Special Issue "Celebrating 50 Years of Viroid Discovery"

A special issue of Cells (ISSN 2073-4409). This special issue belongs to the section "Plant, Algae and Fungi Cell Biology".

Deadline for manuscript submissions: 31 July 2022 | Viewed by 5479

Special Issue Editors

Dr. Ahmed Hadidi
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Guest Editor
Emeritus Lead Scientist, Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
Interests: plant viruses; viroids; molecular virology; molecular biology; genomics; evolution
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Henryk Hanokh Czosnek
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Guest Editor
Emeritus Professor, Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
Interests: plant–virus–insect interactions; plant stress responses; resistance to plant viruses
Special Issues, Collections and Topics in MDPI journals
Prof. Kriton Kalantidis
E-Mail Website
Guest Editor
Institute of Molecular Biology and Biotechnology, University of Crete, 700 13 Heraklion, Greece
Interests: RNAi; RNA silencing; RNA biology; Viroids
Dr. Robert A. Owens
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Guest Editor
Molecular Plant Pathology Laboratory, U.S. Department of Agriculture, Beltsville, MD 200705, USA
Interests: viroids; plant viruses; mobile genetic elements (MGE); RNA trafficking; RNA virus evolution

Special Issue Information

Dear Colleagues,

Theodor O. Diener of the US Department of Agriculture, Beltsville, Maryland, U.S, discovered the first viroid in 1971, the causal agent of potato spindle tuber disease. He showed that the agent is a free RNA of 25,000–110,000 Daltons, much smaller than a viral genome, and that no viral coat proteins were synthesized in infected plants. He concluded that the RNA is too small to contain the genetic information necessary for self-replication and it must rely on host enzymes for its replication. Also, in the U.S., Joseph S. Semancik of the University of California, Riverside, showed in 1972 that the causal agent of citrus exocortis disease is also a viroid of 125, 000 Daltons. By 1977 it was found that viroids cause economically important diseases in vegetable crops, fruit trees, ornamentals and palm species. The host range of viroids has expanded over the years to include grapevine and other cultivated and wild plant species. Viroids, the smallest known infectious agents (246-401 nt) exist as circular and linear RNAs with a high degree of base pairing and replicate autonomously in infected cells. In contrast to viruses, viroids lack capsid proteins, do not code for proteins and are completely dependent on host cellular RNA polymerases and processing enzymes for their replication. Viroids belong to the new order of subviral agents, which currently includes two families, eight genera, and 32 species of viroids. Viroids have had an impact on the science of virology, plant pathology, botany, microbiology, genetics, genomics, molecular biology, and molecular evolution as they represent the frontiers of life.

The objective of this Special Issue is to present a collection of original research, review articles, brief reports, case reports, project reports, communications and hypotheses related to viroid research advances and developments. Viroid topics of particular interest include, but are not limited to, economic impact, characteristics, diseases and viroids associated with plant species, detection and identification methods, transmission, control measures, geographical distribution and epidemiology. 

Dr. Ahmed Hadidi
Prof. Dr. Henryk Hanokh Czosnek
Prof. Dr. Kriton Kalanditis
Dr. Robert A. Owens
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cells is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Viroids
  • economic significance
  • biology
  • structure
  • replication
  • pathogenesis
  • movement
  • proteome and transcriptome
  • RNA silencing
  • origin and evolution
  • taxonomy
  • transmission
  • viroid diseases
  • detection and identification methods
  • control measures
  • CRISPR-Cas genome editing
  • recombinant DNA technology
  • Geographical distribution and epidemiology

Published Papers (7 papers)

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Editorial

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Editorial
Mycoviroids: Fungi as Hosts and Vectors of Viroids
Cells 2022, 11(8), 1335; https://doi.org/10.3390/cells11081335 - 14 Apr 2022
Viewed by 429
Abstract
Viroids were discovered by the American plant pathologist Theodor O [...] Full article
(This article belongs to the Special Issue Celebrating 50 Years of Viroid Discovery)
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Editorial
Viroids, and the Legacy of Ricardo Flores (1947–2020)
Cells 2021, 10(10), 2570; https://doi.org/10.3390/cells10102570 - 28 Sep 2021
Viewed by 528
Abstract
Viroids were discovered by Diener in 1971 [...] Full article
(This article belongs to the Special Issue Celebrating 50 Years of Viroid Discovery)

Research

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Article
The Splicing Variant TFIIIA-7ZF of Viroid-Modulated Transcription Factor IIIA Causes Physiological Irregularities in Transgenic Tobacco and Transient Somatic Depression of “Degradome” Characteristic for Developing Pollen
Cells 2022, 11(5), 784; https://doi.org/10.3390/cells11050784 - 23 Feb 2022
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Abstract
Viroids are small, non-coding, pathogenic RNAs with a significant ability of adaptation to several basic cellular processes in plants. TFIIIA-7ZF, a splicing variant of transcription factor IIIA, is involved in replication of nuclear-replicating viroids by DNA-dependent polymerase II. We overexpressed NbTFIIIA-7ZF from [...] Read more.
Viroids are small, non-coding, pathogenic RNAs with a significant ability of adaptation to several basic cellular processes in plants. TFIIIA-7ZF, a splicing variant of transcription factor IIIA, is involved in replication of nuclear-replicating viroids by DNA-dependent polymerase II. We overexpressed NbTFIIIA-7ZF from Nicotiana benthamiana in tobacco (Nicotiana tabacum) where it caused morphological and physiological deviations like plant stunting, splitting of leaf petioles, pistils or apexes, irregular branching of shoots, formation of double-blade leaves, deformation of main stems, and modification of glandular trichomes. Plant aging and senescence was dramatically delayed in transgenic lines. Factors potentially involved in viroid degradation and elimination in pollen were transiently depressed in transgenic leaves. This depressed “degradome” in young plants involved NtTudor S-like nuclease, dicers, argonoute 5, and pollen extracellular nuclease I showing expression in tobacco anthers and leaves. Analysis of the “degradome” in tobacco leaves transformed with either of two hop viroids confirmed modifications of the “degradome” and TFIIIA expression. Thus, the regulatory network connected to TFIIIA-7ZF could be involved in plant pathogenesis as well as in viroid adaptation to avoid its degradation. These results support the hypothesis on a significant impact of limited TFIIIA-7ZF on viroid elimination in pollen. Full article
(This article belongs to the Special Issue Celebrating 50 Years of Viroid Discovery)
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Article
Revisiting the Non-Coding Nature of Pospiviroids
Cells 2022, 11(2), 265; https://doi.org/10.3390/cells11020265 - 13 Jan 2022
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Abstract
Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in [...] Read more.
Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in terms of size and structure, that were shown to be translated (e.g., cirRNAs, precursors of miRNA, RNA satellites) as well as studies showing that some viroids are located in ribosomes, have reignited the idea that viroids may be translated. In this study, we used advanced bioinformatic analysis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide production but rather to another unknown function that requires further study. Full article
(This article belongs to the Special Issue Celebrating 50 Years of Viroid Discovery)
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Article
Conserved Motifs and Domains in Members of Pospiviroidae
Cells 2022, 11(2), 230; https://doi.org/10.3390/cells11020230 - 11 Jan 2022
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Abstract
In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family Pospiviroidae: their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different [...] Read more.
In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family Pospiviroidae: their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids. Employing the pairwise alignment method used by Keese and Symons and in addition to more recent methods, we tried to reproduce the original results and extent them to further members of Pospiviroidae which were unknown in 1985. Indeed, individual members of Pospiviroidae consist of a patchwork of sequence fragments from the family but the lengths of fragments do not point to consistent points of rearrangement, which is in conflict with the original hypothesis of fixed domain borders. Full article
(This article belongs to the Special Issue Celebrating 50 Years of Viroid Discovery)
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Article
Precisely Monomeric Linear RNAs of Viroids Belonging to Pospiviroid and Hostuviroid Genera Are Infectious Regardless of Transcription Initiation Site and 5′-Terminal Structure
Cells 2021, 10(11), 2971; https://doi.org/10.3390/cells10112971 - 01 Nov 2021
Cited by 2 | Viewed by 563
Abstract
Infectious dimeric RNA transcripts are a powerful tool for reverse genetic analyses in viroid studies. However, the construction of dimeric cDNA clones is laborious and time consuming, especially in mutational analyses by in vitro mutagenesis. In this study, we developed a system to [...] Read more.
Infectious dimeric RNA transcripts are a powerful tool for reverse genetic analyses in viroid studies. However, the construction of dimeric cDNA clones is laborious and time consuming, especially in mutational analyses by in vitro mutagenesis. In this study, we developed a system to synthesize a precisely monomeric linear RNA that could be transcribed in vitro directly from the cDNA clones of four viroid species. The cDNA clones were constructed such that RNA transcription was initiated at the guanine nucleotide of a predicted processing and ligation site in the viroid replication process. Although the transcribed RNAs were considered to possess 5′-triphosphate and 3′-hydroxyl termini, the RNA transcripts were infectious even without in vitro modifications. Additionally, infectivity was detected in the monomeric RNA transcripts, in which transcription was initiated at guanine nucleotides distinct from the predicted processing/ligation site. Moreover, monomeric viroid RNAs bearing 5′-monophosphate, 5′-hydroxyl, or 5′-capped termini were found to be infectious. Northern blot analysis of the pooled total RNA of the plants inoculated with the 5′-terminal modified RNA of potato spindle tuber viroid (PSTVd) indicated that maximum PSTVd accumulation occurred in plants with 5′-monophosphate RNA inoculation, followed by the plants with 5′-triphosphate RNA inoculation. Our system for synthesizing an infectious monomeric linear viroid RNA from a cDNA clone will facilitate mutational analyses by in vitro mutagenesis in viroid research. Full article
(This article belongs to the Special Issue Celebrating 50 Years of Viroid Discovery)
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Review

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Review
Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants
Cells 2021, 10(5), 1187; https://doi.org/10.3390/cells10051187 - 13 May 2021
Cited by 1 | Viewed by 1232
Abstract
Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene [...] Read more.
Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS) and RNA-directed DNA Methylation (RdDM), and the latter has the potential to trigger Transcriptional Gene Silencing (TGS). Over the last three decades, the employment of viroid-based systems has immensely contributed to our understanding of both of these RNAi facets. In this review, we highlight the role of Pospiviroidae in the discovery of RdDM, expound the gradual elucidation through the years of the diverse array of RdDM’s mechanistic details and propose a revised RdDM model based on the cumulative amount of evidence from viroid and non-viroid systems. Full article
(This article belongs to the Special Issue Celebrating 50 Years of Viroid Discovery)
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