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Vashisth S, Kumar P, Chandel VGS, Kumar R, Verma SC, Chandel RS. Unraveling the enigma of root-knot nematodes: from origins to advanced management strategies in agriculture. PLANTA 2024; 260:36. [PMID: 38922545 DOI: 10.1007/s00425-024-04464-5] [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: 03/27/2024] [Accepted: 06/09/2024] [Indexed: 06/27/2024]
Abstract
MAIN CONCLUSION Integrated management strategies, including novel nematicides and resilient cultivars, offer sustainable solutions to combat root-knot nematodes, crucial for safeguarding global agriculture against persistent threats. Root-knot nematodes (RKN) pose a significant threat to a diverse range of host plants, with their obligatory endoparasitic nature leading to substantial agricultural losses. RKN spend much of their lives inside or in contact by secreting plant cell wall-modifying enzymes resulting in the giant cell development for establishing host-parasite relationships. Additionally, inflicting physical harm to host plants, RKN also contributes to disease complexes creation with fungi and bacteria. This review comprehensively explores the origin, history, distribution, and physiological races of RKN, emphasizing their economic impact on plants through gall formation. Management strategies, ranging from cultural and physical to biological and chemical controls, along with resistance mechanisms and marker-assisted selection, are explored. While recognizing the limitations of traditional nematicides, recent breakthroughs in non-fumigant alternatives like fluensulfone, spirotetramat, and fluopyram offer promising avenues for sustainable RKN management. Despite the success of resistance mechanisms like the Mi gene, challenges persist, prompting the need for integrative approaches to tackle Mi-virulent isolates. In conclusion, the review stresses the importance of innovative and resilient control measures for sustainable agriculture, emphasizing ongoing research to address evolving challenges posed by RKN. The integration of botanicals, resistant cultivars, and biological controls, alongside advancements in non-fumigant nematicides, contributes novel insights to the field, laying the ground work for future research directions to ensure the long-term sustainability of agriculture in the face of persistent RKN threats.
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Affiliation(s)
- Sumit Vashisth
- Department of Entomology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vishav Gaurav Singh Chandel
- Department of Entomology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Rakesh Kumar
- Department of Entomology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Subhash Chander Verma
- Department of Entomology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Rajeshwar Singh Chandel
- Department of Entomology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
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Leonetti P, Dallera D, De Marchi D, Candito P, Pasotti L, Macovei A. Exploring the putative microRNAs cross-kingdom transfer in Solanum lycopersicum-Meloidogyne incognita interactions. FRONTIERS IN PLANT SCIENCE 2024; 15:1383986. [PMID: 38784062 PMCID: PMC11114104 DOI: 10.3389/fpls.2024.1383986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
Introduction Plant-pathogen interaction is an inexhaustible source of information on how to sustainably control diseases that negatively affect agricultural production. Meloidogyne incognita is a root-knot nematode (RKN), representing a pest for many crops, including tomato (Solanum lycopersicum). RKNs are a global threat to agriculture, especially under climate change, and RNA technologies offer a potential alternative to chemical nematicides. While endogenous microRNAs have been identified in both S. lycopersicum and M. incognita, and their roles have been related to the regulation of developmental changes, no study has investigated the miRNAs cross-kingdom transfer during this interaction. Methods Here, we propose a bioinformatics pipeline to highlight potential miRNA-dependent cross-kingdom interactions between tomato and M. incognita. Results The obtained data show that nematode miRNAs putatively targeting tomato genes are mostly related to detrimental effects on plant development and defense. Similarly, tomato miRNAs putatively targeting M. incognita biological processes have negative effects on digestion, mobility, and reproduction. To experimentally test this hypothesis, an in vitro feeding assay was carried out using sly-miRNAs selected from the bioinformatics approach. The results show that two tomato miRNAs (sly-miRNA156a, sly-miR169f) soaked by juvenile larvae (J2s) affected their ability to infect plant roots and form galls. This was also coupled with a significant downregulation of predicted target genes (Minc11367, Minc00111), as revealed by a qRT-PCR analysis. Discussions Therefore, the current study expands the knowledge related to the cross-kingdom miRNAs involvement in host-parasite interactions and could pave the way for the application of exogenous plant miRNAs as tools to control nematode infection.
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Affiliation(s)
- Paola Leonetti
- Institute for Sustainable Plant Protection of the National Research Council, Unit of Bari, Bari, Italy
| | - Debora Dallera
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering - Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Davide De Marchi
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering - Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Pamela Candito
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering - Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling, and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering - Centre for Health Technology, University of Pavia, Pavia, Italy
| | - Anca Macovei
- Plant Biotechnology Laboratory, Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
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Noureddine Y, da Rocha M, An J, Médina C, Mejias J, Mulet K, Quentin M, Abad P, Zouine M, Favery B, Jaubert-Possamai S. AUXIN RESPONSIVE FACTOR8 regulates development of the feeding site induced by root-knot nematodes in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5752-5766. [PMID: 37310189 DOI: 10.1093/jxb/erad208] [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: 11/23/2022] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Root-knot nematodes (RKN) from the genus Meloidogyne induce the dedifferentiation of root vascular cells into giant multinucleate feeding cells. These feeding cells result from an extensive reprogramming of gene expression, and auxin is known to be a key player in their development. However, little is known about how the auxin signal is transmitted during giant cell development. Integrative analyses combining transcriptome and small non-coding RNA datasets with the specific sequencing of cleaved transcripts identified genes targeted by miRNAs in tomato (Solanum lycopersicum) galls. The two auxin-responsive transcription factors ARF8A and ARF8B, and their miRNA167 regulators, were identified as robust gene-miRNA pair candidates to be involved in the tomato response to M. incognita. Spatiotemporal expression analysis using promoter-β-glucuronidase (GUS) fusions showed the up-regulation of ARF8A and ARF8B in RKN-induced feeding cells and surrounding cells. The generation and phenotyping of CRISPR (clustered regularly interspaced palindromic repeats) mutants demonstrated the role of ARF8A and ARF8B in giant cell development and allowed the characterization of their downstream regulated genes.
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Affiliation(s)
- Yara Noureddine
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Martine da Rocha
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Jing An
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Clémence Médina
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Joffrey Mejias
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Karine Mulet
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Pierre Abad
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Mohamed Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Bruno Favery
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
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Jiang C, Li Z, Zheng L, Yu Y, Niu D. Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions. MOLECULAR PLANT PATHOLOGY 2023; 24:999-1013. [PMID: 37026481 PMCID: PMC10346379 DOI: 10.1111/mpp.13329] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.
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Affiliation(s)
- Chun‐Hao Jiang
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zi‐Jie Li
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Li‐Yu Zheng
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Yi‐Yang Yu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Dong‐Dong Niu
- Department of Plant Pathology, College of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education/Key Laboratory of Integrated Pest Management on Crops in East China, Ministry of Agriculture/Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
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Raza A, Charagh S, Karikari B, Sharif R, Yadav V, Mubarik MS, Habib M, Zhuang Y, Zhang C, Chen H, Varshney RK, Zhuang W. miRNAs for crop improvement. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107857. [PMID: 37437345 DOI: 10.1016/j.plaphy.2023.107857] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
Climate change significantly impacts crop production by inducing several abiotic and biotic stresses. The increasing world population, and their food and industrial demands require focused efforts to improve crop plants to ensure sustainable food production. Among various modern biotechnological tools, microRNAs (miRNAs) are one of the fascinating tools available for crop improvement. miRNAs belong to a class of small non-coding RNAs playing crucial roles in numerous biological processes. miRNAs regulate gene expression by post-transcriptional target mRNA degradation or by translation repression. Plant miRNAs have essential roles in plant development and various biotic and abiotic stress tolerance. In this review, we provide propelling evidence from previous studies conducted around miRNAs and provide a one-stop review of progress made for breeding stress-smart future crop plants. Specifically, we provide a summary of reported miRNAs and their target genes for improvement of plant growth and development, and abiotic and biotic stress tolerance. We also highlight miRNA-mediated engineering for crop improvement and sequence-based technologies available for the identification of miRNAs associated with stress tolerance and plant developmental events.
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Affiliation(s)
- Ali Raza
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu 225009, China
| | - Vivek Yadav
- College of Horticulture, Northwest Agriculture and Forestry University, Yangling, Shanxi, 712100, China
| | | | - Madiha Habib
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Rd., Islamabad 45500, Pakistan
| | - Yuhui Zhuang
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Hua Chen
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China
| | - Rajeev K Varshney
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China; WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
| | - Weijian Zhuang
- Center of Legume Crop Genetics and Systems Biology, Oil Crops Research Institute, College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, 35002, China.
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Yang F, Ding L, Zhao D, Fan H, Zhu X, Wang Y, Liu X, Duan Y, Chen L. Identification and Functional Analysis of Tomato MicroRNAs in the Biocontrol Bacterium Pseudomonas putida Induced Plant Resistance to Meloidogyne incognita. PHYTOPATHOLOGY 2022; 112:2372-2382. [PMID: 35668060 DOI: 10.1094/phyto-03-21-0101-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Root-knot nematodes (RKNs, Meloidogyne spp.) seriously damage tomato production worldwide, and biocontrol bacteria can induce tomato immunity to RKNs. Our previous studies have revealed that Pseudomonas putida strain Sneb821 can trigger tomato immunity against M. incognita and that several long noncoding RNAs and microRNAs (miRNAs) are involved in this process. However, the molecular functions of the miRNAs in tomato immune responses remain unclear. In this study, deep small RNA sequencing identified 78 differentially expressed miRNAs in tomato plants inoculated with Sneb821 and M. incognita relative to plants inoculated with M. incognita alone; 38 miRNAs were upregulated, and 40 miRNAs were downregulated. The expression levels of six known miRNAs and five novel miRNAs were validated using RT-qPCR assays. These included Sly-miR482d-3p, Sly-miR156e-5p, Sly-miR319a, novel_miR_116, novel_miR_121, and novel_miR_221, which were downregulated, and Sly-miR390a-3p, Sly-miR394-3p, Sly-miR396a-3p, novel_miR_215, and novel_miR_83, which were upregulated in plants treated with Sneb821 and M. incognita. In addition, Sly-miR482d was functionally characterized through gene silencing and overexpression of its target gene NBS-LRR (Solyc05g009750.1) in tomato and by challenging the plants with M. incognita inoculation. The number of second-stage juveniles (J2) inside roots and induced galls were significantly decreased in both Sly-miR482d-silenced plants and Solyc05g009750.1 overexpressing plants, whereas the activity of superoxide dismutase, peroxidase, and hydrogen peroxide content were significantly increased. The results suggest that Sneb821 could inhibit Sly-miR482d expression and thus regulate tomato immune responses against M. incognita infestation. This study provides novel insights into the biocontrol bacteria-mediated tomato immunity to M. incognita that engages with plant miRNAs.
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Affiliation(s)
- Fan Yang
- College of Plant Protection, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Dongling Road 120, Shenyang 110866, China
| | - Ling Ding
- College of Plant Protection, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Dongling Road 120, Shenyang 110866, China
| | - Dan Zhao
- College of Plant Protection, Jilin Agricultural University, Xincheng Road 2888, Jilin 130118, China
| | - Haiyan Fan
- College of Plant Protection, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Dongling Road 120, Shenyang 110866, China
| | - Xiaofeng Zhu
- College of Plant Protection, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, China
| | - Yuanyuan Wang
- College of Biotechnology, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, China
| | - Xiaoyu Liu
- College of Science, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, China
| | - Yuxi Duan
- College of Plant Protection, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, China
| | - Lijie Chen
- College of Plant Protection, Shenyang Agricultural University, Dongling Road 120, Shenyang 110866, China
- Key Laboratory of Protected Horticulture, Shenyang Agricultural University, Ministry of Education, Dongling Road 120, Shenyang 110866, China
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7
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Tomato MicroRNAs and Their Functions. Int J Mol Sci 2022; 23:ijms231911979. [PMID: 36233279 PMCID: PMC9569937 DOI: 10.3390/ijms231911979] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by MIR genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its MIR genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato MIR genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping MIR annotations into an exhaustive and non-redundant atlas of tomato MIR genes. There are 538 candidate and validated MIR genes in the atlas, of which, 169, 18, and 351 code for highly conserved, Solanaceae-specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.
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Bennett M, Piya S, Baum TJ, Hewezi T. miR778 mediates gene expression, histone modification, and DNA methylation during cyst nematode parasitism. PLANT PHYSIOLOGY 2022; 189:2432-2453. [PMID: 35579365 PMCID: PMC9342967 DOI: 10.1093/plphys/kiac228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/27/2022] [Indexed: 05/20/2023]
Abstract
Despite the known critical regulatory functions of microRNAs, histone modifications, and DNA methylation in reprograming plant epigenomes in response to pathogen infection, the molecular mechanisms underlying the tight coordination of these components remain poorly understood. Here, we show how Arabidopsis (Arabidopsis thaliana) miR778 coordinately modulates the root transcriptome, histone methylation, and DNA methylation via post-transcriptional regulation of the H3K9 methyltransferases SU(var)3-9 homolog 5 (SUVH5) and SUVH6 upon infection by the beet cyst nematode Heterodera schachtii. miR778 post-transcriptionally silences SUVH5 and SUVH6 upon nematode infection. Manipulation of the expression of miR778 and its two target genes significantly altered plant susceptibility to H. schachtii. RNA-seq analysis revealed a key role of SUVH5 and SUVH6 in reprograming the transcriptome of Arabidopsis roots upon H. schachtii infection. In addition, chromatin immunoprecipitation (ChIP)-seq analysis established SUVH5 and SUVH6 as the main enzymes mediating H3K9me2 deposition in Arabidopsis roots in response to nematode infection. ChIP-seq analysis also showed that these methyltransferases possess distinct DNA binding preferences in that they are targeting transposable elements under noninfected conditions and protein-coding genes in infected plants. Further analyses indicated that H3K9me2 deposition directed by SUVH5 and SUVH6 contributes to gene expression changes both in roots and in nematode feeding sites and preferentially associates with CG DNA methylation. Together, our results uncovered multi-layered epigenetic regulatory mechanisms coordinated by miR778 during Arabidopsis-H. schachtii interactions.
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Affiliation(s)
- Morgan Bennett
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
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Arbuscular Mycorrhizal Symbiosis Leads to Differential Regulation of Genes and miRNAs Associated with the Cell Wall in Tomato Leaves. BIOLOGY 2022; 11:biology11060854. [PMID: 35741375 PMCID: PMC9219611 DOI: 10.3390/biology11060854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
Arbuscular mycorrhizal symbiosis is an association that provides nutritional benefits to plants. Importantly, it induces a physiological state allowing plants to respond to a subsequent pathogen attack in a more rapid and intense manner. Consequently, mycorrhiza-colonized plants become less susceptible to root and shoot pathogens. This study aimed to identify some of the molecular players and potential mechanisms related to the onset of defense priming by mycorrhiza colonization, as well as miRNAs that may act as regulators of priming genes. The upregulation of cellulose synthases, pectinesterase inhibitors, and xyloglucan endotransglucosylase/hydrolase, as well as the downregulation of a pectinesterase, suggest that the modification and reinforcement of the cell wall may prime the leaves of mycorrhizal plants to react faster and stronger to subsequent pathogen attack. This was confirmed by the findings of miR164a-3p, miR164a-5p, miR171e-5p, and miR397, which target genes and are also related to the biosynthesis or modification of cell wall components. Our findings support the hypothesis that the reinforcement or remodeling of the cell wall and cuticle could participate in the priming mechanism triggered by mycorrhiza colonization, by strengthening the first physical barriers upstream of the pathogen encounter.
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Khanna K, Ohri P, Bhardwaj R. Genetic toolbox and regulatory circuits of plant-nematode associations. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:137-146. [PMID: 34038810 DOI: 10.1016/j.plaphy.2021.05.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/16/2021] [Indexed: 06/12/2023]
Abstract
Plant-nematode associations are the most imperative area of study that forms the basis to understand their regulatory networks and coordinated functional aspects. Nematodes are highly parasitic organisms known so far, to cause relentless damage towards agricultural crops on a global scale. They pierce the roots of host plants and form neo-plastic feeding structures to extract out resources for their functional development. Moreover, they undergo re-differentiation within plant cells to form giant multi-nucleate feeding structures or syncytium. All these processes are facilitated by numerous transcriptomic, proteomic, metabolomic and epigenetic modifications, that regulate different biological attractions among plants and nematodes. Nevertheless, these mechanisms are quite remarkable and have been explored in the present review. Here, we have shed light on genomic as well as genetic approaches to acquire an effective understanding regarding plant-nematode associations. Transcriptomics have revealed an extensive network to unravel feeding mechanism of nematodes through gene-expression programming of target genes. Also, the regulatory circuits of epigenetic alterations through DNA-methylation, non-coding RNAs and histone modifications very well explain epigenetic profiling within plants. Since decades, research have observed many intricacies to elucidate the dynamic nature of epigenetic modulations in plant-nematode attractions. By this review, we have highlighted the functional aspects of small RNAs in inducing plant-nematode parasitism along with the putative role of miRNAs. These RNAs act as chief genetic elements to mediate the expressional changes in plants through post-transcriptional silencing of various effector proteins as well as transcriptional factors. A pragmatic role of miRNAs in modulating gene expression in nematode infection and feeding site development have also been reviewed. Hence, they have been considered master regulators for functional reprogramming the expression during establishment of feeding sites. We have also encapsulated the advancement of genome-broadened DNA-methylation and untangled the nematode mediated dynamic alterations within plant methylome along with assessing transcriptional activities of various genes and transposons. In particular, we have highlighted the role of effector proteins in stimulating epigenetic changes. Finally, we have emerged towards a molecular-based core understanding about plant-nematode associations.
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Affiliation(s)
- Kanika Khanna
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - Puja Ohri
- Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
| | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, Punjab, India.
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Verstraeten B, Atighi MR, Ruiz-Ferrer V, Escobar C, De Meyer T, Kyndt T. Non-coding RNAs in the interaction between rice and Meloidogyne graminicola. BMC Genomics 2021; 22:560. [PMID: 34284724 PMCID: PMC8293575 DOI: 10.1186/s12864-021-07735-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Background Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues. Results We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data. Conclusions To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07735-7.
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Affiliation(s)
| | | | - Virginia Ruiz-Ferrer
- Department of Environmental Science, University of Castilla-La Mancha, Toledo, Spain
| | - Carolina Escobar
- Department of Environmental Science, University of Castilla-La Mancha, Toledo, Spain
| | - Tim De Meyer
- Department of Data Analysis & Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Tina Kyndt
- Department of Biotechnology, Ghent University, Ghent, Belgium.
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12
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Yu Q, Li X, Feng T. GLIDR promotes the progression of glioma by regulating the miR-4677-3p/MAGI2 axis. Exp Cell Res 2021; 406:112726. [PMID: 34237299 DOI: 10.1016/j.yexcr.2021.112726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/17/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023]
Abstract
Gliomas are the most common and fatal primary brain tumors. Growing evidence suggests that long non-coding RNAs (lncRNAs) constitute novel and potential therapeutic targets for glioma. However, the biological role of glioblastoma down-regulated RNA (GLIDR) in glioma remains largely elusive. In the current study, we used quantitative real-time polymerase chain reaction (qRT-PCR) to detect GLIDR expression in glioma cells. Cell counting kit 8 (CCK-8) assay, colony formation assay, JC-1 staining, and flow cytometry were used to evaluate the role of GLIDR in proliferation and apoptosis of glioma cells. Western blotting was performed to assess the effect of GLIDR on the level of apoptosis-related proteins. In addition, bioinformatics prediction, RNA immunoprecipitation (RIP), RNA pull-down, and luciferase reporter gene assays were used to study the regulatory mechanisms of GLIDR in glioma. GLIDR was found to be highly expressed in glioma cells and silencing of GLIDR inhibited cell proliferation and promoted apoptosis. Functionally, GLIDR bound to miR-4677-3p that directly targeted membrane-associated guanylate kinase, WW, and PDZ domain-containing protein 2 (MAGI2). Our data showed that GLIDR affects the proliferation and apoptosis of glioma cells by targeting miR-4677-3p to regulate the expression of MAGI2. In conclusion, our study determined the oncogenic role of GLIDR in glioma, which may provide a new perspective for the treatment of glioma.
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Affiliation(s)
- Qi Yu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xinxing Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tianda Feng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.
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13
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Genome-Wide Screening and Characterization of Non-Coding RNAs in Coffea canephora. Noncoding RNA 2020; 6:ncrna6030039. [PMID: 32932872 PMCID: PMC7549347 DOI: 10.3390/ncrna6030039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 12/25/2022] Open
Abstract
Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that uncovers the ncRNA portion of the C. canephora genome. This study aimed to provide a curated characterization of six ncRNA classes in the Coffea canephora genome. For this purpose, we employed a combination of similarity-based and structural-based computational approaches with stringent curation. Candidate ncRNA loci had expression evidence analyzed using sRNA-seq libraries. We identified 7455 ncRNA loci (6976 with transcriptional evidence) in the C. canephora genome. This comprised of total 115 snRNAs, 1031 snoRNAs, 92 miRNA precursors, 602 tRNAs, 72 rRNAs, and 5064 lncRNAs. For miRNAs, we identified 159 putative high-confidence targets. This study was the most extensive genomic catalog of curated ncRNAs in the Coffea genus. This data might help elaborating more robust hypotheses in future comparative genomic studies as well as gene regulation and genome dynamics, helping to understand the molecular basis of domestication, environmental adaptation, resistance to pests and diseases, and coffee productivity.
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14
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Elucidating micro RNAs role in different plant-pathogen interactions. Mol Biol Rep 2020; 47:8219-8227. [PMID: 32909216 DOI: 10.1007/s11033-020-05810-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/30/2020] [Accepted: 09/03/2020] [Indexed: 01/23/2023]
Abstract
Bacteria, fungi, virus and nematode constitute the primary class of pathogens causing plant diseases. Plant-pathogen interactions are crucial for the identification of the host and pathogen and further establishments of a network of interaction that can cross regulate the gene expressions in both sides. After infection, the correct identification of pathogen through various molecular interactions elicit a defense response against the pathogen by alteration of gene expression by the host. Co-evolution of pathogen gives them the ability to counter the virulence response of the host and pathogen can also modulate the host gene expression pattern to make it more susceptible to the infection. Small non-coding RNA molecules (siRNAs and miRNAs) efficiently modulate gene expression at the transcriptional and post-transcriptional level and play a vital role in host defense. The pathogen can also use this double-sided sward in their defense by deregulating the plant immunity via transcriptional control of plant genes utilizing RNA interference or suppressing the host RNA interference response with the help of various RNA silencing suppressor proteins. This mini-review focused on the miRNAs involvement in host defense and how different families of these non-coding regulatory RNAs regulate the defense response against the pathogen.
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15
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Mani V, Reddy CS, Lee SK, Park S, Ko HR, Kim DG, Hahn BS. Chitin Biosynthesis Inhibition of Meloidogyne incognita by RNAi-Mediated Gene Silencing Increases Resistance to Transgenic Tobacco Plants. Int J Mol Sci 2020; 21:E6626. [PMID: 32927773 PMCID: PMC7555284 DOI: 10.3390/ijms21186626] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/28/2022] Open
Abstract
Meloidogyne incognita is a devastating plant parasitic nematode that causes root knot disease in a wide range of plants. In the present study, we investigated host-induced RNA interference (RNAi) gene silencing of chitin biosynthesis pathway genes (chitin synthase, glucose-6-phosphate isomerase, and trehalase) in transgenic tobacco plants. To develop an RNAi vector, ubiquitin (UBQ1) promoter was directly cloned, and to generate an RNAi construct, expression of three genes was suppressed using the GATEWAY system. Further, transgenic Nicotiana benthamiana lines expressing dsRNA for chitin synthase (CS), glucose-6-phosphate isomerase (GPI), and trehalase 1 (TH1) were generated. Quantitative PCR analysis confirmed endogenous mRNA expression of root knot nematode (RKN) and revealed that all three genes were more highly expressed in the female stage than in eggs and in the parasitic stage. In vivo, transformed roots were challenged with M. incognita. The number of eggs and root knots were significantly decreased by 60-90% in RNAi transgenic lines. As evident, root galls obtained from transgenic RNAi lines exhibited 0.01- to 0.70-fold downregulation of transcript levels of targeted genes compared with galls isolated from control plants. Furthermore, phenotypic characteristics such as female size and width were also marginally altered, while effect of egg mass per egg number in RNAi transgenic lines was reduced. These results indicate the relevance and significance of targeting chitin biosynthesis genes during the nematode lifespan. Overall, our results suggest that further developments in RNAi efficiency in commercially valued crops can be applied to employ RNAi against other plant parasitic nematodes.
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Affiliation(s)
- Vimalraj Mani
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (V.M.); (C.S.R.); (S.-K.L.); (S.P.)
| | - Chinreddy Subramanyam Reddy
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (V.M.); (C.S.R.); (S.-K.L.); (S.P.)
| | - Seon-Kyeong Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (V.M.); (C.S.R.); (S.-K.L.); (S.P.)
| | - Soyoung Park
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (V.M.); (C.S.R.); (S.-K.L.); (S.P.)
| | - Hyoung-Rai Ko
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea;
| | - Dong-Gwan Kim
- Department of Bio-Industry and Bio-Resource Engineering, Sejong University, Seoul 05006, Korea;
| | - Bum-Soo Hahn
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
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16
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Abstract
Epigenetic mechanisms play fundamental roles in regulating numerous biological processes in various developmental and environmental contexts. Three highly interconnected epigenetic control mechanisms, including small noncoding RNAs, DNA methylation, and histone modifications, contribute to the establishment of plant epigenetic profiles. During the past decade, a growing body of experimental work has revealed the intricate, diverse, and dynamic roles that epigenetic modifications play in plant-nematode interactions. In this review, I summarize recent progress regarding the functions of small RNAs in mediating plant responses to infection by cyst and root-knot nematodes, with a focus on the functions of microRNAs. I also recapitulate recent advances in genome-wide DNA methylation analysis and discuss how cyst nematodes induce extensive and dynamic changes in the plant methylome that impact the transcriptional activity of genes and transposable elements. Finally, the potential role of nematode effector proteins in triggering such epigenome changes is discussed.
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Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA;
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17
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Omics applications: towards a sustainable protection of tomato. Appl Microbiol Biotechnol 2020; 104:4185-4195. [PMID: 32185431 DOI: 10.1007/s00253-020-10500-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/20/2020] [Accepted: 02/26/2020] [Indexed: 12/20/2022]
Abstract
Transcriptome data and gene expression analysis have a huge potential in the study of multiple relationships involving plants, pathogens, and pests, including the interactions with beneficial microorganisms such as endophytes or other functional groups. Next-generation sequencing (NGS) and other recent long-read-based sequencing approaches (i.e., nanopore and others) provide unprecedented tools allowing the fast identification of plant information processing systems, in situ and in real time, fundamental for crop management and pest regulation. Other -omics approaches such as metagenomics and metatranscriptomics allow high-resolution insights on the rhizosphere ecology. They may highlight key factors affecting belowground biodiversity or processes, modulating the expression of stress-responsive pathways. The application of miRNAs and other small RNAs is a relatively new field of application, with enormous potential for the selective activation of defense pathways. However, limitations concerning the stability of the RNA molecules and their effective delivery must be overcome.
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18
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Lei P, Han B, Wang Y, Zhu X, Xuan Y, Liu X, Fan H, Chen L, Duan Y. Identification of MicroRNAs That Respond to Soybean Cyst Nematode Infection in Early Stages in Resistant and Susceptible Soybean Cultivars. Int J Mol Sci 2019; 20:E5634. [PMID: 31718001 PMCID: PMC6888636 DOI: 10.3390/ijms20225634] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/06/2019] [Accepted: 11/09/2019] [Indexed: 02/06/2023] Open
Abstract
Soybean cyst nematode (SCN) causes heavy losses to soybean yield. In order to investigate the roles of soybean miRNAs during the early stages of infection (1 and 5 dpi), 24 small RNA libraries were constructed from SCN resistant cultivar Huipizhi (HPZ) and the susceptible Williams 82 (W82) cultivar for high-throughput sequencing. By sequencing the small RNA libraries, a total of 634 known miRNAs were identified, and 252 novel miRNAs were predicted. Altogether, 14 known miRNAs belonging to 13 families, and 26 novel miRNAs were differentially expressed and may respond to SCN infection in HPZ and W82. Similar expression results were also confirmed by qRT-PCR. Further analysis of the biological processes that these potential target genes of differentially expressed miRNAs regulate found that they may be strongly related to plant-pathogen interactions. Overall, soybean miRNAs experience profound changes in early stages of SCN infection in both HPZ and W82. The findings of this study can provide insight into miRNAome changes in both HPZ and W82 at the early stages of infection, and may provide a stepping stone for future SCN management.
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Affiliation(s)
- Piao Lei
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Bing Han
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanyuan Wang
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhu Xuan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyu Liu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Sciences, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lijie Chen
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
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19
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Wu HYL, Song G, Walley JW, Hsu PY. The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling. PLANT PHYSIOLOGY 2019; 181:367-380. [PMID: 31248964 PMCID: PMC6716236 DOI: 10.1104/pp.19.00541] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/10/2019] [Indexed: 05/14/2023]
Abstract
Recent applications of translational control in Arabidopsis (Arabidopsis thaliana) highlight the potential power of manipulating mRNA translation for crop improvement. However, to what extent translational regulation is conserved between Arabidopsis and other species is largely unknown, and the translatome of most crops remains poorly studied. Here, we combined de novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato (Solanum lycopersicum) roots. Exploiting features corresponding to active translation, we discovered widespread unannotated translation events, including 1,329 upstream open reading frames (uORFs) within the 5' untranslated regions of annotated coding genes and 354 small ORFs (sORFs) among unannotated transcripts. uORFs may repress translation of their downstream main ORFs, whereas sORFs may encode signaling peptides. Besides evolutionarily conserved sORFs, we uncovered 96 Solanaceae-specific sORFs, revealing the importance of studying translatomes directly in crops. Proteomic analysis confirmed that some of the unannotated ORFs generate stable proteins in planta. In addition to defining the translatome, our results reveal the global regulation by uORFs and microRNAs. Despite diverging over 100 million years ago, many translational features are well conserved between Arabidopsis and tomato. Thus, our approach provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved and unique translational features, and identifies regulatory mechanisms hidden in a crop genome.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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20
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Ibrahim HMM, Ahmad EM, Martínez-Medina A, Aly MAM. Effective approaches to study the plant-root knot nematode interaction. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 141:332-342. [PMID: 31207494 DOI: 10.1016/j.plaphy.2019.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 05/26/2019] [Accepted: 06/08/2019] [Indexed: 05/24/2023]
Abstract
Plant-parasitic nematodes cause major agricultural losses worldwide. Examining the molecular mechanisms underlying plant-nematode interactions and how plants respond to different invading pathogens is attracting major attention to reduce the expanding gap between agricultural production and the needs of the growing world population. This review summarizes the most recent developments in plant-nematode interactions and the diverse approaches used to improve plant resistance against root knot nematode (RKN). We will emphasize the recent rapid advances in genome sequencing technologies, small interfering RNA techniques (RNAi) and targeted genome editing which are contributing to the significant progress in understanding the plant-nematode interaction mechanisms. Also, molecular approaches to improve plant resistance against nematodes are considered.
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Affiliation(s)
- Heba M M Ibrahim
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt.
| | - Esraa M Ahmad
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Ainhoa Martínez-Medina
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research, Leipzig, Germany
| | - Mohammed A M Aly
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
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21
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Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing. PLoS One 2019; 14:e0212746. [PMID: 30845212 PMCID: PMC6405255 DOI: 10.1371/journal.pone.0212746] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 02/08/2019] [Indexed: 12/31/2022] Open
Abstract
microRNAs represent small endogenous RNAs which are known to play a crucial role in various plant metabolic processes. Carrot being an important vegetable crop, represents one of the richest sources of carotenoids and anthocyanins. Most of the studies on microRNAs have been conducted in the aerial parts of the plants. However, carrot has the rare distinction of storing these compounds in roots. Therefore, carrot represents a good model system to unveil the regulatory roles of miRNAs in the underground edible part of the plant. For the first time, we report the genome wide identification and expression profiling of miRNAs in two contrasting color variants of carrot namely Orange Red and Purple Black using RNA-seq. Illumina sequencing resulted in the generation of 25.5M and 18.9M reads in Orange Red and Purple Black libraries, respectively. In total, 144 and 98 (read count >10), conserved microRNAs and 36 and 66 novel microRNAs were identified in Orange Red and Purple Black, respectively. Functional categorization and differential gene expression revealed the presence of several miRNA genes targeting various secondary metabolic pathways including carotenoid and anthocyanin biosynthetic pathways in the two libraries. 11 known and 2 novel microRNAs were further validated using Stem-Loop PCR and qRT-PCR. Also, target validation was performed for selected miRNA genes using RLM-RACE approach. The present work has laid a foundation towards understanding of various metabolic processes, particularly the color development in carrot. This information can be further employed in targeted gene expression for increasing the carotenoid and anthocyanin content in crop plants.
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22
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Jaubert-Possamai S, Noureddine Y, Favery B. MicroRNAs, New Players in the Plant-Nematode Interaction. FRONTIERS IN PLANT SCIENCE 2019; 10:1180. [PMID: 31681347 PMCID: PMC6811602 DOI: 10.3389/fpls.2019.01180] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/29/2019] [Indexed: 05/04/2023]
Abstract
Plant-parasitic root-knot and cyst nematodes are microscopic worms that cause severe damage to crops and induce major agricultural losses worldwide. These parasites penetrate into host roots and induce the formation of specialized feeding structures, which supply the resources required for nematode development. Root-knot nematodes induce the redifferentiation of five to seven root cells into giant multinucleate feeding cells, whereas cyst nematodes induce the formation of a multinucleate syncytium by targeting a single root cell. Transcriptomic analyses have shown that the induction of these feeding cells by nematodes involves an extensive reprogramming of gene expression within the targeted root cells. MicroRNAs are small noncoding RNAs that act as key regulators of gene expression in eukaryotes by inducing the posttranscriptional silencing of protein coding genes, including many genes encoding transcription factors. A number of microRNAs (miRNAs) displaying changes in expression in root cells in response to nematode infection have recently been identified in various plant species. Modules consisting of miRNAs and the transcription factors they target were recently shown to be required for correct feeding site formation. Examples include miR396 and GRF in soybean syncytia and miR159 and MYB33 in Arabidopsis giant cells. Moreover, some conserved miRNA/target modules seem to have similar functions in feeding site formation in different plant species. These miRNAs may be master regulators of the reprogramming of expression occurring during feeding site formation. This review summarizes current knowledge about the role of these plant miRNAs in plant-nematode interactions.
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23
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Ruiz‐Ferrer V, Cabrera J, Martinez‐Argudo I, Artaza H, Fenoll C, Escobar C. Silenced retrotransposons are major rasiRNAs targets in Arabidopsis galls induced by Meloidogyne javanica. MOLECULAR PLANT PATHOLOGY 2018; 19:2431-2445. [PMID: 30011119 PMCID: PMC6638097 DOI: 10.1111/mpp.12720] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/15/2018] [Accepted: 06/20/2018] [Indexed: 05/18/2023]
Abstract
Root-knot nematodes (RKNs, Meloidogyne spp.) are sedentary biotrophic pathogens that establish within the vascular cylinder of plant roots, forming a gall and inducing several feeding cells, giant cells (GCs), essential for completion of their life cycle. GCs suffer gene expression changes, repeated mitosis and endoreduplication events. Transcriptomics has revealed that an extensive down-regulation of transcripts, a molecular signature of early-developing galls and GCs that is conserved in tomato and Arabidopsis, may be achieved through small RNA (sRNA) gene silencing pathways. The role of some microRNAs (miRNAs) in plant-RKN interactions has recently been addressed, but little is known about the regulatory roles of other sRNA types. Here, we perform a differential accumulation analysis to show which repeat-associated small interfering RNAs (rasiRNAs) are distinctive or enriched in early Arabidopsis galls vs. uninfected roots. Those distinctive from galls are preferentially located in pericentromeric regions with predominant sizes of 24 and 22 nucleotides. Gall-distinctive rasiRNAs target primarily GYPSY and COPIA retrotransposons, which show a marked repression in galls vs. uninfected roots. Infection tests and phenotypic studies of galls from Meloidogyne javanica in Arabidopsis mutants impaired in post-transcriptional gene silencing and/or canonical RNA-directed DNA methylation (RdDM) pathways, as well as quantitative polymerase chain reaction analysis, suggest the implication of canonical and non-canonical RdDM pathways during gall formation, possibly through the regulation of retrotransposons. This process may be crucial for the maintenance of genome integrity during the reprogramming process of galls/GCs from their vascular precursor cells, and/or to ensure a faithful DNA replication during the repeated mitosis/endoreduplication that concurs with feeding site formation.
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Affiliation(s)
- Virginia Ruiz‐Ferrer
- Universidad de Castilla‐ La Mancha. Facultad de Ciencias Ambientales y Bioquímica. Avda. Carlos IIIs/n. 45071. ToledoSpain
| | - Javier Cabrera
- Universidad de Castilla‐ La Mancha. Facultad de Ciencias Ambientales y Bioquímica. Avda. Carlos IIIs/n. 45071. ToledoSpain
| | - Isabel Martinez‐Argudo
- Universidad de Castilla‐ La Mancha. Facultad de Ciencias Ambientales y Bioquímica. Avda. Carlos IIIs/n. 45071. ToledoSpain
| | - Haydeé Artaza
- Faculty of Medicine, Department of Clinical ScienceUniversity of Bergen5020BergenNorway
| | - Carmen Fenoll
- Universidad de Castilla‐ La Mancha. Facultad de Ciencias Ambientales y Bioquímica. Avda. Carlos IIIs/n. 45071. ToledoSpain
| | - Carolina Escobar
- Universidad de Castilla‐ La Mancha. Facultad de Ciencias Ambientales y Bioquímica. Avda. Carlos IIIs/n. 45071. ToledoSpain
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Ali MA, Anjam MS, Nawaz MA, Lam HM, Chung G. Signal Transduction in Plant⁻Nematode Interactions. Int J Mol Sci 2018; 19:ijms19061648. [PMID: 29865232 PMCID: PMC6032140 DOI: 10.3390/ijms19061648] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/26/2018] [Accepted: 05/29/2018] [Indexed: 12/26/2022] Open
Abstract
To successfully invade and infect their host plants, plant parasitic nematodes (PPNs) need to evolve molecular mechanisms to overcome the defense responses from the plants. Nematode-associated molecular patterns (NAMPs), including ascarosides and certain proteins, while instrumental in enabling the infection, can be perceived by the host plants, which then initiate a signaling cascade leading to the induction of basal defense responses. To combat host resistance, some nematodes can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling and also modulate the hosts’ gene expression patterns to facilitate the establishment of nematode feeding sites (NFSs). In this review, we summarized all the known signaling pathways involved in plant–nematode interactions. Specifically, we placed particular focus on the effector proteins from PPNs that mimic the signaling of the defense responses in host plants. Furthermore, we gave an updated overview of the regulation by PPNs of different host defense pathways such as salicylic acid (SA)/jasmonic acid (JA), auxin, and cytokinin and reactive oxygen species (ROS) signaling to facilitate their parasitic successes in plants. This review will enhance the understanding of the molecular signaling pathways involved in both compatible and incompatible plant–nematode interactions.
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Affiliation(s)
- Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan.
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Muhammad Shahzad Anjam
- Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan 66000, Pakistan.
| | | | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
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Koter MD, Święcicka M, Matuszkiewicz M, Pacak A, Derebecka N, Filipecki M. The miRNAome dynamics during developmental and metabolic reprogramming of tomato root infected with potato cyst nematode. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 268:18-29. [PMID: 29362080 DOI: 10.1016/j.plantsci.2017.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/05/2017] [Accepted: 12/09/2017] [Indexed: 05/20/2023]
Abstract
Cyst-forming plant-parasitic nematodes are pests threatening many crops. By means of their secretions cyst nematodes induce the developmental and metabolic reprogramming of host cells that lead to the formation of a syncytium, which is the sole food source for growing nematodes. The in depth micro RNA (miRNA) dynamics in the syncytia induced by Globodera rostochiensis in tomato roots was studied. The miRNAomes were obtained from syncytia covering the early and intermediate developmental stages, and were the subject of differential expression analysis. The expression of 1235 miRNAs was monitored. The fold change (log2FC) ranged from -7.36 to 8.38, indicating that this transcriptome fraction was very variable. Moreover, we showed that the DE (differentially expressed) miRNAs do not fully overlap between the selected time points, suggesting infection stage specific regulation by miRNA. The correctness of RNA-seq expression profiling was confirmed by qRT-PCR (quantitative Real Time Polymerase Chain Reaction) for seven miRNA species. Down- and up-regulated miRNA species, including their isomiRs, were further used to identify their potential targets. Among them there are a large number of transcription factors linked to different aspects of plant development belonging to gene families, such as APETALA2 (AP2), SQUAMOSA (MADS-box), MYB, GRAS, and AUXIN RESPONSE FACTOR (ARF). The substantial portion of potential target genes belong to the NB-LRR and RLK (RECEPTOR-LIKE KINASE) families, indicating the involvement of miRNA mediated regulation in defense responses. We also collected the evidence for target cleavage in the case of 29 miRNAs using one of three alternative methods: 5' RACE (5' Rapid Amplification of cDNA Ends), a search of tasiRNA within our datasets, and the meta-analysis of tomato degradomes in the GEO (Gene Expression Omnibus) database. Eight target transcripts showed a negative correlation with their respective miRNAs at two or three time points. These results indicate a large regulatory potential for miRNAs in tuning the development and defense responses.
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Affiliation(s)
- Marek D Koter
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Magdalena Święcicka
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Mateusz Matuszkiewicz
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Marcin Filipecki
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland.
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Pan X, Nichols RL, Li C, Zhang B. MicroRNA-target gene responses to root knot nematode (Meloidogyne incognita) infection in cotton (Gossypium hirsutum L.). Genomics 2018; 111:383-390. [PMID: 29481843 DOI: 10.1016/j.ygeno.2018.02.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 01/23/2023]
Abstract
MicroRNAs (miRNAs) are a large class of small regulatory RNA molecules, however no study has been performed to elucidate the role of miRNAs in cotton (Gossypium hirsutum) response to the root knot nematode (RKN, Meloidogyne incognita) infection. We selected 28 miRNAs and 8 miRNA target genes to investigate the miRNA-target gene response to M. incognita infection. Our results show that RKN infection significantly affected the expression of several miRNAs and their targeted genes. After 10 days of RKN infection, expression fold changes on miRNA expressions ranged from down-regulated by 33% to upregulated by 406%; meanwhile the expression levels of miRNA target genes were 45.8% to 231%. Three miRNA-target pairs, miR159-MYB, miR319-TCP4 and miR167-ARF8, showed inverse expression patterns between gene targets and their corresponded miRNAs, suggesting miRNA-mediated gene regulation in cotton roots in response to RKN infection.
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Affiliation(s)
- Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | | | - Chao Li
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Comparative Study of Withanolide Biosynthesis-Related miRNAs in Root and Leaf Tissues of Withania somnifera. Appl Biochem Biotechnol 2018; 185:1145-1159. [PMID: 29476318 DOI: 10.1007/s12010-018-2702-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
Abstract
Withania somnifera, popularly known as Indian ginseng, is one of the most important medicinal plants. The plant is well studied in terms of its pharmaceutical activities and genes involved in biosynthetic pathways. However, not much is known about the regulatory mechanism of genes responsible for the production of secondary metabolites. The idea was to identify miRNA transcriptome responsible for the regulation of withanolide biosynthesis, specifically of root and leaf tissues individually. The transcriptome data of in vitro culture of root and leaf tissues of the plant was considered for miRNA identification. A total of 24 and 39 miRNA families were identified in root and leaf tissues, respectively. Out of these, 15 and 27 miRNA families have shown their involvement in different biological functions in root and leaf tissues, respectively. We report here, specific miRNAs and their corresponding target genes for corresponding root and leaf tissues. The target genes have also been analyzed for their role in withanolide metabolism. Endogenous root-miR5140, root-miR159, leaf-miR477, and leaf-miR530 were reported for regulation of withanolide biosynthesis.
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29
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Litholdo CG, Eamens AL, Waterhouse PM. The phenotypic and molecular assessment of the non-conserved Arabidopsis MICRORNA163/S-ADENOSYL-METHYLTRANSFERASE regulatory module during biotic stress. Mol Genet Genomics 2017; 293:503-523. [PMID: 29196849 DOI: 10.1007/s00438-017-1399-9] [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: 08/01/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022]
Abstract
In plants, microRNAs (miRNAs) have evolved in parallel to the protein-coding genes that they target for expression regulation, and miRNA-directed gene expression regulation is central to almost every cellular process. MicroRNA, miR163, is unique to the Arabidopsis genus and is processed into a 24-nucleotide (nt) mature small regulatory RNA (sRNA) from a single precursor transcript transcribed from a single locus, the MIR163 gene. The MIR163 locus is a result of a recent inverted duplication event of one of the five closely related S-ADENOSYL-METHYLTRANSFERASE genes that the mature miR163 sRNA targets for expression regulation. Currently, however, little is known about the role of the miR163/S-ADENOSYL-METHYLTRANSFERASE regulatory module in response to biotic stress. Here, we document the expression domains of MIR163 and the S-ADENOSYL-METHYLTRANSFERASE target genes following fusion of their putative promoter sequences to the β-glucuronidase (GUS) reporter gene and subsequent in planta expression. Further, we report on our phenotypic and molecular assessment of Arabidopsis thaliana plants with altered miR163 accumulation, namely the mir163-1 and mir163-2 insertion knockout mutants and the miR163 overexpression line, the MIR163-OE plant. Finally, we reveal miR163 accumulation and S-ADENOSYL-METHYLTRANSFERASE target gene expression post treatment with the defence elicitors, salicylic acid and jasmonic acid, and following Fusarium oxysporum infection, wounding, and herbivory attack. Together, the work presented here provides a comprehensive new biological insight into the role played by the Arabidopsis genus-specific miR163/S-ADENOSYL-METHYLTRANSFERASE regulatory module in normal A. thaliana development and during the exposure of A. thaliana plants to biotic stress.
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Affiliation(s)
- Celso Gaspar Litholdo
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia. .,Citrus Biotechnology Lab, Centro de Citricultura, Instituto Agronômico de Campinas, Cordeirópolis, SP, 13490-000, Brazil.
| | - Andrew Leigh Eamens
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.,School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Peter Michael Waterhouse
- School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia.,Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, 4001, Australia
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Ali MA, Azeem F, Li H, Bohlmann H. Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1699. [PMID: 29046680 PMCID: PMC5632807 DOI: 10.3389/fpls.2017.01699] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/15/2017] [Indexed: 05/03/2023]
Abstract
Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS) and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.
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Affiliation(s)
- Muhammad A. Ali
- Department of Plant Pathology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- *Correspondence: Muhammad A. Ali ;
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hongjie Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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