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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

A genomic map of PSTVd loop motifs that are essential/critical for replication and systemic trafficking. Superscripts 1 and 2 refer to data from Zhong et al. (2006) and Zhong et al. (2007), respectively. R, replication; T, trafficking. Reproduced with permission from Zhong et al. (2008).
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Figure 5: A genomic map of PSTVd loop motifs that are essential/critical for replication and systemic trafficking. Superscripts 1 and 2 refer to data from Zhong et al. (2006) and Zhong et al. (2007), respectively. R, replication; T, trafficking. Reproduced with permission from Zhong et al. (2008).

Mentions: 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.


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)

A genomic map of PSTVd loop motifs that are essential/critical for replication and systemic trafficking. Superscripts 1 and 2 refer to data from Zhong et al. (2006) and Zhong et al. (2007), respectively. R, replication; T, trafficking. Reproduced with permission from Zhong et al. (2008).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: A genomic map of PSTVd loop motifs that are essential/critical for replication and systemic trafficking. Superscripts 1 and 2 refer to data from Zhong et al. (2006) and Zhong et al. (2007), respectively. R, replication; T, trafficking. Reproduced with permission from Zhong et al. (2008).
Mentions: 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.

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