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Potato Spindle Tuber Viroid RNA-Templated Transcription: Factors and Regulation. Viruses 2018; 10:v10090503. [PMID: 30227597 PMCID: PMC6164485 DOI: 10.3390/v10090503] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/10/2018] [Accepted: 09/15/2018] [Indexed: 12/14/2022] Open
Abstract
Viroids are circular noncoding RNAs that infect plants. Without encoding any protein, these noncoding RNAs contain the necessary genetic information for propagation in hosts. Nuclear-replicating viroids employ DNA-dependent RNA polymerase II (Pol II) for replication, a process that makes a DNA-dependent enzyme recognize RNA templates. Recently, a splicing variant of transcription factor IIIA (TFIIIA-7ZF) was identified as essential for Pol II to replicate potato spindle tuber viroid (PSTVd). The expression of TFIIIA-7ZF, particularly the splicing event, is regulated by a ribosomal protein (RPL5). PSTVd modulates its expression through a direct interaction with RPL5 resulting in optimized expression of TFIIIA-7ZF. This review summarizes the recent discoveries of host factors and regulatory mechanisms underlying PSTVd-templated transcription processes and raises new questions that may help future exploration in this direction. In addition, it briefly compares the machinery and the regulatory mechanism for PSTVd with the replication/transcription system of human hepatitis delta virus.
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2
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Abstract
Mature viroids consist of a noncoding, covalently closed circular RNA that is able to autonomously infect respective host plants. Thus, they must utilize proteins of the host for most biological functions such as replication, processing, transport, and pathogenesis. Therefore, viroids can be regarded as minimal parasites of the host machinery. They have to present to the host machinery the appropriate signals based on either their sequence or their structure. Here, we summarize such sequence and structural features critical for the biological functions of viroids.
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Affiliation(s)
- Gerhard Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
| | - Jean-Pierre Perreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliqueé sur le cancer, Université de Sherbrooke, Québec, Canada.
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3
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Mondragón E, Maher LJ. Anti-Transcription Factor RNA Aptamers as Potential Therapeutics. Nucleic Acid Ther 2015; 26:29-43. [PMID: 26509637 PMCID: PMC4753637 DOI: 10.1089/nat.2015.0566] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transcription factors (TFs) are DNA-binding proteins that play critical roles in regulating gene expression. These proteins control all major cellular processes, including growth, development, and homeostasis. Because of their pivotal role, cells depend on proper TF function. It is, therefore, not surprising that TF deregulation is linked to disease. The therapeutic drug targeting of TFs has been proposed as a frontier in medicine. RNA aptamers make interesting candidates for TF modulation because of their unique characteristics. The products of in vitro selection, aptamers are short nucleic acids (DNA or RNA) that bind their targets with high affinity and specificity. Aptamers can be expressed on demand from transgenes and are intrinsically amenable to recognition by nucleic acid-binding proteins such as TFs. In this study, we review several natural prokaryotic and eukaryotic examples of RNAs that modulate the activity of TFs. These examples include 5S RNA, 6S RNA, 7SK, hepatitis delta virus-RNA (HDV-RNA), neuron restrictive silencer element (NRSE)-RNA, growth arrest-specific 5 (Gas5), steroid receptor RNA activator (SRA), trophoblast STAT utron (TSU), the 3' untranslated region of caudal mRNA, and heat shock RNA-1 (HSR1). We then review examples of unnatural RNA aptamers selected to inhibit TFs nuclear factor-kappaB (NF-κB), TATA-binding protein (TBP), heat shock factor 1 (HSF1), and runt-related transcription factor 1 (RUNX1). The field of RNA aptamers for DNA-binding proteins continues to show promise.
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Affiliation(s)
- Estefanía Mondragón
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
| | - Louis James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
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4
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Hohn T. RNA based viral silencing suppression in plant pararetroviruses. FRONTIERS IN PLANT SCIENCE 2015; 6:398. [PMID: 26113850 PMCID: PMC4462095 DOI: 10.3389/fpls.2015.00398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/18/2015] [Indexed: 05/30/2023]
Abstract
The 35S promoter of cauliflower mosaic virus and that of other plant pararetroviruses gives rise to an RNA, which is both a pre-genome and a polycistronic mRNA. The 600 nucleotide long very structured leader of this RNA is also transcribed separately. The resulting 8S RNA is then converted to a double strand giving rise to a huge set of siRNAs, which suppress silencing. In this Mini-Review I discuss how this versatile stretch of 600 nts constitutes a masterpiece of evolution.
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Affiliation(s)
- Thomas Hohn
- Botanical Institute, University of BaselBasel, Switzerland
- Friedrich Miescher InstituteBasel, Switzerland
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5
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Rao ALN, Kalantidis K. Virus-associated small satellite RNAs and viroids display similarities in their replication strategies. Virology 2015; 479-480:627-36. [PMID: 25731957 DOI: 10.1016/j.virol.2015.02.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/01/2015] [Accepted: 02/10/2015] [Indexed: 12/15/2022]
Abstract
Since the discovery of non-coding, small, highly structured, satellite RNAs (satRNAs) and viroids as subviral pathogens of plants , have been of great interest to molecular biologists as possible living fossils of pre-cellular evolution in an RNA world. Despite extensive studies performed in the last four decades, there is still mystery surrounding the origin and evolutionary relationship between these subviral pathogens. Recent technical advances revealed some commonly shared replication features between these two subviral pathogens. In this review, we discuss our current perception of replication and evolutionary origin of these petite RNA pathogens.
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Affiliation(s)
- A L N Rao
- Department of Plant Pathology & Microbiology, University of California, Riverside, CA 92521-0122, United States.
| | - Kriton Kalantidis
- IMBB-FORTH, Vasilika Vouton, Heraklion, Crete, Greece and Dept. of Biology, University of Crete, Heraklion, Greece
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6
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Hnilicová J, Jirát Matějčková J, Šiková M, Pospíšil J, Halada P, Pánek J, Krásný L. Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria. Nucleic Acids Res 2014; 42:11763-76. [PMID: 25217589 PMCID: PMC4191392 DOI: 10.1093/nar/gku793] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 11/12/2022] Open
Abstract
Small RNAs (sRNAs) are molecules essential for a number of regulatory processes in the bacterial cell. Here we characterize Ms1, a sRNA that is highly expressed in Mycobacterium smegmatis during stationary phase of growth. By glycerol gradient ultracentrifugation, RNA binding assay, and RNA co-immunoprecipitation, we show that Ms1 interacts with the RNA polymerase (RNAP) core that is free of the primary sigma factor (σA) or any other σ factor. This contrasts with the situation in most other species where it is 6S RNA that interacts with RNAP and this interaction requires the presence of σA. The difference in the interaction of the two types of sRNAs (Ms1 or 6S RNA) with RNAP possibly reflects the difference in the composition of the transcriptional machinery between mycobacteria and other species. Unlike Escherichia coli, stationary phase M. smegmatis cells contain relatively few RNAP molecules in complex with σA. Thus, Ms1 represents a novel type of small RNAs interacting with RNAP.
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Affiliation(s)
- Jarmila Hnilicová
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jitka Jirát Matějčková
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Michaela Šiková
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jiří Pospíšil
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Petr Halada
- Department of Molecular Structure Characterization, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Josef Pánek
- Department of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Libor Krásný
- Department of Molecular Genetics of Bacteria, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
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7
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Glouzon JPS, Bolduc F, Wang S, Najmanovich RJ, Perreault JP. Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity. PLoS One 2014; 9:e87297. [PMID: 24498066 PMCID: PMC3907566 DOI: 10.1371/journal.pone.0087297] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 12/24/2013] [Indexed: 01/04/2023] Open
Abstract
Viroids are small circular single-stranded infectious RNAs characterized by a relatively high mutation level. Knowledge of their sequence heterogeneity remains largely elusive and previous studies, using Sanger sequencing, were based on a limited number of sequences. In an attempt to address sequence heterogeneity from a population dynamics perspective, a GF305-indicator peach tree was infected with a single variant of the Avsunviroidae family member Peach latent mosaic viroid (PLMVd). Six months post-inoculation, full-length circular conformers of PLMVd were isolated and deep-sequenced. We devised an original approach to the bioinformatics refinement of our sequence libraries involving important phenotypic data, based on the systematic analysis of hammerhead self-cleavage activity. Two distinct libraries yielded a total of 3,939 different PLMVd variants. Sequence variants exhibiting up to ∼17% of mutations relative to the inoculated viroid were retrieved, clearly illustrating the high level of divergence dynamics within a unique population. While we initially assumed that most positions of the viroid sequence would mutate, we were surprised to discover that ∼50% of positions remained perfectly conserved, including several small stretches as well as a small motif reminiscent of a GNRA tetraloop which are the result of various selective pressures. Using a hierarchical clustering algorithm, the different variants harvested were subdivided into 7 clusters. We found that most sequences contained an average of 4.6 to 6.4 mutations compared to the variant used to initially inoculate the plant. Interestingly, it was possible to reconstitute and compare the sequence evolution of each of these clusters. In doing so, we identified several key mutations. This study provides a reliable pipeline for the treatment of viroid deep-sequencing. It also sheds new light on the extent of sequence variation that a viroid population can sustain, and which may give rise to a quasispecies.
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Affiliation(s)
- Jean-Pierre Sehi Glouzon
- Département d’informatique, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - François Bolduc
- Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Shengrui Wang
- Département d’informatique, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Rafael J. Najmanovich
- Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail: (RJN); (JPP)
| | - Jean-Pierre Perreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail: (RJN); (JPP)
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8
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Abstract
Besides canonical double-strand DNA promoters, multisubunit RNAPs (RNA polymerases) recognize a number of specific single-strand DNA and RNA templates, resulting in synthesis of various types of RNA transcripts. The general recognition principles and the mechanisms of transcription initiation on these templates are not fully understood. To investigate further the molecular mechanisms underlying the transcription of single-strand templates by bacterial RNAP, we selected high-affinity single-strand DNA aptamers that are specifically bound by RNAP holoenzyme, and characterized a novel class of aptamer-based transcription templates. The aptamer templates have a hairpin structure that mimics the upstream part of the open promoter bubble with accordingly placed specific promoter elements. The affinity of the RNAP holoenzyme to such DNA structures probably underlies its promoter-melting activity. Depending on the template structure, the aptamer templates can direct synthesis of productive RNA transcripts or effectively trap RNAP in the process of abortive synthesis, involving DNA scrunching, and competitively inhibit promoter recognition. The aptamer templates provide a novel tool for structure-function studies of transcription initiation by bacterial RNAP and its inhibition.
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9
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Gómez G, Pallás V. Viroids: a light in the darkness of the lncRNA-directed regulatory networks in plants. THE NEW PHYTOLOGIST 2013; 198:10-15. [PMID: 23397958 DOI: 10.1111/nph.12196] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Gustavo Gómez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, CPI - Av. Fausto Elio s/n, 46022, Valencia, Spain
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, CPI - Av. Fausto Elio s/n, 46022, Valencia, Spain
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10
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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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11
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Abstract
Hepatitis delta virus (HDV) is a subviral agent dependent upon hepatitis B virus (HBV). HDV uses the envelope proteins of HBV to achieve assembly and infection of target cells. Otherwise, the replication of the RNA genome of HDV is totally different from that of its helper virus, and involves redirection of host polymerase activity. This chapter is concerned with recent developments in our understanding of the genome replication process.
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Affiliation(s)
- John M Taylor
- Fox Chase Cancer Center, Philadelphia, Pennsylvania, USA
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12
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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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13
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Abstract
Viroids are small, circular RNA pathogens, which infect several crop plants and can cause diseases of economic importance. They do not code for proteins but they contain a number of RNA structural elements, which interact with factors of the host. The resulting set of sophisticated and specific interactions enables them to use the host machinery for their replication and transport, circumvent its defence reactions and alter its gene expression. Although found in plants, viroids have a distant relative in the animal world: hepatitis delta virus (HDV), a satellite virus of hepatitis B virus, which has a similar rod-like structure and replicates in the nucleus of infected cells. Viroids have also a cellular relative: the retroviroids, found in some plants as independent (non-infectious) RNA replicons with a DNA copy. In this review, we summarize recent progress in understanding viroid biology. We discuss the possible role of recently identified viroid-binding host proteins as well as the recent data on the interaction of viroids with one part of the host's defence machinery, the RNA-mediated gene silencing and how this might be connected to viroid replication and pathogenicity.
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Affiliation(s)
- Efthimia Mina Tsagris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, PO Box 1385, 71110 Heraklion, Greece.
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14
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Abrahem A, Pelchat M. Formation of an RNA polymerase II preinitiation complex on an RNA promoter derived from the hepatitis delta virus RNA genome. Nucleic Acids Res 2008; 36:5201-11. [PMID: 18682525 PMCID: PMC2532721 DOI: 10.1093/nar/gkn501] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Although RNA polymerases (RNAPs) are able to use RNA as template, it is unknown how they recognize RNA promoters. In this study, we used an RNA fragment derived from the hepatitis delta virus (HDV) genome as a model to investigate the recognition of RNA promoters by RNAP II. Inhibition of the transcription reaction using an antibody specific to the largest subunit of RNAP II and the direct binding of purified RNAP II to the RNA promoter confirmed the involvement of RNAP II in the reaction. RNA affinity chromatography established that an active RNAP II preinitiation complex forms on the RNA promoter and indicated that this complex contains the core RNAP II subunit and the general transcription factors TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH and TFIIS. Binding assays demonstrated the direct binding of the TATA-binding protein and suggested that this protein is required to nucleate the RNAP II complex on the RNA promoter. Our findings provide a better understanding of the events leading to RNA promoter recognition by RNAP II.
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Affiliation(s)
- Abrahem Abrahem
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
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15
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Motard J, Bolduc F, Thompson D, Perreault JP. The peach latent mosaic viroid replication initiation site is located at a universal position that appears to be defined by a conserved sequence. Virology 2008; 373:362-75. [PMID: 18190946 DOI: 10.1016/j.virol.2007.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Revised: 11/18/2007] [Accepted: 12/10/2007] [Indexed: 10/22/2022]
Abstract
Viroids replicate through a rolling circle mechanism that is exclusively RNA dependent. In this study, we initially revisited the determination of the replication initiation sites of peach latent mosaic viroid (PLMVd). A universal initiation site for each of the PLMVd polarities (position A50/C51 and U284 for the plus and minus strands, respectively) that is shared by a relatively wide repertoire of viroid variants was identified, in agreement with a previous report based on a different methodology. Subsequently, an in vitro selection procedure based on a model rolling circle replication assay was developed. This latter experiment led to the identification of a highly conserved CAGACG box which is reminiscent of the sequence found in the vicinity of the PLMVd initiation sites. The conserved sequence contributes to delineating the initiation site and provides an explanation for the presence of a specific universal initiation site on the PLMVd molecule.
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Affiliation(s)
- Julie Motard
- RNA group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, Quebec, Canada J1H 5N4.
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16
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Gildehaus N, Neußer T, Wurm R, Wagner R. Studies on the function of the riboregulator 6S RNA from E. coli: RNA polymerase binding, inhibition of in vitro transcription and synthesis of RNA-directed de novo transcripts. Nucleic Acids Res 2007; 35:1885-96. [PMID: 17332013 PMCID: PMC1874619 DOI: 10.1093/nar/gkm085] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/30/2007] [Accepted: 01/30/2007] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli 6S RNA represents a non-coding RNA (ncRNA), which, based on the conserved secondary structure and previous functional studies, had been suggested to interfere with transcription. Selective inhibition of sigma-70 holoenzymes, preferentially at extended -10 promoters, but not stationary-phase-specific transcription was described, suggesting a direct role of 6S RNA in the transition from exponential to stationary phase. To elucidate the underlying mechanism, we have analysed 6S RNA interactions with different forms of RNA polymerase by gel retardation and crosslinking. Preferred binding of 6S RNA to Esigma(70) was confirmed, however weaker binding to Esigma(38) was also observed. The crosslinking analysis revealed direct contact between a central 6S RNA sequence element and the beta/beta' and sigma subunits. Promoter complex formation and in vitro transcription analysis with exponential- and stationary-phase-specific promoters and the corresponding holoenzymes demonstrated that 6S RNA interferes with transcription initiation but does not generally distinguish between exponential- and stationary-phase-specific promoters. Moreover, we show for the first time that 6S RNA acts as a template for the transcription of defined RNA molecules in the absence of DNA. In conclusion, this study reveals new aspects of 6S RNA function.
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MESH Headings
- Binding Sites
- DNA-Directed RNA Polymerases/metabolism
- Escherichia coli/genetics
- Gene Expression Regulation, Bacterial
- Promoter Regions, Genetic
- RNA/biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Bacterial/physiology
- RNA, Untranslated/chemistry
- RNA, Untranslated/metabolism
- RNA, Untranslated/physiology
- Sigma Factor/metabolism
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
| | | | | | - Rolf Wagner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, D-40225 Düsseldorf, Germany
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17
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Ding B, Itaya A. Viroid: a useful model for studying the basic principles of infection and RNA biology. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:7-20. [PMID: 17249418 DOI: 10.1094/mpmi-20-0007] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Viroids are small, circular, noncoding RNAs that currently are known to infect only plants. They also are the smallest self-replicating genetic units known. Without encoding proteins and requirement for helper viruses, these small RNAs contain all the information necessary to mediate intracellular trafficking and localization, replication, systemic trafficking, and pathogenicity. All or most of these functions likely result from direct interactions between distinct viroid RNA structural motifs and their cognate cellular factors. In this review, we discuss current knowledge of these RNA motifs and cellular factors. An emerging theme is that the structural simplicity, functional versatility, and experimental tractability of viroid RNAs make viroid-host interactions an excellent model to investigate the basic principles of infection and further the general mechanisms of RNA-templated replication, intracellular and intercellular RNA trafficking, and RNA-based regulation of gene expression. We anticipate that significant advances in understanding viroid-host interactions will be achieved through multifaceted secondary and tertiary RNA structural analyses in conjunction with genetic, biochemical, cellular, and molecular tools to characterize the RNA motifs and cellular factors associated with the processes leading to systemic infection.
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Affiliation(s)
- Biao Ding
- Department of Plant Cellular and Molecular Biology, Plant Biotechnology Center, Ohio State University, 207 Rightmire Hall, 1060 Carmack Road, Columbus 43210, USA.
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18
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Abstract
Noncoding small RNAs regulate gene expression in all organisms, in some cases through direct association with RNA polymerase (RNAP). Here we report that the mechanism of 6S RNA inhibition of transcription is through specific, stable interactions with the active site of Escherichia coli RNAP that exclude promoter DNA binding. In fact, the DNA-dependent RNAP uses bound 6S RNA as a template for RNA synthesis, producing 14-to 20-nucleotide RNA products (pRNA). These results demonstrate that 6S RNA is functionally engaged in the active site of RNAP. Synthesis of pRNA destabilizes 6S RNA-RNAP complexes leading to release of the pRNA-6S RNA hybrid. In vivo, 6S RNA-directed RNA synthesis occurs during outgrowth from the stationary phase and likely is responsible for liberating RNAP from 6S RNA in response to nutrient availability.
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MESH Headings
- Base Sequence
- Binding Sites
- DNA, Bacterial/chemistry
- DNA, Bacterial/metabolism
- DNA-Directed RNA Polymerases/antagonists & inhibitors
- DNA-Directed RNA Polymerases/chemistry
- DNA-Directed RNA Polymerases/metabolism
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Molecular Sequence Data
- Nucleic Acid Conformation
- Promoter Regions, Genetic
- RNA Stability
- RNA, Bacterial/biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Sigma Factor/metabolism
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
- Karen M Wassarman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
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19
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Greco-Stewart VS, Miron P, Abrahem A, Pelchat M. The human RNA polymerase II interacts with the terminal stem-loop regions of the hepatitis delta virus RNA genome. Virology 2006; 357:68-78. [PMID: 16959288 DOI: 10.1016/j.virol.2006.08.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 06/02/2006] [Accepted: 08/07/2006] [Indexed: 12/28/2022]
Abstract
The hepatitis delta virus (HDV) is an RNA virus that depends on DNA-dependent RNA polymerase (RNAP) for its transcription and replication. While it is generally accepted that RNAP II is involved in HDV replication, its interaction with HDV RNA requires confirmation. A monoclonal antibody specific to the carboxy terminal domain of the largest subunit of RNAP II was used to establish the association of RNAP II with both polarities of HDV RNA in HeLa cells. Co-immunoprecipitations using HeLa nuclear extract revealed that RNAP II interacts with HDV-derived RNAs at sites located within the terminal stem-loop domains of both polarities of HDV RNA. Analysis of these regions revealed a strong selection to maintain a rod-like conformation and demonstrated several conserved features. These results provide the first direct evidence of an association between human RNAP II and HDV RNA and suggest two transcription start sites on both polarities of HDV RNA.
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Affiliation(s)
- Valerie S Greco-Stewart
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada K1H 8M5
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Kolonko N, Bannach O, Aschermann K, Hu KH, Moors M, Schmitz M, Steger G, Riesner D. Transcription of potato spindle tuber viroid by RNA polymerase II starts in the left terminal loop. Virology 2006; 347:392-404. [PMID: 16406459 DOI: 10.1016/j.virol.2005.11.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 10/21/2005] [Accepted: 11/28/2005] [Indexed: 01/09/2023]
Abstract
Viroids are single-stranded, circular RNAs of 250 to 400 bases, that replicate autonomously in their host plants but do not code for a protein. Viroids of the family Pospiviroidae, of which potato spindle tuber viroid (PSTVd) is the type strain, are replicated by the host's DNA-dependent RNA polymerase II in the nucleus. To analyze the initiation site of transcription from the (+)-stranded circles into (-)-stranded replication intermediates, we used a nuclear extract from a non-infected cell culture of the host plant S. tuberosum. The (-)-strands, which were de novo-synthesized in the extract upon addition of circular (+)-PSTVd, were purified by affinity chromatography. This purification avoided contamination by host nucleic acids that had resulted in a misassignment of the start site in an earlier study. Primer-extension analysis of the de novo-synthesized (-)-strands revealed a single start site located in the hairpin loop of the left terminal region in circular PSTVd's secondary structure. This start site is supported further by analysis of the infectivity and replication behavior of site-directed mutants in planta.
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Affiliation(s)
- Nadine Kolonko
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Geb. 26.12.U1, Universitätsstr.1, D-40225 Düsseldorf, Germany
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21
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Delgado S, Martínez de Alba AE, Hernández C, Flores R. A short double-stranded RNA motif of Peach latent mosaic viroid contains the initiation and the self-cleavage sites of both polarity strands. J Virol 2005; 79:12934-43. [PMID: 16188995 PMCID: PMC1235847 DOI: 10.1128/jvi.79.20.12934-12943.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The transcription initiation sites of viroid RNAs, despite their relevance for replication and in vivo folding, are poorly characterized. Here we have examined this question for Peach latent mosaic viroid (PLMVd), which belongs to the family of chloroplastic viroids with hammerhead ribozymes (Avsunviroidae), by adapting an RNA ligase-mediated rapid amplification of cDNA ends methodology developed for mapping the genuine capped 5' termini of eukaryotic messenger RNAs. To this aim, the characteristic free 5'-triphosphate group of chloroplastic primary transcripts from PLMVd-infected young fruits was previously capped in vitro with GTP and guanylyltransferase. PLMVd plus and minus initiation sites map at similar double-stranded motifs of 6 to 7 bp that also contain the conserved GUC triplet preceding the self-cleavage site in both polarity strands. Within the branched secondary structures predicted for the two PLMVd strands, this motif is located at the base of a similar long hairpin that presumably contains the promoters for a chloroplastic RNA polymerase. The transcription templates could be the circular viroid RNAs or their most abundant linear counterparts, assuming the involvement of an RNA polymerase able to jump over template discontinuities. Both PLMVd initiation sites were confirmed by applying the same methodology to two purified PLMVd subgenomic RNAs and by primer extension, and they therefore likely reflect the in vivo situation. The location of the PLMVd initiation sites provides a mechanistic view into how the nascent strands may fold and self-cleave during transcription. The approach described here may be extended to other chloroplastic RNA replicons and transcripts accumulating at low levels.
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Affiliation(s)
- Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Spain
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22
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Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA (NEW YORK, N.Y.) 2005; 11:774-84. [PMID: 15811922 PMCID: PMC1370762 DOI: 10.1261/rna.7286705] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Accepted: 02/01/2005] [Indexed: 05/24/2023]
Abstract
6S RNA is an abundant noncoding RNA in Escherichia coli that binds to sigma70 RNA polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. We have computationally identified >100 new 6S RNA homologs in diverse eubacterial lineages. Two abundant Bacillus subtilis RNAs of unknown function (BsrA and BsrB) and cyanobacterial 6Sa RNAs are now recognized as 6S homologs. Structural probing of E. coli 6S RNA and a B. subtilis homolog supports a common secondary structure derived from comparative sequence analysis. The conserved features of 6S RNA suggest that it binds RNA polymerase by mimicking the structure of DNA template in an open promoter complex. Interestingly, the two B. subtilis 6S RNAs are discoordinately expressed during growth, and many proteobacterial 6S RNAs could be cotranscribed with downstream homologs of the E. coli ygfA gene encoding a putative methenyltetrahydrofolate synthetase. The prevalence and robust expression of 6S RNAs emphasize their critical role in bacterial adaptation.
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Affiliation(s)
- Jeffrey E Barrick
- Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520, USA
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23
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Poole AM, Logan DT. Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol Biol Evol 2005; 22:1444-55. [PMID: 15774424 PMCID: PMC7107533 DOI: 10.1093/molbev/msi132] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
RNA repair has now been demonstrated to be a genuine biological process and appears to be present in all three domains of life. In this article, we consider what this might mean for the transition from an early RNA-dominated world to modern cells possessing genetically encoded proteins and DNA. There are significant gaps in our understanding of how the modern protein-DNA world could have evolved from a simpler system, and it is currently uncertain whether DNA genomes evolved once or twice. Against this backdrop, the discovery of RNA repair in modern cells is timely food for thought and brings us conceptually one step closer to understanding how RNA genomes were replaced by DNA genomes. We have examined the available literature on multisubunit RNA polymerase structure and function and conclude that a strong case can be made that the Last Universal Common Ancestor (LUCA) possessed a repair-competent RNA polymerase, which would have been capable of acting on an RNA genome. However, while this lends credibility to the proposal that the LUCA had an RNA genome, the alternative, that LUCA had a DNA genome, cannot be completely ruled out.
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Affiliation(s)
- Anthony M Poole
- Department of Molecular Biology and Functional Genomics, Stockholm University, Stockholm, Sweden.
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Pelchat M, Perreault JP. Binding site of Escherichia coli RNA polymerase to an RNA promoter. Biochem Biophys Res Commun 2004; 319:636-42. [PMID: 15178453 DOI: 10.1016/j.bbrc.2004.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2004] [Indexed: 11/25/2022]
Abstract
The DNA-dependent RNA polymerase (RNAP) from Escherichia coli has previously been reported to specifically initiate transcription from viroid-derived RNA promoters in vitro. In order to gain insight into the molecular mechanism of RNA promoter recognition by this RNAP, we have used nucleic acid intercalators and RNA:protein footprinting experiments to study the interaction between the polymerase and an RNA promoter at the initiation site. Our data revealed that the polymerase binds an external single-stranded loop, rather than a double-stranded region as is the case for DNA templates. Despite this divergence in promoter binding, the model RNA template was bound by both the beta and beta' subunits of the RNAP, as is observed with DNA templates. Most importantly, this work proposes large single-stranded RNA hairpin loops have the potential to be promoters for DNA-dependent RNAP.
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Affiliation(s)
- Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ont., Canada K1H 8M5.
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Tabler M, Tsagris M. Viroids: petite RNA pathogens with distinguished talents. TRENDS IN PLANT SCIENCE 2004; 9:339-348. [PMID: 15231279 DOI: 10.1016/j.tplants.2004.05.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Viroids are small, circular, single-stranded RNA molecules that cause several infectious plant diseases. Viroids do not encode any pathogen-specific peptides but nonetheless, the subviral pathogens replicate autonomously and spread in the plant by recruiting host proteins via functional motifs encoded in their RNA genome. During the past couple of years, considerable progress has been made towards comprehending how viroids interact with their hosts. Here, we summarize recent findings on the structure-function relationships of viroids, their strategies and mechanisms of replication and trafficking, and the identification and characterization of interacting host proteins. We also describe the impact of the RNA silencing machinery of plants on viroid RNAs and how this has started to influence our models of viroid replication and pathogenicity.
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Affiliation(s)
- Martin Tabler
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, PO Box 1527, GR-71110 Heraklion/Crete, Greece.
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Malfitano M, Di Serio F, Covelli L, Ragozzino A, Hernández C, Flores R. Peach latent mosaic viroid variants inducing peach calico (extreme chlorosis) contain a characteristic insertion that is responsible for this symptomatology. Virology 2003; 313:492-501. [PMID: 12954216 DOI: 10.1016/s0042-6822(03)00315-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The involvement of Peach latent mosaic viroid (PLMVd) in an extensive chlorosis of peach known as calico (PC) has been advanced but ultimate proof is lacking. Sequencing of 16 full-length PLMVd cDNA clones of a PC isolate revealed two groups of variants. Nine had a size (336-338 nt) similar to that of typical PLMVd variants of nonsymptomatic and mosaic-inducing isolates, whereas the other 7 were longer (348-351 nt) due to an insertion of 12-13 nt. This insertion was always found in the hairpin loop capping the hammerhead arm, had a limited sequence variability, and folded itself into a hairpin. When three PLMVd dimeric transcripts, two with and the other without the insertion, were slash-inoculated on GF-305 peach seedlings, PC symptoms were produced exclusively by the RNAs containing the insertion, which was conserved in the progeny. These data demonstrate that the agent of PC is PLMVd. Direct support that the 12- to 13-nt insertion contains the PC pathogenicity determinant was obtained by its removal through site-directed mutagenesis from one of the PC-inducing variants. Inoculations with dimeric transcripts of the resulting variant showed that it could replicate but without eliciting symptoms. Our results also suggest that the insertion emerges sporadically de novo.
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Affiliation(s)
- Monica Malfitano
- Dipartimento di Arboricoltura, Botanica, e Patologia Vegetale, Università di Napoli, 80055 Portici, Italy
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