Viroids and Satellites and Their Vector Interactions—This Special Issue Is Dedicated to the Memory of Theodor O. Diener Who Discovered Viroids

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 14578

Special Issue Editors


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Guest Editor
Lead Scientist Emeritus, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
Interests: viroids; viroid diseases; mycoviroids; plant viruses; molecular virology; molecular biology; genomics; origin; evolution
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Guest Editor
Professor Emeritus, 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
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Guest Editor
Professor, Institute of Molecular Biology and Biotechnology, University of Crete, 700 13 Heraklion, Greece
Interests: RNAi; RNA silencing; RNA biology; viroids
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Guest Editor
Distinguished Professor, Jeonbuk National University, Jeonju, Republic of Korea
Interests: molecular analysis of the signaling pathways of resistance elicited by tobacco mosaic virus in tobacco containing the N gene; molecular biology of cucumber mosaic virus, viroids, and satellites
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Many diseases of unknown etiology with symptoms like those caused by plant viruses but for which no virions could be found were described during the early and mid-20th century. In 1971, T.O. Diener demonstrated that the causal agent of potato spindle disease, first described in the early 1920s, is a free RNA of 25,000–110,000 Daltons, which is 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 that it must rely on host enzymes for its replication. In 1972, Joseph S. Semancik and L. G. Weathers reported similar findings for the causal agent of citrus exocortis disease. For such an unconventional agent, the term viroid, suggested by Diener, was adopted in 1972. Diener remarked that the term viroid had earlier been put forward by Altenburg in 1946 to describe possible “...symbionts akin to the viruses...” in animal cells. Viroids are small, covalently closed circular or linear highly structured RNA molecules with a high degree of base paring, replicate autonomously, do not encode proteins, and use pre-existing host-cell RNA polymerase and processing enzymes for replication and pathogenesis. Viroids belong to the order of subviral agents, which currently includes two families, eight genera, and 33 species that have been biologically and molecularly characterized. 

The natural host range of viroids includes vegetables, field and ornamental crops, fruit and palm trees, and grapevines. Recently, it has been shown that apple scar skin viroid naturally infects several species of filamentous fungi in viroid-infected apple trees.  Moreover, under laboratory conditions, few viroids replicated in filamentous fungi. The term mycoviroids was coined for viroids that infect plant pathogenic fungi.

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 leaders of life as they are infectious agents consisting of only 234‒401 ribonucleotides.

In 1961, Basil Kassanis coined the term satellite for the very small virus particles that he found in some cultures of tobacco necrosis virus. He demonstrated that these spherical 17-nm viral satellite particles were unable to replicate in the absence of the larger 30-nm TNV particles. In 1972, Irving R. Schneider described that an RNA dependent on a helper virus for replication and movement was found in association with tobacco ringspot virus and was named “satellite RNA”. In 1972, a devastating epidemic disease swept through the tomato fields of the French Alsace province destroying the crop. The causal agent was not revealed until 1977, when Jacobus M. Kaper clearly demonstrated that RNA 5 of cucumber mosaic virus (CMV) was required to cause the Alsace disease. Because RNA 5 alone cannot cause the disease but needed other CMV RNAs for replication, this CMV RNA was recognized as the first RNA satellite to cause a plant disease. The DNA satellites of geminiviruses were described about two decades later. The first one identified in 1997 was found to be a defective form of a larger satellite designated DNA beta in 2000, one of many since described and now referred to as the Betasatellites of Begomoviruses.

In general, with a few exceptions, most satellites are considered unique and different from either sub-genomic RNAs or viral defective interfering RNAs/DNAs with sequences identical to and derived from part(s) of the viral genome. Historically, satellites were not necessary for the replication of their helper viruses and were thus considered completely redundant. This view, however, has changed to some extent after more than two decades, when satellite-like RNAs were found to be required for their helper viruses’ specific movement within the infected host plant, plant-to-plant transmission, or plant-to-vector transmission.

Alphasatellites of both geminiviruses and nanoviruses are small circular DNAs that depend on their associated viruses for encapsidation, movement, and transmission; however, they are capable of autonomous replication. Hence, they are not true satellites and will not be covered.

Dr. Ahmed Hadidi
Prof. Dr. Henryk Hanokh Czosnek
Prof. Dr. Kriton Kalantidis
Prof. Dr. Peter Palukaitis
Guest Editors

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Keywords

Keywords for Viroids
  • viroids and viroid diseases
  • economic significance
  • biology, and structure
  • replication, and pathogenesis
  • transmission, and mycoviroids
  • epidemiology
  • RNA silencing
  • proteome and transcriptome
  • origin and evolution
  • detection methods and control measures

Keywords for Satellites

  • economic significance
  • biology, replication, and taxonomy
  • origin and evolution
  • satellite RNAs: their involvement in pathogenesis and RNA silencing
  • development and application of satellite-based vectors
  • biology and pathogenesis of satellite viruses
  • large satellite RNAs
  • small linear and small circular satellite RNAs
  • betasatellites of begomoviruses
  • satellites as viral biocontrol agents

Published Papers (9 papers)

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Research

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17 pages, 3848 KiB  
Article
New Insights into Hop Latent Viroid Detection, Infectivity, Host Range, and Transmission
by Osama O. Atallah, Sherin M. Yassin and Jeanmarie Verchot
Viruses 2024, 16(1), 30; https://doi.org/10.3390/v16010030 - 23 Dec 2023
Cited by 2 | Viewed by 3046
Abstract
Hop latent viroid (HLVd), a subviral pathogen from the family Pospiviroidae, is a major threat to the global cannabis industry and is the causative agent for “dudding disease”. Infected plants can often be asymptomatic for a period of growth and then develop [...] Read more.
Hop latent viroid (HLVd), a subviral pathogen from the family Pospiviroidae, is a major threat to the global cannabis industry and is the causative agent for “dudding disease”. Infected plants can often be asymptomatic for a period of growth and then develop symptoms such as malformed and yellowing leaves, as well as stunted growth. During flowering, HLVd-infected plants show reduced levels of valuable metabolites. This study was undertaken to expand our basic knowledge of HLVd infectivity, transmission, and host range. HLVd-specific primers were used for RT-PCR detection in plant samples and were able to detect HLVd in as little as 5 picograms of total RNA. A survey of hemp samples obtained from a diseased production system proved sole infection of HLVd (72%) with no coexistence of hop stunt viroid. HLVd was infectious through successive passage assays using a crude sap or total RNA extract derived from infected hemp. HLVd was also highly transmissible through hemp seeds at rates of 58 to 80%. Host range assays revealed new hosts for HLVd: tomato, cucumber, chrysanthemum, Nicotiana benthamiana, and Arabidopsis thaliana (Col-0). Sequence analysis of 77 isolates revealed only 3 parsimony-informative sites, while 10 sites were detected among all HLVd isolates available in the GenBank. The phylogenetic relationship among HLVd isolates allowed for inferring two major clades based on the genetic distance. Our findings facilitate further studies on host–viroid interaction and viroid management. Full article
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12 pages, 3485 KiB  
Article
Molecular Signature of a Novel Alternanthera Yellow Vein Virus Variant Infecting the Ageratum conyzoides Weed in Oman
by Muhammad Shafiq, Gabrijel Ondrasek, Abdullah Mohammed Al-Sadi and Muhammad Shafiq Shahid
Viruses 2023, 15(12), 2381; https://doi.org/10.3390/v15122381 - 04 Dec 2023
Viewed by 779
Abstract
Alternanthera yellow vein virus (AlYVV), a monopartite begomovirus, has been identified infecting a diverse range of crops and native plants in Pakistan, India, and China. However, distinctive yellow vein symptoms, characteristic of begomovirus infection, were observed on the Ageratum conyzoides weed in [...] Read more.
Alternanthera yellow vein virus (AlYVV), a monopartite begomovirus, has been identified infecting a diverse range of crops and native plants in Pakistan, India, and China. However, distinctive yellow vein symptoms, characteristic of begomovirus infection, were observed on the Ageratum conyzoides weed in Oman, prompting a thorough genomic characterization in this study. The results unveiled a complete genome sequence of 2745 base pairs and an associated betasatellite spanning 1345 base pairs. In addition, Sequence Demarcation Tool analyses indicated the highest nucleotide identity of 92.8% with a previously reported AlYVV-[IN_abalpur_A_17:LC316182] strain, whereas the betasatellite exhibited a 99.8% nucleotide identity with isolates of tomato leaf curl betasatellite. Thus, our findings propose a novel AlYVV Oman virus (AlYVV-OM) variant, emphasizing the need for additional epidemiological surveillance to understand its prevalence and significance in Oman and the broader region. To effectively manage the spread of AlYVV-OM and minimize its potential harm to (agro)ecosystems, future research should focus on elucidating the genetic diversity of AlYVV-OM and its interactions with other begomoviruses. Full article
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11 pages, 2322 KiB  
Article
The Secondary Structure of Potato Spindle Tuber Viroid Determines Its Infectivity in Nicotiana benthamiana
by Yuxin Nie, Yuhong Zhang and Jian Wu
Viruses 2023, 15(12), 2307; https://doi.org/10.3390/v15122307 - 24 Nov 2023
Cited by 1 | Viewed by 895
Abstract
The function of RNAs is determined by their structure. However, studying the relationship between RNA structure and function often requires altering RNA sequences to modify the structures, which leads to the neglect of the importance of RNA sequences themselves. In our research, we [...] Read more.
The function of RNAs is determined by their structure. However, studying the relationship between RNA structure and function often requires altering RNA sequences to modify the structures, which leads to the neglect of the importance of RNA sequences themselves. In our research, we utilized potato spindle tuber viroid (PSTVd), a circular-form non-coding infectious RNA, as a model with which to investigate the role of a specific rod-like structure in RNA function. By generating linear RNA transcripts with different start sites, we established 12 PSTVd forms with different secondary structures while maintaining the same sequence. The RNA secondary structures were predicted using the mfold tool and validated through native PAGE gel electrophoresis after in vitro RNA folding. Analysis using plant infection assays revealed that the formation of a correct rod-like structure is crucial for the successful infection of PSTVd. Interestingly, the inability of PSTVd forms with non-rod-like structures to infect plants could be partially compensated by increasing the amount of linear viroid RNA transcripts, suggesting the existence of additional RNA secondary structures, such as the correct rod-like structure, alongside the dominant structure in the RNA inoculum of these forms. Our study demonstrates the critical role of RNA secondary structures in determining the function of infectious RNAs. Full article
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14 pages, 2581 KiB  
Article
Small Heat Shock Protein (sHsp22.98) from Trialeurodes vaporariorum Plays Important Role in Apple Scar Skin Viroid Transmission
by Savita Chaudhary, Vijayanandraj Selvaraj, Preshika Awasthi, Swati Bhuria, Rituraj Purohit, Surender Kumar and Vipin Hallan
Viruses 2023, 15(10), 2069; https://doi.org/10.3390/v15102069 - 09 Oct 2023
Viewed by 3437
Abstract
Trialeurodes vaporariorum, commonly known as the greenhouse whitefly, severely infests important crops and serves as a vector for apple scar skin viroid (ASSVd). This vector-mediated transmission may cause the spread of infection to other herbaceous crops. For effective management of ASSVd, it is [...] Read more.
Trialeurodes vaporariorum, commonly known as the greenhouse whitefly, severely infests important crops and serves as a vector for apple scar skin viroid (ASSVd). This vector-mediated transmission may cause the spread of infection to other herbaceous crops. For effective management of ASSVd, it is important to explore the whitefly’s proteins, which interact with ASSVd RNA and are thereby involved in its transmission. In this study, it was found that a small heat shock protein (sHsp) from T. vaporariorum, which is expressed under stress, binds to ASSVd RNA. The sHsp gene is 606 bp in length and encodes for 202 amino acids, with a molecular weight of 22.98 kDa and an isoelectric point of 8.95. Intermolecular interaction was confirmed through in silico analysis, using electrophoretic mobility shift assays (EMSAs) and northwestern assays. The sHsp22.98 protein was found to exist in both monomeric and dimeric forms, and both forms showed strong binding to ASSVd RNA. To investigate the role of sHsp22.98 during ASSVd infection, transient silencing of sHsp22.98 was conducted, using a tobacco rattle virus (TRV)-based virus-induced gene silencing system. The sHsp22.98-silenced whiteflies showed an approximate 50% decrease in ASSVd transmission. These results suggest that sHsp22.98 from T. vaporariorum is associated with viroid RNA and plays a significant role in transmission. Full article
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15 pages, 2997 KiB  
Article
Identification of Host Factors Interacting with a γ-Shaped RNA Element from a Plant Virus-Associated Satellite RNA
by Mengjiao Li, Xiaobei Zhang, Kaiyun Huang and Zhiyou Du
Viruses 2023, 15(10), 2039; https://doi.org/10.3390/v15102039 - 01 Oct 2023
Viewed by 989
Abstract
Previously, we identified a highly conserved, γ-shaped RNA element (γRE) from satellite RNAs of cucumber mosaic virus (CMV), and we determined γRE to be structurally required for satRNA survival and the inhibition of CMV replication. It remains unknown how γRE biologically functions. In [...] Read more.
Previously, we identified a highly conserved, γ-shaped RNA element (γRE) from satellite RNAs of cucumber mosaic virus (CMV), and we determined γRE to be structurally required for satRNA survival and the inhibition of CMV replication. It remains unknown how γRE biologically functions. In this work, pull-down assays were used to screen candidates of host factors from Nicotiana benthamiana plants using biotin-labeled γRE as bait. Nine host factors were found to interact specifically with γRE. Then, all of these host factors were down-regulated individually in N. benthamiana plants via tobacco rattle virus-induced gene silencing and tested with infection by GFP-expressing CMV (CMV-gfp) and the isolate T1 of satRNA (sat-T1). Out of nine candidates, three host factors, namely histone H3, GTPase Ran3, and eukaryotic translation initiation factor 4A, were extremely important for infection by CMV-gfp and sat-T1. Moreover, we found that cytosolic glyceraldehyde-3-phosphate dehydrogenase 2 contributed to the replication of CMV and sat-T1, but also negatively regulated CMV 2b activity. Collectively, our work provides essential clues for uncovering the mechanism by which satRNAs inhibit CMV replication. Full article
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Review

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34 pages, 3351 KiB  
Review
Viroids of the Mediterranean Basin
by Maria Kaponi, Panayota E. Kyriakopoulou and Ahmed Hadidi
Viruses 2024, 16(4), 612; https://doi.org/10.3390/v16040612 - 15 Apr 2024
Viewed by 439
Abstract
There has been substantial progress in the Mediterranean countries regarding research on viroids. Twenty-nine viroid species, all belonging to Pospiviroidae and Avsunviroidae genera, have been detected in the Mediterranean Basin. Not only have detection methods, such as reverse transcription-quantitative polymerase chain reaction and [...] Read more.
There has been substantial progress in the Mediterranean countries regarding research on viroids. Twenty-nine viroid species, all belonging to Pospiviroidae and Avsunviroidae genera, have been detected in the Mediterranean Basin. Not only have detection methods, such as reverse transcription-quantitative polymerase chain reaction and next-generation sequencing, been used for viroid detection, along with molecular hybridization techniques allowing for rapid detection, identification, and characterization of known and novel viroids in these countries, but eradication measures have also been taken that allowed for the efficient elimination of certain viroids in a number of Mediterranean countries. The eradication measures were followed as recommended by the European and Mediterranean Plant Protection Organization, which is known by its abbreviation, EPPO. The Mediterranean Region has been a niche for viroids since ancient times due to the warm climate and the socio-cultural conditions that facilitate viroid transmission among different host plant species. Full article
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12 pages, 270 KiB  
Review
Understanding Citrus Viroid Interactions: Experience and Prospects
by Yafei Wang, Yan Shi, Honglian Li and Jiaxin Chang
Viruses 2024, 16(4), 577; https://doi.org/10.3390/v16040577 - 09 Apr 2024
Viewed by 342
Abstract
Citrus is the natural host of at least eight viroid species, providing a natural platform for studying interactions among viroids. The latter manifests as antagonistic or synergistic phenomena. The antagonistic effect among citrus viroids intuitively leads to reduced symptoms caused by citrus viroids, [...] Read more.
Citrus is the natural host of at least eight viroid species, providing a natural platform for studying interactions among viroids. The latter manifests as antagonistic or synergistic phenomena. The antagonistic effect among citrus viroids intuitively leads to reduced symptoms caused by citrus viroids, while the synergistic effect leads to an increase in symptom severity. The interaction phenomenon is complex and interesting, and a deep understanding of the underlying mechanisms induced during this viroid interaction is of great significance for the prevention and control of viroid diseases. This paper summarizes the research progress of citrus viroids in recent years, focusing on the interaction phenomenon and analyzing their interaction mechanisms. It points out the core role of the host RNA silencing mechanism and viroid-derived siRNA (vd-siRNA), and provides suggestions for future research directions. Full article

Other

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12 pages, 8282 KiB  
Commentary
Viroids, Satellite RNAs and Prions: Folding of Nucleic Acids and Misfolding of Proteins
by Gerhard Steger, Detlev Riesner and Stanley B. Prusiner
Viruses 2024, 16(3), 360; https://doi.org/10.3390/v16030360 - 26 Feb 2024
Viewed by 1941
Abstract
Theodor (“Ted”) Otto Diener (* 28 February 1921 in Zürich, Switzerland; † 28 March 2023 in Beltsville, MD, USA) pioneered research on viroids while working at the Plant Virology Laboratory, Agricultural Research Service, USDA, in Beltsville. He coined the name viroid and defined [...] Read more.
Theodor (“Ted”) Otto Diener (* 28 February 1921 in Zürich, Switzerland; † 28 March 2023 in Beltsville, MD, USA) pioneered research on viroids while working at the Plant Virology Laboratory, Agricultural Research Service, USDA, in Beltsville. He coined the name viroid and defined viroids’ important features like the infectivity of naked single-stranded RNA without protein-coding capacity. During scientific meetings in the 1970s and 1980s, viroids were often discussed at conferences together with other “subviral pathogens”. This term includes what are now called satellite RNAs and prions. Satellite RNAs depend on a helper virus and have linear or, in the case of virusoids, circular RNA genomes. Prions, proteinaceous infectious particles, are the agents of scrapie, kuru and some other diseases. Many satellite RNAs, like viroids, are non-coding and exert their function by thermodynamically or kinetically controlled folding, while prions are solely host-encoded proteins that cause disease by misfolding, aggregation and transmission of their conformations into infectious prion isoforms. In this memorial, we will recall the work of Ted Diener on subviral pathogens. Full article
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5 pages, 466 KiB  
Obituary
The Remarkable Legacy of Theodor O. Diener (1921–2023): Preeminent Plant Pathologist and the Discoverer of Viroids
by Robert A. Owens and Ahmed Hadidi
Viruses 2023, 15(9), 1895; https://doi.org/10.3390/v15091895 - 08 Sep 2023
Cited by 1 | Viewed by 1453
Abstract
Theodor (“Ted”) Otto Diener, the discoverer of viroids, died on 28 March 2023 at his home in Beltsville, Maryland, USA [...] Full article
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