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Kwon J, Mori K, Maoka T, Sano T, Nakahara KS. Induction of necrosis symptoms by potato virus X in AGO2-silenced tomato plants associates with reduced transcript accumulation of copper chaperon for superoxide dismutase gene. Virus Res 2024; 348:199436. [PMID: 38996815 PMCID: PMC11315226 DOI: 10.1016/j.virusres.2024.199436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
RNA silencing is a prominent antiviral defense mechanism in plants. When infected with a virus, RNA silencing-deficient plants tend to show exacerbated symptoms along with increased virus accumulation. However, how symptoms are exacerbated is little understood. Here, we investigated the role of the copper chaperon for superoxide dismutase (CCS) 1, in systemic necrosis observed in Argonaute (AGO)2-silenced tomato plants infected with potato virus X (PVX). While infection with the UK3 strain of PVX induced mosaic symptoms in tomato plants, systemic necrosis occurred when AGO2 was silenced. The CCS1 mRNA level was reduced and micro RNA398 (miR398), which potentially target CCS1, was increased in AGO2-knockdown tomato plants infected with PVX-UK3. Ectopic expression of CCS1 using recombinant PVX attenuated necrosis, suggesting that CCS1 alleviates systemic necrosis by activating superoxide dismutases to scavenge reactive oxygen species. Previous reports have indicated a decrease in the levels of CCS1 and superoxide dismutases along with an increased level of miR398 in plants infected with other viruses and viroids, and thus might represent shared regulatory mechanisms that exacerbate symptoms in these plants.
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Affiliation(s)
- Joon Kwon
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Kento Mori
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Tetsuo Maoka
- Institute for Plant Protection, National Agriculture and Food Research Organization (NIPP, NARO), Tsukuba, Ibaraki, 305-8666, Japan
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | - Kenji S Nakahara
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan; Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan.
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2
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Betz R, Heidt S, Figueira-Galán D, Hartmann M, Langner T, Requena N. Alternative splicing regulation in plants by SP7-like effectors from symbiotic arbuscular mycorrhizal fungi. Nat Commun 2024; 15:7107. [PMID: 39160162 PMCID: PMC11333574 DOI: 10.1038/s41467-024-51512-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 08/08/2024] [Indexed: 08/21/2024] Open
Abstract
Most plants in natural ecosystems associate with arbuscular mycorrhizal (AM) fungi to survive soil nutrient limitations. To engage in symbiosis, AM fungi secrete effector molecules that, similar to pathogenic effectors, reprogram plant cells. Here we show that the Glomeromycotina-specific SP7 effector family impacts on the alternative splicing program of their hosts. SP7-like effectors localize at nuclear condensates and interact with the plant mRNA processing machinery, most prominently with the splicing factor SR45 and the core splicing proteins U1-70K and U2AF35. Ectopic expression of these effectors in the crop plant potato and in Arabidopsis induced developmental changes that paralleled to the alternative splicing modulation of a specific subset of genes. We propose that SP7-like proteins act as negative regulators of SR45 to modulate the fate of specific mRNAs in arbuscule-containing cells. Unraveling the communication mechanisms between symbiotic fungi and their host plants will help to identify targets to improve plant nutrition.
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Affiliation(s)
- Ruben Betz
- Joseph Kölreuter Institute for Plant Sciences. Molecular Phytopathology Department, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, Germany
| | - Sven Heidt
- Joseph Kölreuter Institute for Plant Sciences. Molecular Phytopathology Department, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, Germany
| | - David Figueira-Galán
- Joseph Kölreuter Institute for Plant Sciences. Molecular Phytopathology Department, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, Germany
| | - Meike Hartmann
- Joseph Kölreuter Institute for Plant Sciences. Molecular Phytopathology Department, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, Germany
| | - Thorsten Langner
- Max Planck Institute for Biology Tübingen - Max-Planck-Ring 5, Tübingen, Germany
| | - Natalia Requena
- Joseph Kölreuter Institute for Plant Sciences. Molecular Phytopathology Department, Karlsruhe Institute of Technology (KIT) - South Campus, Fritz-Haber-Weg 4, Karlsruhe, Germany.
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Wang Y, Shi Y, Li H, Chang J. Understanding Citrus Viroid Interactions: Experience and Prospects. Viruses 2024; 16:577. [PMID: 38675919 PMCID: PMC11053686 DOI: 10.3390/v16040577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Citrus is the natural host of at least eight viroid species, providing a natural platform for studying interactions among viroids. The latter manifests as antagonistic or synergistic phenomena. The antagonistic effect among citrus viroids intuitively leads to reduced symptoms caused by citrus viroids, while the synergistic effect leads to an increase in symptom severity. The interaction phenomenon is complex and interesting, and a deep understanding of the underlying mechanisms induced during this viroid interaction is of great significance for the prevention and control of viroid diseases. This paper summarizes the research progress of citrus viroids in recent years, focusing on the interaction phenomenon and analyzing their interaction mechanisms. It points out the core role of the host RNA silencing mechanism and viroid-derived siRNA (vd-siRNA), and provides suggestions for future research directions.
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Affiliation(s)
- Yafei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (Y.S.); (H.L.); (J.C.)
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Qiu Y, Wang Y, Wu Y, Yang H, Yang M, Zhou C, Cao M. Effects of RNA silencing during antagonism between citrus exocortis viroid and citrus bark cracking viroid in Etrog citron (Citrus medica). MOLECULAR PLANT PATHOLOGY 2024; 25:e13408. [PMID: 38041680 PMCID: PMC10788473 DOI: 10.1111/mpp.13408] [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: 04/28/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Citrus exocortis viroid (CEVd) and citrus bark cracking viroid (CBCVd) are two important viroids that infect citrus plants and frequently occur as mixed infections in orchards. However, the mechanism of antagonism between the two viroids in mixed infections remains unclear. The CEVd/CBCVd-citron system and small RNA sequencing (sRNA-seq) were used to study the antagonism. When CBCVd was inoculated before CEVd, the CEVd titre was significantly reduced and the symptoms were attenuated. Viroid-derived sRNAs (vd-sRNAs) from CEVd and CBCVd were predominantly 21-nucleotide (nt) and 22-nt in length and had similar 5' base biases. Homologous sequences of the two viroids in the terminal right (TR) region are rich in vd-sRNAs, and the high frequency vd-sRNAs selected from the CBCVd TR region can be used to degrade the transcripts of CEVd in vivo directly. These results suggest that RNA silencing may play an important role in the antagonism of the two viroids, thus deepening our understanding of the molecular interaction of long noncoding RNAs in woody plants.
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Affiliation(s)
- Yuanjian Qiu
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Yafei Wang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouChina
| | - Yujiao Wu
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Han Yang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Mengxue Yang
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Changyong Zhou
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
| | - Mengji Cao
- National Citrus Engineering Research Center, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science CityCitrus Research Institute, Southwest UniversityChongqingChina
- Academy of Agricultural SciencesSouthwest UniversityChongqingChina
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Xie JQ, Zhou X, Jia ZC, Su CF, Zhang Y, Fernie AR, Zhang J, Du ZY, Chen MX. Alternative Splicing, An Overlooked Defense Frontier of Plants with Respect to Bacterial Infection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37916838 DOI: 10.1021/acs.jafc.3c04163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Disease represents a major problem in sustainable agricultural development. Plants interact closely with various microorganisms during their development and in response to the prevailing environment. In particular, pathogenic microorganisms can cause plant diseases, affecting the fertility, yield, and longevity of plants. During the long coevolution of plants and their pathogens, plants have evolved both molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) signaling networks in order to regulate host cells in response to pathogen infestation. Additionally, in the postgenomic era, alternative splicing (AS) has become uncovered as one of the major drivers of proteome diversity, and abnormal RNA splicing is closely associated with bacterial infections. Currently, the complexity of host-bacteria interactions is a much studied area of research that has shown steady progress over the past decade. Although the development of high-throughput sequencing technologies and their application in transcriptomes have revolutionized our understanding of AS, many mechanisms related to host-bacteria interactions remain still unclear. To this end, this review summarizes the changes observed in AS during host-bacteria interactions and outlines potential therapeutics for bacterial diseases based on existing studies. In doing so, we hope to provide guidelines for plant disease management in agriculture.
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Affiliation(s)
- Ji-Qin Xie
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou 550025, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Zi-Chang Jia
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
| | - Chang-Feng Su
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou 550025, China
| | - Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Golm, Germany
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Zhi-Yan Du
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Mo-Xian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, China
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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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Su CF, Das D, Muhammad Aslam M, Xie JQ, Li XY, Chen MX. Eukaryotic splicing machinery in the plant-virus battleground. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1793. [PMID: 37198737 DOI: 10.1002/wrna.1793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/24/2023] [Accepted: 04/19/2023] [Indexed: 05/19/2023]
Abstract
Plant virual infections are mainly caused by plant-virus parasitism which affects ecological communities. Some viruses are highly pathogen specific that can infect only specific plants, while some can cause widespread harm, such as tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV). After a virus infects the host, undergoes a series of harmful effects, including the destruction of host cell membrane receptors, changes in cell membrane components, cell fusion, and the production of neoantigens on the cell surface. Therefore, competition between the host and the virus arises. The virus starts gaining control of critical cellular functions of the host cells and ultimately affects the fate of the targeted host plants. Among these critical cellular processes, alternative splicing (AS) is an essential posttranscriptional regulation process in RNA maturation, which amplify host protein diversity and manipulates transcript abundance in response to plant pathogens. AS is widespread in nearly all human genes and critical in regulating animal-virus interactions. In particular, an animal virus can hijack the host splicing machinery to re-organize its compartments for propagation. Changes in AS are known to cause human disease, and various AS events have been reported to regulate tissue specificity, development, tumour proliferation, and multi-functionality. However, the mechanisms underlying plant-virus interactions are poorly understood. Here, we summarize the current understanding of how viruses interact with their plant hosts compared with humans, analyze currently used and putative candidate agrochemicals to treat plant-viral infections, and finally discussed the potential research hotspots in the future. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Chang-Feng Su
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Mehtab Muhammad Aslam
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ji-Qin Xie
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
| | - Xiang-Yang Li
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Mo-Xian Chen
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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Wang Y, Folimonova SY. Long Noncoding RNAs in Plant-Pathogen Interactions. PHYTOPATHOLOGY 2023; 113:1380-1386. [PMID: 36945729 PMCID: PMC10511663 DOI: 10.1094/phyto-02-23-0051-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Long noncoding RNAs (lncRNAs) are commonly defined as transcripts that lack protein-coding capacity and are longer than 200 nucleotides. Since the emergence of next-generation sequencing technologies in this century, thousands of lncRNAs have been identified from nearly all living organisms. Notably, various pathogens also express their own lncRNAs in host cells during infection. In plants, many lncRNAs exhibit dynamic expression patterns in response to environmental stimuli, including pathogen attacks. In contrast to well-established methods in identifying such lncRNAs, the current understanding of lncRNAs' functional mechanisms is in its infancy. Some lncRNAs serve as precursors for generating small RNAs or serve as target mimics to sequester functional small RNAs, which have been extensively reviewed in the literature. This review focuses on the emerging evidence supporting that certain lncRNAs function as negative or positive regulators of plant immunity. A common theme is that those regulations rely on specific interactions between lncRNAs and key regulatory proteins. Viroids as single-stranded circular noncoding RNAs provide a handle to investigate how RNA local motifs render interaction specificity between lncRNAs and regulatory proteins. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA
| | - Svetlana Y. Folimonova
- Plant Pathology Department, University of Florida, Gainesville, Florida 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611, USA
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Márquez-Molins J, Villalba-Bermell P, Corell-Sierra J, Pallás V, Gomez G. Integrative time-scale and multi-omics analysis of host responses to viroid infection. PLANT, CELL & ENVIRONMENT 2023. [PMID: 37378473 DOI: 10.1111/pce.14647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Viroids are circular RNAs of minimal complexity compelled to subvert plant-regulatory networks to accomplish their infectious process. Studies focused on the response to viroid-infection have mostly addressed specific regulatory levels and considered specifics infection-times. Thus, much remains to be done to understand the temporal evolution and complex nature of viroid-host interactions. Here we present an integrative analysis of the temporal evolution of the genome-wide alterations in cucumber plants infected with hop stunt viroid (HSVd) by integrating differential host transcriptome, sRNAnome and methylome. Our results support that HSVd promotes the redesign of the cucumber regulatory-pathways predominantly affecting specific regulatory layers at different infection-phases. The initial response was characterised by a reconfiguration of the host-transcriptome by differential exon-usage, followed by a progressive transcriptional downregulation modulated by epigenetic changes. Regarding endogenous small RNAs, the alterations were limited and mainly occurred at the late stage. Significant host-alterations were predominantly related to the downregulation of transcripts involved in plant-defence mechanisms, the restriction of pathogen-movement and the systemic spreading of defence signals. We expect that these data constituting the first comprehensive temporal-map of the plant-regulatory alterations associated with HSVd infection could contribute to elucidate the molecular basis of the yet poorly known host-response to viroid-induced pathogenesis.
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Affiliation(s)
- Joan Márquez-Molins
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
- Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Valencia, Spain
| | - Pascual Villalba-Bermell
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
| | - Julia Corell-Sierra
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
| | - Vicente Pallás
- Department of Virologia Molecular y Evolutiva de Plantas, Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València, Valencia, Spain
| | - Gustavo Gomez
- Department of Molecular Interactions and Regulation, Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Parc Científic, Paterna, Spain
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Wang J, Tian P, Sun J, Li B, Jia J, Yuan J, Li X, Gu S, Pang X. CsMYC2 is involved in the regulation of phenylpropanoid biosynthesis induced by trypsin in cucumber (Cucumis sativus) during storage. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:65-74. [PMID: 36701992 DOI: 10.1016/j.plaphy.2023.01.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Trypsin has a new activity of scavenging superoxide anion and generating hydrogen peroxide. Trypsin can significantly improve the storage quality of C. sativus. To illustrate the mechanism of trypsin-induced resistance in fruits and vegetables, an integrated analysis of widely targeted metabolomics and transcriptomics was carried out. Transcriptomic results showed that 1068 genes highly related to phenylpropanoid biosynthesis gathered in the brown module were obtained by WGCNA. In KEGG analysis, differentially expressed genes (DEGs) were also highly enriched in EIP (Environmental Information Processing) pathways "Plant hormone signal transduction (map04075)" and "MAPK signaling pathway-plant (map04016)". Next, 87 genes were identified as the leading edge by GSEA analysis. So far, CsMYC2 was highlighted as a key transcription factor that regulates phenylpropanoid biosynthesis identified by GSEA and WGCNA. Furthermore, the major route of biosynthesis of phenylpropanoid compounds including coumarins, lignins, chlorogenic acid, flavonoids, and derivatives regulated by trypsin was also illustrated by both transcriptomic and metabolomic data. Results of O2PLS showed that CsMYC2 was positively correlated with Rosmarinic acid-3-O-glucoside, Epigallocatechin, Quercetin-3-O-sophoroside (Baimaside), and so on. Correlation between CsMYC2, phenylpropanoid related genes, and metabolites in C. sativus was illustrated by co-expression networks. Roles of CsMYC2 were further checked in C. sativus by VIGS. The results of this study might give new insight into the exploration of the postharvest resistance mechanism of C. sativus induced by trypsin and provide useful information for the subsequent mining of resistance genes in C. sativus.
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Affiliation(s)
- Jie Wang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Pingping Tian
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jiaju Sun
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Bairu Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jingyu Jia
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jiangfeng Yuan
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China; Henan Engineering Research Center of Food Microbiology, Luoyang, 471023, China; National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang, 471000, China.
| | - Shaobin Gu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Xinyue Pang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
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Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. BIOLOGY 2023; 12:172. [PMID: 36829451 PMCID: PMC9952643 DOI: 10.3390/biology12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
Viroids are a unique type of infectious agent, exclusively composed of a relatively small (246-430 nt), highly base-paired, circular, non-coding RNA. Despite the small size and non-coding nature, the more-than-thirty currently known viroid species infectious of higher plants are able to autonomously replicate and move systemically through the host, thereby inducing disease in some plants. After recalling viroid discovery back in the late 60s and early 70s of last century and discussing current hypotheses about their evolutionary origin, this article reviews our current knowledge about these peculiar infectious agents. We describe the highly base-paired viroid molecules that fold in rod-like or branched structures and viroid taxonomic classification in two families, Pospiviroidae and Avsunviroidae, likely gathering nuclear and chloroplastic viroids, respectively. We review current knowledge about viroid replication through RNA-to-RNA rolling-circle mechanisms in which host factors, notably RNA transporters, RNA polymerases, RNases, and RNA ligases, are involved. Systemic movement through the infected plant, plant-to-plant transmission and host range are also discussed. Finally, we focus on the mechanisms of viroid pathogenesis, in which RNA silencing has acquired remarkable importance, and also for the initiation of potential biotechnological applications of viroid molecules.
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Affiliation(s)
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), 46022 Valencia, Spain
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12
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Marquez-Molins J, Juarez-Gonzalez VT, Gomez G, Pallas V, Martinez G. Occurrence of RNA post-transcriptional modifications in plant viruses and viroids and their correlation with structural and functional features. Virus Res 2023; 323:198958. [PMID: 36209921 PMCID: PMC10194119 DOI: 10.1016/j.virusres.2022.198958] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
Post-transcriptional modifications of RNA bases are widespread across all the tree of life and have been linked to RNA maturation, stability, and molecular interactions. RNA modifications have been extensively described in endogenous eukaryotic mRNAs, however, little is known about the presence of RNA modifications in plant viral and subviral RNAs. Here, we used a computational approach to infer RNA modifications in plant-pathogenic viruses and viroids using high-throughput annotation of modified ribonucleotides (HAMR), a software that predicts modified ribonucleotides using high-throughput RNA sequencing data. We analyzed datasets from representative members of different plant viruses and viroids and compared them to plant-endogenous mRNAs. Our approach was able to predict potential RNA chemical modifications (RCMs) in all analyzed pathogens. We found that both DNA and RNA viruses presented a wide range of RCM proportions while viroids had lowest values. Furthermore, we found that for viruses with segmented genomes, some genomic RNAs had a higher proportion of RCM. Interestingly, nuclear-replicating viroids showed most of the predicted modifications located in the pathogenesis region, pointing towards a possible functional role of RCMs in their infectious cycle. Thus, our results strongly suggest that plant viral and subviral RNAs might contain a variety of previously unreported RNA modifications, thus opening a new perspective in the multifaceted process of plant-pathogen interactions.
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Affiliation(s)
- Joan Marquez-Molins
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, Paterna 46980, Spain; Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València, CPI 8E, Av. de los Naranjos s/n, Valencia 46022, Spain
| | - Vasti Thamara Juarez-Gonzalez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 750 07, Sweden
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, Paterna 46980, Spain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València, CPI 8E, Av. de los Naranjos s/n, Valencia 46022, Spain
| | - German Martinez
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 750 07, Sweden.
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Di Serio F, Owens RA, Navarro B, Serra P, Martínez de Alba ÁE, Delgado S, Carbonell A, Gago-Zachert S. Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis. Virus Res 2023; 323:198964. [PMID: 36223861 PMCID: PMC10194176 DOI: 10.1016/j.virusres.2022.198964] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Viroids are small, single-stranded, non-protein coding and circular RNAs able to infect host plants in the absence of any helper virus. They may elicit symptoms in their hosts, but the underlying molecular pathways are only partially known. Here we address the role of post-transcriptional RNA silencing in plant-viroid-interplay, with major emphasis on the involvement of this sequence-specific RNA degradation mechanism in both plant antiviroid defence and viroid pathogenesis. This review is a tribute to the memory of Dr. Ricardo Flores, who largely contributed to elucidate this and other molecular mechanisms involved in plant-viroid interactions.
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Affiliation(s)
- Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy.
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council, Bari 70122, Italy
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Ángel Emilio Martínez de Alba
- Institute for Agribiotechnology Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor 37185, Salamanca, Spain
| | - Sonia Delgado
- Instituto Agroforestal Mediterráneo (IAM-UPV), Camino de Vera, s/n 46022, Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), Valencia 46022, Spain
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale 06120, Germany
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14
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Ma J, Dissanayaka Mudiyanselage SD, Park WJ, Wang M, Takeda R, Liu B, Wang Y. A nuclear import pathway exploited by pathogenic noncoding RNAs. THE PLANT CELL 2022; 34:3543-3556. [PMID: 35877068 PMCID: PMC9516175 DOI: 10.1093/plcell/koac210] [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: 06/07/2022] [Accepted: 07/18/2022] [Indexed: 05/15/2023]
Abstract
The prevailing view of intracellular RNA trafficking in eukaryotic cells is that RNAs transcribed in the nucleus either stay in the nucleus or cross the nuclear envelope, entering the cytoplasm for function. However, emerging evidence illustrates that numerous functional RNAs move in the reverse direction, from the cytoplasm to the nucleus. The mechanism underlying RNA nuclear import has not been well elucidated. Viroids are single-stranded circular noncoding RNAs that infect plants. Using Nicotiana benthamiana, tomato (Solanum lycopersicum), and nuclear-replicating viroids as a model, we showed that cellular IMPORTIN ALPHA-4 (IMPa-4) is likely involved in viroid RNA nuclear import, empirically supporting the involvement of Importin-based cellular pathway in RNA nuclear import. We also confirmed the involvement of a cellular protein (viroid RNA-binding protein 1 [VIRP1]) that binds both IMPa-4 and viroids. Moreover, a conserved C-loop in nuclear-replicating viroids serves as a key signal for nuclear import. Disrupting C-loop impairs VIRP1 binding, viroid nuclear accumulation, and infectivity. Further, C-loop exists in a subviral satellite noncoding RNA that relies on VIRP1 for nuclear import. These results advance our understanding of subviral RNA infection and the regulation of RNA nuclear import.
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Affiliation(s)
- Junfei Ma
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi 39762, USA
| | | | - Woong June Park
- Department of Molecular Biology, Dankook University, Chungnam 31116, Korea
| | - Mo Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agriculture, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Bin Liu
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi 39762, USA
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi 39762, USA
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15
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Joubert M, van den Berg N, Theron J, Swart V. Transcriptomics Advancement in the Complex Response of Plants to Viroid Infection. Int J Mol Sci 2022; 23:ijms23147677. [PMID: 35887025 PMCID: PMC9318114 DOI: 10.3390/ijms23147677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viroids are the smallest plant pathogens, consisting of a single-stranded circular RNA of less than 500 ribonucleotides in length. Despite their noncoding nature, viroids elicit disease symptoms in many economically important plant hosts, and are, thus, a class of pathogens of great interest. How these viroids establish disease within host plants, however, is not yet fully understood. Recent transcriptomic studies have revealed that viroid infection influences the expression of genes in several pathways and processes in plants, including defence responses, phytohormone signalling, cell wall modification, photosynthesis, secondary metabolism, transport, gene expression and protein modification. There is much debate about whether affected pathways signify a plant response to viroid infection, or are associated with the appearance of disease symptoms in these interactions. In this review, we consolidate the findings of viroid–host transcriptome studies to provide an overview of trends observed in the data. When considered together, changes in the gene expression of different hosts upon viroid infection reveal commonalities and differences in diverse interactions. Here, we discuss whether trends in host gene expression can be correlated to plant defence or disease development during viroid infection, and highlight avenues for future research in this field.
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Affiliation(s)
- Melissa Joubert
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Noëlani van den Berg
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Jacques Theron
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Velushka Swart
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
- Correspondence:
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16
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Mejias J, Chen Y, Bazin J, Truong NM, Mulet K, Noureddine Y, Jaubert-Possamai S, Ranty-Roby S, Soulé S, Abad P, Crespi MD, Favery B, Quentin M. Silencing the conserved small nuclear ribonucleoprotein SmD1 target gene alters susceptibility to root-knot nematodes in plants. PLANT PHYSIOLOGY 2022; 189:1741-1756. [PMID: 35385078 PMCID: PMC9237699 DOI: 10.1093/plphys/kiac155] [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: 02/17/2022] [Accepted: 03/08/2022] [Indexed: 06/01/2023]
Abstract
Root-knot nematodes (RKNs) are among the most damaging pests of agricultural crops. Meloidogyne is an extremely polyphagous genus of nematodes that can infect thousands of plant species. A few genes for resistance (R-genes) to RKN suitable for use in crop breeding have been identified, but virulent strains and species of RKN have emerged that render these R-genes ineffective. Secretion of RKN effectors targeting plant functions mediates the reprogramming of root cells into specialized feeding cells, the giant cells, essential for RKN development and reproduction. Conserved targets among plant species define the more relevant strategies for controlling nematode infection. The EFFECTOR18 (EFF18) protein from M. incognita interacts with the spliceosomal small nuclear ribonucleoprotein D1 (SmD1) in Arabidopsis (Arabidopsis thaliana), disrupting its function in alternative splicing regulation and modulating the giant cell transcriptome. We show here that EFF18 is a conserved RKN-specific effector that targets this conserved spliceosomal SmD1 protein in Solanaceae. This interaction modulates alternative splicing events produced by tomato (Solanum lycopersicum) in response to M. incognita infection. The alteration of SmD1 expression by virus-induced gene silencing in Solanaceae affects giant cell formation and nematode development. Thus, our work defines a promising conserved SmD1 target gene to develop broad resistance for the control of Meloidogyne spp. in plants.
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Affiliation(s)
| | | | - Jérémie Bazin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universités Paris Saclay, Evry, Université de Paris, 91192 Gif sur Yvette, France
| | | | - Karine Mulet
- INRAE, Université Côte d’Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Yara Noureddine
- INRAE, Université Côte d’Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | | | - Sarah Ranty-Roby
- INRAE, Université Côte d’Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Salomé Soulé
- INRAE, Université Côte d’Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Pierre Abad
- INRAE, Université Côte d’Azur, CNRS, ISA, F-06903 Sophia Antipolis, France
| | - Martin D Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universités Paris Saclay, Evry, Université de Paris, 91192 Gif sur Yvette, France
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17
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Qing Y, Zheng Y, Mlotshwa S, Smith HN, Wang X, Zhai X, van der Knaap E, Wang Y, Fei Z. Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic changes during tomato domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1536-1550. [PMID: 35514123 DOI: 10.1111/tpj.15798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/23/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Tomato has undergone extensive selections during domestication. Recent progress has shown that genomic structural variants (SVs) have contributed to gene expression dynamics during tomato domestication, resulting in changes of important traits. Here, we performed comprehensive analyses of small RNAs (sRNAs) from nine representative tomato accessions. We demonstrate that SVs substantially contribute to the dynamic expression of the three major classes of plant sRNAs: microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs). Changes in the abundance of phasiRNAs and 24-nucleotide hc-siRNAs likely contribute to the alteration of mRNA gene expression in cis during tomato domestication, particularly for genes associated with biotic and abiotic stress tolerance. We also observe that miRNA expression dynamics are associated with imprecise processing, alternative miRNA-miRNA* selections, and SVs. SVs mainly affect the expression of less-conserved miRNAs that do not have established regulatory functions or low abundant members in highly expressed miRNA families. Our data highlight different selection pressures on miRNAs compared to phasiRNAs and 24-nucleotide hc-siRNAs. Our findings provide insights into plant sRNA evolution as well as SV-based gene regulation during crop domestication. Furthermore, our dataset provides a rich resource for mining the sRNA regulatory network in tomato.
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Affiliation(s)
- You Qing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | | | - Heather N Smith
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Xin Wang
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Xuyang Zhai
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA, 30602, USA
| | - Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, OH, 43210, USA
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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18
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Gómez G, Marquez-Molins J, Martinez G, Pallas V. Plant epigenome alterations: an emergent player in viroid-host interactions. Virus Res 2022; 318:198844. [DOI: 10.1016/j.virusres.2022.198844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 10/18/2022]
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19
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Ma J, Mudiyanselage SDD, Wang Y. Emerging value of the viroid model in molecular biology and beyond. Virus Res 2022; 313:198730. [PMID: 35263622 PMCID: PMC8976779 DOI: 10.1016/j.virusres.2022.198730] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/25/2022] [Accepted: 03/05/2022] [Indexed: 01/21/2023]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. Research in the past five decades has deciphered the viroid genome structures, viroid replication cycles, numerous host factors for viroid infection, viroid motifs for intracellular and intercellular trafficking, interactions with host defense machinery, etc. In this review, we mainly focus on some significant questions that remain to be tackled, centered around (1) how the RNA polymerase II machinery performs transcription on RNA templates of nuclear-replicating viroids, (2) how viroid RNAs coordinate multiple structural elements for diverse functions, and (3) how viroid RNAs activate plant immunity. Research on viroids has led to seminal discoveries in biology, and we expect the research directions outlined in this review to continue providing key knowledge inspiring other areas of biology.
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Affiliation(s)
- Junfei Ma
- Department of Biological Sciences, Mississippi State University, MS 39762, USA
| | | | - Ying Wang
- Department of Biological Sciences, Mississippi State University, MS 39762, USA.
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20
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Li YH, Yang YY, Wang ZG, Chen Z. Emerging Function of Ecotype-Specific Splicing in the Recruitment of Commensal Microbiome. Int J Mol Sci 2022; 23:4860. [PMID: 35563250 PMCID: PMC9100151 DOI: 10.3390/ijms23094860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 12/20/2022] Open
Abstract
In recent years, host-microbiome interactions in both animals and plants has emerged as a novel research area for studying the relationship between host organisms and their commensal microbial communities. The fitness advantages of this mutualistic interaction can be found in both plant hosts and their associated microbiome, however, the driving forces mediating this beneficial interaction are poorly understood. Alternative splicing (AS), a pivotal post-transcriptional mechanism, has been demonstrated to play a crucial role in plant development and stress responses among diverse plant ecotypes. This natural variation of plants also has an impact on their commensal microbiome. In this article, we review the current progress of plant natural variation on their microbiome community, and discuss knowledge gaps between AS regulation of plants in response to their intimately related microbiota. Through the impact of this article, an avenue could be established to study the biological mechanism of naturally varied splicing isoforms on plant-associated microbiome assembly.
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Affiliation(s)
- Yue-Han Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China; (Y.-H.L.); (Y.-Y.Y.)
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161006, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
| | - Yuan-You Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China; (Y.-H.L.); (Y.-Y.Y.)
| | - Zhi-Gang Wang
- School of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161006, China
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
| | - Zhuo Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, China; (Y.-H.L.); (Y.-Y.Y.)
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21
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Li X, Zhang Y, Wu Y, Li B, Sun J, Gu S, Pang X. Lipid metabolism regulated by superoxide scavenger trypsin in
Hylocereus undatus
through multi‐omics analyses. J Food Biochem 2022; 46:e14144. [DOI: 10.1111/jfbc.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 02/24/2022] [Accepted: 03/03/2022] [Indexed: 12/09/2022]
Affiliation(s)
- Xin Li
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
- Key Laboratory of Microbial Resources Exploitation and Utilization Luoyang China
- National Demonstration Center for Experimental Food Processing and Safety Education Luoyang China
| | - Yinyin Zhang
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Ying Wu
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Bairu Li
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Jiaju Sun
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Shaobin Gu
- College of Food and Bioengineering Henan University of Science and Technology Luoyang China
| | - Xinyue Pang
- College of Medical Technology and Engineering Henan University of Science and Technology Luoyang China
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22
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Kochetov AV, Pronozin AY, Shatskaya NV, Afonnikov DA, Afanasenko OS. Potato spindle tuber viroid. Vavilovskii Zhurnal Genet Selektsii 2021; 25:269-275. [PMID: 34901723 PMCID: PMC8628614 DOI: 10.18699/vj21.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 11/24/2022] Open
Abstract
Viroids belong to a very interesting class of molecules attracting researchers in phytopathology and
molecular evolution. Here we review recent literature data concerning the genetics of Potato spindle tuber viroid
(PSTVd) and the mechanisms related to its pathological effect on the host plants. PSTVd can be transmitted vertically through microspores and macrospores, but not with pollen from another infected plant. The 359 nucleotidelong genomic RNA of PSTVd is highly structured and its 3D-conformation is responsible for interaction with host
cellular factors to mediate replication, transport between tissues during systemic infection and the severity of
pathological symptoms. RNA replication is prone to errors and infected plants contain a population of mutated
forms of the PSTVd genome. Interestingly, at 7 DAI, only 25 % of the newly synthesized RNAs were identical to
the master copy, but this proportion increased to up to 70 % at 14 DAI and remained the same afterwards. PSTVd
infection induces the immune response in host plants. There are PSTVd strains with a severe, a moderate or a mild
pathological effect. Interestingly, viroid replication itself does not necessarily induce strong morphological or
physiological symptoms. In the case of PSTVd, disease symptoms may occur due to RNA-interference, which decreases the expression levels of some important cellular regulatory factors, such as, for example, potato StTCP23
from the gibberellic acid pathway with a role in tuber morphogenesis or tomato FRIGIDA-like protein 3 with an
early flowering phenotype. This association between the small segments of viroid genomic RNAs complementary
to the untranslated regions of cellular mRNAs and disease symptoms provides a way for new resistant cultivars to
be developed by genetic editing. To conclude, viroids provide a unique model to reveal the fundamental features
of living systems, which appeared early in evolution and still remain undiscovered.
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Affiliation(s)
- A V Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - A Y Pronozin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N V Shatskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D A Afonnikov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - O S Afanasenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia All-Russian Institute of Plant Protection, Pushkin, St. Petersburg, Russia
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Hadjieva N, Apostolova E, Baev V, Yahubyan G, Gozmanova M. Transcriptome Analysis Reveals Dynamic Cultivar-Dependent Patterns of Gene Expression in Potato Spindle Tuber Viroid-Infected Pepper. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122687. [PMID: 34961158 PMCID: PMC8706270 DOI: 10.3390/plants10122687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
Potato spindle tuber viroid (PSTVd) infects various plants. PSTVd pathogenesis is associated with interference with the cellular metabolism and defense signaling pathways via direct interaction with host factors or via the transcriptional or post-transcriptional modulation of gene expression. To better understand host defense mechanisms to PSTVd infection, we analyzed the gene expression in two pepper cultivars, Capsicum annuum Kurtovska kapia (KK) and Djulunska shipka (DS), which exhibit mild symptoms of PSTVd infection. Deep sequencing-based transcriptome analysis revealed differential gene expression upon infection, with some genes displaying contrasting expression patterns in KK and DS plants. More genes were downregulated in DS plants upon infection than in KK plants, which could underlie the more severe symptoms seen in DS plants. Gene ontology enrichment analysis revealed that most of the downregulated differentially expressed genes in both cultivars were enriched in the gene ontology term photosynthesis. The genes upregulated in DS plants fell in the biological process of gene ontology term defense response. We validated the expression of six overlapping differentially expressed genes that are involved in photosynthesis, plant hormone signaling, and defense pathways by quantitative polymerase chain reaction. The observed differences in the responses of the two cultivars to PSTVd infection expand the understanding of the fine-tuning of plant gene expression that is needed to overcome the infection.
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Genome-wide analysis uncovers tomato leaf lncRNAs transcriptionally active upon Pseudomonas syringae pv. tomato challenge. Sci Rep 2021; 11:24523. [PMID: 34972834 PMCID: PMC8720101 DOI: 10.1038/s41598-021-04005-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/01/2021] [Indexed: 01/27/2023] Open
Abstract
Plants rely on (in)direct detection of bacterial pathogens through plasma membrane-localized and intracellular receptor proteins. Surface pattern-recognition receptors (PRRs) participate in the detection of microbe-associated molecular patterns (MAMPs) and are required for the activation of pattern-triggered immunity (PTI). Pathogenic bacteria, such as Pseudomonas syringae pv. tomato (Pst) deploys ~ 30 effector proteins into the plant cell that contribute to pathogenicity. Resistant plants are capable of detecting the presence or activity of effectors and mount another response termed effector-triggered immunity (ETI). In order to investigate the involvement of tomato’s long non-coding RNAs (lncRNAs) in the immune response against Pst, we used RNA-seq data to predict and characterize those that are transcriptionally active in leaves challenged with a large set of treatments. Our prediction strategy was validated by sequence comparison with tomato lncRNAs described in previous works and by an alternative approach (RT-qPCR). Early PTI (30 min), late PTI (6 h) and ETI (6 h) differentially expressed (DE) lncRNAs were identified and used to perform a co-expression analysis including neighboring (± 100 kb) DE protein-coding genes. Some of the described networks could represent key regulatory mechanisms of photosynthesis, PRR abundance at the cell surface and mitigation of oxidative stress, associated to tomato-Pst pathosystem.
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Li S, Wu ZG, Zhou Y, Dong ZF, Fei X, Zhou CY, Li SF. Changes in metabolism modulate induced by viroid infection in the orchid Dendrobium officinale. Virus Res 2021; 308:198626. [PMID: 34780884 DOI: 10.1016/j.virusres.2021.198626] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/15/2022]
Abstract
Dendrobium officinale is an important traditional Chinese medicinal herb, and the stem tissue is the main medicinal that is harvested from D. officinale. Recently, the first viroid was identified from D. officinale in China, and it has been named Dendrobium viroid (DVd). Whether DVd interferes with metabolic pathways in dendrobium plants and affects the medicinal value of the host is unknown. In this study, metabolomics data from stem tissues supported by transcriptome studies were used to investigate how metabolism modulate of D. officinale is altered by DVd infection. Our results show that metabolism of D. officinale is reprogrammed in many ways during DVd infection, and this is reflected by significant changes in the levels of flavonoids, alkaloids, and phenolic acids. Furthermore, we found that DVd infection significantly decreased the accumulation of flavonoids and alkaloid metabolites in infected stems, and the decreases in these metabolites appears to affect the medicinal components of the infected plants, weakening the host antiviral immune response as well. Conversely, phenolic acids occupy a larger proportion of the up-regulated metabolites from DVd infection in comparison with the mock-inoculated control, and the increase in the total phenolic acids may reflect the activation of the pathogen defense response in D. officinale. Taken together, our results provide an interesting overview and give a better understanding of the relationship between metabolism and DVd infection in the orchid D. officinale.
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Affiliation(s)
- Shuai Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing 400700, China
| | - Zhi-Gang Wu
- School of Pharmacy, Wenzhou Medical University, Wenzhou, 325035, China
| | - Ying Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhen-Fei Dong
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuan Fei
- School of Pharmacy, Wenzhou Medical University, Wenzhou, 325035, China
| | - Chang-Yong Zhou
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing 400700, China
| | - Shi-Fang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Global Survey of the Full-Length Cabbage Transcriptome ( Brassica oleracea Var. capitata L.) Reveals Key Alternative Splicing Events Involved in Growth and Disease Response. Int J Mol Sci 2021; 22:ijms221910443. [PMID: 34638781 PMCID: PMC8508790 DOI: 10.3390/ijms221910443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/25/2022] Open
Abstract
Cabbage (Brassica oleracea L. var. capitata L.) is an important vegetable crop cultivated around the world. Previous studies of cabbage gene transcripts were primarily based on next-generation sequencing (NGS) technology which cannot provide accurate information concerning transcript assembly and structure analysis. To overcome these issues and analyze the whole cabbage transcriptome at the isoform level, PacBio RS II Single-Molecule Real-Time (SMRT) sequencing technology was used for a global survey of the full-length transcriptomes of five cabbage tissue types (root, stem, leaf, flower, and silique). A total of 77,048 isoforms, capturing 18,183 annotated genes, were discovered from the sequencing data generated through SMRT. The patterns of both alternative splicing (AS) and alternative polyadenylation (APA) were comprehensively analyzed. In total, we detected 13,468 genes which had isoforms containing APA sites and 8978 genes which underwent AS events. Moreover, 5272 long non-coding RNAs (lncRNAs) were discovered, and most exhibited tissue-specific expression. In total, 3147 transcription factors (TFs) were detected and 10 significant gene co-expression network modules were identified. In addition, we found that Fusarium wilt, black rot and clubroot infection significantly influenced AS in resistant cabbage. In summary, this study provides abundant cabbage isoform transcriptome data, which promotes reannotation of the cabbage genome, deepens our understanding of their post-transcriptional regulation mechanisms, and can be used for future functional genomic research.
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27
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Li X, Zhang Y, Zhao S, Li B, Cai L, Pang X. Omics analyses indicate the routes of lignin related metabolites regulated by trypsin during storage of pitaya (Hylocereus undatus). Genomics 2021; 113:3681-3695. [PMID: 34509619 DOI: 10.1016/j.ygeno.2021.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 07/30/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
The storage quality of Hylocereus undatus was significantly improved by trypsin, a novel preservative. The transcriptomic results revealed that antioxidant signal pathways were induced, while lignin catabolic process was impeded by trypsin. In addition, the results of protein-protein interaction (PPI) network networks suggested that flavone 3'-O-methyltransferase 1 (OMT1), ferulic acid 5-hydroxylase 1 (CYP84A1), cellulose synthase isomer (CEV1), and 4-coumarate-CoA ligase 3 (4CL3) act as hubs of peroxidases, lignin related proteins, and proteins involved in the phenylpropanoid metabolism (PLPs) induced by trypsin. Trypsin also regulated the biosynthesis of lignin, chlorogenic acid, and flavonoids. Caffeic acid might be the hub in the metabolic network of the early pathways of phenylpropanoid biosynthesis. It has been hypothesized that trypsin might quickly induce lignin biosynthesis and then up-regulated bioactive metabolites to enhance storage quality of H. undatus.
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Affiliation(s)
- Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; Key Laboratory of Microbial Resources Exploitation and Utilization, Luoyang 471023, China; National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang 471000, China
| | - Yinyin Zhang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Shoujing Zhao
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Bairu Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Luning Cai
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China
| | - Xinyue Pang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang 471023, China.
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Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochem Soc Trans 2021; 48:2399-2414. [PMID: 33196096 DOI: 10.1042/bst20190492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.
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Abstract
Viroids are small, single-stranded, circular RNAs infecting plants. Composed of only a few hundred nucleotides and being unable to code for proteins, viroids represent the lowest level of complexity for an infectious agent, even below that of the smallest known viruses. Despite the relatively small size, viroids contain RNA structural elements embracing all the information needed to interact with host factors involved in their infectious cycle, thus providing models for studying structure-function relationships of RNA. Viroids are specifically targeted to nuclei (family Pospiviroidae) or chloroplasts (family Avsunviroidae), where replication based on rolling-circle mechanisms takes place. They move locally and systemically through plasmodesmata and phloem, respectively, and may elicit symptoms in the infected host, with pathogenic pathways linked to RNA silencing and other plant defense responses. In this review, recent advances in the dissection of the complex interplay between viroids and plants are presented, highlighting knowledge gaps and perspectives for future research. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
| | - Ricardo Flores
- Institute of Molecular and Cellular Biology of Plants (UPV-CSIC), Polytechnic University of Valencia, 46022 Valencia, Spain
| | - Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
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30
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Symptom Severity, Infection Progression and Plant Responses in Solanum Plants Caused by Three Pospiviroids Vary with the Inoculation Procedure. Int J Mol Sci 2021; 22:ijms22126189. [PMID: 34201240 PMCID: PMC8273692 DOI: 10.3390/ijms22126189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 11/17/2022] Open
Abstract
Infectious viroid clones consist of dimeric cDNAs used to generate transcripts which mimic the longer-than-unit replication intermediates. These transcripts can be either generated in vitro or produced in vivo by agro-inoculation. We have designed a new plasmid, which allows both inoculation methods, and we have compared them by infecting Solanum lycopersicum and Solanum melongena with clones of Citrus exocortis virod (CEVd), Tomato chlorotic dwarf viroid (TCDVd), and Potato spindle tuber viroid (PSTVd). Our results showed more uniform and severe symptoms in agro-inoculated plants. Viroid accumulation and the proportion of circular and linear forms were different depending on the host and the inoculation method and did not correlate with the symptoms, which correlated with an increase in PR1 induction, accumulation of the defensive signal molecules salicylic (SA) and gentisic (GA) acids, and ribosomal stress in tomato plants. The alteration in ribosome biogenesis was evidenced by both the upregulation of the tomato ribosomal stress marker SlNAC082 and the impairment in 18S rRNA processing, pointing out ribosomal stress as a novel signature of the pathogenesis of nuclear-replicating viroids. In conclusion, this updated binary vector has turned out to be an efficient and reproducible method that will facilitate the studies of viroid–host interactions.
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31
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Nath VS, Mishra AK, Awasthi P, Shrestha A, Matoušek J, Jakse J, Kocábek T, Khan A. Identification and characterization of long non-coding RNA and their response against citrus bark cracking viroid infection in Humulus lupulus. Genomics 2021; 113:2350-2364. [PMID: 34051324 DOI: 10.1016/j.ygeno.2021.05.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/22/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a highly heterogeneous class of non-protein-encoding transcripts that play an essential regulatory role in diverse biological processes, including stress responses. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) poses a major threat to the production of Humulus lupulus (hop) plants. In this study, we systematically investigate the characteristics of the lncRNAs in hop and their role in CBCVd-infection using RNA-sequencing data. Following a stringent filtration criterion, a total of 3598 putative lncRNAs were identified with a high degree of certainty, of which 19% (684) of the lncRNAs were significantly differentially expressed (DE) in CBCVd-infected hop, which were predicted to be mainly involved in plant-pathogen interactions, kinase cascades, secondary metabolism and phytohormone signal transduction. Besides, several lncRNAs and CBCVd-responsive lncRNAs were identified as the precursor of microRNAs and predicted as endogenous target mimics (eTMs) for hop microRNAs involved in CBCVd-infection.
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Affiliation(s)
- Vishnu Sukumari Nath
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Ajay Kumar Mishra
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Praveen Awasthi
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Ankita Shrestha
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jernej Jakse
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Tomáš Kocábek
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Ahamed Khan
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
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Navarro B, Gisel A, Serra P, Chiumenti M, Di Serio F, Flores R. Degradome Analysis of Tomato and Nicotiana benthamiana Plants Infected with Potato Spindle Tuber Viroid. Int J Mol Sci 2021; 22:3725. [PMID: 33918424 PMCID: PMC8038209 DOI: 10.3390/ijms22073725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/16/2022] Open
Abstract
Viroids are infectious non-coding RNAs that infect plants. During infection, viroid RNAs are targeted by Dicer-like proteins, generating viroid-derived small RNAs (vd-sRNAs) that can guide the sequence specific cleavage of cognate host mRNAs via an RNA silencing mechanism. To assess the involvement of these pathways in pathogenesis associated with nuclear-replicating viroids, high-throughput sequencing of sRNAs and degradome analysis were carried out on tomato and Nicotiana benthamiana plants infected by potato spindle tuber viroid (PSTVd). Both hosts develop similar stunting and leaf curling symptoms when infected by PSTVd, thus allowing comparative analyses. About one hundred tomato mRNAs potentially targeted for degradation by vd-sRNAs were initially identified. However, data from biological replicates and comparisons between mock and infected samples reduced the number of bona fide targets-i.e., those identified with high confidence in two infected biological replicates but not in the mock controls-to only eight mRNAs that encode proteins involved in development, transcription or defense. Somewhat surprisingly, results of RT-qPCR assays revealed that the accumulation of only four of these mRNAs was inhibited in the PSTVd-infected tomato. When these analyses were extended to mock inoculated and PSTVd-infected N. benthamiana plants, a completely different set of potential mRNA targets was identified. The failure to identify homologous mRNA(s) targeted by PSTVd-sRNA suggests that different pathways could be involved in the elicitation of similar symptoms in these two species. Moreover, no significant modifications in the accumulation of miRNAs and in the cleavage of their targeted mRNAs were detected in the infected tomato plants with respect to the mock controls. Taken together, these data suggest that stunting and leaf curling symptoms induced by PSTVd are elicited by a complex plant response involving multiple mechanisms, with RNA silencing being only one of the possible components.
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Affiliation(s)
- Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Andreas Gisel
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy;
- International Institute of Tropical Agriculture, Ibadan 200001, Nigeria
| | - Pedro Serra
- Istituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain; (P.S.); (R.F.)
| | - Michela Chiumenti
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy; (B.N.); (M.C.)
| | - Ricardo Flores
- Istituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain; (P.S.); (R.F.)
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Zheng F, Yi W, Liu W, Zhu H, Gong P, Pan Z. A positively charged surface patch on the pestivirus NS3 protease module plays an important role in modulating NS3 helicase activity and virus production. Arch Virol 2021; 166:1633-1642. [PMID: 33787991 DOI: 10.1007/s00705-021-05055-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/08/2021] [Indexed: 10/21/2022]
Abstract
Pestivirus nonstructural protein 3 (NS3) is a multifunctional protein with protease and helicase activities that are essential for virus replication. In this study, we used a combination of biochemical and genetic approaches to investigate the relationship between a positively charged patch on the protease module and NS3 function. The surface patch is composed of four basic residues, R50, K74 and K94 in the NS3 protease domain and H24 in the structurally integrated cofactor NS4APCS. Single-residue or simultaneous four-residue substitutions in the patch to alanine or aspartic acid had little effect on ATPase activity. However, single substitutions of R50, K94 or H24 or a simultaneous four-residue substitution resulted in apparent changes in the helicase activity and RNA-binding ability of NS3. When these mutations were introduced into a classical swine fever virus (CSFV) cDNA clone, a single substitution at K94 or a simultaneous four-residue substitution (Qua_A or Qua_D) impaired the production of infectious virus. Furthermore, the replication efficiency of the CSFV variants was partially correlated with the helicase activity of NS3 in vitro. Our results suggest that the conserved positively charged patch on NS3 plays an important role in modulating the NS3 helicase activity in vitro and CSFV production.
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Affiliation(s)
- Fengwei Zheng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weicheng Yi
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weichi Liu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongchang Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Zishu Pan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Naoi T, Hataya T. Tolerance Even to Lethal Strain of Potato Spindle Tuber Viroid Found in Wild Tomato Species Can Be Introduced by Crossing. PLANTS 2021; 10:plants10030575. [PMID: 33803660 PMCID: PMC8003082 DOI: 10.3390/plants10030575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
To date, natural resistance or tolerance, which can be introduced into crops by crossing, to potato spindle tuber viroid (PSTVd) has not been reported. Additionally, responses to PSTVd infection in many wild tomato species, including some species that can be crossed with PSTVd-susceptible cultivated tomatoes (Solanum lycopersicum var. lycoperaicum), have not been ascertained. The aim of this study was to evaluate responses to PSTVd infection including resistance and tolerance. Accordingly, we inoculated several cultivated and wild tomato species with intermediate and lethal strains of PSTVd. None of the host plants exhibited sufficient resistance to PSTVd to render systemic infection impossible; however, these plants displayed other responses, including tolerance. Further analysis of PSTVd accumulation revealed low accumulation of PSTVd in two wild species, exhibiting high tolerance, even to the lethal strain. Additionally, F1 hybrids generated by crossing a PSTVd-sensitive wild tomato (Solanum lycopersicum var. cerasiforme) with these wild relatives also exhibited tolerance to the lethal PSTVd strain, which is accompanied by low PSTVd accumulation during early infection. These results indicate that the tolerance toward PSTVd in wild species is a dominant trait and can be utilized for tomato breeding by crossing.
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Affiliation(s)
- Takashi Naoi
- Pathogen-Plant Interactions, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan;
| | - Tatsuji Hataya
- Pathogen-Plant Interactions, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Correspondence:
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Herath V, Verchot J. Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum. Int J Mol Sci 2021; 22:2837. [PMID: 33799566 PMCID: PMC8001266 DOI: 10.3390/ijms22062837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
Potato virus X (PVX) belongs to genus Potexvirus. This study characterizes the cellular transcriptome responses to PVX infection in Russet potato at 2 and 3 days post infection (dpi). Among the 1242 differentially expressed genes (DEGs), 268 genes were upregulated, and 37 genes were downregulated at 2 dpi while 677 genes were upregulated, and 265 genes were downregulated at 3 dpi. DEGs related to signal transduction, stress response, and redox processes. Key stress related transcription factors were identified. Twenty-five pathogen resistance gene analogs linked to effector triggered immunity or pathogen-associated molecular pattern (PAMP)-triggered immunity were identified. Comparative analysis with Arabidopsis unfolded protein response (UPR) induced DEGs revealed genes associated with UPR and plasmodesmata transport that are likely needed to establish infection. In conclusion, this study provides an insight on major transcriptional regulatory networked involved in early response to PVX infection and establishment.
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Affiliation(s)
- Venura Herath
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA;
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA;
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36
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Venkataraman S, Badar U, Shoeb E, Hashim G, AbouHaidar M, Hefferon K. An Inside Look into Biological Miniatures: Molecular Mechanisms of Viroids. Int J Mol Sci 2021; 22:2795. [PMID: 33801996 PMCID: PMC8001946 DOI: 10.3390/ijms22062795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022] Open
Abstract
Viroids are tiny single-stranded circular RNA pathogens that infect plants. Viroids do not encode any proteins, yet cause an assortment of symptoms. The following review describes viroid classification, molecular biology and spread. The review also discusses viroid pathogenesis, host interactions and detection. The review concludes with a description of future prospects in viroid research.
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Affiliation(s)
| | | | | | | | | | - Kathleen Hefferon
- Cell and System Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; (S.V.); (U.B.); (E.S.); (G.H.); (M.A.)
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Mejias J, Bazin J, Truong NM, Chen Y, Marteu N, Bouteiller N, Sawa S, Crespi MD, Vaucheret H, Abad P, Favery B, Quentin M. The root-knot nematode effector MiEFF18 interacts with the plant core spliceosomal protein SmD1 required for giant cell formation. THE NEW PHYTOLOGIST 2021; 229:3408-3423. [PMID: 33206370 DOI: 10.1111/nph.17089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/12/2020] [Indexed: 05/11/2023]
Abstract
The root-knot nematode Meloidogyne incognita secretes specific effectors (MiEFF) and induces the redifferentiation of plant root cells into enlarged multinucleate feeding 'giant cells' essential for nematode development. Immunolocalizations revealed the presence of the MiEFF18 protein in the salivary glands of M. incognita juveniles. In planta, MiEFF18 localizes to the nuclei of giant cells demonstrating its secretion during plant-nematode interactions. A yeast two-hybrid approach identified the nuclear ribonucleoprotein SmD1 as a MiEFF18 partner in tomato and Arabidopsis. SmD1 is an essential component of the spliceosome, a complex involved in pre-mRNA splicing and alternative splicing. RNA-seq analyses of Arabidopsis roots ectopically expressing MiEFF18 or partially impaired in SmD1 function (smd1b mutant) revealed the contribution of the effector and its target to alternative splicing and proteome diversity. The comparison with Arabidopsis galls data showed that MiEFF18 modifies the expression of genes important for giant cell ontogenesis, indicating that MiEFF18 modulates SmD1 functions to facilitate giant cell formation. Finally, Arabidopsis smd1b mutants exhibited less susceptibility to M. incognita infection, and the giant cells formed on these mutants displayed developmental defects, suggesting that SmD1 plays an important role in the formation of giant cells and is required for successful nematode infection.
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Affiliation(s)
- Joffrey Mejias
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Jérémie Bazin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universités Paris Saclay - Evry, Université de Paris, Gif sur Yvette, 91192, France
| | - Nhat-My Truong
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-11 8555, Japan
| | - Yongpan Chen
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
- Department of Plant Pathology and Key Laboratory of Pest Monitoring and Green Management of the Ministry of Agriculture, China Agricultural University, Beijing, 100193, China
| | - Nathalie Marteu
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Nathalie Bouteiller
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-11 8555, Japan
| | - Martin D Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Universités Paris Saclay - Evry, Université de Paris, Gif sur Yvette, 91192, France
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, 78000, France
| | - Pierre Abad
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Bruno Favery
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, ISA, Sophia Antipolis, F-06903, France
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Flores R, Navarro B, Delgado S, Serra P, Di Serio F. Viroid pathogenesis: a critical appraisal of the role of RNA silencing in triggering the initial molecular lesion. FEMS Microbiol Rev 2021; 44:386-398. [PMID: 32379313 DOI: 10.1093/femsre/fuaa011] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
The initial molecular lesions through which viroids, satellite RNAs and viruses trigger signal cascades resulting in plant diseases are hotly debated. Since viroids are circular non-protein-coding RNAs of ∼250-430 nucleotides, they appear very convenient to address this issue. Viroids are targeted by their host RNA silencing defense, generating viroid-derived small RNAs (vd-sRNAs) that are presumed to direct Argonaute (AGO) proteins to inactivate messenger RNAs, thus initiating disease. Here, we review the existing evidence. Viroid-induced symptoms reveal a distinction. Those attributed to vd-sRNAs from potato spindle tuber viroid and members of the family Pospiviroidae (replicating in the nucleus) are late, non-specific and systemic. In contrast, those attributed to vd-sRNAs from peach latent mosaic viroid (PLMVd) and other members of the family Avsunviroidae (replicating in plastids) are early, specific and local. Remarkably, leaf sectors expressing different PLMVd-induced chloroses accumulate viroid variants with specific pathogenic determinants. Some vd-sRNAs containing such determinant guide AGO1-mediated cleavage of mRNAs that code for proteins regulating chloroplast biogenesis/development. Therefore, the initial lesions and the expected phenotypes are connected by short signal cascades, hence supporting a cause-effect relationship. Intriguingly, one virus satellite RNA initiates disease through a similar mechanism, whereas in the Pospiviroidae and in plant viruses the situation remains uncertain.
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Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, Via Amendola 122/D, 70126 Bari, Italy
| | - Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos s/n 46010, Valencia, Spain
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Via Amendola 122/D, 70126 Bari, Italy
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Ramesh SV, Yogindran S, Gnanasekaran P, Chakraborty S, Winter S, Pappu HR. Virus and Viroid-Derived Small RNAs as Modulators of Host Gene Expression: Molecular Insights Into Pathogenesis. Front Microbiol 2021; 11:614231. [PMID: 33584579 PMCID: PMC7874048 DOI: 10.3389/fmicb.2020.614231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/19/2020] [Indexed: 02/01/2023] Open
Abstract
Virus-derived siRNAs (vsiRNAs) generated by the host RNA silencing mechanism are effectors of plant’s defense response and act by targeting the viral RNA and DNA in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) pathways, respectively. Contrarily, viral suppressors of RNA silencing (VSRs) compromise the host RNA silencing pathways and also cause disease-associated symptoms. In this backdrop, reports describing the modulation of plant gene(s) expression by vsiRNAs via sequence complementarity between viral small RNAs (sRNAs) and host mRNAs have emerged. In some cases, silencing of host mRNAs by vsiRNAs has been implicated to cause characteristic symptoms of the viral diseases. Similarly, viroid infection results in generation of sRNAs, originating from viroid genomic RNAs, that potentially target host mRNAs causing typical disease-associated symptoms. Pathogen-derived sRNAs have been demonstrated to have the propensity to target wide range of genes including host defense-related genes, genes involved in flowering and reproductive pathways. Recent evidence indicates that vsiRNAs inhibit host RNA silencing to promote viral infection by acting as decoy sRNAs. Nevertheless, it remains unclear if the silencing of host transcripts by viral genome-derived sRNAs are inadvertent effects due to fortuitous pairing between vsiRNA and host mRNA or the result of genuine counter-defense strategy employed by viruses to enhance its survival inside the plant cell. In this review, we analyze the instances of such cross reaction between pathogen-derived vsiRNAs and host mRNAs and discuss the molecular insights regarding the process of pathogenesis.
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Affiliation(s)
- S V Ramesh
- ICAR-Central Plantation Crops Research Institute, Kasaragod, India
| | - Sneha Yogindran
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Prabu Gnanasekaran
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | | | - Stephan Winter
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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SANO T. Progress in 50 years of viroid research-Molecular structure, pathogenicity, and host adaptation. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:371-401. [PMID: 34380915 PMCID: PMC8403530 DOI: 10.2183/pjab.97.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/30/2021] [Indexed: 05/27/2023]
Abstract
Viroids are non-encapsidated, single-stranded, circular RNAs consisting of 246-434 nucleotides. Despite their non-protein-encoding RNA nature, viroids replicate autonomously in host cells. To date, more than 25 diseases in more than 15 crops, including vegetables, fruit trees, and flowers, have been reported. Some are pathogenic but others replicate without eliciting disease. Viroids were shown to have one of the fundamental attributes of life to adapt to environments according to Darwinian selection, and they are likely to be living fossils that have survived from the pre-cellular RNA world. In 50 years of research since their discovery, it was revealed that viroids invade host cells, replicate in nuclei or chloroplasts, and undergo nucleotide mutation in the process of adapting to new host environments. It was also demonstrated that structural motifs in viroid RNAs exert different levels of pathogenicity by interacting with various host factors. Despite their small size, the molecular mechanism of viroid pathogenicity turned out to be more complex than first thought.
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Affiliation(s)
- Teruo SANO
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
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Pang X, Zhao S, Zhang M, Cai L, Zhang Y, Li X. Catechin gallate acts as a key metabolite induced by trypsin in Hylocereus undatus during storage indicated by omics. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:497-507. [PMID: 33257230 DOI: 10.1016/j.plaphy.2020.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
Trypsin is a novel superoxide scavenger. The storage quality of H. undatus was significantly improved by trypsin. To investigate the mechanism of flavonoid metabolism regulated by trypsin, combined analysis of widely targeted metabolomic and transcriptome were performed. GO and KEGG enrichment analyses of the transcriptome profiles of H. undatus revealed that some of the flavonoid related biosynthesis pathways were regulated by up or down patterns with the treatment of trypsin. Correlation analysis of flavonoid related genes expression in H. undatus provided a rationale for the functional significance of them. Furthermore, it has been revealed that the most significantly regulated flavonoid was catechin gallate in metabolomic profiles of H. undatus. The major route of flavonoid biosynthesis regulated by trypsin was also illustrated by both transcriptomic and metabolomic data. Finally, the results of PPI network revealed that C4H, HCT, and CYP75B1 acted as hub proteins involved in flavonoid metabolism regulated by trypsin.
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Affiliation(s)
- Xinyue Pang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Shoujing Zhao
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Min Zhang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Luning Cai
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yinyin Zhang
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, 471023, China; National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang, 471000, China; Henan Engineering Research Center of Food Microbiology, Luoyang, 471023, China.
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42
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Li X, Li B, Guan S, Cai L, Xinyue P. Hub genes and sub-networks of stoma-related genes in Hylocereus undatus through trypsin treatment during storage revealed by transcriptomic analysis. J Food Biochem 2020; 45:e13538. [PMID: 33152799 DOI: 10.1111/jfbc.13538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 10/05/2020] [Indexed: 02/02/2023]
Abstract
To further investigate the preservation mechanisms of trypsin, the synergistic mechanisms of trypsin and stoma-related genes were evaluated in Hylocereus undatus. Trypsin significantly induced the stoma closure and improved the storage quality of H. undatus. Transcriptomic analyses of H. undatus revealed that important antioxidant signal pathway, such as SREBP signaling pathway, cellular response to H2 O2 or cellular response to molecule of bacterial origin, were induced; while responses to water deprivation were impeded by trypsin. These results indicated that trypsin relieved pitaya of pressure of water deprivation and exhibited the protection on pitaya during storage. Furthermore, the analyses of networks of protein-protein interaction suggested that OST1, HK5, AT4G27585, and HIR1 act as hubs of stoma-related proteins induced by trypsin during storage of H. undatus. PRACTICAL APPLICATIONS: Preservation of fruit is becoming increasingly important to the world. Keep the balance of production and scavenging of reactive oxygen species is efficient to improve the storage quality of fruit. Trypsin had a novel superoxide anion scavenging activity and protect fruit cells from cellular injury induced by excess ROS. This article investigates the hub genes and interaction mechanisms of stoma closure induced by trypsin during the storage of H. undatus. The application of trypsin provides a new strategy for the quality control of fruit storage. Trypsin will have a broad market and development potential in the area of food additives.
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Affiliation(s)
- Xin Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China.,Henan Engineering Research Center of Food Microbiology, Luoyang, China.,National Demonstration Center for Experimental Food Processing and Safety Education, Luoyang, China
| | - Bairu Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Suixia Guan
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Luning Cai
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Pang Xinyue
- Medical Technology and Engineering College, Henan University of Science and Technology, Luoyang, China
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43
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Identification and Molecular Mechanisms of Key Nucleotides Causing Attenuation in Pathogenicity of Dahlia Isolate of Potato Spindle Tuber Viroid. Int J Mol Sci 2020; 21:ijms21197352. [PMID: 33027943 PMCID: PMC7583970 DOI: 10.3390/ijms21197352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 09/18/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022] Open
Abstract
While the potato spindle tuber viroid (PSTVd) variant, PSTVd-Dahlia (PSTVd-D or PSTVd-Dwt) induces very mild symptoms in tomato cultivar 'Rutgers', PSTVd-Intermediate (PSTVd-I or PSTVd-Iwt) induces severe symptoms. These two variants differ by nine nucleotides, of which six mutations are located in the terminal left (TL) to the pathogenicity (P) domains. To evaluate the importance of mutations located in the TL to the P domains, ten types of point mutants were created by swapping the nucleotides between the two viroid variants. Bioassay in tomato plants demonstrated that two mutants created on PSTVd-Iwt at positions 42 and 64 resulted in symptom attenuation. Phenotypic and RT-qPCR analysis revealed that mutation at position 42 of PSTVd-Iwt significantly reduced disease severity and accumulation of the viroid, whereas mutation at position 64 showed a significant reduction in stunting when compared to the PSTVd-Iwt infected plant. RT-qPCR analysis on pathogenesis-related protein 1b1 and chalcone synthase genes showed a direct correlation with symptom severity whereas the expansin genes were down-regulated irrespective of the symptom severity. These results indicate that the nucleotides at positions 42 and 64 are in concert with the ones at positions 43, 310, and 311/312, which determines the slower and stable accumulation of PSTVd-D without eliciting excessive host defense responses thus contributing in the attenuation of disease symptom.
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Xu L, Zong X, Wang J, Wei H, Chen X, Liu Q. Transcriptomic analysis reveals insights into the response to Hop stunt viroid (HSVd) in sweet cherry ( Prunus avium L.) fruits. PeerJ 2020; 8:e10005. [PMID: 33005494 PMCID: PMC7513744 DOI: 10.7717/peerj.10005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Hop stunt viroid (HSVd) is a member of the genus Hostuviroid of the family Pospiviroidae and has been found in a wide range of herbaceous and woody hosts. It causes serious dapple fruit symptoms on infected sweet cherry, notably inducing cherry tree decay. In order to better understand the molecular mechanisms of HSVd infection in sweet cherry fruit, transcriptome analysis of HSVd-infected and healthy sweet cherry fruits was carried out. A total of 1,572 differentially expressed genes (DEGs) were identified, involving 961 upregulated DEGs and 611 downregulated DEGs. Functional analysis indicated that the DEGs were mainly involved in plant hormone signal transduction, plant-pathogen interactions, secondary metabolism, and the MAPK signaling pathway. In addition, C2H2 zinc finger, MYB, bHLH, AP2/ERF, C2C2-dof, NAC and WRKY transcription factors can respond to HSVd infection. In order to confirm the high-throughput sequencing results, 16 DEGs were verified by RT-qPCR analysis. The results provided insight into the pathways and genes of sweet cherry fruit in response to HSVd infection.
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Affiliation(s)
- Li Xu
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Xiaojuan Zong
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Jiawei Wang
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Hairong Wei
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Xin Chen
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Qingzhong Liu
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
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Islam S, Bhor SA, Tanaka K, Sakamoto H, Yaeno T, Kaya H, Kobayashi K. Transcriptome Analysis Shows Activation of Stress and Defense Responses by Silencing of Chlorophyll Biosynthetic Enzyme CHLI in Transgenic Tobacco. Int J Mol Sci 2020; 21:E7044. [PMID: 32987929 PMCID: PMC7582866 DOI: 10.3390/ijms21197044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/04/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
In the present study, we have shown the transcriptional changes in a chlorosis model transgenic tobacco plant, i-amiCHLI, in which an artificial micro RNA is expressed in a chemically inducible manner to silence the expression of CHLI genes encoding a subunit of a chlorophyll biosynthetic enzyme. Comparison to the inducer-treated and untreated control non-transformants and untreated i-amiCHLI revealed that 3568 and 3582 genes were up- and down-regulated, respectively, in the inducer-treated i-amiCHLI plants. Gene Ontology enrichment analysis of these differentially expressed genes indicated the upregulation of the genes related to innate immune responses, and cell death pathways, and the downregulation of genes for photosynthesis, plastid organization, and primary and secondary metabolic pathways in the inducer-treated i-amiCHLI plants. The cell death in the chlorotic tissues with a preceding H2O2 production was observed in the inducer-treated i-amiCHLI plants, confirming the activation of the immune response. The involvement of activated innate immune response in the chlorosis development was supported by the comparative expression analysis between the two transgenic chlorosis model systems, i-amiCHLI and i-hpHSP90C, in which nuclear genes encoding different chloroplast proteins were similarly silenced.
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Affiliation(s)
- Shaikhul Islam
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
| | - Sachin Ashok Bhor
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan;
| | - Hikaru Sakamoto
- Faculty of Bio-Industry, Tokyo University of Agriculture, Abashiri, Hokkaido 099-2493, Japan;
| | - Takashi Yaeno
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
- Research Unit for Citromics, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - Hidetaka Kaya
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
- Research Unit for Citromics, Ehime University, Matsuyama, Ehime 790-8566, Japan
| | - Kappei Kobayashi
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime 790-8566, Japan; (S.I.); (S.A.B.); (T.Y.); (H.K.)
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime 790-8566, Japan
- Research Unit for Citromics, Ehime University, Matsuyama, Ehime 790-8566, Japan
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46
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Adkar-Purushothama CR, Perreault JP. Impact of Nucleic Acid Sequencing on Viroid Biology. Int J Mol Sci 2020; 21:ijms21155532. [PMID: 32752288 PMCID: PMC7432327 DOI: 10.3390/ijms21155532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/26/2022] Open
Abstract
The early 1970s marked two breakthroughs in the field of biology: (i) The development of nucleotide sequencing technology; and, (ii) the discovery of the viroids. The first DNA sequences were obtained by two-dimensional chromatography which was later replaced by sequencing using electrophoresis technique. The subsequent development of fluorescence-based sequencing method which made DNA sequencing not only easier, but many orders of magnitude faster. The knowledge of DNA sequences has become an indispensable tool for both basic and applied research. It has shed light biology of viroids, the highly structured, circular, single-stranded non-coding RNA molecules that infect numerous economically important plants. Our understanding of viroid molecular biology and biochemistry has been intimately associated with the evolution of nucleic acid sequencing technologies. With the development of the next-generation sequence method, viroid research exponentially progressed, notably in the areas of the molecular mechanisms of viroids and viroid diseases, viroid pathogenesis, viroid quasi-species, viroid adaptability, and viroid–host interactions, to name a few examples. In this review, the progress in the understanding of viroid biology in conjunction with the improvements in nucleotide sequencing technology is summarized. The future of viroid research with respect to the use of third-generation sequencing technology is also briefly envisaged.
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Nahand JS, Jamshidi S, Hamblin MR, Mahjoubin-Tehran M, Vosough M, Jamali M, Khatami A, Moghoofei M, Baghi HB, Mirzaei H. Circular RNAs: New Epigenetic Signatures in Viral Infections. Front Microbiol 2020; 11:1853. [PMID: 32849445 PMCID: PMC7412987 DOI: 10.3389/fmicb.2020.01853] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Covalent closed circular RNAs (circRNAs) can act as a bridge between non-coding RNAs and coding messenger RNAs. CircRNAs are generated by a back-splicing mechanism during post-transcriptional processing and are abundantly expressed in eukaryotic cells. CircRNAs can act via the modulation of RNA transcription and protein production, and by the sponging of microRNAs (miRNAs). CircRNAs are now thought to be involved in many different biological and pathological processes. Some studies have suggested that the expression of host circRNAs is dysregulated in several types of virus-infected cells, compared to control cells. It is highly likely that viruses can use these molecules for their own purposes. In addition, some viral genes are able to produce viral circRNAs (VcircRNA) by a back-splicing mechanism. However, the viral genes that encode VcircRNAs, and their functions, are poorly studied. In this review, we highlight some new findings about the interaction of host circRNAs and viral infection. Moreover, the potential of VcircRNAs derived from the virus itself, to act as biomarkers and therapeutic targets is summarized.
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Affiliation(s)
- Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Sogol Jamshidi
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, United States.,Department of Dermatology, Harvard Medical School, Boston, MA, United States.,Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marzieh Jamali
- Department of Gynecology and Obstetrics, Mahdieh Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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Naoi T, Kitabayashi S, Kasai A, Sugawara K, Adkar-Purushothama CR, Senda M, Hataya T, Sano T. Suppression of RNA-dependent RNA polymerase 6 in tomatoes allows potato spindle tuber viroid to invade basal part but not apical part including pluripotent stem cells of shoot apical meristem. PLoS One 2020; 15:e0236481. [PMID: 32716919 PMCID: PMC7384629 DOI: 10.1371/journal.pone.0236481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/06/2020] [Indexed: 01/29/2023] Open
Abstract
RNA-dependent RNA polymerase 6 (RDR6) is one of the key factors in plant defense responses and suppresses virus or viroid invasion into shoot apical meristem (SAM) in Nicotiana benthamiana. To evaluate the role of Solanum lycopersicum (Sl) RDR6 upon viroid infection, SlRDR6-suppressed (SlRDR6i) ‘Moneymaker’ tomatoes were generated by RNA interference and inoculated with intermediate or lethal strain of potato spindle tuber viroid (PSTVd). Suppression of SlRDR6 did not change disease symptoms of both PSTVd strains in ‘Moneymaker’ tomatoes. Analysis of PSTVd distribution in shoot apices by in situ hybridization revealed that both PSTVd strains similarly invade the basal part but not apical part including pluripotent stem cells of SAM in SlRDR6i plants at a low rate unlike a previous report in N. benthamiana. In addition, unexpectedly, amount of PSTVd accumulation was apparently lower in SlRDR6i plants than in control tomatoes transformed with empty cassette in early infection especially in the lethal strain. Meanwhile, SlRDR6 suppression did not affect the seed transmission rates of PSTVd. These results indicate that RDR6 generally suppresses PSTVd invasion into SAM in plants, while suppression of RDR6 does not necessarily elevate amount of PSTVd accumulation. Additionally, our results suggest that host factors such as RDR1 other than RDR6 may also be involved in the protection of SAM including pluripotent stem cells from PSTVd invasion and effective RNA silencing causing the decrease of PSTVd accumulation during early infection in tomato plants.
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Affiliation(s)
- Takashi Naoi
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Syoya Kitabayashi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Atsushi Kasai
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Kohei Sugawara
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Charith Raj Adkar-Purushothama
- Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Tatsuji Hataya
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- * E-mail: (TH); (TS)
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
- * E-mail: (TH); (TS)
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49
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Luan W, Dai Y, Li XY, Wang Y, Tao X, Li CX, Mao P, Ma XR. Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid. BMC PLANT BIOLOGY 2020; 20:320. [PMID: 32635887 PMCID: PMC7339384 DOI: 10.1186/s12870-020-02528-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 06/26/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma. RESULTS Here, the RNA-sequencing was implemented to decipher the landscape of tRFs and phasiRNAs in tomato (Solanum lycopersicum) leaves and their responses when foliar spraying exogenous ABA after 24 h. In total, 733 tRFs and 137 phasiRNAs were detected. The tRFs were mainly derived from the tRNAAla transporting alanine, which tended to be cleaved at the 5'terminal guanine site and D loop uracil site to produce tRFAla with length of 20 nt. Most of phasiRNAs originated from NBS-LRR resistance genes. Expression analysis revealed that 156 tRFs and 68 phasiRNAs expressed differentially, respectively. Generally, exogenous ABA mainly inhibited the expression of tRFs and phasiRNAs. Furthermore, integrating analysis of target gene prediction and transcriptome data presented that ABA significantly downregulated the abundance of phsaiRNAs associated with biological and abiotic resistances. Correspondingly, their target genes such as AP2/ERF, WRKY and NBS-LRR, STK and RLK, were mainly up-regulated. CONCLUSIONS Combined with the previous analysis of ABA-response miRNAs, it was speculated that ABA can improve the plant resistances to various stresses by regulating the expression and interaction of small RNAs (such as miRNAs, tRFs, phasiRNAs) and their target genes. This study enriches the plant tRFs and phasiRNAs, providing a vital basis for further investigating ABA response-tRFs and phasiRNAs and their functions in biotic and abiotic stresses.
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Affiliation(s)
- Wei Luan
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Yu Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Cai-Xia Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Ping Mao
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xin-Rong Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu, 610041, Sichuan, People's Republic of China.
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50
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Więsyk A, Lirski M, Fogtman A, Zagórski-Ostoja W, Góra-Sochacka A. Differences in gene expression profiles at the early stage of Solanum lycopersicum infection with mild and severe variants of potato spindle tuber viroid. Virus Res 2020; 286:198090. [PMID: 32634444 DOI: 10.1016/j.virusres.2020.198090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023]
Abstract
Viroids with small, non-coding circular RNA genome can induce diseases in many plant species. The extend of infection symptoms depends on environmental conditions, viroid strain, and host plant species and cultivar. Pathogen recognition leads to massive transcriptional reprogramming to favor defense responses over normal cellular functions. To better understand the interaction between plant host and potato spindle tuber viroid (PSTVd) variants that differ in their virulence, comparative transcriptomic analysis was performed by an RNA-seq approach. The changes of gene expression were analyzed at the time point when subtle symptoms became visible in plants infected with the severe PSTVd-S23 variant, while those infected with the mild PSTVd-M variant looked like non-infected healthy plants. Over 3000 differentially expressed genes (DEGs) were recognized in both infections, but the majority of them were specific for infection with the severe variant. In both infections recognized DEGs were mainly related to biotic stress, hormone metabolism and signaling, transcription regulation, protein degradation, and transport. The DEGs related to cell cycle and microtubule were uniquely down-regulated only in the PSTVd-S23-infected plants. Similarly, expression of transcription factors from C2C2-GATA and growth-regulating factor (GRF) families was only altered upon infection with the severe variant. Both PSTVd variants triggered plant immune response; however expression of genes encoding crucial factors of this process was markedly more changed in the plants infected with the severe variant than in those with the mild one.
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Affiliation(s)
- Aneta Więsyk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland
| | | | - Anna Góra-Sochacka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106, Warsaw, Poland.
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