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Dutta TK, Rupinikrishna K, Akhil VS, Vashisth N, Phani V, Pankaj, Sirohi A, Chinnusamy V. CRISPR/Cas9-induced knockout of an amino acid permease gene (AAP6) reduced Arabidopsis thaliana susceptibility to Meloidogyne incognita. BMC PLANT BIOLOGY 2024; 24:515. [PMID: 38851681 PMCID: PMC11162074 DOI: 10.1186/s12870-024-05175-5] [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: 02/19/2024] [Accepted: 05/20/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Plant-parasitic root-knot nematode (Meloidogyne incognita) causes global yield loss in agri- and horticultural crops. Nematode management options rely on chemical method. However, only a handful of nematicides are commercially available. Resistance breeding efforts are not sustainable because R gene sources are limited and nematodes have developed resistance-breaking populations against the commercially available Mi-1.2 gene-expressing tomatoes. RNAi crops that manage nematode infection are yet to be commercialized because of the regulatory hurdles associated with transgenic crops. The deployment of the CRISPR/Cas9 system to improve nematode tolerance (by knocking out the susceptibility factors) in plants has emerged as a feasible alternative lately. RESULTS In the present study, a M. incognita-responsive susceptibility (S) gene, amino acid permease (AAP6), was characterized from the model plant Arabidodpsis thaliana by generating the AtAAP6 overexpression line, followed by performing the GUS reporter assay by fusing the promoter of AtAAP6 with the β-glucuronidase (GUS) gene. Upon challenge inoculation with M. incognita, overexpression lines supported greater nematode multiplication, and AtAAP6 expression was inducible to the early stage of nematode infection. Next, using CRISPR/Cas9, AtAAP6 was selectively knocked out without incurring any growth penalty in the host plant. The 'Cas9-free' homozygous T3 line was challenge inoculated with M. incognita, and CRISPR-edited A. thaliana plants exhibited considerably reduced susceptibility to nematode infection compared to the non-edited plants. Additionally, host defense response genes were unaltered between edited and non-edited plants, implicating the direct role of AtAAP6 towards nematode susceptibility. CONCLUSION The present findings enrich the existing literature on CRISPR/Cas9 research in plant-nematode interactions, which is quite limited currently while compared with the other plant-pathogen interaction systems.
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Affiliation(s)
- Tushar K Dutta
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Katakam Rupinikrishna
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Voodikala S Akhil
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Neeraj Vashisth
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Victor Phani
- Department of Agricultural Entomology, College of Agriculture, Uttar Banga Krishi Viswavidyalaya (UBKV), Balurghat, 733133, India
| | - Pankaj
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anil Sirohi
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Mascellani Bergo A, Leiss K, Havlik J. Twenty Years of 1H NMR Plant Metabolomics: A Way Forward toward Assessment of Plant Metabolites for Constitutive and Inducible Defenses to Biotic Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8332-8346. [PMID: 38501393 DOI: 10.1021/acs.jafc.3c09362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Metabolomics has become an important tool in elucidating the complex relationship between a plant genotype and phenotype. For over 20 years, nuclear magnetic resonance (NMR) spectroscopy has been known for its robustness, quantitative capabilities, simplicity, and cost-efficiency. 1H NMR is the method of choice for analyzing a broad range of relatively abundant metabolites, which can be used for both capturing the plant chemical profile at one point in time and understanding the pathways that underpin plant defense. This systematic Review explores how 1H NMR-based plant metabolomics has contributed to understanding the role of various compounds in plant responses to biotic stress, focusing on both primary and secondary metabolites. It clarifies the challenges and advantages of using 1H NMR in plant metabolomics, interprets common trends observed, and suggests guidelines for method development and establishing standard procedures.
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Affiliation(s)
- Anna Mascellani Bergo
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16500 Prague, Czechia
| | - Kirsten Leiss
- Business Unit Greenhouse Horticulture, Wageningen University & Research, 2665MV Bleiswijk, Netherlands
| | - Jaroslav Havlik
- Department of Food Science, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 16500 Prague, Czechia
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Guo N, Qu H, Zhi Y, Zhang Y, Cheng S, Chu J, Zhang Z, Xu G. Knockout of amino acid transporter gene OsLHT1 accelerates leaf senescence and enhances resistance to rice blast fungus. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad125. [PMID: 37010326 DOI: 10.1093/jxb/erad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 06/19/2023]
Abstract
Plant amino acid transporters (AATs) regulate not only long-distance transport and reallocation of nitrogen (N) from source to sink organs, but also amount of amino acids in leaves hijacked by invaded pathogens. However, the function of AATs in plant defense responses to pathogen infection remains unknown. In this study, we found that rice amino acid transporter gene OsLHT1 was expressed in leaves and up-regulated by maturing, N starvation and inoculation of blast fungus Magnaporthe oryzae. Knockout of OsLHT1 resulted in development stage- and N supply-dependent premature senescence of leaves at vegetative growth stage. In comparison to wild type, Oslht1 mutant lines showed sustained rusty red spots on fully mature leaf blades irrespective of N supply levels. Notably, no relationship between the severity of leaf rusty red spots and concentration of total N or amino acids was found in Oslht1 mutants at different developmental stages. Disruption of OsLHT1 altered transport and metabolism of amino acids and biosynthesis of flavones and flavonoids, enhanced expression of jasmonic acid- and salicylic acid-related defense genes and production of jasmonic acid and salicylic acid, accumulation of reactive oxygen species. OsLHT1 inactivation dramatically prevented the leaf invasion of M. oryzae, the hemi-biotrophic ascomycete fungus. Overall, these results establish a module connecting the activity of amino acid transporter with leaf metabolism and defense to rice blast fungus.
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Affiliation(s)
- Nan Guo
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, Jiangsu, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongye Qu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Yue Zhi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuyi Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
| | - Shujing Cheng
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China
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Wang Y, Li T, Sun Z, Huang X, Yu N, Tai H, Yang Q. Comparative transcriptome meta-analysis reveals a set of genes involved in the responses to multiple pathogens in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:971371. [PMID: 36186003 PMCID: PMC9521429 DOI: 10.3389/fpls.2022.971371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Maize production is constantly threatened by the presence of different fungal pathogens worldwide. Genetic resistance is the most favorable approach to reducing yield losses resulted from fungal diseases. The molecular mechanism underlying disease resistance in maize remains largely unknown. The objective of this study was to identify key genes/pathways that are consistently associated with multiple fungal pathogen infections in maize. Here, we conducted a meta-analysis of gene expression profiles from seven publicly available RNA-seq datasets of different fungal pathogen infections in maize. We identified 267 common differentially expressed genes (co-DEGs) in the four maize leaf infection experiments and 115 co-DEGs in all the seven experiments. Functional enrichment analysis showed that the co-DEGs were mainly involved in the biosynthesis of diterpenoid and phenylpropanoid. Further investigation revealed a set of genes associated with terpenoid phytoalexin and lignin biosynthesis, as well as potential pattern recognition receptors and nutrient transporter genes, which were consistently up-regulated after inoculation with different pathogens. In addition, we constructed a weighted gene co-expression network and identified several hub genes encoding transcription factors and protein kinases. Our results provide valuable insights into the pathways and genes influenced by different fungal pathogens, which might facilitate mining multiple disease resistance genes in maize.
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Affiliation(s)
- Yapeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Ting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Zedan Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Xiaojian Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Naibing Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Huanhuan Tai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Qin Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
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Joubert M, van den Berg N, Theron J, Swart V. Transcriptomics Advancement in the Complex Response of Plants to Viroid Infection. Int J Mol Sci 2022; 23:ijms23147677. [PMID: 35887025 PMCID: PMC9318114 DOI: 10.3390/ijms23147677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viroids are the smallest plant pathogens, consisting of a single-stranded circular RNA of less than 500 ribonucleotides in length. Despite their noncoding nature, viroids elicit disease symptoms in many economically important plant hosts, and are, thus, a class of pathogens of great interest. How these viroids establish disease within host plants, however, is not yet fully understood. Recent transcriptomic studies have revealed that viroid infection influences the expression of genes in several pathways and processes in plants, including defence responses, phytohormone signalling, cell wall modification, photosynthesis, secondary metabolism, transport, gene expression and protein modification. There is much debate about whether affected pathways signify a plant response to viroid infection, or are associated with the appearance of disease symptoms in these interactions. In this review, we consolidate the findings of viroid–host transcriptome studies to provide an overview of trends observed in the data. When considered together, changes in the gene expression of different hosts upon viroid infection reveal commonalities and differences in diverse interactions. Here, we discuss whether trends in host gene expression can be correlated to plant defence or disease development during viroid infection, and highlight avenues for future research in this field.
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Affiliation(s)
- Melissa Joubert
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Noëlani van den Berg
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Jacques Theron
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Velushka Swart
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
- Correspondence:
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Koo AJ, Arimura GI. Molecular biology of chemical defenses. PLANT MOLECULAR BIOLOGY 2022; 109:351-353. [PMID: 35727520 DOI: 10.1007/s11103-022-01290-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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