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Cherubino Ribeiro TH, Baldrich P, de Oliveira RR, Fernandes-Brum CN, Mathioni SM, de Sousa Cardoso TC, de Souza Gomes M, do Amaral LR, Pimenta de Oliveira KK, Dos Reis GL, Meyers BC, Chalfun-Junior A. The floral development of the allotetraploid Coffea arabica L. correlates with a small RNA dynamic reprogramming. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1848-1863. [PMID: 38488203 DOI: 10.1111/tpj.16713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/05/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]
Abstract
Noncoding and coding RNAs are key regulators of plant growth, development, and stress responses. To investigate the types of transcripts accumulated during the vegetative to reproductive transition and floral development in the Coffea arabica L., we sequenced small RNA libraries from eight developmental stages, up to anthesis. We combined these data with messenger RNA and PARE sequencing of two important development stages that marks the transition of an apparent latent to a rapid growth stage. In addition, we took advantage of multiple in silico tools to characterize genomic loci producing small RNAs such as phasiRNAs, miRNAs, and tRFs. Our differential and co-expression analysis showed that some types of small RNAs such as tRNAs, snoRNAs, snRNAs, and phasiRNAs preferentially accumulate in a stage-specific manner. Members of the miR482/miR2118 superfamily and their 21-nucleotide phasiRNAs originating from resistance genes show a robust co-expression pattern that is maintained across all the evaluated developmental stages. Finally, the majority of miRNAs accumulate in a family stage-specific manner, related to modulated hormonal responses and transcription factor expression.
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Affiliation(s)
- Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | | | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Christiane Noronha Fernandes-Brum
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | | | - Thaís Cunha de Sousa Cardoso
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Matheus de Souza Gomes
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Laurence Rodrigues do Amaral
- Laboratory of Bioinformatics and Molecular Analysis, Federal University of Uberlandia (UFU), Campus Patos de Minas, Lavras, 38700-128, MG, Brazil
| | - Kellen Kauanne Pimenta de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Gabriel Lasmar Dos Reis
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
| | - Blake C Meyers
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
- Division of Plant Sciences and Technology, University of Missouri-Columbia, Columbia, MI, 65211, USA
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Lavras, 37200-000, MG, Brazil
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Zhu X, Kuang Y, Chen Y, Shi J, Cao Y, Hu J, Yu C, Yang F, Tian F, Chen H. miR2118 Negatively Regulates Bacterial Blight Resistance through Targeting Several Disease Resistance Genes in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3815. [PMID: 38005712 PMCID: PMC10675396 DOI: 10.3390/plants12223815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023]
Abstract
Plant miRNAs are a class of noncoding RNA with a length of 21-24 nt that play an important role in plant responses to biotic and abiotic stresses. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious bacterial diseases in rice. Our previous work showed that osa-miR2118b/n was induced by Xoo infection. However, the biological function of miR2118 has not yet been characterized in experiments. Herein, we constructed MIR2118b OE, as well as single and double mutants of MIR2118b/n using CRISPR/Cas9. Further results showed that osa-MIR2118b OE plants exhibited longer lesion lengths than the wild type after Xoo inoculation, while MIR2118 CRISPR plants exhibited shorter lesion lengths than the wild type after Xoo inoculation. Co-transformation experiments in rice protoplasts indicated that osa-miR2118 negatively regulated the transcripts of three nucleotide-binding sites and leucine-rich repeat (NLR) genes (LOC_Os08g42700.1, LOC_Os01g05600.1, and LOC_Os12g37290.1) which are predicted target genes of miR2118, but not the mutated NLR genes with a 3 bp insertion at the center of the binding sites. The transcriptional level of the three NLR genes was reversed relative to osa-miR2118 in the MIR2118b OE and MIR2118b CRISPR plants. The above results demonstrate that osa-miR2118b/n negatively regulates the resistance to bacterial blight through negatively regulating several NLR genes.
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Affiliation(s)
- Xiumei Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Yongjie Kuang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Yutong Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Jia Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Yaqian Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Jixiang Hu
- Jiangsu Coastal Areas Institute of Agricultural Science, Jiangsu Academy of Agricultural Sciences, Yancheng 224002, China;
| | - Chao Yu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.Z.); (Y.K.); (Y.C.); (J.S.); (Y.C.); (C.Y.); (F.Y.); (F.T.)
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3
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von Dahlen JK, Schulz K, Nicolai J, Rose LE. Global expression patterns of R-genes in tomato and potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1216795. [PMID: 37965025 PMCID: PMC10641715 DOI: 10.3389/fpls.2023.1216795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 09/28/2023] [Indexed: 11/16/2023]
Abstract
Introduction As key-players of plant immunity, the proteins encoded by resistance genes (R-genes) recognize pathogens and initiate pathogen-specific defense responses. The expression of some R-genes carry fitness costs and therefore inducible immune responses are likely advantageous. To what degree inducible resistance driven by R-genes is triggered by pathogen infection is currently an open question. Methods In this study we analyzed the expression of 940 R-genes of tomato and potato across 315 transcriptome libraries to investigate how interspecific interactions with microbes influence R-gene expression in plants. Results We found that most R-genes are expressed at a low level. A small subset of R-genes had moderate to high levels of expression and were expressed across many independent libraries, irrespective of infection status. These R-genes include members of the class of genes called NRCs (NLR required for cell death). Approximately 10% of all R-genes were differentially expressed during infection and this included both up- and down-regulation. One factor associated with the large differences in R-gene expression was host tissue, reflecting a considerable degree of tissue-specific transcriptional regulation of this class of genes. Discussion These results call into question the widespread view that R-gene expression is induced upon pathogen attack. Instead, a small core set of R-genes is constitutively expressed, imparting upon the plant a ready-to-detect and defend status.
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Affiliation(s)
- Janina K. von Dahlen
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Kerstin Schulz
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Jessica Nicolai
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Laura E. Rose
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
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López-Márquez D, Del-Espino Á, Ruiz-Albert J, Bejarano ER, Brodersen P, Beuzón CR. Regulation of plant immunity via small RNA-mediated control of NLR expression. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6052-6068. [PMID: 37449766 PMCID: PMC10575705 DOI: 10.1093/jxb/erad268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 07/18/2023]
Abstract
Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses.
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Affiliation(s)
- Diego López-Márquez
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Ángel Del-Espino
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Javier Ruiz-Albert
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
| | - Peter Brodersen
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | - Carmen R Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Depto. Biología Celular, Genética y Fisiología, Málaga, Spain
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5
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Pegler JL, Oultram JMJ, Mann CWG, Carroll BJ, Grof CPL, Eamens AL. Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:1101. [PMID: 36903960 PMCID: PMC10004981 DOI: 10.3390/plants12051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Maksimov IV, Shein MY, Burkhanova GF. RNA Interference in Plant Protection from Fungal and Oomycete Infection. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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7
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Zangishei Z, Annacondia ML, Gundlach H, Didriksen A, Bruckmüller J, Salari H, Krause K, Martinez G. Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain. PLANT PHYSIOLOGY 2022; 190:1242-1259. [PMID: 35861439 PMCID: PMC9516757 DOI: 10.1093/plphys/kiac331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/12/2022] [Indexed: 05/29/2023]
Abstract
Parasitism is a successful life strategy that has evolved independently in several families of vascular plants. The genera Cuscuta and Orobanche represent examples of the two profoundly different groups of parasites: one parasitizing host shoots and the other infecting host roots. In this study, we sequenced and described the overall repertoire of small RNAs from Cuscuta campestris and Orobanche aegyptiaca. We showed that C. campestris contains a number of novel microRNAs (miRNAs) in addition to a conspicuous retention of miRNAs that are typically lacking in other Solanales, while several typically conserved miRNAs seem to have become obsolete in the parasite. One new miRNA appears to be derived from a horizontal gene transfer event. The exploratory analysis of the miRNA population (exploratory due to the absence of a full genomic sequence for reference) from the root parasitic O. aegyptiaca also revealed a loss of a number of miRNAs compared to photosynthetic species from the same order. In summary, our study shows partly similar evolutionary signatures in the RNA silencing machinery in both parasites. Our data bear proof for the dynamism of this regulatory mechanism in parasitic plants.
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Affiliation(s)
| | | | - Heidrun Gundlach
- Helmholtz Zentrum München (HMGU), Plant Genome and Systems Biology (PGSB), Neuherberg 85764, Germany
| | - Alena Didriksen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø 9019, Norway
| | | | - Hooman Salari
- Department of Production Engineering and Plant Genetics, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah 67155, Iran
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8
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Dey S, Sarkar A, Chowdhury S, Singh R, Mukherjee A, Ghosh Z, Kundu P. Heightened miR6024-NLR interactions facilitate necrotrophic pathogenesis in tomato. PLANT MOLECULAR BIOLOGY 2022; 109:717-739. [PMID: 35499677 DOI: 10.1007/s11103-022-01270-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
miR6024 acts as a negative regulator of R genes, hence of Tomato plant immunity, and facilitates disease by the necrotrophic pathogen A. solani. Plant resistance genes or Nucleotide-binding leucine-rich repeat (NLR) genes, integral components of plant disease stress-signaling are targeted by variable groups of miRNAs. However, the significance of miRNA-mediated regulation of NLRs during a pathogen stress response, specifically for necrotrophic fungus, is poorly understood. A thorough examination of Tomato NLRs and miRNAs could map substantial interactions of which half the annotated NLRs were targets of Solanaceae-specific and conserved miRNAs, at the NB subdomain. The Solanaceae-specific miR6024 and its NLR targets analysed in different phytopathogenic stresses revealed differential and mutually antagonistic regulation. Interestingly, miR6024-targeted cleavage of a target NLR also triggered the generation of secondary phased siRNAs which could potentially amplify the defense signal. RNA-seq analysis of leaf tissues from miR6024 overexpressing Tomato plants evidenced a perturbation in the defense transcriptome with the transgenics showing unwarranted immune response-related genes' expression with or without infection with necrotrophic Alternaria solani, though no adverse effect could be observed in the growth and development of the transgenic plants. Transgenic plants exhibited constitutive downregulation of the target NLRs, aggravated disease phenotype with an enhanced lesion, greater ROS generation and hypersusceptibility to A. solani infection, thus establishing that miR6024 negatively impacts plant immune response during necrotrophic pathogenesis. Limited knowledge about the outcome of NLR-miRNA interaction during necrotrophic pathogenesis is a hindrance to the deployment of miRNAs in crop improvement programs. With the elucidation of the necrotrophic disease-synergistic role played by miR6024, it becomes a potent candidate for biotechnological manipulation for the rapid development of pathogen-tolerant solanaceous plants.
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Affiliation(s)
- Sayani Dey
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Arijita Sarkar
- Division of Bioinformatics, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Shreya Chowdhury
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Raghuvir Singh
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Ananya Mukherjee
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India
| | - Pallob Kundu
- Division of Plant Biology, Unified Academic Campus, Bose Institute, EN 80, Bidhan Nagar, Kolkata, West Bengal, 700091, India.
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9
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Zhang X, Ren C, Xue Y, Tian Y, Zhang H, Li N, Sheng C, Jiang H, Bai D. Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Peanut ( Arachis hypogaea L.) Cold Response. FRONTIERS IN PLANT SCIENCE 2022; 13:920195. [PMID: 35720560 PMCID: PMC9203150 DOI: 10.3389/fpls.2022.920195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/06/2022] [Indexed: 05/31/2023]
Abstract
Cold stress is a major environmental factor that affects plant growth and development, as well as fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play crucial roles in various abiotic stresses. Peanuts (Arachis hypogaea L.), one of the most important grain legumes and source of edible oils and proteins, are cultivated in the semi-arid tropical and subtropical regions of the world. To date, there has been no report on the role of miRNAs in the response to cold stress in cultivated peanuts. In this study, we profiled cold-responsive miRNAs in peanuts using deep sequencing in cold-sensitive (WQL20) alongside a tolerant variety (WQL30). A total of 407 known miRNAs and 143 novel peanut-specific miRNAs were identified. The expression of selected known and novel miRNAs was validated by northern blotting and six known cold-responsive miRNAs were revealed. Degradome sequencing identified six cold-responsive miRNAs that regulate 12 target genes. The correlative expression patterns of several miRNAs and their target genes were further validated using qRT-PCR. Our data showed that miR160-ARF, miR482-WDRL, miR2118-DR, miR396-GRF, miR162-DCL, miR1511-SRF, and miR1511-SPIRAL1 modules may mediate cold stress responses. Transient expression analysis in Nicotiana benthamiana found that miR160, miR482, and miR2118 may play positive roles, and miR396, miR162, and miR1511 play negative roles in the regulation of peanut cold tolerance. Our results provide a foundation for understanding miRNA-dependent cold stress response in peanuts. The characterized correlations between miRNAs and their response to cold stress could serve as markers in breeding programs or tools for improving cold tolerance of peanuts.
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Affiliation(s)
- Xin Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
- State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Taiyuan, China
| | - Chao Ren
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Yunyun Xue
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Yuexia Tian
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Huiqi Zhang
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Na Li
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
| | - Cong Sheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Laboratory of Bio-interactions and Crop Health, Nanjing Agricultural University, Nanjing, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dongmei Bai
- Institute of Industrial Crops, Shanxi Agricultural University, Taiyuan, China
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10
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Baldrich P, Bélanger S, Kong S, Pokhrel S, Tamim S, Teng C, Schiebout C, Gurazada SGR, Gupta P, Patel P, Razifard H, Nakano M, Dusia A, Meyers BC, Frank MH. The evolutionary history of small RNAs in Solanaceae. PLANT PHYSIOLOGY 2022; 189:644-665. [PMID: 35642548 PMCID: PMC9157080 DOI: 10.1093/plphys/kiac089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 06/01/2023]
Abstract
The Solanaceae or "nightshade" family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.
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Affiliation(s)
- Patricia Baldrich
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Shuyao Kong
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Suresh Pokhrel
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Saleh Tamim
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Sai Guna Ranjan Gurazada
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
- Corteva Agriscience, Wilmington, Delaware 19805, USA
| | - Pallavi Gupta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Hamid Razifard
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Mayumi Nakano
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Ayush Dusia
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Margaret H Frank
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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11
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Zhang Y, Waseem M, Zeng Z, Xu J, Chen C, Liu Y, Zhai J, Xia R. MicroRNA482/2118, a miRNA superfamily essential for both disease resistance and plant development. THE NEW PHYTOLOGIST 2022; 233:2047-2057. [PMID: 34761409 DOI: 10.1111/nph.17853] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/07/2021] [Indexed: 05/17/2023]
Abstract
MicroRNAs (miRNAs) are a class of 21-24 nucleotides (nt) noncoding small RNAs ubiquitously distributed across the plant kingdom. miR482/2118, one of the conserved miRNA superfamilies originating from gymnosperms, has divergent main functions in core-angiosperms. It mainly regulates NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT (NBS-LRR) genes in eudicots, functioning as an essential component in plant disease resistance; in contrast, it predominantly targets numerous long noncoding RNAs (lncRNAs) in monocot grasses, which are vital for plant reproduction. Usually, miR482/2118 is 22-nt in length, which can trigger the production of phased small interfering RNAs (phasiRNAs) after directed cleavage. PhasiRNAs instigated from target genes of miR482/2118 enhance their roles in corresponding biological processes by cis-regulation on cognate genes and expands their function to other pathways via trans activity on different genes. This review summarizes the origin, biogenesis, conservation, and evolutionary characteristics of the miR482/2118 superfamily and delineates its diverse functions in disease resistance, plant development, stress responses, etc.
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Affiliation(s)
- Yanqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Muhammad Waseem
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Jing Xu
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, Guangdong, 510640, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510640, China
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12
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Han WH, Wang JX, Zhang FB, Liu YX, Wu H, Wang XW. Small RNA and Degradome Sequencing Reveal Important MicroRNA Function in Nicotiana tabacum Response to Bemisia tabaci. Genes (Basel) 2022; 13:361. [PMID: 35205405 PMCID: PMC8871844 DOI: 10.3390/genes13020361] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding regulatory RNAs, are key molecules in many biological and metabolic processes of plant growth, development and stress response via targeting mRNAs. The phloem-feeding insect whitefly Bemisia tabaci (Hemiptera, Aleyrodidae) is a serious pest that causes devastating harm to agricultural production worldwide. However, the function of host miRNAs in the response to whitefly infestation remains unclear. Here, we sequenced the small RNA and degradome of tobacco (Nicotiana tabacum L.), after and before infestation by B. tabaci. We identified 1291 miRNAs belonging to 138 miRNA families including 706 known miRNAs and 585 novel miRNAs. A total of 47 miRNAs were differentially expressed, of which 30 were upregulated and 17 were downregulated by whitefly exposure. Then, computational analysis showed that the target genes of differential miRNAs were involved in R gene regulation, plant innate immunity, plant pathogen defense, the plant hormone signal pathway and abiotic stress tolerance. Furthermore, degradome analysis demonstrated that 253 mRNAs were cleaved by 66 miRNAs. Among them, the targets cleaved by upregulated miR6025, miR160, miR171, miR166 and miR168 are consistent with our prediction, suggesting that pathogen-related miRNAs may function in plant defense against whitefly. Moreover, our results show that plant miRNA response and miRNA-mediated post-transcriptional regulation for phloem-feeding insect infestation are similar to pathogen invasion. Our study provides additional data to further elucidate how host plants respond and defend the phloem-feeding insects.
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Affiliation(s)
| | | | | | | | | | - Xiao-Wei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (W.-H.H.); (J.-X.W.); (F.-B.Z.); (Y.-X.L.); (H.W.)
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13
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Liu W, Cui J, Luan Y. Overexpression of lncRNA08489 enhances tomato immunity against Phytophthora infestans by decoying miR482e-3p. Biochem Biophys Res Commun 2022; 587:36-41. [PMID: 34864393 DOI: 10.1016/j.bbrc.2021.11.079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 01/18/2023]
Abstract
LncRNAs are widely involved in various biological processes of plants. Recent evidences indicated that lncRNAs could act as competing endogenous RNAs (ceRNAs) to adsorb complementary miRNAs in a type of target mimicry, thereby indirectly regulating the target genes of miRNAs. In this study, a lncRNA, lncRNA08489 was identified to be the ceRNA of miR482e-3p in tomato plants. The expression patterns of lncRNA08489 and miR482e-3p showed opposite trends after tomato plants infected with Phytophthora infestans. In tomato leaves overexpressing lncRNA08489 (OE08489), the expression level of miR482e-3p decreased and its target gene, NBS-LRR increased. After infection with P. infestans, the resistance of OE08489 plants was stronger than that of the wild type, and the reactive oxygen species (ROS) scavenging ability of OE08489 plants was significantly improved. Taken together, these results indicated that lncRNA08489 acted as a ceRNA to decoy miR482e-3p and regulate the expression of NBS-LRR to enhance tomato resistance through ROS-scavenging system.
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Affiliation(s)
- Weiwei Liu
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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14
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Li Q, Shah N, Zhou X, Wang H, Yu W, Luo J, Liu Y, Li G, Liu C, Zhang C, Chen P. Identification of Micro Ribonucleic Acids and Their Targets in Response to Plasmodiophora brassicae Infection in Brassica napus. FRONTIERS IN PLANT SCIENCE 2021; 12:734419. [PMID: 34777417 PMCID: PMC8585624 DOI: 10.3389/fpls.2021.734419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/21/2021] [Indexed: 05/24/2023]
Abstract
Clubroot disease, which is caused by the soil-borne pathogen Plasmodiophora brassicae War (P. brassicae), is one of the oldest and most destructive diseases of Brassica and cruciferous crops in the world. Plant microRNAs [micro ribonucleic acids (miRNAs)] play important regulatory roles in several developmental processes. Although the role of plant miRNAs in plant-microbe interaction has been extensively studied, there are only few reports on the specific functions of miRNAs in response to P. brassicae. This study investigated the roles of miRNAs and their targets during P. brassicae infection in a pair of Brassica napus near-isogenic lines (NILs), namely clubroot-resistant line 409R and clubroot-susceptible line 409S. Small RNA sequencing (sRNA-seq) and degradome-seq were performed on root samples of 409R and 409S with or without P. brassicae inoculation. sRNA-seq identified a total of 48 conserved and 72 novel miRNAs, among which 18 had a significant differential expression in the root of 409R, while only one miRNA was differentially expressed in the root of 409S after P. brassicae inoculation. The degradome-seq analysis identified 938 miRNA target transcripts, which are transcription factors, enzymes, and proteins involved in multiple biological processes and most significantly enriched in the plant hormone signal transduction pathway. Between 409R and 409S, we found eight different degradation pathways in response to P. brassicae infection, such as those related to fatty acids. By combining published transcriptome data, we identified a total of six antagonistic miRNA-target pairs in 409R that are responsive to P. brassicae infection and involved in pathways associated with root development, hypersensitive cell death, and chloroplast metabolic synthesis. Our results reveal that P. brassicae infection leads to great changes in miRNA pool and target transcripts. More interestingly, these changes are different between 409R and 409S. Clarification of the crosstalk between miRNAs and their targets may shed new light on the possible mechanisms underlying the pathogen resistance against P. brassicae.
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Affiliation(s)
- Qian Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Nadil Shah
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xueqing Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huiying Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenlin Yu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiajie Luo
- Agricultural Technology Extension Station of Linxiang, Lincang, China
| | - Yajun Liu
- Agricultural Technology Extension Station of Lincang, Lincang, China
| | - Genze Li
- Industrial Crops Institute of Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Chao Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chunyu Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Peng Chen
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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15
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Wu F, Xu J, Gao T, Huang D, Jin W. Molecular mechanism of modulating miR482b level in tomato with botrytis cinerea infection. BMC PLANT BIOLOGY 2021; 21:496. [PMID: 34706648 PMCID: PMC8555085 DOI: 10.1186/s12870-021-03203-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant miRNAs are involved in the response to biotic and abiotic stresses by altering their expression levels, and they play an important role in the regulation of plant resistance to stress. However, the molecular mechanism that regulates the expression levels of miRNAs in plants with biotic and abiotic stress still needs to be explored. Previously, we found that the expression of the miR482 family was changed in tomato infected by Botrytis cinerea. In this study, we investigated and uncovered the mechanism underlying the response of miR482 to B. cinerea infection in tomato. RESULTS First, RT-qPCR was employed to detect the expression patterns of miR482b in tomato infected by B. cinerea, and results showed that miR482b primary transcripts (pri-miR482b) were up-regulated in B. cinerea-infected leaves, but the mature miR482b was down-regulated. Subsequently, we used rapid amplification cDNA end method to amplify the full-length of pri-miR482b. Result showed that the pri-miR482b had two isoforms, with the longer one (consisting 300 bp) having an extra fragment of 53 bp in the 3'-end compared with the shorter one. In vitro Dicer assay indicated that the longer isoform pri-miR482b-x1 had higher efficiency in the post-transcriptional splicing of miRNA than the shorter isoform pri-miR482b-x2. In addition, the transcription level of mature miR482b was much higher in transgenic Arabidopsis overexpressing pri-miR482b-x1 than that in OE pri-miR482b-x2 Arabidopsis. These results confirmed that this extra 53 bp in pri-miR482b-x1 might play a key role in the miR482b biogenesis of post-transcription processing. CONCLUSIONS Extra 53 bp in pri-miR482b-x1 enhanced miR482b biogenesis, which elevated the transcription level of miR482b. This study clarified the response of miR482 to B. cinerea infection in tomato, thereby helping us further understand the molecular mechanisms that regulate the expression levels of other miRNAs.
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Affiliation(s)
- Fangli Wu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jinfeng Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Tiantian Gao
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Diao Huang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Weibo Jin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China.
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16
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Hong Y, Meng J, He X, Zhang Y, Liu Y, Zhang C, Qi H, Luan Y. Editing miR482b and miR482c Simultaneously by CRISPR/Cas9 Enhanced Tomato Resistance to Phytophthora infestans. PHYTOPATHOLOGY 2021; 111:1008-1016. [PMID: 33258411 DOI: 10.1094/phyto-08-20-0360-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Late blight, caused by Phytophthora infestans, is severely damaging to the global tomato industry. Micro-RNAs (miRNAs) have been widely demonstrated to play vital roles in plant resistance by repressing their target genes. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) method has been continuously improved and extensively applied to edit plant genomes. However, editing multiplex miRNAs by CRISPR/Cas9 in tomato has not been studied yet. We knocked out miR482b and miR482c simultaneously in tomato through the multiplex CRISPR/Cas9 system. Two transgenic plants with silenced miR482b and miR482c simultaneously and one transgenic line with silenced miR482b alone were obtained. Compared with wild-type plants, the disease symptoms of three transgenic plants upon infection were reduced, accompanied by increased expression of their common target nucleotide binding site-leucine-rich repeat genes and decreased levels of reactive oxygen species. Furthermore, silencing miR482b and miR482c simultaneously was more resistant than silencing miR482b alone in tomato. More importantly, we found that knocking out miR482b and miR482c can elicit expression perturbation of other miRNAs, suggesting cross-regulation between miRNAs. Our study demonstrated that editing miR482b and miR482c simultaneously with CRISPR/Cas9 is an efficient strategy for generating pathogen-resistant tomatoes, and cross-regulation between miRNAs may reveal the novel mechanism in tomato-P. infestans interactions.
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Affiliation(s)
- Yuhui Hong
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaoli He
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yuanyuan Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yarong Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Chengwei Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Beijing Academy of Agriculture & Forestry Sciences, Beijing 100000, China
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University/Key Laboratory of Protected Horticulture, Ministry of Education/Northern National & Local Joint Engineering Research Center of Horticultural Facilities Design and Application Technology (Liaoning), Shenyang 110866, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
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17
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Andolfo G, D’Agostino N, Frusciante L, Ercolano MR. The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies. Genes (Basel) 2021; 12:genes12020184. [PMID: 33514027 PMCID: PMC7911644 DOI: 10.3390/genes12020184] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/16/2022] Open
Abstract
Tomato (Solanum lycopersicum L.) is a model system for studying the molecular basis of resistance in plants. The investigation of evolutionary dynamics of tomato resistance (R)-loci provides unique opportunities for identifying factors that promote or constrain genome evolution. Nucleotide-binding domain and leucine-rich repeat (NB-LRR) receptors belong to one of the most plastic and diversified families. The vast amount of genomic data available for Solanaceae and wild tomato relatives provides unprecedented insights into the patterns and mechanisms of evolution of NB-LRR genes. Comparative analysis remarked a reshuffling of R-islands on chromosomes and a high degree of adaptive diversification in key R-loci induced by species-specific pathogen pressure. Unveiling NB-LRR natural variation in tomato and in other Solanaceae species offers the opportunity to effectively exploit genetic diversity in genomic-driven breeding programs with the aim of identifying and introducing new resistances in tomato cultivars. Within this motivating context, we reviewed the repertoire of NB-LRR genes available for tomato improvement with a special focus on signatures of adaptive processes. This issue is still relevant and not thoroughly investigated. We believe that the discovery of mechanisms involved in the generation of a gene with new resistance functions will bring great benefits to future breeding strategies.
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Shen E, Chen T, Zhu X, Fan L, Sun J, Llewellyn DJ, Wilson I, Zhu QH. Expansion of MIR482/2118 by a class-II transposable element in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2084-2099. [PMID: 32578284 DOI: 10.1111/tpj.14885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, and their extant diploid progenitors, Gossypium arboreum and Gossypium raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. barbadense, G. hirsutum and G. raimondii, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target-gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives resulted from an initial capture of an MIR482/2118d by a class-II DNA transposable element (TE) in G. raimondii prior to the tetraploidization event, followed by transposition to new genomic locations in G. barbadense, G. hirsutum and G. raimondii. The 'GosTE' involved in the capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily, generating a 3-bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. barbadense and G. hirsutum, suggesting a dynamic co-evolution of miR482/2118 and its NBS-LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.
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Affiliation(s)
- Enhui Shen
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- New Rural Development Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xintian Zhu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Danny J Llewellyn
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Iain Wilson
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qian-Hao Zhu
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
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Analysis of small RNA populations generated in peanut leaves after exogenous application of dsRNA and dsDNA targeting aflatoxin synthesis genes. Sci Rep 2020; 10:13820. [PMID: 32796886 PMCID: PMC7427784 DOI: 10.1038/s41598-020-70618-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 07/27/2020] [Indexed: 11/08/2022] Open
Abstract
Previously, we have shown that RNA interference (RNAi) can prevent aflatoxin accumulation in transformed peanuts. To explore aflatoxin control by exogenous delivery of double-strand RNA (dsRNA) it is necessary to understand the generation of small RNA (sRNA) populations. We sequenced 12 duplicate sRNA libraries of in-vitro-grown peanut plants, 24 and 48 h after exogenous application of five gene fragments (RNAi-5x) related to aflatoxin biosynthesis in Aspergillus flavus. RNAi-5x was applied either as double-stranded RNA (dsRNA) or RNAi plasmid DNA (dsDNA). Small interfering RNAs (siRNAs) derived from RNAi-5x were significantly more abundant at 48 h than at 24 h, and the majority mapped to the fragment of aflatoxin efflux-pump gene. RNAi-5x-specific siRNAs were significantly, three to fivefold, more abundant in dsDNA than dsRNA treatments. Further examination of known micro RNAs related to disease-resistance, showed significant down-regulation of miR399 and up-regulation of miR482 in leaves treated with dsDNA compared to the control. These results show that sRNA sequencing is useful to compare exogenous RNAi delivery methods on peanut plants, and to analyze the efficacy of molecular constructs to generate siRNAs against specific gene targets. This work lays the foundation for non-transgenic delivery of RNAi in controlling aflatoxins in peanut.
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20
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Jiang N, Cui J, Hou X, Yang G, Xiao Y, Han L, Meng J, Luan Y. Sl-lncRNA15492 interacts with Sl-miR482a and affects Solanum lycopersicum immunity against Phytophthora infestans. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1561-1574. [PMID: 32432801 DOI: 10.1111/tpj.14847] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 05/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are involved in the resistance of plants to infection by pathogens via interactions with microRNAs (miRNAs). Long non-coding RNAs are cleaved by miRNAs to produce phased small interfering RNAs (phasiRNAs), which, as competing endogenous RNAs (ceRNAs), function as decoys for mature miRNAs, thus inhibiting their expression, and contain pre-miRNA sequences to produce mature miRNAs. However, whether lncRNAs and miRNAs mediate other molecular mechanisms during plant resistance to pathogens is unknown. In this study, as a positive regulator, Sl-lncRNA15492 from tomato (Solanum lycopersicum Zaofen No. 2) plants affected tomato resistance to Phytophthora infestans. Gain- and loss-of-function experiments and RNA ligase-mediated 5'-amplification of cDNA ends (RLM-5' RACE) also revealed that Sl-miR482a was negatively involved in tomato resistance by targeting Sl-NBS-LRR genes and that silencing of Sl-NBS-LRR1 decreased tomato resistance. Sl-lncRNA15492 inhibited the expression of mature Sl-miR482a, whose precursor was located within the antisense sequence of Sl-lncRNA15492. Further degradome analysis and additional RLM-5' RACE experiments verified that mature Sl-miR482a could also cleave Sl-lncRNA15492. These results provide a mechanism by which lncRNAs might inhibit precursor miRNA expression through antisense strands of lncRNAs, and demonstrate that Sl-lncRNA15492 and Sl-miR482a mutually inhibit the maintenance of Sl-NBS-LRR1 homeostasis during tomato resistance to P. infestans.
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Affiliation(s)
- Ning Jiang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Xinxin Hou
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Guanglei Yang
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Yu Xiao
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Lu Han
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
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21
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Zhao C, Li T, Zhao Y, Zhang B, Li A, Zhao S, Hou L, Xia H, Fan S, Qiu J, Li P, Zhang Y, Guo B, Wang X. Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds. BMC PLANT BIOLOGY 2020; 20:215. [PMID: 32404101 PMCID: PMC7222326 DOI: 10.1186/s12870-020-02426-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 04/30/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND MicroRNAs are important gene expression regulators in plants immune system. Aspergillus flavus is the most common causal agents of aflatoxin contamination in peanuts, but information on the function of miRNA in peanut-A. flavus interaction is lacking. In this study, the resistant cultivar (GT-C20) and susceptible cultivar (Tifrunner) were used to investigate regulatory roles of miRNAs in response to A. flavus growth. RESULTS A total of 30 miRNAs, 447 genes and 21 potential miRNA/mRNA pairs were differentially expressed significantly when treated with A. flavus. A total of 62 miRNAs, 451 genes and 44 potential miRNA/mRNA pairs exhibited differential expression profiles between two peanut varieties. Gene Ontology (GO) analysis showed that metabolic-process related GO terms were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses further supported the GO results, in which many enriched pathways were related with biosynthesis and metabolism, such as biosynthesis of secondary metabolites and metabolic pathways. Correlation analysis of small RNA, transcriptome and degradome indicated that miR156/SPL pairs might regulate the accumulation of flavonoids in resistant and susceptible genotypes. The miR482/2118 family might regulate NBS-LRR gene which had the higher expression level in resistant genotype. These results provided useful information for further understanding the roles of miR156/157/SPL and miR482/2118/NBS-LRR pairs. CONCLUSIONS Integration analysis of the transcriptome, miRNAome and degradome of resistant and susceptible peanut varieties were performed in this study. The knowledge gained will help to understand the roles of miRNAs of peanut in response to A. flavus.
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Affiliation(s)
- Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Tingting Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- Rizhao Experimental High School od Shandong, Rizhao, 276826 PR China
| | - Yuhan Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC USA
| | - Aiqin Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Shoujin Fan
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Jingjing Qiu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-Agricultural Research Service, Tifton, GA 31793 USA
- Department of Plant Pathology, University of Georgia, Tifton, GA USA
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 PR China
- College of Life Sciences, Shandong Normal University, Jinan, 250014 PR China
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22
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Sós‐Hegedűs A, Domonkos Á, Tóth T, Gyula P, Kaló P, Szittya G. Suppression of NB-LRR genes by miRNAs promotes nitrogen-fixing nodule development in Medicago truncatula. PLANT, CELL & ENVIRONMENT 2020; 43:1117-1129. [PMID: 31834628 PMCID: PMC7317971 DOI: 10.1111/pce.13698] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/26/2019] [Accepted: 12/04/2019] [Indexed: 05/29/2023]
Abstract
Plant genomes contain two major classes of innate immune receptors to recognize different pathogens. The pattern recognition receptors perceive conserved pathogen-associated molecular patterns and the resistance genes with nucleotide-binding (NB) and leucine-rich repeat (LRR) domains recognize specific pathogen effectors. The precise regulation of resistance genes is important since the unregulated expression of NB-LRR genes can inhibit growth and may result in autoimmunity in the absence of pathogen infection. It was shown that a subset of miRNAs could target NB-LRR genes and act as an important regulator of plant immunity in the absence of pathogens. Plants not only interact with pathogens, but they can also establish symbiotic interactions with microbes. Nitrogen-fixing symbiotic interaction and nodule formation of legumes may also require the suppression of host defence to prevent immune responses. We found that upon symbiotic interactions, miRNAs repressing NB-LRR expression are upregulated in the developing nodules of Medicago truncatula. Furthermore, we show that the suppression of the activity of the NB-LRR genes targeted by these miRNAs is important during nodule development. Our results suggest that the downregulation of NB-LRR resistance genes in the developing nodule produces a suitable niche that facilitates bacterial colonization and the development of an N-fixing nodule.
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Affiliation(s)
- Anita Sós‐Hegedűs
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Ágota Domonkos
- Department of GeneticsAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Tamás Tóth
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Péter Gyula
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
| | - Péter Kaló
- Department of GeneticsAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
- Institute of Plant BiologyBiological Research CentreSzegedHungary
| | - György Szittya
- Department of Plant BiotechnologyAgricultural Biotechnology Institute, National Agricultural Research and Innovation CenterGödöllőHungary
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23
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Xu X, Chen X, Chen Y, Zhang Q, Su L, Chen X, Chen Y, Zhang Z, Lin Y, Lai Z. Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour. Sci Rep 2020; 10:4626. [PMID: 32170163 PMCID: PMC7069941 DOI: 10.1038/s41598-020-60946-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/07/2020] [Indexed: 11/09/2022] Open
Abstract
miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.
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Affiliation(s)
- Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yan Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qinglin Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liyao Su
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xu Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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24
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Hong YH, Meng J, He XL, Zhang YY, Luan YS. Overexpression of MiR482c in Tomato Induces Enhanced Susceptibility to Late Blight. Cells 2019; 8:E822. [PMID: 31382588 PMCID: PMC6721620 DOI: 10.3390/cells8080822] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 01/18/2023] Open
Abstract
Tomato is the highest-value fruit/vegetable crop worldwide. However, the quality and yield of tomatoes are severely affected by late blight. MicroRNA482s (miR482s) are involved in the plant's immune system. In this study, miR482c was transiently and stably overexpressed in tomatoes in transgenic plants to explore its mechanism in tomato resistance against late blight. Transgenic tomato plants with transiently overexpressed miR482c displayed a larger lesion area than the control plants upon infection. Furthermore, compared with wild-type (WT) tomato plants, the transgenic tomato plants stably overexpressing miR482c displayed a decreased expression of target genes accompanied by lower peroxidase (POD), superoxide dismutase (SOD), and phenylalanine ammonia-lyase (PAL) activity activities and higher malondialdehyde (MDA) content, thereby leading to a decline in reactive oxygen species (ROS) scavenging ability and aggravating the damage of lipid peroxidation product accumulation on the cell membrane, eventually enhancing plant susceptibility. This finding indicates that miR482c may act as a negative regulator in tomato resistance by regulating nucleotide binding sites and leucine-rich repeat (NBS-LRR) expression levels and ROS levels.
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Affiliation(s)
- Yu-Hui Hong
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiao-Li He
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yuan-Yuan Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yu-Shi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
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25
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 360] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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26
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de Vries S, de Vries J, Rose LE. The Elaboration of miRNA Regulation and Gene Regulatory Networks in Plant⁻Microbe Interactions. Genes (Basel) 2019; 10:genes10040310. [PMID: 31010062 PMCID: PMC6523410 DOI: 10.3390/genes10040310] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Plants are exposed to diverse abiotic and biotic stimuli. These require fast and specific integrated responses. Such responses are coordinated at the protein and transcript levels and are incorporated into larger regulatory networks. Here, we focus on the evolution of transcriptional regulatory networks involved in plant–pathogen interactions. We discuss the evolution of regulatory networks and their role in fine-tuning plant defense responses. Based on the observation that many of the cornerstones of immune signaling in angiosperms are also present in streptophyte algae, it is likely that some regulatory components also predate the origin of land plants. The degree of functional conservation of many of these ancient components has not been elucidated. However, ongoing functional analyses in bryophytes show that some components are conserved. Hence, some of these regulatory components and how they are wired may also trace back to the last common ancestor of land plants or earlier. Of course, an understanding of the similarities and differences during the evolution of plant defense networks cannot ignore the lineage-specific coevolution between plants and their pathogens. In this review, we specifically focus on the small RNA regulatory networks involved in fine-tuning of the strength and timing of defense responses and highlight examples of pathogen exploitation of the host RNA silencing system. These examples illustrate well how pathogens frequently target gene regulation and thereby alter immune responses on a larger scale. That this is effective is demonstrated by the diversity of pathogens from distinct kingdoms capable of manipulating the same gene regulatory networks, such as the RNA silencing machinery.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, 38106 Braunschweig, Germany.
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.
- CEPLAS-Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, 40225 Duesseldorf, Germany.
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27
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Han GZ. Origin and evolution of the plant immune system. THE NEW PHYTOLOGIST 2019; 222:70-83. [PMID: 30575972 DOI: 10.1111/nph.15596] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/02/2018] [Indexed: 05/11/2023]
Abstract
Contents Summary 70 I. Introduction 70 II. Ancient associations between plants and microbes 72 III. Evolutionary dynamics of plant-pathogen interactions 74 IV. Evolutionary signature of plant-pathogen interactions 74 V. Origin and evolution of RLK proteins 75 VI. Origin and evolution of NLR proteins 77 VII. Origin and evolution of SA signaling 78 VIII. Origin and evolution of RNA-based defense 79 IX. Perspectives 79 Acknowledgements 80 References 80 SUMMARY: Microbes have engaged in antagonistic associations with plants for hundreds of millions of years. Plants, in turn, have evolved diverse immune strategies to combat microbial pathogens. The conflicts between plants and pathogens result in everchanging coevolutionary cycles known as 'Red Queen' dynamics. These ancient and ongoing plant-pathogen interactions have shaped the evolution of both plant and pathogen genomes. With the recent explosion of plant genome-scale data, comparative analyses provide novel insights into the coevolutionary dynamics of plants and pathogens. Here, we discuss the ancient associations between plants and microbes as well as the evolutionary principles underlying plant-pathogen interactions. We synthesize and review the current knowledge on the origin and evolution of key components of the plant immune system. We also highlight the importance of studying algae and nonflowering land plants in understanding the evolution of the plant immune system.
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Affiliation(s)
- Guan-Zhu Han
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210023, China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
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28
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Seo E, Kim T, Park JH, Yeom SI, Kim S, Seo MK, Shin C, Choi D. Genome-wide comparative analysis in Solanaceous species reveals evolution of microRNAs targeting defense genes in Capsicum spp. DNA Res 2019; 25:561-575. [PMID: 30060137 PMCID: PMC6289781 DOI: 10.1093/dnares/dsy025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/12/2018] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) play roles in various biological processes in plants including growth, development, and disease resistance. Previous studies revealed that some plant miRNAs produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs), and they regulate a cascade of gene expression. We performed a genome-wide comparative analysis of miRNAs in Solanaceous species (pepper, tomato, and potato), from an evolutionary perspective. Microsynteny of miRNAs was analysed based on the genomic loci and their flanking genes and most of the well-conserved miRNA genes maintained microsynteny in Solanaceae. We identified target genes of the miRNAs via degradome analysis and found that several miRNAs target many genes encoding nucleotide-binding leucine-rich repeat (NLR) or receptor-like proteins (RLPs), which are known to be major players in defense responses. In addition, disease-resistance-associated miRNAs trigger phasiRNA production in pepper, indicating amplification of the regulation of disease-resistance gene families. Among these, miR-n033a-3p, whose target NLRs have been duplicated in pepper, targets more NLRs belonging to specific subgroup in pepper than those in potato. miRNAs targeting resistance genes might have evolved to regulate numerous targets in Solanaceae, following expansion of target resistance genes. This study provides an insight into evolutionary relationship between miRNAs and their target defense genes in plants.
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Affiliation(s)
- Eunyoung Seo
- Department of Plant Science, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Taewook Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Seon-In Yeom
- Division of Applied Life Science (BK21 Plus Program), Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Seungill Kim
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Min-Ki Seo
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Chanseok Shin
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Doil Choi
- Department of Plant Science, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
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29
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Jiang N, Cui J, Shi Y, Yang G, Zhou X, Hou X, Meng J, Luan Y. Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato -Phytophthora infestans interaction. HORTICULTURE RESEARCH 2019; 6:28. [PMID: 30729018 PMCID: PMC6355781 DOI: 10.1038/s41438-018-0096-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 05/05/2023]
Abstract
Our previous studies indicated that tomato miR482b could negatively regulate the resistance of tomato to Phytophthora infestans and the expression of miR482b was decreased after inoculation with P. infestans. However, the mechanism by which the accumulation of miR482b is suppressed remains unclear. In this study, we wrote a program to identify 89 long noncoding RNA (lncRNA)-originated endogenous target mimics (eTMs) for 46 miRNAs from our RNA-Seq data. Three tomato lncRNAs, lncRNA23468, lncRNA01308 and lncRNA13262, contained conserved eTM sites for miR482b. When lncRNA23468 was overexpressed in tomato, miR482b expression was significantly decreased, and the expression of the target genes, NBS-LRRs, was significantly increased, resulting in enhanced resistance to P. infestans. Silencing lncRNA23468 in tomato led to the increased accumulation of miR482b and decreased accumulation of NBS-LRRs, as well as reduced resistance to P. infestans. In addition, the accumulation of both miR482b and NBS-LRRs was not significantly changed in tomato plants that overexpressed lncRNA23468 with a mutated eTM site. Based on the VIGS system, a target gene of miR482b, Solyc02g036270.2, was silenced. The disease symptoms of the VIGS-Solyc02g036270.2 tomato plants were in accordance with those of tomato plants in which lncRNA23468 was silenced after inoculation with P. infestans. More severe disease symptoms were found in the modified plants than in the control plants. Our results demonstrate that lncRNAs functioning as eTMs may modulate the effects of miRNAs in tomato and provide insight into how the lncRNA23468-miR482b-NBS-LRR module regulates tomato resistance to P. infestans.
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Affiliation(s)
- Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Yunsheng Shi
- School of Computer Science and Technology, Dalian University of Technology, 116024 Dalian, China
| | - Guanglei Yang
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Xiaoxu Zhou
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Xinxin Hou
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, 116024 Dalian, China
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
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30
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Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato. Proc Natl Acad Sci U S A 2019; 116:2755-2760. [PMID: 30679269 PMCID: PMC6377479 DOI: 10.1073/pnas.1814380116] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Plants, like animals, have complex disease resistance systems in which receptors interact directly or indirectly with effectors of disease produced by pests and pathogens. To minimize the fitness cost of these systems to the plant, there are miRNAs that target the mRNAs of a family of receptor proteins required for disease resistance. Target site mimics of these miRNAs confer enhanced quantitative resistance in tomato against an oomycete and a bacterium. These findings are consistent with a role of the receptor proteins in quantitative disease resistance and show how blocking these miRNAs could be a useful approach in crop protection. Nucleotide binding site leucine-rich repeat (NLR) proteins of the plant innate immune system are negatively regulated by the miR482/2118 family miRNAs that are in a distinct 22-nt class of miRNAs with a double mode of action. First, they cleave the target RNA, as with the canonical 21-nt miRNAs, and second, they trigger secondary siRNA production using the target RNA as a template. Here, we address the extent to which the miR482/2118 family affects expression of NLR mRNAs and disease resistance. We show that structural differences of miR482/2118 family members in tomato (Solanum lycopersicum) are functionally significant. The predicted target of the miR482 subfamily is a conserved motif in multiple NLR mRNAs, whereas for miR2118b, it is a noncoding RNA target formed by rearrangement of several different NLR genes. From RNA sequencing and degradome data in lines expressing short tandem target mimic (STTM) RNAs of miR482/2118, we confirm the different targets of these miRNAs. The effect on NLR mRNA accumulation is slight, but nevertheless, the tomato STTM lines display enhanced resistance to infection with the oomycete and bacterial pathogens. These data implicate an RNA cascade of miRNAs and secondary siRNAs in the regulation of NLR RNAs and show that the encoded NLR proteins have a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized elsewhere. We also illustrate the use of STTM RNA in a biotechnological approach for enhancing quantitative disease resistance in highly bred cultivars.
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Jiang N, Cui J, Yang G, He X, Meng J, Luan Y. Comparative transcriptome analysis shows the defense response networks regulated by miR482b. PLANT CELL REPORTS 2019; 38:1-13. [PMID: 30191311 DOI: 10.1007/s00299-018-2344-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/02/2018] [Indexed: 06/08/2023]
Abstract
The transcriptomic profile in the leaves of miR482b-overexpressing tomato plants revealed that miR482b may suppress alpha-linolenic acid metabolism, cysteine and methionine metabolism, plant-pathogen interaction, and the MAPK pathway to reduce resistance to Phytophthora infestans. Our previous study showed that tomato miR482b acted as a negative regulator during tomato resistance to Phytophthora infestans by silencing NBS-LRR genes. To investigate pathways related to miR482b, the transcriptomic profile of tomato plants that overexpressed miR482b was constructed. A total of 47,124,670 raw sequence reads from the leaves of miR482b-overexpressing tomato plants were generated by Illumina sequencing. A total of 746 genes in miR482b-overexpressing tomato plants were found to show significantly differential expression relative to those in wild-type tomato plants, including 132 up-regulated genes and 614 down-regulated genes. GO and KEGG enrichment analyses showed that plant-pathogen interaction, the MAPK pathway, and the pathways related to JA and ET biosynthesis were affected by miR482b in tomato. qRT-PCR results showed that all the enriched genes in these pathways were down-regulated in tomato plants that overexpressed miR482b and up-regulated in tomato plants that overexpressed an NBS-LRR gene (Soly02g036270.2, the target gene of miR482b). After P. infestans infection, the expression of the enriched genes showed a time-dependent response, and the genes played different roles between resistant tomato (Solanum pimpinellifolium L3708) and tomato susceptible to P. infestans (S. lycopersicum Zaofen No. 2). Our results have, therefore, demonstrated that miR482b is an important component of defense response network. This will also help to identify candidate genes involved in plant-pathogen interaction.
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Affiliation(s)
- Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Guanglei Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Xiaoli He
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China.
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Rose LE, Overdijk EJR, van Damme M. Small RNA molecules and their role in plant disease. EUROPEAN JOURNAL OF PLANT PATHOLOGY 2019; 153:1-14. [PMID: 30880875 PMCID: PMC6394340 DOI: 10.1007/s10658-018-01614-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/01/2018] [Indexed: 05/04/2023]
Abstract
All plant species are subject to disease. Plant diseases are caused by parasites, e.g. viruses, bacteria, oomycetes, parasitic plants, fungi, or nematodes. In all organisms, gene expression is tightly regulated and underpins essential functions and physiology. The coordination and regulation of both host and pathogen gene expression is essential for pathogens to infect and cause disease. One mode of gene regulation is RNA silencing. This biological process is widespread in the natural world, present in plants, animals and several pathogens. In RNA silencing, small (20-40 nucleotides) non-coding RNAs (small-RNAs, sRNAs) accumulate and regulate gene expression transcriptionally or post-transcriptionally in a sequence-specific manner. Regulation of sRNA molecules provides a fast mode to alter gene activity of multiple gene transcripts. RNA silencing is an ancient mechanism that protects the most sensitive part of an organism: its genetic code. sRNA molecules emerged as regulators of plant development, growth and plant immunity. sRNA based RNA silencing functions both within and between organisms. Here we present the described sRNAs from plants and pathogens and discuss how they regulate host immunity and pathogen virulence. We speculate on how sRNA molecules can be exploited to develop disease resistant plants. Finally, the activity of sRNA molecules can be prevented by proteins that suppress RNA silencing. This counter silencing response completes the dialog between plants and pathogens controlling plant disease or resistance outcome on the RNA (controlling gene expression) and protein level.
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Affiliation(s)
- Laura E. Rose
- Institut für Populationsgenetik, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Elysa J. R. Overdijk
- Laboratory of Phytopathology, Wageningen University, P.O. Box 16, Wageningen, 6700 AA The Netherlands
- Laboratory of Cell Biology, Wageningen University, P.O. Box 633, Wageningen, 6700 AP The Netherlands
| | - Mireille van Damme
- Laboratory of Phytopathology, Wageningen University, P.O. Box 16, Wageningen, 6700 AA The Netherlands
- Keygene N.V, Agro Business Park 90, 6708 PW Wageningen, The Netherlands
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Kuźnicki D, Meller B, Arasimowicz-Jelonek M, Braszewska-Zalewska A, Drozda A, Floryszak-Wieczorek J. BABA-Induced DNA Methylome Adjustment to Intergenerational Defense Priming in Potato to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2019; 10:650. [PMID: 31214209 PMCID: PMC6554679 DOI: 10.3389/fpls.2019.00650] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 04/30/2019] [Indexed: 05/21/2023]
Abstract
We provide evidence that alterations in DNA methylation patterns contribute to the regulation of stress-responsive gene expression for an intergenerational resistance of β-aminobutyric acid (BABA)-primed potato to Phytophthora infestans. Plants exposed to BABA rapidly modified their methylation capacity toward genome-wide DNA hypermethylation. De novo induced DNA methylation (5-mC) correlated with the up-regulation of Chromomethylase 3 (CMT3), Domains rearranged methyltransferase 2 (DRM2), and Repressor of silencing 1 (ROS1) genes in potato. BABA transiently activated DNA hypermethylation in the promoter region of the R3a resistance gene triggering its downregulation in the absence of the oomycete pathogen. However, in the successive stages of priming, an excessive DNA methylation state changed into demethylation with the active involvement of potato DNA glycosylases. Interestingly, the 5-mC-mediated changes were transmitted into the next generation in the form of intergenerational stress memory. Descendants of the primed potato, which derived from tubers or seeds carrying the less methylated R3a promoter, showed a higher transcription of R3a that associated with an augmented intergenerational resistance to virulent P. infestans when compared to the inoculated progeny of unprimed plants. Furthermore, our study revealed that enhanced transcription of some SA-dependent genes (NPR1, StWRKY1, and PR1) was not directly linked with DNA methylation changes in the promoter region of these genes, but was a consequence of methylation-dependent alterations in the transcriptional network.
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Affiliation(s)
- Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Agnieszka Braszewska-Zalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, The University of Silesia in Katowice, Katowice, Poland
| | - Andżelika Drozda
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Jolanta Floryszak-Wieczorek
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
- *Correspondence: Jolanta Floryszak-Wieczorek,
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de Vries S, de Vries J, von Dahlen JK, Gould SB, Archibald JM, Rose LE, Slamovits CH. On plant defense signaling networks and early land plant evolution. Commun Integr Biol 2018; 11:1-14. [PMID: 30214675 PMCID: PMC6132428 DOI: 10.1080/19420889.2018.1486168] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 05/28/2018] [Indexed: 12/29/2022] Open
Abstract
All land plants must cope with phytopathogens. Algae face pathogens, too, and it is reasonable to assume that some of the strategies for dealing with pathogens evolved prior to the origin of embryophytes – plant terrestrialization simply changed the nature of the plant-pathogen interactions. Here we highlight that many potential components of the angiosperm defense toolkit are i) found in streptophyte algae and non-flowering embryophytes and ii) might be used in non-flowering plant defense as inferred from published experimental data. Nonetheless, the common signaling networks governing these defense responses appear to have become more intricate during embryophyte evolution. This includes the evolution of the antagonistic signaling pathways of jasmonic and salicylic acid, multiple independent expansions of resistance genes, and the evolution of resistance gene-regulating microRNAs. Future comparative studies will illuminate which modules of the streptophyte defense signaling network constitute the core and which constitute lineage- and/or environment-specific (peripheral) signaling circuits.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Janina K von Dahlen
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany.,iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Sven B Gould
- Institute of Molecular Evolution, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany.,iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany.,Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
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Upson JL, Zess EK, Białas A, Wu CH, Kamoun S. The coming of age of EvoMPMI: evolutionary molecular plant-microbe interactions across multiple timescales. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:108-116. [PMID: 29604609 DOI: 10.1016/j.pbi.2018.03.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 05/11/2023]
Abstract
Plant-microbe interactions are great model systems to study co-evolutionary dynamics across multiple timescales. However, mechanistic research on plant-microbe interactions has often been conducted with little consideration of evolutionary concepts and methods. Conversely, evolutionary research has rarely integrated the range of mechanisms and models from the molecular plant-microbe interactions field. In recent years, the incipient field of evolutionary molecular plant-microbe interactions (EvoMPMI) has emerged to bridge this gap. Here, we report on some of the recent advances in EvoMPMI. In particular, we highlight new systems to study microbe interactions with early diverging land plants, and new findings from studies of adaptive evolution in pathogens and plants. By linking mechanistic and evolutionary research, EvoMPMI promises to expand our understanding of plant-microbe interactions.
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Affiliation(s)
- Jessica L Upson
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Erin K Zess
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | | - Chih-Hang Wu
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.
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36
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Baldrich P, Beric A, Meyers BC. Despacito: the slow evolutionary changes in plant microRNAs. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:16-22. [PMID: 29448158 DOI: 10.1016/j.pbi.2018.01.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/19/2018] [Accepted: 01/23/2018] [Indexed: 05/28/2023]
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression. A handful of miRNAs are broadly conserved in land plants, while the majority are lineage specific; this review describes the processes by which new miRNAs are hypothesized to have emerged. Two major models describe miRNA origins, firstly, de novo emergence via inverted duplication of target gene fragments, and secondly, the expansion and neofunctionalization of existing miRNA families. The occasional acquisition of target sites by previously un-targeted genes adds further dynamism to the process by which miRNAs may shift roles during evolution. Additional factors guiding miRNA evolution include functional constraints on their length and the importance of precursor conservation that is observed in regions above or below the mature miRNA duplex; these regions represent recognition sites for components of biogenesis machinery and direct precursor processing. Insights into the mechanisms of miRNA emergence and divergence are important for understanding plant genome evolution and the impact of miRNA regulatory networks.
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Affiliation(s)
- Patricia Baldrich
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA
| | - Aleksandra Beric
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA; University of Missouri - Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, MO 65211, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, USA; University of Missouri - Columbia, Division of Plant Sciences, 52 Agriculture Lab, Columbia, MO 65211, USA.
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de Vries S, von Dahlen JK, Schnake A, Ginschel S, Schulz B, Rose LE. Broad-spectrum inhibition of Phytophthora infestans by fungal endophytes. FEMS Microbiol Ecol 2018; 94:4925062. [PMID: 29528408 PMCID: PMC5939626 DOI: 10.1093/femsec/fiy037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/05/2018] [Indexed: 11/12/2022] Open
Abstract
Phytophthora infestans is a devastating pathogen of tomato and potato. It readily overcomes resistance genes and applied agrochemicals and hence even today causes large yield losses. Fungal endophytes provide a largely unexplored avenue of control of Phy. infestans. Not only do endophytes produce a wide array of bioactive metabolites, they may also directly compete with and defeat pathogens in planta. Here, we tested 12 fungal endophytes isolated from different plant species in vitro for their production of metabolites with anti- Phytophthora activity. Four well-performing isolates were evaluated for their ability to suppress nine isolates of Phy. infestans on agar medium and in planta. Two endophytes reliably inhibited all Phy. infestans isolates on agar medium, of which Phoma eupatorii isolate 8082 was the most promising. It nearly abolished infection by Phy. infestans in planta. Our data indicate a role for the production of anti-Phytophthora compounds by the fungus and/or an enhanced plant defense response, as evident by an enhanced anthocyanin production. Here, we present a potential biocontrol agent, which can inhibit a broad-spectrum of Phy. infestans isolates. Such broadly acting inhibition is ideal, because it allows for effective control of genetically diverse isolates and may slow the adaptation of Phy. infestans.
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Affiliation(s)
- Sophie de Vries
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Janina K von Dahlen
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Anika Schnake
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Sarah Ginschel
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Barbara Schulz
- Institute of Microbiology, Technische Universitaet Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
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de Vries S, Kukuk A, von Dahlen JK, Schnake A, Kloesges T, Rose LE. Expression profiling across wild and cultivated tomatoes supports the relevance of early miR482/2118 suppression for Phytophthora resistance. Proc Biol Sci 2018; 285:20172560. [PMID: 29491170 PMCID: PMC5832704 DOI: 10.1098/rspb.2017.2560] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/01/2018] [Indexed: 12/15/2022] Open
Abstract
Plants possess a battery of specific pathogen resistance (R-)genes. Precise R-gene regulation is important in the presence and absence of a pathogen. Recently, a microRNA family, miR482/2118, was shown to regulate the expression of a major class of R-genes, nucleotide-binding site leucine-rich repeats (NBS-LRRs). Furthermore, RNA silencing suppressor proteins, secreted by pathogens, prevent the accumulation of miR482/2118, leading to an upregulation of R-genes. Despite this transcriptional release of R-genes, RNA silencing suppressors positively contribute to the virulence of some pathogens. To investigate this paradox, we analysed how the regulation of NBS-LRRs by miR482/2118 has been shaped by the coevolution between Phytophthora infestans and cultivated and wild tomatoes. We used degradome analyses and qRT-PCR to evaluate and quantify the co-expression of miR482/2118 and their NBS-LRR targets. Our data show that miR482/2118-mediated targeting contributes to the regulation of NBS-LRRs in Solanum lycopersicum. Based on miR482/2118 expression profiling in two additional tomato species-with different coevolutionary histories with P. infestans-we hypothesize that pathogen-mediated RNA silencing suppression is most effective in the interaction between S. lycopersicum and P. infestans Furthermore, an upregulation of miR482/2118 early in the infection may increase susceptibility to P. infestans.
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Affiliation(s)
- Sophie de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada NS B3H 4R2
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Andreas Kukuk
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Janina K von Dahlen
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Anika Schnake
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Thorsten Kloesges
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
| | - Laura E Rose
- Institute of Population Genetics, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- iGRAD-Plant Graduate School, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
- Ceplas, Cluster of Excellence in Plant Sciences, Heinrich-Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
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microRNA-mediated R gene regulation: molecular scabbards for double-edged swords. SCIENCE CHINA-LIFE SCIENCES 2018; 61:138-147. [DOI: 10.1007/s11427-017-9237-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 12/04/2017] [Indexed: 11/27/2022]
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40
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Luan Y, Cui J, Li J, Jiang N, Liu P, Meng J. Effective enhancement of resistance to Phytophthora infestans by overexpression of miR172a and b in Solanum lycopersicum. PLANTA 2018; 247:127-138. [PMID: 28884358 DOI: 10.1007/s00425-017-2773-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 09/03/2017] [Indexed: 05/22/2023]
Abstract
Overexpression of miR172a and b in tomato ( Solanum lycopersicum ) Zaofen No. 2 increased resistance to Phytophthora infestans infection by suppressing of an AP2/ERF transcription factor. The miR172 family has been shown to participate in the growth phase transition, flowering time control, abiotic and biotic stresses by regulating the expression of a small group of AP2/ERF transcription factors. In this study, the precursors of miR172a and b were cloned from tomato, Solanum pimpinellifolium L3708. We used the degradome sequencing to determine the cleavage site of miR172 to a member of the AP2/ERF transcription factor family (Solyc11g072600.1.1). qRT-PCR results showed that the expression of AP2/ERF was negatively correlated with the expression of miR172 in S. pimpinellifolium L3708 infected with Phytophthora infestans. Overexpression of miR172a and b in S. lycopersicum Zaofen No. 2 conferred greater resistance to P. infestans infection, as evidenced by decreased disease index, lesion sizes, and P. infestans abundance. The SOD and POD play important roles in scavenging late massive ROS in plant-pathogen interaction. Malonaldehyde (MDA) is widely recognized as an indicator of lipid peroxidation. Membrane damage in plants can be estimated by measuring leakage of electrolytes, which is evaluated by determining relative electrolyte leakage (REL). Less H2O2 and O2-, higher activities of POD and SOD, less MDA content and REL, and higher chlorophyll content and photosynthetic rate were also shown in transgenic plants after inoculation with P. infestans. Our results constitute the first step towards further investigations into the biological function and molecular mechanism of miR172-mediated silencing of AP2/ERF transcription factors in S. lycopersicum-P. infestans interaction and provide a candidate gene for breeding to enhance biotic stress-resistance in S. lycopersicum.
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Affiliation(s)
- Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jie Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ping Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China.
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Ji HM, Zhao M, Gao Y, Cao XX, Mao HY, Zhou Y, Fan WY, Borkovich KA, Ouyang SQ, Liu P. FRG3, a Target of slmiR482e-3p, Provides Resistance against the Fungal Pathogen Fusarium oxysporum in Tomato. FRONTIERS IN PLANT SCIENCE 2018; 9:26. [PMID: 29434609 PMCID: PMC5797444 DOI: 10.3389/fpls.2018.00026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 01/08/2018] [Indexed: 05/20/2023]
Abstract
The vast majority of plant disease resistance (R) genes encode nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins, which specifically determine the plant immune response and have been demonstrated to be targets of several microRNA (miRNA) families. The fungus Fusarium oxysporum f. sp. lycopersici (FOL) causes vascular wilt disease in tomato worldwide. Here, we explored a possible role for FGR3 in tomato defense against FOL. FRG3 is a predicted NBS-LRR like gene that is targeted by slmiR482e-3p, a member of slmiR482 miRNA family. Northern blot data demonstrated that all seven members of the slmiR482 family were regulated in diverse ways after infection by FOL. The ability of FRG3 to be regulated by slmiR482e-3p was confirmed at the transcript level by co-expression studies in Nicotiana benthamiana. A virus-induced gene silencing (VIGS) approach revealed that FRG3 confers resistance to the Motelle tomato cultivar. Taken together, our study has identified a novel R gene, FRG3, which is targeted by slmiR482e-3p at the transcript level, and is necessary for resistance to tomato wilt disease in planta.
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Affiliation(s)
- Hui-Min Ji
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Min Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ying Gao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xin-Xin Cao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Hui-Ying Mao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Yi Zhou
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Wen-Yu Fan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Katherine A. Borkovich
- Department of Plant Pathology and Microbiology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Shou-Qiang Ouyang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Shou-Qiang Ouyang, Peng Liu,
| | - Peng Liu
- Testing Center, Yangzhou University, Yangzhou, China
- *Correspondence: Shou-Qiang Ouyang, Peng Liu,
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Biselli C, Bagnaresi P, Faccioli P, Hu X, Balcerzak M, Mattera MG, Yan Z, Ouellet T, Cattivelli L, Valè G. Comparative Transcriptome Profiles of Near-Isogenic Hexaploid Wheat Lines Differing for Effective Alleles at the 2DL FHB Resistance QTL. FRONTIERS IN PLANT SCIENCE 2018; 9:37. [PMID: 29434615 PMCID: PMC5797473 DOI: 10.3389/fpls.2018.00037] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 01/09/2018] [Indexed: 05/07/2023]
Abstract
Fusarium head blight (FHB), caused by the fungus Fusarium graminearum, represents one of the major wheat diseases worldwide, determining severe yield losses and reduction of grain quality due to the accumulation of mycotoxins. The molecular response associated with the wheat 2DL FHB resistance QTL was mined through a comprehensive transcriptomic analysis of the early response to F. graminearum infection, at 3 days post-inoculation, in spikelets and rachis. The analyses were conducted on two near isogenic lines (NILs) differing for the presence of the 2DL QTL (2-2618, resistant 2DL+ and 2-2890, susceptible null). The general response to fungal infection in terms of mRNAs accumulation trend was similar in both NILs, even though involving an higher number of DEGs in the susceptible NIL, and included down-regulation of the primary and energy metabolism, up-regulation of enzymes implicated in lignin and phenylpropanoid biosynthesis, activation of hormons biosynthesis and signal transduction pathways and genes involved in redox homeostasis and transcriptional regulation. The search for candidate genes with expression profiles associated with the 2DL QTL for FHB resistance led to the discovery of processes differentially modulated in the R and S NILs related to cell wall metabolism, sugar and JA signaling, signal reception and transduction, regulation of the redox status and transcription factors. Wheat FHB response-related miRNAs differentially regulated were also identified as putatively implicated in the superoxide dismutase activities and affecting genes regulating responses to biotic/abiotic stresses and auxin signaling. Altered gene expression was also observed for fungal non-codingRNAs. The putative targets of two of these were represented by the wheat gene WIR1A, involved in resistance response, and a gene encoding a jacalin-related lectin protein, which participate in biotic and abiotic stress response, supporting the presence of a cross-talk between the plant and the fungus.
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Affiliation(s)
- Chiara Biselli
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
- *Correspondence: Chiara Biselli
| | - Paolo Bagnaresi
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Primetta Faccioli
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Xinkun Hu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Margaret Balcerzak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Maria G. Mattera
- Plant Breeding Department, Institute for Sustainable Agriculture, Cordoba, Spain
- Department of Genetics–ETSIAM, University of Cordoba, Cordoba, Spain
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Therese Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Luigi Cattivelli
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Giampiero Valè
- CREA–Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
- CREA–Research Centre for Cereal and Industrial Crops, Vercelli, Italy
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Malik N, George JK. Resistance Genes in Piper colubrinum: In Silico Survey From Leaf Transcriptome and Expression Studies Upon Challenge Inoculation with Phytophthora capsici. Appl Biochem Biotechnol 2017; 184:987-1008. [PMID: 28933036 DOI: 10.1007/s12010-017-2600-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 09/08/2017] [Indexed: 12/24/2022]
Abstract
The oomycetes, Phytophthora capsici, cause foot rot disease in black pepper. Piper colubrinum Link, a distant relative of cultivated black pepper, is highly resistant to this destructive pathogen. Identification of resistance (R) genes in P. colubrinum and the study of its expression profile during interaction with the pathogen can help in understanding the resistance mechanism involved. In the present study, 1289 R gene-related transcripts were mined from P. colubrinum transcriptome, clustered, and classified according to the conserved motifs and domains. Transcripts belonging to four major R gene classes were identified in P. colubrinum, but TIR-NBS-LRR-type R genes were absent. The relative expression of 12 selected R genes was studied using two virulent isolates of P. capsici, and these were found to be upregulated in the initial hours of plant pathogen interaction. The R genes studied were expressed even in aseptically maintained tissue-cultured plants and uninoculated greenhouse-grown plants at basal level suggesting that the plants are geared up with the R gene all the time and are under continuous surveillance for the pathogen and basal level of R gene expression do not require a pathogen trigger. ACT, ATUB, and EIF3E were identified as the most stable reference genes that can be used for real-time PCR study. The present study identified promising R genes in P. colubrinum which can be used in developing Phytophthora-resistant black pepper.
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Affiliation(s)
- Neema Malik
- ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, 673012, India
| | - Johnson K George
- ICAR-Indian Institute of Spices Research, Marikunnu P O, Kozhikode, 673012, India.
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Tang J, Chu C. MicroRNAs in crop improvement: fine-tuners for complex traits. NATURE PLANTS 2017; 3:17077. [PMID: 28665396 DOI: 10.1038/nplants.2017.77] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/28/2017] [Indexed: 05/20/2023]
Abstract
One of the most common challenges for both conventional and modern crop improvement is that the appearance of one desirable trait in a new crop variety is always balanced by the impairment of one or more other beneficial characteristics. The best way to overcome this problem is the flexible utilization of regulatory genes, especially genes that provide more efficient and precise regulation in a targeted manner. MicroRNAs (miRNAs), a type of short non-coding RNA, are promising candidates in this area due to their role as master modulators of gene expression at the post-transcriptional level, targeting messenger RNAs for cleavage or directing translational inhibition in eukaryotes. We herein highlight the current understanding of the biological role of miRNAs in orchestrating distinct agriculturally important traits by summarizing recent functional analyses of 65 miRNAs in 9 major crops worldwide. The integration of current miRNA knowledge with conventional and modern crop improvement strategies is also discussed.
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Affiliation(s)
- Jiuyou Tang
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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de Vries S, von Dahlen JK, Uhlmann C, Schnake A, Kloesges T, Rose LE. Signatures of selection and host-adapted gene expression of the Phytophthora infestans RNA silencing suppressor PSR2. MOLECULAR PLANT PATHOLOGY 2017; 18:110-124. [PMID: 27503598 PMCID: PMC6638260 DOI: 10.1111/mpp.12465] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/07/2016] [Accepted: 08/04/2016] [Indexed: 05/04/2023]
Abstract
Phytophthora infestans is a devastating pathogen in agricultural systems. Recently, an RNA silencing suppressor (PSR2, 'Phytophthora suppressor of RNA silencing 2') has been described in P. infestans. PSR2 has been shown to increase the virulence of Phytophthora pathogens on their hosts. This gene is one of the few effectors present in many economically important Phytophthora species. In this study, we investigated: (i) the evolutionary history of PSR2 within and between species of Phytophthora; and (ii) the interaction between sequence variation, gene expression and virulence. In P. infestans, the highest PiPSR2 expression was correlated with decreased symptom expression. The highest gene expression was observed in the biotrophic phase of the pathogen, suggesting that PSR2 is important during early infection. Protein sequence conservation was negatively correlated with host range, suggesting host range as a driver of PSR2 evolution. Within species, we detected elevated amino acid variation, as observed for other effectors; however, the frequency spectrum of the mutations was inconsistent with strong balancing selection. This evolutionary pattern may be related to the conservation of the host target(s) of PSR2 and the absence of known corresponding R genes. In summary, our study indicates that PSR2 is a conserved effector that acts as a master switch to modify plant gene regulation early during infection for the pathogen's benefit. The conservation of PSR2 and its important role in virulence make it a promising target for pathogen management.
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Affiliation(s)
- Sophie de Vries
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- iGRAD‐Plant Graduate SchoolHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Janina K. von Dahlen
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Constanze Uhlmann
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Anika Schnake
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Thorsten Kloesges
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
| | - Laura E. Rose
- Institute of Population GeneticsHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- iGRAD‐Plant Graduate SchoolHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
- Ceplas, Cluster of Excellence in Plant SciencesHeinrich‐Heine University DuesseldorfDuesseldorf40225Germany
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46
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Wen M, Xie M, He L, Wang Y, Shi S, Tang T. Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa). Genome Biol Evol 2016; 8:3529-3544. [PMID: 27797952 PMCID: PMC5203789 DOI: 10.1093/gbe/evw252] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Differences in expression levels are an important source of phenotypic variation within and between populations. MicroRNAs (miRNAs) are key players in post-transcriptional gene regulation that are important for plant development and stress responses. We surveyed expression variation of miRNAs and mRNAs of six accessions from two rice subspecies Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica using deep sequencing. While more than half (53.7%) of the mature miRNAs exhibit differential expression between grains and seedlings of rice, only 11.0% show expression differences between subspecies, with an additional 2.2% differentiated for the development-by-subspecies interaction. Expression variation is greater for lowly conserved miRNAs than highly conserved miRNAs, whereas the latter show stronger negative correlation with their targets in expression changes between subspecies. Using a permutation test, we identified 51 miRNA–mRNA pairs that correlate negatively or positively in expression level among cultivated rice. Genes involved in various metabolic processes and stress responses are enriched in the differentially expressed genes between rice indica and japonica subspecies. Our results indicate that stabilizing selection is the major force governing miRNA expression in cultivated rice, albeit positive selection may be responsible for much of the between-subspecies expression divergence.
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Affiliation(s)
- Ming Wen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Munan Xie
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | | | - Yushuai Wang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources and Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Zhang Y, Xia R, Kuang H, Meyers BC. The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them. Mol Biol Evol 2016; 33:2692-705. [PMID: 27512116 PMCID: PMC5026261 DOI: 10.1093/molbev/msw154] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
High expression of plant nucleotide binding site leucine-rich repeat (NBS-LRR) defense genes is often lethal to plant cells, a phenotype perhaps associated with fitness costs. Plants implement several mechanisms to control the transcript level of NBS-LRR defense genes. As negative transcriptional regulators, diverse miRNAs target NBS-LRRs in eudicots and gymnosperms. To understand the evolutionary benefits of this miRNA-NBS-LRR regulatory system, we investigated the NBS-LRRs of 70 land plants, coupling this analysis with extensive small RNA data. A tight association between the diversity of NBS-LRRs and miRNAs was found. The miRNAs typically target highly duplicated NBS-LRRs In comparison, families of heterogeneous NBS-LRRs were rarely targeted by miRNAs in Poaceae and Brassicaceae genomes. We observed that duplicated NBS-LRRs from different gene families periodically gave birth to new miRNAs. Most of these newly emerged miRNAs target the same conserved, encoded protein motif of NBS-LRRs, consistent with a model of convergent evolution for these miRNAs. By assessing the interactions between miRNAs and NBS-LRRs, we found nucleotide diversity in the wobble position of the codons in the target site drives the diversification of miRNAs. Taken together, we propose a co-evolutionary model of plant NBS-LRRs and miRNAs hypothesizing how plants balance the benefits and costs of NBS-LRR defense genes.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People's Republic of China Donald Danforth Plant Science Center, St. Louis
| | - Rui Xia
- Donald Danforth Plant Science Center, St. Louis
| | - Hanhui Kuang
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis Division of Plant Sciences, University of Missouri - Columbia
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