1
|
N S, Sano T, Naoi T, R JG. Molecular phylogeny and secondary structure analysis of hop stunt viroid (HSVd) associated with Mulberry (Morus alba) in India. Arch Microbiol 2024; 206:240. [PMID: 38698140 DOI: 10.1007/s00203-024-03966-w] [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: 02/17/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024]
Abstract
Hop stunt viroid (HSVd), a small, single stranded, circular, non-coding infectious RNA known to cause infection in various economically important crop plants. In the present investigation, a study was conducted in the southern part of Karnataka districts of India to detect the possible association of HSVd infection in mulberry plants. A total of 41 mulberry plants showing typical viroid-like symptoms along with asymptomatic samples were collected and screened using conventional Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) using a specific set of HSVd-Fw/ HSVd-Re primers. Out of 41 samples, the study confirmed the presence of HSVd in six samples of mulberry collected from Ramanagara (1 sample), Chikkaballapur (3 samples) and Doddaballapura (2 samples) regions with an expected HSVd amplicon size of ∼ 290-300 nucleotides. The mechanical transmission of HSVd was also confirmed on cucumber (cv. Suyo) seedlings through bioassay, which was reconfirmed by RT-PCR. The amplicons were cloned, sequenced, and the representative nucleotide sequences were deposited in the NCBI GenBank. Subsequently, molecular phylogenetic analysis showed that HSVd mulberry isolates from this study were most closely related to grapevine isolates, indicating a common origin. On the other hand, it was shown to belong to a different group from mulberry isolates so far reported from Iran, Italy, Lebanon, and China. The secondary structure analysis of HSVd mulberry Indian isolates exhibited substitutions in the terminal left, pathogenicity, and variable regions compared to those of the Indian grapevine isolates. As far as this study is concerned, HSVd was detected exclusively in some mulberry plants with viral-like symptoms, but the pathogenesis and symptom expression needs to be further investigated to establish the relationship between HSVd and the disease symptoms in the mulberry plants.
Collapse
Affiliation(s)
- Shilpa N
- Molecular Phytodiagnostic Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570 006, India
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570 006, India
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho, 3, Hirosaki, 036-8561, Japan
| | - Takashi Naoi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho, 3, Hirosaki, 036-8561, Japan
| | - Janardhana G R
- Molecular Phytodiagnostic Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570 006, India.
| |
Collapse
|
2
|
Koonin EV. Circular RNAs from linear viral RNA genomes: A distinct dimension in the virus world. Proc Natl Acad Sci U S A 2024; 121:e2401335121. [PMID: 38349885 PMCID: PMC10895248 DOI: 10.1073/pnas.2401335121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024] Open
Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD20894
| |
Collapse
|
3
|
Chong LC, Lauber C. Viroid-like RNA-dependent RNA polymerase-encoding ambiviruses are abundant in complex fungi. Front Microbiol 2023; 14:1144003. [PMID: 37275138 PMCID: PMC10237039 DOI: 10.3389/fmicb.2023.1144003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 06/07/2023] Open
Abstract
Ambiviruses are hybrid infectious elements encoding the hallmark gene of RNA viruses, the RNA-dependent RNA polymerase, and self-cleaving RNA ribozymes found in many viroids. Ambiviruses are thought to be pathogens of fungi, although the majority of reported genomes have been identified in metatranscriptomes. Here, we present a comprehensive screen for ambiviruses in more than 46,500 fungal transcriptomes from the Sequence Read Archive (SRA). Our data-driven virus discovery approach identified more than 2,500 ambiviral sequences across the kingdom Fungi with a striking expansion in members of the phylum Basidiomycota representing the most complex fungal organisms. Our study unveils a large diversity of unknown ambiviruses with as little as 27% protein sequence identity to known members and sheds new light on the evolution of this distinct class of infectious agents with RNA genomes. No evidence for the presence of ambiviruses in human microbiomes was obtained from a comprehensive screen of respective metatranscriptomes available in the SRA.
Collapse
|
4
|
Lee BD, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M, Simmonds P, Kyrpides N, Gophna U, Dolja VV, Koonin EV. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell 2023; 186:646-661.e4. [PMID: 36696902 PMCID: PMC9911046 DOI: 10.1016/j.cell.2022.12.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
Collapse
Affiliation(s)
- Benjamin D Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Antonio Pedro Camargo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|
5
|
Shilpa N, Dhir S, Janardhana GR. Molecular detection and characterization of Potato spindle tuber viroid (PSTVd) infecting Tomato ( Solanum lycopersicum L.) in Karnataka State of India. Virusdisease 2022; 33:261-269. [PMID: 36277411 PMCID: PMC9481773 DOI: 10.1007/s13337-022-00782-y] [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: 05/09/2022] [Accepted: 07/16/2022] [Indexed: 11/27/2022] Open
Abstract
Potato Spindle Tuber Viroid (PSTVd) is a non-coding, infectious, small, circular RNA known to cause disease in agricultural and horticultural plants. In the present work, an investigation was conducted in the southern districts of Karnataka state to assess the possible pospiviroid infections on tomato plants that are considered natural hosts for viroids. A total of 83 tomato samples showing disease symptoms (virus or viroid-like) along with healthy ones were collected and subjected to viroid detection by conventional Reverse Transcriptase Polymer Chain Reaction (RT-PCR) using universal (Pospi1-RE/Pospi1-FW) and a specific set of primers (3H1/2H1). The study confirmed the presence of PSTVd in one of the samples of tomato collected from Banghatta village of Mandy District, with an expected amplicon of ~ 361 bp. The bioassay conducted on tomato plants (cv. Rutgers) proved the association of PSTVd, which was further confirmed by RT-PCR. The amplicons were cloned, sequenced, and the representative sequences were deposited in the NCBI GenBank. The sequence alignment and secondary structure analysis of the isolated viroid with other reference sequences revealed the variations in the pathogenicity, central conserved region, and Terminal right domains. The variations observed between the isolated PSTVd with that of other Indian isolates support that viroid may have been transmitted among the crop plants, possibly through seed or mechanical means.
Collapse
Affiliation(s)
- N. Shilpa
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006 India
- Molecular Phytodiagnostic Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006 India
| | - Sunny Dhir
- Department of Biotechnology, Maharishi Markandeshwar Engineering College, Maharishi Markandeshwar Deemed to be University, Mullana, Ambala, 133207 India
| | - G. R. Janardhana
- Molecular Phytodiagnostic Laboratory, Department of Studies in Botany, University of Mysore, Manasagangotri, Mysuru, Karnataka 570 006 India
| |
Collapse
|
6
|
The unique carnation stunt-associated pararetroviroid. Virus Res 2022; 312:198709. [DOI: 10.1016/j.virusres.2022.198709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/07/2022] [Accepted: 02/12/2022] [Indexed: 12/12/2022]
|
7
|
Viroids and Viroid-like Circular RNAs: Do They Descend from Primordial Replicators? LIFE (BASEL, SWITZERLAND) 2022; 12:life12010103. [PMID: 35054497 PMCID: PMC8781251 DOI: 10.3390/life12010103] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/09/2023]
Abstract
Viroids are a unique class of plant pathogens that consist of small circular RNA molecules, between 220 and 450 nucleotides in size. Viroids encode no proteins and are the smallest known infectious agents. Viroids replicate via the rolling circle mechanism, producing multimeric intermediates which are cleaved to unit length either by ribozymes formed from both polarities of the viroid genomic RNA or by coopted host RNAses. Many viroid-like small circular RNAs are satellites of plant RNA viruses. Ribozyviruses, represented by human hepatitis delta virus, are larger viroid-like circular RNAs that additionally encode the viral nucleocapsid protein. It has been proposed that viroids are direct descendants of primordial RNA replicons that were present in the hypothetical RNA world. We argue, however, that much later origin of viroids, possibly, from recently discovered mobile genetic elements known as retrozymes, is a far more parsimonious evolutionary scenario. Nevertheless, viroids and viroid-like circular RNAs are minimal replicators that are likely to be close to the theoretical lower limit of replicator size and arguably comprise the paradigm for replicator emergence. Thus, although viroid-like replicators are unlikely to be direct descendants of primordial RNA replicators, the study of the diversity and evolution of these ultimate genetic parasites can yield insights into the earliest stages of the evolution of life.
Collapse
|
8
|
Pérez-Vargas J, Pereira de Oliveira R, Jacquet S, Pontier D, Cosset FL, Freitas N. HDV-Like Viruses. Viruses 2021; 13:1207. [PMID: 34201626 PMCID: PMC8310214 DOI: 10.3390/v13071207] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatitis delta virus (HDV) is a defective human virus that lacks the ability to produce its own envelope proteins and is thus dependent on the presence of a helper virus, which provides its surface proteins to produce infectious particles. Hepatitis B virus (HBV) was so far thought to be the only helper virus described to be associated with HDV. However, recent studies showed that divergent HDV-like viruses could be detected in fishes, birds, amphibians, and invertebrates, without evidence of any HBV-like agent supporting infection. Another recent study demonstrated that HDV can be transmitted and propagated in experimental infections ex vivo and in vivo by different enveloped viruses unrelated to HBV, including hepatitis C virus (HCV) and flaviviruses such as Dengue and West Nile virus. All this new evidence, in addition to the identification of novel virus species within a large range of hosts in absence of HBV, suggests that deltaviruses may take advantage of a large spectrum of helper viruses and raises questions about HDV origins and evolution.
Collapse
Affiliation(s)
- Jimena Pérez-Vargas
- CIRI—Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 allée d’Italie, F-69007 Lyon, France; (J.P.-V.); (R.P.d.O.); (N.F.)
| | - Rémi Pereira de Oliveira
- CIRI—Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 allée d’Italie, F-69007 Lyon, France; (J.P.-V.); (R.P.d.O.); (N.F.)
| | - Stéphanie Jacquet
- LBBE UMR5558 CNRS—Centre National de la Recherche Scientifique, Université de Lyon 1—48 bd du 11 Novembre 1918, 69100 Villeurbanne, France; (S.J.); (D.P.)
| | - Dominique Pontier
- LBBE UMR5558 CNRS—Centre National de la Recherche Scientifique, Université de Lyon 1—48 bd du 11 Novembre 1918, 69100 Villeurbanne, France; (S.J.); (D.P.)
| | - François-Loïc Cosset
- CIRI—Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 allée d’Italie, F-69007 Lyon, France; (J.P.-V.); (R.P.d.O.); (N.F.)
| | - Natalia Freitas
- CIRI—Centre International de Recherche en Infectiologie, Université de Lyon, Université Claude Bernard Lyon 1, Inserm, U1111, CNRS, UMR5308, ENS Lyon, 46 allée d’Italie, F-69007 Lyon, France; (J.P.-V.); (R.P.d.O.); (N.F.)
| |
Collapse
|
9
|
AFM Images of Viroid-Sized Rings That Self-Assemble from Mononucleotides through Wet-Dry Cycling: Implications for the Origin of Life. Life (Basel) 2020; 10:life10120321. [PMID: 33266191 PMCID: PMC7760185 DOI: 10.3390/life10120321] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 11/17/2022] Open
Abstract
It is possible that early life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations reported that wet–dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers. The aim of the study reported here was to visualize the products by atomic force microscopy. In addition to globular oligomers, ring-like structures ranging from 10–200 nm in diameter, with an average around 30–40 nm, were abundant, particularly when nucleotides capable of base pairing were present. The thickness of the rings was consistent with single stranded products, but some had thicknesses indicating base pair stacking. Others had more complex structures in the form of short polymer attachments and pairing of rings. These observations suggest the possibility that base-pairing may promote polymerization during wet–dry cycling followed by solvation of the rings. We conclude that RNA-like rings and structures could have been synthesized non-enzymatically on the prebiotic Earth, with sizes sufficient to fold into ribozymes and genetic molecules required for life to begin.
Collapse
|
10
|
Maurel MC, Leclerc F, Hervé G. Ribozyme Chemistry: To Be or Not To Be under High Pressure. Chem Rev 2019; 120:4898-4918. [DOI: 10.1021/acs.chemrev.9b00457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Sorbonne Université, Muséum National d’Histoire Naturelle, EPHE, F-75005 Paris, France
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, F-91198 Gif-sur-Yvette, France
| | - Guy Hervé
- Laboratoire BIOSIPE, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Campus Pierre et Marie Curie, F-75005 Paris, France
| |
Collapse
|
11
|
Mackie AE, Barbetti MJ, Rodoni B, McKirdy SJ, Jones RAC. Effects of a Potato Spindle Tuber Viroid Tomato Strain on the Symptoms, Biomass, and Yields of Classical Indicator and Currently Grown Potato and Tomato Cultivars. PLANT DISEASE 2019; 103:3009-3017. [PMID: 31567060 DOI: 10.1094/pdis-02-19-0312-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The Chittering strain of potato spindle tuber viroid (PSTVd) infects solanaceous crops and wild plants in the subtropical Gascoyne Horticultural District of Western Australia. Classical PSTVd indicator hosts tomato cultivar Rutgers (R) and potato cultivar Russet Burbank (RB) and currently widely grown tomato cultivars Petula (P) and Swanson (S) and potato cultivars Nadine (N) and Atlantic (A) were inoculated with this strain to study its pathogenicity, quantify fruit or tuber yield losses, and establish whether tomato strains might threaten potato production. In potato foliage, infection caused spindly stems, an upright growth habit, leaves with ruffled margins and reduced size, and upward rolling and twisting of terminal leaflets (RB, A, and N); axillary shoot proliferation (A); severe plant stunting (N and RB); and necrotic spotting of petioles and stems (RB). Tubers from infected plants were tiny (N) or small and "spindle shaped" with (A) or without (RB) cracking. Potato foliage dry weight biomass was decreased by 30 to 44% in A and RB and 37% in N, whereas tuber yield was diminished by 50 to 89% in A, 69 to 71% in RB, and 90% in N. In tomato foliage, infection caused epinasty and rugosity in apical leaves, leaf chlorosis, and plant stunting (S, P, and N); cupped leaves (S and P); and reduced leaf size, flower abortion, and necrosis of midribs, petioles, and stems (R). Mean tomato fruit size was greatly decreased in all three cultivars. Tomato foliage dry weight biomass was diminished by 40 to 53% (P), 42% (S), and 37 to 51% (R). Tomato fruit yield was decreased by 60 to 76% (P), 52% (S), and 64 to 89% (R), respectively. Thus, the tomato strain studied was highly pathogenic to classical indicator and representative current tomato and potato cultivars, causing major losses in fruit and tuber yields. Tomato PSTVd strains, therefore, pose a threat to tomato and potato industries worldwide.
Collapse
Affiliation(s)
- Alison E Mackie
- University of Western Australia School of Agriculture and Environment, Faculty of Science, University of Western Australia, Crawley, Western Australia 6009, Australia
- Department of Primary Industries and Regional Development, Western Australia, Perth, Western Australia 6983, Australia
| | - Martin J Barbetti
- University of Western Australia School of Agriculture and Environment, Faculty of Science, University of Western Australia, Crawley, Western Australia 6009, Australia
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Brendan Rodoni
- AgriBio, Agriculture Victoria, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Simon J McKirdy
- Harry Butler Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Roger A C Jones
- Department of Primary Industries and Regional Development, Western Australia, Perth, Western Australia 6983, Australia
- University of Western Australia Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia
| |
Collapse
|
12
|
Koonin EV, Wolf YI, Katsnelson MI. Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states. Biol Direct 2017; 12:31. [PMID: 29202832 PMCID: PMC5715634 DOI: 10.1186/s13062-017-0202-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/22/2017] [Indexed: 01/02/2023] Open
Abstract
Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic diversity. Here we examine simple thought experiments to demonstrate that both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are evolutionarily unstable. REVIEWERS This article has been reviewed by Yitzhak Pilpel, Bojan Zagrovic, and Eric van Nimwegen.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Mikhail I Katsnelson
- Institute for Molecules and Materials, Radboud University, 6525AJ, Nijmegen, Netherlands
| |
Collapse
|
13
|
Leclerc F, Zaccai G, Vergne J, Řìhovà M, Martel A, Maurel MC. Self-assembly Controls Self-cleavage of HHR from ASBVd (-): a Combined SANS and Modeling Study. Sci Rep 2016; 6:30287. [PMID: 27456224 PMCID: PMC4960562 DOI: 10.1038/srep30287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 01/16/2023] Open
Abstract
In the Avocado Sunblotch Viroid (ASBVd: 249-nt) from the Avsunviroidae family, a symmetric rolling-circle replication operates through an autocatalytic mechanism mediated by hammerhead ribozymes (HHR) embedded in both polarity strands. The concatenated multimeric ASBVd (+) and ASBVd (-) RNAs thus generated are processed by cleavage to unit-length where ASBVd (-) self-cleaves with more efficiency. Absolute scale small angle neutron scattering (SANS) revealed a temperature-dependent dimer association in both ASBVd (-) and its derived 79-nt HHR (-). A joint thermodynamic analysis of SANS and catalytic data indicates the rate-determining step corresponds to the dimer/monomer transition. 2D and 3D models of monomeric and dimeric HHR (-) suggest that the inter-molecular contacts stabilizing the dimer (between HI and HII domains) compete with the intra-molecular ones stabilizing the active conformation of the full-length HHR required for an efficient self-cleavage. Similar competing intra- and inter-molecular contacts are proposed in ASBVd (-) though with a remoter region from an extension of the HI domain.
Collapse
Affiliation(s)
- Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), Dept. of Genome Biology, CEA, CNRS, Université Paris Sud, Gif-sur-Yvette, F-91198, France
| | - Giuseppe Zaccai
- Institut Laue Langevin, Grenoble, F-38042, France.,Institut de Biologie Structurale (IBS), CNRS, Grenoble, F-38044, France.,IBS, CEA, Grenoble, F-38044, France.,IBS, Univ Grenoble Alpes, Grenoble, F-38044, France
| | - Jacques Vergne
- Institut de Systématique, Evolution, Biodiversité ISyEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50 Paris, F-75005, France
| | - Martina Řìhovà
- Institut de Systématique, Evolution, Biodiversité ISyEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50 Paris, F-75005, France.,Institute of Physics, Charles University, Faculty of Mathematics and Physics, Prague 2, CZ-121 16, Czech Republic
| | - Anne Martel
- Institut Laue Langevin, Grenoble, F-38042, France
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité ISyEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50 Paris, F-75005, France
| |
Collapse
|
14
|
A mutual titer-enhancing relationship and similar localization patterns between Citrus exocortis viroid and Hop stunt viroid co-infecting two citrus cultivars. Virol J 2015; 12:142. [PMID: 26377407 PMCID: PMC4574207 DOI: 10.1186/s12985-015-0357-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/13/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Citrus exocortis viroid (CEVd) and Hop stunt viroid (HSVd) are commonly found simultaneously infecting different citrus cultivars in Taiwan. A crucial question to be addressed is how accumulations of these two viroids affect each other in an infected plant. In this study, we investigated the relationship between the two viroids at macroscopic and microscopic levels. METHODS CEVd and HSVd titers were examined by real-time RT-PCR in 17 plants of two citrus cultivars (blood orange and Murcott mandarin) every 3 months (spring, summer, fall and winter) from 2011 to 2013. Three nonparametric tests (Spearman's rank correlation coefficient, Kendall's tau rank correlation coefficient and Hoeffding's inequality) were performed to test the correlation between CEVd and HSVd. Cellular and subcellular localizations of the two viroids were detected by digoxigenin- and colloidal gold-labeled in situ hybridization using light and transmission electron microscopy. RESULTS The two viroids were unevenly distributed in four different types of citrus tissues (rootstock bark, roots, twig bark and leaves). Compared with blood orange, Murcott mandarin was generally more susceptible to CEVd and HSVd infection. Both viroids replicated and preferentially accumulated in the underground tissues of the two citrus cultivars. Except for blood orange at high temperatures, significant positive correlations were observed between the two viroids in specific tissues of both cultivars. Relative to concentrations under single-infection conditions, the CEVd population significantly increased under double infection during half of the 12 monitored seasons; in contrast, the population of HSVd significantly increased under double infection during only one season. At cellular/subcellular levels, the two viroids showed similar localization patterns in four tissues and the cells of these tissues in the two citrus cultivars. CONCLUSIONS Our findings of titer enhancement, localization similarity, and lack of symptom aggravation under CEVd and HSVd double infection suggest that the two viroids have a positive relationship in citrus. The combination of molecular and cellular techniques used in this study provided evidence of titer correlation and localization of co-infecting viroids in the host. These methods may thus be useful tools for exploring viroid-viroid and viroid-host interactions.
Collapse
|
15
|
Development of a duplex one-step RT-qPCR assay for the simultaneous detection of Apple scar skin viroid and plant RNA internal control. J Virol Methods 2015; 221:100-5. [DOI: 10.1016/j.jviromet.2015.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/28/2015] [Accepted: 04/29/2015] [Indexed: 11/19/2022]
|
16
|
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.
Collapse
|
17
|
Lin CY, Wu ML, Shen TL, Yeh HH, Hung TH. Multiplex detection, distribution, and genetic diversity of Hop stunt viroid and Citrus exocortis viroid infecting citrus in Taiwan. Virol J 2015; 12:11. [PMID: 25645458 PMCID: PMC4340875 DOI: 10.1186/s12985-015-0247-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/20/2015] [Indexed: 11/15/2022] Open
Abstract
Background Two citrus viroids, Citrus exocortis viroid (CEVd) and Hop stunt viroid (HSVd), have been reported and become potential threats to the citrus industry in Taiwan. The distributions and infection rates of two viroids have not been investigated since the two diseases were presented decades ago. The genetic diversities and evolutionary relationships of two viroids also remain unclear in the mix citrus planted region. Methods Multiplex RT-PCR was used to detect the two viroids for the first time in seven main cultivars of citrus. Multiplex real-time RT-PCR quantified the distributions of two viroids in four citrus tissues. Sequence alignment and phylogenetic analysis were performed using the ClustalW and MEGA6 (neighbor-joining with p-distance model), respectively. Results HSVd was found more prevalent than CEVd (32.2% vs. 30.4%). Both CEVd and HSVd were commonly found simultaneously in the different citrus cultivars (up to 55%). Results of the multiplex quantitative analysis suggested that uneven distributions of both viroids with twig bark as the most appropriate material for studies involving viroid sampling such as quarantine inspection. Sequence alignment against Taiwanese isolates, along with analysis of secondary structure, revealed the existence of 10 and 5 major mutation sites in CEVd and HSVd, respectively. The mutation sites in CEVd were located at both ends of terminal and variability domains, whereas those in HSVd were situated in left terminal and pathogenicity domains. A phylogenetic analysis incorporating worldwide viroid isolates indicated three and two clusters for the Taiwanese isolates of CEVd and HSVd, respectively. Conclusions Moderately high infection and co-infection rates of two viroids in certain citrus cultivars suggest that different citrus cultivars may play important roles in viroid infection and evolution. These data also demonstrate that two multiplex molecular detection methods developed in the present study provide powerful tools to understand the genetic diversities among viroid isolates and quantify viroids in citrus host. Our field survey can help clarify citrus-viroid relationships as well as develop proper prevention strategies.
Collapse
Affiliation(s)
- Chun-Yi Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan.
| | - Meng-Ling Wu
- Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, 10066, Taiwan.
| | - Tang-Long Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan.
| | - Hsin-Hung Yeh
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Ting-Hsuan Hung
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617, Taiwan.
| |
Collapse
|
18
|
Singh RP. The discovery and eradication of potato spindle tuber viroid in Canada. Virusdisease 2014; 25:415-24. [PMID: 25674616 PMCID: PMC4262315 DOI: 10.1007/s13337-014-0225-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 08/19/2014] [Indexed: 11/28/2022] Open
Abstract
In 1960s, potato spindle tuber was thought to be a viral disease. In 1971, the agent of the disease was characterised as a low-molecular weight infectious ribonucleic acid (RNA), which was named as 'viroid', specifically Potato spindle tuber viroid (PSTVd)). Since then, more than 30 plant diseases in horticultural and ornamental plants have been shown to be caused by different viroids globally. Viroids are single-stranded RNA, covalently closed circular molecule, without any protein coat. They are the smallest known plant pathogen containing RNA genome ranging from 246 nucleotides (Coconut cadang-cadang viroid) to 399 nucleotides (Chrysanthemum chlorotic mottle viroid). Some viroids are located in the plant cell nucleus (pospiviroids) and others in the chloroplast (avsunviroids). With the recognition of pathogenic nature of viroid, specific detection methodologies were developed, which enabled detection of PSTVd in seed-potato tubers prior to their planting in the field, and thus PSTVd was prevented from spreading the disease. As a result, PSTVd was eradicated from Canada in late 1980s. Viroids similar to PSTVd (Pospiviroid) have been discovered and they are detected in symptomless ornamental plants. Although, PSTVd has been eradicated from Canada, there is a strong possibility of viroid introduction from other plants besides potato and tomato and causing PSTVd like diseases.
Collapse
Affiliation(s)
- Rudra P. Singh
- Agriculture and Agri-Food Canada (retired), Fredericton, NB Canada
| |
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
El-Murr N, Maurel MC, Rihova M, Vergne J, Hervé G, Kato M, Kawamura K. Behavior of a hammerhead ribozyme in aqueous solution at medium to high temperatures. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2012; 99:731-8. [PMID: 22915317 DOI: 10.1007/s00114-012-0954-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/28/2022]
Abstract
The "RNA world" hypothesis proposes that--early in the evolution of life--RNA molecules played important roles both in information storage and in enzymatic functions. However, this hypothesis seems to be inconsistent with the concept that life may have emerged under hydrothermal conditions since RNA molecules are considered to be labile under such extreme conditions. Presently, the possibility that the last common ancestor of the present organisms was a hyperthermophilic organism which is important to support the hypothesis of the hydrothermal origin of life has been subject of strong discussions. Consequently, it is of importance to study the behavior of RNA molecules under hydrothermal conditions from the viewpoints of stability, catalytic functions, and storage of genetic information of RNA molecules and determination of the upper limit of temperature where life could have emerged. In the present work, self-cleavage of a natural hammerhead ribozyme was examined at temperatures 10-200 °C. Self-cleavage was investigated in the presence of Mg(2+), which facilitates and accelerates this reaction. Self-cleavage of the hammerhead ribozyme was clearly observed at temperatures up to 60 °C, but at higher temperatures self-cleavage occurs together with hydrolysis and with increasing temperature hydrolysis becomes dominant. The influence of the amount of Mg(2+) on the reaction rate was also investigated. In addition, we discovered that the reaction proceeds in the presence of high concentrations of monovalent cations (Na(+) or K(+)), although very slowly. Furthermore, at high temperatures (above 60 °C), monovalent cations protect the ribozyme against degradation.
Collapse
Affiliation(s)
- Nizar El-Murr
- ER12, ANBioPhy, Fonctions et Interactions des Acides Nucléiques, UPMC Univ Paris 6, 75005, Paris, France
| | | | | | | | | | | | | |
Collapse
|
21
|
Acosta-Leal R, Duffy S, Xiong Z, Hammond RW, Elena SF. Advances in plant virus evolution: translating evolutionary insights into better disease management. PHYTOPATHOLOGY 2011; 101:1136-48. [PMID: 21554186 DOI: 10.1094/phyto-01-11-0017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Recent studies in plant virus evolution are revealing that genetic structure and behavior of virus and viroid populations can explain important pathogenic properties of these agents, such as host resistance breakdown, disease severity, and host shifting, among others. Genetic variation is essential for the survival of organisms. The exploration of how these subcellular parasites generate and maintain a certain frequency of mutations at the intra- and inter-host levels is revealing novel molecular virus-plant interactions. They emphasize the role of host environment in the dynamic genetic composition of virus populations. Functional genomics has identified host factors that are transcriptionally altered after virus infections. The analyses of these data by means of systems biology approaches are uncovering critical plant genes specifically targeted by viruses during host adaptation. Also, a next-generation resequencing approach of a whole virus genome is opening new avenues to study virus recombination and the relationships between intra-host virus composition and pathogenesis. Altogether, the analyzed data indicate that systematic disruption of some specific parameters of evolving virus populations could lead to more efficient ways of disease prevention, eradication, or tolerable virus-plant coexistence.
Collapse
|
22
|
Abstract
Viroids are the smallest known pathogenic agents. They are noncoding, single-stranded, closed-circular, "naked" RNAs, which replicate through RNA-RNA transcription. Viroids of the Avsunviroidae family possess a hammerhead ribozyme in their sequence, allowing self-cleavage during their replication. To date, viroids have only been detected in plant cells. Here, we investigate the replication of Avocado sunblotch viroid (ASBVd) of the Avsunviroidae family in a nonconventional host, the yeast Saccharomyces cerevisiae. We demonstrate that ASBVd RNA strands of both polarities are able to self-cleave and to replicate in a unicellular eukaryote cell. We show that the viroid monomeric RNA is destabilized by the nuclear 3' and the cytoplasmic 5' RNA degradation pathways. For the first time, our results provide evidence that viroids can replicate in other organisms than plants and that yeast contains all of the essential cellular elements for the replication of ASBVd.
Collapse
|
23
|
Abstract
This article addresses some of the questions relating to how hepatitis delta virus (HDV), an agent so far unique in the animal world, might have arisen. HDV was discovered in patients infected with hepatitis B virus (HBV). It generally makes HBV infections more damaging to the liver. It is a subviral satellite agent that depends upon HBV envelope proteins for its assembly and ability to infect new cells. In other aspects of replication, HDV is both independent of and very different from HBV. In addition, the small single-stranded circular RNA genome of HDV, and its mechanism of replication, demonstrate an increasing number of similarities to the viroids - a large family of helper-independent subviral agents that cause pathogenesis in plants.
Collapse
Affiliation(s)
- John Taylor
- Chase Cancer Center, PA 19111, USA, Tel.: +1 215 728 2436, Fax: +1 215 728 2412,
| | - Martin Pelchat
- Department of Biochemistry, Microbiology & Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada, Tel.: +1 613 562 5800 ext. 8846, Fax: +1 613 562 5452,
| |
Collapse
|
24
|
Coleus blumei viroid 6: a new tentative member of the genus Coleviroid derived from natural genome shuffling. Arch Virol 2009; 154:993-7. [PMID: 19434474 DOI: 10.1007/s00705-009-0388-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 04/20/2009] [Indexed: 10/20/2022]
Abstract
Coleus blumei can be infected by several viroids of the genus Coleviroid. One year after detecting a mixed infection of coleus blumei viroid 1 (CbVd-1) and 5 (CbVd-5) in coleus seedlings inoculated with these two viroids, we found an additional viroid-like RNA. Sequence analysis revealed a viroid of 342 nucleotides that contains the central conserved region of coleviroids and is a chimera of the left half of CbVd-3 and the right half of CbVd-5. This new viroid, tentatively referred to as coleus blumei viroid 6 (CbVd-6), appears to have arisen from a natural recombination event or genome shuffling.
Collapse
|
25
|
Percot A, Lecomte S, Vergne J, Maurel MC. Hairpin ribozyme catalysis: A surface-enhanced Raman spectroscopy study. Biopolymers 2009; 91:384-90. [DOI: 10.1002/bip.21143] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
26
|
Hou WY, Sano T, Li F, Wu ZJ, Li L, Li SF. Identification and characterization of a new coleviroid (CbVd-5). Arch Virol 2008; 154:315-20. [PMID: 19112552 DOI: 10.1007/s00705-008-0276-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Accepted: 11/11/2008] [Indexed: 11/28/2022]
Abstract
A viroid-like RNA was detected from coleus (Coleus blumei) in China. It consisted of 274 nucleotides and had 66% sequence identity with a member of the closest known viroid species. The predicted secondary structure is rod-shaped with extensive base pairing, and it has the conserved region characteristic of the genus Coleviroid. Two terminal sequences that are highly conserved among some members of the genus were also identified. The viroid-like RNA was successfully transmitted to coleus by slash-inoculation. This viroid was identified as a new member of the genus Coleviroid, and we tentatively propose the name Coleus blumei viroid 5 (CbVd-5).
Collapse
Affiliation(s)
- Wan-Ying Hou
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West No. 2, Beijing 100193, People's Republic of China
| | | | | | | | | | | |
Collapse
|
27
|
Nakaune R, Nakano M. Identification of a new Apscaviroid from Japanese persimmon. Arch Virol 2008; 153:969-72. [PMID: 18365126 DOI: 10.1007/s00705-008-0073-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 02/27/2008] [Indexed: 11/28/2022]
Abstract
Three viroid-like sequences were detected from Japanese persimmon (Diospyrus kaki Thunb.) by RT-PCR using primers specific for members of the genus Apscaviroid. Based on the sequences, we determined the complete genomic sequences. Two had 92.1-94.3% sequence identity with citrus viroid OS (CVd-OS) and 91.4-96.3% identity with apple fruit crinkle viroid (AFCVd), respectively. Another one, tentatively named persimmon viroid (PVd), had 396 nucleotides and less than 70% sequence identity with known viroids. The secondary structure of PVd is proposed to be rod-like with extensive base pairing and contains the terminal conserved region and the central conserved region characteristic of the genus Apscaviroid. Moreover, we confirmed that the viroids, including PVd, are graft transmissible from persimmon to persimmon and that persimmon is a natural host of these viroids. According to its molecular and biological properties, PVd should be considered a member of a new species in the genus Apscaviroid.
Collapse
Affiliation(s)
- Ryoji Nakaune
- Grape and Persimmon Research Station, National Institute of Fruit Tree Science, National Agriculture and Food Research Organization, Akitsu 301-2, Higashihiroshima, Hiroshima 739-2494, Japan.
| | | |
Collapse
|
28
|
Cohen O, Batuman O, Stanbekova G, Sano T, Mawassi M, Bar-Joseph M. Construction of a multiprobe for the simultaneous detection of viroids infecting citrus trees. Virus Genes 2007; 33:287-92. [PMID: 16990999 DOI: 10.1007/s11262-006-0067-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 01/12/2006] [Indexed: 11/27/2022]
Abstract
Infections with different viroid species are common among cultivated fruit trees and grapevines, and many old-clone citrus varieties contain up to five citrus viroids (CVds) within a single tree. This paper describes the construction of a CVd-Multiprobe consisting of full-length clones of Hop stunt viroid, Citrus exocortis viroid, Citrus bent leaf viroid and CVd-III. The CVd-Multiprobe was tested against RNA transcripts of the four viroids and RNA extracts from plants singly infected with CEVd or HSVd or multiply infected with different CVds. The viroids were effectively diagnosed with the DIG labeled CVd-Multiprobe when tested by Northern hybridization or dot blot analyses. The CVd-Multiprobe does not provide information on the specific viroid resulting in a positive signal. However, this should not be considered as a problem, since most citrus certification programs will discard budwood source trees infected with any of the known CVds.
Collapse
Affiliation(s)
- Oded Cohen
- The S. Tolkowsky laboratory, Department of Virology , Volcani Center, ARO, Bet Dagan, Israel
| | | | | | | | | | | |
Collapse
|
29
|
Abstract
All life forms on Earth share the same biological program based on the DNA/RNA genomes and proteins. The genetic information, recorded in the nucleotide sequence of the DNA and RNA molecule, supplies the language of life which is transferred through the different generations, thus ensuring the perpetuation of genetic information on Earth. The presence of a genetic system is absolutely essential to life. Thus, the appearance in an ancestral era of a nucleic acid-like polymer able to undergo Darwinian evolution indicates the beginning of life on our planet. The building of primordial genetic molecules, whatever they were, required the presence of a protected environment, allowing the synthesis and concentration of precursors (nucleotides), their joining into larger molecules (polynucleotides), the protection of forming polymers against degradation (i.e. by cosmic and UV radiation), thus ensuring their persistence in a changing environment, and the expression of the "biological" potential of the molecule (its capacity to self-replicate and evolve). Determining how these steps occurred and how the primordial genetic molecules originated on Earth is a very difficult problem that still must be resolved. It has long been proposed that surface chemistry, i.e. on clay minerals, could have played a crucial role in the prebiotic formation of molecules basic to life. In the present work, we discuss results obtained in different fields that strengthen the hypothesis of a clay-surface-mediated origin of genetic material.
Collapse
Affiliation(s)
- Enzo Gallori
- Department of Animal Biology and Genetics, University of Florence, Via Romana 17, 50125 Florence, Italy.
| | | | | |
Collapse
|
30
|
Biondi E, Branciamore S, Fusi L, Gago S, Gallori E. Catalytic activity of hammerhead ribozymes in a clay mineral environment: implications for the RNA world. Gene 2006; 389:10-8. [PMID: 17125938 DOI: 10.1016/j.gene.2006.09.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2006] [Revised: 09/11/2006] [Accepted: 09/12/2006] [Indexed: 01/04/2023]
Abstract
The hypothesized RNA-based world would have required the presence of a protected environment in which RNA, or an RNA-like molecule, could originate and express its biological activity. Recent studies have indicated that RNA molecules adsorbed/bound on clay minerals are able to persist in the presence of degrading agents, to interact with surrounding molecules, and to transmit the information contained in their nucleotide sequences. In this study, we assessed the ability of RNA molecules with catalytic activity to perform a specific reaction in a mineral environment. For this purpose, we investigated the self-cleavage reaction of the hammerhead ribozyme of the Avocado Sun Blotch Viroid (ASBVd), both in the monomeric and in dimeric forms. The monomeric transcript was tightly bound on the clay mineral montmorillonite to form a stable complex, while the behaviour of the dimeric transcript was studied in the presence of the clay particles in the reaction mixture. The results indicated that the hammerhead ribozyme was still active when the monomeric transcript was adsorbed on the clay surface, even though its efficiency was reduced to about 20% of that in solution. Moreover, the self-cleavage of clay-adsorbed molecule was significantly enhanced ( approximately four times) by the presence of the 5' reaction product. The self-cleavage reaction of the dimeric transcript in the presence of montmorillonite indicated that the mineral particles protected the RNA molecules against aspecific degradation and increased the rate of cleavage kinetics by about one order of magnitude. These findings corroborate the hypothesis that clay-rich environments would have been a good habitat in which RNA or RNA-like molecules could originate, accumulate and undergo Darwinian evolutionary processes, leading to the first living cells on Earth.
Collapse
Affiliation(s)
- Elisa Biondi
- Department of Animal Biology and Genetics, University of Florence, Florence, Italy
| | | | | | | | | |
Collapse
|
31
|
Flores R, Delgado S, Rodio ME, Ambrós S, Hernández C, Serio FDI. Peach latent mosaic viroid: not so latent. MOLECULAR PLANT PATHOLOGY 2006; 7:209-21. [PMID: 20507441 DOI: 10.1111/j.1364-3703.2006.00332.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
SUMMARY Taxonomy: Peach latent mosaic viroid (PLMVd) is the type species of the genus Pelamoviroid within the family Avsunviroidae of chloroplastic viroids with hammerhead ribozymes. Physical properties: A small circular RNA of 336-351 nt (differences in size result from the absence or presence of certain insertions) adopting a branched conformation stabilized by a pseudoknot between two kissing loops. This particular conformation is most likely responsible for the insolubility of PLMVd in highly saline conditions (in which other viroids adopting a rod-like conformation are soluble). Both polarity strands are able to form hammerhead structures and to self-cleave during replication as predicted by these ribozymes. Biological properties: Although most infections occur without conspicuous symptoms, certain PLMVd isolates induce leaf mosaics, blotches and in the most extreme cases albinism (peach calico, PC), flower streaking, delays in foliation, flowering and ripening, deformations and decolorations of fruits, which usually present cracked sutures and enlarged roundish stones, bud necrosis, stem pitting and premature ageing of the trees, which also adopt a characteristic growing pattern (open habit). The molecular determinant for PC has been mapped at a 12-14-nt insertion that folds into a hairpin capped by a U-rich loop present only in certain variants. PLMVd is horizontally transmitted by the propagation of infected buds and to a lesser extent by pruning tools and aphids, but not by pollen; the viroid is not vertically transmitted through seed. Interesting features: This provides a suitable system for studying how a minimal non-protein-coding catalytic RNA replicates (subverting a DNA-dependent RNA polymerase to transcribe an RNA template), moves, interferes with the metabolism of its host (inciting specific symptoms and a defensive RNA silencing response) and evolves following a quasi-species model characterized by a complex spectrum of variants.
Collapse
Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | | | | | | | | | | |
Collapse
|
32
|
Di Serio F, Daròs JA, Ragozzino A, Flores R. Close structural relationship between two hammerhead viroid-like RNAs associated with cherry chlorotic rusty spot disease. Arch Virol 2006; 151:1539-49. [PMID: 16514498 DOI: 10.1007/s00705-006-0732-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 01/16/2006] [Indexed: 10/25/2022]
Abstract
Analysis of the population of cherry small circular RNAs (cscRNAs) from trees affected by cherry chlorotic rusty spot (CCRS) showed two groups of variants with similar sequence but differing in size (394-415 and 372-377 nt for cscRNA1 and cscRNA2, respectively) because of the presence or absence of a 27-nt fragment folding into a hairpin in their predicted quasi-rod-like secondary structures. These structures were preserved by co-variations and compensatory mutations, as well as by additional complex rearrangements. The variability also preserved the central conserved core and the stability of the helices of the plus and minus hammerhead ribozymes, supporting their role in replication of cscRNAs. The smaller variants most likely derive from the larger through recombination events. Possible functional relationships between cscRNAs and certain mycoviral-like double-stranded RNAs, also associated with CCRS, are discussed.
Collapse
Affiliation(s)
- F Di Serio
- Instituto di Virologia Vegetale del CNR, Sezione di Bari, Bari, Italy
| | | | | | | |
Collapse
|
33
|
Rodio ME, Delgado S, Flores R, Serio FD. Variants of Peach latent mosaic viroid inducing peach calico: uneven distribution in infected plants and requirements of the insertion containing the pathogenicity determinant. J Gen Virol 2006; 87:231-240. [PMID: 16361436 DOI: 10.1099/vir.0.81356-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous characterization of Peach latent mosaic viroid (PLMVd) variants from a single peach calico (PC) isolate showed that PC symptoms are induced by variants with a 12–13 nt insertion at a specific position and folding into a hairpin with a U-rich loop. Here, this study was extended to two other PC isolates. PLMVd variants with insertions similar to those reported previously (type 1), predominated in one isolate (PC-P2). The second (PC-P1), in addition to these variants, contained others with insertions in the same position and of the same size, but with the hairpin capped by a GA-rich loop (type 2). When symptomatic and non-symptomatic tissues from both isolates were used to inoculate GF-305 peach seedlings, they reproduced the phenotype of the inoculum source, indicating that variants differing in pathogenicity are unevenly distributed within single plants. Moreover, characterization of the progeny from inoculations with the PC-P1 source showed that variants with insertions of type 1 and 2 were predominant in the symptomatic and non-symptomatic seedlings, respectively, confirming the association between PC and variants with type 1 but not type 2 insertions. Inoculations with dimeric in vitro transcripts from PLMVd variants with type 1, type 2 and with a chimeric insertion showed that the variant with type 2 insertion was latent and established that the U-rich capping loop has a major role in PC, although the adjacent stem may also have some influence. Insertions can be acquired and lost during infection, suggesting that latent variants can evolve into pathogenic variants and vice versa.
Collapse
Affiliation(s)
- Maria-Elena Rodio
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi and Istituto di Virologia Vegetale del CNR, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Francesco Di Serio
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi and Istituto di Virologia Vegetale del CNR, Sezione di Bari, Via Amendola 165/A, 70126 Bari, Italy
| |
Collapse
|
34
|
Affiliation(s)
- Ian Cooper
- Natural Environment Research Council Centre for Ecology and Hydrology Mansfield Road, Oxford, Oxfordshire OX1 3SR, United Kingdom
| | | |
Collapse
|
35
|
Koonin EV, Martin W. On the origin of genomes and cells within inorganic compartments. Trends Genet 2005; 21:647-54. [PMID: 16223546 PMCID: PMC7172762 DOI: 10.1016/j.tig.2005.09.006] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 08/16/2005] [Accepted: 09/28/2005] [Indexed: 12/30/2022]
Abstract
Building on the model of Russell and Hall for the emergence of life at a warm submarine hydrothermal vent, we suggest that, within a hydrothermally formed system of contiguous iron-sulfide (FeS) compartments, populations of virus-like RNA molecules, which eventually encoded one or a few proteins each, became the agents of both variation and selection. The initial darwinian selection was for molecular self-replication. Combinatorial sorting of genetic elements among compartments would have resulted in preferred proliferation and selection of increasingly complex molecular ensembles--those compartment contents that achieved replication advantages. The last universal common ancestor (LUCA) we propose was not free-living but an inorganically housed assemblage of expressed and replicable genetic elements. The evolution of the enzymatic systems for (i) DNA replication; and (ii) membrane and cell wall biosynthesis, enabled independent escape of the first archaebacterial and eubacterial cells from their hydrothermal hatchery, within which the LUCA itself remained confined.
Collapse
Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| | | |
Collapse
|
36
|
Delgado S, Martínez de Alba AE, Hernández C, Flores R. A short double-stranded RNA motif of Peach latent mosaic viroid contains the initiation and the self-cleavage sites of both polarity strands. J Virol 2005; 79:12934-43. [PMID: 16188995 PMCID: PMC1235847 DOI: 10.1128/jvi.79.20.12934-12943.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The transcription initiation sites of viroid RNAs, despite their relevance for replication and in vivo folding, are poorly characterized. Here we have examined this question for Peach latent mosaic viroid (PLMVd), which belongs to the family of chloroplastic viroids with hammerhead ribozymes (Avsunviroidae), by adapting an RNA ligase-mediated rapid amplification of cDNA ends methodology developed for mapping the genuine capped 5' termini of eukaryotic messenger RNAs. To this aim, the characteristic free 5'-triphosphate group of chloroplastic primary transcripts from PLMVd-infected young fruits was previously capped in vitro with GTP and guanylyltransferase. PLMVd plus and minus initiation sites map at similar double-stranded motifs of 6 to 7 bp that also contain the conserved GUC triplet preceding the self-cleavage site in both polarity strands. Within the branched secondary structures predicted for the two PLMVd strands, this motif is located at the base of a similar long hairpin that presumably contains the promoters for a chloroplastic RNA polymerase. The transcription templates could be the circular viroid RNAs or their most abundant linear counterparts, assuming the involvement of an RNA polymerase able to jump over template discontinuities. Both PLMVd initiation sites were confirmed by applying the same methodology to two purified PLMVd subgenomic RNAs and by primer extension, and they therefore likely reflect the in vivo situation. The location of the PLMVd initiation sites provides a mechanistic view into how the nascent strands may fold and self-cleave during transcription. The approach described here may be extended to other chloroplastic RNA replicons and transcripts accumulating at low levels.
Collapse
Affiliation(s)
- Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Spain
| | | | | | | |
Collapse
|
37
|
Englert M, Beier H. Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Nucleic Acids Res 2005; 33:388-99. [PMID: 15653639 PMCID: PMC546159 DOI: 10.1093/nar/gki174] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Pre-tRNA splicing is an essential process in all eukaryotes. It requires the concerted action of an endonuclease to remove the intron and a ligase for joining the resulting tRNA halves as studied best in the yeast Saccharomyces cerevisiae. Here, we report the first characterization of an RNA ligase protein and its gene from a higher eukaryotic organism that is an essential component of the pre-tRNA splicing process. Purification of tRNA ligase from wheat germ by successive column chromatographic steps has identified a protein of 125 kDa by its potentiality to covalently bind AMP, and by its ability to catalyse the ligation of tRNA halves and the circularization of linear introns. Peptide sequences obtained from the purified protein led to the elucidation of the corresponding proteins and their genes in Arabidopsis and Oryza databases. The plant tRNA ligases exhibit no overall sequence homologies to any known RNA ligases, however, they harbour a number of conserved motifs that indicate the presence of three intrinsic enzyme activities: an adenylyltransferase/ligase domain in the N-terminal region, a polynucleotide kinase in the centre and a cyclic phosphodiesterase domain at the C-terminal end. In vitro expression of the recombinant Arabidopsis tRNA ligase and functional analyses revealed all expected individual activities. Plant RNA ligases are active on a variety of substrates in vitro and are capable of inter- and intramolecular RNA joining. Hence, we conclude that their role in vivo might comprise yet unknown essential functions besides their involvement in pre-tRNA splicing.
Collapse
Affiliation(s)
| | - Hildburg Beier
- To whom correspondence should be addressed. Tel: +49 931 888 4031; Fax: +49 931 888 4028;
| |
Collapse
|
38
|
Flores R, Hernández C, Martínez de Alba AE, Daròs JA, Di Serio F. Viroids and viroid-host interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2005; 43:117-39. [PMID: 16078879 DOI: 10.1146/annurev.phyto.43.040204.140243] [Citation(s) in RCA: 261] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Although they induce symptoms in plants similar to those accompanying virus infections, viroids have unique structural, functional, and evolutionary characteristics. They are composed of a small, nonprotein-coding, single-stranded, circular RNA, with autonomous replication. Viroid species are clustered into the families Pospiviroidae and Avsunviroidae, whose members replicate (and accumulate) in the nucleus and chloroplast, respectively. Viroids replicate in three steps through an RNA-based rolling-circle mechanism: synthesis of longer-than-unit strands catalyzed by host RNA polymerases; processing to unit-length, which in the family Avsunviroidae is mediated by hammerhead ribozymes; and circularization. Within the initially infected cells, viroid RNA must move to its replication organelle, with the resulting progeny then invading adjacent cells through plasmodesmata and reaching distal parts via the vasculature. To carry out these movements, viroids must interact with host factors. The mature viroid RNA could be the primary pathogenic effector or, alternatively, viroids could exert their pathogenic effects via RNA silencing.
Collapse
Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain.
| | | | | | | | | |
Collapse
|
39
|
Hegedus K, Dallmann G, Balázs E. The DNA form of a retroviroid-like element is involved in recombination events with itself and with the plant genome. Virology 2004; 325:277-86. [PMID: 15246267 DOI: 10.1016/j.virol.2004.04.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2004] [Revised: 03/09/2004] [Accepted: 04/19/2004] [Indexed: 11/29/2022]
Abstract
Carnation small viroid-like RNA (CarSV RNA) is unique among plant viroid-like RNAs in having a homologous DNA counterpart. In the present study, we found the most abundant CarSV DNA form (275 nt) coexisting with other smaller and longer-than-unit forms. Further analysis of PCR-amplified products revealed the presence of CarSV DNA-related sequences integrated in the plant genome, fused to microsatellite-like genomic sequences. Six to seven nucleotides at the boundaries in the CarSV DNA sequence could be found in the genomic sequences and also delimiting the boundaries of an enlarged version with partial duplication. This suggests that a common mechanism might have played a role in their emergence, namely, polymerase pausing and switching between stretches of homologous sequences. These plants also contained deleted CarSV DNA mutants with boundaries near those observed with fused sequences.
Collapse
Affiliation(s)
- Krisztina Hegedus
- Agricultural Biotechnology Center, Gödöllo, H-2100 Szent-Györgyi A. u. 4, Hungary
| | | | | |
Collapse
|
40
|
Pelchat M, Perreault JP. Binding site of Escherichia coli RNA polymerase to an RNA promoter. Biochem Biophys Res Commun 2004; 319:636-42. [PMID: 15178453 DOI: 10.1016/j.bbrc.2004.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Indexed: 11/25/2022]
Abstract
The DNA-dependent RNA polymerase (RNAP) from Escherichia coli has previously been reported to specifically initiate transcription from viroid-derived RNA promoters in vitro. In order to gain insight into the molecular mechanism of RNA promoter recognition by this RNAP, we have used nucleic acid intercalators and RNA:protein footprinting experiments to study the interaction between the polymerase and an RNA promoter at the initiation site. Our data revealed that the polymerase binds an external single-stranded loop, rather than a double-stranded region as is the case for DNA templates. Despite this divergence in promoter binding, the model RNA template was bound by both the beta and beta' subunits of the RNAP, as is observed with DNA templates. Most importantly, this work proposes large single-stranded RNA hairpin loops have the potential to be promoters for DNA-dependent RNAP.
Collapse
Affiliation(s)
- Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ont., Canada K1H 8M5.
| | | |
Collapse
|
41
|
Tabler M, Tsagris M. Viroids: petite RNA pathogens with distinguished talents. TRENDS IN PLANT SCIENCE 2004; 9:339-348. [PMID: 15231279 DOI: 10.1016/j.tplants.2004.05.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Viroids are small, circular, single-stranded RNA molecules that cause several infectious plant diseases. Viroids do not encode any pathogen-specific peptides but nonetheless, the subviral pathogens replicate autonomously and spread in the plant by recruiting host proteins via functional motifs encoded in their RNA genome. During the past couple of years, considerable progress has been made towards comprehending how viroids interact with their hosts. Here, we summarize recent findings on the structure-function relationships of viroids, their strategies and mechanisms of replication and trafficking, and the identification and characterization of interacting host proteins. We also describe the impact of the RNA silencing machinery of plants on viroid RNAs and how this has started to influence our models of viroid replication and pathogenicity.
Collapse
Affiliation(s)
- Martin Tabler
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, PO Box 1527, GR-71110 Heraklion/Crete, Greece.
| | | |
Collapse
|
42
|
Qi Y, Pélissier T, Itaya A, Hunt E, Wassenegger M, Ding B. Direct role of a viroid RNA motif in mediating directional RNA trafficking across a specific cellular boundary. THE PLANT CELL 2004; 16:1741-52. [PMID: 15194818 PMCID: PMC514158 DOI: 10.1105/tpc.021980] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2004] [Accepted: 04/14/2004] [Indexed: 05/18/2023]
Abstract
The plasmodesmata and phloem form a symplasmic network that mediates direct cell-cell communication and transport throughout a plant. Selected endogenous RNAs, viral RNAs, and viroids traffic between specific cells or organs via this network. Whether an RNA itself has structural motifs to potentiate trafficking is not well understood. We have used mutational analysis to identify a motif that the noncoding Potato spindle tuber viroid RNA evolved to potentiate its efficient trafficking from the bundle sheath into mesophyll that is vital to establishing systemic infection in tobacco (Nicotiana tabacum). Surprisingly, this motif is not necessary for trafficking in the reverse direction (i.e., from the mesophyll to bundle sheath). It is not required for trafficking between other cell types either. We also found that the requirement for this motif to mediate bundle sheath-to-mesophyll trafficking is dependent on leaf developmental stages. Our results provide genetic evidence that (1) RNA structural motifs can play a direct role in mediating trafficking across a cellular boundary in a defined direction, (2) the bundle sheath-mesophyll boundary serves as a novel regulatory point for RNA trafficking between the phloem and nonvascular tissues, and (3) the symplasmic network remodels its capacity to traffic RNAs during plant development. These findings may help further studies to elucidate the interactions between RNA motifs and cellular factors that potentiate directional trafficking across specific cellular boundaries.
Collapse
Affiliation(s)
- Yijun Qi
- Department of Plant Cellular and Molecular Biology, Plant Biotechnology Center, Ohio State University, Columbus 43210, USA
| | | | | | | | | | | |
Collapse
|
43
|
Flores R, Delgado S, Gas ME, Carbonell A, Molina D, Gago S, De la Peña M. Viroids: the minimal non-coding RNAs with autonomous replication. FEBS Lett 2004; 567:42-8. [PMID: 15165891 DOI: 10.1016/j.febslet.2004.03.118] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2004] [Accepted: 03/07/2004] [Indexed: 10/26/2022]
Abstract
Viroids are small (246-401 nucleotides), non-coding, circular RNAs able to replicate autonomously in certain plants. Viroids are classified into the families Pospiviroidae and Avsunviroidae, whose members replicate in the nucleus and chloroplast, respectively. Replication occurs by an RNA-based rolling-circle mechanism in three steps: (1). synthesis of longer-than-unit strands catalyzed by host DNA-dependent RNA polymerases forced to transcribe RNA templates, (2). processing to unit-length, which in family Avsunviroidae is mediated by hammerhead ribozymes, and (3). circularization either through an RNA ligase or autocatalytically. Disease induction might result from the accumulation of viroid-specific small interfering RNAs that, via RNA silencing, could interfere with normal developmental pathways.
Collapse
Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, 46022 Valencia, Spain.
| | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
During 1970 and 1971, I discovered that a devastating disease of potato plants is not caused by a virus, as had been assumed, but by a new type of subviral pathogen, the viroid. Viroids are so small--one fiftieth of the size of the smallest viruses--that many scientists initially doubted their existence. We now know that viroids cause many damaging diseases of crop plants. Fortunately, new methods that are based on the unique properties of viroids now promise effective control.
Collapse
Affiliation(s)
- Theodor O Diener
- University of Maryland Biotechnology Institute, College Park, Maryland 20742, USA.
| |
Collapse
|
45
|
Daròs JA, Flores R. Arabidopsis thaliana has the enzymatic machinery for replicating representative viroid species of the family Pospiviroidae. Proc Natl Acad Sci U S A 2004; 101:6792-7. [PMID: 15096616 PMCID: PMC404124 DOI: 10.1073/pnas.0401090101] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2003] [Indexed: 11/18/2022] Open
Abstract
Viroids, subviral noncoding RNAs, replicate, move, and incite diseases in plants. Viroids replicate through a rolling-circle mechanism in which oligomeric RNAs of one or both polarities are cleaved and ligated into the circular monomers. Attempts to transmit viroids to Arabidopsis have failed for unknown reasons. To tackle this question, Arabidopsis was transformed with cDNAs expressing dimeric (+) transcripts of representative species of the families Pospiviroidae and Avsunviroidae, which replicate in the nucleus and the chloroplast, respectively. Correct processing to the circular (+) monomers was always observed, demonstrating that Arabidopsis has the appropriate RNase and RNA ligase. Northern blot hybridization also revealed the multimeric (-) RNAs of Citrus exocortis viroid and Hop stunt viroid (HSVd) of the family Pospiviroidae, but not of Avocado sunblotch viroid of the family Avsunviroidae, showing that the first RNA-RNA transcription of the rolling-circle mechanism occurs in Arabidopsis for the two nuclear viroids and that their multimeric (-) RNAs remain unprocessed as in typical hosts. Moreover, transgenic Arabidopsis expressing HSVd dimeric (-) transcripts accumulated the circular (+) monomers, although at low levels, together with the unprocessed primary transcript that served as the template for the second RNA-RNA transcription. Agroinoculation of Arabidopsis with the dimeric (+) Citrus exocortis viroid, HSVd, and Coleus blumei viroid 1 cDNAs showed that these viroids could not move to distal plant parts, in contrast with the situation observed in their experimental hosts. Therefore, deficiencies in movement or low replication appear to be the factors limiting infectivity of some viroids in Arabidopsis.
Collapse
Affiliation(s)
- José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos s/n, 46022 Valencia, Spain
| | | |
Collapse
|
46
|
De la Peña M, Gago S, Flores R. Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J 2004; 22:5561-70. [PMID: 14532128 PMCID: PMC213784 DOI: 10.1093/emboj/cdg530] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Natural hammerhead ribozymes are mostly found in some viroid and viroid-like RNAs and catalyze their cis cleavage during replication. Hammerheads have been manipulated to act in trans and assumed to have a similar catalytic behavior in this artificial context. However, we show here that two natural cis-acting hammerheads self-cleave much faster than trans-acting derivatives and other reported artificial hammerheads. Moreover, modifications of the peripheral loops 1 and 2 of one of these natural hammerheads induced a >100-fold reduction of the self-cleavage constant, whereas engineering a trans-acting artificial hammerhead into a cis derivative by introducing a loop 1 had no effect. These data show that regions external to the central conserved core of natural hammerheads play a role in catalysis, and suggest the existence of tertiary interactions between these peripheral regions. The interactions, determined by the sequence and size of loops 1 and 2 and most likely of helices I and II, must result from natural selection and should be studied in order to better understand the hammerhead requirements in vivo.
Collapse
Affiliation(s)
- Marcos De la Peña
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos s/n, Valencia 46022, Spain
| | | | | |
Collapse
|
47
|
Gozmanova M, Denti MA, Minkov IN, Tsagris M, Tabler M. Characterization of the RNA motif responsible for the specific interaction of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1. Nucleic Acids Res 2003; 31:5534-43. [PMID: 14500815 PMCID: PMC206474 DOI: 10.1093/nar/gkg777] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viroids are small non-coding parasitic RNAs that are able to infect their host plants systemically. This circular naked RNA makes use of host proteins to accomplish its proliferation. Here we analyze the specific binding of the tomato protein Virp1 to the terminal right domain of potato spindle tuber viroid RNA (PSTVd). We find that two asymmetric internal loops within the PSTVd (+) RNA, each composed of the sequence elements 5'-ACAGG and CUCUUCC-5', are responsible for the specific RNA-protein interaction. In view of the nucleotide composition we call this structural element an 'RY motif'. The RY motif located close to the terminal right hairpin loop of the PSTVd secondary structure has an approximately 5-fold stronger binding affinity than the more centrally located RY motif. Simultaneous sequence alterations in both RY motifs abolished the specific binding to Virp1. Mutations in any of the two RY motifs resulted in non-infectious viroid RNA, with the exception of one case, where reversion to sequence wild type took place. In contrast, the simultaneous exchange of two nucleotides within the terminal right hairpin loop of PSTVd had only moderate influence on the binding to Virp1. This variant was infectious and sequence changes were maintained in the progeny. The relevance of the phylogenetic conservation of the RY motif, and sequence elements therein, amongst various genera of the family Pospiviroidae is discussed.
Collapse
Affiliation(s)
- Mariyana Gozmanova
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, PO Box 1527, GR-71110 Heraklion/Crete, Greece
| | | | | | | | | |
Collapse
|
48
|
Gmyl AP, Korshenko SA, Belousov EV, Khitrina EV, Agol VI. Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? RNA (NEW YORK, N.Y.) 2003; 9:1221-1231. [PMID: 13130136 PMCID: PMC1370486 DOI: 10.1261/rna.5111803] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2003] [Accepted: 07/15/2003] [Indexed: 05/24/2023]
Abstract
Biologically important joining of RNA pieces in cells, as exemplified by splicing and some classes of RNA editing, is posttranscriptional, whereas in RNA viruses it is generally believed to occur during viral RNA polymerase-dependent RNA synthesis. Here, we demonstrate the assembly of precise genome of an RNA virus (poliovirus) from its cotransfected fragments, which does not require specific RNA sequences, takes place before generation of the viral RNA polymerase, and occurs in different ways: Apparently unrestricted ligation of the terminal nucleotides, joining of any one of the two entire fragments with the relevant internal nucleotide of its partner, or internal crossovers within the overlapping sequence. Incorporation of the entire 5' or 3' partners into the recombinant RNA is activated by the presence of terminal 3'-phosphate and 5'-OH, respectively. Such postreplicative reactions, fundamentally differing from the known site-specific and structurally demanding cellular RNA rearrangements, might contribute to the origin and evolution of RNA viruses and could generate new RNA species during all stages of biological evolution.
Collapse
Affiliation(s)
- Anatoly P Gmyl
- M.P. Chumakov Institute of Poliomyelitis & Viral Encephalitides, Russian Academy of Medical Sciences, Moscow 142782, Russia
| | | | | | | | | |
Collapse
|
49
|
Qi Y, Ding B. Replication of Potato spindle tuber viroid in cultured cells of tobacco and Nicotiana benthamiana: the role of specific nucleotides in determining replication levels for host adaptation. Virology 2002; 302:445-56. [PMID: 12441088 DOI: 10.1006/viro.2002.1662] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have developed an electroporation protocol to inoculate cultured cells of tobacco and Nicotiana benthamiana with in vitro transcripts of Potato spindle tuber viroid (PSTVd) to characterize viroid structural features that determine replication efficiency at the cellular level. Both (+)- and (-)-strands of PSTVd were detected by Northern blots as early as 6 h postinoculation (h.p.i.). Accumulation of the (+)-circular PSTVd increased very rapidly starting at 24 h.p.i. and continued beyond 6 days postinoculation. Viroid accumulation in individual cells was visualized by in situ hybridization, which showed that 60-70% of the cells were infected. Previous work showed that C259 --> U substitution converted tomato isolate PSTVd(KF440-2) into a strain that is infectious on tobacco (M. Wassenegger, R. L. Spieker, S. Thalmeir, F.-U. Gast, L. Riedel, and H. L. Sänger, 1996. Virology 226, 191-197). Similarly, C259 --> U or U257 --> A substitution in the Intermediate strain (PSTVd(Int)) conferred infectivity in tobacco (Y. Zhu, Y. Qi, Y. Xun, R. Owens, and B. Ding, 2002. Plant Physiol. 130, 138-146). Our replication assays in tobacco-cultured cells demonstrated that U257 --> A and C259 --> U substitutions each enhanced PSTVd replication by 5- to 10-fold. Replacement of U257 with C, but not with G, also led to enhanced replication in tobacco cells. Replacement of C259 with nucleotide A or G did not enhance replication. Elevated accumulation of the (-)- and (+)-strands of these mutants was in part due to enhanced transcription. Interestingly, all of the nucleotide changes did not alter PSTVd replication levels in N. benthamiana cells. These results provide insights about PSTVd structures that modulate replication efficiency in adapting to a specific host.
Collapse
Affiliation(s)
- Yijun Qi
- Department of Plant Biology and Plant Biotechnology Center, The Ohio State University, Columbus, 43210, USA
| | | |
Collapse
|
50
|
Itaya A, Matsuda Y, Gonzales RA, Nelson RS, Ding B. Potato spindle tuber viroid strains of different pathogenicity induces and suppresses expression of common and unique genes in infected tomato. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2002; 15:990-999. [PMID: 12437296 DOI: 10.1094/mpmi.2002.15.10.990] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Viroids are the smallest plant pathogens. These RNAs do not encode proteins and are not encapsidated, and yet they can replicate autonomously, move systemically, and cause diseases in infected plants. Notably, strains of a viroid with subtle differences in nucleotide sequences can cause dramatically different symptoms in infected plants. These features make viroids unique probes to investigate the role of a pathogenic RNA genome in triggering host responses. We conducted a comprehensive analysis of the differential gene expression patterns of tomato plants at various stages of infection by a mild and severe strain of Potato spindle tuber viroid (PSTVd). We also compared tomato gene expression altered by the PSTVd strains with that altered by Tobacco mosaic virus (TMV). Our analyses revealed that the two PSTVd strains altered expression of both common and unique tomato genes. These genes encode products involved in defense/stress response, cell wall structure, chloroplast function, protein metabolism, and other diverse functions. Five genes have unknown functions. Four genes are novel. The expression of some but not all of these genes was also altered by TMV infection. Our results indicate that viroids, although structurally simple, can trigger complex host responses. Further characterization of viroid-altered gene expression in a host plant should help understand viroid pathogenicity and, potentially, the mechanisms of RNA-mediated regulation of plant gene expression.
Collapse
Affiliation(s)
- Asuka Itaya
- Department of Plant Biology and Plant Biotechnology Center, Ohio State University, Columbus 43210, USA
| | | | | | | | | |
Collapse
|