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Chen F, Ma R, Chen XL. Advances of Metabolomics in Fungal Pathogen-Plant Interactions. Metabolites 2019; 9:metabo9080169. [PMID: 31443304 PMCID: PMC6724083 DOI: 10.3390/metabo9080169] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 01/02/2023] Open
Abstract
Plant disease caused by fungus is one of the major threats to global food security, and understanding fungus-plant interactions is important for plant disease control. Research devoted to revealing the mechanisms of fungal pathogen-plant interactions has been conducted using genomics, transcriptomics, proteomics, and metabolomics. Metabolomics research based on mass spectrometric techniques is an important part of systems biology. In the past decade, the emerging field of metabolomics in plant pathogenic fungi has received wide attention. It not only provides a qualitative and quantitative approach for determining the pathogenesis of pathogenic fungi but also helps to elucidate the defense mechanisms of their host plants. This review focuses on the methods and progress of metabolomics research in fungal pathogen-plant interactions. In addition, the prospects and challenges of metabolomics research in plant pathogenic fungi and their hosts are addressed.
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Affiliation(s)
- Fangfang Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ruijing Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiao-Lin Chen
- The Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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52
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Verwaaijen B, Wibberg D, Winkler A, Zrenner R, Bednarz H, Niehaus K, Grosch R, Pühler A, Schlüter A. A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani. Sci Rep 2019; 9:7221. [PMID: 31076623 PMCID: PMC6510776 DOI: 10.1038/s41598-019-43706-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
The leafy green vegetable Lactuca sativa, L. is susceptible to the soil-born fungus Rhizoctonia solani AG1-IB. In a previous study, we reported on the transcriptional response of R. solani AG1-IB (isolate 7/3/14) during the interspecies interaction with L. sativa cv. Tizian by means of RNA sequencing. Here we present the L. sativa transcriptome and metabolome from the same experimental approach. Three distinct interaction zones were sampled and compared to a blank (non-inoculated) sample: symptomless zone 1, zone 2 showing light brown discoloration, and a dark brown zone 3 characterized by necrotic lesions. Throughout the interaction, we observed a massive reprogramming of the L. sativa transcriptome, with 9231 unique genes matching the threshold criteria for differential expression. The lettuce transcriptome of the light brown zone 2 presents the most dissimilar profile compared to the uninoculated zone 4, marking the main stage of interaction. Transcripts putatively encoding several essential proteins that are involved in maintaining jasmonic acid and auxin homeostasis were found to be negatively regulated. These and other indicator transcripts mark a potentially inadequate defence response, leading to a compatible interaction. KEGG pathway mapping and GC-MS metabolome data revealed large changes in amino acid, lignin and hemicellulose related pathways and related metabolites.
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Affiliation(s)
- Bart Verwaaijen
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
- Computational Biology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Anika Winkler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Rita Zrenner
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Hanna Bednarz
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Rita Grosch
- Leibniz-Institute of Vegetable and Ornamental Crops (IGZ), Großbeeren, Germany
| | - Alfred Pühler
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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53
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Cohen SP, Leach JE. Abiotic and biotic stresses induce a core transcriptome response in rice. Sci Rep 2019; 9:6273. [PMID: 31000746 PMCID: PMC6472405 DOI: 10.1038/s41598-019-42731-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/04/2019] [Indexed: 11/26/2022] Open
Abstract
Environmental stresses greatly limit crop yield. With the increase in extreme weather events due to climate change and the constant pressure of diseases and pests, there is an urgent need to develop crop varieties that can tolerate multiple stresses. However, our knowledge of how plants broadly respond to stress is limited. Here, we explore the rice core stress response via meta-analysis of publicly available rice transcriptome data. Our results confirm that rice universally down-regulates photosynthesis in response to both abiotic and biotic stress. Rice also generally up-regulates hormone-responsive genes during stress response, most notably genes in the abscisic acid, jasmonic acid and salicylic acid pathways. We identified several promoter motifs that are likely involved in stress-responsive regulatory mechanisms in rice. With this work, we provide a list of candidate genes to study for improving rice stress tolerance in light of environmental stresses. This work also serves as a proof of concept to show that meta-analysis of diverse transcriptome data is a valid approach to develop robust hypotheses for how plants respond to stress.
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Affiliation(s)
- Stephen P Cohen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, CO, 80523-1177, Fort Collins, USA.,Cell and Molecular Biology Graduate Program, Colorado State University, CO, 80523-1005, Fort Collins, USA
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, CO, 80523-1177, Fort Collins, USA.
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Kanwar P, Jha G. Alterations in plant sugar metabolism: signatory of pathogen attack. PLANTA 2019; 249:305-318. [PMID: 30267150 DOI: 10.1007/s00425-018-3018-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/23/2018] [Indexed: 05/03/2023]
Abstract
This review summarizes the current understanding, future challenges and ongoing quest on sugar metabolic alterations that influence the outcome of plant-pathogen interactions. Intricate cellular and molecular events occur during plant-pathogen interactions. They cause major metabolic perturbations in the host and alterations in sugar metabolism play a pivotal role in governing the outcome of various kinds of plant-pathogen interactions. Sugar metabolizing enzymes and transporters of both host and pathogen origin get differentially regulated during the interactions. Both plant and pathogen compete for utilizing the host sugar metabolic machinery and in turn promote resistant or susceptible responses. However, the kind of sugar metabolism alteration that is beneficial for the host or pathogen is yet to be properly understood. Recently developed tools and methodologies are facilitating research to understand the intricate dynamics of sugar metabolism during the interactions. The present review elaborates current understanding, future challenges and ongoing quest on sugar metabolism, mobilization and regulation during various plant-pathogen interactions.
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Affiliation(s)
- Poonam Kanwar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gopaljee Jha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Kumar R, Swain DM, Yadav SK, Tyagi I, Kumar R, Das J, Ghosh S, Jha G. Bacteria-fungal Confrontation and Fungal Growth Prevention Assay. Bio Protoc 2018; 8:e2694. [PMID: 34179243 DOI: 10.21769/bioprotoc.2694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 11/02/2022] Open
Abstract
There are some bacteria which can grow and multiply at the cost of living fungal biomass. They can potentially utilize fungi as a source of nutrients to forage over them. Such phenomenon is known as bacterial mycophagy, however, its mechanistic insights need to be explored to identify the molecules involved in mycophagy for potential utilization in controlling various fungal diseases. Recently we have demonstrated that a rice-associated bacteria Burkholderia gladioli strain NGJ1 exhibits mycophagous ability on several fungi, including Rhizoctonia solani, the necrotrophic fungal pathogen causing sheath blight disease in rice. We hereby describe our validated and efficient methods used to study B. gladioli strain NGJ1-R. solani interactions. These methodologies would be useful for designing assays to study the confrontation between bacteria and fungi which in turn enable discovery of novel antifungal molecules from such bacteria.
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Affiliation(s)
- Rahul Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Durga Madhab Swain
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sunil Kumar Yadav
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Isha Tyagi
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Rajeev Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Joyati Das
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Srayan Ghosh
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Ghosh S, Kanwar P, Jha G. Identification of candidate pathogenicity determinants of Rhizoctonia solani AG1-IA, which causes sheath blight disease in rice. Curr Genet 2017; 64:729-740. [PMID: 29196814 DOI: 10.1007/s00294-017-0791-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 01/04/2023]
Abstract
Sheath blight disease is one of the predominant diseases of rice and it is caused by the necrotrophic fungal pathogen Rhizoctonia solani. The mechanistic insight about its widespread success as a broad host range pathogen is limited. In this study, we endeavor to identify pathogenicity determinants of R. solani during infection process in rice. Through RNAseq analysis, we identified a total of 65 and 232 R. solani (strain BRS1) genes to be commonly upregulated in three different rice genotypes (PB1, Tetep, and TP309) at establishment and necrotrophic phase, respectively. The induction of genes encoding extracellular protease, ABC transporter, and transcription factors were notable during establishment phase. While during necrotrophic phase, several CAZymes, sugar transporters, cellular metabolism, and protein degradation-related genes were prominently induced. We have also identified few putative secreted effector encoding genes that were upregulated during pathogenesis. The qPCR analysis further validated the phase-specific expression dynamics of some selected putative effectors and pathogenicity-associated genes. Overall, the present study reports identification of key genes and processes that might be crucial for R. solani pathogenesis. The ability to effectively damage host cell wall and survive in hostile plant environment by managing oxidative stress, cytotoxic compounds, etc. is being proposed to be important for pathogenesis of R. solani in rice. The functional characterization of these genes would provide key insights about this important pathosystem and facilitate development of strategies to control this devastating disease.
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Affiliation(s)
- Srayan Ghosh
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Poonam Kanwar
- 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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Swain DM, Yadav SK, Tyagi I, Kumar R, Kumar R, Ghosh S, Das J, Jha G. A prophage tail-like protein is deployed by Burkholderia bacteria to feed on fungi. Nat Commun 2017; 8:404. [PMID: 28864820 PMCID: PMC5581363 DOI: 10.1038/s41467-017-00529-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 07/05/2017] [Indexed: 11/09/2022] Open
Abstract
Some bacteria can feed on fungi, a phenomenon known as mycophagy. Here we show that a prophage tail-like protein (Bg_9562) is essential for mycophagy in Burkholderia gladioli strain NGJ1. The purified protein causes hyphal disintegration and inhibits growth of several fungal species. Disruption of the Bg_9562 gene abolishes mycophagy. Bg_9562 is a potential effector secreted by a type III secretion system (T3SS) and is translocated into fungal mycelia during confrontation. Heterologous expression of Bg_9562 in another bacterial species, Ralstonia solanacearum, confers mycophagous ability in a T3SS-dependent manner. We propose that the ability to feed on fungi conferred by Bg_9562 may help the bacteria to survive in certain ecological niches. Furthermore, considering its broad-spectrum antifungal activity, the protein may be potentially useful in biotechnological applications to control fungal diseases.Some bacteria can feed on live fungi through unclear mechanisms. Here, the authors show that a T3SS-secreted protein, which is homologous to phage tail proteins, allows a Burkholderia gladioli strain to kill and feed on various fungal species.
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Affiliation(s)
- Durga Madhab Swain
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sunil Kumar Yadav
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Isha Tyagi
- 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
| | - Rajeev Kumar
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Srayan Ghosh
- 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
| | - Gopaljee Jha
- Plant Microbe Interactions Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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