthalene acetic acid, NAA), melatonin neither induces Direct repeat 5 DR5 expression in Arabidopsis thaliana roots under normal growth conditions nor suppresses the induction of Alternative oxidase 1a AOX1a in leaves upon Antimycin A treatment, both of which are the hallmarks of auxin action. Additionally, comparative global transcriptome analysis conducted on Arabidopsis treated with melatonin or NAA revealed differences in the number and types of differentially expressed genes. Auxin (4.5 μM) altered the expression of a diverse and large number of genes whereas melatonin at 5 μM had no significant effect but melatonin at 100 μM had a modest effect on transcriptome compared to solvent-treated control. Interestingly, the prominent category of genes differentially expressed upon exposure to melatonin trended towards biotic stress defence pathways while downregulation of key genes related to photosynthesis was observed. CONCLUSION Together these findings indicate that though they are both indolic compounds, melatonin and auxin act through different pathways to alter gene expression in Arabidopsis thaliana. Furthermore, it appears that effects of melatonin enable Arabidopsis thaliana to prioritize biotic stress defence signalling rather than growth. These findings clear the current confusion in the literature regarding the relationship of melatonin and auxin and also have greater implications of utilizing melatonin for improved plant protection.
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Affiliation(s)
- Sajal F Zia
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
- ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Frank Bedon
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - James Whelan
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia
- ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, 3086, Australia
- Centre for Future Landscapes, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC, 3086, Australia.
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Madigan AP, Egidi E, Bedon F, Franks AE, Plummer KM. Bacterial and Fungal Communities Are Differentially Modified by Melatonin in Agricultural Soils Under Abiotic Stress. Front Microbiol 2019; 10:2616. [PMID: 31849848 PMCID: PMC6901394 DOI: 10.3389/fmicb.2019.02616] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/28/2019] [Indexed: 12/29/2022] Open
Abstract
An extensive body of evidence from the last decade has indicated that melatonin enhances plant resistance to a range of biotic and abiotic stressors. This has led to an interest in the application of melatonin in agriculture to reduce negative physiological effects from environmental stresses that affect yield and crop quality. However, there are no reports regarding the effects of melatonin on soil microbial communities under abiotic stress, despite the importance of microbes for plant root health and function. Three agricultural soils associated with different land usage histories (pasture, canola or wheat) were placed under abiotic stress by cadmium (100 or 280 mg kg-1 soil) or salt (4 or 7 g kg-1 soil) and treated with melatonin (0.2 and 4 mg kg-1 soil). Automated Ribosomal Intergenic Spacer Analysis (ARISA) was used to generate Operational Taxonomic Units (OTU) for microbial community analysis in each soil. Significant differences in richness (α diversity) and community structures (β diversity) were observed between bacterial and fungal assemblages across all three soils, demonstrating the effect of melatonin on soil microbial communities under abiotic stress. The analysis also indicated that the microbial response to melatonin is governed by the type of soil and history. The effects of melatonin on soil microbes need to be regarded in potential future agricultural applications.
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Affiliation(s)
- Andrew P. Madigan
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Frank Bedon
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Ashley E. Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
- Centre for Future Landscapes, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
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Johnson S, Jones D, Thrimawithana AH, Deng CH, Bowen JK, Mesarich CH, Ishii H, Won K, Bus VGM, Plummer KM. Whole Genome Sequence Resource of the Asian Pear Scab Pathogen Venturia nashicola. Mol Plant Microbe Interact 2019; 32:1463-1467. [PMID: 31313627 DOI: 10.1094/mpmi-03-19-0067-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Venturia nashicola, the cause of scab disease of Asian pears, is a host-specific, biotrophic fungus. It is restricted to Asia and is regarded as a quarantine threat outside this region. European pear displays nonhost resistance (NHR) to V. nashicola and Asian pears are nonhosts of V. pyrina (the cause of European pear scab disease). The host specificity of these two fungi is likely governed by differences in their effector arsenals, with a subset hypothesized to activate NHR. The Pyrus-Venturia pathosystem provides an opportunity to dissect the underlying genetics of nonhost interactions in this potentially more durable form of resistance. The V. nashicola genome will enable comparisons to other Venturia spp. genomes to identify effectors that potentially activate NHR in the pear scab pathosystem.
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Affiliation(s)
- Shakira Johnson
- La Trobe University, Bundoora, Victoria, Australia
- The Plant Biosecurity Cooperative Research Centre, Canberra, ACT, Australia
| | - Dan Jones
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Amali H Thrimawithana
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Cecilia H Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Joanna K Bowen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Carl H Mesarich
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Hideo Ishii
- Kibi International University, Minami-Awaji, Hyogo, Japan
| | - Kyungho Won
- National Institute of Horticultural and Herbal Science, Rural Development Administration (NIHHS-RDA), Naju, Korea
| | - Vincent G M Bus
- The New Zealand Institute for Plant & Food Research Limited (PFR), Havelock North, New Zealand
| | - Kim M Plummer
- La Trobe University, Bundoora, Victoria, Australia
- The Plant Biosecurity Cooperative Research Centre, Canberra, ACT, Australia
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Abstract
INTRODUCTION The aphid Rhopalosiphum padi L. is a vector of Barley yellow dwarf virus (BYDV) in wheat and other economically important cereal crops. Increased atmospheric CO2 has been shown to alter plant growth and metabolism, enhancing BYDV disease in wheat. However, the biochemical influences on aphid metabolism are not known. OBJECTIVES This work aims to determine whether altered host-plant quality, influenced by virus infection and elevated CO2, impacts aphid weight and metabolism. METHODS Untargeted 1H NMR metabolomics coupled with multivariate statistics were employed to profile the metabolism of R. padi reared on virus-infected and non-infected (sham-inoculated) wheat grown under ambient CO2 (aCO2, 400 µmol mol-1) and future, predicted elevated CO2 (eCO2, 650 µmol mol-1) concentrations. Un-colonised wheat was also profiled to observe changes to host-plant quality (i.e., amino acids and sugars). RESULTS The direct impacts of virus or eCO2 were compared. Virus presence increased aphid weight under aCO2 but decreased weight under eCO2; whilst eCO2 increased non-viruliferous (sham) aphid weight but decreased viruliferous aphid weight. Discriminatory metabolites due to eCO2 were succinate and sucrose (in sham wheat), glucose, choline and betaine (in infected wheat), and threonine, lactate, alanine, GABA, glutamine, glutamate and asparagine (in aphids), irrespective of virus presence. Discriminatory metabolites due to virus presence were alanine, GABA, succinate and betaine (in wheat) and threonine and lactate (in aphids), irrespective of CO2 treatment. CONCLUSION This study confirms that virus and eCO2 alter host-plant quality, and these differences are reflected by aphid weight and metabolism.
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Affiliation(s)
- Simone Vassiliadis
- Agriculture Research Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, 3083, Australia
| | | | - Simone J Rochfort
- Agriculture Research Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
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Young CA, Bock CH, Charlton ND, Mattupalli C, Krom N, Bowen JK, Templeton M, Plummer KM, Wood BW. Evidence for Sexual Reproduction: Identification, Frequency, and Spatial Distribution of Venturia effusa (Pecan Scab) Mating Type Idiomorphs. Phytopathology 2018; 108:837-846. [PMID: 29381450 DOI: 10.1094/phyto-07-17-0233-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Venturia effusa (syn. Fusicladium effusum), causal agent of pecan scab, is the most prevalent pathogen of pecan (Carya illinoinensis), causing severe yield losses in the southeastern United States. V. effusa is currently known only by its asexual (conidial) stage. However, the degree and distribution of genetic diversity observed within and among populations of V. effusa are typical of a sexually reproducing fungal pathogen, and comparable with other dothideomycetes with a known sexual stage, including the closely related apple scab pathogen, V. inaequalis. Using the mating type (MAT) idiomorphs from V. inaequalis, we identified a single MAT gene, MAT1-1-1, in a draft genome of V. effusa. The MAT1-1-1 locus is flanked by two conserved genes encoding a DNA lyase (APN2) and a hypothetical protein. The MAT locus spanning the flanking genes was amplified and sequenced from a subset of 14 isolates, of which 7 contained MAT1-1-1 and the remaining samples contained MAT1-2-1. A multiplex polymerase chain reaction screen was developed to amplify MAT1-1-1, MAT1-2-1, and a conserved reference gene encoding β-tubulin, and used to screen 784 monoconidial isolates of V. effusa collected from 11 populations of pecan across the southeastern United States. A hierarchical sampling protocol representing region, orchard, and tree allowed for analysis of MAT structure at different spatial scales. Analysis of this collection revealed the frequency of the MAT idiomorphs is in a 1:1 equilibrium of MAT1-1:MAT1-2. The apparent equilibrium of the MAT idiomorphs provides impetus for a renewed effort to search for the sexual stage of V. effusa. [Formula: see text] Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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Affiliation(s)
- Carolyn A Young
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
| | - Clive H Bock
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
| | - Nikki D Charlton
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
| | - Chakradhar Mattupalli
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
| | - Nick Krom
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
| | - Joanna K Bowen
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
| | - Matthew Templeton
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
| | - Kim M Plummer
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
| | - Bruce W Wood
- First, third, fourth, and fifth authors: Noble Research Institute, LLC., Ardmore, OK 73401; second and ninth authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; sixth and seventh authors: The New Zealand Institute for Plant & Food Research, Auckland, New Zealand; seventh author: The School of Biological Sciences, University of Auckland, New Zealand; eighth author: Department of Animal, Plant and Soil Sciences, AgriBio, AgriBiosciences Research Centre, La Trobe University, 3086, Victoria, Australia
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10
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Kinoti WM, Constable FE, Nancarrow N, Plummer KM, Rodoni B. Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus. Front Microbiol 2017; 8:1219. [PMID: 28713347 PMCID: PMC5491605 DOI: 10.3389/fmicb.2017.01219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/16/2017] [Indexed: 01/01/2023] Open
Abstract
The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV) was the most frequently detected Ilarvirus, occurring in 48 of the 61 Ilarvirus-positive trees and Prune dwarf virus (PDV) and Apple mosaic virus (ApMV) were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV) was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus-like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus-like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus-like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples, and the need for a standardized approach to accurately determine what constitutes an active, viable virus infection after detection by molecular based methods.
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Affiliation(s)
- Wycliff M. Kinoti
- Biosciences Research Division, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
- AgriBio, School of Applied Systems Biology, La Trobe UniversityMelbourne, VIC, Australia
| | - Fiona E. Constable
- Biosciences Research Division, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
| | - Narelle Nancarrow
- Biosciences Research Division, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
| | - Brendan Rodoni
- Biosciences Research Division, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
- AgriBio, School of Applied Systems Biology, La Trobe UniversityMelbourne, VIC, Australia
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11
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Kinoti WM, Constable FE, Nancarrow N, Plummer KM, Rodoni B. Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing. PLoS One 2017; 12:e0179284. [PMID: 28632759 PMCID: PMC5478126 DOI: 10.1371/journal.pone.0179284] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 05/08/2017] [Indexed: 12/28/2022] Open
Abstract
PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively. The RNA2 had the lowest diversity of sequences compared to RNA1 and RNA3, reflecting the lack of flexibility tolerated by the replicase gene that is encoded by this RNA component. Distinct PNRSV phylo-groups, consisting of closely related clusters of sequence variants, were observed in each of PNRSV RNA1, RNA2 and RNA3. Most plant samples had a single phylo-group for each RNA component. Haplotype network analysis showed that smaller clusters of PNRSV sequence variants were genetically connected to the largest sequence variant cluster within a phylo-group of each RNA component. Some plant samples had sequence variants occurring in multiple PNRSV phylo-groups in at least one of each RNA and these phylo-groups formed distinct clades that represent PNRSV genetic strains. Variants within the same phylo-group of each Prunus plant sample had ≥97% similarity and phylo-groups within a Prunus plant sample and between samples had less ≤97% similarity. Based on the analysis of diversity, a definition of a PNRSV genetic strain was proposed. The proposed definition was applied to determine the number of PNRSV genetic strains in each of the plant samples and the complexity in defining genetic strains in multipartite genome viruses was explored.
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Affiliation(s)
- Wycliff M. Kinoti
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Narelle Nancarrow
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Melbourne, VIC, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Melbourne, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Melbourne, VIC, Australia
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12
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Deng CH, Plummer KM, Jones DAB, Mesarich CH, Shiller J, Taranto AP, Robinson AJ, Kastner P, Hall NE, Templeton MD, Bowen JK. Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range. BMC Genomics 2017; 18:339. [PMID: 28464870 PMCID: PMC5412055 DOI: 10.1186/s12864-017-3699-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/11/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuticular space without penetrating plant cells, it is assumed that effectors that contribute to virulence and determination of host range will be secreted into this plant-pathogen interface. Thus the predicted secretomes of a range of isolates of Venturia with distinct host-ranges were interrogated to reveal putative proteins involved in virulence and pathogenicity. RESULTS Genomes of Venturia pirina (one European pear scab isolate) and Venturia inaequalis (three apple scab, and one loquat scab, isolates) were sequenced and the predicted secretomes of each isolate identified. RNA-Seq was conducted on the apple-specific V. inaequalis isolate Vi1 (in vitro and infected apple leaves) to highlight virulence and pathogenicity components of the secretome. Genes encoding over 600 small secreted proteins (candidate effectors) were identified, most of which are novel to Venturia, with expansion of putative effector families a feature of the genus. Numerous genes with similarity to Leptosphaeria maculans AvrLm6 and the Verticillium spp. Ave1 were identified. Candidates for avirulence effectors with cognate resistance genes involved in race-cultivar specificity were identified, as were putative proteins involved in host-species determination. Candidate effectors were found, on average, to be in regions of relatively low gene-density and in closer proximity to repeats (e.g. transposable elements), compared with core eukaryotic genes. CONCLUSIONS Comparative secretomics has revealed candidate effectors from Venturia fungal plant pathogens that attack pome fruit. Effectors that are putative determinants of host range were identified; both those that may be involved in race-cultivar and host-species specificity. Since many of the effector candidates are in close proximity to repetitive sequences this may point to a possible mechanism for the effector gene family expansion observed and a route to diversification via transposition and repeat-induced point mutation.
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Affiliation(s)
- Cecilia H. Deng
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
| | - Kim M. Plummer
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Plant Biosecurity Cooperative Research Centre, Bruce, ACT Australia
| | - Darcy A. B. Jones
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Present Address: The Centre for Crop and Disease Management, Curtin University, Bentley, Australia
| | - Carl H. Mesarich
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Present Address: Institute of Agriculture & Environment, Massey University, Palmerston North, New Zealand
| | - Jason Shiller
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Present Address: INRA-Angers, Beaucouzé, Cedex, France
| | - Adam P. Taranto
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Plant Sciences Division, Research School of Biology, The Australian National University, Canberra, Australia
| | - Andrew J. Robinson
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative (VLSCI), Victoria, Australia
| | - Patrick Kastner
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
| | - Nathan E. Hall
- Animal, Plant & Soil Sciences Department, AgriBio Centre for AgriBioscience, La Trobe University, Melbourne, Victoria Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative (VLSCI), Victoria, Australia
| | - Matthew D. Templeton
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
- The School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Joanna K. Bowen
- The New Zealand Institute for Plant & Food Research Limited (PFR), Auckland, New Zealand
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13
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Vincent D, Plummer KM, Solomon PS, Lebrun MH, Job D, Rafiqi M. Editorial: How Can Secretomics Help Unravel the Secrets of Plant-Microbe Interactions? Front Plant Sci 2016; 7:1777. [PMID: 27965687 PMCID: PMC5127848 DOI: 10.3389/fpls.2016.01777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/11/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Delphine Vincent
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, La Trobe UniversityBundoora, VIC, Australia
| | - Kim M. Plummer
- Animal, Plant and Soil Sciences Department, AgriBio, La Trobe UniversityBundoora, VIC, Australia
| | - Peter S. Solomon
- Plant Sciences Division, Research School of Biology, The Australian National UniversityCanberra, ACT, Australia
| | - Marc-Henri Lebrun
- Institut National de la Recherche Agronomique-AgroParisTech, UMR INRA1290, Biologie et Gestion des Risques en Agriculture - Champignons Pathogènes des PlantesThiverval-Grignon, France
| | - Dominique Job
- Centre National de la Recherche-Scientifique, UMR5240 Centre Nationnal de la Recherche Scientifique/University Claude Bernard Lyon 1/INSA/Bayer CropScience Joint Laboratory, Bayer CropScienceLyon, France
| | - Maryam Rafiqi
- Jodrell Laboratory, Royal Botanic GardensKew, London, UK
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14
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Dracatos PM, Payne J, Di Pietro A, Anderson MA, Plummer KM. Plant Defensins NaD1 and NaD2 Induce Different Stress Response Pathways in Fungi. Int J Mol Sci 2016; 17:E1473. [PMID: 27598152 PMCID: PMC5037751 DOI: 10.3390/ijms17091473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 08/04/2016] [Accepted: 08/25/2016] [Indexed: 01/05/2023] Open
Abstract
Nicotiana alata defensins 1 and 2 (NaD1 and NaD2) are plant defensins from the ornamental tobacco that have antifungal activity against a variety of fungal pathogens. Some plant defensins interact with fungal cell wall O-glycosylated proteins. Therefore, we investigated if this was the case for NaD1 and NaD2, by assessing the sensitivity of the three Aspergillus nidulans (An) O-mannosyltransferase (pmt) knockout (KO) mutants (An∆pmtA, An∆pmtB, and An∆pmtC). An∆pmtA was resistant to both defensins, while An∆pmtC was resistant to NaD2 only, suggesting NaD1 and NaD2 are unlikely to have a general interaction with O-linked side chains. Further evidence of this difference in the antifungal mechanism was provided by the dissimilarity of the NaD1 and NaD2 sensitivities of the Fusarium oxysporum f. sp. lycopersici (Fol) signalling knockout mutants from the cell wall integrity (CWI) and high osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathways. HOG pathway mutants were sensitive to both NaD1 and NaD2, while CWI pathway mutants only displayed sensitivity to NaD2.
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Affiliation(s)
- Peter M Dracatos
- Plant Breeding Institute Cobbitty, The University of Sydney, Private Bag 4011, Narellan, NSW 2567, Australia.
| | - Jennifer Payne
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
| | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba 14071, Spain.
| | - Marilyn A Anderson
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia.
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, Bundoora, VIC 3083, Australia.
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15
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Vassiliadis S, Plummer KM, Powell KS, Tr Bicki P, Luck JE, Rochfort SJ. The effect of elevated CO 2 and virus infection on the primary metabolism of wheat. Funct Plant Biol 2016; 43:892-902. [PMID: 32480513 DOI: 10.1071/fp15242] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 05/25/2016] [Indexed: 05/27/2023]
Abstract
Atmospheric CO2 concentrations are predicted to double by the end of this century. Although the effects of CO2 fertilisation in crop systems have been well studied, little is known about the specific interactions among plants, pests and pathogens under a changing climate. This growth chamber study focuses on the interactions among Barley yellow dwarf virus (BYDV), its aphid vector (Rhopalosiphum padi) and wheat (Triticum aestivum L. cv. Yitpi) under ambient (aCO2; 400µmolmol-1) or elevated (eCO2; 650µmolmol-1) CO2 concentrations. eCO2 increased the tiller number and biomass of uninoculated plants and advanced the yellowing symptoms of infected plants. Total foliar C content (percentage of the total DW) increased with eCO2 and with sham inoculation (exposed to early herbivory), whereas total N content decreased with eCO2. Liquid chromatography-mass spectrometry approaches were used to quantify the products of primary plant metabolism. eCO2 significantly increased sugars (fructose, mannitol and trehalose), irrespective of disease status, whereas virus infection significantly increased the amino acids essential to aphid diet (histidine, lysine, phenylalanine and tryptophan) irrespective of CO2 concentration. Citric acid was reduced by both eCO2 and virus infection. Both the potential positive and negative biochemical impacts on wheat, aphid and BYDV interactions are discussed.
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Affiliation(s)
- Simone Vassiliadis
- Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Molecular Phenomics, AgriBio, 5 Ring Road, Bundoora, Vic. 3083, Australia
| | - Kim M Plummer
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Vic. 3083, Australia
| | - Kevin S Powell
- DEDJTR, Biosciences Research, Rutherglen Centre, 124 Chiltern Valley Road, Rutherglen, Vic. 3685, Australia
| | - Piotr Tr Bicki
- DEDJTR, Biosciences Research, Horsham Centre, 110 Natimuk Road, Horsham, Vic. 3685, Australia
| | - Jo E Luck
- Plant Biosecurity Cooperative Research Centre, The University of Melbourne, Burnley Campus, 500 Yarra Boulevard, Richmond, Vic. 3121, Australia
| | - Simone J Rochfort
- Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Molecular Phenomics, AgriBio, 5 Ring Road, Bundoora, Vic. 3083, Australia
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16
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Shiller J, Van de Wouw AP, Taranto AP, Bowen JK, Dubois D, Robinson A, Deng CH, Plummer KM. A Large Family of AvrLm6-like Genes in the Apple and Pear Scab Pathogens, Venturia inaequalis and Venturia pirina. Front Plant Sci 2015; 6:980. [PMID: 26635823 PMCID: PMC4646964 DOI: 10.3389/fpls.2015.00980] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/26/2015] [Indexed: 05/19/2023]
Abstract
Venturia inaequalis and V. pirina are Dothideomycete fungi that cause apple scab and pear scab disease, respectively. Whole genome sequencing of V. inaequalis and V. pirina isolates has revealed predicted proteins with sequence similarity to AvrLm6, a Leptosphaeria maculans effector that triggers a resistance response in Brassica napus and B. juncea carrying the resistance gene, Rlm6. AvrLm6-like genes are present as large families (>15 members) in all sequenced strains of V. inaequalis and V. pirina, while in L. maculans, only AvrLm6 and a single paralog have been identified. The Venturia AvrLm6-like genes are located in gene-poor regions of the genomes, and mostly in close proximity to transposable elements, which may explain the expansion of these gene families. An AvrLm6-like gene from V. inaequalis with the highest sequence identity to AvrLm6 was unable to trigger a resistance response in Rlm6-carrying B. juncea. RNA-seq and qRT-PCR gene expression analyses, of in planta- and in vitro-grown V. inaequalis, has revealed that many of the AvrLm6-like genes are expressed during infection. An AvrLm6 homolog from V. inaequalis that is up-regulated during infection was shown (using an eYFP-fusion protein construct) to be localized to the sub-cuticular stroma during biotrophic infection of apple hypocotyls.
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Affiliation(s)
- Jason Shiller
- Animal, Plant and Soil Sciences Department, AgriBio, AgriBiosciences Research Centre, La Trobe University, MelbourneVIC, Australia
| | | | - Adam P. Taranto
- Animal, Plant and Soil Sciences Department, AgriBio, AgriBiosciences Research Centre, La Trobe University, MelbourneVIC, Australia
- Plant Sciences Division, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Joanna K. Bowen
- The New Zealand Institute for Plant and Food Research LimitedAuckland, New Zealand
| | - David Dubois
- School of BioSciences, University of Melbourne, ParkvilleVIC, Australia
| | - Andrew Robinson
- Animal, Plant and Soil Sciences Department, AgriBio, AgriBiosciences Research Centre, La Trobe University, MelbourneVIC, Australia
- Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, MelbourneVIC, Australia
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research LimitedAuckland, New Zealand
| | - Kim M. Plummer
- Animal, Plant and Soil Sciences Department, AgriBio, AgriBiosciences Research Centre, La Trobe University, MelbourneVIC, Australia
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17
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Cooke IR, Jones D, Bowen JK, Deng C, Faou P, Hall NE, Jayachandran V, Liem M, Taranto AP, Plummer KM, Mathivanan S. Proteogenomic analysis of the Venturia pirina (Pear Scab Fungus) secretome reveals potential effectors. J Proteome Res 2014; 13:3635-44. [PMID: 24965097 DOI: 10.1021/pr500176c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A proteogenomic analysis is presented for Venturia pirina, a fungus that causes scab disease on European pear (Pyrus communis). V. pirina is host-specific, and the infection is thought to be mediated by secreted effector proteins. Currently, only 36 V. pirina proteins are catalogued in GenBank, and the genome sequence is not publicly available. To identify putative effectors, V. pirina was grown in vitro on and in cellophane sheets mimicking its growth in infected leaves. Secreted extracts were analyzed by tandem mass spectrometry, and the data (ProteomeXchange identifier PXD000710) was queried against a protein database generated by combining in silico predicted transcripts with six frame translations of a whole genome sequence of V. pirina (GenBank Accession JEMP00000000 ). We identified 1088 distinct V. pirina protein groups (FDR 1%) including 1085 detected for the first time. Thirty novel (not in silico predicted) proteins were found, of which 14 were identified as potential effectors based on characteristic features of fungal effector protein sequences. We also used evidence from semitryptic peptides at the protein N-terminus to corroborate in silico signal peptide predictions for 22 proteins, including several potential effectors. The analysis highlights the utility of proteogenomics in the study of secreted effectors.
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Affiliation(s)
- Ira R Cooke
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University , Melbourne, Victoria 3086, Australia
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18
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Dracatos PM, van der Weerden NL, Carroll KT, Johnson ED, Plummer KM, Anderson MA. Inhibition of cereal rust fungi by both class I and II defensins derived from the flowers of Nicotiana alata. Mol Plant Pathol 2014; 15:67-79. [PMID: 24015961 PMCID: PMC6638682 DOI: 10.1111/mpp.12066] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Defensins are a large family of small, cysteine-rich, basic proteins, produced by most plants and plant tissues. They have a primary function in defence against fungal disease, although other functions have been described. This study reports the isolation and characterization of a class I secreted defensin (NaD2) from the flowers of Nicotiana alata, and compares its antifungal activity with the class II defensin (NaD1) from N. alata flowers, which is stored in the vacuole. NaD2, like all other class I defensins, lacks the C-terminal pro-peptide (CTPP) characteristic of class II defensins. NaD2 is most closely related to Nt-thionin from N. tabacum (96% identical) and shares 81% identity with MtDef4 from alfalfa. The concentration required to inhibit in vitro fungal growth by 50% (IC50 ) was assessed for both NaD1 and NaD2 for the biotrophic basidiomycete fungi Puccinia coronata f. sp. avenae (Pca) and P. sorghi (Ps), the necrotrophic pathogenic ascomycetes Fusarium oxysporum f. sp. vasinfectum (Fov), F. graminearum (Fgr), Verticillium dahliae (Vd) and Thielaviopsis basicola (Tb), and the saprobe Aspergillus nidulans. NaD1 was a more potent antifungal molecule than NaD2 against both the biotrophic and necrotrophic fungal pathogens tested. NaD2 was 5-10 times less effective at killing necrotrophs, but only two-fold less effective on Puccinia species. A new procedure for testing antifungal proteins is described in this study which is applicable to pathogens with spores that are not amenable to liquid culture, such as rust pathogens. Rusts are the most damaging fungal pathogens of many agronomically important crop species (wheat, barley, oats and soybean). NaD1 and NaD2 inhibited urediniospore germination, germ tube growth and germ tube differentiation (appressoria induction) of both Puccinia species tested. NaD1 and NaD2 were fungicidal on Puccinia species and produced stunted germ tubes with a granular cytoplasm. When NaD1 and NaD2 were sprayed onto susceptible oat plants prior to the plants being inoculated with crown rust, they reduced the number of pustules per leaf area, as well as the amount of chlorosis induced by infection. Similar to observations in vitro, NaD1 was more effective as an antifungal control agent than NaD2. Further investigation revealed that both NaD1 and NaD2 permeabilized the plasma membranes of Puccinia spp. This study provides evidence that both secreted (NaD2) and nonsecreted (NaD1) defensins may be useful for broad-spectrum resistance to pathogens.
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Affiliation(s)
- Peter M Dracatos
- Department of Botany, La Trobe University, Melbourne, Vic., 3086, Australia; La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Vic., 3086, Australia
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Bus VG, Rikkerink EH, Caffier V, Durel CE, Plummer KM. Revision of the Nomenclature of the Differential Host-Pathogen Interactions of Venturia inaequalis and Malus. Annu Rev Phytopathol 2011; 49:391-413. [PMID: 0 DOI: 10.1146/annurev-phyto-072910-095339] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The apple scab (Venturia inaequalis–Malus) pathosystem was one of the first systems for which Flor's concept of gene-for-gene (GfG) relationships between the host plant and the pathogen was demonstrated. There is a rich resource of host resistance genes present in Malus germplasm that could potentially be marshalled to confer durable resistance against this most important apple disease. A comprehensive understanding of the host-pathogen interactions occurring in this pathosystem is a prerequisite for effectively manipulating these host resistance factors. An accurate means of identification of specific resistance and consistent use of gene nomenclature is critical for this process. A set of universally available, differentially resistant hosts is described, which will be followed by a set of defined pathogen races at a later stage. We review pertinent aspects of the history of apple scab research, describe the current status and future directions of this research, and resolve some outstanding issues.
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Affiliation(s)
- Vincent G.M. Bus
- The Plant and Food Research Institute of New Zealand, Private Bag 1401, Havelock North 4157, New Zealand
| | - Erik H.A. Rikkerink
- The Plant and Food Research Institute of New Zealand, Private Bag 92169, Auckland 1142, New Zealand
| | - Valérie Caffier
- INRA, UMR77 Pathologie Végétale – PaVé, INRA/ACO/UA, IFR QUASAV, BP 60057, F-49071 Beaucouzé, France
| | - Charles-Eric Durel
- INRA, UMR 1259 Genetics and Horticulture – GenHort, INRA/ACO/UA, IFR QUASAV, BP 60057, F-49071 Beaucouzé, France
| | - Kim M. Plummer
- La Trobe University, Department of Botany, Bundoora, Vic. 3086, Australia
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Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 2011; 7:e1002230. [PMID: 21876677 PMCID: PMC3158057 DOI: 10.1371/journal.pgen.1002230] [Citation(s) in RCA: 647] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/22/2011] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
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Affiliation(s)
- Joelle Amselem
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Ernesto P. Benito
- Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain
| | | | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | - Ronald P. de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Paul S. Dyer
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Fillinger
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Elisabeth Fournier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD – INRA – SupAgro, Montpellier, France
| | - Lilian Gout
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Matthias Hahn
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Linda Kohn
- Biology Department, University of Toronto, Mississauga, Canada
| | - Nicolas Lapalu
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Kim M. Plummer
- Botany Department, La Trobe University, Melbourne, Australia
| | - Jean-Marc Pradier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Emmanuel Quévillon
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Adeline Simon
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Arjen ten Have
- Instituto de Investigaciones Biologicas – CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Bettina Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Paul Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Marion Andrew
- Biology Department, University of Toronto, Mississauga, Canada
| | | | | | - Rolland Beffa
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Isabelle Benoit
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Ourdia Bouzid
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Baptiste Brault
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mathias Choquer
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Jérome Collémare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Pascale Cotton
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Etienne G. Danchin
- Interactions Biotiques et Santé Plantes, UMR5240, INRA – Université de Nice Sophia-Antipolis – CNRS, Sophia-Antipolis, France
| | | | - Angélique Gautier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Corinne Giraud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Tatiana Giraud
- Laboratoire d'Ecologie, Systématique et Evolution, Université Paris-Sud – CNRS – AgroParisTech, Orsay, France
| | - Celedonio Gonzalez
- Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna, Tenerife, Spain
| | - Sandrine Grossetete
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Ulrich Güldener
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | | | - Chinnappa Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Anne Lappartient
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Michaela Leroch
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Caroline Levis
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Evan Mauceli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cécile Neuvéglise
- Biologie Intégrative du Métabolisme Lipidique Microbien, UMR1319, INRA – Micalis – AgroParisTech, Thiverval-Grignon, France
| | - Birgitt Oeser
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Matthew Pearson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Julie Poulain
- GENOSCOPE, Centre National de Séquençage, Evry, France
| | - Nathalie Poussereau
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Hadi Quesneville
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Christine Rascle
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Julia Schumacher
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Adrienne Sexton
- School of Botany, University of Melbourne, Melbourne, Australia
| | - Evelyn Silva
- Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Catherine Sirven
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Darren M. Soanes
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Matt Templeton
- Plant and Food Research, Mt. Albert Research Centre, Auckland, New Zealand
| | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Hebrew University Jerusalem, Rehovot, Israel
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey A. Rollins
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Marc-Henri Lebrun
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Marty Dickman
- Institute for Plant Genomics and Biotechnology, Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
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Souleyre EJF, Marshall SDG, Oakeshott JG, Russell RJ, Plummer KM, Newcomb RD. Biochemical characterisation of MdCXE1, a carboxylesterase from apple that is expressed during fruit ripening. Phytochemistry 2011; 72:564-71. [PMID: 21315388 DOI: 10.1016/j.phytochem.2011.01.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 01/11/2011] [Accepted: 01/12/2011] [Indexed: 05/10/2023]
Abstract
Esters are an important component of apple (Malus×domestica) flavour. Their biosynthesis increases in response to the ripening hormone ethylene, but their metabolism by carboxylesterases (CXEs) is poorly understood. We have identified 16 members of the CXE multigene family from the commercial apple cultivar, 'Royal Gala', that contain all the conserved features associated with CXE members of the α/β hydrolase fold superfamily. The expression of two genes, MdCXE1 and MdCXE16 was characterised in an apple fruit development series and in a transgenic line of 'Royal Gala' (AO3) that is unable to synthesise ethylene in fruit. In wild-type MdCXE1 is expressed at low levels during early stages of fruit development, rising to a peak of expression in apple fruit at harvest maturity. It is not significantly up-regulated by ethylene in the skin of AO3 fruit. MdCXE16 is expressed constitutively in wild-type throughout fruit development, and is up-regulated by ethylene in skin of AO3 fruit. Semi-purified recombinant MdCXE1 was able to hydrolyse a range of 4-methyl umbelliferyl ester substrates that included those containing acyl moieties that are found in esters produced by apple fruit. Kinetic characterisation of MdCXE1 revealed that the enzyme could be inhibited by organophosphates and that its ability to hydrolyse esters showed increasing affinity (K(m)) but decreasing turnover (k(cat)) as substrate acyl carbon length increases from C2 to C16. Our results suggest that MdCXE1 may have an impact on apple flavour through its ability to hydrolyse relevant flavour esters in ripe apple fruit.
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Affiliation(s)
- Edwige J F Souleyre
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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Abstract
UNLABELLED The fungus Venturia inaequalis infects members of the Maloideae, and causes the disease apple scab, the most important disease of apple worldwide. The early elucidation of the gene-for-gene relationship between V. inaequalis and its host Malus has intrigued plant pathologists ever since, with the identification of 17 resistance (R)-avirulence (Avr) gene pairings. The Avr gene products are presumably a subset of the total effector arsenal of V. inaequalis (predominantly proteins secreted in planta assumed to facilitate infection). The supposition that effectors from V. inaequalis act as suppressors of plant defence is supported by the ability of the pathogen to penetrate the cuticle and differentiate into large pseudoparenchymatous structures, termed stromata, in the subcuticular space, without the initiation of an effective plant defence response. If effectors can be identified that are essential for pathogenicity, the corresponding R genes will be durable and would add significant value to breeding programmes. An R gene cluster in Malus has been cloned, but no V. inaequalis effectors have been characterized at the molecular level. However, the identification of effectors is likely to be facilitated by the resolution of the whole genome sequence of V. inaequalis. TAXONOMY Teleomorph: Venturia inaequalis Cooke (Wint.); Kingdom Fungi; Phylum Ascomycota; Subphylum Euascomycota; Class Dothideomycetes; Family Venturiaceae; genus Venturia; species inaequalis. Anamorph: Fusicladium pomi (Fr.) Lind or Spilocaea pomi (Fr.). LIFE CYCLE: V. inaequalis is a hemibiotroph and overwinters as pseudothecia (sexual fruiting bodies) following a phase of saprobic growth in fallen leaf tissues. The primary inoculum consists of ascospores, which germinate and penetrate the cuticle. Stromata are formed above the epidermal cells but do not penetrate them. Cell wall-degrading enzymes are only produced late in the infection cycle, raising the as yet unanswered question as to how V. inaequalis gains nutrients from the host. Conidia (secondary inoculum) arise from the upper surface of the stromata, and are produced throughout the growing season, initiating multiple rounds of infection. VENTURIA INAEQUALIS AS A MODEL PATHOGEN OF A WOODY HOST: V. inaequalis can be cultured and is amenable to crossing in vitro, enabling map-based cloning strategies. It can be transformed readily, and functional analyses can be conducted by gene silencing. Expressed sequence tag collections are available to aid in gene identification. These will be complemented by the whole genome sequence, which, in turn, will contribute to the comparative analysis of different races of V. inaequalis and plant pathogens within the Dothideomycetes.
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Affiliation(s)
- Joanna K Bowen
- The New Zealand Institute for Plant & Food Research Limited, Mt. Albert Research Centre, Private Bag 92 169, Auckland 1142, New Zealand.
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Bowen JK, Mesarich CH, Rees-George J, Cui W, Fitzgerald A, Win J, Plummer KM, Templeton MD. Candidate effector gene identification in the ascomycete fungal phytopathogen Venturia inaequalis by expressed sequence tag analysis. Mol Plant Pathol 2009; 10:431-48. [PMID: 19400844 PMCID: PMC6640279 DOI: 10.1111/j.1364-3703.2009.00543.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The hemi-biotrophic fungus Venturia inaequalis infects members of the Maloideae, causing the economically important apple disease, scab. The plant-pathogen interaction of Malus and V. inaequalis follows the gene-for-gene model. cDNA libraries were constructed, and bioinformatic analysis of the resulting expressed sequence tags (ESTs) was used to characterize potential effector genes. Effectors are small proteins, secreted in planta, that are assumed to facilitate infection. Therefore, a cDNA library was constructed from a compatible interaction. To distinguish pathogen from plant sequences, the library was probed with genomic DNA from V. inaequalis to enrich for pathogen genes, and cDNA libraries were constructed from in vitro-grown material. A suppression subtractive hybridization library enriched for cellophane-induced genes was included, as growth on cellophane may mimic that in planta, with the differentiation of structures resembling those formed during plant colonization. Clustering of ESTs from the in planta and in vitro libraries indicated a fungal origin of the resulting non-redundant sequence. A total of 937 ESTs was classified as putatively fungal, which could be assembled into 633 non-redundant sequences. Sixteen new candidate effector genes were identified from V. inaequalis based on features common to characterized effector genes from filamentous fungi, i.e. they encode a small, novel, cysteine-rich protein, with a putative signal peptide. Three of the 16 candidates, in particular, conformed to most of the protein structural characteristics expected of fungal effectors and showed significant levels of transcriptional up-regulation during in planta growth. In addition to candidate effector genes, this collection of ESTs represents a valuable genomic resource for V. inaequalis.
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Affiliation(s)
- Joanna K Bowen
- The New Zealand Institute for Plant and Food Research Limited, Mt. Albert Research Centre, Auckland, New Zealand.
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Kucheryava N, Bowen JK, Sutherland PW, Conolly JJ, Mesarich CH, Rikkerink EH, Kemen E, Plummer KM, Hahn M, Templeton MD. Two novel Venturia inaequalis genes induced upon morphogenetic differentiation during infection and in vitro growth on cellophane. Fungal Genet Biol 2008; 45:1329-39. [DOI: 10.1016/j.fgb.2008.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 07/09/2008] [Accepted: 07/15/2008] [Indexed: 11/29/2022]
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Tong X, Zhang X, Plummer KM, Stowell KM, Sullivan PA, Farley PC. GcSTUA, an APSES transcription factor, is required for generation of appressorial turgor pressure and full pathogenicity of Glomerella cingulata. Mol Plant Microbe Interact 2007; 20:1102-11. [PMID: 17849713 DOI: 10.1094/mpmi-20-9-1102] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Glomerella cingulata, which infects a number of different hosts, gains entry to the plant tissue by means of an appressorium. Turgor pressure generated within the appressorium forces a penetration peg through the plant cuticle. A visible lesion forms as the fungus continues to grow within the host. A G. cingulata homolog (GcSTUA) of the genes encoding Asm1, Phd1, Sok2, Efg1, and StuA transcription factors in Magnaporthe grisea and other fungi was cloned and shown to be required for infection of intact apple fruit and penetration of onion epidermal cells. Mobilization of glycogen and triacylglycerol during formation of appressoria by the GcSTUA deletion mutant appeared normal and melanization of the maturing appressoria was also indistinguishable from that of the wild type. However, GcSTUA was essential for the generation of normal turgor pressure within the appressorium. As is the case for its homologs in other fungi, GcSTUA also was required for the formation of aerial hyphae, efficient conidiation, and the formation of perithecia (sexual reproductive structures).
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Affiliation(s)
- XingZhang Tong
- Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand
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Simons JL, Napoli CA, Janssen BJ, Plummer KM, Snowden KC. Analysis of the DECREASED APICAL DOMINANCE genes of petunia in the control of axillary branching. Plant Physiol 2007; 143:697-706. [PMID: 17158589 PMCID: PMC1803742 DOI: 10.1104/pp.106.087957] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 11/29/2006] [Indexed: 05/12/2023]
Abstract
Control of branch development is a major determinant of architecture in plants. Branching in petunia (Petunia hybrida) is controlled by the DECREASED APICAL DOMINANCE (DAD) genes. Gene functions were investigated by plant grafting, morphology studies, double-mutant characterization, and gene expression analysis. Both dad1-1 and dad3 increased branching mutants can be reverted to a near-wild-type phenotype by grafting to a wild-type or a dad2 mutant root stock, indicating that both genes affect the production of a graft-transmissible substance that controls branching. Expression of the DAD1 gene in the stems of grafted plants, detected by quantitative reverse transcription-polymerase chain reaction correlates with the branching phenotype of the plants. The dad2-1 mutant cannot be reverted by grafting, indicating that this gene acts predominantly in the shoot of the plant. Double-mutant analysis indicates that the DAD2 gene acts in the same pathway as the DAD1 and DAD3 genes because the dad1-1dad2-1 and dad2-1dad3 double mutants are indistinguishable from the dad2-1 mutant. However, the dad1-1dad3 double mutant has an additive phenotype, with decreased height of the plants, delayed flowering, and reduced germination rates compared to the single mutants. This result, together with the observation that the dad1-1 and dad3 mutants cannot be reverted by grafting to each other, suggests that the DAD1 and DAD3 genes act in the same pathway, but not in a simple stepwise fashion.
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Affiliation(s)
- Joanne L Simons
- HortResearch, Private Bag 92169, Mt. Albert, Auckland, New Zealand
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Ileperuma NR, Marshall SDG, Squire CJ, Baker HM, Oakeshott JG, Russell RJ, Plummer KM, Newcomb RD, Baker EN. High-resolution crystal structure of plant carboxylesterase AeCXE1, from Actinidia eriantha, and its complex with a high-affinity inhibitor paraoxon. Biochemistry 2007; 46:1851-9. [PMID: 17256879 DOI: 10.1021/bi062046w] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carboxylesterases (CXEs) are widely distributed in plants, where they have been implicated in roles that include plant defense, plant development, and secondary metabolism. We have cloned, overexpressed, purified, and crystallized a carboxylesterase from the kiwifruit species Actinidia eriantha (AeCXE1). The structure of AeCXE1 was determined by X-ray crystallography at 1.4 A resolution. The crystal structure revealed that AeCXE1 is a member of the alpha/beta-hydrolase fold superfamily, most closely related structurally to the hormone-sensitive lipase subgroup. The active site of the enzyme, located in an 11 A deep hydrophobic gorge, contains the conserved catalytic triad residues Ser169, Asp276, and His306. Kinetic analysis using artificial ester substrates showed that the enzyme can hydrolyze a range of carboxylester substrates with acyl groups ranging from C2 to C16, with a preference for butyryl moieties. This preference was supported by the discovery of a three-carbon acyl adduct bound to the active site Ser169 in the native structure. AeCXE1 was also found to be inhibited by organophosphates, with paraoxon (IC50 = 1.1 muM) a more potent inhibitor than dimethylchlorophosphate (DMCP; IC50 = 9.2 muM). The structure of AeCXE1 with paraoxon bound was determined at 2.3 A resolution and revealed that the inhibitor binds covalently to the catalytic serine residue, with virtually no change in the structure of the enzyme. The structural information for AeCXE1 provides a basis for addressing the wider functional roles of carboxylesterases in plants.
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Turner CT, Davy MW, MacDiarmid RM, Plummer KM, Birch NP, Newcomb RD. RNA interference in the light brown apple moth, Epiphyas postvittana (Walker) induced by double-stranded RNA feeding. Insect Mol Biol 2006; 15:383-91. [PMID: 16756557 DOI: 10.1111/j.1365-2583.2006.00656.x] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
RNA interference (RNAi) or gene silencing is typically induced in insects by the injection of double-stranded RNAs (dsRNAs), short interfering RNAs, or through the use of hairpin constructs in transgenic insects. Here we demonstrate in the horticultural pest, Epiphyas postvittana (Lepidoptera: Tortricidae), that RNAi can be triggered by oral delivery of dsRNA to larvae. Transcript levels of a larval gut carboxylesterase gene (EposCXE1) were reduced to less than half that of controls within 2 days of being fed EposCXE1 dsRNA. Transcript levels of the pheromone binding protein gene (EposPBP1) were reduced in adult antennae by feeding larvae EposPBP1 dsRNA. Knockdown of EposPBP1 transcripts was observed for the first 2 days after adult eclosion but recovered to wild-type levels at 4 days posteclosion. The potential mechanisms involved in the initiation, movement and amplification of the silencing signal are discussed.
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Affiliation(s)
- C T Turner
- The Horticulture and Food Research Institute of New Zealand Ltd, Auckland, New Zealand
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Abstract
The study of gene function in filamentous fungi is a field of research that has made great advances in very recent years. A number of transformation and gene manipulation strategies have been developed and applied to a diverse and rapidly expanding list of economically important filamentous fungi and oomycetes. With the significant number of fungal genomes now sequenced or being sequenced, functional genomics promises to uncover a great deal of new information in coming years. This review discusses recent advances that have been made in examining gene function in filamentous fungi and describes the advantages and limitations of the different approaches.
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Affiliation(s)
- Richard J Weld
- National Centre for Advanced Bio-Protection Technologies, PO Box 84, Lincoln University, Canterbury 8150, New Zealand.
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Bus VGM, Laurens FND, van de Weg WE, Rusholme RL, Rikkerink EHA, Gardiner SE, Bassett HCM, Kodde LP, Plummer KM. The Vh8 locus of a new gene-for-gene interaction between Venturia inaequalis and the wild apple Malus sieversii is closely linked to the Vh2 locus in Malus pumila R12740-7A. New Phytol 2005; 166:1035-49. [PMID: 15869661 DOI: 10.1111/j.1469-8137.2005.01395.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The wild apple (Malus sieversii) is a large-fruited species from Central Asia, which is used as a source of scab resistance in cultivar breeding. Phytopathological tests with races of Venturia inaequalis were performed to differentiate scab-resistance genes in Malus as well as an avirulence gene in the pathogen. A novel gene-for-gene interaction between V. inaequalis and Malus was identified. The locus of the scab-resistance gene Vh8 is linked with, or possibly allelic to, that of the Vh2 gene in Malus pumila Russian apple R12740-7A, at the lower end of linkage group 2 of Malus. Race 8 isolate NZ188B.2 is compatible with Vh8, suggesting the loss or modification of the complementary AvrVh8 gene, while isolate 1639 overcomes both Vh2 and Vh8, but is incompatible with at least one other gene not detected by any of the other race isolates tested. Our research is the first to differentiate scab-resistance genes in a putative gene cluster in apple with the aid of races of V. inaequalis.
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Affiliation(s)
- Vincent G M Bus
- The Horticulture and Food Research Institute of New Zealand Ltd, Hawkes Bay Research Centre, Havelock North, Private Bag 1401, New Zealand.
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Fitzgerald A, Van Kan JAL, Plummer KM. Simultaneous silencing of multiple genes in the apple scab fungus, Venturia inaequalis, by expression of RNA with chimeric inverted repeats. Fungal Genet Biol 2004; 41:963-71. [PMID: 15341918 DOI: 10.1016/j.fgb.2004.06.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2004] [Accepted: 06/28/2004] [Indexed: 11/24/2022]
Abstract
RNA-mediated gene silencing has been demonstrated in plants, animals, and more recently in filamentous fungi. Here, we report high frequency, RNA-mediated gene silencing in the apple scab fungus, Venturia inaequalis. The green fluorescent protein (GFP) transgene was silenced in a GFP-expressing transformant. An endogenous gene, trihydroxynaphthalene reductase (THN), involved in melanin biosynthesis, was also silenced. Silencing of these two genes resulted in obvious phenotypes in vitro. High frequency gene silencing was achieved using hairpin constructs for the GFP or the THN genes transferred by Agrobacterium (71 and 61%, respectively). THN-silenced transformants exhibited a distinctive light brown phenotype and maintained the ability to infect apple. Of significance was the simultaneous silencing of the two genes from a single chimeric, inverted repeat hairpin construct. Silencing of both genes with this construct occurred at a frequency of 51% of all the transformants. All 125 colonies silenced for the GFP gene were also silenced for THN. As THN and GFP silenced transformants have readily detectable phenotypes, the genes have utility as markers for gene silencing. Simultaneous, multiple gene silencing, utilising such marker genes, will enable the development of high through-put screening for functional genomics. This chimeric technology will be particularly valuable when linked with silenced genes that have no obvious phenotype in vitro.
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Affiliation(s)
- Anna Fitzgerald
- Plant Health and Development, Horticulture and Food Research Institute of New Zealand Ltd., Auckland, New Zealand
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Marshall SDG, Putterill JJ, Plummer KM, Newcomb RD. The carboxylesterase gene family from Arabidopsis thaliana. J Mol Evol 2004; 57:487-500. [PMID: 14738307 DOI: 10.1007/s00239-003-2492-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2003] [Accepted: 05/12/2003] [Indexed: 11/29/2022]
Abstract
Carboxylesterases hydrolyze esters of short-chain fatty acids and have roles in animals ranging from signal transduction to xenobiotic detoxification. In plants, however, little is known of their roles. We have systematically mined the genome from the model plant Arabidopsis thaliana for carboxylesterase genes and studied their distribution in the genome and expression profile across a range of tissues. Twenty carboxylesterase genes (AtCXE) were identified. The AtCXE family shares conserved sequence motifs and secondary structure characteristics with carboxylesterases and other members of the larger alpha/beta hydrolase fold superfamily of enzymes. Phylogenetic analysis of the AtCXE genes together with other plant carboxylesterases distinguishes seven distinct clades, with an Arabidopsis thaliana gene represented in six of the seven clades. The AtCXE genes are widely distributed across the genome (present in four of five chromosomes), with the exception of three clusters of tandemly duplicated genes. Of the interchromosomal duplication events, two have been mediated through newly identified partial chromosomal duplication events that also include other genes surrounding the AtCXE loci. Eighteen of the 20 AtCXE genes are expressed over a broad range of tissues, while the remaining 2 (unrelated) genes are expressed only in the flowers and siliques. Finally, hypotheses for the functional roles of the AtCXE family members are presented based on the phylogenetic relationships with other plant carboxylesterases of known function, their expression profile, and knowledge of likely esterase substrates found in plants.
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Affiliation(s)
- Sean D G Marshall
- Mt Albert Research Centre, HortResearch, Private Bag 92 169, Mt Albert, Auckland, New Zealand
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Fitzgerald AM, Mudge AM, Gleave AP, Plummer KM. Agrobacterium and PEG-mediated transformation of the phytopathogen Venturia inaequalis. Mycol Res 2003; 107:803-10. [PMID: 12967207 DOI: 10.1017/s0953756203008086] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report the development of two new transformation systems, polyethylene glycol (PEG)-mediated transformation of protoplasts and Agrobacterium tumefaciens-mediated transformation of mycelium, for the filamentous ascomycete Venturia inaequalis. New binary vectors have been created for the latter. Although transformation was initially achieved using a PEG-mediated method, this was superseded by the A. tumefaciens-mediated approach. The advantages of the latter include: ease of the protocol, no requirement for protoplasts; higher transformation efficiency; and single-site integration. A comparison between the two transformation methods is presented.
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Affiliation(s)
- Anna M Fitzgerald
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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Stehmann C, Pennycook S, Plummer KM. Molecular Identification of a Sexual Interloper: The Pear Pathogen, Venturia pirina, has Sex on Apple. Phytopathology 2001; 91:633-641. [PMID: 18942992 DOI: 10.1094/phyto.2001.91.7.633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Venturia pirina (the pear scab pathogen) and V. inaequalis (the apple scab pathogen) were detected as ascospores discharged from apple leaf litter in New Zealand (spring 1998). Pseudothecia of both species were located on dead apple leaves; however, only those of V. inaequalis were associated with scab lesions. V. pirina was identified by rDNA sequence analyses, because morphological characters could not distinguish this fungus from V. asperata (a rare saprophyte on apple) and other Venturia spp. pathogenic on rosaceous fruit trees. Species-specific polymerase chain reaction primers designed to the 18S end of the internal transcribed spacer 1 region differentiated Venturia fruit tree pathogens reliably. V. pirina field isolates were pathogenic on pear, but only weak saprophytes on apple. In rare instances, when appressoria of V. pirina appeared to penetrate the cuticle of apple leaves, epidermal cells responded with a localized hypersensitive response (HR). To our knowledge, this is the first report of induction of HR-like events by V. pirina on its nonhost, apple, and also the first record of sexual reproduction of V. pirina on apple. It is assumed that V. pirina pseudothecia formed from saprophytic lesions in senescing apple leaves when active defense mechanisms such as HR were no longer induced.
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Crowhurst RN, Binnie SJ, Bowen JK, Hawthorne BT, Plummer KM, Rees-George J, Rikkerink EH, Templeton MD. Effect of disruption of a cutinase gene (cutA) on virulence and tissue specificity of Fusarium solani f. sp. cucurbitae race 2 toward Cucurbita maxima and C. moschata. Mol Plant Microbe Interact 1997; 10:355-368. [PMID: 9100380 DOI: 10.1094/mpmi.1997.10.3.355] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A 3.9-kb genomic DNA fragment from the cucurbit pathogen Fusarium solani f. sp. cucurbitae race 2 was cloned. Sequence analysis revealed an open reading frame of 690 nucleotides interrupted by a single 51-bp intron. The nucleotide and predicted amino acid sequences showed 92 and 98% identity, respectively, to those of the cutA gene of the pea pathogen F. solani f. sp. pisi. A gene replacement vector was constructed and used to generate cutA- mutants that were detected with a polymerase chain reaction (PCR) assay. Seventy-one cutA- mutants were identified among the 416 transformants screened. Vector integration was assessed by Southern analysis in 23 of these mutants. PCR and Southern analysis data showed the level of homologous integration was 14%. Disruption of the cutA locus in mutants was confirmed by RNA gel blot hybridization. Neither virulence on Cucurbita maxima cv. Delica at any of six different inoculum concentrations, nor pathogenicity on intact fruit of four different species or cultivars of cucurbit or hypocotyl tissue of C. maxima cv. Crown, was found to be affected by disruption of the cutA gene.
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Affiliation(s)
- R N Crowhurst
- Molecular Genetics Group, Horticulture and Food Research Institute of New Zealand Ltd., Auckland.
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Abstract
Pulsed field gel electrophoresis experiments show that chromosomal length polymorphisms are produced during meiosis in the ascomycetous plant pathogen Leptosphaeria maculans. Homologues in tetrads of L. maculans were identified on the basis of their binding to chromosome-specific probes that included beta-tubulin, nitrate reductase, 18S ribosomal DNA and two Random Amplified Polymorphic DNA (RAPD) markers. Changes in size of homologues were followed during meiosis. Significant karyotype variation was evident due to the random assortment of parental homologues of different sizes. In most cases, the progeny had the same-sized homologues as the parents; however, in some instances novel-sized homologues were detected that varied in size from those of the parents by up to 50 kb. Our results are consistent with the hypothesis that these novel chromosomal length polymorphisms are produced by reciprocal recombination between parental homologous chromosomes of unequal sizes.
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Affiliation(s)
- K M Plummer
- Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, VIC, Australia
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Salisbury PA, Ballinger DJ, Wratten N, Plummer KM, Howlett BJ. Blackleg disease on oilseed Brassica in Australia: a review. ACTA ACUST UNITED AC 1995. [DOI: 10.1071/ea9950665] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Blackleg, caused by the fungus Leptosphaeria maculans, is the major disease of canola (Brassica napus) in Australia. The development of blackleg-resistant B. napus varieties has been a major factor in the resurgence of the industry nationwide. The main sources of resistance used in Australian public breeding programs are Japanese spring varieties and French winter varieties. In these programs, all early generation material is screened in field blackleg nurseries sown on, or adjacent to, infested canola stubble from the previous season. Little is known about the genetic control of resistance, and the mechanisms responsible for generating pathogenic variability of L. maculans isolates in Australia is largely uncharacterised. Australian B. napus varieties are the most blackleg-resistant spring varieties in the world. Apart from growing blackleg-resistant varieties, other strategies that minimise infection and delay any breakdown in varietal resistance include growing canola on the same area only once every 3 years, destroying stubble, and eradicating volunteer plants between cropping seasons. Additionally, strategic use of chemicals can provide effective control to supplement varietal resistance in areas prone to severe blackleg infestation.
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Abstract
Chromosomal DNA of Australian field-isolates of the phytopathogenic ascomycete Leptosphaeria maculans was resolved by pulsed-field gel electrophoresis. All isolates examined had highly variable karyotypes. Ascospores (sexual spores) derived from single pseudothecia (sexual fruiting bodies) isolated from Brassica napus (oilseed rape) stubble were analyzed. In two tetrads four distinct karyotypes were observed, with only one chromosomal DNA band in common to all the members of each tetrad. Although isolates had highly variable karyotypes, two overall patterns were present. In one pattern there were at least 12 chromosomal DNA bands, the largest being greater than 2.2 Mb in size; in the other there were more than 15 chromosomal DNA bands, the largest being about 2.0 Mb. The chromosomal DNA preparations included mitochondrial DNA which migrated as a diffuse band between 0.10 and 0.15 Mb in size, and DNA molecules of 8 and 9 kb in size.
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Affiliation(s)
- K M Plummer
- Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, Victoria, Australia
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