Viroid-like RNAs from cherry trees affected by leaf scorch disease: further data supporting their association with mycoviral double-stranded RNAs

Minoia, Sofía; Navarro, Beatriz; Covelli, L.; Barone, Maria Vittoria; García-Becedas, M. T.; Ragozzino, A.; Alioto, D.; Flores, Ricardo; Serio, Francesco Di

doi:10.1007/s00705-013-1843-z

Cited by 15 publications

(12 citation statements)

References 14 publications

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“…Attempted amplifications by RT-PCR, using different primer pairs, of Vd-LRNAs larger than FHVd-LR in the Oahu isolates have so far been unsuccessful, suggesting the absence of larger coinfecting Vd-LRNAs. Moreover, the two cscRNAs coinfecting cherry trees were not simultaneously observed in all the studied isolates, with some of them being infected by only one (Minoia et al, 2014).…”

Section: Discussionmentioning

confidence: 87%

“…Indeed, HRzs in both polarity strands have been reported in three Vd-LsatRNAs and in all viroids classified in the family Avsunviroidae. HRzs were also found in both polarity strands of two Vd-LRNAs whose nature remains unclear (grapevine hammerhead Vd-LRNA and cscRNAs, which possibly are a viroid and two Vd-LsatRNAs of a mycovirus, respectively) (Alioto et al, 2003;Wu et al, 2012;Minoia et al, 2014). Fig hammerhead viroid-like RNA assumes a rod-like conformation of minimal free energy, the relevance in vivo of which is supported by the variability observed in the FHVd-LR population accumulating in fig tissues.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Novel Fig-Associated Viroid-Like RNAs Containing Hammerhead Ribozymes in Both Polarity Strands Identified by High-Throughput Sequencing

Olmedo-Velarde

Navarro

et al. 2020

Front. Microbiol.

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Based on high-throughput sequencing (HTS) data, the existence of viroid-like RNAs (Vd-LRNAs) associated with fig trees grown in the Hawaiian Islands has been predicted. One of these RNAs has been characterized as a circular RNA ranging in size from 357 to 360 nucleotides. Structural and biochemical features of this RNA, tentatively named fig hammerhead viroid-like RNA (FHVd-LR), markedly resemble those previously reported for several viroids and viroid-like satellite RNAs (Vd-LsatRNAs), which are non-proteincoding RNAs infecting their hosts autonomously and in combination with a helper virus, respectively. The full-length sequence of FHVd-LR variants was determined by RT-PCR, cloning, and sequencing. Despite a low global sequence identity with known viroids and Vd-LsatRNAs, FHVd-LR contains a hammerhead ribozyme (HRz) in each polarity strand. Northern blot hybridization assays identified the circular and linear forms of both polarity strands of FHVd-LR and showed that one strand, assigned the (+) polarity, accumulates at higher levels than the (−) polarity strand in vivo. The (+) polarity RNA assumes a rodlike secondary structure of minimal free energy with the conserved domains of the HRzs located in opposition to each other, a feature typical of several viroids and Vd-LRNAs. The HRzs of both FHVd-LR polarity strands were shown to be active in vitro during transcription, self-cleaving the RNAs at the predicted sites. These data, together with the sequence variability observed in the cloned and sequenced full-length variants, indicate that FHVd-LR is a novel viroid or Vd-LsatRNA. According to HTS data, the coexistence of FHVd-LR of different sizes in the same host cannot be excluded. The relationships of FHVd-LR with previously reported viroids and Vd-LsatRNAs, and the need to perform bioassays to conclusively clarify the biological nature of this circular RNA, are discussed.

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Section: Discussionmentioning

confidence: 87%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Novel Fig-Associated Viroid-Like RNAs Containing Hammerhead Ribozymes in Both Polarity Strands Identified by High-Throughput Sequencing

Olmedo-Velarde

Navarro

et al. 2020

Front. Microbiol.

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“…Thus, varieties of fungi, including phytopathogenic, mycorrhizal, and endophytic fungi, could possibly serve as the reservoir or biological vector of viroids. Except for certain mycoviruses with viroid-like RNA satellites (86,87), viroid or self-replicating viroidlike agents have not been found in fungi. Presumably, the common use of dsRNA fractions that exclude low-molecular-weight RNAs for mycovirus identifications or viral metagenomics may have prevented the discovery of viroids from fungi.…”

Section: Discussionmentioning

confidence: 99%

Symptomatic plant viroid infections in phytopathogenic fungi

Wei

Bian

Andika

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Viroids are pathogenic agents that have a small, circular noncoding RNA genome. They have been found only in plant species; therefore, their infectivity and pathogenicity in other organisms remain largely unexplored. In this study, we investigate whether plant viroids can replicate and induce symptoms in filamentous fungi. Seven plant viroids representing viroid groups that replicate in either the nucleus or chloroplast of plant cells were inoculated to three plant pathogenic fungi, Cryphonectria parasitica, Valsa mali, and Fusarium graminearum. By transfection of fungal spheroplasts with viroid RNA transcripts, each of the three, hop stunt viroid (HSVd), iresine 1 viroid, and avocado sunblotch viroid, can stably replicate in at least one of those fungi. The viroids are horizontally transmitted through hyphal anastomosis and vertically through conidia. HSVd infection severely debilitates the growth of V. mali but not that of the other two fungi, while in F. graminearum and C. parasitica, with deletion of dicer-like genes, the primary components of the RNA-silencing pathway, HSVd accumulation increases. We further demonstrate that HSVd can be bidirectionally transferred between F. graminearum and plants during infection. The viroids also efficiently infect fungi and induce disease symptoms when the viroid RNAs are exogenously applied to the fungal mycelia. These findings enhance our understanding of viroid replication, host range, and pathogenicity, and of their potential spread to other organisms in nature.plant viroid | fungus | transmission | pathogenicity V iroids are infectious pathogenic agents possessing small, nonencapsidated, circular single-stranded RNAs that, to date, have been found to naturally infect only plants (1, 2). Viroids infect a wide variety of higher plant species, causing devastating diseases in many crops, particularly vegetables, fruits, and ornamental plants (3). In crop plants, viroids are known to spread by vegetative propagation; by mechanical agricultural practices; and, in certain cases, through seeds, pollen, and insect transmission (3, 4). As viroids do not encode any proteins and do not require a helper agent for their multiplication and survival, the biological activities of viroids are entirely dependent on direct interactions of their RNA genome or its derivatives with cellular host components (5-9). Viroid replication or processing of its RNAs in the yeast, Saccharomyces cerevisiae, and cyanobacterium, Nostoc (Nostocales), have been demonstrated (10-12).Currently, at least 34 viroid species have been identified and are classified into two families, Avsunviroidae and Pospiviroidae (13-15). The members of Avsunviroidae (type species: Avocado sunblotch viroid) replicate in the chloroplasts or plastids through symmetric rolling-circle replication using the host nuclear-encoded polymerase. Their RNAs form highly branched secondary structures and have ribozyme activities. Members of Pospiviroidae (type species: Potato spindle tuber viroid) replicate and accumulate in the nucleus th...

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“…1997 , 2006 ). Further supporting such a scenario, viroid-like RNAs similar to cscRNA1, and always in close association with similar mycoviral dsRNAs, have been identified in different cherry cultivars growing in Spain and Italy ( Minoia et al. 2014 ).…”

Section: Viroid-like Catalytic Rnas From Plants and Animals: Support ...mentioning

confidence: 71%

A scenario for the emergence of protoviroids in the RNA world and for their further evolution into viroids and viroid-like RNAs by modular recombinations and mutations

et al. 2022

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Viroids are tiny, circular and non-coding RNAs that are able to replicate and systemically infect plants. The smallest known pathogens, they have been proposed to represent survivors from the RNA world that likely preceded the cellular world currently dominating life on the earth. Although the small, circular and compact nature of viroid genomes, some of which are also endowed with catalytic activity mediated by hammerhead ribozymes, support this proposal, the lack of feasible evolutionary routes and the identification of hammerhead ribozymes in a large number of DNA genomes of organisms along the tree of life has led some to question such a proposal. Here, we reassess the origin and subsequent evolution of viroids by complementing phylogenetic reconstructions with molecular data, including the primary and higher-order structure of the genomic RNAs, their replication and recombination mechanisms and selected biological information. Features of some viroid-like RNAs found in plants, animal, and possibly fungi are also considered. The resulting evolutionary scenario supports the emergence of protoviroids in the RNA world, mainly as replicative modules, followed by further increase in genome complexity based on module/domain shuffling and combination, and mutation. Such a modular evolutionary scenario would have facilitated the inclusion in the protoviroid genomes of complex RNA structures (or coding sequences, as in the case of hepatitis ∂ virus and delta-like agents), likely needed for their adaptation from the RNA world to a life based on cells, thus generating the ancestors of current infectious viroids and viroid-like RNAs. Other non-infectious viroid-like RNAs, such as retroviroid-like RNA elements and retrozymes, could also be derived from protoviroids if their reverse transcription and integration into viral or eukaryotic DNA, respectively, are considered as a possible key step in their evolution. Comparison of evidence supporting a general and modular evolutionary model for viroids and viroid-like RNAs with that favoring alternative scenarios provides reasonable reasons to keep alive the hypothesis that these small RNA pathogens may be relics of a precellular world.

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Viroid-like RNAs from cherry trees affected by leaf scorch disease: further data supporting their association with mycoviral double-stranded RNAs

Cited by 15 publications

References 14 publications

Novel Fig-Associated Viroid-Like RNAs Containing Hammerhead Ribozymes in Both Polarity Strands Identified by High-Throughput Sequencing

Novel Fig-Associated Viroid-Like RNAs Containing Hammerhead Ribozymes in Both Polarity Strands Identified by High-Throughput Sequencing

Symptomatic plant viroid infections in phytopathogenic fungi

A scenario for the emergence of protoviroids in the RNA world and for their further evolution into viroids and viroid-like RNAs by modular recombinations and mutations

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