Analysis of the population structure of three phenotypically different PSTVd isolates

Góra, A.; Candresse, Thierry; Zagórski, W.

doi:10.1007/bf01379128

Cited by 39 publications

(26 citation statements)

References 39 publications

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“…However, the limited sequence heterogeneity detected in members of the family Pospiviroidae (Góra et al, 1994), the replication of which is mediated by the multi-subunit nuclear RNA polymerase II (Mühlbach and Sänger, 1979; Flores and Semancik, 1982; Schindler and Mühlbach, 1992), has precluded the implementation of this approach for validating their proposed secondary structure.…”

Section: Rod-like Versus Branched Secondary Structure: In Vivo Evidencementioning

confidence: 99%

Viroids: From Genotype to Phenotype Just Relying on RNA Sequence and Structural Motifs

Flores¹,

Serra²,

Minoia³

et al. 2012

Front. Microbio.

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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.

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Section: Rod-like Versus Branched Secondary Structure: In Vivo Evidencementioning

confidence: 99%

Viroids: From Genotype to Phenotype Just Relying on RNA Sequence and Structural Motifs

Flores¹,

Serra²,

Minoia³

et al. 2012

Front. Microbio.

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“…Substitutions in the lower strand of the CCR have been found in some PSTVd isolates (Owens et al, 1992), but not in viroids of the ASSVd group. On the other hand, no change has been reported so far in the upper strand of any member, or sequence variant, of the viroid groups whose type members are PSTVd (Schn61zer et al, 1985;Puchta et al, 1990 a;Gdra et al, 1994) and ASSVd (Koltunow & Rezaian, 1989;Puchta et al, 1990 b), or the more recently described Coleus blumei viroid 1 (Spieker et al, 1990), showing that the Ag0 ~ G substitution is unique in this regard.…”

mentioning

confidence: 94%

Pear blister canker viroid: sequence variability and causal role in pear blister canker disease

Ambrós

Desvignes

Llácer

et al. 1995

Journal of General Virology

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The sequences of several cDNA clones of pear blister canker viroid (PBCVd) P1914T and P47A isolates have been determined. Seven out of eight P1914T clones analysed have a constant sequence which differs at six positions from that of the P2098T isolate reported previously. The remaining P1914T clone (8) has a single nucleotide substitution. The same six changes have been also observed in most of the ten P47A clones sequenced.However, some P47A clones show additional variability in positions on both strands of the central conserved region (CCR) and in another conserved sequence at the left-terminal region. This is the first report of a change affecting the upper strand of a viroid CCR. Reasons why such a change is tolerated are discussed. Infectivity bioassays have demonstrated that PBCVd is the causal agent of PBC disease.

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“…Members of the Pospiviroidae family replicate in the nucleus by host DNA-dependent RNA polymerase II [1]. The lack of proof-reading activity of the plant polymerase(s), the large population size, and the rapid rate of RNA replication have been suggested to result in genetic polymorphism, as demonstrated in various viroids including PSTVd [16,17,18], Citric exocortis viroid (CEVd) [19,20], Hop stunt viroid (HSVd) [21], Australian grapevine viroid (AGVd) [22], Pear blister canker viroid [23], Peach latent mosaic viroid (PLMVd) [24,25], Grapevine yellow speckle viroid- 1 (GYSVd-1) [26], and Chrysanthemum stunt viroid (CSVd) [27]. In this study, the genetic variants of TCDVd and PSTVd in tomato plants were investigated and analyzed.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

Nie

2012

Viruses

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The sequence polymorphism and population structure of Tomato chlorotic dwarf viroid (TCDVd) (isolate Trust) and Potato tuber spindle viroid (PSTVd) (isolate FN) in tomato plants were investigated. Of the 9 and 35 TCDVd clones sequenced from 2 different TCDVd-infected plants, 2 and 4 sequence variants were identified, respectively, leading to a total of 4 sequence variants of 360 nucleotides in length. Variant I was identical to AF162131, the first TCDVd sequence to be reported, and the rest exhibited 1 to 3 nucleotide differences, all in the TR domain, from AF162131/variant I. Of the 33 and 29 PSTVd clones sequenced from 2 different PSTVd-infected plants, 8 and 9 sequence variants were found, respectively, leading to a total of 15 variants ranging in length from 356 to 359 nucleotides. The variant I was identical to EF044303, a PSTVd reported in Russia. The rest exhibited 1 to 11 nucleotide differences scattering in all five domains from EF044303/variant I. The results demonstrated for the first time that TCDVd, like many other viroids including PSTVd, exists in host plants as a collective group comprised of various sequence variants. However, in comparison to PSTVd, TCDVd is less polymorphic in tomato plants as fewer variants and lower haplotype/nucleotide diversities were observed.

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Analysis of the population structure of three phenotypically different PSTVd isolates

Cited by 39 publications

References 39 publications

Viroids: From Genotype to Phenotype Just Relying on RNA Sequence and Structural Motifs

Viroids: From Genotype to Phenotype Just Relying on RNA Sequence and Structural Motifs

Pear blister canker viroid: sequence variability and causal role in pear blister canker disease

Analysis of Sequence Polymorphism and Population Structure of Tomato chlorotic dwarf viroid and Potato spindle tuber viroid in Viroid-Infected Tomato Plants

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