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Abstract
The characterization of the elusive disease agent of the potato spindle tuber disease, potato spindle tuber viroid (PSTVd), was aided by the ability to obtain large amounts of infected tomato tissue in a simple bioassay where PSTVd was easily mechanically transmissible to an alternate herbaceous host in which it thrived and produced dramatic symptoms in a relatively short period (Diener, Viroids. Handbook of plant virus infections: comparative diagnosis. Elsevier/North-Holland, Amsterdam, pp 913-934, 1981; Diener, Virology 45:411-428, 1971; Raymer and O'Brien, Am Pot J, 39:401-408, 1962). Reactions in the primary, or secondary, herbaceous indicator host can range from asymptomatic to severe depending upon the viroid strain, host species, and environmental conditions and can provide evidence of a viroid infection, but do not permit identification of the viroid in question. Further characterization by molecular hybridization, RT-PCR, and sequence analysis is used to determine the etiology of the disease agent. In this chapter, methods are described for mechanical inoculation of viroids to herbaceous hosts to determine the viroid nature of diseases and the experimental host range of the viroid or to shorten the time required for obtaining relatively large amounts of viroid for subsequent purification and characterization.
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Affiliation(s)
- Rosemarie W Hammond
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Molecular Plant Pathology Laboratory, Beltsville, MD, USA.
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2
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Matoušek J, Steinbachová L, Drábková LZ, Kocábek T, Potěšil D, Mishra AK, Honys D, Steger G. Elimination of Viroids from Tobacco Pollen Involves a Decrease in Propagation Rate and an Increase of the Degradation Processes. Int J Mol Sci 2020; 21:E3029. [PMID: 32344786 PMCID: PMC7216239 DOI: 10.3390/ijms21083029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/19/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
Some viroids-single-stranded, non-coding, circular RNA parasites of plants-are not transmissible through pollen to seeds and to next generation. We analyzed the cause for the elimination of apple fruit crinkle viroid (AFCVd) and citrus bark cracking viroid (CBCVd) from male gametophyte cells of Nicotiana tabacum by RNA deep sequencing and molecular methods using infected and transformed tobacco pollen tissues at different developmental stages. AFCVd was not transferable from pollen to seeds in reciprocal pollinations, due to a complete viroid eradication during the last steps of pollen development and fertilization. In pollen, the viroid replication pathway proceeds with detectable replication intermediates, but is dramatically depressed in comparison to leaves. Specific and unspecific viroid degradation with some preference for (-) chains occurred in pollen, as detected by analysis of viroid-derived small RNAs, by quantification of viroid levels and by detection of viroid degradation products forming "comets" on Northern blots. The decrease of viroid levels during pollen development correlated with mRNA accumulation of several RNA-degrading factors, such as AGO5 nuclease, DICER-like and TUDOR S-like nuclease. In addition, the functional status of pollen, as a tissue with high ribosome content, could play a role during suppression of AFCVd replication involving transcription factors IIIA and ribosomal protein L5.
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Affiliation(s)
- Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Lenka Záveská Drábková
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Tomáš Kocábek
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic;
| | - Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Department of Molecular Genetics, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic; (J.M.); (T.K.); (A.K.M.)
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague 6, Czech Republic; (L.S.); (L.Z.D.); (D.H.)
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany
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3
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Steger G, Riesner D. Viroid research and its significance for RNA technology and basic biochemistry. Nucleic Acids Res 2019; 46:10563-10576. [PMID: 30304486 PMCID: PMC6237808 DOI: 10.1093/nar/gky903] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/24/2018] [Indexed: 12/27/2022] Open
Abstract
Viroids were described 47 years ago as the smallest RNA molecules capable of infecting plants and autonomously self-replicating without an encoded protein. Work on viroids initiated the development of a number of innovative methods. Novel chromatographic and gelelectrophoretic methods were developed for the purification and characterization of viroids; these methods were later used in molecular biology, gene technology and in prion research. Theoretical and experimental studies of RNA folding demonstrated the general biological importance of metastable structures, and nuclear magnetic resonance spectroscopy of viroid RNA showed the partially covalent nature of hydrogen bonds in biological macromolecules. RNA biochemistry and molecular biology profited from viroid research, such as in the detection of RNA as template of DNA-dependent polymerases and in mechanisms of gene silencing. Viroids, the first circular RNA detected in nature, are important for studies on the much wider spectrum of circular RNAs and other non-coding RNAs.
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Affiliation(s)
- Gerhard Steger
- Department of Biology, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Detlev Riesner
- Department of Biology, Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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Brass JRJ, Owens RA, Matoušek J, Steger G. Viroid quasispecies revealed by deep sequencing. RNA Biol 2017; 14:317-325. [PMID: 28027000 PMCID: PMC5367258 DOI: 10.1080/15476286.2016.1272745] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/04/2016] [Accepted: 12/12/2016] [Indexed: 10/20/2022] Open
Abstract
Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250-400 nucleotides, depending on viroid species. Members of the family Pospiviroidae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts. Viroids induce the production of viroid-specific small RNAs (vsRNA) that can direct (post-)transcriptional gene silencing against host transcripts or genomic sequences. Here, we used deep-sequencing to analyze vsRNAs from plants infected with different PSTVd variants to elucidate the PSTVd quasipecies evolved during infection. We recovered several novel as well as previously known PSTVd variants that were obviously competent in replication and identified common strand-specific mutations. The calculated mean error rate per nucleotide position was less than [Formula: see text], quite comparable to the value of [Formula: see text] reported for a member of Avsunviroidae. The resulting error threshold allows the synthesis of longer-than-unit-length replication intermediates as required by the asymmetric rolling-circle mechanism of members of Pospiviroidae.
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Affiliation(s)
- Joseph R. J. Brass
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Robert A. Owens
- United States Department of Agriculture, Agricultural Research Service, Molecular Plant Pathology Laboratory, Beltsville, MD, USA
| | - Jaroslav Matoušek
- Biology Centre, CAS, v. v. i., Institute of Plant Molecular Biology, Branišovská, České Budějovice, Czech Republic
| | - Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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Kovalskaya N, Owens R, Baker CJ, Deahl K, Hammond RW. Application of a modified EDTA-mediated exudation technique and guttation fluid analysis for Potato spindle tuber viroid RNA detection in tomato plants (Solanum lycopersicum). J Virol Methods 2013; 198:75-81. [PMID: 24388932 DOI: 10.1016/j.jviromet.2013.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/26/2013] [Accepted: 12/17/2013] [Indexed: 11/29/2022]
Abstract
Potato spindle tuber viroid (PSTVd) is a small plant pathogenic circular RNA that does not encode proteins, replicates autonomously, and traffics systemically in infected plants. Long-distance transport occurs by way of the phloem; however, one report in the literature describes the presence of viroid RNA in the xylem ring of potato tubers. In this study, a modified method based on an EDTA-mediated phloem exudation technique was applied for detection of PSTVd in the phloem of infected tomato plants. RT-PCR, nucleic acid sequencing, and Southern blot analyses of RT-PCR products verified the presence of viroid RNA in phloem exudates. In addition, the guttation fluid collected from the leaves of PSTVd-infected tomato plants was analyzed revealing the absence of viroid RNA in the xylem sap. To our knowledge, this is the first report of PSTVd RNA detection in phloem exudates obtained by the EDTA-mediated exudation technique.
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Affiliation(s)
- Natalia Kovalskaya
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA; Institute of Ecological Soil Science of MV Lomonosov Moscow State University, Moscow 119991, Russia
| | - Robert Owens
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - C Jacyn Baker
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Kenneth Deahl
- Genetic Improvement of Fruits and Vegetables Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Rosemarie W Hammond
- Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA.
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6
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Füssy Z, Patzak J, Stehlík J, Matoušek J. Imbalance in expression of hop (Humulus lupulus) chalcone synthase H1 and its regulators during hop stunt viroid pathogenesis. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:688-695. [PMID: 23395540 DOI: 10.1016/j.jplph.2012.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 06/01/2023]
Abstract
Viroid-derived small RNAs generated during hop stunt viroid (HSVd) pathogenesis may induce the symptoms found in the hop cultivar "Admiral", including observed shifts in phenylpropanoid metabolites and changes in petiole coloration. Using quantitative RT-PCR, we examined hop lupulin gland-specific genes that have been shown to be involved in phenylpropanoid metabolism, for altered expression in response to infection with two HSVd isolates, HSVd-g and CPFVd. Most notably, the expression of a gene encoding a key enzyme for phenylpropanoid synthesis, naringenin-chalcone synthase H1 (chs_H1), decreased up to 40-fold in infected samples. In addition, a marked decrease in the expression of HlbHLH2 and an increase in the expression of HlMyb3 were observed. These two genes encode transcription factors that form a ternary complex with HlWDR1 for chs_H1 promoter activation. In a transient expression assay, a decrease in the ternary complex potential to activate the chs_H1 promoter was observed upon the decrease of HlbHLH2 expression. In addition, targeting of the chs_H1 transcript by vd-sRNAs may contribute to these expression changes. Our data show that HSVd infection causes a significant imbalance in the expression of phenylpropanoid metabolite-affecting genes via a complex mechanism, possibly involving regulatory disorders and direct targeting by vd-sRNA.
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Affiliation(s)
- Zoltán Füssy
- University of South Bohemia, Faculty of Science, Branišovská 31, 370 05 České Budějovice, Czech Republic.
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7
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Abstract
Viroids are the smallest autonomous infectious nucleic acids known today. They are non-coding, unencapsidated, circular RNAs with sizes ranging from 250 to 400 nucleotides and infect certain plants. These RNAs are transcribed by rolling-circle mechanisms in the plant host's nuclei (Pospiviroidae) or chloroplasts (Avsunviroidae). Since viroids lack any open reading frame, their pathogenicity has for a long time been a conundrum. Recent findings, however, show that viroid infection is associated with the appearance of viroid-specific small RNA (vsRNA). These have sizes similar to endogenous small interfering RNA and microRNA and thus might alter the normal gene expression in the host plant. In this review we will summarize the current knowledge on vsRNA and discuss the current hypotheses how they connect to the induced symptoms, which vary dramatically, depending on both the plant cultivar and the viroid strain.
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Affiliation(s)
- Christian Hammann
- Heisenberg Research Group Ribogenetics, Technical University of Darmstadt, Darmstadt, Germany.
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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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9
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Scientific Opinion on the assessment of the risk of solanaceous pospiviroids for the EU territory and the identification and evaluation of risk management options. EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2330] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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10
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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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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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12
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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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13
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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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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.
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15
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Abstract
Viroids are single-stranded, circular, and noncoding RNAs that infect plants. They replicate in the nucleus or chloroplast and then traffic cell-to-cell through plasmodesmata and long distance through the phloem to establish systemic infection. They also cause diseases in certain hosts. All functions are mediated directly by the viroid RNA genome or genome-derived RNAs. I summarize recent advances in the understanding of viroid structures and cellular factors enabling these functions, emphasizing conceptual developments, major knowledge gaps, and future directions. Newly emerging experimental systems and research tools are discussed that are expected to enable significant progress in a number of key areas. I highlight examples of groundbreaking contributions of viroid research to the development of new biological principles and offer perspectives on using viroid models to continue advancing some frontiers of life science.
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Affiliation(s)
- Biao Ding
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, Columbus, Ohio 43210, USA.
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Matousek J, Orctová L, Skopek J, Pesina K, Steger G. Elimination of hop latent viroid upon developmental activation of pollen nucleases. Biol Chem 2008; 389:905-18. [PMID: 18627315 DOI: 10.1515/bc.2008.096] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Hop latent viroid (HLVd) is not transmissible through hop generative tissues and seeds. Here we describe the process of HLVd elimination during development of hop pollen. HLVd propagates in uninucleate hop pollen, but is eliminated at stages following first pollen mitosis during pollen vacuolization and maturation. Only traces of HLVd were detected by RT-PCR in mature pollen after anthesis and no viroid was detectable in in vitro germinating pollen, suggesting complete degradation of circular and linear HLVd forms. The majority of the degraded HLVd RNA in immature pollen included discrete products in the range of 230-100 nucleotides and therefore did not correspond to siRNAs. HLVd eradication from pollen correlated with developmental expression of a pollen nuclease and specific RNAses. Activity of the pollen nuclease HBN1 was maximal during the vacuolization step and decreased in mature pollen. Total RNAse activity increased continuously up to the final steps of pollen maturation. HBN1 mRNA, which is abundant at the uninucleate microspore stage, encodes a protein of 300 amino acids (34.1 kDa, isoeletric point 5.1). Sequence comparisons revealed that HBN1 is a homolog of S1-like bifunctional plant endonucleases. The developmentally activated HBN1 and pollen ribonucleases could participate in the mechanism of HLVd recognition and degradation.
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Affiliation(s)
- Jaroslav Matousek
- Biological Center AS CR vvi, Institute of Plant Molecular Biology, Branisovská 31, Ceské Budejovice, Czech Republic
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Vegetative propagation and its possible role as a genetic bottleneck in the shaping of the apple fruit crinkle viroid populations in apple and hop plants. Virus Genes 2008; 37:298-303. [PMID: 18770018 DOI: 10.1007/s11262-008-0270-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2008] [Accepted: 07/31/2008] [Indexed: 10/21/2022]
Abstract
Apple fruit crinkle viroid (AFCVd) infects apples and hops. To analyze the genetic diversity of AFCVd, nine apple and six hop isolates were collected from several locations in Japan. In total, 76 independent cDNA clones were used for sequencing and phylogenetic analyses. Two major population clusters were identified. The first consisted of all four hop isolates from Akita and some from Yamagata. The second cluster consisted of some Yamagata hop and all apple isolates. On the basis of the polymorphism found in the nucleotide insertion between positions 142/143 of the AFCVd genome and the history of hop cultivation in the region, it appears likely that one of the AFCVd populations that pre-existed in the Yamagata hops served as a "founder" for the Akita hop cluster. In this scenario, a genetic bottleneck caused by vegetative propagation played an important role in the shaping of viroid populations in a cultivated crop.
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