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Jimenez-Lopez JC, Singh KB, Clemente A, Czubinski J, Ochatt S, Von Wettberg E, Smýkal P. Editorial: Legumes for global food security - volume II. Front Plant Sci 2023; 14:1273600. [PMID: 37794927 PMCID: PMC10545871 DOI: 10.3389/fpls.2023.1273600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Affiliation(s)
- Jose C. Jimenez-Lopez
- Department of Stress, Development and Signaling in Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Karam B. Singh
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Perth, WA, Australia
| | - Alfonso Clemente
- Department of Nutrition and Sustainable Animal Production, Estación Experimental del Zaidin, Spanish National Research Council (CSIC), Granada, Spain
| | - Jaroslaw Czubinski
- Department of Biochemistry and Food Analysis, Poznan University of Life Sciences, Poznan, Poland
| | - Sergio Ochatt
- Agroécologie, Institut National de Recherche pour l’Agriculture, l’alimentation et l’Environnement (INRAE), Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Eric Von Wettberg
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, United States
| | - Petr Smýkal
- Department of Botany, Palacký University in Olomouc, Olomouc, Czechia
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Lima-Cabello E, Escudero-Feliu J, Peralta-Leal A, Garcia-Fernandez P, Siddique KHM, Singh KB, Núñez MI, León J, Jimenez-Lopez JC. β-Conglutins' Unique Mobile Arm Is a Key Structural Domain Involved in Molecular Nutraceutical Properties of Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2023; 24:7676. [PMID: 37108842 PMCID: PMC10143110 DOI: 10.3390/ijms24087676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Narrow-leafed lupin (NLL; Lupinus angustifolius L.) has multiple nutraceutical properties that may result from unique structural features of β-conglutin proteins, such as the mobile arm at the N-terminal, a structural domain rich in α-helices. A similar domain has not been found in other vicilin proteins of legume species. We used affinity chromatography to purify recombinant complete and truncated (without the mobile arm domain, tβ5 and tβ7) forms of NLL β5 and β7 conglutin proteins. We then used biochemical and molecular biology techniques in ex vivo and in vitro systems to evaluate their anti-inflammatory activity and antioxidant capacity. The complete β5 and β7 conglutin proteins decreased pro-inflammatory mediator levels (e.g., nitric oxide), mRNA expression levels (iNOS, TNFα, IL-1β), and the protein levels of pro-inflammatory cytokine TNF-α, interleukins (IL-1β, IL-2, IL-6, IL-8, IL-12, IL-17, IL-27), and other mediators (INFγ, MOP, S-TNF-R1/-R2, and TWEAK), and exerted a regulatory oxidative balance effect in cells as demonstrated in glutathione, catalase, and superoxide dismutase assays. The truncated tβ5 and tβ7 conglutin proteins did not have these molecular effects. These results suggest that β5 and β7 conglutins have potential as functional food components due to their anti-inflammatory and oxidative cell state regulatory properties, and that the mobile arm of NLL β-conglutin proteins is a key domain in the development of nutraceutical properties, making NLL β5 and β7 excellent innovative candidates as functional foods.
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Affiliation(s)
- Elena Lima-Cabello
- Spanish National Research Council (CSIC), Estacion Experimental del Zaidin, Department of Stress, Development and Signaling in Plants, E-18008 Granada, Spain
| | - Julia Escudero-Feliu
- Spanish National Research Council (CSIC), Estacion Experimental del Zaidin, Department of Stress, Development and Signaling in Plants, E-18008 Granada, Spain
- Biosanitary Research Institute of Granada (ibs. GRANADA), E-18012 Granada, Spain
| | - Andreina Peralta-Leal
- Spanish National Research Council (CSIC), Estacion Experimental del Zaidin, Department of Stress, Development and Signaling in Plants, E-18008 Granada, Spain
| | - Pedro Garcia-Fernandez
- Research Centre for Information and Communications Technologies (CITIC-UGR), University of Granada, E-18071 Granada, Spain
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
| | - Karam B. Singh
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
- CSIRO Agriculture and Food, Floreat, WA 6014, Australia
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Maria I. Núñez
- Biosanitary Research Institute of Granada (ibs. GRANADA), E-18012 Granada, Spain
- Biopathology and Regenerative Medicine Institute (IBIMER), University of Granada, E-18100 Granada, Spain
- Department of Radiology and Physical Medicine, Faculty of Medicine, University of Granada, E-18016 Granada, Spain
| | - Josefa León
- Biosanitary Research Institute of Granada (ibs. GRANADA), E-18012 Granada, Spain
- Clinical Management Unit of Digestive Disease and UNAI, San Cecilio University Hospital, E-18006 Granada, Spain
| | - Jose C. Jimenez-Lopez
- Spanish National Research Council (CSIC), Estacion Experimental del Zaidin, Department of Stress, Development and Signaling in Plants, E-18008 Granada, Spain
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
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Garg G, Kamphuis LG, Bayer PE, Kaur P, Dudchenko O, Taylor CM, Frick KM, Foley RC, Gao L, Aiden EL, Edwards D, Singh KB. A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits. Plant J 2022; 111:1252-1266. [PMID: 35779281 PMCID: PMC9544533 DOI: 10.1111/tpj.15885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 06/02/2023]
Abstract
Narrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten-free, non-genetically modified, alternative protein source to soybean (Glycine max) and as such has gained interest as a human food ingredient. Here, we present a chromosome-length reference genome for the species and a pan-genome assembly comprising 55 NLL lines, including Australian and European cultivars, breeding lines and wild accessions. We present the core and variable genes for the species and report on the absence of essential mycorrhizal associated genes. The genome and pan-genomes of NLL and its close relative white lupin (Lupinus albus) are compared. Furthermore, we provide additional evidence supporting LaRAP2-7 as the key alkaloid regulatory gene for NLL and demonstrate the NLL genome is underrepresented in classical NLR disease resistance genes compared to other sequenced legume species. The NLL genomic resources generated here coupled with previously generated RNA sequencing datasets provide new opportunities to fast-track lupin crop improvement.
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Affiliation(s)
- Gagan Garg
- CSIRO Agriculture and FoodFloreatWA6014Australia
| | - Lars G. Kamphuis
- CSIRO Agriculture and FoodFloreatWA6014Australia
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWA6009Australia
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWA6102Australia
| | - Philipp E. Bayer
- The School of Biological SciencesUniversity of Western AustraliaCrawleyWA6009Australia
| | - Parwinder Kaur
- School of Agriculture and Environment, University of Western AustraliaCrawleyWA6009Australia
| | - Olga Dudchenko
- Center for Genome Architecture, Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
- Center for Theoretical Biological PhysicsRice UniversityHoustonTX77005USA
| | - Candy M. Taylor
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWA6009Australia
- School of Agriculture and Environment, University of Western AustraliaCrawleyWA6009Australia
| | - Karen M. Frick
- CSIRO Agriculture and FoodFloreatWA6014Australia
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | | | | | - Erez Lieberman Aiden
- School of Agriculture and Environment, University of Western AustraliaCrawleyWA6009Australia
- Center for Genome Architecture, Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
- Center for Theoretical Biological PhysicsRice UniversityHoustonTX77005USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTechPudongChina
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - David Edwards
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWA6009Australia
- The School of Biological SciencesUniversity of Western AustraliaCrawleyWA6009Australia
| | - Karam B. Singh
- CSIRO Agriculture and FoodFloreatWA6014Australia
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWA6009Australia
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWA6102Australia
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Edwards O, Jander G, Ochman H, Schuurink R, Singh KB. Insects Co-opt Host Genes to Overcome Plant Defences. Fac Rev 2022; 11:10. [PMID: 35574173 DOI: 10.12703/r-01-000007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Insect pests of plants, such as whiteflies, cause immense economic damage both through direct feeding and by transmitting viruses. In a major breakthrough, a paper by Xia et al.1 shows that some whiteflies have co-opted a gene from their plant host that has helped them neutralize a key component of the plant's defense. Plants produce a range of toxins as part of their defense against insect predation, and Xia et al. 1 show that, through a horizontal gene transfer (HGT) event from plant to insect, some whiteflies have acquired a gene whose original function was to protect the plants themselves from such damaging toxins through chemical modification that converts them to less harmful forms. Targeting of this gene in whiteflies using RNAi technology provided effective resistance in this ground-breaking study, which should lead others interested in crop protection to explore genes that have been transferred from plants to insects.
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John E, Jacques S, Phan HTT, Liu L, Pereira D, Croll D, Singh KB, Oliver RP, Tan KC. Variability in an effector gene promoter of a necrotrophic fungal pathogen dictates epistasis and effector-triggered susceptibility in wheat. PLoS Pathog 2022; 18:e1010149. [PMID: 34990464 PMCID: PMC8735624 DOI: 10.1371/journal.ppat.1010149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/26/2021] [Indexed: 12/31/2022] Open
Abstract
The fungus Parastagonospora nodorum uses proteinaceous necrotrophic effectors (NEs) to induce tissue necrosis on wheat leaves during infection, leading to the symptoms of septoria nodorum blotch (SNB). The NEs Tox1 and Tox3 induce necrosis on wheat possessing the dominant susceptibility genes Snn1 and Snn3B1/Snn3D1, respectively. We previously observed that Tox1 is epistatic to the expression of Tox3 and a quantitative trait locus (QTL) on chromosome 2A that contributes to SNB resistance/susceptibility. The expression of Tox1 is significantly higher in the Australian strain SN15 compared to the American strain SN4. Inspection of the Tox1 promoter region revealed a 401 bp promoter genetic element in SN4 positioned 267 bp upstream of the start codon that is absent in SN15, called PE401. Analysis of the world-wide P. nodorum population revealed that a high proportion of Northern Hemisphere isolates possess PE401 whereas the opposite was observed in representative P. nodorum isolates from Australia and South Africa. The presence of PE401 removed the epistatic effect of Tox1 on the contribution of the SNB 2A QTL but not Tox3. PE401 was introduced into the Tox1 promoter regulatory region in SN15 to test for direct regulatory roles. Tox1 expression was markedly reduced in the presence of PE401. This suggests a repressor molecule(s) binds PE401 and inhibits Tox1 transcription. Infection assays also demonstrated that P. nodorum which lacks PE401 is more pathogenic on Snn1 wheat varieties than P. nodorum carrying PE401. An infection competition assay between P. nodorum isogenic strains with and without PE401 indicated that the higher Tox1-expressing strain rescued the reduced virulence of the lower Tox1-expressing strain on Snn1 wheat. Our study demonstrated that Tox1 exhibits both 'selfish' and 'altruistic' characteristics. This offers an insight into a complex NE-NE interaction that is occurring within the P. nodorum population. The importance of PE401 in breeding for SNB resistance in wheat is discussed.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Huyen T. T. Phan
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Lifang Liu
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
| | - Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Karam B. Singh
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, Western Australia, Australia
| | | | - Kar-Chun Tan
- Centre for Crop and Disease Management, Curtin University, Bentley, Perth, Western Australia, Australia
- Curtin University, Bentley, Perth, Western Australia, Australia
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Taylor CM, Garg G, Berger JD, Ribalta FM, Croser JS, Singh KB, Cowling WA, Kamphuis LG, Nelson MN. A Trimethylguanosine Synthase1-like (TGS1) homologue is implicated in vernalisation and flowering time control. Theor Appl Genet 2021; 134:3411-3426. [PMID: 34258645 PMCID: PMC8440268 DOI: 10.1007/s00122-021-03910-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/06/2021] [Indexed: 05/30/2023]
Abstract
KEY MESSAGE A plant-specific Trimethylguanosine Synthase1-like homologue was identified as a candidate gene for the efl mutation in narrow-leafed lupin, which alters phenology by reducing vernalisation requirement. The vernalisation pathway is a key component of flowering time control in plants from temperate regions but is not well understood in the legume family. Here we examined vernalisation control in the temperate grain legume species, narrow-leafed lupin (Lupinus angustifolius L.), and discovered a candidate gene for an ethylene imine mutation (efl). The efl mutation changes phenology from late to mid-season flowering and additionally causes transformation from obligate to facultative vernalisation requirement. The efl locus was mapped to pseudochromosome NLL-10 in a recombinant inbred line (RIL) mapping population developed by accelerated single seed descent. Candidate genes were identified in the reference genome, and a diverse panel of narrow-leafed lupins was screened to validate mutations specific to accessions with efl. A non-synonymous SNP mutation within an S-adenosyl-L-methionine-dependent methyltransferase protein domain of a Trimethylguanosine Synthase1-like (TGS1) orthologue was identified as the candidate mutation giving rise to efl. This mutation caused substitution of an amino acid within an established motif at a position that is otherwise highly conserved in several plant families and was perfectly correlated with the efl phenotype in F2 and F6 genetic population and a panel of diverse accessions, including the original efl mutant. Expression of the TGS1 homologue did not differ between wild-type and efl genotypes, supporting altered functional activity of the gene product. This is the first time a TGS1 orthologue has been associated with vernalisation response and flowering time control in any plant species.
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Affiliation(s)
- Candy M Taylor
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Gagan Garg
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA, 6014, Australia
| | - Jens D Berger
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA, 6014, Australia
| | - Federico M Ribalta
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
| | - Janine S Croser
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Karam B Singh
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA, 6014, Australia
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia
| | - Wallace A Cowling
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6009, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Lars G Kamphuis
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA, 6014, Australia
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia
| | - Matthew N Nelson
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Floreat, WA, 6014, Australia
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Belt K, Foley RC, O'Sullivan CA, Roper MM, Singh KB, Thatcher LF. A Plant Stress-Responsive Bioreporter Coupled With Transcriptomic Analysis Allows Rapid Screening for Biocontrols of Necrotrophic Fungal Pathogens. Front Mol Biosci 2021; 8:708530. [PMID: 34540894 PMCID: PMC8446517 DOI: 10.3389/fmolb.2021.708530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Streptomyces are soil-borne Actinobacteria known to produce a wide range of enzymes, phytohormones, and metabolites including antifungal compounds, making these microbes fitting for use as biocontrol agents in agriculture. In this study, a plant reporter gene construct comprising the biotic stress-responsive glutathione S-transferase promoter GSTF7 linked to a luciferase output (GSTF7:luc) was used to screen a collection of Actinobacteria candidates for manipulation of plant biotic stress responses and their potential as biocontrol agents. We identified a Streptomyces isolate (KB001) as a strong candidate and demonstrated successful protection against two necrotrophic fungal pathogens, Sclerotinia sclerotiorum and Rhizoctonia solani, but not against a bacterial pathogen (Pseudomonas syringe). Treatment of Arabidopsis plants with either KB001 microbial culture or its secreted compounds induced a range of stress and defense response-related genes like pathogenesis-related (PR) and hormone signaling pathways. Global transcriptomic analysis showed that both treatments shared highly induced expression of reactive oxygen species and auxin signaling pathways at 6 and 24 h posttreatment, while some other responses were treatment specific. This study demonstrates that GSTF7 is a suitable marker for the rapid and preliminary screening of beneficial bacteria and selection of candidates with potential for application as biocontrols in agriculture, including the Streptomyces KB001 that was characterized here, and could provide protection against necrotrophic fungal pathogens.
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Affiliation(s)
- Katharina Belt
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Floreat, WA, Australia
| | - Rhonda C Foley
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Floreat, WA, Australia
| | - Cathryn A O'Sullivan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, St Lucia, QLD, Australia
| | - Margaret M Roper
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Floreat, WA, Australia
| | - Karam B Singh
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Floreat, WA, Australia
| | - Louise F Thatcher
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Acton, ACT, Australia
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Sperschneider J, Jones AW, Nasim J, Xu B, Jacques S, Zhong C, Upadhyaya NM, Mago R, Hu Y, Figueroa M, Singh KB, Stone EA, Schwessinger B, Wang MB, Taylor JM, Dodds PN. The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylation. BMC Biol 2021; 19:203. [PMID: 34526021 PMCID: PMC8444563 DOI: 10.1186/s12915-021-01123-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Background Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms of epigenetic silencing in the fungal kingdom have remained elusive. Results We use sRNA sequencing and methylation data to gain insight into epigenetics in the dikaryotic fungus Puccinia graminis f. sp. tritici (Pgt), which causes the devastating stem rust disease on wheat. We use Hi-C data to define the Pgt centromeres and show that they are repeat-rich regions (~250 kb) that are highly diverse in sequence between haplotypes and, like in plants, are enriched for young TEs. DNA cytosine methylation is particularly active at centromeres but also associated with genome-wide control of young TE insertions. Strikingly, over 90% of Pgt sRNAs and several RNAi genes are differentially expressed during infection. Pgt induces waves of functionally diversified sRNAs during infection. The early wave sRNAs are predominantly 21 nts with a 5′ uracil derived from genes. In contrast, the late wave sRNAs are mainly 22-nt sRNAs with a 5′ adenine and are strongly induced from centromeric regions. TEs that overlap with late wave sRNAs are more likely to be methylated, both inside and outside the centromeres, and methylated TEs exhibit a silencing effect on nearby genes. Conclusions We conclude that rust fungi use an epigenetic silencing pathway that might have similarity with RdDM in plants. The Pgt RNAi machinery and sRNAs are under tight temporal control throughout infection and might ensure genome stability during sporulation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01123-z.
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Affiliation(s)
- Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, Australia. .,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
| | - Ashley W Jones
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Jamila Nasim
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Bo Xu
- Thermo Fisher Scientific, 5 Caribbean Drive, Scoresby, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Australia
| | - Chengcheng Zhong
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Narayana M Upadhyaya
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Yiheng Hu
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Karam B Singh
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Australia.,Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, Australia
| | - Eric A Stone
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | - Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia
| | - Ming-Bo Wang
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Jennifer M Taylor
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
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John E, Singh KB, Oliver RP, Tan K. Transcription factor control of virulence in phytopathogenic fungi. Mol Plant Pathol 2021; 22:858-881. [PMID: 33973705 PMCID: PMC8232033 DOI: 10.1111/mpp.13056] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 09/22/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Plant-pathogenic fungi are a significant threat to economic and food security worldwide. Novel protection strategies are required and therefore it is critical we understand the mechanisms by which these pathogens cause disease. Virulence factors and pathogenicity genes have been identified, but in many cases their roles remain elusive. It is becoming increasingly clear that gene regulation is vital to enable plant infection and transcription factors play an essential role. Efforts to determine their regulatory functions in plant-pathogenic fungi have expanded since the annotation of fungal genomes revealed the ubiquity of transcription factors from a broad range of families. This review establishes the significance of transcription factors as regulatory elements in plant-pathogenic fungi and provides a systematic overview of those that have been functionally characterized. Detailed analysis is provided on regulators from well-characterized families controlling various aspects of fungal metabolism, development, stress tolerance, and the production of virulence factors such as effectors and secondary metabolites. This covers conserved transcription factors with either specialized or nonspecialized roles, as well as recently identified regulators targeting key virulence pathways. Fundamental knowledge of transcription factor regulation in plant-pathogenic fungi provides avenues to identify novel virulence factors and improve our understanding of the regulatory networks linked to pathogen evolution, while transcription factors can themselves be specifically targeted for disease control. Areas requiring further insight regarding the molecular mechanisms and/or specific classes of transcription factors are identified, and direction for future investigation is presented.
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Affiliation(s)
- Evan John
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern AustraliaAustralia
| | - Richard P. Oliver
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kar‐Chun Tan
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern AustraliaAustralia
- School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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Kidd BN, Foley R, Singh KB, Anderson JP. Foliar resistance to Rhizoctonia solani in Arabidopsis is compromised by simultaneous loss of ethylene, jasmonate and PEN2 mediated defense pathways. Sci Rep 2021; 11:2546. [PMID: 33510286 PMCID: PMC7843637 DOI: 10.1038/s41598-021-81858-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/06/2021] [Indexed: 11/09/2022] Open
Abstract
Rhizoctonia solani causes damaging yield losses on most major food crops. R. solani isolates belonging to anastomosis group 8 (AG8) are soil-borne, root-infecting pathogens with a broad host range. AG8 isolates can cause disease on wheat, canola and legumes, however Arabidopsis thaliana is heretofore thought to possess non-host resistance as A. thaliana ecotypes, including the reference strain Col-0, are resistant to AG8 infection. Using a mitochondria-targeted redox sensor (mt-roGFP2) and cell death staining, we demonstrate that both AG8 and a host isolate (AG2-1) of R. solani are able to infect A. thaliana roots. Above ground tissue of A. thaliana was found to be resistant to AG8 but not AG2. Genetic analysis revealed that ethylene, jasmonate and PENETRATION2-mediated defense pathways work together to provide resistance to AG8 in the leaves which subsequently enable tolerance of root infections. Overall, we demonstrate a significant difference in defense capabilities of above and below ground tissue in providing resistance to R. solani AG8 in Arabidopsis.
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Affiliation(s)
- Brendan N Kidd
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, Australia.,Australian Reseach Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Rhonda Foley
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, Australia
| | - Karam B Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, Australia.,Department of Environment and Agriculture, Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia.,The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Jonathan P Anderson
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, Australia. .,The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
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11
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Jacques S, Sperschneider J, Garg G, Thatcher LF, Gao LL, Kamphuis LG, Singh KB. A functional genomics approach to dissect spotted alfalfa aphid resistance in Medicago truncatula. Sci Rep 2020; 10:22159. [PMID: 33335168 PMCID: PMC7746763 DOI: 10.1038/s41598-020-78904-z] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/01/2020] [Indexed: 12/03/2022] Open
Abstract
Aphids are virus-spreading insect pests affecting crops worldwide and their fast population build-up and insecticide resistance make them problematic to control. Here, we aim to understand the molecular basis of spotted alfalfa aphid (SAA) or Therioaphis trifolii f. maculata resistance in Medicago truncatula, a model organism for legume species. We compared susceptible and resistant near isogenic Medicago lines upon SAA feeding via transcriptome sequencing. Expression of genes involved in defense and stress responses, protein kinase activity and DNA binding were enriched in the resistant line. Potentially underlying some of these changes in gene expression was the finding that members of the MYB, NAC, AP2 domain and ERF transcription factor gene families were differentially expressed in the resistant versus susceptible lines. A TILLING population created in the resistant cultivar was screened using exome capture sequencing and served as a reverse genetics tool to functionally characterise genes involved in the aphid resistance response. This screening revealed three transcription factors (a NAC, AP2 domain and ERF) as important regulators in the defence response, as a premature stop-codon in the resistant background led to a delay in aphid mortality and enhanced plant susceptibility. This combined functional genomics approach will facilitate the future development of pest resistant crops by uncovering candidate target genes that can convey enhanced aphid resistance.
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Affiliation(s)
- Silke Jacques
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia.,Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2600, Australia
| | - Gagan Garg
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
| | | | - Ling-Ling Gao
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
| | - Lars G Kamphuis
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia.,Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia.,The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Karam B Singh
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia. .,Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia. .,The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia.
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12
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Jimenez-Lopez JC, Singh KB, Clemente A, Nelson MN, Ochatt S, Smith PMC. Editorial: Legumes for Global Food Security. Front Plant Sci 2020; 11:926. [PMID: 32733508 PMCID: PMC7359862 DOI: 10.3389/fpls.2020.00926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/05/2020] [Indexed: 05/30/2023]
Affiliation(s)
- Jose C. Jimenez-Lopez
- Department of Biochemistry, Cell & Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Karam B. Singh
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Perth, WA, Australia
| | - Alfonso Clemente
- Department of Physiology and Biochemistry of Animal Nutrition, Estación Experimental del Zaidín, Spanish National Research Council (CSIC), Granada, Spain
| | - Matthew N. Nelson
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Perth, WA, Australia
| | - Sergio Ochatt
- Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne, Dijon, France
| | - Penelope M. C. Smith
- Legumes for Sustainable Agriculture, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia
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13
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Zhang L, Kamphuis LG, Guo Y, Jacques S, Singh KB, Gao LL. Ethylene Is Not Essential for R-Gene Mediated Resistance but Negatively Regulates Moderate Resistance to Some Aphids in Medicago truncatula. Int J Mol Sci 2020; 21:ijms21134657. [PMID: 32629952 PMCID: PMC7369913 DOI: 10.3390/ijms21134657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 05/30/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 02/02/2023] Open
Abstract
Ethylene is important for plant responses to environmental factors. However, little is known about its role in aphid resistance. Several types of genetic resistance against multiple aphid species, including both moderate and strong resistance mediated by R genes, have been identified in Medicago truncatula. To investigate the potential role of ethylene, a M. truncatula ethylene- insensitive mutant, sickle, was analysed. The sickle mutant occurs in the accession A17 that has moderate resistance to Acyrthosiphon kondoi, A. pisum and Therioaphis trifolii. The sickle mutant resulted in increased antibiosis-mediated resistance against A. kondoi and T. trifolii but had no effect on A. pisum. When sickle was introduced into a genetic background carrying resistance genes, AKR (A. kondoi resistance), APR (A. pisum resistance) and TTR (T. trifolii resistance), it had no effect on the strong aphid resistance mediated by these genes, suggesting that ethylene signaling is not essential for their function. Interestingly, for the moderate aphid resistant accession, the sickle mutant delayed leaf senescence following aphid infestation and reduced the plant biomass losses caused by both A. kondoi and T. trifolii. These results suggest manipulation of the ethylene signaling pathway could provide aphid resistance and enhance plant tolerance against aphid feeding.
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Affiliation(s)
- Lijun Zhang
- CSIRO Agriculture and Food, Wembley, WA 6014, Australia; (L.Z.); (L.G.K.); (Y.G.); (S.J.)
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China
| | - Lars G. Kamphuis
- CSIRO Agriculture and Food, Wembley, WA 6014, Australia; (L.Z.); (L.G.K.); (Y.G.); (S.J.)
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA 6009, Australia
| | - Yanqiong Guo
- CSIRO Agriculture and Food, Wembley, WA 6014, Australia; (L.Z.); (L.G.K.); (Y.G.); (S.J.)
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China
| | - Silke Jacques
- CSIRO Agriculture and Food, Wembley, WA 6014, Australia; (L.Z.); (L.G.K.); (Y.G.); (S.J.)
- College of Plant Protection, Shanxi Agricultural University, Taigu 030801, China
| | - Karam B. Singh
- CSIRO Agriculture and Food, Wembley, WA 6014, Australia; (L.Z.); (L.G.K.); (Y.G.); (S.J.)
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA 6009, Australia
- Correspondence: (K.B.S.); (L.-L.G.); Tel.:+61-8-9333-6320 (K.B.S.); Fax: +61-8-9387-8991 (K.B.S.)
| | - Ling-Ling Gao
- CSIRO Agriculture and Food, Wembley, WA 6014, Australia; (L.Z.); (L.G.K.); (Y.G.); (S.J.)
- Correspondence: (K.B.S.); (L.-L.G.); Tel.:+61-8-9333-6320 (K.B.S.); Fax: +61-8-9387-8991 (K.B.S.)
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Jacques S, Reidy-Crofts J, Sperschneider J, Kamphuis LG, Gao LL, Edwards OR, Singh KB. An RNAi supplemented diet as a reverse genetics tool to control bluegreen aphid, a major pest of legumes. Sci Rep 2020; 10:1604. [PMID: 32005880 PMCID: PMC6994723 DOI: 10.1038/s41598-020-58442-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 06/14/2019] [Accepted: 01/14/2020] [Indexed: 11/25/2022] Open
Abstract
Aphids are important agricultural pests causing major yield losses worldwide. Since aphids can rapidly develop resistance to chemical insecticides there is an urgent need to find alternative aphid pest management strategies. Despite the economic importance of bluegreen aphid (Acyrthosiphon kondoi), very few genetic resources are available to expand our current understanding and help find viable control solutions. An artificial diet is a desirable non-invasive tool to enable the functional characterisation of genes in bluegreen aphid and discover candidate target genes for future use in RNA interference (RNAi) mediated crop protection against aphids. To date no artificial diet has been developed for bluegreen aphid, so we set out to develop a suitable diet by testing and optimising existing diets. Here, we describe an artificial diet for rearing bluegreen aphid and also provide a proof of concept for the supplementation of the diet with RNAi molecules targeting the salivary gland transcript C002 and gap gene hunchback, resulting in bluegreen aphid mortality which has not yet been documented in this species. Managing this pest, for example via RNAi delivery through artificial feeding will be a major improvement to test bluegreen aphid candidate target genes for future pest control and gain significant insights into bluegreen aphid gene function.
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Affiliation(s)
- Silke Jacques
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
- Curtin University, Centre for Crop and Disease Management, Bentley, WA, 6102, Australia
| | - Jenny Reidy-Crofts
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2600, Australia
| | - Lars G Kamphuis
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
- Curtin University, Centre for Crop and Disease Management, Bentley, WA, 6102, Australia
| | - Ling-Ling Gao
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
| | - Owain R Edwards
- Centre for Environment and Life Sciences, CSIRO Land and Water, Floreat, WA, 6014, Australia
| | - Karam B Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Floreat, WA, 6014, Australia.
- Curtin University, Centre for Crop and Disease Management, Bentley, WA, 6102, Australia.
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15
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Kamphuis LG, Klingler JP, Jacques S, Gao LL, Edwards OR, Singh KB. Additive and epistatic interactions between AKR and AIN loci conferring bluegreen aphid resistance and hypersensitivity in Medicago truncatula. J Exp Bot 2019; 70:4887-4902. [PMID: 31087095 PMCID: PMC6760273 DOI: 10.1093/jxb/erz222] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
Aphids, including the bluegreen aphid (BGA; Acyrthosiphon kondoi), are important pests in agriculture. Two BGA resistance genes have been identified in the model legume Medicago truncatula, namely AKR (Acyrthosiphon kondoi resistance) and AIN (Acyrthosiphon induced necrosis). In this study, progeny derived from a cross between a resistant accession named Jester and a highly susceptible accession named A20 were used to study the interaction between the AKR and AIN loci with respect to BGA performance and plant response to BGA infestation. These studies demonstrated that AKR and AIN have additive effects on the BGA resistance phenotype. However, AKR exerts dominant suppression epistasis on AIN-controlled macroscopic necrotic lesions. Nevertheless, both AKR and AIN condition production of H2O2 at the BGA feeding site. Electrical penetration graph analysis demonstrated that AKR prevents phloem sap ingestion, irrespective of the presence of AIN. Similarly, the jasmonic acid defense signaling pathway is recruited by AKR, irrespective of AIN. This research identifies an enhancement of aphid resistance through gene stacking, and insights into the interaction of distinct resistance genes against insect pests.
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Affiliation(s)
- Lars G Kamphuis
- CSIRO Agriculture and Food, Floreat, Australia
- UWA Institute of Agriculture, Crawley, Australia
- Curtin University, Centre for Crop and Disease Management, Bentley, Australia
| | | | - Silke Jacques
- CSIRO Agriculture and Food, Floreat, Australia
- Curtin University, Centre for Crop and Disease Management, Bentley, Australia
| | | | | | - Karam B Singh
- CSIRO Agriculture and Food, Floreat, Australia
- UWA Institute of Agriculture, Crawley, Australia
- Curtin University, Centre for Crop and Disease Management, Bentley, Australia
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16
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Frick KM, Foley RC, Siddique KHM, Singh KB, Kamphuis LG. The role of jasmonate signalling in quinolizidine alkaloid biosynthesis, wounding and aphid predation response in narrow-leafed lupin. Funct Plant Biol 2019; 46:443-454. [PMID: 30940332 DOI: 10.1071/fp18278] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 01/17/2019] [Indexed: 05/24/2023]
Abstract
Quinolizidine alkaloids (QAs) are toxic secondary metabolites produced in lupin species that protect the plant against insects. They form in vegetative tissues and accumulate to a different extent in the grains: high levels in 'bitter' narrow-leafed lupin (NLL) and low levels in 'sweet' NLL. Grain QA levels vary considerably, and sometimes exceed the industry limit for food and feed purposes. We hypothesised that jasmonates regulate QA biosynthesis in response to environmental stresses such as wounding and aphid predation, which may explain non-genetic variability in grain QA levels. Methyl jasmonate (MeJA)-inducible genes were identified and verified in NLL. Exogenous MeJA application-induced expression of QA biosynthetic genes and QA levels for bitter, but not sweet NLL. Although MeJA-inducible genes responded to wounding, the expression of QA biosynthetic genes was not induced for bitter and sweet NLL. We assessed the effect of aphid predation on QA production for two cultivars - one moderately resistant and one susceptible to aphid predation. Although MeJA-inducible genes responded to aphid predation, no change in QA levels was found for either cultivar. These findings offer insights into the regulation of QA biosynthesis in bitter and sweet NLL and concludes that aphids are not a concern for increasing grain QAs in NLL cultivars.
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Affiliation(s)
- Karen M Frick
- UWA School of Agriculture and Environment, The University of Western Australia, LB 5005, Perth, WA 6001, Australia; and CSIRO Agriculture and Food, 147 Underwood Avenue, Floreat, WA 6014, Australia; and The UWA Institute of Agriculture, The University of Western Australia, LB 5005, Perth, WA 6001, Australia; and Present address: Section for Plant Biochemistry, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Rhonda C Foley
- CSIRO Agriculture and Food, 147 Underwood Avenue, Floreat, WA 6014, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, LB 5005, Perth, WA 6001, Australia
| | - Karam B Singh
- CSIRO Agriculture and Food, 147 Underwood Avenue, Floreat, WA 6014, Australia; and The UWA Institute of Agriculture, The University of Western Australia, LB 5005, Perth, WA 6001, Australia; and Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Lars G Kamphuis
- CSIRO Agriculture and Food, 147 Underwood Avenue, Floreat, WA 6014, Australia; and The UWA Institute of Agriculture, The University of Western Australia, LB 5005, Perth, WA 6001, Australia; and Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia; and Corresponding author.
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Thatcher LF, Singh KB. The Arabidopsis altered in stress response2 is Impaired in Resistance to Root and Leaf Necrotrophic Fungal Pathogens. Plants (Basel) 2019; 8:E60. [PMID: 30862010 PMCID: PMC6473459 DOI: 10.3390/plants8030060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
The Arabidopsis thaliana Glutathione S-transferase Phi8 (GSTF8) gene is recognised as a marker for early defence and stress responses. To identify regulators of these responses, a forward genetic screen for Arabidopsis mutants with up-regulated GSTF8 promoter activity was conducted by screening a mutagenized population containing a GSTF8 promoter fragment fused to the luciferase reporter gene (GSTF8:LUC). We previously identified several enhanced stress response (esr) mutants from this screen that conferred constitutive GSTF8:LUC activity and increased resistance to several pathogens and/or insects pests. Here we identified a further mutant constitutively expressing GSTF8:LUC and termed altered in stress response2 (asr2). Unlike the esr mutants, asr2 was more susceptible to disease symptom development induced by two necrotrophic fungal pathogens; the root pathogen Fusarium oxysporum, and the leaf pathogen Alternaria brassicicola. The asr2 allele was mapped to a 2.1 Mbp region of chromosome 2 and narrowed to four candidate loci.
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Affiliation(s)
- Louise F Thatcher
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913, Australia.
| | - Karam B Singh
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913, Australia.
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia.
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DeBoer K, Melser S, Sperschneider J, Kamphuis LG, Garg G, Gao LL, Frick K, Singh KB. Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development. BMC Genomics 2019; 20:135. [PMID: 30764773 PMCID: PMC6376761 DOI: 10.1186/s12864-019-5521-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 02/20/2018] [Accepted: 02/07/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown. RESULTS By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse. CONCLUSION This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development.
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Affiliation(s)
- Kathleen DeBoer
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
| | - Su Melser
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Present address: INSERM U1215, Neurocentre Magendie, Bordeaux, France
| | - Jana Sperschneider
- Centre for Genomics, Metabolomics and Bioinformatics (CGMB), The Australian National University, Canberra, ACT 2601 Australia
| | - Lars G. Kamphuis
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Curtin University, Centre for Crop and Disease Management, Department of Environment and Agriculture, Bentley, WA 6102 Australia
| | - Gagan Garg
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
| | - Ling-Ling Gao
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
| | - Karen Frick
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- The School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Karam B. Singh
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
- CSIRO Agriculture and Food, Private Bag 5, Wembley, WA 6913 Australia
- Curtin University, Centre for Crop and Disease Management, Department of Environment and Agriculture, Bentley, WA 6102 Australia
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Taylor CM, Kamphuis LG, Zhang W, Garg G, Berger JD, Mousavi‐Derazmahalleh M, Bayer PE, Edwards D, Singh KB, Cowling WA, Nelson MN. INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow-leafed lupin (Lupinus angustifolius L.). Plant Cell Environ 2019; 42:174-187. [PMID: 29677403 PMCID: PMC7379684 DOI: 10.1111/pce.13320] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 01/12/2018] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 05/02/2023]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) cultivation was transformed by 2 dominant vernalization-insensitive, early flowering time loci known as Ku and Julius (Jul), which allowed expansion into shorter season environments. However, reliance on these loci has limited genetic and phenotypic diversity for environmental adaptation in cultivated lupin. We recently predicted that a 1,423-bp deletion in the cis-regulatory region of LanFTc1, a FLOWERING LOCUS T (FT) homologue, derepressed expression of LanFTc1 and was the underlying cause of the Ku phenotype. Here, we surveyed diverse germplasm for LanFTc1 cis-regulatory variation and identified 2 further deletions of 1,208 and 5,162 bp in the 5' regulatory region, which overlap the 1,423-bp deletion. Additionally, we confirmed that no other polymorphisms were perfectly associated with vernalization responsiveness. Phenotyping and gene expression analyses revealed that Jul accessions possessed the 5,162-bp deletion and that the Jul and Ku deletions were equally capable of removing vernalization requirement and up-regulating gene expression. The 1,208-bp deletion was associated with intermediate phenology, vernalization responsiveness, and gene expression and therefore may be useful for expanding agronomic adaptation of lupin. This insertion/deletion series may also help resolve how the vernalization response is mediated at the molecular level in legumes.
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Affiliation(s)
- Candy M. Taylor
- UWA School of Agriculture and EnvironmentThe University of Western AustraliaPerthWestern Australia6009Australia
| | - Lars G. Kamphuis
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern Australia6014Australia
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern Australia6102Australia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern Australia6009Australia
| | - Weilu Zhang
- UWA School of Agriculture and EnvironmentThe University of Western AustraliaPerthWestern Australia6009Australia
| | - Gagan Garg
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern Australia6014Australia
| | - Jens D. Berger
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern Australia6014Australia
| | - Mahsa Mousavi‐Derazmahalleh
- UWA School of Agriculture and EnvironmentThe University of Western AustraliaPerthWestern Australia6009Australia
| | - Philipp E. Bayer
- School of Biological SciencesThe University of Western AustraliaPerthWestern Australia6009Australia
| | - David Edwards
- School of Biological SciencesThe University of Western AustraliaPerthWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern Australia6009Australia
| | - Karam B. Singh
- Agriculture and FoodCommonwealth Scientific and Industrial Research OrganisationFloreatWestern Australia6014Australia
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWestern Australia6102Australia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern Australia6009Australia
| | - Wallace A. Cowling
- UWA School of Agriculture and EnvironmentThe University of Western AustraliaPerthWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern Australia6009Australia
| | - Matthew N. Nelson
- UWA School of Agriculture and EnvironmentThe University of Western AustraliaPerthWestern Australia6009Australia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern Australia6009Australia
- Natural Capital and Plant HealthRoyal Botanic Gardens, KewArdinglyWest SussexRH17 6TNUK
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Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. Mol Plant Pathol 2018; 19:2094-2110. [PMID: 29569316 PMCID: PMC6638006 DOI: 10.1111/mpp.12682] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 05/14/2023]
Abstract
Plant-pathogenic fungi secrete effector proteins to facilitate infection. We describe extensive improvements to EffectorP, the first machine learning classifier for fungal effector prediction. EffectorP 2.0 is now trained on a larger set of effectors and utilizes a different approach based on an ensemble of classifiers trained on different subsets of negative data, offering different views on classification. EffectorP 2.0 achieves an accuracy of 89%, compared with 82% for EffectorP 1.0 and 59.8% for a small size classifier. Important features for effector prediction appear to be protein size, protein net charge as well as the amino acids serine and cysteine. EffectorP 2.0 decreases the number of predicted effectors in secretomes of fungal plant symbionts and saprophytes by 40% when compared with EffectorP 1.0. However, EffectorP 1.0 retains value, and combining EffectorP 1.0 and 2.0 results in a stringent classifier with a low false positive rate of 9%. EffectorP 2.0 predicts significant enrichments of effectors in 12 of 13 sets of infection-induced proteins from diverse fungal pathogens, whereas a small cysteine-rich classifier detects enrichment in only seven of 13. EffectorP 2.0 will fast track the prioritization of high-confidence effector candidates for functional validation and aid in improving our understanding of effector biology. EffectorP 2.0 is available at http://effectorp.csiro.au.
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Affiliation(s)
- Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and FoodPerth, WA 6014Australia
| | - Peter N. Dodds
- Black Mountain Laboratories, CSIRO Agriculture and FoodCanberra, ACT 2601Australia
| | - Donald M. Gardiner
- CSIRO Agriculture and FoodQueensland Bioscience PrecinctBrisbane, Qld 4067Australia
| | - Karam B. Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and FoodPerth, WA 6014Australia
- Department of Environment and Agriculture, Centre for Crop and Disease ManagementCurtin UniversityBentley, WA 6102Australia
| | - Jennifer M. Taylor
- Black Mountain Laboratories, CSIRO Agriculture and FoodCanberra, ACT 2601Australia
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Frick KM, Foley RC, Kamphuis LG, Siddique KHM, Garg G, Singh KB. Characterization of the genetic factors affecting quinolizidine alkaloid biosynthesis and its response to abiotic stress in narrow-leafed lupin (Lupinus angustifolius L.). Plant Cell Environ 2018; 41:2155-2168. [PMID: 29473655 DOI: 10.1111/pce.13172] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 12/19/2017] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Quinolizidine alkaloids (QAs) are toxic secondary metabolites that complicate the end use of narrow-leafed lupin (NLL; Lupinus angustifolius L.) grain, as levels sometimes exceed the industry limit for its use as a food and feed source. The genotypic and environmental influences on QA production in NLL are poorly understood. Here, the expression of QA biosynthetic genes was analysed in vegetative and reproductive tissues of bitter (high QA) and sweet (low QA) accessions. It was demonstrated that sweet accessions are characterized by lower QA biosynthetic gene expression exclusively in leaf and stem tissues than bitter NLL, consistent with the hypothesis that QAs are predominantly produced in aerial tissues and transported to seeds, rather than synthesized within the seed itself. This analysis informed our identification of additional candidate genes involved in QA biosynthesis. Drought and temperature stress are two major abiotic stresses that often occur during NLL pod set. Hence, we assessed the effect of drought, increased temperature, and their combination, on QA production in three sweet NLL cultivars. A cultivar-specific response to drought and temperature in grain QA levels was observed, including the identification of a cultivar where alkaloid levels did not change with these stress treatments.
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Affiliation(s)
- Karen M Frick
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6001, Australia
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Rhonda C Foley
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
| | - Lars G Kamphuis
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
| | - Gagan Garg
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
| | - Karam B Singh
- CSIRO Agriculture and Food, Floreat, WA, 6014, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, 6102, Australia
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Mousavi-Derazmahalleh M, Bayer PE, Nevado B, Hurgobin B, Filatov D, Kilian A, Kamphuis LG, Singh KB, Berger JD, Hane JK, Edwards D, Erskine W, Nelson MN. Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin. Theor Appl Genet 2018; 131:887-901. [PMID: 29353413 PMCID: PMC5852200 DOI: 10.1007/s00122-017-3045-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 11/10/2017] [Indexed: 05/18/2023]
Abstract
KEY MESSAGE This first pan-Mediterranean analysis of genetic diversity in wild narrow-leafed lupin revealed strong East-West genetic differentiation of populations, an historic eastward migration, and signatures of genetic adaptation to climatic variables. Most grain crops suffer from a narrow genetic base, which limits their potential for adapting to new challenges such as increased stresses associated with climate change. Plant breeders are returning to the wild ancestors of crops and their close relatives to broaden the genetic base of their crops. Understanding the genetic adaptation of these wild relatives will help plant breeders most effectively use available wild diversity. Here, we took narrow-leafed lupin (Lupinus angustifolius L.) as a model to understand adaptation in a wild crop ancestor. A set of 142 wild accessions of narrow-leafed lupin from across the Mediterranean basin were subjected to genotyping-by-sequencing using Diversity Arrays Technology. Phylogenetic, linkage disequilibrium and demographic analyses were employed to explore the history of narrow-leafed lupin within the Mediterranean region. We found strong genetic differentiation between accessions from the western and eastern Mediterranean, evidence of an historic West to East migration, and that eastern Mediterranean narrow-leafed lupin experienced a severe and recent genetic bottleneck. We showed that these two populations differ for flowering time as a result of local adaptation, with the West flowering late while the East flowers early. A genome-wide association study identified single nucleotide polymorphism markers associated with climatic adaptation. Resolving the origin of wild narrow-leafed lupin and how its migration has induced adaptation to specific regions of the Mediterranean serves as a useful resource not only for developing narrow-leafed lupin cultivars with greater resilience to a changing climate, but also as a model which can be applied to other legumes.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Philipp E. Bayer
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Bhavna Hurgobin
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | | | - Lars G. Kamphuis
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - Karam B. Singh
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - Jens D. Berger
- CSIRO Agriculture and Food, Wembley, WA 6913 Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - James K. Hane
- CCDM Bioinformatics, Centre for Crop Disease Management, Curtin University, Bentley, WA 6102 Australia
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
| | - William Erskine
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
- Centre for Plant Genetics and Breeding, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Matthew N. Nelson
- UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009 Australia
- Natural Capital and Plant Health, Royal Botanic Gardens Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
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Sperschneider J, Dodds PN, Singh KB, Taylor JM. ApoplastP: prediction of effectors and plant proteins in the apoplast using machine learning. New Phytol 2018; 217:1764-1778. [PMID: 29243824 DOI: 10.1111/nph.14946] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/07/2017] [Indexed: 05/18/2023]
Abstract
The plant apoplast is integral to intercellular signalling, transport and plant-pathogen interactions. Plant pathogens deliver effectors both into the apoplast and inside host cells, but no computational method currently exists to discriminate between these localizations. We present ApoplastP, the first method for predicting whether an effector or plant protein localizes to the apoplast. ApoplastP uncovers features of apoplastic localization common to both effectors and plant proteins, namely depletion in glutamic acid, acidic amino acids and charged amino acids and enrichment in small amino acids. ApoplastP predicts apoplastic localization in effectors with a sensitivity of 75% and a false positive rate of 5%, improving the accuracy of cysteine-rich classifiers by > 13%. ApoplastP does not depend on the presence of a signal peptide and correctly predicts the localization of unconventionally secreted proteins. The secretomes of fungal saprophytes as well as necrotrophic, hemibiotrophic and extracellular fungal pathogens are enriched for predicted apoplastic proteins. Rust pathogens have low proportions of predicted apoplastic proteins, but these are highly enriched for predicted effectors. ApoplastP pioneers apoplastic localization prediction using machine learning. It will facilitate functional studies and will be valuable for predicting if an effector localizes to the apoplast or if it enters plant cells.
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Affiliation(s)
- Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, 6014, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Karam B Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, 6014, Australia
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, WA, 6102, Australia
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
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Lima-Cabello E, Morales-Santana S, Foley RC, Melser S, Alché V, Siddique KH, Singh KB, Alché JD, Jimenez-Lopez JC. Ex vivo and in vitro assessment of anti-inflammatory activity of seed β-conglutin proteins from Lupinus angustifolius. J Funct Foods 2018. [DOI: 10.1016/j.jff.2017.11.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Anderson JP, Sperschneider J, Win J, Kidd B, Yoshida K, Hane J, Saunders DGO, Singh KB. Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors. Sci Rep 2017; 7:10410. [PMID: 28874693 PMCID: PMC5585356 DOI: 10.1038/s41598-017-10405-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/07/2017] [Indexed: 11/17/2022] Open
Abstract
Rhizoctonia solani is a fungal pathogen causing substantial damage to many of the worlds’ largest food crops including wheat, rice, maize and soybean. Despite impacting global food security, little is known about the pathogenicity mechanisms employed by R. solani. To enable prediction of effectors possessing either broad efficacy or host specificity, a combined secretome was constructed from a monocot specific isolate, a dicot specific isolate and broad host range isolate infecting both monocot and dicot hosts. Secretome analysis suggested R. solani employs largely different virulence mechanisms to well-studied pathogens, despite in many instances infecting the same host plants. Furthermore, the secretome of the broad host range AG8 isolate may be shaped by maintaining functions for saprophytic life stages while minimising opportunities for host plant recognition. Analysis of possible co-evolution with host plants and in-planta up-regulation in particular, aided identification of effectors including xylanase and inhibitor I9 domain containing proteins able to induce cell death in-planta. The inhibitor I9 domain was more abundant in the secretomes of a wide range of necrotising fungi relative to biotrophs. These findings provide novel targets for further dissection of the virulence mechanisms and potential avenues to control this under-characterised but important pathogen.
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Affiliation(s)
- Jonathan P Anderson
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia. .,The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia.
| | | | - Joe Win
- The Sainsbury Laboratory, Norwich, UK
| | - Brendan Kidd
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia
| | | | - James Hane
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia.,Curtin University, Bentley, Western Australia, Australia
| | - Diane G O Saunders
- The Sainsbury Laboratory, Norwich, UK.,The John Innes Centre, Norwich, UK
| | - Karam B Singh
- CSIRO Agriculture and Food, Floreat, Western Australia, Australia.,The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
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Liu Y, Hassan S, Kidd BN, Garg G, Mathesius U, Singh KB, Anderson JP. Ethylene Signaling Is Important for Isoflavonoid-Mediated Resistance to Rhizoctonia solani in Roots of Medicago truncatula. Mol Plant Microbe Interact 2017; 30:691-700. [PMID: 28510484 DOI: 10.1094/mpmi-03-17-0057-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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
The root-infecting necrotrophic fungal pathogen Rhizoctoniasolani causes significant disease to all the world's major food crops. As a model for pathogenesis of legumes, we have examined the interaction of R. solani AG8 with Medicago truncatula. RNAseq analysis of the moderately resistant M. truncatula accession A17 and highly susceptible sickle (skl) mutant (defective in ethylene sensing) identified major early transcriptional reprogramming in A17. Responses specific to A17 included components of ethylene signaling, reactive oxygen species metabolism, and consistent upregulation of the isoflavonoid biosynthesis pathway. Mass spectrometry revealed accumulation of the isoflavonoid-related compounds liquiritigenin, formononetin, medicarpin, and biochanin A in A17. Overexpression of an isoflavone synthase in M. truncatula roots increased isoflavonoid accumulation and resistance to R. solani. Addition of exogenous medicarpin suggested this phytoalexin may be one of several isoflavonoids required to contribute to resistance to R. solani. Together, these results provide evidence for the role of ethylene-mediated accumulation of isoflavonoids during defense against root pathogens in legumes. The involvement of ethylene signaling and isoflavonoids in the regulation of both symbiont-legume and pathogen-legume interactions in the same tissue may suggest tight regulation of these responses are required in the root tissue.
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Affiliation(s)
- Yao Liu
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
- 2 Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Samira Hassan
- 3 Research School of Biology, Australian National University, Canberra, Australian Capital Territory; and
| | - Brendan N Kidd
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
| | - Gagan Garg
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
| | - Ulrike Mathesius
- 3 Research School of Biology, Australian National University, Canberra, Australian Capital Territory; and
| | - Karam B Singh
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
- 4 The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia
| | - Jonathan P Anderson
- 1 CSIRO Agriculture and Food, Floreat, Western Australia
- 4 The UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia
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Dixit M, Singh KB, Prakash R, Singh D. Functional block of IL-17 cytokine promotes bone healing by augmenting FOXO1 and ATF4 activity in cortical bone defect model. Osteoporos Int 2017; 28:2207-2220. [PMID: 28341898 DOI: 10.1007/s00198-017-4012-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/15/2017] [Indexed: 01/08/2023]
Abstract
UNLABELLED We determine the effect of interleukin (IL)-17 neutralizing antibody on new bone regeneration. Anti-IL-17 antibody promoted new bone regeneration in cortical bone defect model by augmenting FOXO1 and ATF4 activity thereby decreasing oxidative stress. Our study demonstrates the bone healing and regeneration potential of neutralizing IL-17antibody in osteoporotic fractures. INTRODUCTION The immune system plays important role in the fracture healing process. However, fracture healing is prolonged in disorders associated with systemic inflammation. Fracture healing is decelerated in osteoporosis, condition linked with systemic inflammation. Bone regeneration therapies like recombinant human BMP2 are associated with serious side effects. Studies have been carried out where agents like denosumab and infliximab enhance bone regeneration in osteoporotic conditions. Our previous studies show the osteoprotective and immunoprotective effects of neutralizing IL-17 antibody. Here, we determine the effect of IL-17 neutralizing antibody on new bone regeneration and compare its efficacy with known osteoporotic therapies. METHODS For the study, female BALB/c mice were ovariectomized or sham operated and left for a month followed by a 0.6-mm drill-hole injury in femur mid-diaphysis. The treatment was commenced next day onwards with anti-IL-17, anti-RANKL (Receptor activator of nuclear factor kappa-B ligand), parathyroid hormone (PTH), or alendronate for a period of 3, 10, or 21 days. Animals were then autopsied, and femur bones were dissected out for micro-CT scanning, confocal microscopy, and gene and protein expression studies. RESULTS Micro-CT analysis showed that anti-IL-17 antibody promoted bone healing at days 10 and 21, and the healing effect observed was significantly better than Ovx, anti-RANKL antibody, and ALN, and equal to PTH. Anti-IL-17 also enhanced new bone regeneration as assessed by calcein-labeling studies. Additionally, anti-IL-17 therapy enhanced expression of osteogenic markers and decreased oxidative stress at the injury site. CONCLUSION Overall, our study demonstrates bone healing and regeneration potential of neutralizing IL-17 antibody in osteoporotic fractures.
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Affiliation(s)
- M Dixit
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Lucknow, India
| | - K B Singh
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Lucknow, India
| | - R Prakash
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Lucknow, India
| | - D Singh
- Division of Endocrinology and Centre for Research in Anabolic Skeletal Targets in Health and Illness (ASTHI), CSIR-Central Drug Research Institute, B.S. 10/1, Sector-10, Jankipuram Extension, Lucknow, India.
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Belt K, Huang S, Thatcher LF, Casarotto H, Singh KB, Van Aken O, Millar AH. Salicylic Acid-Dependent Plant Stress Signaling via Mitochondrial Succinate Dehydrogenase. Plant Physiol 2017; 173:2029-2040. [PMID: 28209841 PMCID: PMC5373042 DOI: 10.1104/pp.16.00060] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 02/14/2017] [Indexed: 05/19/2023]
Abstract
Mitochondria are known for their role in ATP production and generation of reactive oxygen species, but little is known about the mechanism of their early involvement in plant stress signaling. The role of mitochondrial succinate dehydrogenase (SDH) in salicylic acid (SA) signaling was analyzed using two mutants: disrupted in stress response1 (dsr1), which is a point mutation in SDH1 identified in a loss of SA signaling screen, and a knockdown mutant (sdhaf2) for SDH assembly factor 2 that is required for FAD insertion into SDH1. Both mutants showed strongly decreased SA-inducible stress promoter responses and low SDH maximum capacity compared to wild type, while dsr1 also showed low succinate affinity, low catalytic efficiency, and increased resistance to SDH competitive inhibitors. The SA-induced promoter responses could be partially rescued in sdhaf2, but not in dsr1, by supplementing the plant growth media with succinate. Kinetic characterization showed that low concentrations of either SA or ubiquinone binding site inhibitors increased SDH activity and induced mitochondrial H2O2 production. Both dsr1 and sdhaf2 showed lower rates of SA-dependent H2O2 production in vitro in line with their low SA-dependent stress signaling responses in vivo. This provides quantitative and kinetic evidence that SA acts at or near the ubiquinone binding site of SDH to stimulate activity and contributes to plant stress signaling by increased rates of mitochondrial H2O2 production, leading to part of the SA-dependent transcriptional response in plant cells.
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Affiliation(s)
- Katharina Belt
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia (K.B., S.H., O.V.A., A.H.M.)
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Wembley, Washington 6913, Australia (L.F.T., H.C., K.B.S.); and
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Washington 6009, Australia (K.B.S.)
| | - Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia (K.B., S.H., O.V.A., A.H.M.)
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Wembley, Washington 6913, Australia (L.F.T., H.C., K.B.S.); and
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Washington 6009, Australia (K.B.S.)
| | - Louise F Thatcher
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia (K.B., S.H., O.V.A., A.H.M.)
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Wembley, Washington 6913, Australia (L.F.T., H.C., K.B.S.); and
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Washington 6009, Australia (K.B.S.)
| | - Hayley Casarotto
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia (K.B., S.H., O.V.A., A.H.M.)
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Wembley, Washington 6913, Australia (L.F.T., H.C., K.B.S.); and
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Washington 6009, Australia (K.B.S.)
| | - Karam B Singh
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia (K.B., S.H., O.V.A., A.H.M.)
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Wembley, Washington 6913, Australia (L.F.T., H.C., K.B.S.); and
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Washington 6009, Australia (K.B.S.)
| | - Olivier Van Aken
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia (K.B., S.H., O.V.A., A.H.M.)
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Wembley, Washington 6913, Australia (L.F.T., H.C., K.B.S.); and
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Washington 6009, Australia (K.B.S.)
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, Faculty of Science, Bayliss Building M316, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia (K.B., S.H., O.V.A., A.H.M.)
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Wembley, Washington 6913, Australia (L.F.T., H.C., K.B.S.); and
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Washington 6009, Australia (K.B.S.)
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Sperschneider J, Catanzariti AM, DeBoer K, Petre B, Gardiner DM, Singh KB, Dodds PN, Taylor JM. LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell. Sci Rep 2017; 7:44598. [PMID: 28300209 PMCID: PMC5353544 DOI: 10.1038/srep44598] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [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: 12/01/2016] [Accepted: 02/09/2017] [Indexed: 12/17/2022] Open
Abstract
Pathogens secrete effector proteins and many operate inside plant cells to enable infection. Some effectors have been found to enter subcellular compartments by mimicking host targeting sequences. Although many computational methods exist to predict plant protein subcellular localization, they perform poorly for effectors. We introduce LOCALIZER for predicting plant and effector protein localization to chloroplasts, mitochondria, and nuclei. LOCALIZER shows greater prediction accuracy for chloroplast and mitochondrial targeting compared to other methods for 652 plant proteins. For 107 eukaryotic effectors, LOCALIZER outperforms other methods and predicts a previously unrecognized chloroplast transit peptide for the ToxA effector, which we show translocates into tobacco chloroplasts. Secretome-wide predictions and confocal microscopy reveal that rust fungi might have evolved multiple effectors that target chloroplasts or nuclei. LOCALIZER is the first method for predicting effector localisation in plants and is a valuable tool for prioritizing effector candidates for functional investigations. LOCALIZER is available at http://localizer.csiro.au/.
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Affiliation(s)
- Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - Ann-Maree Catanzariti
- Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Kathleen DeBoer
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Donald M. Gardiner
- Queensland Bioscience Precinct, CSIRO Agriculture and Food, Brisbane, QLD, Australia
| | - Karam B. Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - Peter N. Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Jennifer M. Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
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Hane JK, Ming Y, Kamphuis LG, Nelson MN, Garg G, Atkins CA, Bayer PE, Bravo A, Bringans S, Cannon S, Edwards D, Foley R, Gao L, Harrison MJ, Huang W, Hurgobin B, Li S, Liu C, McGrath A, Morahan G, Murray J, Weller J, Jian J, Singh KB. A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution. Plant Biotechnol J 2017; 15:318-330. [PMID: 27557478 PMCID: PMC5316927 DOI: 10.1111/pbi.12615] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 08/12/2016] [Accepted: 08/20/2016] [Indexed: 05/18/2023]
Abstract
Lupins are important grain legume crops that form a critical part of sustainable farming systems, reducing fertilizer use and providing disease breaks. It has a basal phylogenetic position relative to other crop and model legumes and a high speciation rate. Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten-free. We report the draft genome assembly (609 Mb) of NLL cultivar Tanjil, which has captured >98% of the gene content, sequences of additional lines and a dense genetic map. Lupins are unique among legumes and differ from most other land plants in that they do not form mycorrhizal associations. Remarkably, we find that NLL has lost all mycorrhiza-specific genes, but has retained genes commonly required for mycorrhization and nodulation. In addition, the genome also provided candidate genes for key disease resistance and domestication traits. We also find evidence of a whole-genome triplication at around 25 million years ago in the genistoid lineage leading to Lupinus. Our results will support detailed studies of legume evolution and accelerate lupin breeding programmes.
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Affiliation(s)
- James K. Hane
- CSIRO AgricultureWembleyWAAustralia
- Department of Environment and AgricultureCCDM BioinformaticsCentre for Crop and Disease ManagementCurtin UniversityBentleyWAAustralia
- Curtin Institute for ComputationCurtin UniversityBentleyWAAustralia
| | - Yao Ming
- Department of Plant and Animal Genome ResearchBeijing Genome InstituteShenzhenChina
| | - Lars G. Kamphuis
- CSIRO AgricultureWembleyWAAustralia
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWAAustralia
| | - Matthew N. Nelson
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWAAustralia
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
- Present address: Royal Botanic Gardens KewNatural Capital and Plant HealthArdinglyRH17 6TNUK
| | | | - Craig A. Atkins
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWAAustralia
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
| | - Armando Bravo
- Boyce Thompson Institute for Plant ResearchIthacaNYUSA
| | | | - Steven Cannon
- USDA‐ARS Corn Insects and Crop Genetics Research UnitCrop Genome Informatics LabIowa State UniversityAmesIAUSA
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - David Edwards
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
- University of QueenslandBrisbaneQldAustralia
| | | | | | | | - Wei Huang
- Department of AgronomyIowa State UniversityAmesIAUSA
| | - Bhavna Hurgobin
- School of Plant BiologyUniversity of Western AustraliaCrawleyWAAustralia
- University of QueenslandBrisbaneQldAustralia
| | - Sean Li
- Data61CSIROCanberraACTAustralia
| | | | | | - Grant Morahan
- Centre for Diabetes ResearchUniversity of Western AustraliaCrawleyWAAustralia
| | | | - James Weller
- School of Biological SciencesUniversity of TasmaniaHobartTASAustralia
| | - Jianbo Jian
- Department of Plant and Animal Genome ResearchBeijing Genome InstituteShenzhenChina
| | - Karam B. Singh
- CSIRO AgricultureWembleyWAAustralia
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWAAustralia
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31
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Lima-Cabello E, Alche V, Foley RC, Andrikopoulos S, Morahan G, Singh KB, Alche JD, Jimenez-Lopez JC. Narrow-leafed lupin (Lupinus angustifolius
L.) β-conglutin proteins modulate the insulin signaling pathway as potential type 2 diabetes treatment and inflammatory-related disease amelioration. Mol Nutr Food Res 2017; 61. [DOI: 10.1002/mnfr.201600819] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Elena Lima-Cabello
- Plant Reproductive Biology Laboratory; Deptartment of Biochemistry; Cell & Molecular Biology of Plants, Estacion Experimental del Zaidin; Spanish National Research Council (CSIC); Granada Spain
| | - Victor Alche
- Andalusian Health System; Health Center “Villanueva de las Torres”; Granada Spain
| | - Rhonda C. Foley
- The Commonwealth Scientific and Industrial Research Organisation (CSIRO); Agriculture and Food; Centre for Environment and Life Sciences (CELS); Floreat; WA Australia
| | - Sofianos Andrikopoulos
- Department of Medicine; Heidelberg Repatriation Hospital; The University of Melbourne; Heidelberg West VIC Australia
| | - Grant Morahan
- Harry Perkins Institute of Medical Research; Centre for Diabetes Research; The University of Western Australia; Perth WA Australia
| | - Karam B. Singh
- The Commonwealth Scientific and Industrial Research Organisation (CSIRO); Agriculture and Food; Centre for Environment and Life Sciences (CELS); Floreat; WA Australia
- The UWA Institute of Agriculture; The University of Western Australia; Perth WA Australia
| | - Juan D. Alche
- Plant Reproductive Biology Laboratory; Deptartment of Biochemistry; Cell & Molecular Biology of Plants, Estacion Experimental del Zaidin; Spanish National Research Council (CSIC); Granada Spain
| | - Jose C. Jimenez-Lopez
- Plant Reproductive Biology Laboratory; Deptartment of Biochemistry; Cell & Molecular Biology of Plants, Estacion Experimental del Zaidin; Spanish National Research Council (CSIC); Granada Spain
- The UWA Institute of Agriculture; The University of Western Australia; Perth WA Australia
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Frick KM, Kamphuis LG, Siddique KHM, Singh KB, Foley RC. Quinolizidine Alkaloid Biosynthesis in Lupins and Prospects for Grain Quality Improvement. Front Plant Sci 2017; 8:87. [PMID: 28197163 PMCID: PMC5281559 DOI: 10.3389/fpls.2017.00087] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/16/2017] [Indexed: 05/21/2023]
Abstract
Quinolizidine alkaloids (QAs) are toxic secondary metabolites found within the genus Lupinus, some species of which are commercially important grain legume crops including Lupinus angustifolius (narrow-leafed lupin, NLL), L. luteus (yellow lupin), L. albus (white lupin), and L. mutabilis (pearl lupin), with NLL grain being the most largely produced of the four species in Australia and worldwide. While QAs offer the plants protection against insect pests, the accumulation of QAs in lupin grain complicates its use for food purposes as QA levels must remain below the industry threshold (0.02%), which is often exceeded. It is not well understood what factors cause grain QA levels to exceed this threshold. Much of the early work on QA biosynthesis began in the 1970-1980s, with many QA chemical structures well-characterized and lupin cell cultures and enzyme assays employed to identify some biosynthetic enzymes and pathway intermediates. More recently, two genes associated with these enzymes have been characterized, however, the QA biosynthetic pathway remains only partially elucidated. Here, we review the research accomplished thus far concerning QAs in lupin and consider some possibilities for further elucidation and manipulation of the QA pathway in lupin crops, drawing on examples from model alkaloid species. One breeding strategy for lupin is to produce plants with high QAs in vegetative tissues while low in the grain in order to confer insect resistance to plants while keeping grain QA levels within industry regulations. With the knowledge achieved on alkaloid biosynthesis in other plant species in recent years, and the recent development of genomic and transcriptomic resources for NLL, there is considerable scope to facilitate advances in our knowledge of QAs, leading to the production of improved lupin crops.
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Affiliation(s)
- Karen M. Frick
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- School of Plant Biology, The University of Western AustraliaCrawley, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Lars G. Kamphuis
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | | | - Karam B. Singh
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
- The UWA Institute of Agriculture, The University of Western AustraliaPerth, WA, Australia
| | - Rhonda C. Foley
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Commonwealth Scientific and Industrial Research OrganisationFloreat, WA, Australia
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Jimenez-Lopez JC, Melser S, DeBoer K, Thatcher LF, Kamphuis LG, Foley RC, Singh KB. Narrow-Leafed Lupin ( Lupinus angustifolius) β1- and β6-Conglutin Proteins Exhibit Antifungal Activity, Protecting Plants against Necrotrophic Pathogen Induced Damage from Sclerotinia sclerotiorum and Phytophthora nicotianae. Front Plant Sci 2016; 7:1856. [PMID: 28018392 PMCID: PMC5161055 DOI: 10.3389/fpls.2016.01856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/24/2016] [Indexed: 05/27/2023]
Abstract
Vicilins (7S globulins) are seed storage proteins and constitute the main protein family in legume seeds, particularly in narrow-leafed lupin (Lupinus angustifolius L.; NLL), where seven vicilin genes, called β1- to β7-conglutin have been identified. Vicilins are involved in germination processes supplying amino acids for seedling growth and plant development, as well as in some cases roles in plant defense and protection against pathogens. The roles of NLL β-conglutins in plant defense are unknown. Here the potential role of five NLL β-conglutin family members in protection against necrotrophic fungal pathogens was investigated and it was demonstrated that recombinant purified 6xHis-tagged β1- and β6-conglutin proteins exhibited the strongest in vitro growth inhibitory activity against a range of necrotrophic fungal pathogens compared to β2, β3, and β4 conglutins. To examine activity in vivo, two representative necrotrophic pathogens, the fungus Sclerotinia sclerotiorum and oomycete Phytophthora nicotianae were used. Transient expression of β1- and β6-conglutin proteins in Nicotiana benthamiana leaves demonstrated in vivo growth suppression of both of these pathogens, resulting in low percentages of hyphal growth and elongation in comparison to control treated leaves. Cellular studies using β1- and β6-GFP fusion proteins showed these conglutins localized to the cell surface including plasmodesmata. Analysis of cellular death following S. sclerotiorum or P. nicotianae revealed both β1- and β6-conglutins suppressed pathogen induced cell death in planta and prevented pathogen induced suppression of the plant oxidative burst as determined by protein oxidation in infected compared to mock-inoculated leaves.
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Affiliation(s)
- Jose C. Jimenez-Lopez
- The Institute of Agriculture, The University of Western Australia, PerthWA, Australia
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estacion Experimental del Zaidin, Spanish National Research CouncilGranada, Spain
| | - Su Melser
- Centre for Environment and Life Sciences, Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, FloreatWA, Australia
| | - Kathleen DeBoer
- The Institute of Agriculture, The University of Western Australia, PerthWA, Australia
- Centre for Environment and Life Sciences, Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, FloreatWA, Australia
| | - Louise F. Thatcher
- Centre for Environment and Life Sciences, Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, FloreatWA, Australia
| | - Lars G. Kamphuis
- The Institute of Agriculture, The University of Western Australia, PerthWA, Australia
- Centre for Environment and Life Sciences, Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, FloreatWA, Australia
| | - Rhonda C. Foley
- Centre for Environment and Life Sciences, Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, FloreatWA, Australia
| | - Karam B. Singh
- The Institute of Agriculture, The University of Western Australia, PerthWA, Australia
- Centre for Environment and Life Sciences, Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, FloreatWA, Australia
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Thatcher LF, Williams AH, Garg G, Buck SAG, Singh KB. Transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. medicaginis during colonisation of resistant and susceptible Medicago truncatula hosts identifies differential pathogenicity profiles and novel candidate effectors. BMC Genomics 2016; 17:860. [PMID: 27809762 PMCID: PMC5094085 DOI: 10.1186/s12864-016-3192-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 06/15/2016] [Accepted: 10/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pathogenic members of the Fusarium oxysporum species complex are responsible for vascular wilt disease on many important crops including legumes, where they can be one of the most destructive disease causing necrotrophic fungi. We previously developed a model legume-infecting pathosystem based on the reference legume Medicago truncatula and a pathogenic F. oxysporum forma specialis (f. sp.) medicaginis (Fom). To dissect the molecular pathogenicity arsenal used by this root-infecting pathogen, we sequenced its transcriptome during infection of a susceptible and resistant host accession. RESULTS High coverage RNA-Seq of Fom infected root samples harvested from susceptible (DZA315) or resistant (A17) M. truncatula seedlings at early or later stages of infection (2 or 7 days post infection (dpi)) and from vegetative (in vitro) samples facilitated the identification of unique and overlapping sets of in planta differentially expressed genes. This included enrichment, particularly in DZA315 in planta up-regulated datasets, for proteins associated with sugar, protein and plant cell wall metabolism, membrane transport, nutrient uptake and oxidative processes. Genes encoding effector-like proteins were identified, including homologues of the F. oxysporum f. sp. lycopersici Secreted In Xylem (SIX) proteins, and several novel candidate effectors based on predicted secretion, small protein size and high in-planta induced expression. The majority of the effector candidates contain no known protein domains but do share high similarity to predicted proteins predominantly from other F. oxysporum ff. spp. as well as other Fusaria (F. solani, F. fujikori, F. verticilloides, F. graminearum and F. pseudograminearum), and from another wilt pathogen of the same class, a Verticillium species. Overall, this suggests these novel effector candidates may play important roles in Fusaria and wilt pathogen virulence. CONCLUSION Combining high coverage in planta RNA-Seq with knowledge of fungal pathogenicity protein features facilitated the identification of differentially expressed pathogenicity associated genes and novel effector candidates expressed during infection of a resistant or susceptible M. truncatula host. The knowledge from this first in depth in planta transcriptome sequencing of any F. oxysporum ff. spp. pathogenic on legumes will facilitate the dissection of Fusarium wilt pathogenicity mechanisms on many important legume crops.
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Affiliation(s)
- Louise F. Thatcher
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Angela H. Williams
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009 Australia
| | - Gagan Garg
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Sally-Anne G. Buck
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
| | - Karam B. Singh
- CSIRO Agriculture and Food, Centre for Environment and Life Sciences, Wembley, Western Australia 6913 Australia
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009 Australia
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Kamphuis LG, Guo SM, Gao LL, Singh KB. Genetic Mapping of a Major Resistance Gene to Pea Aphid (Acyrthosipon pisum) in the Model Legume Medicago truncatula. Int J Mol Sci 2016; 17:E1224. [PMID: 27483247 PMCID: PMC5000622 DOI: 10.3390/ijms17081224] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 01/05/2023] Open
Abstract
Resistance to the Australian pea aphid (PA; Acyrthosiphon pisum) biotype in cultivar Jester of the model legume Medicago truncatula is mediated by a single dominant gene and is phloem-mediated. The genetic map position for this resistance gene, APR (Acyrthosiphon pisum resistance), is provided and shows that APR maps 39 centiMorgans (cM) distal of the A. kondoi resistance (AKR) locus, which mediates resistance to a closely related species of the same genus bluegreen aphid (A. kondoi). The APR region on chromosome 3 is dense in classical nucleotide binding site leucine-rich repeats (NLRs) and overlaps with the region harbouring the RAP1 gene which confers resistance to a European PA biotype in the accession Jemalong A17. Further screening of a core collection of M. truncatula accessions identified seven lines with strong resistance to PA. Allelism experiments showed that the single dominant resistance to PA in M. truncatula accessions SA10481 and SA1516 are allelic to SA10733, the donor of the APR locus in cultivar Jester. While it remains unclear whether there are multiple PA resistance genes in an R-gene cluster or the resistance loci identified in the other M. truncatula accessions are allelic to APR, the introgression of APR into current M. truncatula cultivars will provide more durable resistance to PA.
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Affiliation(s)
- Lars G Kamphuis
- Commenwealth Scientific and Industrial Research Organisation, Agriculture and Food, 147 Underwood Avenue, Floreat, WA 6014, Australia.
- University of Western Australia Insititute of Agriculture, 35 Stirling Highway, Crawley, WA 6009, Australia.
| | - Su-Min Guo
- Commenwealth Scientific and Industrial Research Organisation, Agriculture and Food, 147 Underwood Avenue, Floreat, WA 6014, Australia.
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
| | - Ling-Ling Gao
- Commenwealth Scientific and Industrial Research Organisation, Agriculture and Food, 147 Underwood Avenue, Floreat, WA 6014, Australia.
| | - Karam B Singh
- Commenwealth Scientific and Industrial Research Organisation, Agriculture and Food, 147 Underwood Avenue, Floreat, WA 6014, Australia.
- University of Western Australia Insititute of Agriculture, 35 Stirling Highway, Crawley, WA 6009, Australia.
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36
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Anderson JP, Hane JK, Stoll T, Pain N, Hastie ML, Kaur P, Hoogland C, Gorman JJ, Singh KB. Mass-spectrometry data for Rhizoctonia solani proteins produced during infection of wheat and vegetative growth. Data Brief 2016; 8:267-71. [PMID: 27331100 PMCID: PMC4906030 DOI: 10.1016/j.dib.2016.05.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 03/23/2016] [Revised: 05/11/2016] [Accepted: 05/19/2016] [Indexed: 11/02/2022] Open
Abstract
Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato, legumes and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. The data described in this article is derived from applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Comparisons of the data for sample types in this set will be useful to identify metabolic pathway changes as the fungus switches from saprophytic to a pathogenic lifestyle or pathogenicity related proteins contributing to the ability to cause disease on wheat. The data set is deposited in the PRIDE archive under identifier PRIDE: PXD002806.
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Affiliation(s)
- Jonathan P Anderson
- CSIRO Agriculture, Floreat, Western Australia; The University of Western Australia Institute of Agriculture, Crawley, Western Australia
| | | | - Thomas Stoll
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Marcus L Hastie
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Christine Hoogland
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Jeffrey J Gorman
- Protein Discovery Centre, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Karam B Singh
- CSIRO Agriculture, Floreat, Western Australia; The University of Western Australia Institute of Agriculture, Crawley, Western Australia
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37
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Sperschneider J, Gardiner DM, Dodds PN, Tini F, Covarelli L, Singh KB, Manners JM, Taylor JM. EffectorP: predicting fungal effector proteins from secretomes using machine learning. New Phytol 2016; 210:743-61. [PMID: 26680733 DOI: 10.1111/nph.13794] [Citation(s) in RCA: 250] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/05/2015] [Indexed: 05/02/2023]
Abstract
Eukaryotic filamentous plant pathogens secrete effector proteins that modulate the host cell to facilitate infection. Computational effector candidate identification and subsequent functional characterization delivers valuable insights into plant-pathogen interactions. However, effector prediction in fungi has been challenging due to a lack of unifying sequence features such as conserved N-terminal sequence motifs. Fungal effectors are commonly predicted from secretomes based on criteria such as small size and cysteine-rich, which suffers from poor accuracy. We present EffectorP which pioneers the application of machine learning to fungal effector prediction. EffectorP improves fungal effector prediction from secretomes based on a robust signal of sequence-derived properties, achieving sensitivity and specificity of over 80%. Features that discriminate fungal effectors from secreted noneffectors are predominantly sequence length, molecular weight and protein net charge, as well as cysteine, serine and tryptophan content. We demonstrate that EffectorP is powerful when combined with in planta expression data for predicting high-priority effector candidates. EffectorP is the first prediction program for fungal effectors based on machine learning. Our findings will facilitate functional fungal effector studies and improve our understanding of effectors in plant-pathogen interactions. EffectorP is available at http://effectorp.csiro.au.
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Affiliation(s)
- Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture, Perth, 6014, WA, Australia
| | - Donald M Gardiner
- Queensland Bioscience Precinct, CSIRO Agriculture, Brisbane, 4067, QLD, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture, Canberra, 2601, ACT, Australia
| | - Francesco Tini
- Queensland Bioscience Precinct, CSIRO Agriculture, Brisbane, 4067, QLD, Australia
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, 06121, Umbria, Italy
| | - Lorenzo Covarelli
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, 06121, Umbria, Italy
| | - Karam B Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture, Perth, 6014, WA, Australia
| | - John M Manners
- Black Mountain Laboratories, CSIRO Agriculture, Canberra, 2601, ACT, Australia
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture, Canberra, 2601, ACT, Australia
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38
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Foley RC, Kidd BN, Hane JK, Anderson JP, Singh KB. Reactive Oxygen Species Play a Role in the Infection of the Necrotrophic Fungi, Rhizoctonia solani in Wheat. PLoS One 2016; 11:e0152548. [PMID: 27031952 PMCID: PMC4816451 DOI: 10.1371/journal.pone.0152548] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 11/05/2015] [Accepted: 03/16/2016] [Indexed: 01/18/2023] Open
Abstract
Rhizoctonia solani is a nectrotrophic fungal pathogen that causes billions of dollars of damage to agriculture worldwide and infects a broad host range including wheat, rice, potato and legumes. In this study we identify wheat genes that are differentially expressed in response to the R. solani isolate, AG8, using microarray technology. A significant number of wheat genes identified in this screen were involved in reactive oxygen species (ROS) production and redox regulation. Levels of ROS species were increased in wheat root tissue following R. solani infection as determined by Nitro Blue Tetrazolium (NBT), 3,3'-diaminobenzidine (DAB) and titanium sulphate measurements. Pathogen/ROS related genes from R. solani were also tested for expression patterns upon wheat infection. TmpL, a R. solani gene homologous to a gene associated with ROS regulation in Alternaria brassicicola, and OAH, a R. solani gene homologous to oxaloacetate acetylhydrolase which has been shown to produce oxalic acid in Sclerotinia sclerotiorum, were highly induced in R. solani when infecting wheat. We speculate that the interplay between the wheat and R. solani ROS generating proteins may be important for determining the outcome of the wheat/R. solani interaction.
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Affiliation(s)
- Rhonda C. Foley
- CSIRO Agriculture, Centre for Environment and Life Sciences, Floreat, WA, Australia
| | - Brendan N. Kidd
- CSIRO Agriculture, Centre for Environment and Life Sciences, Floreat, WA, Australia
| | - James K. Hane
- CSIRO Agriculture, Centre for Environment and Life Sciences, Floreat, WA, Australia
| | - Jonathan P. Anderson
- CSIRO Agriculture, Centre for Environment and Life Sciences, Floreat, WA, Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Karam B. Singh
- CSIRO Agriculture, Centre for Environment and Life Sciences, Floreat, WA, Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
- * E-mail:
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39
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Williams AH, Sharma M, Thatcher LF, Azam S, Hane JK, Sperschneider J, Kidd BN, Anderson JP, Ghosh R, Garg G, Lichtenzveig J, Kistler HC, Shea T, Young S, Buck SAG, Kamphuis LG, Saxena R, Pande S, Ma LJ, Varshney RK, Singh KB. Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors. BMC Genomics 2016; 17:191. [PMID: 26945779 PMCID: PMC4779268 DOI: 10.1186/s12864-016-2486-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 10/26/2015] [Accepted: 02/17/2016] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world's second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. RESULTS Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. CONCLUSIONS We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn't share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.
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Affiliation(s)
- Angela H Williams
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Louise F Thatcher
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Sarwar Azam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - James K Hane
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
- Department of Environment and Agriculture, Curtin Institute for Computation, and CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin University, Perth, WA, 6102, Australia.
| | - Jana Sperschneider
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Brendan N Kidd
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Jonathan P Anderson
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Raju Ghosh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Gagan Garg
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Judith Lichtenzveig
- Department of Environment and Agriculture, Pulse Pathology and Genetics, Centre for Crop and Disease Management and Curtin Institute for Computation, Curtin University, Perth, WA, 6102, Australia.
| | - H Corby Kistler
- USDA-ARS, Cereal Disease Laboratory, University of Minnesota, St Paul, MN, 55108, USA.
| | | | - Sarah Young
- The Broad Institute, Cambridge, MA, 02141, USA.
| | - Sally-Anne G Buck
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Lars G Kamphuis
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
| | - Rachit Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Suresh Pande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Rajeev K Varshney
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad, 502324, Telangana, India.
| | - Karam B Singh
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, WA, 6913, Australia.
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Thatcher LF, Gao LL, Singh KB. Jasmonate Signalling and Defence Responses in the Model Legume Medicago truncatula-A Focus on Responses to Fusarium Wilt Disease. Plants (Basel) 2016; 5:E11. [PMID: 27135231 PMCID: PMC4844425 DOI: 10.3390/plants5010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 12/05/2022]
Abstract
Jasmonate (JA)-mediated defences play important roles in host responses to pathogen attack, in particular to necrotrophic fungal pathogens that kill host cells in order to extract nutrients and live off the dead plant tissue. The root-infecting fungal pathogen Fusarium oxysporum initiates a necrotrophic growth phase towards the later stages of its lifecycle and is responsible for devastating Fusarium wilt disease on numerous legume crops worldwide. Here we describe the use of the model legume Medicago truncatula to study legume-F. oxysporum interactions and compare and contrast this against knowledge from other model pathosystems, in particular Arabidopsis thaliana-F. oxysporum interactions. We describe publically-available genomic, transcriptomic and genetic (mutant) resources developed in M. truncatula that enable dissection of host jasmonate responses and apply aspects of these herein during the M. truncatula--F. oxysporum interaction. Our initial results suggest not all components of JA-responses observed in M. truncatula are shared with Arabidopsis in response to F. oxysporum infection.
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Affiliation(s)
- Louise F Thatcher
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, Western Australia 6913, Australia.
| | - Ling-Ling Gao
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, Western Australia 6913, Australia.
| | - Karam B Singh
- CSIRO Agriculture, Centre for Environment and Life Sciences, Wembley, Western Australia 6913, Australia.
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia.
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Anderson JP, Hane JK, Stoll T, Pain N, Hastie ML, Kaur P, Hoogland C, Gorman JJ, Singh KB. Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts. Mol Cell Proteomics 2016; 15:1188-203. [PMID: 26811357 PMCID: PMC4824849 DOI: 10.1074/mcp.m115.054502] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Indexed: 11/22/2022] Open
Abstract
Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility to R. solani when expressed in Nicotiana benthamiana. In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806.
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Affiliation(s)
- Jonathan P Anderson
- From the ‡CSIRO Agriculture, Floreat, Western Australia; §The University of Western Australia Institute of Agriculture, Crawley, Western Australia
| | - James K Hane
- From the ‡CSIRO Agriculture, Floreat, Western Australia
| | - Thomas Stoll
- ¶QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Nicholas Pain
- From the ‡CSIRO Agriculture, Floreat, Western Australia
| | - Marcus L Hastie
- ¶QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | | | - Jeffrey J Gorman
- ¶QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Karam B Singh
- From the ‡CSIRO Agriculture, Floreat, Western Australia; §The University of Western Australia Institute of Agriculture, Crawley, Western Australia;
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Fischer K, Dieterich R, Nelson MN, Kamphuis LG, Singh KB, Rotter B, Krezdorn N, Winter P, Wehling P, Ruge-Wehling B. Characterization and mapping of LanrBo: a locus conferring anthracnose resistance in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet 2015; 128:2121-30. [PMID: 26169875 DOI: 10.1007/s00122-015-2572-3] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/23/2015] [Indexed: 05/15/2023]
Abstract
A novel and highly effective source of anthracnose resistance in narrow-leafed lupin was identified. Resistance was shown to be governed by a single dominant locus. Molecular markers have been developed, which can be used for selecting resistant genotypes in lupin breeding. A screening for anthracnose resistance of a set of plant genetic resources of narrow-leafed lupin (Lupinus angustifolius L.) identified the breeding line Bo7212 as being highly resistant to anthracnose (Colletotrichum lupini). Segregation analysis indicated that the resistance of Bo7212 is inherited by a single dominant locus. The corresponding resistance gene was given the designation LanrBo. Previously published molecular anchor markers allowed us to locate LanrBo on linkage group NLL-11 of narrow-leafed lupin. Using information from RNAseq data obtained with inoculated resistant vs. susceptible lupin entries as well as EST-sequence information from the model genome Lotus japonicus, additional SNP and EST markers linked to LanrBo were derived. A bracket of two LanrBo-flanking markers allows for precise marker-assisted selection of the novel resistance gene in narrow-leafed lupin breeding programs.
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Affiliation(s)
- Kristin Fischer
- Julius Kühn-Institut, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, Germany.
| | | | - Matthew N Nelson
- School of Plant Biology, The University of Western Australia, Crawley, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
| | - Lars G Kamphuis
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
- CSIRO, Agriculture Flagship, Wembley, Australia
| | - Karam B Singh
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Australia
- CSIRO, Agriculture Flagship, Wembley, Australia
| | | | | | | | - Peter Wehling
- Julius Kühn-Institut, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, Germany
| | - Brigitte Ruge-Wehling
- Julius Kühn-Institut, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, Germany
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Rawlinson C, Kamphuis LG, Gummer JPA, Singh KB, Trengove RD. A rapid method for profiling of volatile and semi-volatile phytohormones using methyl chloroformate derivatisation and GC-MS. Metabolomics 2015; 11:1922-1933. [PMID: 26491427 PMCID: PMC4605965 DOI: 10.1007/s11306-015-0837-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/27/2015] [Indexed: 01/10/2023]
Abstract
Phytohormones are central components of complex signalling networks in plants. The interplay between these metabolites, which include abscisic acid (ABA), auxin (IAA), ethylene, jasmonic acid (JA) and salicylic acid (SA), regulate plant growth and development and modulate responses to biotic and abiotic stress. Few methods of phytohormone profiling can adequately quantify a large range of plant hormones simultaneously and without the requirement for laborious or highly specialised extraction protocols. Here we describe the development and validation of a phytohormone profiling protocol, based on methyl-chloroformate derivatisation of the plant metabolites and analysis by gas chromatography/mass spectrometry (GC-MS). We describe the analysis of 11 metabolites, either plant phytohormones or intermediates of phytohormone metabolism; ABA, azelaic acid, IAA, JA and SA, and the phytohormone precursors 1-aminocyclopropane 1-carboxylic acid, benzoic acid, cinnamic acid, 13-epi-12-oxophytodienoic acid (13-epi-OPDA), linoleic acid and linolenic acid, and validate the isolation from foliar tissue of the model legume Medicago truncatula. The preparation is insensitive to the presence of water, facilitating measurement of the volatile metabolites. Quantitation was linear over four orders of magnitude, and the limits of detection between two and 10 ng/mL for all measured metabolites using a single quadrupole GC-MS.
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Affiliation(s)
- Catherine Rawlinson
- Separation Science and Metabolomics Laboratory, Division of Research and Development, Murdoch University, Murdoch, WA 6150 Australia
- Metabolomics Australia, Murdoch University Node, Murdoch University, Murdoch, WA 6150 Australia
| | - Lars G. Kamphuis
- CSIRO Agriculture Flagship, Private Bag No. 5, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
| | - Joel P. A. Gummer
- Separation Science and Metabolomics Laboratory, Division of Research and Development, Murdoch University, Murdoch, WA 6150 Australia
- Metabolomics Australia, Murdoch University Node, Murdoch University, Murdoch, WA 6150 Australia
| | - Karam B. Singh
- CSIRO Agriculture Flagship, Private Bag No. 5, Wembley, WA 6913 Australia
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009 Australia
| | - Robert D. Trengove
- Separation Science and Metabolomics Laboratory, Division of Research and Development, Murdoch University, Murdoch, WA 6150 Australia
- Metabolomics Australia, Murdoch University Node, Murdoch University, Murdoch, WA 6150 Australia
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Sperschneider J, Dodds PN, Gardiner DM, Manners JM, Singh KB, Taylor JM. Advances and challenges in computational prediction of effectors from plant pathogenic fungi. PLoS Pathog 2015; 11:e1004806. [PMID: 26020524 PMCID: PMC4447458 DOI: 10.1371/journal.ppat.1004806] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jana Sperschneider
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia
- * E-mail:
| | - Peter N. Dodds
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
| | - Donald M. Gardiner
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - John M. Manners
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
| | - Karam B. Singh
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - Jennifer M. Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
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45
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Sperschneider J, Gardiner DM, Thatcher LF, Lyons R, Singh KB, Manners JM, Taylor JM. Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity. Genome Biol Evol 2015; 7:1613-27. [PMID: 25994930 PMCID: PMC4494044 DOI: 10.1093/gbe/evv092] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pathogens and hosts are in an ongoing arms race and genes involved in host–pathogen interactions are likely to undergo diversifying selection. Fusarium plant pathogens have evolved diverse infection strategies, but how they interact with their hosts in the biotrophic infection stage remains puzzling. To address this, we analyzed the genomes of three Fusarium plant pathogens for genes that are under diversifying selection. We found a two-speed genome structure both on the chromosome and gene group level. Diversifying selection acts strongly on the dispensable chromosomes in Fusarium oxysporum f. sp. lycopersici and on distinct core chromosome regions in Fusarium graminearum, all of which have associations with virulence. Members of two gene groups evolve rapidly, namely those that encode proteins with an N-terminal [SG]-P-C-[KR]-P sequence motif and proteins that are conserved predominantly in pathogens. Specifically, 29 F. graminearum genes are rapidly evolving, in planta induced and encode secreted proteins, strongly pointing toward effector function. In summary, diversifying selection in Fusarium is strongly reflected as genomic footprints and can be used to predict a small gene set likely to be involved in host–pathogen interactions for experimental verification.
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Affiliation(s)
- Jana Sperschneider
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia
| | - Donald M Gardiner
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Louise F Thatcher
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia
| | - Rebecca Lyons
- CSIRO Agriculture Flagship, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
| | - Karam B Singh
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Perth, Western Australia, Australia University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia, Australia
| | - John M Manners
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
| | - Jennifer M Taylor
- CSIRO Agriculture Flagship, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia
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Thatcher LF, Kamphuis LG, Hane JK, Oñate-Sánchez L, Singh KB. The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress. PLoS One 2015; 10:e0126978. [PMID: 25985302 PMCID: PMC4436139 DOI: 10.1371/journal.pone.0126978] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [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: 01/14/2015] [Accepted: 04/09/2015] [Indexed: 11/25/2022] Open
Abstract
Glutathione S-transferases (GSTs) play important roles in the protection of cells against toxins and oxidative damage where one Arabidopsis member, GSTF8, has become a commonly used marker gene for early stress and defense responses. A GSTF8 promoter fragment fused to the luciferase reporter gene was used in a forward genetic screen for Arabidopsis mutants with up-regulated GSTF8 promoter activity. This identified the esr1-1 (enhanced stress response 1) mutant which also conferred increased resistance to the fungal pathogen Fusarium oxysporum. Through positional cloning, the ESR1 gene was found to encode a KH-domain containing RNA-binding protein (At5g53060). Whole transcriptome sequencing of esr1-1 identified altered expression of genes involved in responses to biotic and abiotic stimuli, hormone signaling pathways and developmental processes. In particular was an overall significant enrichment for jasmonic acid (JA) mediated processes in the esr1-1 down-regulated dataset. A subset of these genes were tested for MeJA inducibility and we found the expression of some but not all were reduced in esr1-1. The esr1-1 mutant was not impaired in other aspects of JA-signalling such as JA- sensitivity or development, suggesting ESR1 functions in specific components of the JA-signaling pathway. Examination of salicylic acid (SA) regulated marker genes in esr1-1 showed no increase in basal or SA induced expression suggesting repression of JA-regulated genes is not due to antagonistic SA-JA crosstalk. These results define new roles for KH-domain containing proteins with ESR1 unlinking JA-mediated growth and defense responses.
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Affiliation(s)
- Louise F. Thatcher
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Wembley, Western Australia, Australia
| | - Lars G. Kamphuis
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Wembley, Western Australia, Australia
- The Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
| | - James K. Hane
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Wembley, Western Australia, Australia
| | - Luis Oñate-Sánchez
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Wembley, Western Australia, Australia
| | - Karam B. Singh
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Wembley, Western Australia, Australia
- The Institute of Agriculture, The University of Western Australia, Crawley, Western Australia, Australia
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Foley RC, Jimenez-Lopez JC, Kamphuis LG, Hane JK, Melser S, Singh KB. Analysis of conglutin seed storage proteins across lupin species using transcriptomic, protein and comparative genomic approaches. BMC Plant Biol 2015; 15:106. [PMID: 25902794 PMCID: PMC4407355 DOI: 10.1186/s12870-015-0485-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 03/30/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND The major proteins in lupin seeds are conglutins that have primary roles in supplying carbon, sulphur and nitrogen and energy for the germinating seedling. They fall into four families; α, β, γ and δ. Interest in these conglutins is growing as family members have been shown to have beneficial nutritional and pharmaceutical properties. RESULTS An in-depth transcriptome and draft genome from the narrow-leafed lupin (NLL; Lupinus angustifolius) variety, Tanjil, were examined and 16 conglutin genes were identified. Using RNAseq data sets, the structure and expression of these 16 conglutin genes were analysed across eight lupin varieties from five lupin species. Phylogenic analysis suggest that the α and γ conglutins diverged prior to lupin speciation while β and δ members diverged both prior and after speciation. A comparison of the expression of the 16 conglutin genes was performed, and in general the conglutin genes showed similar levels of RNA expression among varieties within species, but quite distinct expression patterns between lupin species. Antibodies were generated against the specific conglutin families and immunoblot analyses were used to compare the levels of conglutin proteins in various tissues and during different stages of seed development in NLL, Tanjil, confirming the expression in the seed. This analysis showed that the conglutins were expressed highly at the mature seed stage, in all lupin species, and a range of polypeptide sizes were observed for each conglutin family. CONCLUSIONS This study has provided substantial information on the complexity of the four conglutin families in a range of lupin species in terms of their gene structure, phylogenetic relationships as well as their relative RNA and protein abundance during seed development. The results demonstrate that the majority of the heterogeneity of conglutin polypeptides is likely to arise from post-translational modification from a limited number of precursor polypeptides rather than a large number of different genes. Overall, the results demonstrate a high degree of plasticity for conglutin expression during seed development in different lupin species.
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Affiliation(s)
- Rhonda C Foley
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Floreat, WA, Australia.
| | - Jose C Jimenez-Lopez
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
| | - Lars G Kamphuis
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Floreat, WA, Australia.
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
| | - James K Hane
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Floreat, WA, Australia.
- Current address: Curtin Institute for Computation and Centre for Crop & Disease Management, Department of Environment & Agriculture, Curtin University, Bentley, Western Australia, Australia.
| | - Su Melser
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Floreat, WA, Australia.
| | - Karam B Singh
- CSIRO Agriculture Flagship, Centre for Environment and Life Sciences, Floreat, WA, Australia.
- The UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
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Kamphuis LG, Hane JK, Nelson MN, Gao L, Atkins CA, Singh KB. Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers. Plant Biotechnol J 2015; 13:14-25. [PMID: 25060816 PMCID: PMC4309465 DOI: 10.1111/pbi.12229] [Citation(s) in RCA: 38] [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: 03/04/2014] [Revised: 05/27/2014] [Accepted: 06/12/2014] [Indexed: 05/18/2023]
Abstract
Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome-derived gene-based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome-derived markers and 66 BAC-end sequence-derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map.
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Affiliation(s)
- Lars G Kamphuis
- CSIRO Plant IndustryWembley, WA, Australia
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
| | | | - Matthew N Nelson
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
- The School of Plant Biology, University of Western AustraliaCrawley, WA, Australia
| | | | - Craig A Atkins
- The School of Plant Biology, University of Western AustraliaCrawley, WA, Australia
| | - Karam B Singh
- CSIRO Plant IndustryWembley, WA, Australia
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
- *Correspondence (Tel +61 8 9333 6320; fax +61 8 9383 9673; email )
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49
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Sperschneider J, Williams AH, Hane JK, Singh KB, Taylor JM. Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors. Front Plant Sci 2015; 6:1168. [PMID: 26779196 PMCID: PMC4688413 DOI: 10.3389/fpls.2015.01168] [Citation(s) in RCA: 27] [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] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 12/07/2015] [Indexed: 05/03/2023]
Abstract
The steadily increasing number of sequenced fungal and oomycete genomes has enabled detailed studies of how these eukaryotic microbes infect plants and cause devastating losses in food crops. During infection, fungal and oomycete pathogens secrete effector molecules which manipulate host plant cell processes to the pathogen's advantage. Proteinaceous effectors are synthesized intracellularly and must be externalized to interact with host cells. Computational prediction of secreted proteins from genomic sequences is an important technique to narrow down the candidate effector repertoire for subsequent experimental validation. In this study, we benchmark secretion prediction tools on experimentally validated fungal and oomycete effectors. We observe that for a set of fungal SwissProt protein sequences, SignalP 4 and the neural network predictors of SignalP 3 (D-score) and SignalP 2 perform best. For effector prediction in particular, the use of a sensitive method can be desirable to obtain the most complete candidate effector set. We show that the neural network predictors of SignalP 2 and 3, as well as TargetP were the most sensitive tools for fungal effector secretion prediction, whereas the hidden Markov model predictors of SignalP 2 and 3 were the most sensitive tools for oomycete effectors. Thus, previous versions of SignalP retain value for oomycete effector prediction, as the current version, SignalP 4, was unable to reliably predict the signal peptide of the oomycete Crinkler effectors in the test set. Our assessment of subcellular localization predictors shows that cytoplasmic effectors are often predicted as not extracellular. This limits the reliability of secretion predictions that depend on these tools. We present our assessment with a view to informing future pathogenomics studies and suggest revised pipelines for secretion prediction to obtain optimal effector predictions in fungi and oomycetes.
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Affiliation(s)
- Jana Sperschneider
- CSIRO Agriculture Flagship, Centre for Environment and Life SciencesPerth, WA, Australia
- *Correspondence: Jana Sperschneider
| | - Angela H. Williams
- CSIRO Agriculture Flagship, Centre for Environment and Life SciencesPerth, WA, Australia
- The Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
| | - James K. Hane
- Department of Environment and Agriculture, CCDM Bioinformatics, Centre for Crop and Disease Management, Curtin UniversityPerth, WA, Australia
- Curtin Institute for Computation, Curtin UniversityPerth, WA, Australia
| | - Karam B. Singh
- CSIRO Agriculture Flagship, Centre for Environment and Life SciencesPerth, WA, Australia
- The Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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Zhang B, Van Aken O, Thatcher L, De Clercq I, Duncan O, Law SR, Murcha MW, van der Merwe M, Seifi HS, Carrie C, Cazzonelli C, Radomiljac J, Höfte M, Singh KB, Van Breusegem F, Whelan J. The mitochondrial outer membrane AAA ATPase AtOM66 affects cell death and pathogen resistance in Arabidopsis thaliana. Plant J 2014; 80:709-727. [PMID: 25227923 DOI: 10.1111/tpj.12665] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 06/03/2023]
Abstract
One of the most stress-responsive genes encoding a mitochondrial protein in Arabidopsis (At3g50930) has been annotated as AtBCS1 (cytochrome bc1 synthase 1), but was previously functionally uncharacterised. Here, we show that the protein encoded by At3g50930 is present as a homo-multimeric protein complex on the outer mitochondrial membrane and lacks the BCS1 domain present in yeast and mammalian BCS1 proteins, with the sequence similarity restricted to the AAA ATPase domain. Thus we propose to re-annotate this protein as AtOM66 (Outer Mitochondrial membrane protein of 66 kDa). While transgenic plants with reduced AtOM66 expression appear to be phenotypically normal, AtOM66 over-expression lines have a distinct phenotype, showing strong leaf curling and reduced starch content. Analysis of mitochondrial protein content demonstrated no detectable changes in mitochondrial respiratory complex protein abundance. Consistent with the stress inducible expression pattern, over-expression lines of AtOM66 are more tolerant to drought stress but undergo stress-induced senescence earlier than wild type. Genome-wide expression analysis revealed a constitutive induction of salicylic acid-related (SA) pathogen defence and cell death genes in over-expression lines. Conversely, expression of SA marker gene PR-1 was reduced in atom66 plants, while jasmonic acid response genes PDF1.2 and VSP2 have increased transcript abundance. In agreement with the expression profile, AtOM66 over-expression plants show increased SA content, accelerated cell death rates and are more tolerant to the biotrophic pathogen Pseudomonas syringae, but more susceptible to the necrotrophic fungus Botrytis cinerea. In conclusion, our results demonstrate a role for AtOM66 in cell death and amplifying SA signalling.
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Affiliation(s)
- Botao Zhang
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Bayliss Building M316, 35 Stirling Highway, Crawley, WA, 6009, Australia; Department of Botany, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Bundoora, Vic., 3086, Australia
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