Viroid research and its significance for RNA technology and basic biochemistry

Steger, Gerhard; Riesner, Detlev

doi:10.1093/nar/gky903

Cited by 25 publications

(27 citation statements)

References 182 publications

(163 reference statements)

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“…Due to their extreme simplicity, viroids appear very appropriate to tackle this question. They are circular, non-proteincoding RNAs of 246-434 nucleotides (nt), which infect and frequently cause disease in certain higher plants [1][2][3][4][5][6]. Those within the family Pospiviroidae, like potato spindle tuber viroid (PSTVd), have a central conserved region (CCR), lack hammerhead ribozymes and replicate in the nucleus through an asymmetric RNA-RNA rolling-circle mechanism [7,8].…”

Section: Introductionmentioning

confidence: 99%

How sequence variants of a plastid-replicating viroid with one single nucleotide change initiate disease in its natural host

et al. 2019

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Understanding how viruses and subviral agents initiate disease is central to plant pathology. Whether RNA silencing mediates the primary lesion triggered by viroids (small non-protein-coding RNAs), or just intermediate-late steps of a signaling cascade, remains unsolved. While most variants of the plastidreplicating peach latent mosaic viroid (PLMVd) are asymptomatic, some incite peach mosaics or albinism (peach calico, PC). We have previously shown that two 21-nt small RNAs (PLMVd-sRNAs) containing a 12-13-nt PC-associated insertion guide cleavage, via RNA silencing, of the mRNA encoding a heatshock protein involved in chloroplast biogenesis. To gain evidence supporting that such event is the initial lesion, and more specifically, that different chloroses have different primary causes, here we focused on a PLMVd-induced peach yellow mosaic (PYM) expressed in leaf sectors interspersed with others green. First, sequencing PLMVd-cDNAs from both sectors and bioassays mapped the PYM determinant at one nucleotide, a notion further sustained by the phenotype incited by other natural and artificial PLMVd variants. And second, sRNA deep-sequencing and RNA ligase-mediated RACE identified one PLMVd-sRNA with the PYM-associated change that guides cleavage, as predicted by RNA silencing, of the mRNA encoding a thylakoid translocase subunit required for chloroplast development. RT-qPCR showed lower accumulation of this mRNA in PYM-expressing tissues. Remarkably, PLMVd-sRNAs triggering PYM and PC have 5ʹ-terminal Us, involving Argonaute 1 in what likely are the initial alterations eliciting distinct chloroses.

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Section: Introductionmentioning

confidence: 99%

How sequence variants of a plastid-replicating viroid with one single nucleotide change initiate disease in its natural host

et al. 2019

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“…Owing to their similarities with conventional viruses, viroids, virusoids or satellites are often referred to as sub-viral particles. Viroids are the smallest phytopathogens with rod or dumb-bell shaped unencapsidated infectious RNA that however, do not synthesize any proteins[ 31 ]. Viriods do not have a capsid or outer envelope, but, as with viruses, can reproduce only within a host cell.…”

Section: Viroids Virusoids or Satellitesmentioning

confidence: 99%

Geometric architecture of viruses

Parvez¹

2020

WJV

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In the current SARS-CoV-2 disease (COVID-19) pandemic, the structural understanding of new emerging viruses in relation to developing effective treatment and interventions are very necessary. Viruses present remarkable differences in geometric shapes, sizes, molecular compositions and organizations. A detailed structural knowledge of a virion is essential for understanding the mechanisms of capsid assembly/disassembly, antigenicity, cell-receptor interaction, and designing therapeutic strategies. X-ray crystallography, cryo-electron microscopy and molecular simulations have elucidated atomic-level structure of several viruses. In view of this, a recently determined crystal structure of SARS-CoV-2 nucleocapsid has revealed its architecture and self-assembly very similar to that of the SARS-CoV-1 and the Middle-East respiratory syndrome virus (MERS-CoV). In structure determination, capsid symmetry is an important factor greatly contributing to its stability and balance between the packaged genome and envelope. Since the capsid protein subunits are asymmetrical, the maximum number of inter-subunit interactions can be established only when they are arranged symmetrically. Therefore, a stable capsid must be in a perfect symmetry and lowest possible free-energy. Isometric virions are spherical but geometrically icosahedrons as compared to complex virions that are both isometric and helical. Enveloped icosahedral or helical viruses are very common in animals but rare in plants and bacteria. Icosahedral capsids are defined by triangulation number ( T = 1, 3, 4, 13, etc .), i.e ., the identical equilateral-triangles formed of subunits. Biologically significant defective capsids with or without nucleic acids are common in enveloped alpha-, flavi- and hepadnaviruses. The self-assembling, stable and non-infectious virus-like particles have been widely exploited as vaccine candidates and therapeutic molecules delivery vehicles.

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“…The area of a heat map below the diagonal presents the difference map created by subtracting PSTVd CProps from the CProps of the model presented above the diagonal. PSTVd will be used for comparison analysis, as this motif has the most experimental evidence for its proposed structure (Zhong et al 2008;Steger and Riesner 2018). Figure 5 shows CProps for the PSTVd SRD and the HSVd mSRD.…”

Section: Communication Propensity Indicates Stable Srds and Msrds Havmentioning

confidence: 99%

In silico survey of the central conserved regions in viroids of the Pospiviroidae family for conserved asymmetric loop structures

Freidhoff

Bruist

2019

RNA

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Viroids are the smallest replicative pathogens, consisting of RNA circles (∼300 nucleotides) that require host machinery to replicate. Structural RNA elements recruit these host factors. Currently, many of these structural elements and the nature of their interactions are unknown. All Pospiviroidae have homology in the central conserved region (CCR). The CCR of potato spindle tuber viroid (PSTVd) contains a sarcin/ricin domain (SRD), the only viroid structural element with an unequivocal replication role. We assumed that every member of this family uses this region to recruit host factors, and that each CCR has an SRD-like asymmetric loop within it. Potential SRD or SRD-like motifs were sought in the CCR of each Pospiviroidae member as follows. Motif location in each CCR was predicted with MUSCLE alignment and Vienna RNAfold. Viroid-specific models of SRD-like motifs were built by superimposing noncanonical base pairs and nucleotides on a model of an SRD. The RNA geometry search engine FR3D was then used to find nucleotide groups close to the geometry suggested by this superimposition. Atomic resolution structures were assembled using the molecular visualization program Chimera, and the stability of each motif was assessed with molecular dynamics (MD). Some models required a protonated cytosine. To be stable within a cell, the pK a of that cytosine must be shifted up. Constant pH-replica exchange MD analysis showed such a shift in the proposed structures. These data show that every Pospiviroidae member could form a motif that resembles an SRD in its CCR, and imply there could be undiscovered mimics of other RNA domains.

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Viroid research and its significance for RNA technology and basic biochemistry

Cited by 25 publications

References 182 publications

How sequence variants of a plastid-replicating viroid with one single nucleotide change initiate disease in its natural host

How sequence variants of a plastid-replicating viroid with one single nucleotide change initiate disease in its natural host

Geometric architecture of viruses

In silico survey of the central conserved regions in viroids of the Pospiviroidae family for conserved asymmetric loop structures

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