DNA probe

How do viroids replicate? Which enzyme system do they use? Currently, a DNA probe has been made and the investigation is now on for the sequences that are targeted in the uninfected plant, as well as in the infected plant. The site of synthesis in the cell is also unknown. In the case of PSTV it has been shown that the nucleolus is the site of accumulation but the actual site of synthesis unknown (Gosmanova et al. , 2003). Sequence analysis has revealed sequence similarities to introns in certain classes of plant cell genes, namely introns of mitochondrial and ribosomal RNAs.

These similarities are composed of short conserved sequences which place restrictions on secondary and tertiary structure of all these RNAs. Some of these introns have been discovered to be self-splicing, that is the parental RNA acts as a catalyst to facilitate excision of a circular offspring intron RNA and a shortened linear RNA. Diener has proposed that viroids and virusoids may represent plant gene introns which have escaped from their genes during evolution. However, it is more likely that similarity in structure influences the same mechanisms of processing.

Viroids have been cloned into m13 and their DNA is equally infective. Single changes in nucleotide sequences can either enhance or lessen their pathogenicity. Most of the observed changes are located in one or two specific areas of the viroid structure, termed the virulence or pathogenicity-modulating domains. Further analysis shows remarkable similarity between end of transposable element and retroviruses and viroids. All contain uninterrupted stretches of 11-18 purines bases and a centrally conserved region. Center bordered by almost perfect repeat. Similar to copia.

More tips here – Gene Splicing

Could viroids be derived from retroviruses that have lost a large component part or could they be moveable genetic elements-transposons? Small virus is dependant for its replication on co-infection with an unrelated, yet specific, helper virus that provides the replicase. There is no sequence similarity between the helper virus and the satellite virus. Example is tobacco necrosis satellite virus. Two viruses, tobacco necrosis virus and its satellite, STNV, are two unrelated viruses in terms of capsid and nucleic acid structure. TNV is a typical infectious virus that carries all its needed information in its single RNA molecule.

STNV is non-infectious on its own, however it is a small icosahedral particle, consisting of 60 protein molecules. It contains an RNA of . 4 x106 daltons that appears to be monocistronic RNA coding only for its coat protein. All of the satellite viruses carry information for the coat protein. STNV is an obligate parasite of a TNV. This dependence is specific, since no other virus can be substituted. TNV is a typical icosahedron plant virus. TNV normally infects plant roots. The STNV contains only 1239nt and acts as a monocistronic mRNA for the synthesis of its 22kD coat protein.

Another example of a satellite virus is satellite tobacco mosaic virus, which is somewhat smaller and contains two ORFs. One of these is the capsid protein, the other unknown function. A number of other satellite viruses have been discovered. Very much like the case of adeno-associated viruses in mammals. These viruses are dependent on the replication of adenovirus or herpes virus. Likewise delta hepatitis virus appears to be a satellite virus.. It is like a satellite RNA since it requires hepatitis virus for transmission although not for replication. It is circular RNA of about 1678 nucleotides.

The agent appears to replicate like a viroid. However it does contain information for a protein antigen. It is thus more similar to a defective virus, or satellite RNA. That STNV is a specific obligative parasite is illustrated by the inability of other viruses to act as helper, and the variation in the ability of certain TNV strains to support the replication of different strains of STNV.


Gozmanova M, Denti MA, Minkov IN, Tsagris M, Tabler M: Characterization of the RNA motif responsible for the specific interaction of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1.

Nucleic Acids Res 2003, 31:5534-5543. Flores R, Delgado S, Gas ME, Carbonell A, Molina D, Gago S, De la Pena M: Viroids: the minimal non-coding RNAs with autonomous replication. FEBS Lett 2004, 567:42-48. Simon AE, Roossinck MJ, Havelda Z: Plant virus satellite and defective interfering RNAs: new paradigms for a new century. Annu Rev Phytopathol 2004, 42:415-437. Taylor JM: Replication of human hepatitis delta virus: recent developments. Trends Microbiol 2003, 11:185-190.

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