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Kälin C, Piombo E, Bourras S, Brantestam AK, Dubey M, Elfstrand M, Karlsson M. Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea. BMC PLANT BIOLOGY 2024; 24:144. [PMID: 38413860 PMCID: PMC10900555 DOI: 10.1186/s12870-024-04817-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Aphanomyces euteiches is a soil-borne oomycete that causes root rot in pea and other legume species. Symptoms of Aphanomyces root rot (ARR) include root discoloration and wilting, leading to significant yield losses in pea production. Resistance to ARR is known to be polygenic but the roles of single genes in the pea immune response are still poorly understood. This study uses transcriptomics to elucidate the immune response of two pea genotypes varying in their levels of resistance to A. euteiches. RESULTS In this study, we inoculated roots of the pea (P. sativum L.) genotypes 'Linnea' (susceptible) and 'PI180693' (resistant) with two different A. euteiches strains varying in levels of virulence. The roots were harvested at 6 h post-inoculation (hpi), 20 hpi and 48 hpi, followed by differential gene expression analysis. Our results showed a time- and genotype-dependent immune response towards A. euteiches infection, involving several WRKY and MYB-like transcription factors, along with genes associated with jasmonic acid (JA) and abscisic acid (ABA) signaling. By cross-referencing with genes segregating with partial resistance to ARR, we identified 39 candidate disease resistance genes at the later stage of infection. Among the genes solely upregulated in the resistant genotype 'PI180693', Psat7g091800.1 was polymorphic between the pea genotypes and encoded a Leucine-rich repeat receptor-like kinase reminiscent of the Arabidopsis thaliana FLAGELLIN-SENSITIVE 2 receptor. CONCLUSIONS This study provides new insights into the gene expression dynamics controlling the immune response of resistant and susceptible pea genotypes to A. euteiches infection. We present a set of 39 candidate disease resistance genes for ARR in pea, including the putative immune receptor Psat7g091800.1, for future functional validation.
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Affiliation(s)
- Carol Kälin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Salim Bourras
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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2
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Sita K, Sehgal A, HanumanthaRao B, Nair RM, Vara Prasad PV, Kumar S, Gaur PM, Farooq M, Siddique KHM, Varshney RK, Nayyar H. Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance. FRONTIERS IN PLANT SCIENCE 2017; 8:1658. [PMID: 29123532 PMCID: PMC5662899 DOI: 10.3389/fpls.2017.01658] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/08/2017] [Indexed: 05/20/2023]
Abstract
Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can result in heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology, and reproductive growth of plants. High-temperature stress at the time of the reproductive stage is becoming a severe limitation for production of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change. The reproductive period is vital in the life cycle of all plants and is susceptible to high-temperature stress as various metabolic processes are adversely impacted during this phase, which reduces crop yield. Food legumes exposed to high-temperature stress during reproduction show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to smaller seeds and poor yields. Through various breeding techniques, heat tolerance in major legumes can be enhanced to improve performance in the field. Omics approaches unravel different mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward high-temperature stress.
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Affiliation(s)
- Kumari Sita
- Department of Botany, Panjab University, Chandigarh, India
| | | | | | | | - P. V. Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, United States
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Muhammad Farooq
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
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3
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Zargar SM, Mahajan R, Nazir M, Nagar P, Kim ST, Rai V, Masi A, Ahmad SM, Shah RA, Ganai NA, Agrawal GK, Rakwal R. Common bean proteomics: Present status and future strategies. J Proteomics 2017; 169:239-248. [DOI: 10.1016/j.jprot.2017.03.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 11/30/2022]
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4
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Chen T, Zhou B, Duan L, Zhu H, Zhang Z. MtMAPKK4 is an essential gene for growth and reproduction of Medicago truncatula. PHYSIOLOGIA PLANTARUM 2017; 159:492-503. [PMID: 27935060 DOI: 10.1111/ppl.12533] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/09/2016] [Accepted: 11/13/2016] [Indexed: 06/06/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are universal signaling modules in eukaryotes, including yeasts, animals and plants. They are involved in responses to various biotic and abiotic stresses, hormones, cell division and developmental processes. A MAPK cascade is composed of three functionally tiered protein kinases, namely MAPK, MAPK kinases (MAPKKs) and MAPK kinase kinases (MAPKKKs). These kinases have been intensively studied for their roles in developmental and physiological processes in various organisms. In this study, a Medicago truncatula MtMAPKK4 mutant with the tobacco retrotransposon Tnt1 insertion was identified using reverse genetics methods. No homozygous progeny could be produced by self-pollination of mapkk4/+ heterozygotes for 5 generations. Heterozygous mapkk4/+ mutant plants exhibited growth retardation, chlorosis symptoms and significantly reduced numbers of infection threads and nodules. The interaction between MtMAPKK4 and MtMAPK3/6 occurred both in yeast and in planta. Green fluorescent protein-tagged MtMAPKK4, MtMAPK3 and MtMAPK6 were all localized to membranes, cytoplasm and nuclei. Expression of MtMAPKK4, MtMAPK3 and MtMAPK6 was detected in various tissues of M. truncatula plants at the nodule maturation stage. Transcript levels of these genes were decreased in roots at the early symbiotic stage.
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Affiliation(s)
- Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P R China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P R China
| | - Bo Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P R China
| | - Liujian Duan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P R China
| | - Hui Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P R China
| | - Zhongming Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P R China
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5
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Sita K, Sehgal A, HanumanthaRao B, Nair RM, Vara Prasad PV, Kumar S, Gaur PM, Farooq M, Siddique KHM, Varshney RK, Nayyar H. Food Legumes and Rising Temperatures: Effects, Adaptive Functional Mechanisms Specific to Reproductive Growth Stage and Strategies to Improve Heat Tolerance. FRONTIERS IN PLANT SCIENCE 2017. [PMID: 29123532 DOI: 10.3389/flps.2017.01658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Ambient temperatures are predicted to rise in the future owing to several reasons associated with global climate changes. These temperature increases can result in heat stress- a severe threat to crop production in most countries. Legumes are well-known for their impact on agricultural sustainability as well as their nutritional and health benefits. Heat stress imposes challenges for legume crops and has deleterious effects on the morphology, physiology, and reproductive growth of plants. High-temperature stress at the time of the reproductive stage is becoming a severe limitation for production of grain legumes as their cultivation expands to warmer environments and temperature variability increases due to climate change. The reproductive period is vital in the life cycle of all plants and is susceptible to high-temperature stress as various metabolic processes are adversely impacted during this phase, which reduces crop yield. Food legumes exposed to high-temperature stress during reproduction show flower abortion, pollen and ovule infertility, impaired fertilization, and reduced seed filling, leading to smaller seeds and poor yields. Through various breeding techniques, heat tolerance in major legumes can be enhanced to improve performance in the field. Omics approaches unravel different mechanisms underlying thermotolerance, which is imperative to understand the processes of molecular responses toward high-temperature stress.
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Affiliation(s)
- Kumari Sita
- Department of Botany, Panjab University, Chandigarh, India
| | | | | | | | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, United States
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Muhammad Farooq
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- The UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
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6
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Goossens J, De Geyter N, Walton A, Eeckhout D, Mertens J, Pollier J, Fiallos-Jurado J, De Keyser A, De Clercq R, Van Leene J, Gevaert K, De Jaeger G, Goormachtig S, Goossens A. Isolation of protein complexes from the model legume Medicago truncatula by tandem affinity purification in hairy root cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:476-489. [PMID: 27377668 DOI: 10.1111/tpj.13258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/21/2016] [Accepted: 06/30/2016] [Indexed: 05/26/2023]
Abstract
Tandem affinity purification coupled to mass spectrometry (TAP-MS) is one of the most powerful techniques to isolate protein complexes and elucidate protein interaction networks. Here, we describe the development of a TAP-MS strategy for the model legume Medicago truncatula, which is widely studied for its ability to produce valuable natural products and to engage in endosymbiotic interactions. As biological material, transgenic hairy roots, generated through Agrobacterium rhizogenes-mediated transformation of M. truncatula seedlings, were used. As proof of concept, proteins involved in the cell cycle, transcript processing and jasmonate signalling were chosen as bait proteins, resulting in a list of putative interactors, many of which confirm the interologue concept of protein interactions, and which can contribute to biological information about the functioning of these bait proteins in planta. Subsequently, binary protein-protein interactions among baits and preys, and among preys were confirmed by a systematic yeast two-hybrid screen. Together, by establishing a M. truncatula TAP-MS platform, we extended the molecular toolbox of this model species.
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Affiliation(s)
- Jonas Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Nathan De Geyter
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alan Walton
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Dominique Eeckhout
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jan Mertens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jennifer Fiallos-Jurado
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Annick De Keyser
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Rebecca De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Jelle Van Leene
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Gent, Belgium
| | - Geert De Jaeger
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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7
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Rodríguez-Celma J, Lattanzio G, Villarroya D, Gutierrez-Carbonell E, Ceballos-Laita L, Rencoret J, Gutiérrez A, Del Río JC, Grusak MA, Abadía A, Abadía J, López-Millán AF. Effects of Fe deficiency on the protein profiles and lignin composition of stem tissues from Medicago truncatula in absence or presence of calcium carbonate. J Proteomics 2016; 140:1-12. [PMID: 27045941 DOI: 10.1016/j.jprot.2016.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/07/2016] [Accepted: 03/10/2016] [Indexed: 12/26/2022]
Abstract
UNLABELLED Iron deficiency is a yield-limiting factor with major implications for crop production, especially in soils with high CaCO3. Because stems are essential for the delivery of nutrients to the shoots, the aim of this work was to study the effects of Fe deficiency on the stem proteome of Medicago truncatula. Two-dimensional electrophoresis separation of stem protein extracts resolved 276 consistent spots in the whole experiment. Iron deficiency in absence or presence of CaCO3 caused significant changes in relative abundance in 10 and 31 spots, respectively, and 80% of them were identified by mass spectrometry. Overall results indicate that Fe deficiency by itself has a mild effect on the stem proteome, whereas Fe deficiency in the presence of CaCO3 has a stronger impact and causes changes in a larger number of proteins, including increases in stress and protein metabolism related proteins not observed in the absence of CaCO3. Both treatments resulted in increases in cell wall related proteins, which were more intense in the presence of CaCO3. The increases induced by Fe-deficiency in the lignin per protein ratio and changes in the lignin monomer composition, assessed by pyrolysis-gas chromatography-mass spectrometry and microscopy, respectively, further support the existence of cell wall alterations. BIOLOGICAL SIGNIFICANCE In spite of being essential for the delivery of nutrients to the shoots, our knowledge of stem responses to nutrient deficiencies is very limited. The present work applies 2-DE techniques to unravel the response of this understudied tissue to Fe deficiency. Proteomics data, complemented with mineral, lignin and microscopy analyses, indicate that stems respond to Fe deficiency by increasing stress and defense related proteins, probably in response of mineral and osmotic unbalances, and eliciting significant changes in cell wall composition. The changes observed are likely to ultimately affect solute transport and distribution to the leaves.
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Affiliation(s)
- Jorge Rodríguez-Celma
- Plant Nutrition Department, Aula Dei Experimental Station (CSIC), P.O. Box 13034, E-50080, Zaragoza, Spain
| | - Giuseppe Lattanzio
- Plant Nutrition Department, Aula Dei Experimental Station (CSIC), P.O. Box 13034, E-50080, Zaragoza, Spain
| | - Dido Villarroya
- Plant Nutrition Department, Aula Dei Experimental Station (CSIC), P.O. Box 13034, E-50080, Zaragoza, Spain
| | - Elain Gutierrez-Carbonell
- Plant Nutrition Department, Aula Dei Experimental Station (CSIC), P.O. Box 13034, E-50080, Zaragoza, Spain
| | - Laura Ceballos-Laita
- Plant Nutrition Department, Aula Dei Experimental Station (CSIC), P.O. Box 13034, E-50080, Zaragoza, Spain
| | - Jorge Rencoret
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), Reina Mercedes 10, E-41012 Sevilla, Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), Reina Mercedes 10, E-41012 Sevilla, Spain
| | - José C Del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), Reina Mercedes 10, E-41012 Sevilla, Spain
| | - Michael A Grusak
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030, USA
| | - Anunciación Abadía
- Plant Nutrition Department, Aula Dei Experimental Station (CSIC), P.O. Box 13034, E-50080, Zaragoza, Spain
| | - Javier Abadía
- Plant Nutrition Department, Aula Dei Experimental Station (CSIC), P.O. Box 13034, E-50080, Zaragoza, Spain
| | - Ana-Flor López-Millán
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030, USA.
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8
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Ramalingam A, Kudapa H, Pazhamala LT, Weckwerth W, Varshney RK. Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:1116. [PMID: 26734026 PMCID: PMC4689856 DOI: 10.3389/fpls.2015.01116] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/25/2015] [Indexed: 05/19/2023]
Abstract
The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several studies on proteomics and metabolomics in model and crop legumes have been discussed. Additionally, applications of advanced proteomics and metabolomics approaches have also been included in this review for future applications in legume research. The integration of these "omics" approaches will greatly support the identification of accurate biomarkers in legume smart breeding programs.
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Affiliation(s)
- Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Lekha T Pazhamala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Hyderabad, India
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna Vienna, Austria
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, India; School of Plant Biology and Institute of Agriculture, The University of Western AustraliaCrawley, WA, Australia
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9
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Rathi D, Gayen D, Gayali S, Chakraborty S, Chakraborty N. Legume proteomics: Progress, prospects, and challenges. Proteomics 2015; 16:310-27. [DOI: 10.1002/pmic.201500257] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/19/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Divya Rathi
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
| | - Dipak Gayen
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
| | - Saurabh Gayali
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research; Aruna Asaf Ali Marg New Delhi India
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10
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Gil-Quintana E, Lyon D, Staudinger C, Wienkoop S, González EM. Medicago truncatula and Glycine max: Different Drought Tolerance and Similar Local Response of the Root Nodule Proteome. J Proteome Res 2015; 14:5240-51. [PMID: 26503705 PMCID: PMC4673605 DOI: 10.1021/acs.jproteome.5b00617] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Indexed: 12/14/2022]
Abstract
Legume crops present important agronomical and environmental advantages mainly due to their capacity to reduce atmospheric N2 to ammonium via symbiotic nitrogen fixation (SNF). This process is very sensitive to abiotic stresses such as drought, but the mechanism underlying this response is not fully understood. The goal of the current work is to compare the drought response of two legumes with high economic impact and research importance, Medicago truncatula and Glycine max, by characterizing their root nodule proteomes. Our results show that, although M. truncatula exhibits lower water potential values under drought conditions compared to G. max, SNF declined analogously in the two legumes. Both of their nodule proteomes are very similar, and comparable down-regulation responses in the diverse protein functional groups were identified (mainly proteins related to the metabolism of carbon, nitrogen, and sulfur). We suggest lipoxygenases and protein turnover as newly recognized players in SNF regulation. Partial drought conditions applied to a split-root system resulted in the local down-regulation of the entire proteome of drought-stressed nodules in both legumes. The high degree of similarity between both legume proteomes suggests that the vast amount of research conducted on M. truncatula could be applied to economically important legume crops, such as soybean.
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Affiliation(s)
- Erena Gil-Quintana
- Department
of Environmental Sciences, Public University
of Navarra, E-31006 Pamplona, Spain
| | - David Lyon
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Christiana Staudinger
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Stefanie Wienkoop
- Department
of Molecular Systems Biology, University
of Vienna, Althanstrasse
14, 1090 Vienna, Austria
| | - Esther M. González
- Department
of Environmental Sciences, Public University
of Navarra, E-31006 Pamplona, Spain
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11
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Hu J, Rampitsch C, Bykova NV. Advances in plant proteomics toward improvement of crop productivity and stress resistancex. FRONTIERS IN PLANT SCIENCE 2015; 6:209. [PMID: 25926838 PMCID: PMC4396383 DOI: 10.3389/fpls.2015.00209] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/16/2015] [Indexed: 05/14/2023]
Abstract
Abiotic and biotic stresses constrain plant growth and development negatively impacting crop production. Plants have developed stress-specific adaptations as well as simultaneous responses to a combination of various abiotic stresses with pathogen infection. The efficiency of stress-induced adaptive responses is dependent on activation of molecular signaling pathways and intracellular networks by modulating expression, or abundance, and/or post-translational modification (PTM) of proteins primarily associated with defense mechanisms. In this review, we summarize and evaluate the contribution of proteomic studies to our understanding of stress response mechanisms in different plant organs and tissues. Advanced quantitative proteomic techniques have improved the coverage of total proteomes and sub-proteomes from small amounts of starting material, and characterized PTMs as well as protein-protein interactions at the cellular level, providing detailed information on organ- and tissue-specific regulatory mechanisms responding to a variety of individual stresses or stress combinations during plant life cycle. In particular, we address the tissue-specific signaling networks localized to various organelles that participate in stress-related physiological plasticity and adaptive mechanisms, such as photosynthetic efficiency, symbiotic nitrogen fixation, plant growth, tolerance and common responses to environmental stresses. We also provide an update on the progress of proteomics with major crop species and discuss the current challenges and limitations inherent to proteomics techniques and data interpretation for non-model organisms. Future directions in proteomics research toward crop improvement are further discussed.
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Affiliation(s)
- Junjie Hu
- Department of Biology, Memorial University of Newfoundland, St. John’sNL, Canada
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
| | - Christof Rampitsch
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
| | - Natalia V. Bykova
- Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, MordenMB, Canada
- *Correspondence: Natalia V. Bykova, Cereal Proteomics, Cereal Research Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
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Kiirika LM, Schmitz U, Colditz F. The alternative Medicago truncatula defense proteome of ROS-defective transgenic roots during early microbial infection. FRONTIERS IN PLANT SCIENCE 2014; 5:341. [PMID: 25101099 PMCID: PMC4101433 DOI: 10.3389/fpls.2014.00341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 06/26/2014] [Indexed: 05/29/2023]
Abstract
ROP-type GTPases of plants function as molecular switches within elementary signal transduction pathways such as the regulation of ROS synthesis via activation of NADPH oxidases (RBOH-respiratory burst oxidase homolog in plants). Previously, we reported that silencing of the Medicago truncatula GTPase MtROP9 led to reduced ROS production and suppressed induction of ROS-related enzymes in transgenic roots (MtROP9i) infected with pathogenic (Aphanomyces euteiches) and symbiotic microorganisms (Glomus intraradices, Sinorhizobium meliloti). While fungal infections were enhanced, S. meliloti infection was drastically impaired. In this study, we investigate the temporal proteome response of M. truncatula MtROP9i transgenic roots during the same microbial interactions under conditions of deprived potential to synthesize ROS. In comparison with control roots (Mtvector), we present a comprehensive proteomic analysis using sensitive MS protein identification. For four early infection time-points (1, 3, 5, 24 hpi), 733 spots were found to be different in abundance: 213 spots comprising 984 proteins (607 unique) were identified after S. meliloti infection, 230 spots comprising 796 proteins (580 unique) after G. intraradices infection, and 290 spots comprising 1240 proteins (828 unique) after A. euteiches infection. Data evaluation by GelMap in combination with a heatmap tool allowed recognition of key proteome changes during microbial interactions under conditions of hampered ROS synthesis. Overall, the number of induced proteins in MtROP9i was low as compared with controls, indicating a dual function of ROS in defense signaling as well as alternative response patterns activated during microbial infection. Qualitative analysis of induced proteins showed that enzymes linked to ROS production and scavenging were highly induced in control roots, while in MtROP9i the majority of proteins were involved in alternative defense pathways such as cell wall and protein degradation.
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Affiliation(s)
| | | | - Frank Colditz
- Department of Plant Molecular Biology, Institute of Plant Genetics, Leibniz University HannoverHannover, Germany
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Affiliation(s)
- Jesús Jorrín-Novo
- Agricultural and Plant Proteomics, Biochemistry and Molecular Biology, University of Córdoba, Cordoba, Spain.
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Kiirika LM, Behrens C, Braun HP, Colditz F. The Mitochondrial Complexome of Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2013; 4:84. [PMID: 23596449 PMCID: PMC3625726 DOI: 10.3389/fpls.2013.00084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 03/21/2013] [Indexed: 05/30/2023]
Abstract
Legumes (Fabaceae, Leguminosae) are unique in their ability to carry out an elaborate endosymbiotic nitrogen fixation process with rhizobia proteobacteria. The symbiotic nitrogen fixation enables the host plants to grow almost independently of any other nitrogen source. Establishment of symbiosis requires adaptations of the host cellular metabolism, here foremost of the energy metabolism mainly taking place in mitochondria. Since the early 1990s, the galegoid legume Medicago truncatula Gaertn. is a well-established model for studying legume biology, but little is known about the protein complement of mitochondria from this species. An initial characterization of the mitochondrial proteome of M. truncatula (Jemalong A17) was published recently. In the frame of this study, mitochondrial protein complexes were characterized using Two-dimensional (2D) Blue native (BN)/SDS-PAGE. From 139 detected spots, the "first hit" (=most abundant) proteins of 59 spots were identified by mass spectrometry. Here, we present a comprehensive analysis of the mitochondrial "complexome" (the "protein complex proteome") of M. truncatula via 2D BN/SDS-PAGE in combination with highly sensitive MS protein identification. In total, 1,485 proteins were identified within 158 gel spots, representing 467 unique proteins. Data evaluation by the novel GelMap annotation tool allowed recognition of protein complexes of low abundance. Overall, at least 36 mitochondrial protein complexes were found. To our knowledge several of these complexes were described for the first time in Medicago. The data set is accessible under http://www.gelmap.de/medicago/. The mitochondrial protein complex proteomes of Arabidopsis available at http://www.gelmap.de/arabidopsis/ and Medicago are compared.
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Affiliation(s)
- Leonard Muriithi Kiirika
- Department of Plant Molecular Biology, Institute for Plant Genetics, Leibniz University HannoverHannover, Germany
| | - Christof Behrens
- Department of Plant Proteomics, Institute for Plant Genetics, Leibniz University HannoverHannover, Germany
| | - Hans-Peter Braun
- Department of Plant Proteomics, Institute for Plant Genetics, Leibniz University HannoverHannover, Germany
| | - Frank Colditz
- Department of Plant Molecular Biology, Institute for Plant Genetics, Leibniz University HannoverHannover, Germany
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Kiirika LM, Bergmann HF, Schikowsky C, Wimmer D, Korte J, Schmitz U, Niehaus K, Colditz F. Silencing of the Rac1 GTPase MtROP9 in Medicago truncatula stimulates early mycorrhizal and oomycete root colonizations but negatively affects rhizobial infection. PLANT PHYSIOLOGY 2012; 159:501-16. [PMID: 22399646 PMCID: PMC3375982 DOI: 10.1104/pp.112.193706] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 03/06/2012] [Indexed: 05/03/2023]
Abstract
RAC/ROP proteins (ρ-related GTPases of plants) are plant-specific small G proteins that function as molecular switches within elementary signal transduction pathways, including the regulation of reactive oxygen species (ROS) generation during early microbial infection via the activation of NADPH oxidase homologs of plants termed RBOH (for respiratory burst oxidase homolog). We investigated the role of Medicago truncatula Jemalong A17 small GTPase MtROP9, orthologous to Medicago sativa Rac1, via an RNA interference silencing approach. Composite M. truncatula plants (MtROP9i) whose roots have been transformed by Agrobacterium rhizogenes carrying the RNA interference vector were generated and infected with the symbiotic arbuscular mycorrhiza fungus Glomus intraradices and the rhizobial bacterium Sinorhizobium meliloti as well as with the pathogenic oomycete Aphanomyces euteiches. MtROP9i transgenic lines showed a clear growth-reduced phenotype and revealed neither ROS generation nor MtROP9 and MtRBOH gene expression after microbial infection. Coincidently, antioxidative compounds were not induced in infected MtROP9i roots, as documented by differential proteomics (two-dimensional differential gel electrophoresis). Furthermore, MtROP9 knockdown clearly promoted mycorrhizal and A. euteiches early hyphal root colonization, while rhizobial infection was clearly impaired. Infected MtROP9i roots showed, in part, extremely swollen noninfected root hairs and reduced numbers of deformed nodules. S. meliloti nodulation factor treatments of MtROP9i led to deformed root hairs showing progressed swelling of its upper regions or even of the entire root hair and spontaneous constrictions but reduced branching effects occurring only at swollen root hairs. These results suggest a key role of Rac1 GTPase MtROP9 in ROS-mediated early infection signaling.
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Affiliation(s)
| | | | | | | | | | | | | | - Frank Colditz
- Leibniz University of Hannover, Institute for Plant Genetics, Department III, Plant Molecular Biology, D–30419 Hannover, Germany (L.M.K., C.S., D.W., J.K., U.S., F.C.); University of Bielefeld, Department 7, Proteome and Metabolome Research, D–33615 Bielefeld, Germany (H.F.B., K.N.)
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The mitochondrial proteome of the model legume Medicago truncatula. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1658-68. [DOI: 10.1016/j.bbapap.2011.08.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 08/08/2011] [Accepted: 08/15/2011] [Indexed: 11/23/2022]
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Rodríguez-Celma J, Vázquez-Reina S, Orduna J, Abadía A, Abadía J, Álvarez-Fernández A, López-Millán AF. Characterization of Flavins in Roots of Fe-Deficient Strategy I Plants, with a Focus on Medicago truncatula. ACTA ACUST UNITED AC 2011; 52:2173-89. [DOI: 10.1093/pcp/pcr149] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Lei Z, Dai X, Watson BS, Zhao PX, Sumner LW. A legume specific protein database (LegProt) improves the number of identified peptides, confidence scores and overall protein identification success rates for legume proteomics. PHYTOCHEMISTRY 2011; 72:1020-1027. [PMID: 21353266 DOI: 10.1016/j.phytochem.2011.01.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/17/2011] [Accepted: 01/19/2011] [Indexed: 05/30/2023]
Abstract
A legume specific protein database (LegProt) has been created containing sequences from seven legume species, i.e., Glycine max, Lotus japonicus, Medicago sativa, Medicago truncatula, Lupinusalbus, Phaseolus vulgaris, and Pisum sativum. The database consists of amino acid sequences translated from predicted gene models and 6-frame translations of tentative consensus (TC) sequences assembled from expressed sequence tags (ESTs) and singleton ESTs. This database was queried using mass spectral data for protein identification and identification success rates were compared to the NCBI nr database. Specifically, Mascot MS/MS ion searches of tandem nano-LC Q-TOFMS/MS mass spectral data showed that relative to the NCBI nr protein database, the LegProt database yielded a 54% increase in the average protein score (i.e., from NCBI nr 480 to LegProt 739) and a 50% increase in the average number of matched peptides (i.e., from NCBI nr 8 to LegProt 12). The overall identification success rate also increased from 88% (NCBI nr) to 93% (LegProt). Mascot peptide mass fingerprinting (PMF) searches of the LegProt database using MALDI-TOFMS data yielded a significant increase in the identification success rate from 19% (NCBI nr) to 34% (LegProt) while the average scores and average number of matched peptides showed insignificant changes. The results demonstrate that the LegProt database significantly increases legume protein identification success rates and the confidence levels compared to the commonly used NCBI nr. These improvements are primarily due to the presence of a large number of legume specific TC sequences in the LegProt database that were not found in NCBI nr. The LegProt database is freely available for download (http://bioinfo.noble.org/manuscript-support/legumedb) and will serve as a valuable resource for legume proteomics.
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Affiliation(s)
- Zhentian Lei
- Plant Biology Division, The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
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Rodríguez-Celma J, Lattanzio G, Grusak MA, Abadía A, Abadía J, López-Millán AF. Root responses of Medicago truncatula plants grown in two different iron deficiency conditions: changes in root protein profile and riboflavin biosynthesis. J Proteome Res 2011; 10:2590-601. [PMID: 21370931 DOI: 10.1021/pr2000623] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Iron deficiency is a yield-limiting factor with major implications for field crop production in one-third of the world's agricultural areas, especially those with high soil CaCO(3). In the present work, a two-dimensional gel electrophoresis proteomic approach was combined with a study on the riboflavin synthesis pathway, including qPCR and riboflavin determination, to investigate Fe-deficiency responses in Medicago truncatula plants grown with and without CaCO(3). Iron deficiency caused a de novo accumulation of DMRLs and GTPcII, proteins involved in riboflavin biosynthesis, as well as marked increases in root riboflavin concentrations and in the expression of four genes from the riboflavin biosynthetic pathway. Two novel changes found were the increased accumulation of proteins related to N recycling and protein catabolism. Other identified changes were consistent with previously found increases in glycolysis, TCA cycle, and stress-related processes. All effects were more marked in the presence of CaCO(3). Our results show that the riboflavin biosynthesis pathway was up-regulated at the genomic, proteomic, and metabolomic levels under both Fe-deficiency treatments, especially in the presence of CaCO(3). Results also indicate that N recycling occurs in M. truncatula upon Fe deficiency, possibly constituting an additional anaplerotic N and C source for the synthesis of secondary metabolites, carboxylates, and others.
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Affiliation(s)
- Jorge Rodríguez-Celma
- Plant Nutrition Department, Aula Dei Experimental Station (CSIC), P.O. Box 13034, E-50080, Zaragoza, Spain
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