1
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Iwata T, Kishikawa T, Seimiya T, Notoya G, Suzuki T, Shibata C, Miyakawa Y, Odawara N, Funato K, Tanaka E, Yamagami M, Sekiba K, Otsuka M, Koike K, Fujishiro M. Satellite double-stranded RNA induces mesenchymal transition in pancreatic cancer by regulating alternative splicing. J Biol Chem 2024; 300:105742. [PMID: 38346537 PMCID: PMC10943486 DOI: 10.1016/j.jbc.2024.105742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/26/2023] [Accepted: 01/29/2024] [Indexed: 03/11/2024] Open
Abstract
Human satellite II (HSATII), composed of tandem repeats in pericentromeric regions, is aberrantly transcribed in epithelial cancers, particularly pancreatic cancer. Dysregulation of repetitive elements in cancer tissues can facilitate incidental dsRNA formation; however, it remains controversial whether dsRNAs play tumor-promoting or tumor-suppressing roles during cancer progression. Therefore, we focused on the double-stranded formation of HSATII RNA and explored its molecular function. The overexpression of double-stranded HSATII (dsHSATII) RNA promoted mesenchymal-like morphological changes and enhanced the invasiveness of pancreatic cancer cells. We identified an RNA-binding protein, spermatid perinuclear RNA-binding protein (STRBP), which preferentially binds to dsHSATII RNA rather than single-stranded HSATII RNA. The mesenchymal transition of dsHSATII-expressing cells was rescued by STRBP overexpression. Mechanistically, STRBP is involved in the alternative splicing of genes associated with epithelial-mesenchymal transition (EMT). We also confirmed that isoform switching of CLSTN1, driven by dsHSATII overexpression or STRBP depletion, induced EMT-like morphological changes. These findings reveal a novel tumor-promoting function of dsHSATII RNA, inducing EMT-like changes and cell invasiveness, thus enhancing our understanding of the biological significance of aberrant expression of satellite arrays in malignant tumors.
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Affiliation(s)
- Takuma Iwata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiro Kishikawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Takahiro Seimiya
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genso Notoya
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsunori Suzuki
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chikako Shibata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yu Miyakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nariaki Odawara
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuyoshi Funato
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Tanaka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mari Yamagami
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuma Sekiba
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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2
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Li M, Zhang X, Huang K, Du Z. Identification of Host Factors Interacting with a γ-Shaped RNA Element from a Plant Virus-Associated Satellite RNA. Viruses 2023; 15:2039. [PMID: 37896816 PMCID: PMC10611174 DOI: 10.3390/v15102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Previously, we identified a highly conserved, γ-shaped RNA element (γRE) from satellite RNAs of cucumber mosaic virus (CMV), and we determined γRE to be structurally required for satRNA survival and the inhibition of CMV replication. It remains unknown how γRE biologically functions. In this work, pull-down assays were used to screen candidates of host factors from Nicotiana benthamiana plants using biotin-labeled γRE as bait. Nine host factors were found to interact specifically with γRE. Then, all of these host factors were down-regulated individually in N. benthamiana plants via tobacco rattle virus-induced gene silencing and tested with infection by GFP-expressing CMV (CMV-gfp) and the isolate T1 of satRNA (sat-T1). Out of nine candidates, three host factors, namely histone H3, GTPase Ran3, and eukaryotic translation initiation factor 4A, were extremely important for infection by CMV-gfp and sat-T1. Moreover, we found that cytosolic glyceraldehyde-3-phosphate dehydrogenase 2 contributed to the replication of CMV and sat-T1, but also negatively regulated CMV 2b activity. Collectively, our work provides essential clues for uncovering the mechanism by which satRNAs inhibit CMV replication.
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Affiliation(s)
| | | | | | - Zhiyou Du
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
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3
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Timcheva K, Dufour S, Touat-Todeschini L, Burnard C, Carpentier MC, Chuffart F, Merret R, Helsmoortel M, Ferré S, Grézy A, Couté Y, Rousseaux S, Khochbin S, Vourc'h C, Bousquet-Antonelli C, Kiernan R, Seigneurin-Berny D, Verdel A. Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression. Cell Rep 2022; 41:111784. [PMID: 36516773 DOI: 10.1016/j.celrep.2022.111784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/01/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
Heat stress (HS) induces a cellular response leading to profound changes in gene expression. Here, we show that human YTHDC1, a reader of N6-methyladenosine (m6A) RNA modification, mostly associates to the chromatin fraction and that HS induces a redistribution of YTHDC1 across the genome, including to heat-induced heat shock protein (HSP) genes. YTHDC1 binding to m6A-modified HSP transcripts co-transcriptionally promotes expression of HSPs. In parallel, hundreds of the genes enriched in YTHDC1 during HS have their transcripts undergoing YTHDC1- and m6A-dependent intron retention. Later, YTHDC1 concentrates within nuclear stress bodies (nSBs) where it binds to m6A-modified SATIII non-coding RNAs, produced in an HSF1-dependent manner upon HS. These findings reveal that YTHDC1 plays a central role in a chromatin-associated m6A-based reprogramming of gene expression during HS. Furthermore, they support the model where the subsequent and temporary sequestration of YTHDC1 within nSBs calibrates the timing of this YTHDC1-dependent gene expression reprogramming.
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Affiliation(s)
- Kalina Timcheva
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Solenne Dufour
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Leila Touat-Todeschini
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Callum Burnard
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Marie-Christine Carpentier
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Florent Chuffart
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Rémy Merret
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Marion Helsmoortel
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Sabrina Ferré
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Aude Grézy
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Yohann Couté
- University Grenoble Alpes, Inserm, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Sophie Rousseaux
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Saadi Khochbin
- Epigenetic Regulations, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Claire Vourc'h
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France
| | - Cécile Bousquet-Antonelli
- University Perpignan Via Domitia, LGDP-UMR5096, 58 Av. Paul Alduy, 66860 Perpignan, France; CNRS LGDP-UMR5096, UPVD, 58 Av. Paul Alduy, 66860 Perpignan, France
| | - Rosemary Kiernan
- Gene Regulation Laboratory, Institut de Génétique Humaine, UMR9002, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Daphné Seigneurin-Berny
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
| | - André Verdel
- RNA, Epigenetics and Stress, Institut pour l'Avancée des Biosciences, CR UGA/Inserm U1209/CNRS UMR5309, Site Santé - Allée des Alpes, 38700 La Tronche, France.
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4
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Abstract
Yellow dwarf viruses are the most economically important and widespread viruses of cereal crops. Although they share common biological properties such as phloem limitation and obligate aphid transmission, the replication machinery and associated cis-acting signals of these viruses fall into two unrelated taxa represented by Barley yellow dwarf virus and Cereal yellow dwarf virus. Here, we explain the reclassification of these viruses based on their very different genomes. We also provide an overview of viral protein functions and their interactions with the host and vector, replication mechanisms of viral and satellite RNAs, and the complex gene expression strategies. Throughout, we point out key unanswered questions in virus evolution, structural biology, and genome function and replication that, when answered, may ultimately provide new tools for virus management.
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Affiliation(s)
- W Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA;
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
| | - Zachary Lozier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA;
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
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5
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Mrkvová M, Hančinský R, Predajňa L, Alaxin P, Achs A, Tomašechová J, Šoltys K, Mihálik D, Olmos A, Ruiz-García AB, Glasa M. High-Throughput Sequencing Discloses the Cucumber Mosaic Virus (CMV) Diversity in Slovakia and Reveals New Hosts of CMV from the Papaveraceae Family. Plants (Basel) 2022; 11:1665. [PMID: 35807616 PMCID: PMC9269241 DOI: 10.3390/plants11131665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Cucumber mosaic virus (CMV; Cucumovirus, Bromoviridae) is an omnipresent virus characterized by a large host range and high genetic variability. Using high-throughput sequencing, we have characterized near complete genomes of 14 Slovak CMV variants from different plant hosts. Of these, three variants originated from the Papaveraceae species (oilseed poppy, common poppy and great celandine), previously poorly described as CMV natural hosts. Based on a BLAST search and phylogenetic analysis, the Slovak CMV isolates can be divided into two genetically different Groups, Ia and II, respectively. The SL50V variant, characterized by a divergent RNA2 sequence, potentially represents a reassortant variant. In four samples (T101, SL50V, CP2, MVU2-21), the presence of satellite CMV RNA was identified along with CMV. Although mechanically transmitted to experimental cucumber plants, the role of satellite RNA in the symptomatology observed could not be established due to a complex infection of original hosts with different viruses.
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Affiliation(s)
- Michaela Mrkvová
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (R.H.); (P.A.); (J.T.); (D.M.)
- National Agricultural and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 92168 Piešt’any, Slovakia
| | - Richard Hančinský
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (R.H.); (P.A.); (J.T.); (D.M.)
- National Agricultural and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 92168 Piešt’any, Slovakia
| | - Lukáš Predajňa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovakia; (L.P.); (A.A.)
| | - Peter Alaxin
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (R.H.); (P.A.); (J.T.); (D.M.)
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovakia; (L.P.); (A.A.)
| | - Adam Achs
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovakia; (L.P.); (A.A.)
| | - Jana Tomašechová
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (R.H.); (P.A.); (J.T.); (D.M.)
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovakia; (L.P.); (A.A.)
| | - Katarína Šoltys
- Department of Microbiology and Virology, Comenius University in Bratislava, Ilkovičova 6, 84104 Bratislava, Slovakia;
| | - Daniel Mihálik
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (R.H.); (P.A.); (J.T.); (D.M.)
- National Agricultural and Food Centre, Research Institute of Plant Production, Bratislavská cesta 122, 92168 Piešt’any, Slovakia
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.O.); (A.B.R.-G.)
| | - Ana Belén Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra, Moncada-Náquera Km 4.5, 46113 Moncada, Spain; (A.O.); (A.B.R.-G.)
| | - Miroslav Glasa
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia; (M.M.); (R.H.); (P.A.); (J.T.); (D.M.)
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovakia; (L.P.); (A.A.)
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Huang YW, Lee CW, Lin NS, Cuong HV, Hu CC, Hsu YH. First Report of Distinct Bamboo mosaic virus (BaMV) Isolates Infecting Bambusa funghomii in Vietnam and the Identification of a Highly Variable Region in the BaMV Genome. Viruses 2022; 14:698. [PMID: 35458428 PMCID: PMC9032891 DOI: 10.3390/v14040698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
New isolates of the Bamboo mosaic virus (BaMV) were identified in Bambusa funghomii bamboo in Vietnam. Sequence analyses revealed that the Vietnam isolates are distinct from all known BaMV strains, sharing the highest sequence identities (about 77%) with the Yoshi isolates reported in California, USA. Unique satellite RNAs were also found to be associated with the BaMV Vietnam isolates. A possible recombination event was detected in the genome of BaMV-VN2. A highly variable region was identified in the ORF1 gene, in between the methyl transferase domain and helicase domain. These results revealed the presence of unique BaMV isolates in an additional bamboo species in one more country, Vietnam, and provided evidence in support of the possible involvement of environmental or host factors in the diversification and evolution of BaMV.
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Affiliation(s)
- Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung 40227, Taiwan; (Y.-W.H.); (C.-W.L.)
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chin-Wei Lee
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung 40227, Taiwan; (Y.-W.H.); (C.-W.L.)
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Ha Viet Cuong
- Department of Plant Pathology, Research Center for Tropic Plant Diseases, Vietnam National University of Agriculture, Hanoi 100915, Vietnam;
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung 40227, Taiwan; (Y.-W.H.); (C.-W.L.)
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, 250 Kuo-Kuang Rd, Taichung 40227, Taiwan; (Y.-W.H.); (C.-W.L.)
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
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7
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Cao M, Zhang S, Liao R, Wang X, Xuan Z, Zhan B, Li Z, Zhang J, Du X, Tang Z, Li S, Zhou Y. Spatial Virome Analysis of Zanthoxylum armatum Trees Affected With the Flower Yellowing Disease. Front Microbiol 2021; 12:702210. [PMID: 34305869 PMCID: PMC8298004 DOI: 10.3389/fmicb.2021.702210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/07/2021] [Indexed: 11/29/2022] Open
Abstract
Zanthoxylum armatum is an important woody crop with multiple applications in pharmaceutics, cosmetics, and food industries. With continuous increases in the plantation area, integrated pest management is required for scale production when diseases caused by biotic factors such as pests and pathogens have become new problems, one of which is the infectious flower yellowing disease (FYD). Here, isolates of a new illarvirus (3) and a new nepovirus-associated subviral satellite RNA (12) were identified in Z. armatum, in addition to 38 new isolates of four previously reported RNA viruses. Sequence variation can be observed in viral/subviral quasispecies and among predominant isolates from the same or different samples and geographic origins. Intriguingly, RNA sequencing of different diseased trees invariably showed an extraordinary pattern of particularly high reads accumulation of the green Sichuan pepper-nepovirus (GSPNeV) and the satellite RNA in symptomatic tissues. In addition, we also examined small RNAs of the satellite RNA, which show similar patterns to those of coinfecting viruses. This study provides further evidence to support association of the FYD with viral/subviral infections and deepens our understanding of the diversity and molecular characteristics of the viruses and satellite, as well as their interactions with the host.
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Affiliation(s)
- Mengji Cao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Song Zhang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Ruiling Liao
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Xiaoru Wang
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Zhiyou Xuan
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Binhui Zhan
- State Key Laboratory of Biology for Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqi Li
- Jiangjin Agricultural Technology Extension Station, Chongqing, China
| | - Jie Zhang
- Bishan Modern Agricultural Development Promotion Center, Chongqing, China
| | - Xinnian Du
- Zhaotong Forestry and Grassland Pest Monitoring and Testing Center, Yunnan, China
| | - Zhengsen Tang
- Zhaotong Forestry and Grassland Pest Monitoring and Testing Center, Yunnan, China
| | - Shifang Li
- State Key Laboratory of Biology for Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yan Zhou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, China
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8
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Mills WK, Lee YCG, Kochendoerfer AM, Dunleavy EM, Karpen GH. RNA from a simple-tandem repeat is required for sperm maturation and male fertility in Drosophila melanogaster. eLife 2019; 8:48940. [PMID: 31687931 PMCID: PMC6879302 DOI: 10.7554/elife.48940] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/03/2019] [Indexed: 11/26/2022] Open
Abstract
Tandemly-repeated DNAs, or satellites, are enriched in heterochromatic regions of eukaryotic genomes and contribute to nuclear structure and function. Some satellites are transcribed, but we lack direct evidence that specific satellite RNAs are required for normal organismal functions. Here, we show satellite RNAs derived from AAGAG tandem repeats are transcribed in many cells throughout Drosophila melanogaster development, enriched in neurons and testes, often localized within heterochromatic regions, and important for viability. Strikingly, we find AAGAG transcripts are necessary for male fertility, and that AAGAG RNA depletion results in defective histone-protamine exchange, sperm maturation and chromatin organization. Since these events happen late in spermatogenesis when the transcripts are not detected, we speculate that AAGAG RNA in primary spermatocytes ‘primes’ post-meiosis steps for sperm maturation. In addition to demonstrating essential functions for AAGAG RNAs, comparisons between closely related Drosophila species suggest that satellites and their transcription evolve quickly to generate new functions.
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Affiliation(s)
- Wilbur Kyle Mills
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Yuh Chwen G Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | | | - Elaine M Dunleavy
- Centre for Chromosome Biology, National University of Ireland, Galway, Ireland
| | - Gary H Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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9
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Cao X, Liu S, Yu C, Li X, Yuan X. A new strategy of using satellite RNA to control viral plant diseases: post-inoculation with satellite RNA attenuates symptoms derived from pre-infection with its helper virus. Plant Biotechnol J 2019; 17:1856-1858. [PMID: 31050095 PMCID: PMC6737017 DOI: 10.1111/pbi.13145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/14/2019] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Xinran Cao
- Department of Plant PathologyCollege of Plant ProtectionShandong Agricultural UniversityShandong Province Key Laboratory of Agricultural MicrobiologyTai'anChina
- Yantai Agricultural Technology Extension CenterYantaiChina
| | - Shanshan Liu
- Department of Plant PathologyCollege of Plant ProtectionShandong Agricultural UniversityShandong Province Key Laboratory of Agricultural MicrobiologyTai'anChina
| | - Chengming Yu
- Department of Plant PathologyCollege of Plant ProtectionShandong Agricultural UniversityShandong Province Key Laboratory of Agricultural MicrobiologyTai'anChina
| | - Xiangdong Li
- Department of Plant PathologyCollege of Plant ProtectionShandong Agricultural UniversityShandong Province Key Laboratory of Agricultural MicrobiologyTai'anChina
| | - Xuefeng Yuan
- Department of Plant PathologyCollege of Plant ProtectionShandong Agricultural UniversityShandong Province Key Laboratory of Agricultural MicrobiologyTai'anChina
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10
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Wrzesińska B, Dai Vu L, Gevaert K, De Smet I, Obrępalska-Stęplowska A. Peanut Stunt Virus and Its Satellite RNA Trigger Changes in Phosphorylation in N. benthamiana Infected Plants at the Early Stage of the Infection. Int J Mol Sci 2018; 19:E3223. [PMID: 30340407 PMCID: PMC6214028 DOI: 10.3390/ijms19103223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/11/2018] [Accepted: 10/16/2018] [Indexed: 11/16/2022] Open
Abstract
Signaling in host plants is an integral part of a successful infection by pathogenic RNA viruses. Therefore, identifying early signaling events in host plants that play an important role in establishing the infection process will help our understanding of the disease process. In this context, phosphorylation constitutes one of the most important post-translational protein modifications, regulating many cellular signaling processes. In this study, we aimed to identify the processes affected by infection with Peanut stunt virus (PSV) and its satellite RNA (satRNA) in Nicotiana benthamiana at the early stage of pathogenesis. To achieve this, we performed proteome and phosphoproteome analyses on plants treated with PSV and its satRNA. The analysis of the number of differentially phosphorylated proteins showed strong down-regulation in phosphorylation in virus-treated plants (without satRNA). Moreover, proteome analysis revealed more down-regulated proteins in PSV and satRNA-treated plants, which indicated a complex dependence between proteins and their modifications. Apart from changes in photosynthesis and carbon metabolism, which are usually observed in virus-infected plants, alterations in proteins involved in RNA synthesis, transport, and turnover were observed. As a whole, this is the first community (phospho)proteome resource upon infection of N. benthamiana with a cucumovirus and its satRNA and this resource constitutes a valuable data set for future studies.
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Affiliation(s)
- Barbara Wrzesińska
- Institute of Plant Protection-National Research Institute, Department of Entomology, Animal Pests and Biotechnology, Władysława Węgorka 20, 60-318 Poznań, Poland.
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium.
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium.
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.
- VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium.
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium.
- VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Ghent, Belgium.
| | - Aleksandra Obrępalska-Stęplowska
- Institute of Plant Protection-National Research Institute, Department of Entomology, Animal Pests and Biotechnology, Władysława Węgorka 20, 60-318 Poznań, Poland.
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11
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Obrępalska-Stęplowska A, Zmienko A, Wrzesińska B, Goralski M, Figlerowicz M, Zyprych-Walczak J, Siatkowski I, Pospieszny H. The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA. Viruses 2018; 10:E449. [PMID: 30142955 PMCID: PMC6165542 DOI: 10.3390/v10090449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 01/22/2023] Open
Abstract
Peanut stunt virus (PSV) is a widespread disease infecting legumes. The PSV strains are classified into four subgroups and some are defined by the association of satellite RNAs (satRNAs). In the case of PSV, the presence of satRNAs alters the symptoms of disease in infected plants. In this study, we elucidated the plant response to PSV-G strain, which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA, which exacerbated pathogenesis in Nicotiana benthamiana. To explain the mechanisms underlying PSV infection and symptoms exacerbation caused by satRNA, we carried out transcriptome profiling of N. benthamiana challenged by PSV-G and satRNA using species-specific microarrays. Co-infection of plants with PSV-G + satRNA increased the number of identified differentially expressed genes (DEGs) compared with the number identified in PSV-G-infected plants. In both treatments, the majority of up-regulated DEGs were engaged in translation, ribosome biogenesis, RNA metabolism, and response to stimuli, while the down-regulated DEGs were required for photosynthesis. The presence of satRNA in PSV-G-infected plants caused different trends in expression of DEGs associated with phosphorylation, ATP binding, and plasma membrane.
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Affiliation(s)
- Aleksandra Obrępalska-Stęplowska
- Department of Entomology, Animal Pests and Biotechnology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
- Institute of Computing Science, Faculty of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965 Poznań, Poland.
| | - Barbara Wrzesińska
- Department of Entomology, Animal Pests and Biotechnology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
| | - Michal Goralski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
- Institute of Computing Science, Faculty of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965 Poznań, Poland.
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, University of Life Sciences in Poznań, Wojska Polskiego 28 Street, 60-637 Poznań, Poland.
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, University of Life Sciences in Poznań, Wojska Polskiego 28 Street, 60-637 Poznań, Poland.
| | - Henryk Pospieszny
- Department of Virology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
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Abstract
Nucleus is the residence and place of work for a plethora of long noncoding RNAs. Here, we provide a summary of the functions and functional mechanisms of several relatively well studied examples of nuclear long noncoding RNAs (lncRNAs) in the nucleus, such as Xist, NEAT1, MALAT1 and TERRA. The recently identified novel EIciRNA is also highlighted. These nuclear lncRNAs play a variety of roles with diverse molecular mechanisms in animal cells. We also discuss insights and concerns about current and future studies of nuclear lnc RNAs.
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Affiliation(s)
- Bin Yu
- a The CAS Key Laboratory of Innate Immunity and Chronic Disease , CAS Center for Excellence in Molecular Cell Science , School of Life Sciences , University of Science and Technology of China , Hefei , Anhui Province , China
| | - Ge Shan
- a The CAS Key Laboratory of Innate Immunity and Chronic Disease , CAS Center for Excellence in Molecular Cell Science , School of Life Sciences , University of Science and Technology of China , Hefei , Anhui Province , China
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13
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Abstract
Satellite RNAs (satRNAs) are sub-viral agents that may interact with their cognate helper virus (HV) and host plant synergistically and/or antagonistically. SatRNAs totally depend on the HV for replication, so satRNAs and HV usually evolve similar secondary or tertiary RNA structures that are recognized by a replication complex, although satRNAs and HV do not share an appreciable sequence homology. The satRNAs of Bamboo mosaic virus (satBaMV), the only satRNAs of the genus Potexvirus, have become one of the models of how satRNAs can modulate HV replication and virus-induced symptoms. In this review, we summarize the molecular mechanisms underlying the interaction of interfering satBaMV and BaMV. Like other satRNAs, satBaMV mimics the secondary structures of 5'- and 3'-untranslated regions (UTRs) of BaMV as a molecular pretender. However, a conserved apical hairpin stem loop (AHSL) in the 5'-UTR of satBaMV was found as the key determinant for downregulating BaMV replication. In particular, two unique nucleotides (C60 and C83) in the AHSL of satBaMVs determine the satBaMV interference ability by competing for the replication machinery. Thus, transgenic plants expressing interfering satBaMV could confer resistance to BaMV, and interfering satBaMV could be used as biological-control agent. Unlike two major anti-viral mechanisms, RNA silencing and salicylic acid-mediated immunity, our findings in plants by in vivo competition assay and RNA deep sequencing suggested replication competition is involved in this transgenic satBaMV-mediated BaMV interference. We propose how a single nucleotide of satBaMV can make a great change in BaMV pathogenicity and the underlying mechanism.
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Affiliation(s)
- Kuan-Yu Lin
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
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Xu J, Liu D, Zhang Y, Wang Y, Han C, Li D, Yu JL, Wang XB. Improved Pathogenicity of a Beet Black Scorch Virus Variant by Low Temperature and Co-infection with Its Satellite RNA. Front Microbiol 2016; 7:1771. [PMID: 27867378 PMCID: PMC5095503 DOI: 10.3389/fmicb.2016.01771] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/21/2016] [Indexed: 01/26/2023] Open
Abstract
Co-infection of none-coding satellite RNAs (sat-RNAs) usually inhibits replication and attenuates disease symptoms of helper viruses. However, we find that the sat-RNA of Beet black scorch virus (BBSV) and low temperature (18°C) additively enhance the systemic infection of BBSV in Nicotiana benthamiana. Northern blotting hybridization revealed a relatively reduced accumulation of BBSV-derived small interfering RNAs (siRNAs) in presence of sat-RNA as compared to that of BBSV alone. Cloning and sequencing of total small RNAs showed that more than 50% of the total small RNAs sequenced from BBSV-infected plants were BBSV-siRNAs, whereas the abundance of sat-siRNAs were higher than BBSV-siRNAs in the sat-RNA co-infected plants, indicating that the sat-RNA occupies most of the silencing components and possibly relieves the RNA silencing-mediated defense against BBSV. Interestingly, the 5' termini of siRNAs derived from BBSV and sat-RNA were dominated by Uridines (U) and Adenines (A), respectively. Besides, the infection of BBSV alone and with sat-RNA induce down-regulation of miR168 and miR403, respectively, which leads to high accumulation of their targets, Argonaute 1 (AGO1) and AGO2. Our work reveals the profiles of siRNAs of BBSV and sat-RNA and provides an additional clue to investigate the complicated interaction between the helper virus and sat-RNA.
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Affiliation(s)
- Jin Xu
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural SciencesBeijing, China
| | - Deshui Liu
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Yongliang Zhang
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Ying Wang
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Chenggui Han
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Jia-Lin Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
| | - Xian-Bing Wang
- State Key Laboratory of Agro-Biotechnology, China Agricultural UniversityBeijing, China
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15
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Obrępalska-Stęplowska A, Renaut J, Planchon S, Przybylska A, Wieczorek P, Barylski J, Palukaitis P. Corrigendum: Effect of temperature on the pathogenesis, accumulation of viral and satellite RNAs and on plant proteome in peanut stunt virus and satellite RNA-infected plants. Front Plant Sci 2016; 7:839. [PMID: 27375674 PMCID: PMC4894900 DOI: 10.3389/fpls.2016.00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 05/27/2016] [Indexed: 06/06/2023]
Abstract
[This corrects the article on p. 903 in vol. 6, PMID: 26579153.].
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Affiliation(s)
| | - Jenny Renaut
- Department of Environmental Research and Innovation, Integrative Biology Facility, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Sebastien Planchon
- Department of Environmental Research and Innovation, Integrative Biology Facility, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Arnika Przybylska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection—National Research InstitutePoznań, Poland
| | - Przemysław Wieczorek
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection—National Research InstitutePoznań, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz UniversityPoznań, Poland
| | - Peter Palukaitis
- Department of Horticultural Sciences, Seoul Women UniversitySeoul, South Korea
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Chaturvedi S, Rao ALN. A shift in plant proteome profile for a Bromodomain containing RNA binding Protein (BRP1) in plants infected with Cucumber mosaic virus and its satellite RNA. J Proteomics 2016; 131:1-7. [PMID: 26463137 DOI: 10.1016/j.jprot.2015.09.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/03/2015] [Accepted: 09/30/2015] [Indexed: 12/18/2022]
Abstract
Host proteins are the integral part of a successful infection caused by a given RNA virus pathogenic to plants. Therefore, identification of crucial host proteins playing an important role in establishing the infection process is likely to help in devising approaches to curbing disease spread. Cucumber mosaic virus (Q-CMV) and its satellite RNA (QsatRNA) are important pathogens of many economically important crop plants worldwide. In a previous study, we demonstrated the biological significance of a Bromodomain containing RNA-binding Protein (BRP1) in the infection cycle of QsatRNA, making BRP1 an important host protein to study. To further shed a light on the mechanistic role of BRP1 in the replication of Q-CMV and QsatRNA, we analyzed the Nicotiana benthamiana host protein interactomes either for BRP1 alone or in the presence of Q-CMV or QsatRNA. Co-immunoprecipitation, followed by LC-MS/MS analysis of BRP1-FLAG on challenging with Q-CMV or QsatRNA has led us to observe a shift in the host protein interactome of BRP1. We discuss the significance of these results in relation to Q-CMV and its QsatRNA infection cycle. BIOLOGICAL SIGNIFICANCE Host proteins play an important role in replication and infection of eukaryotic cells by a wide-range of RNA viruses pathogenic to humans, animals and plants. Since a given eukaryotic cell typically contains ~30,000 different proteins, recent advances made in proteomics and bioinformatics approaches allowed the identification of host proteins critical for viral replication and pathogenesis. Although Cucumber mosaic virus (CMV) and its satRNA are well characterized at molecular level, information concerning the network of host factors involved in their replication and pathogenesis is still on its infancy. We have recently observed that a Bromodomain containing host protein (BRP1) is obligatory to transport satRNA to the nucleus. Consequently, it is imperative to apply proteomics and bioinformatics approaches in deciphering how host interactome network regulates the replication of CMV and its satRNA. In this study, first we established the importance of BRP1 in CMV replication. Then, application of co-immunoprecipitation in conjunction with LC-MS/MS allowed the identification of a wide range of host proteins that are associated with the replication of CMV and its satRNA. Interestingly, a shift in the plant proteome was observed when plants infected with CMV were challenged with its satRNA.
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Affiliation(s)
- Sonali Chaturvedi
- Department of Plant Pathology & Microbiology, University of California, Riverside, CA 92521, United States
| | - A L N Rao
- Department of Plant Pathology & Microbiology, University of California, Riverside, CA 92521, United States.
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17
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Sõmera M, Sarmiento C, Truve E. Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae. Viruses 2015; 7:3076-115. [PMID: 26083319 PMCID: PMC4488728 DOI: 10.3390/v7062761] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/18/2015] [Accepted: 06/02/2015] [Indexed: 12/26/2022] Open
Abstract
The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.
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Affiliation(s)
- Merike Sõmera
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Cecilia Sarmiento
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Erkki Truve
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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18
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Shen WX, Au PCK, Shi BJ, Smith NA, Dennis ES, Guo HS, Zhou CY, Wang MB. Satellite RNAs interfere with the function of viral RNA silencing suppressors. Front Plant Sci 2015; 6:281. [PMID: 25964791 PMCID: PMC4408847 DOI: 10.3389/fpls.2015.00281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/08/2015] [Indexed: 05/05/2023]
Abstract
Viral satellite RNAs (satRNAs) are small subviral RNAs and depend on the helper virus for replication and spread. satRNAs can attenuate helper virus-induced symptoms, the mechanism of which remains unclear. Here, we show that two virus-encoded suppressors of RNA silencing (VSRs), Cucumber mosaic virus (CMV) 2b and Tombusvirus P19, suppress hairpin RNA (hpRNA)-induced silencing of a β-glucuronidase (GUS) gene in Nicotiana benthamiana. This suppression can be overcome by CMV Y-satellite RNA (Y-Sat) via the Y-Sat-derived small interfering RNAs (siRNAs), which bind to the VSRs and displace the bound hpGUS-derived siRNAs. We also show that microRNA target gene expression in N. tabacum was elevated by CMV infection, presumably due to function of the 2b VSR, but this upregulation of microRNA target genes was reversed in the presence of Y-Sat. These results suggest that satRNA infection minimizes the effect of VSRs on host siRNA and microRNA-directed silencing. Our results suggest that the high abundance of satRNA-derived siRNAs contributes to symptom attenuation by binding helper virus-encoded VSRs, minimizing the capacity of the VSRs to bind host siRNA and miRNA and interfere with their function.
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Affiliation(s)
- Wan-Xia Shen
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
- Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
| | - Phil Chi Khang Au
- Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
| | - Bu-Jun Shi
- Department of Plant Science, Waite Institute, Adelaide UniversityGlen Osmond, SA, Australia
| | - Neil A. Smith
- Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of SciencesBeijing, China
| | - Chang-Yong Zhou
- National Citrus Engineering Research Center, Citrus Research Institute, Southwest UniversityChongqing, China
| | - Ming-Bo Wang
- Commonwealth Scientific and Industrial Research Organisation Plant IndustryCanberra, ACT, Australia
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19
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Obrępalska-Stęplowska A, Renaut J, Planchon S, Przybylska A, Wieczorek P, Barylski J, Palukaitis P. Effect of temperature on the pathogenesis, accumulation of viral and satellite RNAs and on plant proteome in peanut stunt virus and satellite RNA-infected plants. Front Plant Sci 2015; 6:903. [PMID: 26579153 PMCID: PMC4625170 DOI: 10.3389/fpls.2015.00903] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/09/2015] [Indexed: 05/08/2023]
Abstract
Temperature is an important environmental factor influencing plant development in natural and diseased conditions. The growth rate of plants grown at C27°C is more rapid than for plants grown at 21°C. Thus, temperature affects the rate of pathogenesis progression in individual plants. We have analyzed the effect of temperature conditions (either 21°C or 27°C during the day) on the accumulation rate of the virus and satellite RNA (satRNA) in Nicotiana benthamiana plants infected by peanut stunt virus (PSV) with and without its satRNA, at four time points. In addition, we extracted proteins from PSV and PSV plus satRNA-infected plants harvested at 21 dpi, when disease symptoms began to appear on plants grown at 21°C and were well developed on those grown at 27°C, to assess the proteome profile in infected plants compared to mock-inoculated plants grown at these two temperatures, using 2D-gel electrophoresis and mass spectrometry approaches. The accumulation rate of the viral RNAs and satRNA was more rapid at 27°C at the beginning of the infection and then rapidly decreased in PSV-infected plants. At 21 dpi, PSV and satRNA accumulation was higher at 21°C and had a tendency to increase further. In all studied plants grown at 27°C, we observed a significant drop in the identified proteins participating in photosynthesis and carbohydrate metabolism at the proteome level, in comparison to plants maintained at 21°C. On the other hand, the proteins involved in protein metabolic processes were all more abundant in plants grown at 27°C. This was especially evident when PSV-infected plants were analyzed, where increase in abundance of proteins involved in protein synthesis, degradation, and folding was revealed. In mock-inoculated and PSV-infected plants we found an increase in abundance of the majority of stress-related differently-regulated proteins and those associated with protein metabolism. In contrast, in PSV plus satRNA-infected plants the shift in the temperature barely increased the level of stress-related proteins.
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Affiliation(s)
- Aleksandra Obrępalska-Stęplowska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection – National Research InstitutePoznań, Poland
- *Correspondence: Aleksandra Obrępalska-Stęplowska
| | - Jenny Renaut
- Department Environmental Research and Innovation, Integrative Biology Facility, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Sebastien Planchon
- Department Environmental Research and Innovation, Integrative Biology Facility, Luxembourg Institute of Science and TechnologyBelvaux, Luxembourg
| | - Arnika Przybylska
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection – National Research InstitutePoznań, Poland
| | - Przemysław Wieczorek
- Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection – National Research InstitutePoznań, Poland
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz UniversityPoznań, Poland
| | - Peter Palukaitis
- Department of Horticultural Sciences, Seoul Women UniversitySeoul, South Korea
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20
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Liou MR, Huang YW, Hu CC, Lin NS, Hsu YH. A dual gene-silencing vector system for monocot and dicot plants. Plant Biotechnol J 2014; 12:330-43. [PMID: 24283212 DOI: 10.1111/pbi.12140] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/18/2013] [Accepted: 10/14/2013] [Indexed: 05/16/2023]
Abstract
Plant virus-based gene-silencing vectors have been extensively and successfully used to elucidate functional genomics in plants. However, only limited virus-induced gene-silencing (VIGS) vectors can be used in both monocot and dicot plants. Here, we established a dual gene-silencing vector system based on Bamboo mosaic virus (BaMV) and its satellite RNA (satBaMV). Both BaMV and satBaMV vectors could effectively silence endogenous genes in Nicotiana benthamiana and Brachypodium distachyon. The satBaMV vector could also silence the green fluorescent protein (GFP) transgene in GFP transgenic N. benthamiana. GFP transgenic plants co-agro-inoculated with BaMV and satBaMV vectors carrying sulphur and GFP genes, respectively, could simultaneously silence both genes. Moreover, the silenced plants could still survive with the silencing of genes essential for plant development such as heat-shock protein 90 (Hsp90) and Hsp70. In addition, the satBaMV- but not BaMV-based vector could enhance gene-silencing efficiency in newly emerging leaves of N. benthamiana deficient in RNA-dependant RNA polymerase 6. The dual gene-silencing vector system of BaMV and satBaMV provides a novel tool for comparative functional studies in monocot and dicot plants.
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Affiliation(s)
- Ming-Ru Liou
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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21
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Cho S, Cho Y, Lee S, Kim J, Yum H, Kim SC, Cho BK. Current challenges in bacterial transcriptomics. Genomics Inform 2013; 11:76-82. [PMID: 23843773 PMCID: PMC3704930 DOI: 10.5808/gi.2013.11.2.76] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 05/20/2013] [Accepted: 05/23/2013] [Indexed: 11/29/2022] Open
Abstract
Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.
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Affiliation(s)
- Suhyung Cho
- Department of Biological Sciences and KAIST Institute for the BioCentury, Intelligent Synthetic Biology Center, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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Hu CC, Hsu YH, Lin NS. Satellite RNAs and Satellite Viruses of Plants. Viruses 2009; 1:1325-50. [PMID: 21994595 DOI: 10.3390/v1031325] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 12/07/2009] [Accepted: 12/07/2009] [Indexed: 12/24/2022] Open
Abstract
The view that satellite RNAs (satRNAs) and satellite viruses are purely molecular parasites of their cognate helper viruses has changed. The molecular mechanisms underlying the synergistic and/or antagonistic interactions among satRNAs/satellite viruses, helper viruses, and host plants are beginning to be comprehended. This review aims to summarize the recent achievements in basic and practical research, with special emphasis on the involvement of RNA silencing mechanisms in the pathogenicity, population dynamics, and, possibly, the origin(s) of these subviral agents. With further research following current trends, the comprehensive understanding of satRNAs and satellite viruses could lead to new insights into the trilateral interactions among host plants, viruses, and satellites.
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Sikora EJ, Gudauskas RT, Murphy JF, Porch DW, Andrianifahanana M, Zehnder GW, Bauske EM, Kemble JM, Lester DF. A Multivirus Epidemic of Tomatoes in Alabama. Plant Dis 1998; 82:117-120. [PMID: 30857044 DOI: 10.1094/pdis.1998.82.1.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
During 1992, a multivirus epidemic reduced tomato production by as much as 25% in the major tomato-growing region of Alabama. Estimated yield losses of 100% resulted from the epidemic in over 250 ha in two counties of North Alabama. Cucumber mosaic cucumovirus (CMV), alone or in combination with potato potyvirus Y (PVY) and/or tobacco etch potyvirus (TEV), was responsible for the crop failure. CMV was detected alone or in combination with PVY and/or TEV in over 70% of the samples tested and was present in 90% of the fields surveyed. In 1993, 21 tomato fields were monitored weekly from transplanting through harvest for CMV, PVY, TEV, tobacco mosaic tobamovirus, and tomato spotted wilt tospovirus. All 5 viruses were detected, with CMV occurring most frequently. Incidence of CMV at the 61% level or higher was found in 16 of the 21 fields surveyed. Tomatoes transplanted in April and May were least effected and had relatively low virus incidence until late in their development. Tomatoes transplanted in June and July were infected at an earlier age, had the highest virus incidence, were the most severely affected, and suffered the greatest loss in yield. In 1994,Aphis gossypii, the cotton aphid, was the most common virus vector found during an aphid monitoring/virus spread study. Populations of A. gossypii peaked in late June, immediately preceding a period of rapid CMV incidence and spread.
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Affiliation(s)
| | | | - John F Murphy
- Assistant Professor, Department of Plant Pathology, Auburn University, Auburn, AL 36849
| | - Daniel W Porch
- Associate County Agent, Blount County, Oneonta, AL 35121
| | | | | | - Ellen M Bauske
- Extension Associate, Department of Horticulture, Auburn University
| | - Joseph M Kemble
- Assistant Professor, Department of Horticulture, Auburn University
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