Viroid-specific small RNA in plant disease

Hammann, Christian; Steger, Gerhard

doi:10.4161/rna.19810

Cited by 50 publications

(50 citation statements)

References 98 publications

(112 reference statements)

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“…First, viroid infection results in the genomic RNA progeny folding upon itself into collapsed secondary structures and in the production of dsRNAs, either replicative intermediates or RDR products. Northern hybridizations have detected viroid-derived sRNAs (vd-sRNAs), with properties akin to those of the host and virus sRNAs generated by DCLs, accompanying infections by representative members of the two viroid families; these vd-sRNAs have been subsequently sequenced by conventional and high-throughput approaches (44,45). Second, the expression of a reporter gene and the accumulation in infected plants of the genomic viroid RNA appear to be repressed by vdsRNAs in a sequence-specific mode (46)(47)(48)(49).…”

mentioning

confidence: 99%

Specific Argonautes Selectively Bind Small RNAs Derived from Potato Spindle Tuber Viroid and Attenuate Viroid Accumulation In Vivo

Minoia

Carbonell

Serio

et al. 2014

J Virol

100

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The identification of viroid-derived small RNAs (vd-sRNAs) of 21 to 24 nucleotides (nt) in plants infected by viroids (infectious non-protein-coding RNAs of just 250 to 400 nt) supports their targeting by Dicer-like enzymes, the first host RNA-silencing barrier. However, whether viroids, like RNA viruses, are also targeted by the RNA-induced silencing complex (RISC) remains controversial. At the RISC core is one Argonaute (AGO) protein that, guided by endogenous or viral sRNAs, targets complementary RNAs. To examine whether AGO proteins also load vd-sRNAs, leaves of Nicotiana benthamiana infected by potato spindle tuber viroid (PSTVd) were agroinfiltrated with plasmids expressing epitope-tagged versions of AGO1, AGO2, AGO3, AGO4, AGO5, AGO6, AGO7, AGO9, and AGO10 from Arabidopsis thaliana. Immunoprecipitation analyses of the agroinfiltrated halos revealed that all AGOs except AGO6, AGO7, and AGO10 associated with vd-sRNAs: AGO1, AGO2, and AGO3 preferentially with those of 21 and 22 nt, while AGO4, AGO5, and AGO9 additionally bound those of 24 nt. Deep-sequencing analyses showed that sorting of vd-sRNAs into AGO1, AGO2, AGO4, and AGO5 depended essentially on their 5=-terminal nucleotides, with the profiles of the corresponding AGO-loaded vd-sRNAs adopting specific hot spot distributions along the viroid genome. Furthermore, agroexpression of AGO1, AGO2, AGO4, and AGO5 on PSTVd-infected tissue attenuated the level of the genomic RNAs, suggesting that they, or their precursors, are RISC targeted. In contrast to RNA viruses, PSTVd infection of N. benthamiana did not affect miR168-mediated regulation of the endogenous AGO1, which loaded vd-sRNAs with specificity similar to that of its A. thaliana counterpart. V iroids, despite having minimal genomes restricted to a nonprotein-coding single-stranded RNA (ssRNA) of only ϳ250 to 400 nucleotides (nt), can parasitize the higher plants they infect and replicate, spread systemically, and frequently incite disease (1-3). Most of the approximately 30 viroids characterized so far, including the type species potato spindle tuber viroid (PSTVd) (4, 5), have been assigned to the family Pospiviroidae on the basis of a rod-like (or quasi-rod-like) secondary structure with a central conserved region (CCR) and replication in the nucleus through an asymmetric rolling-circle mechanism with double-stranded RNA (dsRNA) intermediates (6-10). This mechanism is catalyzed by the RNA polymerase II forced to transcribe RNA templates (11-13), an RNase most likely of class III (14), and the DNA ligase 1 redirected to act as an RNA ligase (15), with the CCR playing a critical role in the cleavage of the oligomeric plus strands generated by the rolling-circle mechanism (14) and in the ligation (circularization) of the resulting monomeric plus strands (16). The remaining four viroids, members of the family Avsunviroidae, display a quasi-rod-like or clearly branched secondary structure without a CCR but with hammerhead ribozymes in both polarity strands; these catalytic RNA motifs mediate se...

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mentioning

confidence: 99%

Specific Argonautes Selectively Bind Small RNAs Derived from Potato Spindle Tuber Viroid and Attenuate Viroid Accumulation In Vivo

Minoia

Carbonell

Serio

et al. 2014

J Virol

100

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“…As discussed earlier, such impaired motifs might be operational in systems where a mechanism is required that can be used as on/off switch . The reaction of the PLMVd HHRz, on the other hand, appears to be constitutively on, in line with its function as an RNA endonuclease in processing of multimeric viroid transcripts during rolling circle replication (Branch and Robertson 1984;Tabler and Tsagris 2004;Hammann and Steger 2012). In a new genome database search, we have recently looked for G17-containing HHRz motifs and identified a series of such motifs in several organisms (C Seehafer, A Kalweit, and C Hammann, unpubl.).…”

Section: Discussionmentioning

confidence: 99%

“…The variability of tertiary interacting motifs became even further apparent in several recent database searches for novel HHRz motifs carried out in this and other laboratories Rojas et al 2000;Gräf et al 2005;Przybilski et al 2005;Martick et al 2008;De la Peña and Garcia-Robles 2010;Jimenez et al 2011;Perreault et al 2011;Seehafer et al 2011). While the HHRz was originally discovered in subviral plant pathogens (Hutchins et al 1986;Prody et al 1986;Hammann and Steger 2012), the aforementioned searches have revealed many, predominantly eukaryotic species, with genomically encoded HHRz motifs (for recent review, see .…”

Section: Introductionmentioning

confidence: 99%

G17-modified hammerhead ribozymes are active in vitro and in vivo

Kalweit

Hammann

2013

RNA

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Natural hammerhead ribozymes (HHRz) feature tertiary interactions between hairpin loops or bulges in two of three helices that surround the catalytic core of conserved nucleotides. Their conservation was originally established on minimal versions lacking the tertiary interactions. While those sequence requirements in general also apply to natural versions, we show here differences for the HHRz cleavage site N17. A guanosine at this position strongly impairs cleavage activity in minimal versions, whereas we observe for the G17 variants of four tertiary stabilized HHRz significant cleavage and ligation activity in vitro. Kinetic analyses of these variants revealed a reduced rate and extent of cleavage, compared with wild-type sequences, while variants with distorted tertiary interactions cleaved at a reduced rate, but to the same extent. Contrary to this, G17 variants exhibit similar in vitro ligation activity as compared with the respective wild-type motif. To also address the catalytic performance of these motifs in vivo, we have inserted HHRz cassettes in the lacZ gene and tested this β-galactosidase reporter in Dictyostelium discoideum. In colorimetric assays, we observe differences in the enzymatic activity of β-galactosidase, which correlate well with the activity of the different HHRz variants in vitro and which can be unambiguously attributed to ribozyme cleavage by primer extension analysis.

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“…These vd-sRNAs are structurally similar to host microRNAs and small interfering RNAs [37,43,44], the key effectors of RNA silencing [4], thus supporting the involvement of this RNA-based regulatory network in plant-viroid interactions (reviewed by [27,30,47]). Besides contributing to further dissecting the molecular events underlying viroid infection, these findings also have major implications for disease diagnosis.…”

Section: Validity Of Recognized Species Of Genus Pospiviroidmentioning

confidence: 99%

Current status of viroid taxonomy

Serio

Flores

Verhoeven³

et al. 2014

Arch Virol

161

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Viroids are the smallest autonomous infectious nucleic acids known so far. With a small circular RNA genome of about 250-400 nt, which apparently does not code for any protein, viroids replicate and move systemically in host plants. Since the discovery of the first viroid almost forty-five years ago, many different viroids have been isolated, characterized and, frequently, identified as the causal agents of plant diseases. The first viroid classification scheme was proposed in the early 1990s and adopted by the International Committee on Taxonomy of Viruses (ICTV) a few years later. Here, the current viroid taxonomy scheme and the criteria for viroid species demarcation are discussed, highlighting the main taxonomic questions currently under consideration by the ICTV Viroid Study Group. The impact of correct taxonomic annotation of viroid sequence variants is also addressed, taking into consideration the increasing application of nextgeneration sequencing and bioinformatics for known and previously unrecognized viroids.

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Viroid-specific small RNA in plant disease

Cited by 50 publications

References 98 publications

Specific Argonautes Selectively Bind Small RNAs Derived from Potato Spindle Tuber Viroid and Attenuate Viroid Accumulation In Vivo

Specific Argonautes Selectively Bind Small RNAs Derived from Potato Spindle Tuber Viroid and Attenuate Viroid Accumulation In Vivo

G17-modified hammerhead ribozymes are active in vitro and in vivo

Current status of viroid taxonomy

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