Viroid 

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Viroid
Scientific classification
(unranked): Subviral agents
(unranked): Viroid
Families

Pospiviroidae
Avsunviroidae

Viroids are plant pathogens that consist of a short stretch (a few hundred nucleobases) of highly complementary, circular, single-stranded RNA without the protein coat that is typical for viruses. The smallest discovered is a 220 nucleobase scRNA (small cytoplasmic RNA) associated with the rice yellow mottle sobemovirus (RYMV).1 In comparison, the genome of the smallest known viruses capable of causing an infection by themselves are around 2 kilobases in size. The human pathogen hepatitis D is similar to viroids.2

Viroids were discovered and given this name by Theodor Otto Diener, a plant pathologist at the Agricultural Research Service in Maryland, in 1971.345

Viroid RNA does not code for any protein.6 The replication mechanism involves RNA polymerase II, an enzyme normally associated with synthesis of messenger RNA from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid's RNA as template. Some viroids are ribozymes, having catalytic properties which allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.7

The first viroid to be identified was the potato spindle tuber viroid (PSTVd). Some 33 species have been identified.

Primary8 and secondary structure of the PSTVd viroid:

Primary Structure 


  1   CGGAACUAAA CUCGUGGUUC CUGUGGUUCA CACCUGACCU CCUGAGCAGA AAAGAAAAAA
 61   GAAGGCGGCU CGGAGGAGCG CUUCAGGGAU CCCCGGGGAA ACCUGGAGCG AACUGGCAAA
121   AAAGGACGGU GGGGAGUGCC CAGCGGCCGA CAGGAGUAAU UCCCGCCGAA ACAGGGUUUU
181   CACCCUUCCU UUCUUCGGGU GUCCUUCCUC GCGCCCGCAG GACCACCCCU CGCCCCCUUU
241   GCGCUGUCGC UUCGGCUACU ACCCGGUGGA AACAACUGAA GCUCCCGAGA ACCGCUUUUU
301   CUCUAUCUUA CUUGCUUCGG GGCGAGGGUG UUUAGCCCUU GGAACCGCAG UUGGUUCCU
Secondary Structure


Putative secondary structure of the PSTVd viroid


Contents

Taxonomy

Viroids and RNA silencing

There has long been confusion over how viroids are able to induce symptoms in plants without encoding any protein products within their sequences. Evidence now suggests that RNA silencing is involved in the process. First, changes to the viroid genome can dramatically alter its virulence.9 This reflects the fact that any siRNAs produced would have less complementary base pairing with target messenger RNA. Secondly, siRNAs corresponding to sequences from viroid genomes have been isolated from infected plants.10 Finally, transgenic expression of the noninfectious hpRNA of potato spindle tuber viroid develops all the corresponding viroid like symptoms.11

This evidence indicates that when viroids replicate via a double stranded intermediate RNA, they are targeted by a dicer enzyme and cleaved into siRNAs that are then loaded onto the RNA-induced silencing complex. The viroid siRNAs actually contain sequences capable of complementary base pairing with the plant's own messenger RNAs and induction of degradation or inhibition of translation is what causes the classic viroid symptoms.

See also

References

  1. ^ Collins RF, Gellatly DL, Sehgal OP, Abouhaidar MG (1998). "Self-cleaving circular RNA associated with rice yellow mottle virus is the smallest viroid-like RNA". Virology 241 (2): 269–75. doi:10.1006/viro.1997.8962. PMID 9499801. 
  2. ^ Rocheleau L, Pelchat M (2006). "The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research". BMC Microbiol. 6: 24. doi:10.1186/1471-2180-6-24. PMID 16519798. 
  3. ^ Diener TO (August 1971). "Potato spindle tuber "virus". IV. A replicating, low molecular weight RNA". Virology 45 (2): 411–28. PMID 5095900, http://linkinghub.elsevier.com/retrieve/pii/0042-6822(71)90342-4. 
  4. ^ |url=http://www.ars.usda.gov/is/timeline/viroid.htm |title=ARS Research Timeline - Tracking the Elusive Viroid |date=2006-03-02 |accessdate=2007-07-18}}
  5. ^ Discovery of Viroids
  6. ^ Tsagris EM, de Alba AE, Gozmanova M, Kalantidis K (September 2008). "Viroids". Cell. Microbiol.. doi:10.1111/j.1462-5822.2008.01231.x. PMID 18764915. 
  7. ^ Daròs JA, Elena SF, Flores R (2006). "Viroids: an Ariadne's thread into the RNA labyrinth". EMBO Rep. 7 (6): 593–8. doi:10.1038/sj.embor.7400706. PMID 16741503. 
  8. ^ Schrader O, Baumstark T, Riesner D (2003). "A mini-RNA containing the tetraloop, wobble-pair and loop E motifs of the central conserved region of potato spindle tuber viroid is processed into a minicircle". Nucleic Acids Res. 31 (3): 988–98. doi:10.1093/nar/gkg193. PMID 12560495. 
  9. ^ Elizabeth Dickson, Hugh D. Robertson, C. L. Niblett, R. K. Horst & Milton Zaitlin (1979). "Minor differences between nucleotide sequences of mild and severe strains of potato spindle tuber viroid". Nature 277: 60–62. doi:10.1038/277060a0. 
  10. ^ Papaefthimiou I, Hamilton A, Denti M, Baulcombe D, Tsagris M, Tabler M (2001). "Replicating potato spindle tuber viroid RNA is accompanied by short RNA fragments that are characteristic of post-transcriptional gene silencing". Nucleic Acids Res. 29 (11): 2395–400. doi:10.1093/nar/29.11.2395. PMID 11376158, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=55696. 
  11. ^ Wang MB, Bian XY, Wu LM, et al (2004). "On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites". Proc. Natl. Acad. Sci. U.S.A. 101 (9): 3275–80. doi:10.1073/pnas.0400104101. PMID 14978267, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=365780. 

External links

Viroids:details