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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

Geometric classification of RNA base-pairing. The upper panel shows that each nucleotide base has three edges (Watson–Crick, Hoogsteen, and sugar) that can potentially form hydrogen bonds with one of the three edges of another base. Thus, each base is represented by a triangle and can potentially pair with up to three other bases. The interacting bases can pair with a cis or trans relative orientation of their glycosidic bonds; this is illustrated in the lower panels for the cis and trans orientations of nucleotides pairing at the Hoogsteen edge of one base and the sugar edge of the second base. In these base-pairs, the Watson–Crick edges of the interacting bases are available for further interactions – with other RNAs, proteins, or small molecules. The cross and circle in the triangle where the Hoogsteen and sugar edges meet indicate 5′ → 3′ and 3′ → 5′ orientations, respectively, of the sugar-phosphodiester backbones relative to the plane of the page. W–C, Watson–Crick edge; H, Hoogsteen edge; SE, sugar edge. Reproduced with permission from Zhong et al. (2006).
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Figure 4: Geometric classification of RNA base-pairing. The upper panel shows that each nucleotide base has three edges (Watson–Crick, Hoogsteen, and sugar) that can potentially form hydrogen bonds with one of the three edges of another base. Thus, each base is represented by a triangle and can potentially pair with up to three other bases. The interacting bases can pair with a cis or trans relative orientation of their glycosidic bonds; this is illustrated in the lower panels for the cis and trans orientations of nucleotides pairing at the Hoogsteen edge of one base and the sugar edge of the second base. In these base-pairs, the Watson–Crick edges of the interacting bases are available for further interactions – with other RNAs, proteins, or small molecules. The cross and circle in the triangle where the Hoogsteen and sugar edges meet indicate 5′ → 3′ and 3′ → 5′ orientations, respectively, of the sugar-phosphodiester backbones relative to the plane of the page. W–C, Watson–Crick edge; H, Hoogsteen edge; SE, sugar edge. Reproduced with permission from Zhong et al. (2006).

Mentions: There is an increasing appreciation that the small RNA motifs seemingly unstructured due to the absence of Watson–Crick base-pairs – one example being the loops in the rod-like secondary structure of PSTVd – are instead stabilized by alternative interactions. Actually, each RNA base can form hydrogen bonds with another base via one of the three edges (Watson–Crick, Hoogsteen, and sugar), with their glycosidic bonds being oriented cis or trans relative to each other (Figure 4; Leontis and Westhof, 2001). Isosteric (that is, similar in shape) relationships for each base-pairing family are compiled in isostericity matrices that provide the rationale for explaining and predicting recurrent three-dimensional (3D) motifs in non-homologous RNAs, wherein they are more conserved in structure (their nucleotides adopt similar spatial arrangements) than in sequence (Leontis et al., 2002). This approach has been used to validate a 3D model of PSTVd loop E inferred from comparative sequence analysis as well as from NMR and X-ray crystal structures of similar motifs in other RNAs and, besides, it has allowed the design of disruptive and compensatory mutations; functional analyses of such mutants in vitro and in vivo has shown that the structural integrity of this element of tertiary structure is critical for accumulation (Zhong et al., 2006). RNA signatures also regulate short (cell-to-cell) and long distance movement of viroids through the plasmodesmata and phloem, respectively. More specifically: (i) unidirectional PSTVd trafficking from the bundle sheath to mesophyll in young tobacco leaves demands a bipartite RNA motif (Qi et al., 2004), (ii) entry of PSTVd from non-vascular into phloem tissue to initiate systemic infection is mediated by an U/C motif (forming a water-inserted cis Watson–Crick/Watson–Crick base-pair flanked by short conventional helices), a 3D model based on comparisons with X-ray crystal structures of similar motifs in rRNAs and supported by combined mutagenesis and co-variation analyses (Zhong et al., 2007), and (iii) trafficking from palisade mesophyll to spongy mesophyll requires an RNA motif called loop 6 (consisting of the sequence 5′-CGA-3′…5′-GAC-3′ flanked on both sides by cis Watson–Crick G/C and G/U wobble base-pairs) the 3D model of which, describing all non-Watson–Crick base-pairs, has been derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA X-ray crystal structure database (Takeda et al., 2011). Finally, extending this approach, a genome-wide mutational analysis has identified loops/bulges in PSTVd that are essential or important for autonomous replication in single cells (protoplasts) or for systemic trafficking, thus providing a framework for future studies on RNA motifs that regulate these two functional properties in PSTVd and perhaps in other RNAs (Zhong et al., 2008; Figure 5). In conclusion, significant advances in understanding viroid-host relationships should be expected from a comprehensive dissection of viroid RNA structural motifs and, particularly, on how they interact with their cognate cellular factors (Takeda and Ding, 2009; Ding, 2010).


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)

Geometric classification of RNA base-pairing. The upper panel shows that each nucleotide base has three edges (Watson–Crick, Hoogsteen, and sugar) that can potentially form hydrogen bonds with one of the three edges of another base. Thus, each base is represented by a triangle and can potentially pair with up to three other bases. The interacting bases can pair with a cis or trans relative orientation of their glycosidic bonds; this is illustrated in the lower panels for the cis and trans orientations of nucleotides pairing at the Hoogsteen edge of one base and the sugar edge of the second base. In these base-pairs, the Watson–Crick edges of the interacting bases are available for further interactions – with other RNAs, proteins, or small molecules. The cross and circle in the triangle where the Hoogsteen and sugar edges meet indicate 5′ → 3′ and 3′ → 5′ orientations, respectively, of the sugar-phosphodiester backbones relative to the plane of the page. W–C, Watson–Crick edge; H, Hoogsteen edge; SE, sugar edge. Reproduced with permission from Zhong et al. (2006).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Geometric classification of RNA base-pairing. The upper panel shows that each nucleotide base has three edges (Watson–Crick, Hoogsteen, and sugar) that can potentially form hydrogen bonds with one of the three edges of another base. Thus, each base is represented by a triangle and can potentially pair with up to three other bases. The interacting bases can pair with a cis or trans relative orientation of their glycosidic bonds; this is illustrated in the lower panels for the cis and trans orientations of nucleotides pairing at the Hoogsteen edge of one base and the sugar edge of the second base. In these base-pairs, the Watson–Crick edges of the interacting bases are available for further interactions – with other RNAs, proteins, or small molecules. The cross and circle in the triangle where the Hoogsteen and sugar edges meet indicate 5′ → 3′ and 3′ → 5′ orientations, respectively, of the sugar-phosphodiester backbones relative to the plane of the page. W–C, Watson–Crick edge; H, Hoogsteen edge; SE, sugar edge. Reproduced with permission from Zhong et al. (2006).
Mentions: There is an increasing appreciation that the small RNA motifs seemingly unstructured due to the absence of Watson–Crick base-pairs – one example being the loops in the rod-like secondary structure of PSTVd – are instead stabilized by alternative interactions. Actually, each RNA base can form hydrogen bonds with another base via one of the three edges (Watson–Crick, Hoogsteen, and sugar), with their glycosidic bonds being oriented cis or trans relative to each other (Figure 4; Leontis and Westhof, 2001). Isosteric (that is, similar in shape) relationships for each base-pairing family are compiled in isostericity matrices that provide the rationale for explaining and predicting recurrent three-dimensional (3D) motifs in non-homologous RNAs, wherein they are more conserved in structure (their nucleotides adopt similar spatial arrangements) than in sequence (Leontis et al., 2002). This approach has been used to validate a 3D model of PSTVd loop E inferred from comparative sequence analysis as well as from NMR and X-ray crystal structures of similar motifs in other RNAs and, besides, it has allowed the design of disruptive and compensatory mutations; functional analyses of such mutants in vitro and in vivo has shown that the structural integrity of this element of tertiary structure is critical for accumulation (Zhong et al., 2006). RNA signatures also regulate short (cell-to-cell) and long distance movement of viroids through the plasmodesmata and phloem, respectively. More specifically: (i) unidirectional PSTVd trafficking from the bundle sheath to mesophyll in young tobacco leaves demands a bipartite RNA motif (Qi et al., 2004), (ii) entry of PSTVd from non-vascular into phloem tissue to initiate systemic infection is mediated by an U/C motif (forming a water-inserted cis Watson–Crick/Watson–Crick base-pair flanked by short conventional helices), a 3D model based on comparisons with X-ray crystal structures of similar motifs in rRNAs and supported by combined mutagenesis and co-variation analyses (Zhong et al., 2007), and (iii) trafficking from palisade mesophyll to spongy mesophyll requires an RNA motif called loop 6 (consisting of the sequence 5′-CGA-3′…5′-GAC-3′ flanked on both sides by cis Watson–Crick G/C and G/U wobble base-pairs) the 3D model of which, describing all non-Watson–Crick base-pairs, has been derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA X-ray crystal structure database (Takeda et al., 2011). Finally, extending this approach, a genome-wide mutational analysis has identified loops/bulges in PSTVd that are essential or important for autonomous replication in single cells (protoplasts) or for systemic trafficking, thus providing a framework for future studies on RNA motifs that regulate these two functional properties in PSTVd and perhaps in other RNAs (Zhong et al., 2008; Figure 5). In conclusion, significant advances in understanding viroid-host relationships should be expected from a comprehensive dissection of viroid RNA structural motifs and, particularly, on how they interact with their cognate cellular factors (Takeda and Ding, 2009; Ding, 2010).

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