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Priyadarshini P, Kalwan G, Kohli D, Kumar D, Bharadwaj C, Gaikwad K, Jain PK. Small RNA sequencing analysis provides novel insights into microRNA-mediated regulation of defense responses in chickpea against Fusarium wilt infection. PLANTA 2025; 261:23. [PMID: 39751997 DOI: 10.1007/s00425-024-04599-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 12/19/2024] [Indexed: 01/04/2025]
Abstract
MAIN CONCLUSION Small RNA sequencing analysis in two chickpea genotypes, JG 62 (Fusarium wilt-susceptible) and WR 315 (Fusarium wilt-resistant), under Fusarium wilt stress led to identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. A miRNA, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction. Fusarium wilt (FW) of chickpea (Cicer arietinum L.) caused by Fusarium oxysporum f. sp. ciceris (Foc) is a destructive soil-borne disease that severely reduces the chickpea yield and quality globally. In the present study, we have investigated microRNAs and the microRNA/target gene crosstalk involved in chickpea resistance to FW. The control and stress samples from two genotypes, JG 62 (FW-susceptible) and WR 315 (FW-resistant), collected at 10 days post-inoculation (dpi), were selected for small RNA sequencing. A total of 12 libraries were constructed and sequenced using Illumina HiSeq 2500 platform. The sequencing and in silico analyses revealed the identification of 544 miRNAs which included 406 known and 138 novel miRNAs. A total of 50 miRNAs were physically co-localized with Foc-resistance QTLs present on chromosome 2 (also known as Foc hotspot). A total of 115 miRNAs showed differential expression in both the genotypes across different combinations. Prediction and functional annotation of miRNA targets revealed their role in transcription regulation, disease resistance, defense response, metabolism, etc. Ten miRNAs and their targets were validated using poly(A)-based qRT-PCR in two genotypes grown under lab and field conditions. Many miRNAs and their targets showed genotype-specific expression. The expression profiling also highlighted, both, similar and different expression patterns for the same sets of miRNA and mRNA at different stages of Foc infection. A high correlation in expression patterns of the miRNAs and their targets in lab- and field-grown plant samples was observed. Interestingly, Car-miR398 targeted copper chaperone for superoxide dismutase (CCS) that, in turn, regulated superoxide dismutase (SOD) activity during chickpea-Foc interaction. The cleavage site in targets was mapped for three miRNAs by analyzing publicly available degradome data for chickpea. The study, for the first time, provides novel insights into microRNA-mediated regulation of resistance and susceptibility mechanisms in chickpea against FW and opens up avenues for the development of the wilt-resistant cultivars in chickpea.
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Affiliation(s)
- Parichita Priyadarshini
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, Delhi, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, Delhi, India
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, 284003, Uttar Pradesh, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, Delhi, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, Delhi, India
| | - Deshika Kohli
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, Delhi, India
| | - Deepesh Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, Delhi, India
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, Delhi, India
| | - C Bharadwaj
- Division of Genetics, ICAR- Indian Agricultural Research Institute, New Delhi, 110012, Delhi, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, Delhi, India
| | - Pradeep Kumar Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, Delhi, India.
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Yadav P, Sharma K, Tiwari N, Saxena G, Asif MH, Singh S, Kumar M. Comprehensive transcriptome analyses of Fusarium-infected root xylem tissues to decipher genes involved in chickpea wilt resistance. 3 Biotech 2023; 13:390. [PMID: 37942053 PMCID: PMC10630269 DOI: 10.1007/s13205-023-03803-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023] Open
Abstract
Fusarium wilt is the most destructive soil-borne disease that poses a major threat to chickpea production. To comprehensively understand the interaction between chickpea and Fusarium oxysporum, the xylem-specific transcriptome analysis of wilt-resistant (WR315) and wilt-susceptible (JG62) genotypes at an early timepoint (4DPI) was investigated. Differential expression analysis showed that 1368 and 348 DEGs responded to pathogen infection in resistant and susceptible genotypes, respectively. Both genotypes showed transcriptional reprogramming in response to Foc2, but the responses in WR315 were more severe than in JG62. Results of the KEGG pathway analysis revealed that most of the DEGS in both genotypes with enrichment in metabolic pathways, secondary metabolite biosynthesis, plant hormone signal transduction, and carbon metabolism. Genes associated with defense-related metabolites synthesis such as thaumatin-like protein 1b, cysteine-rich receptor-like protein kinases, MLP-like proteins, polygalacturonase inhibitor 2-like, ethylene-responsive transcription factors, glycine-rich cell wall structural protein-like, beta-galactosidase-like, subtilisin-like protease, thioredoxin-like protein, chitin elicitor receptor kinase-like, proline transporter-like, non-specific lipid transfer protein and sugar transporter were mostly up-regulated in resistant as compared to susceptible genotypes. The results of this study provide disease resistance genes, which would be helpful in understanding the Foc resistance mechanism in chickpea. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03803-9.
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Affiliation(s)
- Pooja Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Kritika Sharma
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Nikita Tiwari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Garima Saxena
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Mehar H. Asif
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Swati Singh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Manoj Kumar
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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de Almeida NM, de Almeida AAF, de Almeida Santos N, Mora-Ocampo IY, Pirovani CP. Leaf proteomic profiles in cacao scion-rootstock combinations tolerant and intolerant to cadmium toxicity. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:107987. [PMID: 37722279 DOI: 10.1016/j.plaphy.2023.107987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023]
Abstract
Cd contamination in cacao beans is one of the major problems faced by cocoa producing countries in Latin America. Cacao scion-rootstock combinations influence the Cd accumulation in the shoot of the plant. The objective of this work was to carry out a comparative analysis between cacao scion rootstock combinations (CCN 51/BN 34, CCN 51/PS 13.19, CCN 51/PH 16 and CCN 51/CCN 51), contrasting for tolerance to cadmium (Cd) toxicity, by means of leaf proteomic profiles, in order to elucidate molecular mechanisms involved in tolerance to Cd toxicity. Cacao scion-rootstock combinations were grown in soil with 150 mg Cd kg-1 soil, together with the control treatment. Leaf samples were collected 96 h after treatments were applied. There were alterations in the leaf proteome of the cacao scion-rootstock combinations, whose molecular responses to Cd toxicity varied depending on the combination. Leaf proteomic analyzes provided important information regarding the molecular mechanisms involved in the tolerance and intolerance of cacao scion-rootstock combinations to Cd toxicity. Enzymatic and non-enzymatic antioxidant systems, efficient for eliminating ROS, especially the expressions of APX and SOD, in addition to the increase in the abundance of metalloproteins, such as ferredoxins, rubredoxin, ALMT, Trx-1 and ABC-transporter were key mechanisms used in the Cd detoxification in cacao scion-rootstock combinations tolerant to Cd toxicity. Carboxylic acid metabolism, glucose activation and signal transduction were also important processes in the responses of cacao scion-rootstock combinations to Cd toxicity. The results confirmed CCN 51/BN 34 as a cacao scion-rootstock combination efficient in tolerance to Cd toxicity.
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Affiliation(s)
- Nicolle Moreira de Almeida
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Alex-Alan Furtado de Almeida
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Nayara de Almeida Santos
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Irma Yuliana Mora-Ocampo
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
| | - Carlos Priminho Pirovani
- Department of Biological Sciences, State University of Santa Cruz, Highway Jorge Amado, Km 16, 45662-900, Ilhéus, BA, Brazil.
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Choubey VK, Sakure AA, Kumar S, Vaja MB, Mistry JG, Patel DA. Proteomics profiling and in silico analysis of peptides identified during Fusarium oxysporum infection in castor (Ricinus communis). PHYTOCHEMISTRY 2023:113776. [PMID: 37393971 DOI: 10.1016/j.phytochem.2023.113776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/04/2023]
Abstract
Castor is industrially important non-edible oil seeds crop severely affected by soil borne pathogen Fusarium oxysporum f. sp. ricini which causes heavy economic losses among the castor growing states in India and worldwide. The development of Fusarium wilt resistant varieties in castor is also challenging because the genes identified for resistance are recessive in nature. Unlike transcriptomics and genomics, proteomics is always a method of choice for quick identification of novel proteins expressed during biological events. Therefore, comparative proteomic approach was employed for identification of proteins released in resistant genotype during Fusarium infection. Protein was extracted from inoculated 48-1 resistant and JI-35 susceptible genotype and subjected to 2D-gel electrophoresis coupled with RPLC-MS/MS. This analysis resulted in 18 unique peptides in resistant genotype and 8 unique peptides in susceptible genotype were identified through MASCOT search database. The real time expression study showed that 5 genes namely CCR 1, Germin like protein 5-1, RPP8, Laccase 4 and Chitinase like 6 was found highly up-regulated during Fusarium oxysporum infection. Furthermore, end point PCR analysis of c-DNA showed amplification of three genes namely Chitinase 6 like, RPP8 and β-glucanase exclusively in resistant genotype indicating that these genes may be involved in resistance phenomenon in castor. Up-regulation of CCR-1 and Laccase 4 involved in lignin biosynthesis provides mechanical strength and may help to prevent the entry of fungal mycelia and protein Germin like 5-1 helps to neutralized ROS by SOD activity. The clear role of these genes can be further confirmed through functional genomics for castor improvement and also for development of transgenic in different crops for wilt resistance.
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Affiliation(s)
- Vikash Kumar Choubey
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, Gujarat, India
| | - Amar A Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, Gujarat, India.
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, Gujarat, India
| | - Mahesh B Vaja
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, Gujarat, India
| | - Jigar G Mistry
- Department of Genetics & Plant Breeding, BACA, Anand Agricultural University, Anand, 388110, Gujarat, India
| | - D A Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, Gujarat, India
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Proteometabolomic Analysis Reveals Molecular Features Associated with Grain Size and Antioxidant Properties amongst Chickpea (Cicer arietinum L.) Seeds Genotypes. Antioxidants (Basel) 2022; 11:antiox11101850. [DOI: 10.3390/antiox11101850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Legumes are an essential source of nutrients that complement energy and protein requirements in the human diet. They also contribute to the intake of bioactive compounds such as polyphenols, whose content can vary depending on cultivars and genotypes. We conducted a comparative proteomics and metabolomics study to determine if there were significant variations in relevant nutraceutical compounds in the five genotypes of Kabuli-type chickpea grains. We performed an isobaric tandem mass tag (TMT) couple to synchronous precursor selection (SPS)-MS3 method along with a targeted and untargeted metabolomics approach based on accurate mass spectrometry. We observed an association between the overproduction of proteins involved in starch, lipid, and amino acid metabolism with gibberellin accumulation in large grains. In contrast, we visualized the over-accumulation of proteins associated with water deprivation in small grains. It was possible to visualize in small grains the over-accumulation of some phenolics such as vanillin, salicylic acid, protocatechuic acid, 4-coumaric acid, 4-hydroxybenzoic acid, vanillic acid, ferulic acid, and kaempferol 3-O-glucoside as well as the amino acid l-phenylalanine. The activated phenolic pathway was associated with the higher antioxidant capacity of small grains. Small grains consumption could be advantageous due to their nutraceutical properties.
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Nag P, Paul S, Shriti S, Das S. Defence response in plants and animals against a common fungal pathogen, Fusarium oxysporum. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100135. [PMID: 35909626 PMCID: PMC9325751 DOI: 10.1016/j.crmicr.2022.100135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 03/24/2022] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
Fusarium oxysporum species complex (FOSC) is considered one of the most devastating plant pathogen. FOSC is an emerging pathogen of immunocompromised individuals. Mycotoxins produced by FOSC predisposes the host to other pathogens. Comparative immune reactions in plant and invertebrate show that several antimicrobial peptides (AMPs) and secondary metabolites maybe used as control against Fusarium infection.
Plant pathogens emerging as threat to human and animal health has been a matter of concern within the scientific community. Fusarium oxysporum, predominantly a phytopathogen, can infect both plants and animals. As a plant pathogen, F. oxysporum is one of the most economically damaging pathogen. In humans, F. oxysporum can infect immunocompromised individuals and is increasingly being considered as a problematic pathogen. Mycotoxins produced by F. oxysporum supress the innate immune pathways in both plants and animals. Hence, F. oxysporum is the perfect example for studying similarities and differences between defence strategies adopted by plants and animals. In this review we will discuss the innate immune response of plant and animal hosts for protecting against F. oxysporum infection. Such studies will be helpful for identifying genes, protein and metabolites with antifungal properties suitable for protecting humans.
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Medina-Puche L, Martínez-Rivas FJ, Molina-Hidalgo FJ, García-Gago JA, Mercado JA, Caballero JL, Muñoz-Blanco J, Blanco-Portales R. Ectopic expression of the atypical HLH FaPRE1 gene determines changes in cell size and morphology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110830. [PMID: 33691964 DOI: 10.1016/j.plantsci.2021.110830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 05/22/2023]
Abstract
PACLOBUTRAZOL RESISTANCE (PRE) genes code atypical HLH transcriptional regulators characterized by the absence of a DNA-binding domain but present an HLH dimerization domain. In vegetative tissues, the function of these HLH proteins has been related with cell elongation processes. In strawberry, three FaPRE genes are expressed, two of them (FaPRE2 and FaPRE3) in vegetative tissues while FaPRE1 is fruit receptacle-specific. Ubiquitous FaPRE1 accumulation produced elongated flower receptacles and plants due to the elongation of the main aerial vegetative organs, with the exception of leaves. Histological analysis clearly demonstrated that the observed phenotype was due to significant changes in the parenchymal cell's morphology. In addition, transcriptomic studies of the transgenic elongated flower receptacles allowed to identify a small group of differentially expressed genes that encode cell wall-modifying enzymes. Together, the data seem to indicate that, in the strawberry plant vegetative organs, FaPRE proteins could modulate the expression of genes related with the determination of the size and shape of the parenchymal cells.
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Affiliation(s)
- L Medina-Puche
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - F J Martínez-Rivas
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - F J Molina-Hidalgo
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - J A García-Gago
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Biología Vegetal, Universidad de Málaga, Málaga, Spain.
| | - J A Mercado
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), Departamento de Biología Vegetal, Universidad de Málaga, Málaga, Spain.
| | - J L Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - J Muñoz-Blanco
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
| | - R Blanco-Portales
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa C-6, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, Córdoba, Spain.
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Jain A, Chatterjee A, Das S. Synergistic consortium of beneficial microorganisms in rice rhizosphere promotes host defense to blight-causing Xanthomonas oryzae pv. oryzae. PLANTA 2020; 252:106. [PMID: 33205288 DOI: 10.1007/s00425-020-03515-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/05/2020] [Indexed: 06/11/2023]
Abstract
Rice plants primed with beneficial microbes Bacillus amyloliquefaciens and Aspergillus spinulosporus with biocontrol potential against Xanthomonas oryzae pv. oryzae, provided protection from disease by reprogramming host defence response under pathogen challenge. Plant-beneficial microbe interactions taking place in the rhizosphere are widely used for growth promotion and mitigation of biotic stresses in plants. The present study aims to evaluate the defense network induced by beneficial microorganisms in the rice rhizosphere, and the three-way interaction involved upon inoculation with dreadful bacteria Xanthomonas oryzae pv. oryzae (Xoo). Differential expression of defense-related enzymes, proteins, and genes in rice variety Swarna primed with a microbial consortium of Bacillus amyloliquefaciens and Aspergillus spinulosporus were quantified in the presence and absence of Xoo. The time-based expression profile alterations in leaves under the five distinct treatments "(unprimed unchallenged, unprimed Xoo challenged, B. amyloliquefaciens primed and challenged, A. spinulosporus primed and challenged, B. amyloliquefaciens and A. spinulosporus consortium primed and challenged)" revealed differential early upregulation of SOD, PAL, PO, PPO activities and TPC content in beneficial microbes primed plants in comparison to unprimed challenged plants. The enhanced defense response in all the rice plants recruited with beneficial microbe was also reflected by reduced plant mortality and an increased plant dry biomass and chlorophyll content. Also, more than 550 protein spots were observed per gel by PD Quest software, a total of 55 differentially expressed protein spots were analysed used MALDI-TOF MS, out of which 48 spots were recognized with a significant score with direct or supporting roles in stress alleviation and disease resistance. qRT-PCR was carried out to compare the biochemical and proteomic data to mRNA levels. We conclude that protein biogenesis and alleviated resistance response may contribute to improved biotic stress adaptation. These results might accelerate the functional regulation of the Xoo-receptive proteins in the presence of beneficial rhizospheric microbes and their computation as promising molecular markers for superior disease management.
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Affiliation(s)
- Akansha Jain
- Division of Plant Biology, Bose Institute Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, 700054, India
| | - Anwesha Chatterjee
- Vijaygarh Jyotish Ray College, Jadavpur, Kolkata, West Bengal, 700032, India
| | - Sampa Das
- Division of Plant Biology, Bose Institute Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, 700054, India.
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Zorrilla-Fontanesi Y, Pauwels L, Panis B, Signorelli S, Vanderschuren H, Swennen R. Strategies to revise agrosystems and breeding to control Fusarium wilt of banana. NATURE FOOD 2020; 1:599-604. [PMID: 37128105 DOI: 10.1038/s43016-020-00155-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/26/2020] [Indexed: 05/03/2023]
Abstract
The recent emergence of the fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), the deadly strain that causes Fusarium wilt of banana, has put the banana production chain for export under threat. Here, we propose research priorities and complementary strategies and challenges for effective and efficient mitigation management of Fusarium wilt. Our strategies include diversifying the agrosystems to increase crop resilience, as well as using precision breeding approaches to rapidly assess and introduce disease-resistance genes to develop stable and complete Foc resistance in commercial banana cultivars.
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Affiliation(s)
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics (Technologiepark 71), Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology (Technologiepark 71), Ghent, Belgium
| | - Bart Panis
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- Bioversity International, Heverlee, Belgium
| | - Santiago Signorelli
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
- The School of Molecular Sciences, Faculty of Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Hervé Vanderschuren
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium.
- Plant Genetics Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium.
| | - Rony Swennen
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven, Leuven, Belgium.
- Bioversity International, Heverlee, Belgium.
- International Institute of Tropical Agriculture (IITA), C/o The Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania.
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Jain A, Singh HB, Das S. Deciphering plant-microbe crosstalk through proteomics studies. Microbiol Res 2020; 242:126590. [PMID: 33022544 DOI: 10.1016/j.micres.2020.126590] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 08/21/2020] [Accepted: 08/21/2020] [Indexed: 11/25/2022]
Abstract
Proteomic approaches are being used to elucidate a better discretion of interactions occurring between host, pathogen, and/or beneficial microorganisms at the molecular level. Application of proteomic techniques, unravel pathogenicity, stress-related, and antioxidant proteins expressed amid plant-microbe interactions and good information have been generated. It is being perceived that a fine regulation of protein expression takes place for effective pathogen recognition, induction of resistance, and maintenance of host integrity. However, our knowledge of molecular plant-microbe interactions is still incomplete and inconsequential. This review aims to provide insight into numerous ways used for proteomic investigation including peptide/protein identification, separation, and quantification during host defense response. Here, we highlight the current progress in proteomics of defense responses elicited by bacterial, fungal, and viral pathogens in plants along with which the proteome level changes induced by beneficial microorganisms are also discussed.
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Affiliation(s)
- Akansha Jain
- Division of Plant Biology, Bose Institute Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, 700054, West Bengal, India.
| | - Harikesh Bahadur Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, 221005, India.
| | - Sampa Das
- Division of Plant Biology, Bose Institute Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, 700054, West Bengal, India.
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Gupta S, Mishra SK, Misra S, Pandey V, Agrawal L, Nautiyal CS, Chauhan PS. Revealing the complexity of protein abundance in chickpea root under drought-stress using a comparative proteomics approach. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 151:88-102. [PMID: 32203884 DOI: 10.1016/j.plaphy.2020.03.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 05/02/2023]
Abstract
Global warming has reached an alarming situation, which led to a dangerous climatic condition. The irregular rainfalls and land degradation are the significant consequences of these climatic changes causing a decrease in crop productivity. The effect of drought and its tolerance mechanism, a comparative roots proteomic analysis of chickpea seedlings grown under hydroponic conditions for three weeks, performed at different time points using 2-Dimensional gel electrophoresis (2-DE). After PD-Quest analysis, 110 differentially expressed spots subjected to MALDI-TOF/TOF and 75 spots identified with a significant score. These identified proteins classified into eight categories based on their functional annotation. Proteins involved in carbon and energy metabolism comprised 23% of total identified proteins include mainly glyceraldehyde-3-phosphate dehydrogenase, malate dehydrogenase, transaldolase, and isocitrate dehydrogenase. Proteins related to stress response (heat-shock protein, CS domain protein, and chitinase 2-like) contributed 16% of total protein spots followed by 13% involved in protein metabolism (adenosine kinase 2, and protein disulfide isomerase). ROS metabolism contributed 13% (glutathione S-transferase, ascorbate peroxidase, and thioredoxin), and 9% for signal transduction (actin-101, and 14-3-3-like protein B). Five percent protein identified for secondary metabolism (cinnamoyl-CoA reductase-1 and chalcone-flavononeisomerase 2) and 7% for nitrogen (N) and amino acid metabolism (glutamine synthetase and homocysteine methyltransferase). The abundance of some proteins validated by using Western blotting and Real-Time-PCR. The detailed information for drought-responsive root protein(s) through comparative proteomics analysis can be utilized in the future for genetic improvement programs to develop drought-tolerant chickpea lines.
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Affiliation(s)
- Swati Gupta
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shashank Kumar Mishra
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Sankalp Misra
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vivek Pandey
- Plant Ecology and Environmental Sciences, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Lalit Agrawal
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Department of Agriculture and Allied Sciences, Doon Business School, Dehradun, 248001, India.
| | - Chandra Shekhar Nautiyal
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
| | - Puneet Singh Chauhan
- Microbial Technology Division, Council of Scientific and Industrial Research-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India.
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Defense Response in Chickpea Pod Wall due to Simulated Herbivory Unfolds Differential Proteome Profile. Protein J 2020; 39:240-257. [PMID: 32356273 DOI: 10.1007/s10930-020-09899-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The pod wall of legumes is known to protect the developing seeds from pests and pathogens. However, the mechanism of conferring defense against insects has not yet been deciphered. Here, we have utilized 2-dimensional gel electrophoresis (2D-GE) coupled with mass spectrometry (MS/MS) to identify over expressed proteins in the pod wall of two different cultivars (commercial cultivar: JG 11 and tolerant cultivar: ICC 506-EB) of chickpea after 12 h of application of Helicoverpa armigera oral secretions (simulated herbivory). The assays were performed with a view that larvae are a voracious feeder and cause substantial damage to the pod within 12 h. A total of 600 reproducible protein spots were detected on gels, and the comparative analysis helped identify 35 (12 up-regulated, 23 down-regulated) and 20 (10 up-regulated, 10 down-regulated) differentially expressed proteins in JG 11 and ICC 506-EB, respectively. Functional classification of protein spots of each cultivar after MS/MS indicated that the differentially expressed proteins were associated with various metabolic activities. Also, stress-related proteins such as mannitol dehydrogenase (MADH), disease resistance-like protein-CSA1, serine/threonine kinase (D6PKL2), endoglucanase-19 etc. were up-regulated due to simulated herbivory. The proteins identified with a possible role in defense were further analyzed using the STRING database to advance our knowledge on their interacting partners. It decoded the involvement of several reactive oxygen species (ROS) scavengers and other proteins involved in cell wall reinforcement. The biochemical analysis also confirmed the active role of ROS scavengers during simulated herbivory. Thus, our study provides valuable new insights on chickpea-H.armigera interactions at the protein level.
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iTRAQ-Based Proteomic Analysis of Watermelon Fruits in Response to Cucumber green mottle mosaic virus Infection. Int J Mol Sci 2020; 21:ijms21072541. [PMID: 32268502 PMCID: PMC7178218 DOI: 10.3390/ijms21072541] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 01/07/2023] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) is an important viral pathogen on cucurbit plants worldwide, which can cause severe fruit decay symptoms on infected watermelon (usually called “watermelon blood flesh”). However, the molecular mechanism of this disease has not been well understood. In this study, we employed the isobaric tags for relative and absolute quantitation (iTRAQ) technique to analyze the proteomic profiles of watermelon fruits in response to CGMMV infection. A total of 595 differentially accumulated proteins (DAPs) were identified, of which 404 were upregulated and 191 were downregulated. Functional annotation analysis showed that these DAPs were mainly involved in photosynthesis, carbohydrate metabolism, secondary metabolite biosynthesis, plant–pathogen interaction, and protein synthesis and turnover. The accumulation levels of several proteins related to chlorophyll metabolism, pyruvate metabolism, TCA cycle, heat shock proteins, thioredoxins, ribosomal proteins, translation initiation factors, and elongation factors were strongly affected by CGMMV infection. Furthermore, a correlation analysis was performed between CGMMV-responsive proteome and transcriptome data of watermelon fruits obtained in our previous study, which could contribute to comprehensively elucidating the molecular mechanism of “watermelon blood flesh”. To confirm the iTRAQ-based proteome data, the corresponding transcripts of ten DAPs were validated by determining their abundance via quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). These results could provide a scientific basis for in-depth understanding of the pathogenic mechanisms underlying CGMMV-induced “watermelon blood flesh”, and lay the foundation for further functional exploration and verification of related genes and proteins.
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Caballo C, Castro P, Gil J, Millan T, Rubio J, Die JV. Candidate genes expression profiling during wilting in chickpea caused by Fusarium oxysporum f. sp. ciceris race 5. PLoS One 2019; 14:e0224212. [PMID: 31644597 PMCID: PMC6808423 DOI: 10.1371/journal.pone.0224212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/08/2019] [Indexed: 01/23/2023] Open
Abstract
Chickpea production may be seriously threatened by Fusarium wilt, a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. ciceris. F. oxysporum race 5 is the most important race in the Mediterranean basin. Recently, the region responsible for resistance race 5 has been delimited within a region on chromosome 2 that spans 820 kb. To gain a better understanding of this genomic region, we used a transcriptomic approach based on quantitative real-time PCR to analyze the expression profiles of 22 selected candidate genes. We used a pair of near-isogenic lines (NILs) differing in their sensitivity to Fusarium race 5 (resistant vs susceptible) to monitor the transcriptional changes over a time-course experiment (24, 48, and 72 hours post inoculation, hpi). Qualitative differences occurred during the timing of regulation. A cluster of 12 genes were induced by the resistant NIL at 24 hpi, whereas a second cluster contained 9 genes induced by the susceptible NIL at 48 hpi. Their possible functions in the molecular defence of chickpea is discussed. Our study provides new insight into the molecular defence against Fusarium race 5 and demonstrates that development of NILs is a rich resource to facilitate the detection of candidate genes. The new genes regulated here may be useful against other Fusarium races.
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Affiliation(s)
- Cristina Caballo
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, Córdoba, Spain
| | - Patricia Castro
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Juan Gil
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Teresa Millan
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
| | - Josefa Rubio
- Área de Genómica y Biotecnología, IFAPA, Alameda del Obispo, Córdoba, Spain
| | - Jose V. Die
- Department of Genetics - ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, Spain
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15
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Chakraborty J, Ghosh P, Sen S, Nandi AK, Das S. CaMPK9 increases the stability of CaWRKY40 transcription factor which triggers defense response in chickpea upon Fusarium oxysporum f. sp. ciceri Race1 infection. PLANT MOLECULAR BIOLOGY 2019; 100:411-431. [PMID: 30953279 DOI: 10.1007/s11103-019-00868-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 04/01/2019] [Indexed: 05/28/2023]
Abstract
Physical interaction and phosphorylation by CaMPK9 protects the degradation of CaWRKY40 that induces resistance response in chickpea to Fusarium wilt disease by modulating the transcription of defense responsive genes. WRKY transcription factors (TFs) are the global regulators of plant defense signaling that modulate immune responses in host plants by regulating transcription of downstream target genes upon challenged by pathogens. However, very little is known about immune responsive role of Cicer arietinum L. (Ca) WRKY TFs particularly. Using two contrasting chickpea genotypes with respect to resistance against Fusarium oxysporum f. sp. ciceri Race1 (Foc1), we demonstrate transcript accumulation of different CaWRKYs under multiple stresses and establish that CaWRKY40 triggers defense. CaWRKY40 overexpressing chickpea mounts resistance to Foc1 by positively modulating the defense related gene expression. EMSA, ChIP assay and real-time PCR analyses suggest CaWRKY40 binds at the promoters and positively regulates transcription of CaDefensin and CaWRKY33. Further studies revealed that mitogen Activated Protein Kinase9 (CaMPK9) phosphorylates CaWRKY40 by directly interacting with its two canonical serine residues. Interestingly, CaMPK9 is unable to interact with CaWRKY40 when the relevant two serine residues were replaced by alanine. Overexpression of serine mutated WRKY40 isoform in chickpea fails to provide resistance against Foc1. Mutated WRKY40Ser.224/225 to AA overexpressing chickpea resumes its ability to confer resistance against Foc1 after application of 26S proteasomal inhibitor MG132, suggests that phosphorylation is essential to protect CaWRKY40 from proteasomal degradation. CaMPK9 silencing also led to susceptibility in chickpea to Foc1. Altogether, our results elucidate positive regulatory roles of CaMPK9 and CaWRKY40 in modulating defense response in chickpea upon Foc1 infection.
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Affiliation(s)
- Joydeep Chakraborty
- Division of Plant Biology, Bose Institute, Centenary Campus, P-1/12, CIT Scheme-VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India
| | - Prithwi Ghosh
- Division of Plant Biology, Bose Institute, Centenary Campus, P-1/12, CIT Scheme-VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Senjuti Sen
- Division of Plant Biology, Bose Institute, Centenary Campus, P-1/12, CIT Scheme-VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India
| | - Ashis Kumar Nandi
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sampa Das
- Division of Plant Biology, Bose Institute, Centenary Campus, P-1/12, CIT Scheme-VIIM, Kankurgachi, Kolkata, West Bengal, 700054, India.
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16
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Ashraf N, Basu S, Narula K, Ghosh S, Tayal R, Gangisetty N, Biswas S, Aggarwal PR, Chakraborty N, Chakraborty S. Integrative network analyses of wilt transcriptome in chickpea reveal genotype dependent regulatory hubs in immunity and susceptibility. Sci Rep 2018; 8:6528. [PMID: 29695764 PMCID: PMC5916944 DOI: 10.1038/s41598-018-19919-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/05/2018] [Indexed: 12/12/2022] Open
Abstract
Host specific resistance and non-host resistance are two plant immune responses to counter pathogen invasion. Gene network organizing principles leading to quantitative differences in resistant and susceptible host during host specific resistance are poorly understood. Vascular wilt caused by root pathogen Fusarium species is complex and governed by host specific resistance in crop plants, including chickpea. Here, we temporally profiled two contrasting chickpea genotypes in disease and immune state to better understand gene expression switches in host specific resistance. Integrative gene-regulatory network elucidated tangible insight into interaction coordinators leading to pathway determination governing distinct (disease or immune) phenotypes. Global network analysis identified five major hubs with 389 co-regulated genes. Functional enrichment revealed immunome containing three subnetworks involving CTI, PTI and ETI and wilt diseasome encompassing four subnetworks highlighting pathogen perception, penetration, colonization and disease establishment. These subnetworks likely represent key components that coordinate various biological processes favouring defence or disease. Furthermore, we identified core 76 disease/immunity related genes through subcellular analysis. Our regularized network with robust statistical assessment captured known and unexpected gene interaction, candidate novel regulators as future biomarkers and first time showed system-wide quantitative architecture corresponding to genotypic characteristics in wilt landscape.
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Affiliation(s)
- Nasheeman Ashraf
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swaraj Basu
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sudip Ghosh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rajul Tayal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nagaraju Gangisetty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sushmita Biswas
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pooja R Aggarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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17
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Saabale PR, Dubey SC, Priyanka K, Sharma TR. Analysis of differential transcript expression in chickpea during compatible and incompatible interactions with Fusarium oxysporum f. sp . ciceris Race 4. 3 Biotech 2018; 8:111. [PMID: 29430372 DOI: 10.1007/s13205-018-1128-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/19/2018] [Indexed: 11/24/2022] Open
Abstract
The present study reports the transcriptome analysis of resistance (WR315) and susceptible (JG62) genotypes of chickpea in response to Fusarium oxysporum f. sp. ciceris (Foc) race 4 using the method of suppression subtractive hybridization. Altogether, 162 chickpea-expressed sequence tags (ESTs) were identified from two libraries and analyzed to catalog eight functional categories. These ESTs could be assembled into 18 contigs and 144 singletons with 10 contigs and 68 singletons from compatible and 8 contigs and 70 singletons from incompatible interaction. The largest category consisted of ESTs which encode for proteins related to hypothetical proteins (22.8%), followed by energy and metabolism (20.3%)-related genes, defense and cell rescue-related genes (17.9%) and signal transduction-related genes (16%). Among them, 17.1 and 18.7% were defense-related genes in compatible and incompatible interaction, respectively. These ESTs mainly includes various putative genes related to oxidative burst, pathogenesis and secondary metabolism. Induction of putative superoxide dismutase, metallothionein, 4-coumarate-CoA ligase, heat shock proteins and cysteine proteases indicated oxidative burst after infection. The ESTs belonged to various functional categories which were directly and indirectly associated with defense signaling pathways. Quantitative and semi-quantitative polymerase chain reaction exhibited differential expression of candidate genes and detected higher levels in incompatible interaction compared to compatible interaction. The present study revealed partial molecular mechanism associated with the resistance in chickpea against Foc, which is the key to design a strategy for incorporation of resistance via either biotechnological means or introgression of resistance genes.
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Affiliation(s)
- Parasappa R Saabale
- 1Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110 012 India
- 2Present Address: Regional Research Centre, Indian Institute of Pulses Research, Dharwad, 580005 India
| | - Sunil C Dubey
- 1Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110 012 India
- 3Present Address: Division of Plant Quarantine, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110 012 India
| | - Kumari Priyanka
- 1Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110 012 India
| | - Tilak R Sharma
- 4National Research Centre on Plant Biotechnology, LBS Centre, IARI, New Delhi, 110 012 India
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18
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Carneiro JMT, Chacón-Madrid K, Galazzi RM, Campos BK, Arruda SCC, Azevedo RA, Arruda MAZ. Evaluation of silicon influence on the mitigation of cadmium-stress in the development of Arabidopsis thaliana through total metal content, proteomic and enzymatic approaches. J Trace Elem Med Biol 2017; 44:50-58. [PMID: 28965600 DOI: 10.1016/j.jtemb.2017.05.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/18/2017] [Accepted: 05/30/2017] [Indexed: 12/20/2022]
Abstract
The mitigation of Cd-stress through Si addition to Arabidopsis thaliana cultivation is evaluated in terms of total metal content, proteomic and enzymatic approaches. Four different treatment are evaluated: TC (control, without Si or Cd addition), T1 (with Si addition), T2 (with Cd addition), and T3 (with Si and Cd addition). Through the total determination of Cd and Si in Arabidopsis leaves, the Cd concentration decreased by half when T2 is compared with T3 treatment. In terms of proteomic approach, some differential protein species are achieved by comparative proteomics through 2-D DIGE of all treatments evaluated. Fifty six differential abundant proteins spots (abundance factor ≥1.5) are detected, and 32 of them accurately characterized and identified through nESI-LC-MS/MS. These proteins are differentially produced due to Cd and/or Si treatments, which mainly include proteins associated with disease/defense, energy and metabolism. The most difference in the abundance of proteins is found due to the presence or absence of Si in plants treated with Cd. Regarding the enzymatic approaches, a major increase is found on APX, CAT and GR activities (5.0, 3.5, and 1.5-fold, respectively). The same is observed for the MDA concentration because an increase of 3-fold is found when TC are compared to those treated with T2. However, when T3 plants are evaluated, the enzymes activities are similar to TC plants. Differences ranging from 6.5 to 21% are detected considering the activity of SOD in the treatments (T1-T3 x TC). The decreased activities of CAT, APX and GR and lower MDA concentration indicate a lower reactive oxygen species production in plants treated with Cd and Si. Based on a proteomics point of view it is possible to conclude that Si-Cd interactions occur at protein level and allow plants to respond effectively to the Cd toxicity, revealing the active involvement of Si on mechanisms involved in Si-induced Cd tolerance in Arabidopsis plants. Additionally, from an enzymatic point of view, it is possible to conclude that Si positively interferes diminishing the negative effects of Cd in Arabidopsis by decreasing the reactive oxygen species generation and increasing the antioxidative enzyme activity.
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Affiliation(s)
- Josiane M T Carneiro
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Katherine Chacón-Madrid
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Rodrigo M Galazzi
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Bruna K Campos
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Sandra C C Arruda
- Department of Genetics, Laboratory of Biochemistry and Genetics of Plants, Escola Superior de Agricultura Luiz de Queiroz, ESALQ-University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Ricardo A Azevedo
- Department of Genetics, Laboratory of Biochemistry and Genetics of Plants, Escola Superior de Agricultura Luiz de Queiroz, ESALQ-University of São Paulo, 13400-970, Piracicaba, SP, Brazil
| | - Marco A Z Arruda
- Spectrometry, Sample Preparation and Mechanization Group-GEPAM, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil; National Institute of Science and Technology for Bioanalytics, Institute of Chemistry, University of Campinas-Unicamp, P.O. Box 6154, 13083-970, Campinas, SP, Brazil.
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19
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Gupta S, Bhar A, Chatterjee M, Ghosh A, Das S. Transcriptomic dissection reveals wide spread differential expression in chickpea during early time points of Fusarium oxysporum f. sp. ciceri Race 1 attack. PLoS One 2017; 12:e0178164. [PMID: 28542579 PMCID: PMC5460890 DOI: 10.1371/journal.pone.0178164] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 05/09/2017] [Indexed: 12/19/2022] Open
Abstract
Plants' reaction to underground microorganisms is complex as sessile nature of plants compels them to prioritize their responses to diverse microorganisms both pathogenic and symbiotic. Roots of important crops are directly exposed to diverse microorganisms, but investigations involving root pathogens are significantly less. Thus, more studies involving root pathogens and their target crops are necessitated to enrich the understanding of underground interactions. Present study reported the molecular complexities in chickpea during Fusarium oxysporum f. sp. ciceri Race 1 (Foc1) infection. Transcriptomic dissections using RNA-seq showed significantly differential expression of molecular transcripts between infected and control plants of both susceptible and resistant genotypes. Radar plot analyses showed maximum expressional undulations after infection in both susceptible and resistant plants. Gene ontology and functional clustering showed large number of transcripts controlling basic metabolism of plants. Network analyses demonstrated defense components like peptidyl cis/trans isomerase, MAP kinase, beta 1,3 glucanase, serine threonine kinase, patatin like protein, lactolylglutathione lyase, coproporphyrinogen III oxidase, sulfotransferases; reactive oxygen species regulating components like respiratory burst oxidase, superoxide dismutases, cytochrome b5 reductase, glutathione reductase, thioredoxin reductase, ATPase; metabolism regulating components, myo inositol phosphate, carboxylate synthase; transport related gamma tonoplast intrinsic protein, and structural component, ubiquitins to serve as important nodals of defense signaling network. These nodal molecules probably served as hub controllers of defense signaling. Functional characterization of these hub molecules would not only help in developing better understanding of chickpea-Foc1 interaction but also place them as promising candidates for resistance management programs against vascular wilt of legumes.
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Affiliation(s)
- Sumanti Gupta
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
| | - Anirban Bhar
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
| | - Moniya Chatterjee
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
| | - Amartya Ghosh
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
| | - Sampa Das
- Division of Plant Biology, Bose Institute, Centenary Campus, P 1/12, CIT Scheme, VII-M, Kankurgachi, Kolkata, West Bengal, India
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20
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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: 4.0] [Reference Citation Analysis] [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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Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry. Biochem Res Int 2016; 2016:1049462. [PMID: 27144024 PMCID: PMC4842031 DOI: 10.1155/2016/1049462] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/27/2016] [Accepted: 03/20/2016] [Indexed: 11/17/2022] Open
Abstract
Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana.
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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: 7.4] [Reference Citation Analysis] [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, SWITZERLAND) 2016; 5:E11. [PMID: 27135231 PMCID: PMC4844425 DOI: 10.3390/plants5010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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Belowground Defence Strategies Against Fusarium oxysporum. BELOWGROUND DEFENCE STRATEGIES IN PLANTS 2016. [DOI: 10.1007/978-3-319-42319-7_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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Narula K, Pandey A, Gayali S, Chakraborty N, Chakraborty S. Birth of plant proteomics in India: a new horizon. J Proteomics 2015; 127:34-43. [PMID: 25920368 DOI: 10.1016/j.jprot.2015.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 01/02/2023]
Abstract
UNLABELLED In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. BIOLOGICAL SIGNIFICANCE The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Aarti Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Zingde SM. Has Proteomics come of age in India? J Proteomics 2015; 127:3-6. [PMID: 25748142 DOI: 10.1016/j.jprot.2015.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/25/2015] [Indexed: 12/24/2022]
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