Viroids: Small Noncoding Infectious RNAs with the Remarkable Ability of Autonomous Replication

Daròs, José‐Antonio

doi:10.1007/978-3-319-32919-2_13

Cited by 14 publications

(10 citation statements)

References 164 publications

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“…Viroids are small, circular, non-protein-coding infectious RNAs that have the ability to replicate autonomously when inoculated into higher plants. Their genomic RNAs range in size from 246 to 401 nucleotides (nt) (Flores et al, 2015 ; Daròs, 2016 ; Gago-Zachert, 2016 ), and some viroids infect economically important crops where they can cause devastating diseases. The symptoms of viroid diseases include chlorosis, epinasty, leaf deformation and necrosis, stunting, fruit distortion, and plant death (Flores et al, 2005 ).…”

Section: Introductionmentioning

confidence: 99%

Global Transcriptomic Changes Induced by Infection of Cucumber (Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid

Xia

Hou

et al. 2017

Front. Microbiol.

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Fifteen years after transfer to hops, hop stunt viroid-grapevine (HSVd-g) was replaced by HSVd-hop (HSVd-h), a sequence variant that contains changes at five different positions. HSVd-g54 is a laboratory mutant derived from HSVd-g that differs from its progenitor by a single G to A substitution at position 54. While infection by HSVd-h induces only mild stunting in cucumber (Cucumis sativus L.), HSVd-g54 induces much more severe symptoms in this indicator host. Comparison of transcriptome profiles of cucumber infected with HSVd-h or HSVd-g54 with those of mock-inoculated controls obtained by whole transcriptome shotgun sequencing revealed that many genes related to photosynthesis were down-regulated following infection. In contrast, genes encoding RNA-dependent RNA polymerase 1 (CsRDR1), especially CsRDR1c1 and CsRDR1c2, as well as those related to basal defense responses were up-regulated. Expression of genes associated with phytohormone signaling pathways were also altered, indicating that viroid infection initiates a complex array of changes in the host transcriptome. HSVd-g54 induced an earlier and stronger response than HSVd-h, and further examination of these differences will contribute to a better understanding of the mechanisms that determine viroid pathogenicity.

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Section: Introductionmentioning

confidence: 99%

Global Transcriptomic Changes Induced by Infection of Cucumber (Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid

Xia

Hou

et al. 2017

Front. Microbiol.

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“…Then the viroid progeny moves cell-to-cell through the plasmodesmata, the channels that traverse the cell walls of plant cells, and long-distance through the phloem to establish a systemic infection in the host plant frequently inducing a disease. The more than 30 viroid species known to date are classified into two families, Pospiviroidae and Avsunviroidae , depending on the presence of particular domains in the viroid molecule; more specifically a central conserved region (CCR) that is present in all members of the family Pospiviroidae , but is missing in those of the Avsunviroidae , and hammerhead ribozymes that are exclusive of this last family ( Flores et al, 2015 ; Daròs, 2016b ; Steger and Perreault, 2016 ; Brass et al, 2017 ; Giguère and Perreault, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Mutational Analysis of Eggplant Latent Viroid RNA Circularization by the Eggplant tRNA Ligase in Escherichia coli

2018

Self Cite

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Eggplant latent viroid (ELVd) is a relatively small non-coding circular RNA that induces asymptomatic infections in eggplants (Solanum melongena L.). Like other viroid species that belong to the family Avsunviroidae, ELVd contains hammerhead ribozymes in the strands of both polarities that self-cleave RNAs producing terminal 5′-hydroxyl and 2′,3′-cyclic phosphodiester groups. Available experimental data indicate that ELVd replicates in the chloroplasts of infected cells through a symmetric rolling-circle mechanism, in which RNA circularization is catalyzed by the chloroplastic isoform of the tRNA ligase. In this work, a mutational analysis was performed to gain insight into the sequence and structural requirements of the tRNA ligase-mediated circularization of ELVd RNAs. In the predicted minimum free energy conformation of the monomeric linear ELVd RNA intermediate of plus (+) polarity, the ligation site is located in the lower part of an opened internal loop, which is present in a quasi-rod-like structure that occupies the center of the molecule. The mutations analyzed herein consisted of punctual nucleotide substitutions and deletions surrounding the ligation site on the upper and lower strands of the ELVd quasi-double-stranded structure. Computational predictions of the mutated ELVd conformations indicated different degrees of distortions compared to the minimum free energy conformation of the wild-type ELVd linear monomer of + polarity. When these mutant RNAs were expressed in Escherichia coli, they were all circularized by the eggplant tRNA ligase with approximately the same efficiency as the wild-type ELVd, except for those that directly affected the ribozyme domain. These results suggest that the viroid ribozyme domains, in addition to self-cleavage, are also involved in the tRNA ligase-mediated circularization of the monomeric linear replication intermediates.

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“…The ml (+) RNA is then ligated into the circular (+) RNA. It has been demonstrated by Nohales et al (2012) that the viroids force host DNA-ligase, most likely DNA-ligase I, to act as RNA ligase to circularize the ml (+) strand RNA [ 22 , 23 ].…”

Section: Viroidsmentioning

confidence: 99%

Long Noncoding RNAs in Plant Viroids and Viruses: A Review

Shrestha

Bujarski

2020

Pathogens

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Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle mechanism. Viroids interact with host processes in complex ways, emerging as one of the most productive tools for studying the functions of lncRNAs. Defective (D) RNAs, another category of lnc RNAs, are found in a variety of plant RNA viruses, most of which are noncoding. These are derived from and are replicated by the helper virus. D RNA-virus interactions evolve into mutually beneficial combinations, enhancing virus fitness via competitive advantages of moderated symptoms. Yet the satellite RNAs are single-stranded and include either large linear protein-coding ss RNAs, small linear ss RNAs, or small circular ss RNAs (virusoids). The satellite RNAs lack sequence homology to the helper virus, but unlike viroids need a helper virus to replicate and encapsidate. They can attenuate symptoms via RNA silencing and enhancement of host defense, but some can be lethal as RNA silencing suppressor antagonists. Moreover, selected viruses produce lncRNAs by incomplete degradation of genomic RNAs. They do not replicate but may impact viral infection, gene regulation, and cellular functions. Finally, the host plant lncRNAs can also contribute during plant-virus interactions, inducing plant defense and the regulation of gene expression, often in conjunction with micro and/or circRNAs.

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Viroids: Small Noncoding Infectious RNAs with the Remarkable Ability of Autonomous Replication

Cited by 14 publications

References 164 publications

Global Transcriptomic Changes Induced by Infection of Cucumber (Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid

Global Transcriptomic Changes Induced by Infection of Cucumber (Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid

Mutational Analysis of Eggplant Latent Viroid RNA Circularization by the Eggplant tRNA Ligase in Escherichia coli

Long Noncoding RNAs in Plant Viroids and Viruses: A Review

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