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Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs.

Flores R, Serra P, Minoia S, Di Serio F, Navarro B - Front Microbiol (2012)

Bottom Line: As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers.Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae.Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC) Valencia, Spain.

ABSTRACT
As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

No MeSH data available.


Related in: MedlinePlus

Structural features of viroids. Upper and middle panels, schemes of the characteristic rod-like secondary structures of the genomic RNAs of Potato spindle tuber viroid (PSTVd) and Hop stunt viroid (HSVd) respectively (family Pospiviroidae). The approximate location of the five structural domains – terminal left (TL), pathogenic (P), central (C), variable (V), and terminal right (TR) – is indicated, as well as that of the central conserved region (CCR), the terminal conserved region (TCR), and the terminal conserved hairpin (TCH). Lower panel, scheme of the multibranched secondary structure of the genomic RNA of Peach latent mosaic viroid (PLMVd; family Avsunviroidae), in which the sequences conserved in most natural hammerhead ribozymes are boxed with black and white backgrounds for the (+) and (−) polarities, respectively; the kissing-loop interaction is indicated with lines, and the characteristic 12-nt hairpin insertion of the reference variant containing the pathogenicity determinant of an extreme chlorosis (peach calico) is highlighted with blue color. For a more detailed representation of the PSTVd secondary structure see Figure 5.
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Figure 1: Structural features of viroids. Upper and middle panels, schemes of the characteristic rod-like secondary structures of the genomic RNAs of Potato spindle tuber viroid (PSTVd) and Hop stunt viroid (HSVd) respectively (family Pospiviroidae). The approximate location of the five structural domains – terminal left (TL), pathogenic (P), central (C), variable (V), and terminal right (TR) – is indicated, as well as that of the central conserved region (CCR), the terminal conserved region (TCR), and the terminal conserved hairpin (TCH). Lower panel, scheme of the multibranched secondary structure of the genomic RNA of Peach latent mosaic viroid (PLMVd; family Avsunviroidae), in which the sequences conserved in most natural hammerhead ribozymes are boxed with black and white backgrounds for the (+) and (−) polarities, respectively; the kissing-loop interaction is indicated with lines, and the characteristic 12-nt hairpin insertion of the reference variant containing the pathogenicity determinant of an extreme chlorosis (peach calico) is highlighted with blue color. For a more detailed representation of the PSTVd secondary structure see Figure 5.

Mentions: Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides paired through canonical Watson–Crick interactions are flanked by loops of apparently unpaired nucleotides. Circularity facilitates intramolecular folding, and together, the two features afford protection against both exonucleases (demanding free termini), and endonucleases (acting preferentially on single-stranded regions). This peculiar secondary structure became evident upon sequencing PSTVd: thermodynamics-based predictions, RNase, and bisulfite probing in vitro, and electron microscopy revealed that the 359-nt PSTVd RNA adopts a rod-like secondary structure with a width roughly similar to that of a double-stranded DNA (Sogo et al., 1973; Sänger et al., 1976; Gross et al., 1978; Riesner et al., 1979; Figure 1). Additional support for this view was provided when similar structures of maximal base-pairing were predicted for two other viroids related to PSTVd but different in size and with just 60–73% nucleotide sequence identity: Chrysanthemum Stunt viroid (CSVd), and Citrus exocortis viroid (CEVd; Haseloff and Symons, 1981; Gross et al., 1982). Although probing with nucleases and dimethyl sulfate supplied evidence for a bifurcation in the left-terminal domain of the PSTVd rod-like structure (Gast et al., 1996), subsequent nuclear magnetic resonance (NMR) analysis of the 69-nt forming this domain, confirmed by temperature-gradient gel electrophoresis, and UV melting experiments, sustain the elongated rod form as the thermodynamically favored conformation (Dingley et al., 2003). Further supporting this notion, recent application of SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) – a relatively novel technique that interrogates local backbone RNA flexibility in solution at single-nucleotide resolution (Merino et al., 2005; Weeks and Mauger, 2011) and permits coupling these data to computer-assisted structure prediction – has failed to reveal the presence of Y-shaped, or cruciform structures in CEVd and some other members of the family Pospiviroidae (Xu et al., 2012). However, despite this evidence, the universality of the rod-like structure of viroids should not be taken for granted within this family, as illustrated by early results indicating that the most stable secondary structure predicted for Pear blister canker viroid (PBCVd) is cruciform and that none of the other energetically close conformations are elongated (Hernández et al., 1992).


Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs.

Flores R, Serra P, Minoia S, Di Serio F, Navarro B - Front Microbiol (2012)

Structural features of viroids. Upper and middle panels, schemes of the characteristic rod-like secondary structures of the genomic RNAs of Potato spindle tuber viroid (PSTVd) and Hop stunt viroid (HSVd) respectively (family Pospiviroidae). The approximate location of the five structural domains – terminal left (TL), pathogenic (P), central (C), variable (V), and terminal right (TR) – is indicated, as well as that of the central conserved region (CCR), the terminal conserved region (TCR), and the terminal conserved hairpin (TCH). Lower panel, scheme of the multibranched secondary structure of the genomic RNA of Peach latent mosaic viroid (PLMVd; family Avsunviroidae), in which the sequences conserved in most natural hammerhead ribozymes are boxed with black and white backgrounds for the (+) and (−) polarities, respectively; the kissing-loop interaction is indicated with lines, and the characteristic 12-nt hairpin insertion of the reference variant containing the pathogenicity determinant of an extreme chlorosis (peach calico) is highlighted with blue color. For a more detailed representation of the PSTVd secondary structure see Figure 5.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376415&req=5

Figure 1: Structural features of viroids. Upper and middle panels, schemes of the characteristic rod-like secondary structures of the genomic RNAs of Potato spindle tuber viroid (PSTVd) and Hop stunt viroid (HSVd) respectively (family Pospiviroidae). The approximate location of the five structural domains – terminal left (TL), pathogenic (P), central (C), variable (V), and terminal right (TR) – is indicated, as well as that of the central conserved region (CCR), the terminal conserved region (TCR), and the terminal conserved hairpin (TCH). Lower panel, scheme of the multibranched secondary structure of the genomic RNA of Peach latent mosaic viroid (PLMVd; family Avsunviroidae), in which the sequences conserved in most natural hammerhead ribozymes are boxed with black and white backgrounds for the (+) and (−) polarities, respectively; the kissing-loop interaction is indicated with lines, and the characteristic 12-nt hairpin insertion of the reference variant containing the pathogenicity determinant of an extreme chlorosis (peach calico) is highlighted with blue color. For a more detailed representation of the PSTVd secondary structure see Figure 5.
Mentions: Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides paired through canonical Watson–Crick interactions are flanked by loops of apparently unpaired nucleotides. Circularity facilitates intramolecular folding, and together, the two features afford protection against both exonucleases (demanding free termini), and endonucleases (acting preferentially on single-stranded regions). This peculiar secondary structure became evident upon sequencing PSTVd: thermodynamics-based predictions, RNase, and bisulfite probing in vitro, and electron microscopy revealed that the 359-nt PSTVd RNA adopts a rod-like secondary structure with a width roughly similar to that of a double-stranded DNA (Sogo et al., 1973; Sänger et al., 1976; Gross et al., 1978; Riesner et al., 1979; Figure 1). Additional support for this view was provided when similar structures of maximal base-pairing were predicted for two other viroids related to PSTVd but different in size and with just 60–73% nucleotide sequence identity: Chrysanthemum Stunt viroid (CSVd), and Citrus exocortis viroid (CEVd; Haseloff and Symons, 1981; Gross et al., 1982). Although probing with nucleases and dimethyl sulfate supplied evidence for a bifurcation in the left-terminal domain of the PSTVd rod-like structure (Gast et al., 1996), subsequent nuclear magnetic resonance (NMR) analysis of the 69-nt forming this domain, confirmed by temperature-gradient gel electrophoresis, and UV melting experiments, sustain the elongated rod form as the thermodynamically favored conformation (Dingley et al., 2003). Further supporting this notion, recent application of SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) – a relatively novel technique that interrogates local backbone RNA flexibility in solution at single-nucleotide resolution (Merino et al., 2005; Weeks and Mauger, 2011) and permits coupling these data to computer-assisted structure prediction – has failed to reveal the presence of Y-shaped, or cruciform structures in CEVd and some other members of the family Pospiviroidae (Xu et al., 2012). However, despite this evidence, the universality of the rod-like structure of viroids should not be taken for granted within this family, as illustrated by early results indicating that the most stable secondary structure predicted for Pear blister canker viroid (PBCVd) is cruciform and that none of the other energetically close conformations are elongated (Hernández et al., 1992).

Bottom Line: As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers.Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae.Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

View Article: PubMed Central - PubMed

Affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC) Valencia, Spain.

ABSTRACT
As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunviroidae adopt multibranched conformations occasionally stabilized by kissing-loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunviroidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures - either global or local - determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

No MeSH data available.


Related in: MedlinePlus