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Prajapati MR, Thapa P, Diksha D, Sharma SK, Gupta N, Baranwal VK. Complete genome sequence of grapevine yellow speckle viroid 3, a novel apscaviroid infecting grapevine, characterized by high-throughput sequencing. Arch Virol 2024; 169:194. [PMID: 39249561 DOI: 10.1007/s00705-024-06128-x] [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: 04/04/2024] [Accepted: 07/25/2024] [Indexed: 09/10/2024]
Abstract
A novel grapevine viroid was discovered in an asymptomatic grapevine of Indian rootstocks. The whole genome sequence of the viroid (370 nt) was determined by high-throughput sequencing as well as RT-PCR followed by cloning and Sanger sequencing. The terminal conserved region (TCR), central conserved region (CCR) upper strand, and CCR lower strand are conserved regions found in the viroid that are unique to the members of the genus Apscaviroid. Based on our findings and the demarcation criteria for viroids, the novel viroid, which we have tentatively named "grapevine yellow speckle viroid 3" is a putative new member of the genus Apscaviroid.
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Affiliation(s)
| | - Pooja Thapa
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Damini Diksha
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Nitika Gupta
- ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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2
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Hao J, Ma J, Wang Y. Understanding viroids, endogenous circular RNAs, and viroid-like RNAs in the context of biogenesis. PLoS Pathog 2024; 20:e1012299. [PMID: 38935625 PMCID: PMC11210808 DOI: 10.1371/journal.ppat.1012299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024] Open
Affiliation(s)
- Jie Hao
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Junfei Ma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Ying Wang
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
- Plant Molecular and Cell Biology Program, University of Florida, Gainesville, Florida, United States of America
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3
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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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4
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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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5
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Nie Y, Zhang Y, Wu J. The Secondary Structure of Potato Spindle Tuber Viroid Determines Its Infectivity in Nicotiana benthamiana. Viruses 2023; 15:2307. [PMID: 38140547 PMCID: PMC10748084 DOI: 10.3390/v15122307] [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: 09/08/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
The function of RNAs is determined by their structure. However, studying the relationship between RNA structure and function often requires altering RNA sequences to modify the structures, which leads to the neglect of the importance of RNA sequences themselves. In our research, we utilized potato spindle tuber viroid (PSTVd), a circular-form non-coding infectious RNA, as a model with which to investigate the role of a specific rod-like structure in RNA function. By generating linear RNA transcripts with different start sites, we established 12 PSTVd forms with different secondary structures while maintaining the same sequence. The RNA secondary structures were predicted using the mfold tool and validated through native PAGE gel electrophoresis after in vitro RNA folding. Analysis using plant infection assays revealed that the formation of a correct rod-like structure is crucial for the successful infection of PSTVd. Interestingly, the inability of PSTVd forms with non-rod-like structures to infect plants could be partially compensated by increasing the amount of linear viroid RNA transcripts, suggesting the existence of additional RNA secondary structures, such as the correct rod-like structure, alongside the dominant structure in the RNA inoculum of these forms. Our study demonstrates the critical role of RNA secondary structures in determining the function of infectious RNAs.
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Affiliation(s)
| | | | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (Y.N.); (Y.Z.)
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Ma J, Dissanayaka Mudiyanselage SD, Hao J, Wang Y. Cellular roadmaps of viroid infection. Trends Microbiol 2023; 31:1179-1191. [PMID: 37349206 PMCID: PMC10592528 DOI: 10.1016/j.tim.2023.05.014] [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: 03/16/2023] [Revised: 05/28/2023] [Accepted: 05/31/2023] [Indexed: 06/24/2023]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. According to the International Committee on Taxonomy of Viruses, there are 44 viroids known to date. Notably, more than 20 000 distinct viroid-like RNA sequences have recently been identified in existing sequencing datasets, suggesting an unprecedented complexity in biological roles of viroids and viroid-like RNAs. Interestingly, a human pathogen, hepatitis delta virus (HDV), also replicates via a rolling circle mechanism like viroids. Therefore, knowledge of viroid infection is informative for research on HDV and other viroid-like RNAs reported from various organisms. Here, we summarize recent advancements in understanding viroid shuttling among subcellular compartments for completing replication cycles, emphasizing regulatory roles of RNA motifs and structural dynamics in diverse biological processes. We also compare the knowledge of viroid intracellular trafficking with known pathways governing cellular RNA movement in cells. Future investigations on regulatory RNA structures and cognate factors in regulating viroid subcellular trafficking and replication will likely provide new insights into RNA structure-function relationships and facilitate the development of strategies controlling RNA localization and function in cells.
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Affiliation(s)
- Junfei Ma
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Jie Hao
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA.
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7
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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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8
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Chong LC, Lauber C. Viroid-like RNA-dependent RNA polymerase-encoding ambiviruses are abundant in complex fungi. Front Microbiol 2023; 14:1144003. [PMID: 37275138 PMCID: PMC10237039 DOI: 10.3389/fmicb.2023.1144003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
Ambiviruses are hybrid infectious elements encoding the hallmark gene of RNA viruses, the RNA-dependent RNA polymerase, and self-cleaving RNA ribozymes found in many viroids. Ambiviruses are thought to be pathogens of fungi, although the majority of reported genomes have been identified in metatranscriptomes. Here, we present a comprehensive screen for ambiviruses in more than 46,500 fungal transcriptomes from the Sequence Read Archive (SRA). Our data-driven virus discovery approach identified more than 2,500 ambiviral sequences across the kingdom Fungi with a striking expansion in members of the phylum Basidiomycota representing the most complex fungal organisms. Our study unveils a large diversity of unknown ambiviruses with as little as 27% protein sequence identity to known members and sheds new light on the evolution of this distinct class of infectious agents with RNA genomes. No evidence for the presence of ambiviruses in human microbiomes was obtained from a comprehensive screen of respective metatranscriptomes available in the SRA.
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Lee BD, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M, Simmonds P, Kyrpides N, Gophna U, Dolja VV, Koonin EV. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell 2023; 186:646-661.e4. [PMID: 36696902 PMCID: PMC9911046 DOI: 10.1016/j.cell.2022.12.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
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Affiliation(s)
- Benjamin D Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Antonio Pedro Camargo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Ribeiro TP, Vasquez DDN, Macedo LLP, Lourenço-Tessutti IT, Valença DC, Oliveira-Neto OB, Paes-de-Melo B, Rodrigues-Silva PL, Firmino AAP, Basso MF, Lins CBJ, Neves MR, Moura SM, Tripode BMD, Miranda JE, Silva MCM, Grossi-de-Sa MF. Stabilized Double-Stranded RNA Strategy Improves Cotton Resistance to CBW ( Anthonomus grandis). Int J Mol Sci 2022; 23:13713. [PMID: 36430188 PMCID: PMC9691246 DOI: 10.3390/ijms232213713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/11/2022] Open
Abstract
Cotton is the most important crop for fiber production worldwide. However, the cotton boll weevil (CBW) is an insect pest that causes significant economic losses in infested areas. Current control methods are costly, inefficient, and environmentally hazardous. Herein, we generated transgenic cotton lines expressing double-stranded RNA (dsRNA) molecules to trigger RNA interference-mediated gene silencing in CBW. Thus, we targeted three essential genes coding for chitin synthase 2, vitellogenin, and ecdysis-triggering hormone receptor. The stability of expressed dsRNAs was improved by designing a structured RNA based on a viroid genome architecture. We transformed cotton embryos by inserting a promoter-driven expression cassette that overexpressed the dsRNA into flower buds. The transgenic cotton plants were characterized, and positive PCR transformed events were detected with an average heritability of 80%. Expression of dsRNAs was confirmed in floral buds by RT-qPCR, and the T1 cotton plant generation was challenged with fertilized CBW females. After 30 days, data showed high mortality (around 70%) in oviposited yolks. In adult insects fed on transgenic lines, chitin synthase II and vitellogenin showed reduced expression in larvae and adults, respectively. Developmental delays and abnormalities were also observed in these individuals. Our data remark on the potential of transgenic cotton based on a viroid-structured dsRNA to control CBW.
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Affiliation(s)
- Thuanne P. Ribeiro
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- Biotechnology and Molecular Biology Department, Federal University of Brasilia (UnB), Brasilia 70910-900, DF, Brazil
| | - Daniel D. N. Vasquez
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- Genetic and Molecular Biology Department, Catholic University of Brasilia (UCB), Brasilia 71966-700, DF, Brazil
| | - Leonardo L. P. Macedo
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Embrapa, Brasilia 70770-917, DF, Brazil
| | - Isabela T. Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Embrapa, Brasilia 70770-917, DF, Brazil
| | - David C. Valença
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
| | - Osmundo B. Oliveira-Neto
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Embrapa, Brasilia 70770-917, DF, Brazil
- Biochemistry and Molecular Biology Department, Integrated Faculties of the Educational Union of Planalto Central, Brasilia 70675-760, DF, Brazil
| | - Bruno Paes-de-Melo
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Embrapa, Brasilia 70770-917, DF, Brazil
| | | | - Alexandre A. P. Firmino
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- Max Planck Institute Molecular Plant Physiol, 14476 Potsdam, Germany
| | - Marcos F. Basso
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Embrapa, Brasilia 70770-917, DF, Brazil
| | - Camila B. J. Lins
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
| | - Maysa R. Neves
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
| | - Stefanie M. Moura
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Embrapa, Brasilia 70770-917, DF, Brazil
| | | | | | - Maria C. M. Silva
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Embrapa, Brasilia 70770-917, DF, Brazil
| | - Maria F. Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasilia 70770-917, DF, Brazil
- Genetic and Molecular Biology Department, Catholic University of Brasilia (UCB), Brasilia 71966-700, DF, Brazil
- National Institute of Science and Technology (INCT Plant Stress Biotech), Embrapa, Brasilia 70770-917, DF, Brazil
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11
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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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12
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Dissanayaka Mudiyanselage SD, Ma J, Pechan T, Pechanova O, Liu B, Wang Y. A remodeled RNA polymerase II complex catalyzing viroid RNA-templated transcription. PLoS Pathog 2022; 18:e1010850. [PMID: 36121876 PMCID: PMC9521916 DOI: 10.1371/journal.ppat.1010850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/29/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
Viroids, a fascinating group of plant pathogens, are subviral agents composed of single-stranded circular noncoding RNAs. It is well-known that nuclear-replicating viroids exploit host DNA-dependent RNA polymerase II (Pol II) activity for transcription from circular RNA genome to minus-strand intermediates, a classic example illustrating the intrinsic RNA-dependent RNA polymerase activity of Pol II. The mechanism for Pol II to accept single-stranded RNAs as templates remains poorly understood. Here, we reconstituted a robust in vitro transcription system and demonstrated that Pol II also accepts minus-strand viroid RNA template to generate plus-strand RNAs. Further, we purified the Pol II complex on RNA templates for nano-liquid chromatography-tandem mass spectrometry analysis and identified a remodeled Pol II missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9, contrasting to the canonical 12-subunit Pol II or the 10-subunit Pol II core on DNA templates. Interestingly, the absence of Rpb9, which is responsible for Pol II fidelity, explains the higher mutation rate of viroids in comparison to cellular transcripts. This remodeled Pol II is active for transcription with the aid of TFIIIA-7ZF and appears not to require other canonical general transcription factors (such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and TFIIS), suggesting a distinct mechanism/machinery for viroid RNA-templated transcription. Transcription elongation factors, such as FACT complex, PAF1 complex, and SPT6, were also absent in the reconstituted transcription complex. Further analyses of the critical zinc finger domains in TFIIIA-7ZF revealed the first three zinc finger domains pivotal for RNA template binding. Collectively, our data illustrated a distinct organization of Pol II complex on viroid RNA templates, providing new insights into viroid replication, the evolution of transcription machinery, as well as the mechanism of RNA-templated transcription.
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Affiliation(s)
| | - Junfei Ma
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Tibor Pechan
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Olga Pechanova
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Bin Liu
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, United States of America
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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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14
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Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators? LIFE (BASEL, SWITZERLAND) 2022; 12:life12010103. [PMID: 35054497 PMCID: PMC8781251 DOI: 10.3390/life12010103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/09/2023]
Abstract
Viroids are a unique class of plant pathogens that consist of small circular RNA molecules, between 220 and 450 nucleotides in size. Viroids encode no proteins and are the smallest known infectious agents. Viroids replicate via the rolling circle mechanism, producing multimeric intermediates which are cleaved to unit length either by ribozymes formed from both polarities of the viroid genomic RNA or by coopted host RNAses. Many viroid-like small circular RNAs are satellites of plant RNA viruses. Ribozyviruses, represented by human hepatitis delta virus, are larger viroid-like circular RNAs that additionally encode the viral nucleocapsid protein. It has been proposed that viroids are direct descendants of primordial RNA replicons that were present in the hypothetical RNA world. We argue, however, that much later origin of viroids, possibly, from recently discovered mobile genetic elements known as retrozymes, is a far more parsimonious evolutionary scenario. Nevertheless, viroids and viroid-like circular RNAs are minimal replicators that are likely to be close to the theoretical lower limit of replicator size and arguably comprise the paradigm for replicator emergence. Thus, although viroid-like replicators are unlikely to be direct descendants of primordial RNA replicators, the study of the diversity and evolution of these ultimate genetic parasites can yield insights into the earliest stages of the evolution of life.
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15
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Lee BD, Neri U, Oh CJ, Simmonds P, Koonin EV. ViroidDB: a database of viroids and viroid-like circular RNAs. Nucleic Acids Res 2022; 50:D432-D438. [PMID: 34751403 PMCID: PMC8728161 DOI: 10.1093/nar/gkab974] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/31/2022] Open
Abstract
We introduce ViroidDB, a value-added database that attempts to collect all known viroid and viroid-like circular RNA sequences into a single resource. Spanning about 10 000 unique sequences, ViroidDB includes viroids, retroviroid-like elements, small circular satellite RNAs, ribozyviruses, and retrozymes. Each sequence's secondary structure, ribozyme content, and cluster membership are predicted via a custom pipeline optimized for handling circular RNAs. The data can be explored via a purpose-built user interface that features visualizations, multiple sequence alignments, and a portal for downloading bulk data. Users can browse the data by sequence type, taxon, or typo-tolerant search of metadata fields. The database is freely accessible at https://viroids.org.
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MESH Headings
- Base Sequence
- Databases, Nucleic Acid
- Internet
- Metadata
- Nucleic Acid Conformation
- Plant Diseases/virology
- Plants/virology
- RNA, Catalytic/chemistry
- RNA, Catalytic/classification
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Circular/chemistry
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Viral/chemistry
- RNA, Viral/classification
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sequence Alignment
- Software
- Viroids/classification
- Viroids/genetics
- Viroids/metabolism
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Affiliation(s)
- Benjamin D Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD 20894, USA
- Nuffield Department of Medicine, University of Oxford, Oxford OX1, UK
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD 20894, USA
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16
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Koonin EV, Dolja VV, Krupovic M, Kuhn JH. Viruses Defined by the Position of the Virosphere within the Replicator Space. Microbiol Mol Biol Rev 2021; 85:e0019320. [PMID: 34468181 PMCID: PMC8483706 DOI: 10.1128/mmbr.00193-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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Wei T, Ding SW. Editorial overview: Mechanisms in the molecular interactions of plants with viruses and viroids. Curr Opin Virol 2021; 49:27-29. [PMID: 34029991 DOI: 10.1016/j.coviro.2021.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Taiyun Wei
- Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shou-Wei Ding
- Department of Microbiology and Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants. Cells 2021; 10:cells10051187. [PMID: 34067940 PMCID: PMC8152041 DOI: 10.3390/cells10051187] [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: 04/15/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems.
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