Avsunviroidae family: Viroids containing hammerhead ribozymes

Flores, Ricardo; Daròs, José‐Antonio; Hernández, Carmen

doi:10.1016/s0065-3527(00)55006-4

Cited by 122 publications

(115 citation statements)

References 175 publications

(253 reference statements)

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“…Viroids are divided into two families, Pospiviroidae and Avsunviroidae, whose members replicate and accumulate in the nucleus and the chloroplast, respectively. The classification scheme is supported by other criteria which in members of the family Avsunviroidae include self-cleavage, mediated by hammerhead ribozymes, of the oligomeric RNA intermediates of both polarities resulting from replication through a rollingcircle mechanism (Flores et al 2000(Flores et al , 2004.…”

Section: Introductionmentioning

confidence: 99%

A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability

Gago

Peña²,

Flores³

2005

RNA

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Chrysanthemum chlorotic mottle viroid (CChMVd) RNA (398-401 nucleotides) can form hammerhead ribozymes that play a functional role in its replication through a rolling-circle mechanism. In contrast to most other viroids, which adopt rod-like or quasi-rod-like secondary structures of minimal free energy, the computer-predicted conformations of CChMVd and Peach latent mosaic viroid (PLMVd) RNAs are branched. Moreover, the covariations found in a number of natural CChMVd variants support that the same or a closely related conformation exists in vivo. Here we report that the CChMVd natural variability also supports that the branched conformation is additionally stabilized by a kissing-loop interaction resembling another one proposed in PLMVd from in vitro assays. Moreover, site-directed mutagenesis combined with bioassays and progeny analysis showed that: (1) single CChMVd mutants affecting the kissing loops had low or no infectivity at all, whereas infectivity was recovered in double mutants restoring the interaction; (2) mutations affecting the structure of the regions adjacent to the kissing loops reverted to wild type or led to rearranged stems, also supporting their interaction; and (3) the interchange between 4 nucleotides of each of the two kissing loops generated a viable CChMVd variant with eight mutations. PAGE analysis under denaturing and nondenaturing conditions revealed that the kissing-loop interaction determines proper in vitro folding of CChMVd RNA. Preservation of a similar kissing-loop interaction in two hammerhead viroids with an overall low sequence similarity suggests that it facilitates in vivo the adoption and stabilization of a compact folding critical for viroid viability.

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Section: Introductionmentioning

confidence: 99%

A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability

Gago

Peña²,

Flores³

2005

RNA

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“…RNAs of (+, arbitrarily the most abundant strand in vivo) and (À) polarity can form active hammerhead ribozymes (Fig. 2) that are involved in replication [1,2]. …”

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confidence: 99%

ICTV Virus Taxonomy Profile: Avsunviroidae

Serio

Matoušek

et al. 2018

Journal of General Virology

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Members of the family Avsunviroidae have a single-stranded circular RNA genome that adopts a rod-like or branched conformation and can form, in the strands of either polarity, hammerhead ribozymes involved in their replication in plastids through a symmetrical RNA-RNA rolling-circle mechanism. These viroids lack the central conserved region typical of members of the family Pospiviroidae. The family Avsunviroidae includes three genera, Avsunviroid, Pelamoviroid and Elaviroid, with a total of four species. This is a summary of the ICTV Report on the taxonomy of the family Avsunviroidae, which is available at http://www.ictv.global/report/avsunviroidae. GENOMEMembers of the family Avsunviroidae have a circular singlestranded RNA genome of 246 to 401 nt, which may assume rod-like, quasi-rod-like or branched conformations in silico or in vitro, with indirect or direct evidence supporting similar conformations in vivo (Table 1, Fig. 1). Viroid G+C content is >50 % except for avocado sunblotch viroid (38 %). RNAs of (+, arbitrarily the most abundant strand in vivo) and (À) polarity can form active hammerhead ribozymes (Fig. 2) that are involved in replication [1,2]. REPLICATIONReplication takes place in plastids, mostly chloroplasts, through a symmetrical rolling-circle mechanism. A nuclearencoded plastid RNA polymerase, conscripted to transcribe RNA templates instead of its physiological DNA template, synthesizes oligomeric viroid RNAs of both polarities. These oligomers are self-cleaved co-transcriptionally by the embedded hammerhead ribozymes, thereby generating linear monomeric RNAs that are subsequently circularized by a tRNA ligase. This enzyme, like the nuclear-encoded plastid RNA polymerase, is encoded in the nucleus and translocated into plastids. TAXONOMYThe type of hammerhead structure, the genome G+C content and its solubility in 2 M LiCl, together with clustering in phylogenetic trees derived from whole genome sequences, are used as genus demarcation criteria.

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“…Without encoding proteins and encapsidation, the small (250-to 400-nt), circular, and noncoding viroid RNAs replicate to high levels in a host cell, move from cell to cell and from organ to organ to establish systemic infection, and can cause devastating diseases (21,(29)(30)(31)83). Therefore, these infectious RNAs are exposed to almost every conceivable means of cellular surveillance, detection, and destruction.…”

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A Structured Viroid RNA Serves as a Substrate for Dicer-Like Cleavage To Produce Biologically Active Small RNAs but Is Resistant to RNA-Induced Silencing Complex-Mediated Degradation

Itaya¹,

Zhong²,

Bundschuh

et al. 2007

J Virol

185

177

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RNA silencing is a potent means of antiviral defense in plants and animals. A hallmark of this defense response is the production of 21-to 24-nucleotide viral small RNAs via mechanisms that remain to be fully understood. Many viruses encode suppressors of RNA silencing, and some viral RNAs function directly as silencing suppressors as counterdefense. The occurrence of viroid-specific small RNAs in infected plants suggests that viroids can trigger RNA silencing in a host, raising the question of how these noncoding and unencapsidated RNAs survive cellular RNA-silencing systems. We address this question by characterizing the production of small RNAs of Potato spindle tuber viroid (srPSTVds) and investigating how PSTVd responds to RNA silencing. Our molecular and biochemical studies provide evidence that srPSTVds were derived mostly from the secondary structure of viroid RNAs. Replication of PSTVd was resistant to RNA silencing, although the srPSTVds were biologically active in guiding RNA-induced silencing complex (RISC)-mediated cleavage, as shown with a sensor system. Further analyses showed that without possessing or triggering silencing suppressor activities, the PSTVd secondary structure played a critical role in resistance to RISC-mediated cleavage. These findings support the hypothesis that some infectious RNAs may have evolved specific secondary structures as an effective means to evade RNA silencing in addition to encoding silencing suppressor activities. Our results should have important implications in further studies on RNA-based mechanisms of host-pathogen interactions and the biological constraints that shape the evolution of infectious RNA structures.A major focus of current biology is to understand how a pathogen has evolved mechanisms to achieve a balance among several interrelated activities that are crucial to establish a full infection: evading or suppressing host defense, minimizing destructive interference of host metabolism, and maximizing utilization of host factors to support replication and systemic spread. A full understanding of these mechanisms is not only necessary to build a foundation for developing technologies to combat pathogen diseases but also can provide fundamental mechanistic insights into the regulation of basic cellular processes.Recent studies have discovered small RNA-mediated gene silencing as a powerful antiviral mechanism in plants and animals (6,22,25,47,49,50,72,77,84,(87)(88)(89)98). Furthermore, small RNA-mediated gene silencing plays essential roles in regulating a wide variety of growth and development processes (4-6, 11, 13, 17, 23, 28, 42). A key mediator of RNA silencing is several classes of 21-to 24-nucleotide (nt) small RNAs.MicroRNAs (miRNAs) are produced by cleavage of hairpin RNA precursors encoded by the genome of an organism. Short interfering RNAs (siRNAs) are generated by cleavage of double-stranded RNAs (dsRNAs) that may originate from several sources, including cellular genomes, viral replication intermediates, aberrant cellular RNAs, overexpresse...

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Avsunviroidae family: Viroids containing hammerhead ribozymes

Cited by 122 publications

References 175 publications

A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability

A kissing-loop interaction in a hammerhead viroid RNA critical for its in vitro folding and in vivo viability

ICTV Virus Taxonomy Profile: Avsunviroidae

A Structured Viroid RNA Serves as a Substrate for Dicer-Like Cleavage To Produce Biologically Active Small RNAs but Is Resistant to RNA-Induced Silencing Complex-Mediated Degradation

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