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Marquez‐Molins J, Gomez G, Pallas V. Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid-host interactions. MOLECULAR PLANT PATHOLOGY 2021; 22:153-162. [PMID: 33305492 PMCID: PMC7814962 DOI: 10.1111/mpp.13022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
TAXONOMY Hop stunt viroid (HSVd) is the type species of the genus Hostuviroid (family Pospiviroidae). The other species of this genus is Dahlia latent viroid, which presents an identical central conserved region (CCR) but lacks other structural hallmarks present in Hop stunt viroid. HSVd replication occurs in the nucleus through an asymmetric rolling-circle model as in the other members of the family Pospiviroidae, which also includes the genera Pospiviroid, Cocadviroid, Apscaviroid, and Coleoviroid. PHYSICAL PROPERTIES Hop stunt viroid consists of a single-stranded, circular RNA of 295-303 nucleotides depending on isolates and sequence variants. The most stable secondary structure is a rod-like or quasi-rod-like conformation with two characteristic domains: a CCR and a terminal conserved hairpin similar to that of cocadviroids. HSVd lacks a terminal conserved region. HOSTS AND SYMPTOMS HSVd infects a very broad range of natural hosts and has been reported to be the causal agent of five different diseases (citrus cachexia, cucumber pale fruit, peach and plum apple apricot distortion, and hop stunt). It is distributed worldwide. TRANSMISSION HSVd is transmitted mechanically and by seed.
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Affiliation(s)
- Joan Marquez‐Molins
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas, Universitat de ValènciaPaternaSpain
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas, Universitat Politècnica de ValènciaValenciaSpain
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas, Universitat de ValènciaPaternaSpain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas, Universitat Politècnica de ValènciaValenciaSpain
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Zhang Z, Xia C, Matsuda T, Taneda A, Murosaki F, Hou W, Owens RA, Li S, Sano T. Effects of Host-Adaptive Mutations on Hop Stunt Viroid Pathogenicity and Small RNA Biogenesis. Int J Mol Sci 2020; 21:ijms21197383. [PMID: 33036282 PMCID: PMC7582576 DOI: 10.3390/ijms21197383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 01/02/2023] Open
Abstract
Accidental transmission of hop stunt viroid (HSVd) from grapevine to hop has led to several epidemics of hop stunt disease with convergent evolution of HSVd-g(rape) into HSVd-h(op) containing five mutations. However, the biological function of these five mutations remains unknown. In this study, we compare the biological property of HSVd-g and HSVd-h by bioassay and analyze HSVd-specific small RNA (HSVd-sRNA) using high-throughput sequencing. The bioassay indicated an association of these five mutations with differences in infectivity, replication capacity, and pathogenicity between HSVd-g and HSVd-h, e.g., HSVd-g induced more severe symptoms than HSVd-h in cucumber. Site-directed mutagenesis of HSVd-g showed that the mutation at position 54 increased pathogenicity. HSVd-sRNA analysis of cucumber and hop plants infected with different HSVd variants showed that several sRNA species containing adaptive nucleotides were specifically down-regulated in plants infected with HSVd-h. Several HSVd-sRNAs containing adaptive mutations were predicted to target cucumber genes, but changes in the levels of these genes were not directly correlated with changes in symptom expression. Furthermore, expression levels of two other cucumber genes targeted by HSVd-RNAs, encoding ethylene-responsive transcription factor ERF011, and trihelix transcription factor GTL2, were altered by HSVd infection. The possible relationship between these two genes to HSVd pathogenicity is discussed.
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Affiliation(s)
- Zhixiang Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Changjian Xia
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Takahiro Matsuda
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
| | - Akito Taneda
- Graduate School of Science and Technology, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan;
| | - Fumiko Murosaki
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
| | - Wanying Hou
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Robert A. Owens
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA;
| | - Shifang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
- Environment and Plant Protection Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (S.L.); (T.S.)
| | - Teruo Sano
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
- Correspondence: (S.L.); (T.S.)
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Visser M, Cook G, Burger JT, Maree HJ. In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection. Virol J 2017; 14:200. [PMID: 29058618 PMCID: PMC5651572 DOI: 10.1186/s12985-017-0871-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/16/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Small RNA (sRNA) associated gene regulation has been shown to play a significant role during plant-pathogen interaction. In commercial citrus orchards co-infection of Citrus tristeza virus (CTV) and viroids occur naturally. METHODS A next-generation sequencing-based approach was used to study the sRNA and transcriptional response in grapefruit to the co-infection of CTV and Citrus dwarfing viroid. RESULTS The co-infection resulted in a difference in the expression of a number of sRNA species when comparing healthy and infected plants; the majority of these were derived from transcripts processed in a phased manner. Several RNA transcripts were also differentially expressed, including transcripts derived from two genes, predicted to be under the regulation of sRNAs. These genes are involved in plant hormone systems; one in the abscisic acid, and the other in the cytokinin regulatory pathway. Additional analysis of virus- and viroid-derived small-interfering RNAs (siRNAs) showed areas on the pathogen genomes associated with increased siRNA synthesis. Most interestingly, the starting position of the p23 silencing suppressor's sub-genomic RNA generated a siRNA hotspot on the CTV genome. CONCLUSIONS This study showed the involvement of various genes, as well as endogenous and exogenous RNA-derived sRNA species in the plant-defence response. The results highlighted the role of sRNA-directed plant hormone regulation during biotic stress, as well as a counter-response of plants to virus suppressors of RNA-silencing.
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Affiliation(s)
- Marike Visser
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Glynnis Cook
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Citrus Research International, Nelspruit, South Africa
| | - Johan T. Burger
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa
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Guo S, Wong SM. Deep sequencing analysis reveals a TMV mutant with a poly(A) tract reduces host defense responses in Nicotiana benthamiana. Virus Res 2017; 239:126-135. [PMID: 28082213 DOI: 10.1016/j.virusres.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/07/2017] [Accepted: 01/08/2017] [Indexed: 12/24/2022]
Abstract
Tobacco mosaic virus (TMV) possesses an upstream pseudoknotted domain (UPD), which is important for replication. After substituting the UPD with an internal poly(A) tract (43 nt), a mutant TMV-43A was constructed. TMV-43A replicated slower than TMV and induced a non-lethal mosaic symptom in Nicotiana benthamiana. In this study, deep sequencing was performed to detect the differences of small RNA profiles between TMV- and TMV-43A-infected N. benthamiana. The results showed that TMV-43A produced lesser amount of virus-derived interfering RNAs (vsiRNAs) than that of TMV. However, the distributions of vsiRNAs generation hotspots between TMV and TMV-43A were similar. Expression of genes related to small RNA biogenesis in TMV-43A-infected N. benthamiana was significantly lower than that of TMV, which leads to generation of lesser vsiRNAs. The expressions of host defense response genes were up-regulated after TMV infection, as compared to TMV-43A-infected plants. Host defense response to TMV-43A infection was lower than that to TMV. The absence of UPD might contribute to the reduced host response to TMV-43A. Our study provides valuable information in the role of the UPD in eliciting host response genes after TMV infection in N. benthamiana. (187 words).
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Affiliation(s)
- Song Guo
- Department of Biological Sciences, National University of Singapore, Republic of Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Republic of Singapore; Temasek Life Sciences Laboratory, Singapore, Republic of Singapore; National University of Singapore Research Institute in Suzhou, Jiangsu, People's Republic of China.
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Lv DQ, Liu SW, Zhao JH, Zhou BJ, Wang SP, Guo HS, Fang YY. Replication of a pathogenic non-coding RNA increases DNA methylation in plants associated with a bromodomain-containing viroid-binding protein. Sci Rep 2016; 6:35751. [PMID: 27767195 PMCID: PMC5073342 DOI: 10.1038/srep35751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/30/2016] [Indexed: 12/23/2022] Open
Abstract
Viroids are plant-pathogenic molecules made up of single-stranded circular non-coding RNAs. How replicating viroids interfere with host silencing remains largely unknown. In this study, we investigated the effects of a nuclear-replicating Potato spindle tuber viroid (PSTVd) on interference with plant RNA silencing. Using transient induction of silencing in GFP transgenic Nicotiana benthamiana plants (line 16c), we found that PSTVd replication accelerated GFP silencing and increased Virp1 mRNA, which encodes bromodomain-containing viroid-binding protein 1 and is required for PSTVd replication. DNA methylation was increased in the GFP transgene promoter of PSTVd-replicating plants, indicating involvement of transcriptional gene silencing. Consistently, accelerated GFP silencing and increased DNA methylation in the of GFP transgene promoter were detected in plants transiently expressing Virp1. Virp1 mRNA was also increased upon PSTVd infection in natural host potato plants. Reduced transcript levels of certain endogenous genes were also consistent with increases in DNA methylation in related gene promoters in PSTVd-infected potato plants. Together, our data demonstrate that PSTVd replication interferes with the nuclear silencing pathway in that host plant, and this is at least partially attributable to Virp1. This study provides new insights into the plant-viroid interaction on viroid pathogenicity by subverting the plant cell silencing machinery.
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MESH Headings
- DNA Methylation
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Green Fluorescent Proteins/genetics
- Plant Diseases/genetics
- Plant Diseases/virology
- Plant Proteins/metabolism
- Plants, Genetically Modified
- Promoter Regions, Genetic
- RNA Interference
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Untranslated/biosynthesis
- RNA, Viral/biosynthesis
- RNA-Binding Proteins/metabolism
- Solanum tuberosum/metabolism
- Solanum tuberosum/virology
- Nicotiana/genetics
- Nicotiana/metabolism
- Nicotiana/virology
- Viroids/genetics
- Viroids/pathogenicity
- Viroids/physiology
- Virus Replication/genetics
- Virus Replication/physiology
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Affiliation(s)
- Dian-Qiu Lv
- Virus-free Seedling Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences Postdoctoral Programme, Harbin, China
| | - Shang-Wu Liu
- Virus-free Seedling Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bang-Jun Zhou
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shao-Peng Wang
- Virus-free Seedling Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Yuan Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Su X, Fu S, Qian Y, Zhang L, Xu Y, Zhou X. Discovery and small RNA profile of Pecan mosaic-associated virus, a novel potyvirus of pecan trees. Sci Rep 2016; 6:26741. [PMID: 27226228 PMCID: PMC4880897 DOI: 10.1038/srep26741] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/06/2016] [Indexed: 11/08/2022] Open
Abstract
A novel potyvirus was discovered in pecan (Carya illinoensis) showing leaf mosaic symptom through the use of deep sequencing of small RNAs. The complete genome of this virus was determined to comprise of 9,310 nucleotides (nt), and shared 24.0% to 58.9% nucleotide similarities with that of other Potyviridae viruses. The genome was deduced to encode a single open reading frame (polyprotein) on the plus strand. Phylogenetic analysis based on the whole genome sequence and coat protein amino acid sequence showed that this virus is most closely related to Lettuce mosaic virus. Using electron microscopy, the typical Potyvirus filamentous particles were identified in infected pecan leaves with mosaic symptoms. Our results clearly show that this virus is a new member of the genus Potyvirus in the family Potyviridae. The virus is tentatively named Pecan mosaic-associated virus (PMaV). Additionally, profiling of the PMaV-derived small RNA (PMaV-sRNA) showed that the most abundant PMaV-sRNAs were 21-nt in length. There are several hotspots for small RNA production along the PMaV genome; two 21-nt PMaV-sRNAs starting at 811 nt and 610 nt of the minus-strand genome were highly repeated.
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Affiliation(s)
- Xiu Su
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin’an 311300, China
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Yajuan Qian
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Liqin Zhang
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin’an 311300, China
| | - Yi Xu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310029, 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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Chen S, Jiang G, Wu J, Liu Y, Qian Y, Zhou X. Characterization of a Novel Polerovirus Infecting Maize in China. Viruses 2016; 8:E120. [PMID: 27136578 PMCID: PMC4885075 DOI: 10.3390/v8050120] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/20/2016] [Accepted: 04/22/2016] [Indexed: 12/17/2022] Open
Abstract
A novel virus, tentatively named Maize Yellow Mosaic Virus (MaYMV), was identified from the field-grown maize plants showing yellow mosaic symptoms on the leaves collected from the Yunnan Province of China by the deep sequencing of small RNAs. The complete 5642 nucleotide (nt)-long genome of the MaYMV shared the highest nucleotide sequence identity (73%) to Maize Yellow Dwarf Virus-RMV. Sequence comparisons and phylogenetic analyses suggested that MaYMV represents a new member of the genus Polerovirus in the family Luteoviridae. Furthermore, the P0 protein encoded by MaYMV was demonstrated to inhibit both local and systemic RNA silencing by co-infiltration assays using transgenic Nicotiana benthamiana line 16c carrying the GFP reporter gene, which further supported the identification of a new polerovirus. The biologically-active cDNA clone of MaYMV was generated by inserting the full-length cDNA of MaYMV into the binary vector pCB301. RT-PCR and Northern blot analyses showed that this clone was systemically infectious upon agro-inoculation into N. benthamiana. Subsequently, 13 different isolates of MaYMV from field-grown maize plants in different geographical locations of Yunnan and Guizhou provinces of China were sequenced. Analyses of their molecular variation indicate that the 3' half of P3-P5 read-through protein coding region was the most variable, whereas the coat protein- (CP-) and movement protein- (MP-)coding regions were the most conserved.
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Affiliation(s)
- Sha Chen
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Guangzhuang Jiang
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jianxiang Wu
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Yong Liu
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha 410125, China.
| | - Yajuan Qian
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Xueping Zhou
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, 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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