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Moelling K. What contemporary viruses tell us about evolution: a personal view. Arch Virol 2013; 158:1833-48. [PMID: 23568292 PMCID: PMC3755228 DOI: 10.1007/s00705-013-1679-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 02/14/2013] [Indexed: 12/11/2022]
Abstract
Recent advances in information about viruses have revealed novel and surprising properties such as viral sequences in the genomes of various organisms, unexpected amounts of viruses and phages in the biosphere, and the existence of giant viruses mimicking bacteria. Viruses helped in building genomes and are driving evolution. Viruses and bacteria belong to the human body and our environment as a well-balanced ecosystem. Only in unbalanced situations do viruses cause infectious diseases or cancer. In this article, I speculate about the role of viruses during evolution based on knowledge of contemporary viruses. Are viruses our oldest ancestors?
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Affiliation(s)
- Karin Moelling
- Max Planck Institute for Molecular Genetics, Ihnestr 63-73, 14195, Berlin, Germany.
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52
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Poojari S, Alabi OJ, Fofanov VY, Naidu RA. A leafhopper-transmissible DNA virus with novel evolutionary lineage in the family geminiviridae implicated in grapevine redleaf disease by next-generation sequencing. PLoS One 2013; 8:e64194. [PMID: 23755117 PMCID: PMC3673993 DOI: 10.1371/journal.pone.0064194] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/10/2013] [Indexed: 01/25/2023] Open
Abstract
A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms.
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Affiliation(s)
- Sudarsana Poojari
- Department of Plant Pathology, Washington State University, Irrigated Agriculture Research and Extension Center, Prosser, Washington, United States of America
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53
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Verhoeven JTJ, Meekes ETM, Roenhorst JW, Flores R, Serra P. Dahlia latent viroid: a recombinant new species of the family Pospiviroidae posing intriguing questions about its origin and classification. J Gen Virol 2012; 94:711-719. [PMID: 23255620 DOI: 10.1099/vir.0.048751-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A viroid-like RNA has been detected in two asymptomatic dahlia accessions by return and double PAGE. It appeared smaller than Chrysanthemum stunt viroid and Potato spindle tuber viroid, the two members of the genus Pospiviroid, family Pospiviroidae, reported in this ornamental previously. RT-PCR with primers designed for amplifying all pospiviroids produced no amplicons, but RT-PCR with random primers revealed a 342 nt RNA. The sequence of this RNA was confirmed with specific primers, which additionally revealed its presence in many dahlia cultivars. The RNA was named Dahlia latent viroid (DLVd) because it replicates autonomously, but symptomlessly, in dahlia and shares maximum sequence identity with other viroids of less than 56 %. Furthermore, DLVd displays characteristic features of the family Pospiviroidae: a predicted rod-like secondary structure of minimum free energy with a central conserved region (CCR), and the ability to form the metastable structures hairpins I and II. Its CCR is identical to that of Hop stunt viroid (HSVd, genus Hostuviroid). However, DLVd: (i) has the terminal conserved region present in members of the genus Pospiviroid, but absent in HSVd, and (ii) lacks the terminal conserved hairpin present in HSVd. Phylogenetic reconstructions indicate that HSVd and Pepper chat fruit viroid (genus Pospiviroid) are the closest relatives of DLVd, but DLVd differs from these viroids in its host range, restricted to dahlia so far. Therefore, while DLVd fulfils the criteria to be a novel species of the family Pospiviroidae, its recombinant origin makes assignment to the genera Pospiviroid or Hostuviroid problematic.
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Affiliation(s)
- Jacobus Th J Verhoeven
- National Plant Protection Organization, National Reference Centre, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Ellis T M Meekes
- Naktuinbouw, P.O. Box 40, 2370 AA Roelofarendsveen, The Netherlands
| | - Johanna W Roenhorst
- National Plant Protection Organization, National Reference Centre, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain
| | - Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain
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54
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Alabi OJ, Zheng Y, Jagadeeswaran G, Sunkar R, Naidu RA. High-throughput sequence analysis of small RNAs in grapevine (Vitis vinifera L.) affected by grapevine leafroll disease. MOLECULAR PLANT PATHOLOGY 2012; 13:1060-76. [PMID: 22827483 PMCID: PMC6638782 DOI: 10.1111/j.1364-3703.2012.00815.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Grapevine leafroll disease (GLRD) is one of the most economically important virus diseases of grapevine (Vitis spp.) worldwide. In this study, we used high-throughput sequencing of cDNA libraries made from small RNAs (sRNAs) to compare profiles of sRNA populations recovered from own-rooted Merlot grapevines with and without GLRD symptoms. The data revealed the presence of sRNAs specific to Grapevine leafroll-associated virus 3, Hop stunt viroid (HpSVd), Grapevine yellow speckle viroid 1 (GYSVd-1) and Grapevine yellow speckle viroid 2 (GYSVd-2) in symptomatic grapevines and sRNAs specific only to HpSVd, GYSVd-1 and GYSVd-2 in nonsymptomatic grapevines. In addition to 135 previously identified conserved microRNAs in grapevine (Vvi-miRs), we identified 10 novel and several candidate Vvi-miRs in both symptomatic and nonsymptomatic grapevine leaves based on the cloning of miRNA star sequences. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) of selected conserved Vvi-miRs indicated that individual members of an miRNA family are differentially expressed in symptomatic and nonsymptomatic leaves. The high-resolution mapping of sRNAs specific to an ampelovirus and three viroids in mixed infections, the identification of novel Vvi-miRs and the modulation of certain conserved Vvi-miRs offers resources for the further elucidation of compatible host-pathogen interactions and for the provision of ecologically relevant information to better understand host-pathogen-environment interactions in a perennial fruit crop.
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Affiliation(s)
- Olufemi J Alabi
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, USA
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55
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Tessitori M, Rizza S, Reina A, Causarano G, Di Serio F. The genetic diversity of Citrus dwarfing viroid populations is mainly dependent on the infected host species. J Gen Virol 2012; 94:687-693. [PMID: 23152366 DOI: 10.1099/vir.0.048025-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
As with viruses, viroids infect their hosts as polymorphic populations of variants. Identifying possible sources of genetic variability is significant in the case of the species Citrus dwarfing viroid (CDVd) which has been proposed as a dwarfing agent for high-density citrus plantings. Here, a natural CDVd isolate (CMC) was used as an inoculum source for long-term (25 years) and short-term (1 year) bioassays in different citrus host species. Characterization of progenies indicated that the genetic stability of CDVd populations was high in certain hosts (trifoliate orange, Troyer citrange, Etrog citron, Navelina sweet orange), which preserve viroid populations similar to the original CMC isolate even after 25 years. By contrast, CDVd variant populations in Interdonato lemon and Volkamer lemon were completely different to those in the inoculated sources, highlighting how influential the host is on the genetic variability of CDVd populations. Implications for risk assessment of CDVd as a dwarfing agent are discussed. The GenBank/EMBL/DDBJ accession numbers for the complete sequences of the Citrus dwarfing viroid variants are JF970266.1 forH2-2, JF970267.1 for H2-7, EU938647.1 for H6-2, EU938651.1 forH6-10, JF970268.1 for H10-7, EU938652.1 for H14-13, EU938653.1for H14-14, JF970269.1 for H14-16, EU938648.1 for H15-9,EU938649.1 for H16-2, JF970265.1 for H16-9, EU938654.1 forH16-13, EU938650.1 for H20-3, JF970270.1 for H20-7, EU938641.1for PR-1, EU938642.1 for PR-3, EU938643.1 for PR-7, EU938644.1for CR-1, EU938639.1 for VR-4, JF12070.1 for VR-15, JF812069.1LS-4, EU938640.1 for LS-10 and JF970264.1 for LS-11.
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Affiliation(s)
- Matilde Tessitori
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari - Sez. Fitopatologia e Genetica agraria, Università di Catania, 95123 Catania, Italy
| | - Serena Rizza
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari - Sez. Fitopatologia e Genetica agraria, Università di Catania, 95123 Catania, Italy
| | - Antonella Reina
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari - Sez. Fitopatologia e Genetica agraria, Università di Catania, 95123 Catania, Italy
| | - Giovanni Causarano
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari - Sez. Fitopatologia e Genetica agraria, Università di Catania, 95123 Catania, Italy
| | - Francesco Di Serio
- Istituto di Virologia Vegetale, UOS Bari, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
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56
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Rizza S, Conesa A, Juarez J, Catara A, Navarro L, Duran-Vila N, Ancillo G. Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection. MOLECULAR PLANT PATHOLOGY 2012; 13:852-64. [PMID: 22420919 PMCID: PMC6638686 DOI: 10.1111/j.1364-3703.2012.00794.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Viroids are small (246-401 nucleotides), single-stranded, circular RNA molecules that infect several crop plants and can cause diseases of economic importance. Citrus are the hosts in which the largest number of viroids have been identified. Citrus exocortis viroid (CEVd), the causal agent of citrus exocortis disease, induces considerable losses in citrus crops. Changes in the gene expression profile during the early (pre-symptomatic) and late (post-symptomatic) stages of Etrog citron infected with CEVd were investigated using a citrus cDNA microarray. MaSigPro analysis was performed and, on the basis of gene expression profiles as a function of the time after infection, the differentially expressed genes were classified into five clusters. FatiScan analysis revealed significant enrichment of functional categories for each cluster, indicating that viroid infection triggers important changes in chloroplast, cell wall, peroxidase and symporter activities.
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Affiliation(s)
- Serena Rizza
- Department of Phytosanitary Sciences and Technologies-University of Catania, Via S. Sofia 102, 95123 Catania, Italy
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57
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Nohales MÁ, Molina-Serrano D, Flores R, Daròs JA. Involvement of the chloroplastic isoform of tRNA ligase in the replication of viroids belonging to the family Avsunviroidae. J Virol 2012; 86:8269-76. [PMID: 22623792 PMCID: PMC3421689 DOI: 10.1128/jvi.00629-12] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 05/15/2012] [Indexed: 11/20/2022] Open
Abstract
Avocado sunblotch viroid, peach latent mosaic viroid, chrysanthemum chlorotic mottle viroid, and eggplant latent viroid (ELVd), the four recognized members of the family Avsunviroidae, replicate through the symmetric pathway of an RNA-to-RNA rolling-circle mechanism in chloroplasts of infected cells. Viroid oligomeric transcripts of both polarities contain embedded hammerhead ribozymes that, during replication, mediate their self-cleavage to monomeric-length RNAs with 5'-hydroxyl and 2',3'-phosphodiester termini that are subsequently circularized. We report that a recombinant version of the chloroplastic isoform of the tRNA ligase from eggplant (Solanum melongena L.) efficiently catalyzes in vitro circularization of the plus [(+)] and minus [(-)] monomeric linear replication intermediates from the four Avsunviroidae. We also show that while this RNA ligase specifically recognizes the genuine monomeric linear (+) ELVd replication intermediate, it does not do so with five other monomeric linear (+) ELVd RNAs with their ends mapping at different sites along the molecule, despite containing the same 5'-hydroxyl and 2',3'-phosphodiester terminal groups. Moreover, experiments involving transient expression of a dimeric (+) ELVd transcript in Nicotiana benthamiana Domin plants preinoculated with a tobacco rattle virus-derived vector to induce silencing of the plant endogenous tRNA ligase show a significant reduction of ELVd circularization. In contrast, circularization of a viroid replicating in the nucleus occurring through a different pathway is unaffected. Together, these results support the conclusion that the chloroplastic isoform of the plant tRNA ligase is the host enzyme mediating circularization of both (+) and (-) monomeric linear intermediates during replication of the viroids belonging to the family Avsunviroidae.
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Affiliation(s)
- María-Ángeles Nohales
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), Valencia, Spain
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58
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Flores R, Serra P, Minoia S, Di Serio F, Navarro B. Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs. Front Microbiol 2012; 3:217. [PMID: 22719735 PMCID: PMC3376415 DOI: 10.3389/fmicb.2012.00217] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 05/28/2012] [Indexed: 11/13/2022] Open
Abstract
As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson–Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures – either global or local – determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.
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Affiliation(s)
- Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC) Valencia, Spain
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59
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Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, Di Serio F. Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:991-1003. [PMID: 22332758 DOI: 10.1111/j.1365-313x.2012.04940.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
How viroids, tiny non-protein-coding RNAs (~250-400 nt), incite disease is unclear. One hypothesis is that viroid-derived small RNAs (vd-sRNAs; 21-24 nt) resulting from the host defensive response, via RNA silencing, may target for cleavage cell mRNAs and trigger a signal cascade, eventually leading to symptoms. Peach latent mosaic viroid (PLMVd), a chloroplast-replicating viroid, is particularly appropriate to tackle this question because it induces an albinism (peach calico, PC) strictly associated with variants containing a specific 12-14-nt hairpin insertion. By dissecting albino and green leaf sectors of Prunus persica (peach) seedlings inoculated with PLMVd natural and artificial variants, and cloning their progeny, we have established that the hairpin insertion sequence is involved in PC. Furthermore, using deep sequencing, semi-quantitative RT-PCR and RNA ligase-mediated rapid amplification of cDNA ends (RACE), we have determined that two PLMVd-sRNAs containing the PC-associated insertion (PC-sRNA8a and PC-sRNA8b) target for cleavage the mRNA encoding the chloroplastic heat-shock protein 90 (cHSP90), thus implicating RNA silencing in the modulation of host gene expression by a viroid. Chloroplast malformations previously reported in PC-expressing tissues are consistent with the downregulation of cHSP90, which participates in chloroplast biogenesis and plastid-to-nucleus signal transduction in Arabidopsis. Besides PC-sRNA8a and PC-sRNA8b, both deriving from the less-abundant PLMVd (-) strand, we have identified other PLMVd-sRNAs potentially targeting peach mRNAs. These results also suggest that sRNAs derived from other PLMVd regions may downregulate additional peach genes, ultimately resulting in other symptoms or in a more favorable host environment for viroid infection.
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Affiliation(s)
- Beatriz Navarro
- Istituto di Virologia Vegetale-CNR, Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy
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60
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61
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Bojić T, Beeharry Y, Zhang DJ, Pelchat M. Tomato RNA polymerase II interacts with the rod-like conformation of the left terminal domain of the potato spindle tuber viroid positive RNA genome. J Gen Virol 2012; 93:1591-1600. [PMID: 22422064 DOI: 10.1099/vir.0.041574-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potato spindle tuber viroid (PSTVd) is a small, single-stranded, circular, non-coding RNA pathogen. Host DNA-dependent RNA polymerase II (RNAP II) was proposed to be critical for its replication, but no interaction site for RNAP II on the PSTVd RNA genome was identified. Using a co-immunoprecipitation strategy involving a mAb specific for the conserved heptapeptide (i.e. YSPTSPS) located at the carboxy-terminal domain of the largest subunit of RNAP II, we established the interaction of tomato RNAP II with PSTVd RNA and showed that RNAP II associates with the left terminal domain of PSTVd (+) RNA. RNAP II did not interact with any of several PSTVd (-) RNAs tested. Deletion and site-directed mutagenesis of a shortened model PSTVd (+) RNA fragment were used to identify the role of specific nucleotides and structural motifs in this interaction. Our results provide evidence for the interaction of a RNAP II complex from a natural host with the rod-like conformation of the left terminal domain of PSTVd (+) RNA.
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Affiliation(s)
- Teodora Bojić
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Yasnee Beeharry
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Da Jiang Zhang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
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62
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Ding B. Viroids: self-replicating, mobile, and fast-evolving noncoding regulatory RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 1:362-75. [PMID: 21956936 DOI: 10.1002/wrna.22] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Viroids are small, circular, and noncoding RNAs that infect plants. They replicate in the nucleus or chloroplast and then traffic from cell to cell and from organ to organ to establish systemic infection. Viroids achieve nearly all of the biological functions by directly interacting with host cellular factors. Viroid replication, together with replication of human hepatitis delta virus, demonstrates the biological novelty and significance of RNA-dependent RNA polymerase activities of DNA-dependent RNA polymerases. Viroid systemic infection uncovers a new biological principle--the role of three-dimensional RNA structural motifs mediating RNA trafficking between specific cells. Viroid diseases are virtually the consequences of host gene regulation by noncoding RNAs. A viroid RNA has the highest in vivo mutation rate among all known nucleic acid replicons. The host range of many viroids is expanding, essentially as a result of continuing and fast evolution of noncoding sequences/structures to gain new biological functions. Here, I discuss recent progress in these areas, emphasizing the broad significance of viroid research to the discovery of fundamental biological principles.
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Affiliation(s)
- Biao Ding
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Center for RNA Biology, and Molecular, Cellular and Developmental Biology Program, The Ohio State University, 207 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210, USA.
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63
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Molina-Serrano D, Marqués J, Nohales MÁ, Flores R, Daròs JA. A chloroplastic RNA ligase activity analogous to the bacterial and archaeal 2´-5' RNA ligase. RNA Biol 2012; 9:326-33. [PMID: 22336712 DOI: 10.4161/rna.19218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Bacteria and archaea contain a 2'-5' RNA ligase that seals in vitro 2',3'-cyclic phosphodiester and 5'-hydroxyl RNA termini, generating a 2',5'-phosphodiester bond. In our search for an RNA ligase able to circularize the monomeric linear replication intermediates of viroids belonging to the family Avsunviroidae, which replicate in the chloroplast, we have identified in spinach (Spinacea oleracea L.) chloroplasts a new RNA ligase activity whose properties resemble those of the bacterial and archaeal 2'-5' RNA ligase. The spinach chloroplastic RNA ligase recognizes the 5'-hydroxyl and 2',3'-cyclic phosphodiester termini of Avocado sunblotch viroid and Eggplant latent viroid RNAs produced by hammerhead-mediated self-cleavage, yielding circular products linked through an atypical, most likely 2',5'-phosphodiester, bond. The enzyme neither requires divalent cations as cofactors, nor NTPs as substrate. The reaction apparently reaches equilibrium at a low ratio between the final circular product and the linear initial substrate. Even if its involvement in viroid replication seems unlikely, the identification of a 2'-5' RNA ligase activity in higher plant chloroplasts, with properties very similar to an analogous enzyme widely distributed in bacterial and archaeal proteomes, is intriguing and suggests an important biological role so far unknown.
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Affiliation(s)
- Diego Molina-Serrano
- Instituto de Biología Molecular y Celular de Plantas-Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Avenida de los Naranjos, Valencia, Spain
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64
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Kurup R, Kurup PA. A cholesterol and actinide dependent shadow biosphere of archaea and viroids in autoimmune diseases. Immunobiology 2012; 217:316-20. [PMID: 22137029 DOI: 10.1016/j.imbio.2011.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 10/18/2011] [Indexed: 11/29/2022]
Abstract
Endogenous digoxin has been related to the pathogenesis of multiple sclerosis and other autoimmune diseases like systemic lupus erythematosis and rheumatoid arthritis. The possibility of endogenous digoxin synthesis by archaea with a mevalonate pathway and cholesterol catabolism was considered. 10 cases each of multiple sclerosis and other autoimmune diseases like systemic lupus erythematosis and rheumatoid arthritis before starting treatment and 10 age and sex matched healthy controls from general population were chosen for the study. Cholesterol substrate was added to the plasma of the patients and the generation of cytochrome F420, free RNA, free DNA, polycyclic aromatic hydrocarbon, hydrogen peroxide, serotonin, pyruvate, ammonia, glutamate, cytochrome C, hexokinase, ATP synthase, HMG CoA reductase, digoxin and bile acids were studied. The changes with the addition of antibiotics and cerium to the patient's plasma were also studied. The statistical analysis was done by ANOVA. The parameters mentioned above were increased the patient's plasma with addition of cholesterol substrate. The addition of antibiotics to the patient's plasma caused a decrease in all the parameters while addition of cerium increased their levels. An actinide dependent shadow biosphere of archaea and viroids is described in multiple sclerosis and other autoimmune diseases like systemic lupus erythematosis and rheumatoid arthritis contributing to their pathogenesis.
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Affiliation(s)
- Ravikumar Kurup
- The Metabolic Disorders Research Centre, TC 4/1525, Gouri Sadan, Kattu Road, North of Cliff House, Kowdiar PO, Trivandrum, Kerala, India.
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65
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Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, Di Serio F. Viroids: how to infect a host and cause disease without encoding proteins. Biochimie 2012; 94:1474-80. [PMID: 22738729 DOI: 10.1016/j.biochi.2012.02.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
Abstract
Despite being composed by a single-stranded, circular, non-protein-coding RNA of just 246-401 nucleotides (nt), viroids can incite in their host plants symptoms similar to those caused by DNA and RNA viruses, which have genomes at least 20-fold bigger and encode proteins. On the other hand, certain non-protein-coding plant satellite RNAs display structural similarities with viroids but for replication and transmission they need to parasitize specific helper viruses (modifying concomitantly the symptoms they induce). While phenotypic alterations accompanying infection by viruses may partly result from expressing the proteins they code for, how the non-protein-coding viroids (and satellite RNAs) cause disease remains a conundrum. Initial ideas on viroid pathogenesis focused on a direct interaction of the genomic RNA with host proteins resulting in their malfunction. With the advent of RNA silencing, it was alternatively proposed that symptoms could be produced by viroid-derived small RNAs (vd-sRNAs) -generated by the host defensive machinery- targeting specific host mRNA or DNA sequences for post-transcriptional or transcriptional gene silencing, respectively, a hypothesis that could also explain pathogenesis of non-protein-coding satellite RNAs. Evidence sustaining this view has been circumstantial, but recent data provide support for it in two cases: i) the yellow symptoms associated with a specific satellite RNA result from a 22-nt small RNA (derived from the 24-nt fragment of the satellite genome harboring the pathogenic determinant), which is complementary to a segment of the mRNA of the chlorophyll biosynthetic gene CHLI and targets it for cleavage by the RNA silencing machinery, and ii) two 21-nt vd-sRNAS containing the pathogenic determinant of the albino phenotype induced by a chloroplast-replicating viroid target for cleavage the mRNA coding for the chloroplastic heat-shock protein 90 via RNA silencing too. This evidence, which is compelling for the satellite RNA, does not exclude alternative mechanisms.
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Affiliation(s)
- Beatriz Navarro
- Istituto di Virologia Vegetale (CNR), Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy
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66
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Pallas V, Martinez G, Gomez G. The interaction between plant viroid-induced symptoms and RNA silencing. Methods Mol Biol 2012; 894:323-43. [PMID: 22678590 DOI: 10.1007/978-1-61779-882-5_22] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
A large body of evidence has lead to the suggestive proposal of a potential interplay between viroid-induced pathogenesis and RNA silencing regulatory mechanisms. A variety of techniques have been used to examine this interaction. This chapter outlines the use of a green fluorescent protein (GFP) sensor, containing viroid-specific sequence targets to study this phenomenon. In addition, a symptomatic transgenic line of Nicotiana benthamiana that expresses and processes Hop stunt viroid (HSVd) is used as stocks in grafting assays with the rdr6i-Nb lines, in which the RNA-dependent RNA polymerase 6 (NbRDR6) is constitutively silenced. The combination of the use of a viroid-specific GFP-sensor, the grafting assays with plants silenced for the RDR6 and the analysis of siRNAs allows to address how to monitor viroid-specific RNA silencing and how to associate this regulatory pathway with symptom expression.
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Affiliation(s)
- Vicente Pallas
- Instituto de Biologia Moleculaire y Celular de Plantas, Valencia, Spain.
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67
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Bateman A, Agrawal S, Birney E, Bruford EA, Bujnicki JM, Cochrane G, Cole JR, Dinger ME, Enright AJ, Gardner PP, Gautheret D, Griffiths-Jones S, Harrow J, Herrero J, Holmes IH, Huang HD, Kelly KA, Kersey P, Kozomara A, Lowe TM, Marz M, Moxon S, Pruitt KD, Samuelsson T, Stadler PF, Vilella AJ, Vogel JH, Williams KP, Wright MW, Zwieb C. RNAcentral: A vision for an international database of RNA sequences. RNA (NEW YORK, N.Y.) 2011; 17:1941-6. [PMID: 21940779 PMCID: PMC3198587 DOI: 10.1261/rna.2750811] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.
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Affiliation(s)
- Alex Bateman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom
- Corresponding author.E-mail .
| | - Shipra Agrawal
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore 560 100, India
- BioCOS Life Sciences Private Limited, Bangalore 560 100, India
| | - Ewan Birney
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Elspeth A. Bruford
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Janusz M. Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109 Warsaw, Poland
- Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Umultowska 89, 61-614 Poznan, Poland
| | - Guy Cochrane
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - James R. Cole
- Microbial Ecology Center, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | - Marcel E. Dinger
- Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD 4072, Australia
| | - Anton J. Enright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Paul P. Gardner
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Daniel Gautheret
- Institut de Génétique et Microbiologie–UMR CNRS 8621, Université Paris-Sud–Bâtiment 400, 91405 Orsay Cedex, France
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, M13 9PT, United Kingdom
| | - Jen Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Javier Herrero
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Ian H. Holmes
- Department of Bioengineering, University of California, Berkeley, California 94720-1762, USA
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, 30050, Taiwan
| | - Krystyna A. Kelly
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Paul Kersey
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Ana Kozomara
- Faculty of Life Sciences, University of Manchester, Michael Smith Building, Manchester, M13 9PT, United Kingdom
| | - Todd M. Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Manja Marz
- RNA Bioinformatics Group, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany
| | - Simon Moxon
- University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Kim D. Pruitt
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
| | - Tore Samuelsson
- Department of Medical Biochemistry, University of Goteborg, Medicinareg. 9A, S-405 30 Goteborg, Sweden
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, 04009 Leipzig, Germany
| | - Albert J. Vilella
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Jan-Hinnerk Vogel
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Kelly P. Williams
- Sandia National Laboratories, MS 9291, Livermore, California 94551-0969, USA
| | - Mathew W. Wright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, United Kingdom
| | - Christian Zwieb
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3901, USA
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68
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Rey FA. Virus/host interactions: a strong force driving the diversification of cellular organisms. Curr Opin Microbiol 2011; 14:445-8. [DOI: 10.1016/j.mib.2011.07.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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69
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Smith NA, Eamens AL, Wang MB. Viral small interfering RNAs target host genes to mediate disease symptoms in plants. PLoS Pathog 2011; 7:e1002022. [PMID: 21573142 PMCID: PMC3088724 DOI: 10.1371/journal.ppat.1002022] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 02/15/2011] [Indexed: 12/25/2022] Open
Abstract
The Cucumber mosaic virus (CMV) Y-satellite RNA (Y-Sat) has a small non-protein-coding RNA genome that induces yellowing symptoms in infected Nicotiana tabacum (tobacco). How this RNA pathogen induces such symptoms has been a longstanding question. We show that the yellowing symptoms are a result of small interfering RNA (siRNA)-directed RNA silencing of the chlorophyll biosynthetic gene, CHLI. The CHLI mRNA contains a 22-nucleotide (nt) complementary sequence to the Y-Sat genome, and in Y-Sat-infected plants, CHLI expression is dramatically down-regulated. Small RNA sequencing and 5' RACE analyses confirmed that this 22-nt sequence was targeted for mRNA cleavage by Y-Sat-derived siRNAs. Transformation of tobacco with a RNA interference (RNAi) vector targeting CHLI induced Y-Sat-like symptoms. In addition, the symptoms of Y-Sat infection can be completely prevented by transforming tobacco with a silencing-resistant variant of the CHLI gene. These results suggest that siRNA-directed silencing of CHLI is solely responsible for the Y-Sat-induced symptoms. Furthermore, we demonstrate that two Nicotiana species, which do not develop yellowing symptoms upon Y-Sat infection, contain a single nucleotide polymorphism within the siRNA-targeted CHLI sequence. This suggests that the previously observed species specificity of Y-Sat-induced symptoms is due to natural sequence variation in the CHLI gene, preventing CHLI silencing in species with a mismatch to the Y-Sat siRNA. Taken together, these findings provide the first demonstration of small RNA-mediated viral disease symptom production and offer an explanation of the species specificity of the viral disease.
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MESH Headings
- Agrobacterium tumefaciens/genetics
- Amino Acid Sequence
- Down-Regulation
- Gene Silencing
- High-Throughput Nucleotide Sequencing
- Host-Pathogen Interactions
- Lyases/genetics
- Molecular Sequence Data
- Plant Diseases/genetics
- Plant Diseases/virology
- Plant Viruses/physiology
- Plants, Genetically Modified/enzymology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/virology
- Plasmids
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Satellite/genetics
- RNA, Satellite/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Nicotiana/enzymology
- Nicotiana/genetics
- Nicotiana/virology
- Virus Replication
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70
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Diermann N, Matoušek J, Junge M, Riesner D, Steger G. Characterization of plant miRNAs and small RNAs derived from potato spindle tuber viroid (PSTVd) in infected tomato. Biol Chem 2011; 391:1379-90. [PMID: 21087089 DOI: 10.1515/bc.2010.148] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To defend against invading pathogens, plants possess RNA silencing mechanisms involving small RNAs (miRNAs, siRNAs). Also viroids - plant infectious, non-coding, unencapsidated RNA - cause the production of viroid-specific small RNAs (vsRNA), but viroids do escape the cytoplasmic silencing mechanism. Viroids with minor sequence variations can produce different symptoms in infected plants, suggesting an involvement of vsRNAs in symptom production. We analyzed by deep sequencing the spectrum of vsRNAs induced by the PSTVd strain AS1, which causes strong symptoms such as dwarfing and necrosis upon infection of tomato plants cv Rutgers. Indeed, vsRNAs found with highest frequency mapped to the pathogenicity-modulating domain of PSTVd, supporting an involvement of vsRNAs in symptom production. Furthermore, in PSTVd AS1-infected plants the accumulation of some endogenous miRNAs, which are involved in leaf development via regulation of transcription factors, is suppressed. The latter finding supports the hypothesis that a miRNA-dependent (mis)regulation of transcription factors causes the viroid symptoms.
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Affiliation(s)
- Natalie Diermann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
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71
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Desbiez C, Moury B, Lecoq H. The hallmarks of "green" viruses: do plant viruses evolve differently from the others? INFECTION GENETICS AND EVOLUTION 2011; 11:812-24. [PMID: 21382520 DOI: 10.1016/j.meegid.2011.02.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 02/22/2011] [Accepted: 02/24/2011] [Indexed: 12/13/2022]
Abstract
All viruses are obligatory parasites that must develop tight interactions with their hosts to complete their infectious cycle. Viruses infecting plants share many structural and functional similarities with those infecting other organisms, particularly animals and fungi. Quantitative data regarding their evolutionary mechanisms--generation of variability by mutation and recombination, changes in populations by selection and genetic drift have been obtained only recently, and appear rather similar to those measured for animal viruses.This review presents an update of our knowledge of the phylogenetic and evolutionary characteristics of plant viruses and their relation to their plant hosts, in comparison with viruses infecting other organisms.
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Affiliation(s)
- C Desbiez
- INRA, Unité de Pathologie Végétale UR407, F-84140 Montfavet, France.
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72
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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.
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73
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Takeda R, Petrov AI, Leontis NB, Ding B. A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana. THE PLANT CELL 2011; 23:258-72. [PMID: 21258006 PMCID: PMC3051236 DOI: 10.1105/tpc.110.081414] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 12/13/2010] [Accepted: 12/25/2010] [Indexed: 05/04/2023]
Abstract
Cell-to-cell trafficking of RNA is an emerging biological principle that integrates systemic gene regulation, viral infection, antiviral response, and cell-to-cell communication. A key mechanistic question is how an RNA is specifically selected for trafficking from one type of cell into another type. Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) required for trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana leaves. This motif, called loop 6, has the sequence 5'-CGA-3'...5'-GAC-3' flanked on both sides by cis Watson-Crick G/C and G/U wobble base pairs. We present a three-dimensional (3D) structural model of loop 6 that specifies all non-Watson-Crick base pair interactions, derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA x-ray crystal structure database. The model is supported by available chemical modification patterns, natural sequence conservation/variations in PSTVd isolates and related species, and functional characterization of all possible mutants for each of the loop 6 base pairs. Our findings and approaches have broad implications for studying the 3D RNA structural motifs mediating trafficking of diverse RNA species across specific cellular boundaries and for studying the structure-function relationships of RNA motifs in other biological processes.
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Affiliation(s)
- Ryuta Takeda
- Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
| | - Anton I. Petrov
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Neocles B. Leontis
- Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403
| | - Biao Ding
- Molecular, Cellular, and Developmental Biology Program, Ohio State University, Columbus, Ohio 43210
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, Ohio State University, Columbus, Ohio 43210
- The Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
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74
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Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 2010; 6:e1001233. [PMID: 21151960 PMCID: PMC2996334 DOI: 10.1371/journal.pgen.1001233] [Citation(s) in RCA: 709] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 11/02/2010] [Indexed: 12/02/2022] Open
Abstract
Human genome-wide association studies have linked single nucleotide polymorphisms (SNPs) on chromosome 9p21.3 near the INK4/ARF (CDKN2a/b) locus with susceptibility to atherosclerotic vascular disease (ASVD). Although this locus encodes three well-characterized tumor suppressors, p16INK4a, p15INK4b, and ARF, the SNPs most strongly associated with ASVD are ∼120 kb from the nearest coding gene within a long non-coding RNA (ncRNA) known as ANRIL (CDKN2BAS). While individuals homozygous for the atherosclerotic risk allele show decreased expression of ANRIL and the coding INK4/ARF transcripts, the mechanism by which such distant genetic variants influence INK4/ARF expression is unknown. Here, using rapid amplification of cDNA ends (RACE) and analysis of next-generation RNA sequencing datasets, we determined the structure and abundance of multiple ANRIL species. Each of these species was present at very low copy numbers in primary and cultured cells; however, only the expression of ANRIL isoforms containing exons proximal to the INK4/ARF locus correlated with the ASVD risk alleles. Surprisingly, RACE also identified transcripts containing non-colinear ANRIL exonic sequences, whose expression also correlated with genotype and INK4/ARF expression. These non-polyadenylated RNAs resisted RNAse R digestion and could be PCR amplified using outward-facing primers, suggesting they represent circular RNA structures that could arise from by-products of mRNA splicing. Next-generation DNA sequencing and splice prediction algorithms identified polymorphisms within the ASVD risk interval that may regulate ANRIL splicing and circular ANRIL (cANRIL) production. These results identify novel circular RNA products emanating from the ANRIL locus and suggest causal variants at 9p21.3 regulate INK4/ARF expression and ASVD risk by modulating ANRIL expression and/or structure. Unbiased studies of the human genome have identified strong genetic determinants of atherosclerotic vascular disease (ASVD) on chromosome 9p21.3. This region of the genome does not encode genes previously linked to ASVD, but does contain the INK4/ARF tumor suppressor locus. Products of the INK4/ARF locus regulate cell division, a process thought to be important in ASVD pathology. We and others have suggested that genetic variants in 9p21.3 influence INK4/ARF gene expression; however, the mechanisms by which these distant polymorphisms (>100,000 bp away) influence transcription of the locus is unknown. The ASVD–associated genetic variants lie within the predicted structure of a non-coding RNA (ncRNA) called ANRIL. Based upon recent work suggesting that other ncRNAs can repress nearby coding genes, we considered the possibility that ANRIL structure may regulate INK4/ARF gene expression. Coupling molecular analysis with state-of-the-art sequencing technologies in a wide variety of cell types from normal human donors and cancer cells, we found that ANRIL encodes a heterogeneous species of rare RNA transcripts. Moreover, we identified novel, circular ANRIL isoforms (cANRIL) whose expression correlated with INK4/ARF transcription and ASVD risk. These studies suggest a new model wherein ANRIL structure influences INK4/ARF expression and susceptibility to atherosclerosis.
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Affiliation(s)
- Christin E. Burd
- The Curriculum in Toxicology, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - William R. Jeck
- Department of Genetics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Yan Liu
- Department of Genetics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Hanna K. Sanoff
- The Division of Hematology and Oncology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Zefeng Wang
- Department of Pharmacology, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Norman E. Sharpless
- The Curriculum in Toxicology, The Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Genetics, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- Department of Medicine, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
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75
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Eiras M. VIROIDES, PEQUENOS RNAS PATOGÊNICOS CAPAZES DE REPLICAÇÃO AUTÔNOMA: MODELOS MOLECULARES PARA O ESTUDO DE INTERAÇÕES PATÓGENO-HOSPEDEIRO E EVOLUÇÃO. ARQUIVOS DO INSTITUTO BIOLÓGICO 2010. [DOI: 10.1590/1808-1657v77p7512010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RESUMO Os viroides, apesar de serem constituídos por um pequeno RNA de fita simples, fortemente estruturado, circular, que não codifica proteínas, são capazes de se replicar de maneira autônoma em plantas superiores e causar doença interagindo diretamente com fatores do hospedeiro. Nesta revisão, serão apresentados e discutidos alguns dos mais recentes trabalhos envolvendo a interação de viroides com fatores do hospedeiro, incluindo aspectos relacionados à replicação, movimento e patogênese, além de suas características evolutivas. Nos últimos anos, alguns grupos de pesquisa têm se aventurado na busca por fatores do hospedeiro e mecanismos moleculares relacionados ao ciclo infeccioso dos viroides, tentando desvendar como esses pequenos RNAs interagem com o hospedeiro induzindo sintomas. Os viroides não codificam proteínas supressoras de silenciamento e, portanto, devem garantir sua existência utilizando estratégias baseadas em sua estrutura secundária, na compartimentalização em organelas, associação com fatores do hospedeiro e eficiência na replicação. A complexidade do ciclo infeccioso desses minúsculos RNAs indica que muitas interações desses patógenos com fatores do hospedeiro ainda devem ser identificadas.
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Affiliation(s)
- M. Eiras
- Instituto Biológico, Centro de Pesquisa e Desenvolvimento de Sanidade Vegetal, Brasil
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76
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Wiesyk A, Candresse T, Zagorski W, Gora-Sochacka A. Use of randomly mutagenized genomic cDNA banks of potato spindle tuber viroid to screen for viable versions of the viroid genome. J Gen Virol 2010; 92:457-66. [DOI: 10.1099/vir.0.026286-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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77
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Teune JH, Steger G. NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome. J Nucleic Acids 2010; 2010. [PMID: 20871826 PMCID: PMC2943127 DOI: 10.4061/2010/495904] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 06/10/2010] [Accepted: 06/29/2010] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNA) are small regulatory, noncoding RNA molecules that are transcribed
as primary miRNAs (pri-miRNA) from eukaryotic genomes. At least in plants, their
regulatory activity is mediated through base-pairing with protein-coding messenger RNAs
(mRNA) followed by mRNA degradation or translation repression.
We describe NOVOMIR, a program for the identification of miRNA genes in plant
genomes. It uses a series of filter steps and a statistical model to discriminate a pre-miRNA
from other RNAs and does rely neither on prior knowledge of a miRNA target nor on
comparative genomics. The sensitivity and specificity of NOVOMIR for detection of premiRNAs
from Arabidopsis thaliana is ~0.83 and ~0.99, respectively. Plant pre-miRNAs
are more heterogeneous with respect to size and structure than animal pre-miRNAs. Despite
these difficulties, NOVOMIR is well suited to perform searches for pre-miRNAs on a
genomic scale. NOVOMIR is written in Perl and relies on two additional, free programs for prediction
of RNA secondary structure (RNALFOLD, RNASHAPES).
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Affiliation(s)
- Jan-Hendrik Teune
- Institut für Physikalische Biologie, Universitätsstr. 1, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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78
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Martinez G, Donaire L, Llave C, Pallas V, Gomez G. High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem. MOLECULAR PLANT PATHOLOGY 2010; 11:347-59. [PMID: 20447283 PMCID: PMC6640512 DOI: 10.1111/j.1364-3703.2009.00608.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Small RNA (sRNA)-guided processes, referred to as RNA silencing, regulate endogenous and exogenous gene expression. In plants and some animals, these processes are noncell autonomous and can operate beyond the site of initiation. Viroids, the smallest self-replicating plant pathogens known, are inducers, targets and evaders of this regulatory mechanism and, consequently, the presence of viroid-derived sRNAs (vd-sRNAs) is usually associated with viroid infection. However, the pathways involved in the biogenesis of vd-sRNAs are largely unknown. Here, we analyse, by high-throughput pyrosequencing, the profiling of the Hop stunt viroid (HSVd) vd-sRNAs recovered from the leaves and phloem of infected cucumber (Cucumis sativus) plants. HSVd vd-sRNAs are mostly 21 and 22 nucleotides in length and derived equally from plus and minus HSVd RNA strands. The widespread distribution of vd-sRNAs across the genome reveals that the totality of the HSVd RNA genome contributes to the formation of vd-sRNAs. Our sequence data suggest that viroid-derived double-stranded RNA functions as one of the main precursors of vd-sRNAs. Remarkably, phloem vd-sRNAs accumulated preferentially as 22-nucleotide species with a consensus sequence over-represented. This bias in size and sequence in the HSVd vd-sRNA population recovered from phloem exudate suggests the existence of a selective trafficking of vd-sRNAs to the phloem tissue of infected cucumber plants.
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Affiliation(s)
- German Martinez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, CPI, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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79
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Vachev T, Ivanova D, Minkov I, Tsagris M, Gozmanova M. Trafficking of the Potato spindle tuber viroid between tomato and Orobanche ramosa. Virology 2010; 399:187-93. [DOI: 10.1016/j.virol.2009.12.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 08/11/2009] [Accepted: 12/12/2009] [Indexed: 10/19/2022]
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80
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Di Serio F, Martínez de Alba AE, Navarro B, Gisel A, Flores R. RNA-dependent RNA polymerase 6 delays accumulation and precludes meristem invasion of a viroid that replicates in the nucleus. J Virol 2010; 84:2477-89. [PMID: 20015979 PMCID: PMC2820905 DOI: 10.1128/jvi.02336-09] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 12/08/2009] [Indexed: 12/23/2022] Open
Abstract
The detection of viroid-derived small RNAs (vd-sRNAs) similar to the small interfering RNAs (siRNAs, 21 to 24 nucleotides [nt]) in plants infected by nuclear-replicating members of the family Pospiviroidae (type species, Potato spindle tuber viroid [PSTVd]) indicates that they are inducers and targets of the RNA-silencing machinery of their hosts. RNA-dependent RNA polymerase 6 (RDR6) catalyzes an amplification circuit producing the double-stranded precursors of secondary siRNAs. Recently, the role of RDR6 in restricting systemic spread of certain RNA viruses and precluding their invasion of the apical growing tip has been documented using RDR6-silenced Nicotiana benthamiana (NbRDR6i) plants. Here we show that RDR6 is also engaged in regulating PSTVd levels: accumulation of PSTVd genomic RNA was increased in NbRDR6i plants with respect to the wild-type controls (Nbwt) early in infection, whereas this difference decreased or disappeared in later infection stages. Moreover, in situ hybridization revealed that RDR6 is involved in restricting PSTVd access in floral and vegetative meristems, thus providing firm genetic evidence for an antiviroid RNA silencing mechanism. RNA gel blot hybridization and deep sequencing showed in wt and RDR6i backgrounds that PSTVd sRNAs (i) accumulate to levels paralleling their genomic RNA, (ii) display similar patterns with prevailing 22- or 21-nt plus-strand species, and (iii) adopt strand-specific hot spot profiles along the genomic RNA. Therefore, the surveillance mechanism restraining entry of some RNA viruses into meristems likely also controls PSTVd access in N. benthamiana. Unexpectedly, deep sequencing also disclosed in NbRDR6i plants a profile of RDR6-derived siRNA dominated by 21-nt plus-strand species mapping within a narrow window of the hairpin RNA stem expressed transgenically for silencing RDR6, indicating that minus-strand siRNAs silencing the NbRDR6 mRNA represent a minor fraction of the total siRNA population.
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Affiliation(s)
- Francesco Di Serio
- Istituto di Virologia Vegetale (CNR), Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politécnica, Avenida de los Naranjos, 46022 Valencia, Spain, Istituto di Tecnologie Biomediche (CNR), Via Amendola 122/D, 70126 Bari, Italy
| | - Angel-Emilio Martínez de Alba
- Istituto di Virologia Vegetale (CNR), Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politécnica, Avenida de los Naranjos, 46022 Valencia, Spain, Istituto di Tecnologie Biomediche (CNR), Via Amendola 122/D, 70126 Bari, Italy
| | - Beatriz Navarro
- Istituto di Virologia Vegetale (CNR), Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politécnica, Avenida de los Naranjos, 46022 Valencia, Spain, Istituto di Tecnologie Biomediche (CNR), Via Amendola 122/D, 70126 Bari, Italy
| | - Andreas Gisel
- Istituto di Virologia Vegetale (CNR), Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politécnica, Avenida de los Naranjos, 46022 Valencia, Spain, Istituto di Tecnologie Biomediche (CNR), Via Amendola 122/D, 70126 Bari, Italy
| | - Ricardo Flores
- Istituto di Virologia Vegetale (CNR), Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy, Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politécnica, Avenida de los Naranjos, 46022 Valencia, Spain, Istituto di Tecnologie Biomediche (CNR), Via Amendola 122/D, 70126 Bari, Italy
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81
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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.
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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,
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82
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Evolution and diversity of the human hepatitis d virus genome. Adv Bioinformatics 2010:323654. [PMID: 20204073 PMCID: PMC2829689 DOI: 10.1155/2010/323654] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 12/11/2009] [Indexed: 12/17/2022] Open
Abstract
Human hepatitis delta virus (HDV) is the smallest RNA virus in genome. HDV genome is divided into a viroid-like sequence and a protein-coding sequence which could have originated from different resources and the HDV genome was eventually constituted through RNA recombination. The genome subsequently diversified through accumulation of mutations selected by interactions between the mutated RNA and proteins with host factors to successfully form the infectious virions. Therefore, we propose that the conservation of HDV nucleotide sequence is highly related with its functionality. Genome analysis of known HDV isolates shows that the C-terminal coding sequences of large delta antigen (LDAg) are the highest diversity than other regions of protein-coding sequences but they still retain biological functionality to interact with the heavy chain of clathrin can be selected and maintained. Since viruses interact with many host factors, including escaping the host immune response, how to design a program to predict RNA genome evolution is a great challenging work.
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83
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Bolduc F, Hoareau C, St-Pierre P, Perreault JP. In-depth sequencing of the siRNAs associated with peach latent mosaic viroid infection. BMC Mol Biol 2010; 11:16. [PMID: 20158907 PMCID: PMC2830927 DOI: 10.1186/1471-2199-11-16] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 02/16/2010] [Indexed: 11/21/2022] Open
Abstract
Background It has been observed that following viroid infection, there is an accumulation of viroid-derived siRNAs in infected plants. Some experimental results suggest that these small RNAs may be produced by the plant defense system to protect it from infection, indicating that viroids can elicit the RNA-silencing pathways. The objective of this study is to identify in the peach latent mosaic viroid (PLMVd), a model RNA genome, the regions that are most susceptible to RNA interference machinery. Results The RNA isolated from an infected tree have been used to sequence in parallel viroid species and small non-coding RNA species. Specifically, PLMVd RNAs were amplified, cloned and sequenced according to a conventional approach, while small non-coding RNAs were determined by high-throughput sequencing. The first led to the typing of 18 novel PLMVd variants. The second provided a library of small RNAs including 880 000 sequences corresponding to PLMVd-derived siRNAs, which makes up 11.2% of the sequences of the infected library. These siRNAs contain mainly 21-22 nucleotide RNAs and are equivalently distributed between the plus and the minus polarities of the viroid. They cover the complete viroid genome, although the amount varies depending on the regions. These regions do not necessarily correlate with the double-stranded requirement to be a substrate for Dicer-like enzymes. We noted that some sequences encompass the hammerhead self-cleavage site, indicating that the circular conformers could be processed by the RNA-silencing machinery. Finally, a bias in the relative abundance of the nature of the 5' nucleotides was observed (A, U >> G, C). Conclusions The approach used provided us a quantitative representation of the PLMVd-derived siRNAs retrieved from infected peach trees. These siRNAs account for a relatively large proportion of the small non-coding RNAs. Surprisingly, the siRNAs from some regions of the PLMVd genome appear over-represented, although these regions are not necessarily forming sufficiently long double-stranded structures to satisfy Dicer-like criteria for substrate specificity. Importantly, this large library of siRNAs gave several hints as to the components of the involved silencing machinery.
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Affiliation(s)
- François Bolduc
- RNA group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de santé, Université de Sherbrooke, Sherbrooke, QC, J1H 5N4, Canada
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84
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Wang Y, Ding B. Viroids: small probes for exploring the vast universe of RNA trafficking in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:28-39. [PMID: 20074138 DOI: 10.1111/j.1744-7909.2010.00900.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cell-to-cell and long-distance trafficking of RNA is a rapidly evolving frontier of integrative plant biology that broadly impacts studies on plant growth and development, spread of infectious agents and plant defense responses. The fundamental questions being pursued at the forefronts revolve around function, mechanism and evolution. In the present review, we will first use specific examples to illustrate the biological importance of cell-to-cell and long-distance trafficking of RNA. We then focus our discussion on research findings obtained using viroids that have advanced our understanding of the underlying mechanisms involved in RNA trafficking. We further use viroid examples to illustrate the great diversity of trafficking machinery evolved by plants, as well as the promise for new insights in the years ahead. Finally, we discuss the prospect of integrating findings from different experimental systems to achieve a systems-based understanding of RNA trafficking function, mechanism and evolution.
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Affiliation(s)
- Ying Wang
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, Columbus, OH 43210, USA
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85
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Ivanova D, Vachev T, Baev V, Minkov I, Gozmanova M. Identification of Potato Spindle Tuber Viroid Small RNA in Orobanche Ramosaby Microarray. BIOTECHNOL BIOTEC EQ 2010. [DOI: 10.1080/13102818.2010.10817829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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86
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Kawaguchi-Ito Y, Li SF, Tagawa M, Araki H, Goshono M, Yamamoto S, Tanaka M, Narita M, Tanaka K, Liu SX, Shikata E, Sano T. Cultivated grapevines represent a symptomless reservoir for the transmission of hop stunt viroid to hop crops: 15 years of evolutionary analysis. PLoS One 2009; 4:e8386. [PMID: 20041179 PMCID: PMC2793511 DOI: 10.1371/journal.pone.0008386] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 11/19/2009] [Indexed: 11/22/2022] Open
Abstract
Hop stunt was a mysterious disorder that first emerged in the 1940s in commercial hops in Japan. To investigate the origin of this disorder, we infected hops with natural Hop stunt viroid (HpSVd) isolates derived from four host species (hop, grapevine, plum and citrus), which except for hop represent possible sources of the ancestral viroid. These plants were maintained for 15 years, then analyzed the HpSVd variants present. Here we show that the variant originally found in cultivated grapevines gave rise to various combinations of mutations at positions 25, 26, 54, 193, and 281. However, upon prolonged infection, these variants underwent convergent evolution resulting in a limited number of adapted mutants. Some of them showed nucleotide sequences identical to those currently responsible for hop stunt epidemics in commercial hops in Japan, China, and the United States. Therefore, these results indicate that we have successfully reproduced the original process by which a natural HpSVd variant naturally introduced into cultivated hops was able to mutate into the HpSVd variants that are currently present in commercial hops. Furthermore, and importantly, we have identified cultivated grapevines as a symptomless reservoir in which HSVd can evolve and be transmitted to hop crops to cause epidemics.
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Affiliation(s)
- Yoko Kawaguchi-Ito
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Shi-Fang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Masaya Tagawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Hiroyuki Araki
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Masafumi Goshono
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Shingen Yamamoto
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Mayumi Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Masako Narita
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Kazuaki Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Sheng-Xue Liu
- Key Oasis Eco-agriculture Laboratory of Xinjiang Production and Construction Group, Shihezi, People's Republic of China
| | - Eishiro Shikata
- Graduate School of Agriculture, Japan Academy, Hokkaido University, Sapporo, Japan
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
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87
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Di Serio F, Gisel A, Navarro B, Delgado S, Martínez de Alba ÁE, Donvito G, Flores R. Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis. PLoS One 2009; 4:e7539. [PMID: 19847296 PMCID: PMC2760764 DOI: 10.1371/journal.pone.0007539] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 09/25/2009] [Indexed: 01/03/2023] Open
Abstract
Northern-blot hybridization and low-scale sequencing have revealed that plants infected by viroids, non-protein-coding RNA replicons, accumulate 21–24 nt viroid-derived small RNAs (vd-sRNAs) similar to the small interfering RNAs, the hallmarks of RNA silencing. These results strongly support that viroids are elicitors and targets of the RNA silencing machinery of their hosts. Low-scale sequencing, however, retrieves partial datasets and may lead to biased interpretations. To overcome this restraint we have examined by deep sequencing (Solexa-Illumina) and computational approaches the vd-sRNAs accumulating in GF-305 peach seedlings infected by two molecular variants of Peach latent mosaic viroid (PLMVd) inciting peach calico (albinism) and peach mosaic. Our results show in both samples multiple PLMVd-sRNAs, with prevalent 21-nt (+) and (−) RNAs presenting a biased distribution of their 5′ nucleotide, and adopting a hotspot profile along the genomic (+) and (−) RNAs. Dicer-like 4 and 2 (DCL4 and DCL2, respectively), which act hierarchically in antiviral defense, likely also mediate the genesis of the 21- and 22-nt PLMVd-sRNAs. More specifically, because PLMVd replicates in plastids wherein RNA silencing has not been reported, DCL4 and DCL2 should dice the PLMVd genomic RNAs during their cytoplasmic movement or the PLMVd-dsRNAs generated by a cytoplasmic RNA-dependent RNA polymerase (RDR), like RDR6, acting in concert with DCL4 processing. Furthermore, given that vd-sRNAs derived from the 12–14-nt insertion containing the pathogenicity determinant of peach calico are underrepresented, it is unlikely that symptoms may result from the accidental targeting of host mRNAs by vd-sRNAs from this determinant guiding the RNA silencing machinery.
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Affiliation(s)
| | - Andreas Gisel
- Istituto di Tecnologie Biomediche del CNR, Bari, Italy
| | | | - Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Valencia, Spain
| | | | | | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Valencia, Spain
- * E-mail:
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88
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Takeda R, Ding B. Viroid intercellular trafficking: RNA motifs, cellular factors and broad impacts. Viruses 2009; 1:210-21. [PMID: 21994546 PMCID: PMC3185492 DOI: 10.3390/v1020210] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 12/30/2022] Open
Abstract
Viroids are noncoding RNAs that infect plants. In order to establish systemic infection, these RNAs must traffic from an initially infected host cell into neighboring cells and ultimately throughout a whole plant. Recent studies have identified structural motifs in a viroid that are required for trafficking, enabling further studies on the mechanisms of their function. Some cellular proteins interact with viroids in vivo and may play a role in viroid trafficking, which can now be directly tested by using a virus-induced gene silencing system that functions efficiently in plant species from which these factors were identified. This review discusses these recent advances, unanswered questions and the use of viroid infection as an highly productive model to elucidate mechanisms of RNA trafficking that is of broad biological significance.
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Affiliation(s)
- Ryuta Takeda
- Department of Plant Cellular and Molecular Biology and Molecular, Cellular and Developmental Biology Program, Ohio State University, 207 Rightmire Hall, 1060 Carmack Road, Columbus, 43210 USA; E-Mail:
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89
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Gómez G, Martínez G, Pallás V. Interplay between viroid-induced pathogenesis and RNA silencing pathways. TRENDS IN PLANT SCIENCE 2009; 14:264-9. [PMID: 19375972 DOI: 10.1016/j.tplants.2009.03.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 02/20/2009] [Accepted: 03/02/2009] [Indexed: 05/22/2023]
Abstract
Of all known plant pathogens, viroids have the lowest biological complexity. Their genome consists of a naked RNA without protein-encoding capacity. However, viroids contain sufficient genetic information to establish infection in susceptible hosts. The process by which this tiny RNA subverts the plant cell machinery by coercing the host to express symptoms of viroid infection is the 'Holy Grail' that has been searched for since the first viroid-induced disease was described. Recently, a large body of evidence has led to the emergent view that RNA silencing has a crucial role in viroid pathogenesis and evolution. Here, we chronologically analyse the relevant findings supporting this idea and propose a model to explain the possible interrelation between the trans-acting small interfering RNA (ta-siRNA) biogenesis pathway and viroid replication and pathogenesis.
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Affiliation(s)
- Gustavo Gómez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, Edificio 8 E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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90
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Abstract
The key to the discovery of the Hepatitis D Virus (HDV) was the description in Turin, Italy in the mid-1970s of the delta antigen and antibody in carriers of the hepatitis B surface antigen. The new antigen was first thought to be a marker of the Hepatitis B Virus (HBV) and in view of its intricate true nature, it would have possibly died away as another odd antigenic subtype of HBV, like many that were described in the 1970s. Fortunately, instead, a collaboration started in 1978 between the Turin group, and the National Institute of Health and Georgetown University in the US. With American facilities and expertise this collaboration led just a year later, in 1979, to the unfolding of an unexpected and amazing chapter in virology. Experiments in chimpanzees demonstrated that the delta antigen was not a component of the HBV but of a separate defective virus requiring HBV for its infection; it was named the hepatitis D virus to conform to the nomenclature of hepatitis viruses and classified within the genus Deltavirus. The animal experiments were also seminal in proposing to future clinical interpretation, the paradigm of a pathogenic infection (hepatitis D), that could develop only in HBV-infected patients, was mainly transmitted by superinfection of HDV on chronic HBV carriers and had the ability to strongly inhibit the helper HBV. The discovery of the HDV has driven three directions of further research: (1) The understanding of the replicative and infectious mechanisms of the HDV. (2) The assessment of its epidemiological and medical impact. (3) The search for a therapy for chronic hepatitis D (CHD). This review summarizes the progress achieved in each field of research in the thirty years that have passed since the discovery of HDV.
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Affiliation(s)
- Mario Rizzetto
- Division of Gastroenterology, Molinette-University of Turin, Corso Bramante, Turin 10126, Italy.
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91
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Mota S, Mendes M, Freitas N, Penque D, Coelho AV, Cunha C. Proteome analysis of a human liver carcinoma cell line stably expressing hepatitis delta virus ribonucleoproteins. J Proteomics 2008; 72:616-27. [PMID: 19136081 DOI: 10.1016/j.jprot.2008.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 12/03/2008] [Accepted: 12/04/2008] [Indexed: 01/26/2023]
Abstract
Hepatitis delta virus (HDV) infects human hepatocytes already infected with the hepatitis B virus increasing about ten fold the risk of cirrhosis and fulminant hepatitis. The lack of an appropriate cell culture system capable of supporting virus replication has so far impaired the detailed investigation of the HDV biology including the identification of host factors involved in pathogenesis. Here, we made use of a HDV cDNA stably transfected cell line, Huh7-D12, in a proteomic approach to identify the changes in the protein expression profiles in human liver cells that arise as a consequence of HDV replication. Total protein extracts from Huh7-D12 cells and of the corresponding non transfected human liver carcinoma cell line, Huh7, were separated by 2-DE. Differentially expressed spots were identified by MALDI-TOF followed by database searching. We identified 23 differentially expressed proteins of which 15 were down regulated and 8 up regulated in Huh7-D12 cells. These proteins were found to be involved in different cellular pathways. The down regulation of the histone H1-binding protein and of triosephosphate isomerase was confirmed by Real time PCR, and the up regulation of the La protein and lamin A/C was validated by western blot.
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Affiliation(s)
- Sérgio Mota
- Unidade de Biologia Molecular, Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical, Rua da Junqueira 96, Lisbon, Portugal
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