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Wu J, Bisaro DM. Potato spindle tuber viroid (PSTVd) loop 27 mutants promote cell-to-cell movement and phloem unloading of the wild type: Insights into RNA-based viroid interactions. Virology 2024; 597:110137. [PMID: 38897019 DOI: 10.1016/j.virol.2024.110137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/29/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
Variations in infection progression with concurrent or prior infections by different viruses, viroids, or their strains are evident, but detailed investigations into viroid variant interactions are lacking. We studied potato spindle tuber viroid intermediate strain (PSTVd-I) to explore variant interactions. Two mutants, U177A/A182U (AU, replication- and trafficking-competent) and U178G/U179G (GG, replication-competent but trafficking-defective) on loop 27 increased cell-to-cell movement of wild-type (WT) PSTVd without affecting replication. In mixed infection assays, both mutants accelerated WT phloem unloading, while only AU promoted it in separate leaf assays, suggesting that enhancement of WT infection is not due to systemic signals. The mutants likely enhance WT infection due to their loop-specific functions, as evidenced by the lack of impact on WT infection seen with the distantly located G347U (UU) mutant. This study provides the first comprehensive analysis of viroid variant interactions, highlighting the prolonged phloem unloading process as a significant barrier to systemic spread.
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Affiliation(s)
- Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China; Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China; Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH, USA.
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2
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Wu J, Zhang Y, Nie Y, Yan F, Zirbel CL, Bisaro DM. RNA three-dimensional structure drives the sequence organization of potato spindle tuber viroid quasispecies. PLoS Pathog 2024; 20:e1012142. [PMID: 38574111 PMCID: PMC11020406 DOI: 10.1371/journal.ppat.1012142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/16/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
RNA viruses and viroids exist and evolve as quasispecies due to error-prone replication. Quasispecies consist of a few dominant master sequences alongside numerous variants that contribute to genetic diversity. Upon environmental changes, certain variants within quasispecies have the potential to become the dominant sequences, leading to the emergence of novel infectious strains. However, the emergence of new infectious variants remains unpredictable. Using mutant pools prepared by saturation mutagenesis of selected stem and loop regions, our study of potato spindle tuber viroid (PSTVd) demonstrates that mutants forming local three-dimensional (3D) structures similar to the wild type (WT) are more likely to accumulate in PSTVd quasispecies. The selection mechanisms underlying this biased accumulation are likely associated with cell-to-cell movement and long-distance trafficking. Moreover, certain trafficking-defective PSTVd mutants can be spread by functional sister genomes in the quasispecies. Our study reveals that the RNA 3D structure of stems and loops constrains the evolution of viroid quasispecies. Mutants with a structure similar to WT have a higher likelihood of being maintained within the quasispecies and can potentially give rise to novel infectious variants. These findings emphasize the potential of targeting RNA 3D structure as a more robust approach to defend against viroid infections.
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Affiliation(s)
- Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Yuhong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Yuxin Nie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Craig L. Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - David M. Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
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Wu J, Bisaro DM. Cell-cell communication and initial population composition shape the structure of potato spindle tuber viroid quasispecies. THE PLANT CELL 2024; 36:1036-1055. [PMID: 38252648 PMCID: PMC10980348 DOI: 10.1093/plcell/koae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/19/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
RNA viruses and viroids replicate with high mutation rates, forming quasispecies, population of variants centered around dominant sequences. The mechanisms governing quasispecies remain unclear. Plasmodesmata regulate viroid movement and were hypothesized to impact viroid quasispecies. Here, we sequenced the progeny of potato spindle tuber viroid intermediate (PSTVd-I) strain from mature guard cells lacking plasmodesmal connections and from in vitro-cultivated mesophyll cell protoplasts from systemic leaves of early-infected tomato (Solanum lycopersicum) plants. Remarkably, more variants accumulated in guard cells compared to whole leaves. Similarly, after extended cell culture, we observed more variants in cultivated mesophyll protoplasts. Coinfection and single-cell sequencing experiments demonstrated that the same plant cell can be infected multiple times by the same or different PSTVd sequences. To study the impact of initial population composition on PSTVd-I quasispecies, we conducted coinfections with PSTVd-I and variants. Two inoculum ratios (10:1 or 1:10) established quasispecies with or without PSTVd-I as the master sequence. In the absence of the master sequence, the percentage of novel variants initially increased. Moreover, a 1:1 PSTVd-I/variant RNA ratio resulted in PSTVd-I dominating (>50%), while the variants reached 20%. After PSTVd-I-only infection, the variants reached around 10%, while after variant-only infection, the variants were significantly more than 10%. These results emphasize the role of cell-to-cell communication and initial population composition in shaping PSTVd quasispecies.
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Affiliation(s)
- Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
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4
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Han K, Jia Z, Zhang Y, Zhou H, Bu S, Chen J, Yan D, Qi R, Yan F, Wu J. Chloroplast clustering around the nucleus induced by OMP24 overexpression unexpectedly promoted PSTVd infection in Nicotiana benthamiana. MOLECULAR PLANT PATHOLOGY 2023; 24:1552-1559. [PMID: 37695572 PMCID: PMC10632781 DOI: 10.1111/mpp.13385] [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: 04/18/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 09/12/2023]
Abstract
Chloroplast clustering around the nucleus is a well-known mechanism that occurs in response to various biotic and abiotic stresses and is believed to be a mechanism of defence against pathogens in plants. This phenomenon is accompanied by increased production of reactive oxygen species (ROS), which can help to destroy invading pathogens. However, the function of chloroplast clustering during viroid infection is unclear. Here, we report that, although the infection by potato spindle tuber viroid (PSTVd) failed to induce chloroplast clustering, chloroplast clustering caused by the overexpression of the Nicotiana benthamiana chloroplast outer membrane protein 24 (NbOMP24) promoted the infection by PSTVd, a viroid pathogen, in N. benthamiana. Interestingly, H2 O2 treatment, which caused increased ROS accumulation, showed no significant effects on PSTVd infection. Moreover, NbOMP24 protein showed no direct interaction with PSTVd. We propose that perinuclear chloroplast clustering induced by NbOMP24 provides a favourable environment for PSTVd infection. These findings highlight the complexity of chloroplast clustering-mediated plant-pathogen interactions and the need for further research to fully understand these mechanisms.
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Affiliation(s)
- Kelei Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroproductsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
- Institute of Plant Protection and Agro‐Products Safety, Anhui Academy of Agricultural SciencesHefeiChina
| | - Zhaoxing Jia
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroproductsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Yuhong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroproductsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Huijie Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroproductsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Shan Bu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroproductsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroproductsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Dankan Yan
- Institute of Plant Protection and Agro‐Products Safety, Anhui Academy of Agricultural SciencesHefeiChina
| | - Rende Qi
- Institute of Plant Protection and Agro‐Products Safety, Anhui Academy of Agricultural SciencesHefeiChina
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroproductsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of AgroproductsInstitute of Plant Virology, Ningbo UniversityNingboChina
- Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang ProvinceInstitute of Plant Virology, Ningbo UniversityNingboChina
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5
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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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6
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Heeney M, Frank MH. The mRNA mobileome: challenges and opportunities for deciphering signals from the noise. THE PLANT CELL 2023; 35:1817-1833. [PMID: 36881847 DOI: 10.1093/plcell/koad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 05/30/2023]
Abstract
Organismal communication entails encoding a message that is sent over space or time to a recipient cell, where that message is decoded to activate a downstream response. Defining what qualifies as a functional signal is essential for understanding intercellular communication. In this review, we delve into what is known and unknown in the field of long-distance messenger RNA (mRNA) movement and draw inspiration from the field of information theory to provide a perspective on what defines a functional signaling molecule. Although numerous studies support the long-distance movement of hundreds to thousands of mRNAs through the plant vascular system, only a small handful of these transcripts have been associated with signaling functions. Deciphering whether mobile mRNAs generally serve a role in plant communication has been challenging, due to our current lack of understanding regarding the factors that influence mRNA mobility. Further insight into unsolved questions regarding the nature of mobile mRNAs could provide an understanding of the signaling potential of these macromolecules.
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Affiliation(s)
- Michelle Heeney
- Plant Biology Section, School of Integrative Plant Science, Cornell University, 14853 Ithaca, NY, USA
| | - Margaret H Frank
- Plant Biology Section, School of Integrative Plant Science, Cornell University, 14853 Ithaca, NY, USA
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7
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Jeynes-Cupper K, Catoni M. Long distance signalling and epigenetic changes in crop grafting. FRONTIERS IN PLANT SCIENCE 2023; 14:1121704. [PMID: 37021313 PMCID: PMC10067726 DOI: 10.3389/fpls.2023.1121704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Humans have used grafting for more than 4000 years to improve plant production, through physically joining two different plants, which can continue to grow as a single organism. Today, grafting is becoming increasingly more popular as a technique to increase the production of herbaceous horticultural crops, where rootstocks can introduce traits such as resistance to several pathogens and/or improving the plant vigour. Research in model plants have documented how long-distance signalling mechanisms across the graft junction, together with epigenetic regulation, can produce molecular and phenotypic changes in grafted plants. Yet, most of the studied examples rely on proof-of-concept experiments or on limited specific cases. This review explores the link between research findings in model plants and crop species. We analyse studies investigating the movement of signalling molecules across the graft junction and their implications on epigenetic regulation. The improvement of genomics analyses and the increased availability of genetic resources has allowed to collect more information on potential benefits of grafting in horticultural crop models. Ultimately, further research into this topic will enhance our ability to use the grafting technique to exploit genetic and epigenetic variation in crops, as an alternative to traditional breeding.
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Affiliation(s)
| | - Marco Catoni
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- Institute for Sustainable Plant Protection, National Research Council of Italy, Torino, Italy
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8
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Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. BIOLOGY 2023; 12:biology12020172. [PMID: 36829451 PMCID: PMC9952643 DOI: 10.3390/biology12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
Viroids are a unique type of infectious agent, exclusively composed of a relatively small (246-430 nt), highly base-paired, circular, non-coding RNA. Despite the small size and non-coding nature, the more-than-thirty currently known viroid species infectious of higher plants are able to autonomously replicate and move systemically through the host, thereby inducing disease in some plants. After recalling viroid discovery back in the late 60s and early 70s of last century and discussing current hypotheses about their evolutionary origin, this article reviews our current knowledge about these peculiar infectious agents. We describe the highly base-paired viroid molecules that fold in rod-like or branched structures and viroid taxonomic classification in two families, Pospiviroidae and Avsunviroidae, likely gathering nuclear and chloroplastic viroids, respectively. We review current knowledge about viroid replication through RNA-to-RNA rolling-circle mechanisms in which host factors, notably RNA transporters, RNA polymerases, RNases, and RNA ligases, are involved. Systemic movement through the infected plant, plant-to-plant transmission and host range are also discussed. Finally, we focus on the mechanisms of viroid pathogenesis, in which RNA silencing has acquired remarkable importance, and also for the initiation of potential biotechnological applications of viroid molecules.
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9
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Tobacco mosaic virus movement protein complements a Potato spindle tuber viroid RNA mutant impaired for mesophyll entry but not mutants unable to enter the phloem. PLoS Pathog 2022; 18:e1011062. [PMID: 36574436 PMCID: PMC9829174 DOI: 10.1371/journal.ppat.1011062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 01/09/2023] [Accepted: 12/12/2022] [Indexed: 12/29/2022] Open
Abstract
Tobacco mosaic virus movement protein (TMV MP) is essential for virus spread between cells. To accomplish its task, TMV MP binds viral RNA, interacts with components of the cytoskeleton, and increases the size exclusion limit (SEL) of plasmodesmata. Plasmodesmata are gated intercellular channels that allow passage of small molecules and macromolecules, including RNA and protein, between plant cells. Moreover, plasmodesmata are diverse and those connecting different cell types appear to have unique mechanisms to regulate macromolecular trafficking, which likely contributes to the establishment of distinct cell boundaries. Consequently, TMV MP might be competent to mediate RNA transport through some but not all plasmodesmal gates. Due to a lack of viral mutants defective for movement between specific cell types, the ability of TMV MP in this regard is incompletely understood. In contrast, a number of trafficking impaired Potato spindle tuber viroid (PSTVd) mutants have been identified. PSTVd is a systemically infectious non-coding RNA that nevertheless can perform all functions required for replication as well as cell-to-cell and systemic spread. Previous studies have shown that PSTVd employs different structure and sequence elements to move between diverse cell types in host plants, and mutants defective for transport between specific cell types have been identified. Therefore, PSTVd may serve as a tool to analyze the functions of MPs of viral and cellular origin. To probe the RNA transport activity of TMV MP, transgenic plants expressing the protein were inoculated with PSTVd mutants. Remarkably, TMV MP complemented a PSTVd mutant defective for mesophyll entry but could not support two mutants impaired for phloem entry, suggesting it fails to productively interface with plasmodesmata at the phloem boundary and that additional viral and host factors may be required. Consistent with this idea, TMV co-infection, but not the combination of MP and coat protein (CP) expression, was able to complement one of the phloem entry mutants. These observations suggest that phloem loading is a critical impediment to establishing systemic infection that could involve the entire ensemble of TMV proteins. They also demonstrate a novel strategy for analysis of MPs.
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10
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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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11
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Kehr J, Morris RJ, Kragler F. Long-Distance Transported RNAs: From Identity to Function. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:457-474. [PMID: 34910585 DOI: 10.1146/annurev-arplant-070121-033601] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
There is now a wealth of data, from different plants and labs and spanning more than two decades, which unequivocally demonstrates that RNAs can be transported over long distances, from the cell where they are transcribed to distal cells in other tissues. Different types of RNA molecules are transported, including micro- and messenger RNAs. Whether these RNAs are selected for transport and, if so, how they are selected and transported remain, in general, open questions. This aspect is likely not independent of the biological function and relevance of the transported RNAs, which are in most cases still unclear. In this review, we summarize the experimental data supporting selectivity or nonselectivity of RNA translocation and review the evidence for biological functions. After discussing potential issues regarding the comparability between experiments, we propose criteria that need to be critically evaluated to identify important signaling RNAs.
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Affiliation(s)
- Julia Kehr
- Department of Biology, Institute for Plant Sciences and Microbiology, Universität Hamburg, Hamburg, Germany;
| | - Richard J Morris
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom;
| | - Friedrich Kragler
- Department II, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany;
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12
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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] [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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Abstract
Systemic RNA trafficking widely exists in plants and is critical for integrating the healthy development and responses to environmental cues. Viroids, single-stranded circular noncoding RNAs that infect plants, have been used as a model to delineate the mechanism underlying systemic RNA trafficking. Recent work on viroids has shown that structural motifs are critical to direct RNA trafficking through distinct cellular boundaries. Here, we describe the methods for generating mutational variants using site-directed mutagenesis and infection assays to unravel the function of RNA motifs. This approach can be modified to study other RNA motif-based biological processes.
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Affiliation(s)
- Heather N Smith
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Junfei Ma
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA.
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14
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Ma J, Wang Y. Studies on Viroid Shed Light on the Role of RNA Three-Dimensional Structural Motifs in RNA Trafficking in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:836267. [PMID: 35401640 PMCID: PMC8983868 DOI: 10.3389/fpls.2022.836267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/23/2022] [Indexed: 05/05/2023]
Abstract
RNAs play essential roles in various biological processes. Mounting evidence has demonstrated that RNA subcellular localization and intercellular/systemic trafficking govern their functions in coordinating plant growth at the organismal level. While numerous types of RNAs (i.e., mRNAs, small RNAs, rRNAs, tRNAs, and long noncoding RNAs) have been found to traffic in a non-cell-autonomous fashion within plants, the underlying regulatory mechanism remains unclear. Viroids are single-stranded circular noncoding RNAs, which entirely rely on their RNA motifs to exploit cellular machinery for organelle entry and exit, cell-to-cell movement through plasmodesmata, and systemic trafficking. Viroids represent an excellent model to dissect the role of RNA three-dimensional (3D) structural motifs in regulating RNA movement. Nearly two decades of studies have found multiple RNA 3D motifs responsible for viroid nuclear import as well as trafficking across diverse cellular boundaries in plants. These RNA 3D motifs function as "keys" to unlock cellular and subcellular barriers and guide RNA movement within a cell or between cells. Here, we summarize the key findings along this line of research with implications for future studies on RNA trafficking in plants.
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15
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Steger G. Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing. Methods Mol Biol 2022; 2316:331-371. [PMID: 34845705 DOI: 10.1007/978-1-0716-1464-8_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Viroids are small non-coding RNAs that require a special sequence and structure to be replicated and transported by the host machinery. Many of these features can be predicted and later experimentally verified. Here, we will present workflows to predict viroid structures and draw the predicted structures in a pleasing and descriptive way using recently developed software.
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Affiliation(s)
- Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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16
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Lezzhov AA, Morozov SY, Solovyev AG. Phloem Exit as a Possible Control Point in Selective Systemic Transport of RNA. FRONTIERS IN PLANT SCIENCE 2021; 12:739369. [PMID: 34899773 PMCID: PMC8660857 DOI: 10.3389/fpls.2021.739369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/28/2021] [Indexed: 06/01/2023]
Affiliation(s)
- Alexander A. Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Sergey Y. Morozov
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- Department of Virology, Faculty of Biology, Moscow State University, Moscow, Russia
| | - Andrey G. Solovyev
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
- Department of Virology, Faculty of Biology, Moscow State University, Moscow, Russia
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Steinbachová L, Matoušek J, Steger G, Matoušková H, Radišek S, Honys D. Transformation of Seed Non-Transmissible Hop Viroids in Nicotiana benthamiana Causes Distortions in Male Gametophyte Development. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112398. [PMID: 34834761 PMCID: PMC8624972 DOI: 10.3390/plants10112398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/22/2021] [Accepted: 11/03/2021] [Indexed: 05/27/2023]
Abstract
Viroids are small, non-coding, parasitic RNAs that promote developmental distortions in sensitive plants. We analyzed pollen of Nicotiana benthamiana after infection and/or ectopic transformation with cDNAs of citrus bark cracking viroid (CBCVd), apple fruit crinkle viroid (AFCVd) and potato spindle tuber viroid (PSTVd) variant AS1. These viroids were seed non-transmissible in N. benthamiana. All viroids propagated to high levels in immature anthers similar to leaves, while their levels were drastically reduced by approximately 3.6 × 103, 800 and 59 times in mature pollen of CBCVd, AFCVd and PSTVd infected N. benthamiana, respectively, in comparison to leaves. These results suggest similar elimination processes during male gametophyte development as in the Nicotiana tabacum we presented in our previous study. Mature pollen of N. benthamiana showed no apparent defects in infected plants although all three viroids induced strong pathological symptoms on leaves. While Nicotiana species have naturally bicellular mature pollen, we noted a rare occurrence of mature pollen with three nuclei in CBCVd-infected N. benthamiana. Changes in the expression of ribosomal marker proteins in AFCVd-infected pollen were detected, suggesting some changes in pollen metabolism. N. benthamiana transformed with 35S-driven viroid cDNAs showed strong symptoms including defects in pollen development. A large number of aborted pollen (34% and 62%) and a slight increase of young pollen grains (8% and 15%) were found in mature pollen of AFCVd and CBCVd transformants, respectively, in comparison to control plants (3.9% aborted pollen and 0.3% young pollen). Moreover, pollen grains with malformed nuclei or trinuclear pollen were found in CBCVd-transformed plants. Our results suggest that "forcing" overexpression of seed non-transmissible viroid led to strong pollen pathogenesis. Viroid adaptation to pollen metabolism can be assumed as an important factor for viroid transmissibility through pollen and seeds.
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Affiliation(s)
- Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic;
| | - Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (H.M.)
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, D-40204 Düsseldorf, Germany;
| | - Helena Matoušková
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (H.M.)
| | - Sebastjan Radišek
- Slovenian Institute of Hop Research and Brewing, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia;
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic;
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Abstract
Viroids are small, single-stranded, circular RNAs infecting plants. Composed of only a few hundred nucleotides and being unable to code for proteins, viroids represent the lowest level of complexity for an infectious agent, even below that of the smallest known viruses. Despite the relatively small size, viroids contain RNA structural elements embracing all the information needed to interact with host factors involved in their infectious cycle, thus providing models for studying structure-function relationships of RNA. Viroids are specifically targeted to nuclei (family Pospiviroidae) or chloroplasts (family Avsunviroidae), where replication based on rolling-circle mechanisms takes place. They move locally and systemically through plasmodesmata and phloem, respectively, and may elicit symptoms in the infected host, with pathogenic pathways linked to RNA silencing and other plant defense responses. In this review, recent advances in the dissection of the complex interplay between viroids and plants are presented, highlighting knowledge gaps and perspectives for future research. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Beatriz Navarro
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
| | - Ricardo Flores
- Institute of Molecular and Cellular Biology of Plants (UPV-CSIC), Polytechnic University of Valencia, 46022 Valencia, Spain
| | - Francesco Di Serio
- Institute for Sustainable Plant Protection, National Research Council of Italy; I-70126 Bari, Italy;
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Wang T, Li X, Zhang X, Wang Q, Liu W, Lu X, Gao S, Liu Z, Liu M, Gao L, Zhang W. RNA Motifs and Modification Involve in RNA Long-Distance Transport in Plants. Front Cell Dev Biol 2021; 9:651278. [PMID: 33869208 PMCID: PMC8047152 DOI: 10.3389/fcell.2021.651278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 02/22/2021] [Indexed: 01/31/2023] Open
Abstract
A large number of RNA molecules have been found in the phloem of higher plants, and they can be transported to distant organelles through the phloem. RNA signals are important cues to be evolving in fortification strategies by long-distance transportation when suffering from various physiological challenges. So far, the mechanism of RNA selectively transportation through phloem cells is still in progress. Up to now, evidence have shown that several RNA motifs including Polypyrimidine (poly-CU) sequence, transfer RNA (tRNA)-related sequence, Single Nucleotide Mutation bound with specific RNA binding proteins to form Ribonucleotide protein (RNP) complexes could facilitate RNA mobility in plants. Furthermore, some RNA secondary structure such as tRNA-like structure (TLS), untranslation region (UTR) of mRNA, stem-loop structure of pre-miRNA also contributed to the mobility of RNAs. Latest researchs found that RNA methylation such as methylated 5′ cytosine (m5C) played an important role in RNA transport and function. These studies lay a theoretical foundation to uncover the mechanism of RNA transport. We aim to provide ideas and clues to inspire future research on the function of RNA motifs in RNA long-distance transport, furthermore to explore the underlying mechanism of RNA systematic signaling.
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Affiliation(s)
- Tao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaojing Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Qing Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Xiaohong Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Shunli Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Zixi Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Mengshuang Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing, China
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Venkataraman S, Badar U, Shoeb E, Hashim G, AbouHaidar M, Hefferon K. An Inside Look into Biological Miniatures: Molecular Mechanisms of Viroids. Int J Mol Sci 2021; 22:2795. [PMID: 33801996 PMCID: PMC8001946 DOI: 10.3390/ijms22062795] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022] Open
Abstract
Viroids are tiny single-stranded circular RNA pathogens that infect plants. Viroids do not encode any proteins, yet cause an assortment of symptoms. The following review describes viroid classification, molecular biology and spread. The review also discusses viroid pathogenesis, host interactions and detection. The review concludes with a description of future prospects in viroid research.
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Affiliation(s)
| | | | | | | | | | - Kathleen Hefferon
- Cell and System Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; (S.V.); (U.B.); (E.S.); (G.H.); (M.A.)
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21
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SANO T. Progress in 50 years of viroid research-Molecular structure, pathogenicity, and host adaptation. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2021; 97:371-401. [PMID: 34380915 PMCID: PMC8403530 DOI: 10.2183/pjab.97.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/30/2021] [Indexed: 05/27/2023]
Abstract
Viroids are non-encapsidated, single-stranded, circular RNAs consisting of 246-434 nucleotides. Despite their non-protein-encoding RNA nature, viroids replicate autonomously in host cells. To date, more than 25 diseases in more than 15 crops, including vegetables, fruit trees, and flowers, have been reported. Some are pathogenic but others replicate without eliciting disease. Viroids were shown to have one of the fundamental attributes of life to adapt to environments according to Darwinian selection, and they are likely to be living fossils that have survived from the pre-cellular RNA world. In 50 years of research since their discovery, it was revealed that viroids invade host cells, replicate in nuclei or chloroplasts, and undergo nucleotide mutation in the process of adapting to new host environments. It was also demonstrated that structural motifs in viroid RNAs exert different levels of pathogenicity by interacting with various host factors. Despite their small size, the molecular mechanism of viroid pathogenicity turned out to be more complex than first thought.
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Affiliation(s)
- Teruo SANO
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
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22
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Wu J, Bisaro DM. Biased Pol II fidelity contributes to conservation of functional domains in the Potato spindle tuber viroid genome. PLoS Pathog 2020; 16:e1009144. [PMID: 33351860 PMCID: PMC7787683 DOI: 10.1371/journal.ppat.1009144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/06/2021] [Accepted: 11/10/2020] [Indexed: 01/25/2023] Open
Abstract
Accurate calculation of mutation rates for viruses and viroids is necessary for evolutionary studies and to evaluate adaptation potential. However, estimation of in vivo mutation rates is complicated by selection, which leads to loss or proliferation of certain mutations. To minimize this concern, lethal mutations, including nonsense and non-synonymous mutations, have been used to determine mutation rates for several viruses and viroids, including Potato spindle tuber viroid (PSTVd). However, this approach has limitations, including focus on a relatively small number of genome sites and the possibility that mutations may not actually be lethal or may be maintained by wild type individuals. To avoid selection bias altogether, we sequenced minus-strand PSTVd dimers from concatemeric replication intermediates. The underlying rationale is that mutations found in only one of the monomers were likely generated de novo during RNA polymerase II (Pol II) transcription of the circular plus-strand RNA genome. This approach yielded an apparent Pol II error rate of ~1/1837 nucleotides per transcription cycle, and an estimated mutation rate of ~1/919 nucleotides for a single replication cycle. Remarkably, de novo mutations were nearly absent from the most conserved, replication-critical regions of the PSTVd genome, suggesting that sequence conservation is a consequence of both essential function and template optimization for greater Pol II fidelity. Such biased fidelity may constitute a novel strategy to ensure population success while allowing abundant sampling of sequence space in other genome regions. Comparison with variants in progeny populations derived from a cloned, wild type PSTVd master sequence revealed that most de novo mutations were lost through selection. Polymerase errors are the major source of variation in virus and viroid genomes, and as a consequence polymerase error rates are major determinants of adaptation potential. Accurate calculation of in vivo mutation rates is complicated by selection. To circumvent this issue, dimeric PSTVd minus-strand replication intermediates generated in vivo by host RNA polymerase II (Pol II) were sequenced to identify de novo mutations. This analysis revealed a very high error rate for Pol II transcribing genomic PSTVd RNA, leading to an extremely high mutation rate. Remarkably, however, de novo mutations were rare in the most highly conserved, replication-critical genome regions, suggesting these sequences are selected for both function and enhanced transcription fidelity. This biased fidelity may reveal a novel strategy to ensure population survival while maximizing adaptation potential. Further, comparison of mutations identified by minus-strand dimer sequencing with mutations observed in progeny variants derived from wild type PSTVd showed that most de novo mutations were lost through selection.
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Affiliation(s)
- Jian Wu
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - David M. Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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23
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Ivanov AV, Shmyglya IV, Zherdev AV, Dzantiev BB, Safenkova IV. The Challenge for Rapid Detection of High-Structured Circular RNA: Assay of Potato Spindle Tuber Viroid Based on Recombinase Polymerase Amplification and Lateral Flow Tests. PLANTS 2020; 9:plants9101369. [PMID: 33076508 PMCID: PMC7650583 DOI: 10.3390/plants9101369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 01/14/2023]
Abstract
An assay was developed to detect the potato spindle tuber viroid (PSTVd), a dangerous plant pathogen that causes crop damage resulting in economic losses in the potato agriculture sector. The assay was based on the reverse transcription and recombinase polymerase amplification (RT-RPA) of PSTVd RNA coupled with amplicon detection via lateral flow assay (LFA). Primers labeled with fluorescein and biotin were designed for RT-RPA for effective recognition of the loop regions in the high-structured circular RNA of PSTVd. The labeled DNA amplicon was detected using lateral flow test strips consisting of a conjugate of gold nanoparticles with antibodies specific to fluorescein and streptavidin in the test zone. The RT-RPA-LFA detected 106 copies of in vitro transcribed PSTVd RNA in reaction or up to 1:107 diluted extracts of infected plant leaves. The assay took 30 min, including the RT-RPA stage and the LFA stage. The testing of healthy and infected potato samples showed full concordance between the developed RT-RPA-LFA and quantitative reverse transcription polymerase chain reaction (RT-qPCR) and the commercial kit. The obtained results proved the feasibility of using the developed assay to detect PSTVd from a natural source.
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Affiliation(s)
- Aleksandr V. Ivanov
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.I.); (A.V.Z.); (I.V.S.)
| | - Irina V. Shmyglya
- A. G. Lorch Russian Potato Research Center, Kraskovo 140051, Russia;
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.I.); (A.V.Z.); (I.V.S.)
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.I.); (A.V.Z.); (I.V.S.)
- Correspondence: ; Tel.: +7-495-954-3142
| | - Irina V. Safenkova
- A.N. Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia; (A.V.I.); (A.V.Z.); (I.V.S.)
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24
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Tolstyko EA, Lezzhov AA, Morozov SY, Solovyev AG. Phloem transport of structured RNAs: A widening repertoire of trafficking signals and protein factors. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110602. [PMID: 32900440 DOI: 10.1016/j.plantsci.2020.110602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/20/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
The conducting sieve tubes of the phloem consist of sieve elements (SEs), which are enucleate cells incapable of transcription and translation. Nevertheless, SEs contain a large variety of RNAs, and long-distance RNA trafficking via the phloem has been documented. The phloem transport of certain RNAs, as well as the further unloading of these RNAs at target tissues, is essential for plant individual development and responses to environmental cues. The translocation of such RNAs via the phloem is believed to be directed by RNA structural elements serving as phloem transport signals (PTSs), which are recognized by proteins that direct the PTS-containing RNAs into the phloem translocation pathway. The ability of phloem transport has been reported for several classes of structured RNAs including viroids, genuine tRNAs, mRNAs with tRNA sequences embedded into mRNA untranslated regions, tRNA-like structures in the genomic RNAs of plant viruses, and micro-RNA (miRNA) precursors (pri-miRNA). Here, three distinct types of such RNAs are discussed, along with the proteins that may specifically interact with these structures in the phloem. Three-dimensional (3D) motifs, which are characteristic of imperfect RNA duplexes, are discussed as elements of phloem-mobile structured RNAs specifically recognized by proteins involved in phloem transport, thus serving as PTSs.
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Affiliation(s)
- Eugeny A Tolstyko
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia
| | - Alexander A Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119991, Russia
| | - Sergey Y Morozov
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia
| | - Andrey G Solovyev
- Department of Virology, Biological Faculty, Moscow State University, Moscow, 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119992, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia.
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25
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Wu J, Zhou C, Li J, Li C, Tao X, Leontis NB, Zirbel CL, Bisaro DM, Ding B. Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA. Nucleic Acids Res 2020; 48:3134-3155. [PMID: 32083649 PMCID: PMC7102988 DOI: 10.1093/nar/gkaa100] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/03/2020] [Accepted: 02/18/2020] [Indexed: 01/19/2023] Open
Abstract
While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). Deep sequencing PSTVd genomes from plants inoculated with a cloned master sequence revealed naturally occurring variants, and showed that G/U pairs are maintained to the same extent as canonical WC base pairs. Comprehensive mutational analysis demonstrated that nearly all G/U pairs are critical for replication and/or systemic spread. Two selected G/U pairs were found to be required for PSTVd entry into, but not for exit from, the host vascular system. This study identifies critical roles for G/U pairs in the survival of an infectious RNA, and increases understanding of structure-based regulation of replication and trafficking of pathogen and cellular RNAs.
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Affiliation(s)
- Jian Wu
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.,Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Cuiji Zhou
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - James Li
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Chun Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaorong Tao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Neocles B Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - David M Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.,Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Biao Ding
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, USA.,Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, OH 43210, USA
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26
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Evidence Supporting That RNA Polymerase II Catalyzes De Novo Transcription Using Potato Spindle Tuber Viroid Circular RNA Templates. Viruses 2020; 12:v12040371. [PMID: 32230827 PMCID: PMC7232335 DOI: 10.3390/v12040371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
Transcription is a fundamental process that mediates the interplay between genetic information and phenotype. Emerging evidence indicates that RNA polymerase II (Pol II) can catalyze transcription using both DNA and RNA templates. It is well established that Pol II initiates de novo transcription on DNA templates. However, it is unclear whether Pol II performs de novo transcription or relies on primers for initiation (primed transcription) on RNA templates. Using potato spindle tuber viroid (PSTVd) as a model, we presented evidence showing that circular PSTVd templates are critical for the synthesis of longer-than-unit-length (-)-strand products, which supports the de novo transcription based on the asymmetric rolling circle model of PSTVd replication. We further showed that the crucial factor for primed transcription, transcription factor IIS (TFIIS), is dispensable for PSTVd replication in cells. Together, our data support the de novo transcription on PSTVd RNA templates catalyzed by Pol II. This result has significant implications in understanding the mechanism and machinery underlying Pol II-catalyzed transcription using other RNA templates.
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27
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Lu X, Liu W, Wang T, Zhang J, Li X, Zhang W. Systemic Long-Distance Signaling and Communication Between Rootstock and Scion in Grafted Vegetables. FRONTIERS IN PLANT SCIENCE 2020; 11:460. [PMID: 32431719 PMCID: PMC7214726 DOI: 10.3389/fpls.2020.00460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/27/2020] [Indexed: 05/06/2023]
Abstract
Grafting is widely used in fruit, vegetable, and flower propagation to improve biotic and abiotic stress resistance, yield, and quality. At present, the systemic changes caused by grafting, as well as the mechanisms and effects of long-distance signal transport between rootstock and scion have mainly been investigated in model plants (Arabidopsis thaliana and Nicotiana benthamiana). However, these aspects of grafting vary when different plant materials are grafted, so the study of model plants provides only a theoretical basis and reference for the related research of grafted vegetables. The dearth of knowledge about the transport of signaling molecules in grafted vegetables is inconsistent with the rapid development of large-scale vegetable production, highlighting the need to study the mechanisms regulating the rootstock-scion interaction and long-distance transport. The rapid development of molecular biotechnology and "omics" approaches will allow researchers to unravel the physiological and molecular mechanisms involved in the rootstock-scion interaction in vegetables. We summarize recent progress in the study of the physiological aspects (e.g., hormones and nutrients) of the response in grafted vegetables and focus in particular on long-distance molecular signaling (e.g., RNA and proteins). This review provides a theoretical basis for studies of the rootstock-scion interaction in grafted vegetables, as well as provide guidance for rootstock breeding and selection to meet specific demands for efficient vegetable production.
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Wu J, Leontis NB, Zirbel CL, Bisaro DM, Ding B. A three-dimensional RNA motif mediates directional trafficking of Potato spindle tuber viroid from epidermal to palisade mesophyll cells in Nicotiana benthamiana. PLoS Pathog 2019; 15:e1008147. [PMID: 31644572 PMCID: PMC6827988 DOI: 10.1371/journal.ppat.1008147] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/04/2019] [Accepted: 10/14/2019] [Indexed: 12/15/2022] Open
Abstract
Potato spindle tuber viroid (PSTVd) is a circular non-coding RNA of 359 nucleotides that replicates and spreads systemically in host plants, thus all functions required to establish an infection are mediated by sequence and structural elements in the genome. The PSTVd secondary structure contains 26 Watson-Crick base-paired stems and 27 loops. Most of the loops are believed to form three-dimensional (3D) structural motifs through non-Watson-Crick base pairing, base stacking, and other local interactions. Homology-based prediction using the JAR3D online program revealed that loop 27 (nucleotides 177-182) most likely forms a 3D structure similar to the loop of a conserved hairpin located in the 3' untranslated region of histone mRNAs in animal cells. This stem-loop, which is involved in 3'-end maturation, is not found in polyadenylated plant histone mRNAs. Mutagenesis showed that PSTVd genomes containing base substitutions in loop 27 predicted by JAR3D to disrupt the 3D structure were unable to replicate in Nicotiana benthamiana leaves following mechanical rub inoculation, with one exception: a U178G/U179G double mutant was replication-competent and able to spread within the upper epidermis of inoculated leaves, but was confined to this cell layer. Remarkably, direct delivery of the U178G/U179G mutant into the vascular system by needle puncture inoculation allowed it to spread systemically and enter mesophyll cells and epidermal cells of upper leaves. These findings highlight the importance of RNA 3D structure for PSTVd replication and intercellular trafficking and indicate that loop 27 is required for epidermal exit, but not epidermal entry or transit between other cell types. Thus, requirements for RNA trafficking between epidermal and underlying palisade mesophyll cells are unique and directional. Our findings further suggest that 3D structure and RNA-protein interactions constrain RNA sequence evolution, and validate JAR3D as a tool to predict RNA 3D structure.
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Affiliation(s)
- Jian Wu
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, Infectious Diseases Institute, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Neocles B. Leontis
- Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - Craig L. Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - David M. Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, Infectious Diseases Institute, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Biao Ding
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, Infectious Diseases Institute, and Graduate Program in Molecular, Cellular, and Developmental Biology, The Ohio State University, Columbus, Ohio, United States of America
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Lezzhov AA, Atabekova AK, Tolstyko EA, Lazareva EA, Solovyev AG. RNA phloem transport mediated by pre-miRNA and viral tRNA-like structures. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 284:99-107. [PMID: 31084885 DOI: 10.1016/j.plantsci.2019.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
Phloem-mobile mRNAs are assumed to contain sequence elements directing RNA to the phloem translocation pathway. One of such elements is represented by tRNA sequences embedded in untranslated regions of many mRNAs, including those proved to be mobile. Genomic RNAs of a number of plant viruses possess a 3'-terminal tRNA-like structures (TLSs) only distantly related to genuine tRNAs, but nevertheless aminoacylated and capable of interaction with some tRNA-binding proteins. Here, we elaborated an experimental system for analysis of RNA phloem transport based on an engineered RNA of Potato virus X capable of replication, but not encapsidation and movement in plants. The TLSs of Brome mosaic virus, Tobacco mosaic virus and Turnip yellow mosaic virus were demonstrated to enable the phloem transport of foreign RNA. A miRNA precursor, pre-miR390b, was also found to render RNA competent for the phloem transport. In line with this, sequences of miRNA precursors were identified in a Cucurbita maxima phloem transcriptome, supporting the hypothesis that, at least in some cases, miRNA phloem signaling can involve miRNA precursors. Collectively, the data presented here suggest that RNA molecules can be directed into the phloem translocation pathway by structured RNA elements such as those of viral TLSs and miRNA precursors.
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Affiliation(s)
- Alexander A Lezzhov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119991, Russia
| | - Anastasia K Atabekova
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119234, Russia
| | - Eugeny A Tolstyko
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119234, Russia
| | - Ekaterina A Lazareva
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119234, Russia
| | - Andrey G Solovyev
- Department of Virology, Biological Faculty, Moscow State University, Moscow 119234, Russia; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia; Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow 119991, Russia.
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Moreno M, Vázquez L, López-Carrasco A, Martín-Gago J, Flores R, Briones C. Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy. RNA Biol 2019; 16:295-308. [PMID: 30734641 PMCID: PMC6380281 DOI: 10.1080/15476286.2019.1572436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 12/11/2018] [Accepted: 01/17/2019] [Indexed: 11/01/2022] Open
Abstract
Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.
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Affiliation(s)
- M. Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - L. Vázquez
- Departamento de Superficies y Recubrimientos, Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid, Spain
| | - A. López-Carrasco
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | - J.A. Martín-Gago
- Departamento de Superficies y Recubrimientos, Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid, Spain
| | - R. Flores
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | - C. Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
- Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Spain
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Chrysanthemum Stunt Viroid Resistance in Chrysanthemum. Viruses 2018; 10:v10120719. [PMID: 30562919 PMCID: PMC6315827 DOI: 10.3390/v10120719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/17/2022] Open
Abstract
Chrysanthemum stunt viroid (CSVd) is one of the most severe threats in Chrysanthemum morifolium production. Over the last decade, several studies have reported the natural occurrence of CSVd resistance in chrysanthemum germplasms. Such CSVd-resistant germplasms are desirable for the stable production of chrysanthemum plants. Current surveys include finding new resistant chrysanthemum cultivars, breeding, and revealing resistant mechanisms. We review the progress, from discovery to current status, of CSVd-resistance studies, while introducing information on the improvement of associated inoculation and diagnostic techniques.
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Reagan BC, Ganusova EE, Fernandez JC, McCray TN, Burch-Smith TM. RNA on the move: The plasmodesmata perspective. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:1-10. [PMID: 30107876 DOI: 10.1016/j.plantsci.2018.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/25/2018] [Accepted: 07/04/2018] [Indexed: 05/11/2023]
Abstract
It is now widely accepted that plant RNAs can have effects at sites far away from their sites of synthesis. Cellular mRNA transcripts, endogenous small RNAs and defense-related small RNAs all move from cell to cell via plasmodesmata (PD), and may even move long distances in the phloem. Despite their small size, PD have complicated substructures, and the area of the pore available for RNA trafficking can be remarkably small. The intent of this review is to bring into focus the role of PD in cell-to-cell and long distance communication in plants. We consider how cellular RNAs could move through the cell to the PD and thence through PD. The protein composition of PD and the possible roles of PD proteins in RNA trafficking are also discussed. Recent evidence for RNA metabolism in organelles acting as a factor in controlling PD flux is also presented, highlighting new aspects of plant intra- and intercellular communication. It is clear that while the phenomenon of RNA mobility is common and essential, many questions remain, and these have been highlighted throughout this review.
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Affiliation(s)
- Brandon C Reagan
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States
| | - Elena E Ganusova
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States
| | - Jessica C Fernandez
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States
| | - Tyra N McCray
- School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, United States
| | - Tessa M Burch-Smith
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States; School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996, United States.
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Allelic RNA Motifs in Regulating Systemic Trafficking of Potato Spindle Tuber Viroid. Viruses 2018; 10:v10040160. [PMID: 29601476 PMCID: PMC5923454 DOI: 10.3390/v10040160] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 01/07/2023] Open
Abstract
Intercellular RNA trafficking has been shown as a widely-existing phenomenon that has significant functions in many aspects of biology. Viroids, circular noncoding RNAs that cause plant diseases, have been a model to dissect the role of RNA structural motifs in regulating intercellular RNA trafficking in plants. Recent studies on potato spindle tuber viroid (PSTVd) showed that the RNA motif loop 19 is important for PSTVd to spread from palisade to spongy mesophyll in infected leaves. Here, we performed saturated mutational analysis to uncover all possible functional variants of loop 19 and exploit this data to pinpoint to a three-dimensional structural model of this motif. Interestingly, we found that two distinct structural motifs can replace loop 19 and retain the systemic trafficking capacity. One of the alternative structures rapidly emerged from the inoculation using a loop 19 abolished mutant that is not capable of systemic trafficking. Our observation indicates the flexibility of multiple structural arrangements interchangeably exerting similar function at a particular RNA locus. Taken together, this study deepens the understanding of RNA structural motifs-regulated viroid RNA trafficking, which has broad implications for studying RNA intercellular trafficking as well.
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Tsushima T, Sano T. A point-mutation of Coleus blumei viroid 1 switches the potential to transmit through seed. J Gen Virol 2018; 99:393-401. [DOI: 10.1099/jgv.0.001013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Taro Tsushima
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
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Wang Y, Zirbel CL, Leontis NB, Ding B. RNA 3-dimensional structural motifs as a critical constraint of viroid RNA evolution. PLoS Pathog 2018; 14:e1006801. [PMID: 29470541 PMCID: PMC5823408 DOI: 10.1371/journal.ppat.1006801] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, United States of America
- * E-mail: (YW); (CLZ); (NBL)
| | - Craig L. Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio, United States of America
- * E-mail: (YW); (CLZ); (NBL)
| | - Neocles B. Leontis
- Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
- * E-mail: (YW); (CLZ); (NBL)
| | - Biao Ding
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
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36
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Nabeshima T, Doi M, Hosokawa M. Comparative Analysis of Chrysanthemum Stunt Viroid Accumulation and Movement in Two Chrysanthemum ( Chrysanthemum morifolium) Cultivars with Differential Susceptibility to the Viroid Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:1940. [PMID: 29250083 PMCID: PMC5715398 DOI: 10.3389/fpls.2017.01940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Chrysanthemum stunt viroid (CSVd) was inoculated into two chrysanthemum (Chrysanthemum morifolium) cultivars, the CSVd-susceptible cultivar Piato and the CSVd-resistant cultivar Mari Kazaguruma. For CSVd inoculation, grafting and Agrobacterium-mediated inoculation were used. In grafting experiments, CSVd was detectable in Mari Kazaguruma after grafting onto infected Piato, but after removal of infected rootstocks, CSVd could not be detected in the uppermost leaves. In agroinfection experiments, CSVd systemic infection was observed in Piato but not in Mari Kazaguruma. However, agro-inoculated leaves of Mari Kazaguruma accumulated circular CSVd RNA to levels equivalent to those in Piato at 7 days post-inoculation. In situ detection of CSVd in inoculated leaves revealed that CSVd was absent in phloem of Mari Kazaguruma, while CSVd strongly localized to this site in Piato. We hypothesize that CSVd resistance in Mari Kazaguruma relates not to CSVd replication but to CSVd movement in leaves.
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López-Carrasco A, Ballesteros C, Sentandreu V, Delgado S, Gago-Zachert S, Flores R, Sanjuán R. Different rates of spontaneous mutation of chloroplastic and nuclear viroids as determined by high-fidelity ultra-deep sequencing. PLoS Pathog 2017; 13:e1006547. [PMID: 28910391 PMCID: PMC5614642 DOI: 10.1371/journal.ppat.1006547] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 09/26/2017] [Accepted: 07/22/2017] [Indexed: 01/19/2023] Open
Abstract
Mutation rates vary by orders of magnitude across biological systems, being higher for simpler genomes. The simplest known genomes correspond to viroids, subviral plant replicons constituted by circular non-coding RNAs of few hundred bases. Previous work has revealed an extremely high mutation rate for chrysanthemum chlorotic mottle viroid, a chloroplast-replicating viroid. However, whether this is a general feature of viroids remains unclear. Here, we have used high-fidelity ultra-deep sequencing to determine the mutation rate in a common host (eggplant) of two viroids, each representative of one family: the chloroplastic eggplant latent viroid (ELVd, Avsunviroidae) and the nuclear potato spindle tuber viroid (PSTVd, Pospiviroidae). This revealed higher mutation frequencies in ELVd than in PSTVd, as well as marked differences in the types of mutations produced. Rates of spontaneous mutation, quantified in vivo using the lethal mutation method, ranged from 1/1000 to 1/800 for ELVd and from 1/7000 to 1/3800 for PSTVd depending on sequencing run. These results suggest that extremely high mutability is a common feature of chloroplastic viroids, whereas the mutation rates of PSTVd and potentially other nuclear viroids appear significantly lower and closer to those of some RNA viruses. Spontaneous mutations are the ultimate source of genetic variation and their characterization provides fundamental information about evolutionary processes. The highest mutation rate so far described corresponds to a hammerhead viroid infecting plant chloroplasts. Viroids are plant-exclusive parasites constituted by 250–400 nt-long, non-protein-coding RNAs, and are divided into two families with distinct mechanisms of replication and localization: chloroplastic (Avsunviroidae), and nuclear (Pospiviroidae). Here, we have used high-fidelity ultra-deep sequencing to compare side by side the mutation rates of one representative member of each viroid family in the same host. We found that the mutation rate of the nuclear viroid was several fold lower than that of the chloroplastic viroid.
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Affiliation(s)
- Amparo López-Carrasco
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Cristina Ballesteros
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, València, Spain
| | | | - Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Selma Gago-Zachert
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
- Department of Molecular Signal Processing, Leibniz Institute for Plant Biochemistry, Halle (Saale), Germany
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, València, Spain
- Departamento de Genética, Universitat de València, València, Spain
- * E-mail:
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López-Carrasco A, Flores R. Dissecting the secondary structure of the circular RNA of a nuclear viroid in vivo: A "naked" rod-like conformation similar but not identical to that observed in vitro. RNA Biol 2017; 14:1046-1054. [PMID: 27574720 PMCID: PMC5680722 DOI: 10.1080/15476286.2016.1223005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/05/2016] [Accepted: 08/08/2016] [Indexed: 02/04/2023] Open
Abstract
With a minimal (250-400 nt), non-protein-coding, circular RNA genome, viroids rely on sequence/structural motifs for replication and colonization of their host plants. These motifs are embedded in a compact secondary structure whose elucidation is crucial to understand how they function. Viroid RNA structure has been tackled in silico with algorithms searching for the conformation of minimal free energy, and in vitro by probing in solution with RNases, dimethyl sulphate and bisulphite, and with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), which interrogates the RNA backbone at single-nucleotide resolution. However, in vivo approaches at that resolution have not been assayed. Here, after confirming by 3 termodynamics-based predictions and by in vitro SHAPE that the secondary structure adopted by the infectious monomeric circular (+) RNA of potato spindle tuber viroid (PSTVd) is a rod-like conformation with double-stranded segments flanked by loops, we have probed it in vivo with a SHAPE modification. We provide direct evidence that a similar, but not identical, rod-like conformation exists in PSTVd-infected leaves of Nicotiana benthamiana, verifying the long-standing view that this RNA accumulates in planta as a "naked" form rather than tightly associated with protecting host proteins. However, certain nucleotides of the central conserved region, including some of the loop E involved in key functions such as replication, are more SHAPE-reactive in vitro than in vivo. This difference is most likely due to interactions with proteins mediating some of these functions, or to structural changes promoted by other factors of the in vivo habitat.
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Affiliation(s)
- Amparo López-Carrasco
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
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Viability and genetic stability of potato spindle tuber viroid mutants with indels in specific loops of the rod-like secondary structure. Virus Res 2017; 240:94-100. [PMID: 28778395 DOI: 10.1016/j.virusres.2017.07.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 01/17/2023]
Abstract
Maintenance of the rod-like structure of potato spindle tuber viroid (PSTVd), which contains over 20 loops and bulges between double-stranded helices, is important for viroid biology. To study tolerance to modifications of the stem-loop structures and PSTVd capacity for mutation repair, we have created 6 mutants carrying 3-4 nucleotides deletions or insertions at three unique restriction sites, EagI, StyI and AvaII. Differences in the infectivity of these in vitro generated PSTVd mutants can result from where the mutations map, as well as from the extent to which the secondary structure of the molecule is affected. Deletion or insertion of 4 nucleotides at the EagI and StyI sites led to loss of infectivity. However, mutants with deletion (PSTVd-Ava-del) or insertion (PSTVd-Ava-in) of 3 nucleotides (221GAC223), at the AvaII site (loop 20) were viable but not genetically stable. In all analyzed plants, reversion to the wild type PSTVd-S23 sequence was observed for the PSTVd-Ava-in mutant a few weeks after agroinfiltration. Analysis of PSTVd-Ava-del progeny allowed the identification of 10 new sequence variants carrying various modifications, some of them having retained the original three nucleotide deletion at the AvaII site. Interestingly, other variants gained three nucleotides in the deletion site but did not revert to the original wild type sequence. The genetic stability of the progeny PSTVd-Ava-del sequence variants was evaluated in tomato leaves (early infection) and in both leaves and roots (late infection), respectively.
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Abstract
The plant vascular system plays a central role in coordinating physiological and developmental events through delivery of both essential nutrients and long-distance signaling agents. The enucleate phloem sieve tube system of the angiosperms contains a broad spectrum of RNA species. Grafting and transcriptomics studies have indicated that several thousand mRNAs move long distances from source organs to meristematic sink tissues. Ribonucleoprotein complexes play a pivotal role as stable RNA-delivery systems for systemic translocation of cargo RNA. In this review, we assess recent progress in the characterization of phloem and plasmodesmal transport as an integrated local and systemic communication network. We discuss the roles of phloem-mobile small RNAs in epigenetic events, including meristem development and genome stability, and the delivery of mRNAs to specific tissues in response to environmental inputs. A large body of evidence now supports a model in which phloem-mobile RNAs act as critical components of gene regulatory networks involved in plant growth, defense, and crop yield at the whole-plant level.
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Affiliation(s)
- Byung-Kook Ham
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616; ,
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616; ,
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Modelling the three-dimensional structure of the right-terminal domain of pospiviroids. Sci Rep 2017; 7:711. [PMID: 28386073 PMCID: PMC5429643 DOI: 10.1038/s41598-017-00764-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/13/2017] [Indexed: 12/20/2022] Open
Abstract
Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to present sequence or structural features to exploit host proteins. Viroid binding protein 1 (Virp1) is indispensable for replication of pospiviroids, the largest genus of viroids, in a host plant as well as in protoplasts. Virp1 is known to bind at two sites in the terminal right (TR) domain of pospiviroids; each site consists of a purine- (R-) and a pyrimidine- (Y-)rich motif that are partially base-paired to each other. Here we model the important structural features of the domain and show that it contains an internal loop of two Y · Y cis Watson-Crick/Watson-Crick (cWW) pairs, an asymmetric internal loop including a cWW and a trans Watson/Hoogsteen pair, and a thermodynamically quite stable hairpin loop with several stacking interactions. These features are discussed in connection to the known biological functions of the TR domain.
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Jiang D, Wang M, Li S. Functional analysis of a viroid RNA motif mediating cell-to-cell movement in Nicotiana benthamiana. J Gen Virol 2017; 98:121-125. [PMID: 27902342 DOI: 10.1099/jgv.0.000630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cell-to-cell trafficking through different cellular layers is a key process for various RNAs including those of plant viruses and viroids, but the regulatory mechanisms involved are still not fully elucidated and good model systems are important. Here, we analyse the function of a simple RNA motif (termed 'loop19') in potato spindle tuber viroid (PSTVd) which is required for trafficking in Nicotiana benthamiana leaves. Northern blotting, reverse transcriptase PCR (RT-PCR) and in situ hybridization analyses demonstrated that unlike wild-type PSTVd, which was present in the nuclei in all cell types, the trafficking-defective loop19 mutants were visible only in the nuclei of upper epidermal and palisade mesophyll cells, which shows that PSTVd loop19 plays a role in mediating RNA trafficking from palisade to spongy mesophyll cells in N.benthamiana leaves. Our findings and approaches have broad implications for studying the RNA motifs mediating trafficking of RNAs across specific cellular boundaries in other biological systems.
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Affiliation(s)
- Dongmei Jiang
- Center for Applied Plant Sciences, Ohio State University, Columbus, OH 43210, USA
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
| | - Meng Wang
- Beijing Research Center for Agricultural Standards and Testing, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
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Abstract
Mature viroids consist of a noncoding, covalently closed circular RNA that is able to autonomously infect respective host plants. Thus, they must utilize proteins of the host for most biological functions such as replication, processing, transport, and pathogenesis. Therefore, viroids can be regarded as minimal parasites of the host machinery. They have to present to the host machinery the appropriate signals based on either their sequence or their structure. Here, we summarize such sequence and structural features critical for the biological functions of viroids.
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Affiliation(s)
- Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
| | - Jean-Pierre Perreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliqueé sur le cancer, Université de Sherbrooke, Québec, Canada.
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Hua L, Song Y, Kim N, Laing C, Wang JTL, Schlick T. CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking. PLoS One 2016; 11:e0147097. [PMID: 26789998 PMCID: PMC4720362 DOI: 10.1371/journal.pone.0147097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/29/2015] [Indexed: 01/01/2023] Open
Abstract
RNA junctions are important structural elements of RNA molecules. They are formed when three or more helices come together in three-dimensional space. Recent studies have focused on the annotation and prediction of coaxial helical stacking (CHS) motifs within junctions. Here we exploit such predictions to develop an efficient alignment tool to handle RNA secondary structures with CHS motifs. Specifically, we build upon our Junction-Explorer software for predicting coaxial stacking and RNAJAG for modelling junction topologies as tree graphs to incorporate constrained tree matching and dynamic programming algorithms into a new method, called CHSalign, for aligning the secondary structures of RNA molecules containing CHS motifs. Thus, CHSalign is intended to be an efficient alignment tool for RNAs containing similar junctions. Experimental results based on thousands of alignments demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools. CHSalign yields a high score when aligning two RNA secondary structures with similar CHS motifs or helical arrangement patterns, and a low score otherwise. This new method has been implemented in a web server, and the program is also made freely available, at http://bioinformatics.njit.edu/CHSalign/.
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Affiliation(s)
- Lei Hua
- Bioinformatics Laboratory, Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Yang Song
- Bioinformatics Laboratory, Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Namhee Kim
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Christian Laing
- Bioinformatics Laboratory, Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Jason T. L. Wang
- Bioinformatics Laboratory, Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
- * E-mail: (JW); (TS)
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York, United States of America
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
- * E-mail: (JW); (TS)
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Saplaoura E, Kragler F. Mobile Transcripts and Intercellular Communication in Plants. DEVELOPMENTAL SIGNALING IN PLANTS 2016; 40:1-29. [DOI: 10.1016/bs.enz.2016.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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46
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Itaya A, Lucas WJ, Qi Y, Qu F, Wang Y, Zhong X, Liu CM. In memory of Professor Biao Ding (1960-2015). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2015; 57:730-731. [PMID: 26182880 DOI: 10.1111/jipb.12381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Asuka Itaya
- Agriculture and Agri-Food Canada, Ottawa, Canada
| | - William J Lucas
- Department of Plant Biology, University of California, Davis, USA
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Feng Qu
- Department of Plant Pathology, Ohio State University, Columbus, USA
| | - Ying Wang
- Department of Molecular Genetics, Ohio State University, Columbus, USA
| | - Xuehua Zhong
- Wisconsin Institute for Discovery & Laboratory of Genetics, University of Wisconsin, Madison, USA
| | - Chun-Ming Liu
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Bani-Hashemian SM, Pensabene-Bellavia G, Duran-Vila N, Serra P. Phloem restriction of viroids in three citrus hosts is overcome by grafting with Etrog citron: potential involvement of a translocatable factor. J Gen Virol 2015; 96:2405-2410. [PMID: 25888624 DOI: 10.1099/vir.0.000154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viroid systemic spread involves cell-to-cell movement from initially infected cells via plasmodesmata, long-distance movement within the phloem and again cell-to-cell movement to invade distal tissues including the mesophyll. Citrus exocortis viroid (CEVd), hop stunt viroid, citrus bent leaf viroid, citrus dwarfing viroid, citrus bark cracking viroid and citrus viroid V remained phloem restricted when singly infecting Citrus karna, Citrus aurantium and Poncirus trifoliata, but not Etrog citron, where they were additionally detected in mesophyll protoplasts. However, when CEVd-infected C. karna was side-grafted with Etrog citron--with the resulting plants being composed of a C. karna stock and an Etrog citron branch--the viroid was detected in mesophyll protoplasts of the former, thus indicating that the ability of Etrog citron to support viroid invasion of non-vascular tissues was transferred to the stock. Further results suggest that a translocatable factor from Etrog citron mediates this viroid trafficking.
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Affiliation(s)
- Seyed Mehdi Bani-Hashemian
- Departamento de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
- Iran Citrus Research Institute, 46915-335 Ramsar, Iran
| | - Giovanni Pensabene-Bellavia
- Departamento de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
- José Morera S.L., Pl. Almansa 1-1°, 46001 Valencia, Spain
| | - Nuria Duran-Vila
- Departamento de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (UPV - CSIC), 46022 Valencia, Spain
- Departamento de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
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Viroids, the simplest RNA replicons: How they manipulate their hosts for being propagated and how their hosts react for containing the infection. Virus Res 2015; 209:136-45. [PMID: 25738582 DOI: 10.1016/j.virusres.2015.02.027] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/23/2015] [Accepted: 02/23/2015] [Indexed: 12/31/2022]
Abstract
The discovery of viroids about 45 years ago heralded a revolution in Biology: small RNAs comprising around 350 nt were found to be able to replicate autonomously-and to incite diseases in certain plants-without encoding proteins, fundamental properties discriminating these infectious agents from viruses. The initial focus on the pathological effects usually accompanying infection by viroids soon shifted to their molecular features-they are circular molecules that fold upon themselves adopting compact secondary conformations-and then to how they manipulate their hosts to be propagated. Replication of viroids-in the nucleus or chloroplasts through a rolling-circle mechanism involving polymerization, cleavage and circularization of RNA strands-dealt three surprises: (i) certain RNA polymerases are redirected to accept RNA instead of their DNA templates, (ii) cleavage in chloroplastic viroids is not mediated by host enzymes but by hammerhead ribozymes, and (iii) circularization in nuclear viroids is catalyzed by a DNA ligase redirected to act upon RNA substrates. These enzymes (and ribozymes) are most probably assisted by host proteins, including transcription factors and RNA chaperones. Movement of viroids, first intracellularly and then to adjacent cells and distal plant parts, has turned out to be a tightly regulated process in which specific RNA structural motifs play a crucial role. More recently, the advent of RNA silencing has brought new views on how viroids may cause disease and on how their hosts react to contain the infection; additionally, viroid infection may be restricted by other mechanisms. Representing the lowest step on the biological size scale, viroids have also attracted considerable interest to get a tentative picture of the essential characteristics of the primitive replicons that populated the postulated RNA world.
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Minoia S, Navarro B, Delgado S, Di Serio F, Flores R. Viroid RNA turnover: characterization of the subgenomic RNAs of potato spindle tuber viroid accumulating in infected tissues provides insights into decay pathways operating in vivo. Nucleic Acids Res 2015; 43:2313-25. [PMID: 25662219 PMCID: PMC4344493 DOI: 10.1093/nar/gkv034] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While biogenesis of viroid RNAs is well-known, how they decay is restricted to data involving host RNA silencing. Here we report an alternative degradation pathway operating on potato spindle tuber viroid (PSTVd), the type species of nuclear-replicating viroids (family Pospiviroidae). Northern-blot hybridizations with full- and partial-length probes revealed a set of PSTVd (+) subgenomic (sg)RNAs in early-infected eggplant, some partially overlapping and reaching levels comparable to those of the genomic circular and linear forms. Part of the PSTVd (+) sgRNAs were also observed in Nicotiana benthamiana (specifically in the nuclei) and tomato, wherein they have been overlooked due to their low accumulation. Primer extensions of representative (+) sgRNAs failed to detect a common 5′ terminus, excluding that they could result from aborted transcription initiated at one specific site. Supporting this view, 5′- and 3′-RACE indicated that the (+) sgRNAs have 5′-OH and 3′-P termini most likely generated by RNase-mediated endonucleolytic cleavage of longer precursors. These approaches also unveiled PSTVd (−) sgRNAs with features similar to their (+) counterparts. Our results provide a mechanistic insight on how viroid decay may proceed in vivo during replication, and suggest that synthesis and decay of PSTVd strands might be coupled as in mRNA.
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Affiliation(s)
- Sofia Minoia
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Beatriz Navarro
- Istituto per la Protezione Sostenibile delle Piante, UOS Bari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, UOS Bari, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, Spain
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50
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Kovalskaya N, Hammond RW. Molecular biology of viroid-host interactions and disease control strategies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 228:48-60. [PMID: 25438785 DOI: 10.1016/j.plantsci.2014.05.006] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/26/2014] [Accepted: 05/14/2014] [Indexed: 06/04/2023]
Abstract
Viroids are single-stranded, covalently closed, circular, highly structured noncoding RNAs that cause disease in several economically important crop plants. They replicate autonomously and move systemically in host plants with the aid of the host machinery. In addition to symptomatic infections, viroids also cause latent infections where there is no visual evidence of infection in the host; however, transfer to a susceptible host can result in devastating disease. While there are non-hosts for viroids, no naturally occurring durable resistance has been observed in most host species. Current effective control methods for viroid diseases include detection and eradication, and cultural controls. In addition, heat or cold therapy combined with meristem tip culture has been shown to be effective for elimination of viroids for some viroid-host combinations. An understanding of viroid-host interactions, host susceptibility, and non-host resistance could provide guidance for the design of viroid-resistant plants. Efforts to engineer viroid resistance into host species have been underway for several years, and include the use of antisense RNA, antisense RNA plus ribozymes, a dsRNase, and siRNAs, among others. The results of those efforts and the challenges associated with creating viroid resistant plants are summarized in this review.
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Affiliation(s)
- Natalia Kovalskaya
- USDA ARS BARC Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA
| | - Rosemarie W Hammond
- USDA ARS BARC Molecular Plant Pathology Laboratory, Beltsville, MD 20705, USA.
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