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Comprehensive secondary structure elucidation of four genera of the family Pospiviroidae.

Giguère T, Adkar-Purushothama CR, Perreault JP - PLoS ONE (2014)

Bottom Line: Recently, the technique of high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity.In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed.Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here.

View Article: PubMed Central - PubMed

Affiliation: Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada.

ABSTRACT
Viroids are small, circular, single stranded RNA molecules that infect plants. Since they are non-coding, their structures play a critical role in their life cycles. To date, little effort has been spend on elucidating viroid structures in solution due to both the experimental difficulties and the time-consuming nature of the methodologies implicated. Recently, the technique of high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity. In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed. Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here.

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The most stable structure for a viroid from the genus Cocadviroid.The final structural model of CCCVd obtained by SHAPE and folded by the RNAstructure software. The nucleotides in black denote those of low SHAPE reactivities (0–0.40) Those in orange are of intermediate reactivities (0.40–0.85) and those in red are highly reactive (>0.85). The different regions are delimited by the full lines.
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pone-0098655-g003: The most stable structure for a viroid from the genus Cocadviroid.The final structural model of CCCVd obtained by SHAPE and folded by the RNAstructure software. The nucleotides in black denote those of low SHAPE reactivities (0–0.40) Those in orange are of intermediate reactivities (0.40–0.85) and those in red are highly reactive (>0.85). The different regions are delimited by the full lines.

Mentions: The genus Cocadviroid is composed of four species, the Coconut cadang cadang viroid (CCCVd), the Coconut tinangaja viroid (CTiVd), the Hop latent viroid (HLVd) and CVd-IV. Previously, structure of CVd-IV was elucidated using SHAPE [24]. In the present work, the structure of CCCVd, the type species of the genus, was elucidated. Unlike other viroids, CCCVd is known to possess two fast and two slow monomeric forms, (in terms of their electrophoretic mobilities) [29]. Here, one of the fast (246 nt) isomers was probed by SHAPE as it appears in the early stages of the disease and can induce severe symptoms in palms [29]. The probing results of the two distinct RNA strands were almost identical, with 98.0% of unambiguous nucleotides being obtained (Figure S3). The final structure revealed 16.7% variation in nucleotide pairings when it was compared to the computer predicted structure. The structure is characterized by the presence of a relatively large internal loop located in the P region (formed by the residues from nt 23–31 in the upper strand and nt 216–226 in the lower strand). This loop contains multiple adenosine residues, indicating the presence of a large A-motif in CCCVd. Moreover, the CCR of CCCVd contained a loop E structure, a feature characteristic of the genus Pospiviroid (Figure 3). A comparison of the structure of CCCVd with that of the previously probed CVd-IV [24] demonstrated the structural features of the genus, namely that both viroids exhibited similar structures in the CCR with both a loop E and an A-motif being present in the P region.


Comprehensive secondary structure elucidation of four genera of the family Pospiviroidae.

Giguère T, Adkar-Purushothama CR, Perreault JP - PLoS ONE (2014)

The most stable structure for a viroid from the genus Cocadviroid.The final structural model of CCCVd obtained by SHAPE and folded by the RNAstructure software. The nucleotides in black denote those of low SHAPE reactivities (0–0.40) Those in orange are of intermediate reactivities (0.40–0.85) and those in red are highly reactive (>0.85). The different regions are delimited by the full lines.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4045682&req=5

pone-0098655-g003: The most stable structure for a viroid from the genus Cocadviroid.The final structural model of CCCVd obtained by SHAPE and folded by the RNAstructure software. The nucleotides in black denote those of low SHAPE reactivities (0–0.40) Those in orange are of intermediate reactivities (0.40–0.85) and those in red are highly reactive (>0.85). The different regions are delimited by the full lines.
Mentions: The genus Cocadviroid is composed of four species, the Coconut cadang cadang viroid (CCCVd), the Coconut tinangaja viroid (CTiVd), the Hop latent viroid (HLVd) and CVd-IV. Previously, structure of CVd-IV was elucidated using SHAPE [24]. In the present work, the structure of CCCVd, the type species of the genus, was elucidated. Unlike other viroids, CCCVd is known to possess two fast and two slow monomeric forms, (in terms of their electrophoretic mobilities) [29]. Here, one of the fast (246 nt) isomers was probed by SHAPE as it appears in the early stages of the disease and can induce severe symptoms in palms [29]. The probing results of the two distinct RNA strands were almost identical, with 98.0% of unambiguous nucleotides being obtained (Figure S3). The final structure revealed 16.7% variation in nucleotide pairings when it was compared to the computer predicted structure. The structure is characterized by the presence of a relatively large internal loop located in the P region (formed by the residues from nt 23–31 in the upper strand and nt 216–226 in the lower strand). This loop contains multiple adenosine residues, indicating the presence of a large A-motif in CCCVd. Moreover, the CCR of CCCVd contained a loop E structure, a feature characteristic of the genus Pospiviroid (Figure 3). A comparison of the structure of CCCVd with that of the previously probed CVd-IV [24] demonstrated the structural features of the genus, namely that both viroids exhibited similar structures in the CCR with both a loop E and an A-motif being present in the P region.

Bottom Line: Recently, the technique of high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity.In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed.Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here.

View Article: PubMed Central - PubMed

Affiliation: Département de biochimie, Faculté de médecine et des sciences de la santé, Pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada.

ABSTRACT
Viroids are small, circular, single stranded RNA molecules that infect plants. Since they are non-coding, their structures play a critical role in their life cycles. To date, little effort has been spend on elucidating viroid structures in solution due to both the experimental difficulties and the time-consuming nature of the methodologies implicated. Recently, the technique of high-throughput selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) was adapted for the probing of the members of family Avsunviroidae, all of whom replicate in the chloroplast and demonstrate ribozyme activity. In the present work, twelve viroid species belonging to four different genera of the family Pospiviroidae, whose members are characterized by the presence of a central conserved region (CCR) and who replicate in nucleus of the host, were probed. Given that the structures of five distinct viroid species from the family Pospiviroidae have been previously reported, an overview of the different structural characteristics for all genera and the beginning of a manual classification of the different viroids based on their structural features are presented here.

Show MeSH