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Pandey P, Patil M, Priya P, Senthil-Kumar M. When two negatives make a positive: the favorable impact of the combination of abiotic stress and pathogen infection on plants. J Exp Bot 2024; 75:674-688. [PMID: 37864841 DOI: 10.1093/jxb/erad413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
Combined abiotic and biotic stresses modify plant defense signaling, leading to either the activation or suppression of defense responses. Although the majority of combined abiotic and biotic stresses reduce plant fitness, certain abiotic stresses reduce the severity of pathogen infection in plants. Remarkably, certain pathogens also improve the tolerance of some plants to a few abiotic stresses. While considerable research focuses on the detrimental impact of combined stresses on plants, the upside of combined stress remains hidden. This review succinctly discusses the interactions between abiotic stresses and pathogen infection that benefit plant fitness. Various factors that govern the positive influence of combined abiotic stress and pathogen infection on plant performance are also discussed. In addition, we provide a brief overview of the role of pathogens, mainly viruses, in improving plant responses to abiotic stresses. We further highlight the critical nodes in defense signaling that guide plant responses during abiotic stress towards enhanced resistance to pathogens. Studies on antagonistic interactions between abiotic and biotic stressors can uncover candidates in host plant defense that may shield plants from combined stresses.
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Affiliation(s)
- Prachi Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi 110067, India
| | - Mahesh Patil
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi 110067, India
| | - Piyush Priya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi 110067, India
| | - Muthappa Senthil-Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi 110067, India
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Dwivedi V, Pal L, Singh S, Singh NP, Parida SK, Chattopadhyay D. The chickpea WIP2 gene underlying a major QTL contributes to lateral root development. J Exp Bot 2024; 75:642-657. [PMID: 37158162 DOI: 10.1093/jxb/erad171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
Abstract
Lateral roots are a major component of root system architecture, and lateral root count (LRC) positively contributes to yield under drought in chickpea. To understand the genetic regulation of LRC, a biparental mapping population derived from two chickpea accessions having contrasting LRCs was genotyped by sequencing, and phenotyped to map four major quantitative trait loci (QTLs) contributing to 13-32% of the LRC trait variation. A single- nucleotide polymorphism tightly linked to the locus contributing to highest trait variation was located on the coding region of a gene (CaWIP2), orthologous to NO TRANSMITTING TRACT/WIP domain protein 2 (NTT/WIP2) gene of Arabidopsis thaliana. A polymorphic simple sequence repeat (SSR) in the CaWIP2 promoter showed differentiation between low versus high LRC parents and mapping individuals, suggesting its utility for marker-assisted selection. CaWIP2 promoter showed strong expression in chickpea apical root meristem and lateral root primordia. Expression of CaWIP2 under its native promoter in the Arabidopsis wip2wip4wip5 mutant rescued its rootless phenotype to produce more lateral roots than the wild-type plants, and led to formation of amyloplasts in the columella. CaWIP2 expression also induced the expression of genes that regulate lateral root emergence. Our study identified a gene-based marker for LRC which will be useful for developing drought-tolerant, high-yielding chickpea varieties.
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Affiliation(s)
- Vikas Dwivedi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Lalita Pal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shilpi Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nagendra Pratap Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Naik J, Tyagi S, Rajput R, Kumar P, Pucker B, Bisht NC, Misra P, Stracke R, Pandey A. Flavonols affect the interrelated glucosinolate and camalexin biosynthetic pathways in Arabidopsis thaliana. J Exp Bot 2024; 75:219-240. [PMID: 37813680 DOI: 10.1093/jxb/erad391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/04/2023] [Indexed: 10/11/2023]
Abstract
Flavonols are structurally and functionally diverse biomolecules involved in plant biotic and abiotic stress tolerance, pollen development, and inhibition of auxin transport. However, their effects on global gene expression and signaling pathways are unclear. To explore the roles of flavonol metabolites in signaling, we performed comparative transcriptome and targeted metabolite profiling of seedlings from the flavonol-deficient Arabidopsis loss-of-function mutant flavonol synthase1 (fls1) with and without exogenous supplementation of flavonol derivatives (kaempferol, quercetin, and rutin). RNA-seq results indicated that flavonols modulate various biological and metabolic pathways, with significant alterations in camalexin and aliphatic glucosinolate synthesis. Flavonols negatively regulated camalexin biosynthesis but appeared to promote the accumulation of aliphatic glucosinolates via transcription factor-mediated up-regulation of biosynthesis genes. Interestingly, upstream amino acid biosynthesis genes involved in methionine and tryptophan synthesis were altered under flavonol deficiency and exogenous supplementation. Quercetin treatment significantly up-regulated aliphatic glucosinolate biosynthesis genes compared with kaempferol and rutin. In addition, expression and metabolite analysis of the transparent testa7 mutant, which lacks hydroxylated flavonol derivatives, clarified the role of quercetin in the glucosinolate biosynthesis pathway. This study elucidates the molecular mechanisms by which flavonols interfere with signaling pathways, their molecular targets, and the multiple biological activities of flavonols in plants.
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Affiliation(s)
- Jogindra Naik
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shivi Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ruchika Rajput
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pawan Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Boas Pucker
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, 33615 Bielefeld, Germany
| | - Naveen C Bisht
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Prashant Misra
- Plant Sciences and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
| | - Ralf Stracke
- Faculty of Biology, Genetics and Genomics of Plants, Bielefeld University, 33615 Bielefeld, Germany
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Priya P, Patil M, Pandey P, Singh A, Babu VS, Senthil-Kumar M. Stress combinations and their interactions in plants database: a one-stop resource on combined stress responses in plants. Plant J 2023; 116:1097-1117. [PMID: 37824297 DOI: 10.1111/tpj.16497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/23/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
We have developed a compendium and interactive platform, named Stress Combinations and their Interactions in Plants Database (SCIPDb; http://www.nipgr.ac.in/scipdb.php), which offers information on morpho-physio-biochemical (phenome) and molecular (transcriptome and metabolome) responses of plants to different stress combinations. SCIPDb is a plant stress informatics hub for data mining on phenome, transcriptome, trait-gene ontology, and data-driven research for advancing mechanistic understanding of combined stress biology. We analyzed global phenome data from 939 studies to delineate the effects of various stress combinations on yield in major crops and found that yield was substantially affected under abiotic-abiotic stresses. Transcriptome datasets from 36 studies hosted in SCIPDb identified novel genes, whose roles have not been earlier established in combined stress. Integretome analysis under combined drought-heat stress pinpointed carbohydrate, amino acid, and energy metabolism pathways as the crucial metabolic, proteomic, and transcriptional components in plant tolerance to combined stress. These examples illustrate the application of SCIPDb in identifying novel genes and pathways involved in combined stress tolerance. Further, we showed the application of this database in identifying novel candidate genes and pathways for combined drought and pathogen stress tolerance. To our knowledge, SCIPDb is the only publicly available platform offering combined stress-specific omics big data visualization tools, such as an interactive scrollbar, stress matrix, radial tree, global distribution map, meta-phenome analysis, search, BLAST, transcript expression pattern table, Manhattan plot, and co-expression network. These tools facilitate a better understanding of the mechanisms underlying plant responses to combined stresses.
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Affiliation(s)
- Piyush Priya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110067, India
| | - Mahesh Patil
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110067, India
| | - Prachi Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110067, India
| | - Anupriya Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110067, India
| | - Vishnu Sudha Babu
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110067, India
| | - Muthappa Senthil-Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi, 110067, India
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Singh SK, Shree A, Verma S, Singh K, Kumar K, Srivastava V, Singh R, Saxena S, Singh AP, Pandey A, Verma PK. The nuclear effector ArPEC25 from the necrotrophic fungus Ascochyta rabiei targets the chickpea transcription factor CaβLIM1a and negatively modulates lignin biosynthesis, increasing host susceptibility. Plant Cell 2023; 35:1134-1159. [PMID: 36585808 PMCID: PMC10015165 DOI: 10.1093/plcell/koac372] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 12/02/2022] [Accepted: 12/21/2022] [Indexed: 05/29/2023]
Abstract
Fungal pathogens deploy a barrage of secreted effectors to subvert host immunity, often by evading, disrupting, or altering key components of transcription, defense signaling, and metabolic pathways. However, the underlying mechanisms of effectors and their host targets are largely unexplored in necrotrophic fungal pathogens. Here, we describe the effector protein Ascochyta rabiei PEXEL-like Effector Candidate 25 (ArPEC25), which is secreted by the necrotroph A. rabiei, the causal agent of Ascochyta blight disease in chickpea (Cicer arietinum), and is indispensable for virulence. After entering host cells, ArPEC25 localizes to the nucleus and targets the host LIM transcription factor CaβLIM1a. CaβLIM1a is a transcriptional regulator of CaPAL1, which encodes phenylalanine ammonia lyase (PAL), the regulatory, gatekeeping enzyme of the phenylpropanoid pathway. ArPEC25 inhibits the transactivation of CaβLIM1a by interfering with its DNA-binding ability, resulting in negative regulation of the phenylpropanoid pathway and decreased levels of intermediates of lignin biosynthesis, thereby suppressing lignin production. Our findings illustrate the role of fungal effectors in enhancing virulence by targeting a key defense pathway that leads to the biosynthesis of various secondary metabolites and antifungal compounds. This study provides a template for the study of less explored necrotrophic effectors and their host target functions.
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Affiliation(s)
- Shreenivas Kumar Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ankita Shree
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sandhya Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kunal Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kamal Kumar
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vikas Srivastava
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ritu Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Samiksha Saxena
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Agam Prasad Singh
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ashutosh Pandey
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Plant Immunity Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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Agrawal R, Sharma M, Dwivedi N, Maji S, Thakur P, Junaid A, Fajkus J, Laxmi A, Thakur JK. MEDIATOR SUBUNIT17 integrates jasmonate and auxin signaling pathways to regulate thermomorphogenesis. Plant Physiol 2022; 189:2259-2280. [PMID: 35567489 PMCID: PMC9342970 DOI: 10.1093/plphys/kiac220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/20/2022] [Indexed: 05/16/2023]
Abstract
Plant adjustment to environmental changes involves complex crosstalk between extrinsic and intrinsic cues. In the past two decades, extensive research has elucidated the key roles of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and the phytohormone auxin in thermomorphogenesis. In this study, we identified a previously unexplored role of jasmonate (JA) signaling components, the Mediator complex, and their integration with auxin signaling during thermomorphogenesis in Arabidopsis (Arabidopsis thaliana). Warm temperature induces expression of JA signaling genes including MYC2, but, surprisingly, this transcriptional activation is not JA dependent. Warm temperature also promotes accumulation of the JA signaling receptor CORONATINE INSENSITIVE1 (COI1) and degradation of the JA signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9, which probably leads to de-repression of MYC2, enabling it to contribute to the expression of MEDIATOR SUBUNIT17 (MED17). In response to warm temperature, MED17 occupies the promoters of thermosensory genes including PIF4, YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE19 (IAA19), and IAA29. Moreover, MED17 facilitates enrichment of H3K4me3 on the promoters of PIF4, YUC8, IAA19, and IAA29 genes. Interestingly, both occupancy of MED17 and enrichment of H3K4me3 on these thermomorphogenesis-related promoters are dependent on PIF4 (or PIFs). Altered accumulation of COI1 under warm temperature in the med17 mutant suggests the possibility of a feedback mechanism. Overall, this study reveals the role of the Mediator complex as an integrator of JA and auxin signaling pathways during thermomorphogenesis.
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Affiliation(s)
- Rekha Agrawal
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Mohan Sharma
- Signalling Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Pallabi Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Alim Junaid
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ashverya Laxmi
- Signalling Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, New Delhi 110067, India
- Plant Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
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Halder K, Chaudhuri A, Abdin MZ, Majee M, Datta A. Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses. Plants (Basel) 2022; 11:1449. [PMID: 35684223 PMCID: PMC9182740 DOI: 10.3390/plants11111449] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Plants' stress response machinery is characterized by an intricate network of signaling cascades that receive and transmit environmental cues and ultimately trigger transcriptional reprogramming. The family of epigenetic regulators that are the key players in the stress-induced signaling cascade comprise of chromatin remodelers, histone modifiers, DNA modifiers and regulatory non-coding RNAs. Changes in the histone modification and DNA methylation lead to major alterations in the expression level and pattern of stress-responsive genes to adjust with abiotic stress conditions namely heat, cold, drought and salinity. The spotlight of this review falls primarily on the chromatin restructuring under severe abiotic stresses, crosstalk between epigenetic regulators along with a brief discussion on stress priming in plants.
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Affiliation(s)
- Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Malik Z. Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
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Singh RK, Prasad A, Muthamilarasan M, Parida SK, Prasad M. Breeding and biotechnological interventions for trait improvement: status and prospects. Planta 2020; 252:54. [PMID: 32948920 PMCID: PMC7500504 DOI: 10.1007/s00425-020-03465-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/12/2020] [Indexed: 05/06/2023]
Abstract
Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
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Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Yadav SK, Das J, Kumar R, Jha G. Calcium regulates the mycophagous ability of Burkholderia gladioli strain NGJ1 in a type III secretion system-dependent manner. BMC Microbiol 2020; 20:216. [PMID: 32689944 PMCID: PMC7372643 DOI: 10.1186/s12866-020-01897-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 07/12/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND A rice associated bacterium Burkholderia gladioli strain NGJ1 demonstrates mycophagy, a phenomenon wherein bacteria feed on fungi. Previously, we have reported that NGJ1 utilizes type III secretion system (T3SS) to deliver a prophage tail-like protein (Bg_9562) into fungal cells to establish mycophagy. RESULTS In this study, we report that calcium ion concentration influences the mycophagous ability of NGJ1 on Rhizoctonia solani, an important fungal pathogen. The calcium limiting condition promotes mycophagy while high calcium environment prevents it. The expression of various T3SS apparatus encoding genes of NGJ1 was induced and secretion of several potential T3SS effector proteins (including Bg_9562) into extracellular milieu was triggered under calcium limiting condition. Using LC-MS/MS proteome analysis, we identified several calcium regulated T3SS effector proteins of NGJ1. The expression of genes encoding some of these effector proteins was upregulated during mycophagous interaction of NGJ1 with R. solani. Further, mutation of one of these genes (endo-β-1, 3- glucanase) rendered the mutant NGJ1 bacterium defective in mycophagy while complementation with full length copy of the gene restored its mycophagous activity. CONCLUSION Our study provides evidence that low calcium environment triggers secretion of various T3SS effectors proteins into the extracellular milieu and suggests the importance of cocktail of these proteins in promoting mycophagy.
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Affiliation(s)
- Sunil Kumar Yadav
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Joyati Das
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rahul Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Aggarwal PR, Nag P, Choudhary P, Chakraborty N, Chakraborty S. Genotype-independent Agrobacterium rhizogenes-mediated root transformation of chickpea: a rapid and efficient method for reverse genetics studies. Plant Methods 2018; 14:55. [PMID: 29988950 PMCID: PMC6034309 DOI: 10.1186/s13007-018-0315-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 06/02/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Chickpea (Cicer arietinum L.), an important legume crop is one of the major source of dietary protein. Developing an efficient and reproducible transformation method is imperative to expedite functional genomics studies in this crop. Here, we present an optimized and detailed procedure for Agrobacterium rhizogenes-mediated root transformation of chickpea. RESULTS Transformation positive roots were obtained on selection medium after two weeks of A. rhizogenes inoculation. Expression of green fluorescent protein further confirmed the success of transformation. We demonstrate that our method adequately transforms chickpea roots at early developmental stage with high efficiency. In addition, root transformation was found to be genotype-independent and the efficacy of our protocol was highest in two (Annigiri and JG-62) of the seven tested chickpea genotypes. Next, we present the functional analysis of chickpea hairy roots by expressing Arabidopsis TRANSPARENT TESTA 2 (AtTT2) gene involved in proanthocyanidins biosynthesis. Overexpression of AtTT2 enhanced the level of proanthocyanidins in hairy roots that led to the decreased colonization of fungal pathogen, Fusarium oxysporum. Furthermore, the induction of transgenic roots does not affect functional studies involving infection of roots by fungal pathogen. CONCLUSIONS Transgenic roots expressing genes of interest will be useful in downstream functional characterization using reverse genetics studies. It requires 1 day to perform the root transformation protocol described in this study and the roots expressing transgene can be maintained for 3-4 weeks, providing sufficient time for further functional studies. Overall, the current methodology will greatly facilitate the functional genomics analyses of candidate genes in root-rhizosphere interaction in this recalcitrant but economically important legume crop.
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Affiliation(s)
- Pooja Rani Aggarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Papri Nag
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Pooja Choudhary
- 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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