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MeSH Review

Viroids

 
 
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Disease relevance of Viroids

  • RNA polymerase II is implicated in the RNA-templated RNA synthesis during replication of viroids and Hepatitis Delta Virus (HDV); however, neither the RNA template nor protein factor requirements for this process are well defined [1].
  • Sequence homology was found by computer analysis between potato spindle tuber viroid (PSTV) RNA and U3B snRNA of Novikoff hepatoma cells [2].
  • Four viral genera including five potato viruses [(carlavirus (PVS), polerovirus (PLRV), potexvirus (PVX), potyvirus (PVA and PVY))] and a viroid genus including a viroid genome (pospiviroid (PSTVd)) were used to develop various formats of m-RT-PCR [3].
  • Digoxigenin-labelled molecular probe for the simultaneous detection of three potato pathogens: potato spindle tuber viroid (PSTVd), potato virus Y (PVY), and potato leafroll virus (PLRV) [4].
  • After convincing evidence was obtained showing that scrapie infectivity depends upon a protein component, the term "prion" was introduced to distinguish these infectious pathogens from others, including viroids and viruses [5].
 

High impact information on Viroids

  • DNA-dependent RNA polymerase II of plant origin transcribes viroid RNA into full-length copies [6].
  • Isolated nuclei from green leaf tissue of tomato plants infected with potato spindle tuber viroid (PSTVd) were bound to microscope slides, fixed with formaldehyde and hybridized with biotinylated transcripts of cloned PSTVd cDNA [7].
  • The previously described induction of RdRP activity upon viroid infection is shown to be correlated with an increased steady state level of the corresponding mRNA [8].
  • Five lines of pac1 potato (Solanum tuberosum L., cultivar Russet Burbank) challenged with potato spindle tuber viroid (PSTVd) suppressed PSTVd infection and accumulation [9].
  • Potato spindle tuber viroid can be separated into two fractions by polyacrylamide gelelectrophoresis in the presence of formamide and urea [10].
 

Chemical compound and disease context of Viroids

  • The ability to purify viroid conformational isomers from polyacrylamide gels will facilitate biochemical studies aimed at identifying host components interacting with RNAs of the viroid replication complex, which may not all be present in the most thermodynamically favored rodlike structure of mature viroids [11].
  • In the course of a study on the variability of this viroid a natural sequence variant has been characterized in which the hammerhead structure of the plus polarity strand has the sequence CCGA instead of the conserved uridine turn motif CUGA present in the catalytic pocket of all natural hammerhead structures [12].
  • However, NASBA in the presence of inosine 5'-triphosphate successfully amplified the cRNAs to viroids in total nucleic acid extracts from citrus plants [13].
  • Under certain conditions this guanosine-specific endoribonuclease proved to be capable of processing the longer-than-unit-length, precursor-like viroid RNA transcript by cleaving out a linear 358 nucleotide long product and ligating that to a circular RNA molecule [14].
  • Studies on the primary and secondary structure of potato spindle tuber viroid: products of digestion with ribonuclease A and ribonuclease T1, and modification with bisulfite [15].
 

Biological context of Viroids

  • In plants, posttranscriptional gene silencing (PTGS) has been reported for cytoplasmic RNAs from endogenous nuclear genes, transgenes, viruses, and, recently, for a viroid with nuclear replication and accumulation [16].
  • Sequence homology between potato spindle tuber viroid and U3B snRNA [2].
  • The citrus exocortis viroid (approximately 350 nucleotides) is degraded by hot formamide hydrolysis to fragments ranging from small oligonucleotides to near full lengths, and subsequently labelled to high specific activity by enzymatically attaching 32P to the 5'-end of each molecule [17].
  • The most stable rod-like secondary structure of this viroid has 53 G:C, 29 A:U and 5 G:U base pairs with a minimum free energy (at 25 degrees C) of -81.2 kcal/mol (-339.4 kJ/mol) [18].
 

Gene context of Viroids

  • We have addressed this issue in chrysanthemum chlorotic mottle viroid (CChMVd), whose (+) hammerhead has an extra A (A10) between the conserved A9 and the quasi-conserved G10 [19].
  • Potato spindle tuber viroid (PSTV), a small infectios RNA, has been completely digested with RNase T1 and RNase A, and the resulting oligonucleotides have been sequenced using 5'-terminal 32p-labelling with gamma-32p ATP and T4 polynucleotide kinase, fingerprinting and controlled nuclease P1 digestion [15].
  • 8. The values of the apparent reaction enthalpies of the different viroid species range between 3,140 and 3,770 kJ/mol [20].
  • Transcripts of (+) and (-) polarity, from unit up to sixfold length, were synthesized from DNA clones of the potato spindle tuber viroid (PSTV) with the SP6 transcription system [21].
  • These homologous regions fall within the particular domains in the viroid domain model which has been previously proposed by Keese and Symons(Proc. Natl. Acad. Sci. USA. 82, 4582-4586, 1985) [22].
 

Analytical, diagnostic and therapeutic context of Viroids

  • Inosine 5'-triphosphate can dramatically increase the yield of NASBA products targeting GC-rich and intramolecular base-paired viroid RNA [13].
  • Viroid cDNA was then synthesized and amplified using viroid specific primers in RT-PCR assays and the amplified viroid cDNA (amplicon) was digoxigenin (DIG) -labelled during the amplification process [23].
  • In situ hybridization experiments were carried out to detect avocado sunblotch viroid (ASBVd) in foliar tissue of avocado, using a digoxigenin-labelled RNA probe complementary to the ASBVd-RNA in sections of aldehyde-fixed, LRGold-embedded leaf samples [24].
  • Run-off transcription of the PCR product allows the synthesis of exact-length linear viroid RNA which can be circularised by T4 RNA ligase following an enzymic modification of the 5' triphosphate to a monophosphate [25].
  • Potato spindle tuber viroid: circular dichroism spectrum and physical chemical studies of its interaction with ethidium bromide [26].

References

  1. Specific HDV RNA-templated transcription by pol II in vitro. Filipovska, J., Konarska, M.M. RNA (2000) [Pubmed]
  2. Sequence homology between potato spindle tuber viroid and U3B snRNA. Kiss, T., Pósfai, J., Solymosy, F. FEBS Lett. (1983) [Pubmed]
  3. Detection of multiple potato viruses using an oligo(dT) as a common cDNA primer in multiplex RT-PCR. Nie, X., Singh, R.P. J. Virol. Methods (2000) [Pubmed]
  4. Digoxigenin-labelled molecular probe for the simultaneous detection of three potato pathogens: potato spindle tuber viroid (PSTVd), potato virus Y (PVY), and potato leafroll virus (PLRV). Wełnicki, M., Zekanowski, C., Zagórski, W. Acta Biochim. Pol. (1994) [Pubmed]
  5. Prion encephalopathies of animals and humans. Prusiner, S.B. Dev. Biol. Stand. (1993) [Pubmed]
  6. DNA-dependent RNA polymerase II of plant origin transcribes viroid RNA into full-length copies. Rackwitz, H.R., Rohde, W., Sänger, H.L. Nature (1981) [Pubmed]
  7. Imaging of viroids in nuclei from tomato leaf tissue by in situ hybridization and confocal laser scanning microscopy. Harders, J., Lukács, N., Robert-Nicoud, M., Jovin, T.M., Riesner, D. EMBO J. (1989) [Pubmed]
  8. Isolation of an RNA-directed RNA polymerase-specific cDNA clone from tomato. Schiebel, W., Pélissier, T., Riedel, L., Thalmeir, S., Schiebel, R., Kempe, D., Lottspeich, F., Sänger, H.L., Wassenegger, M. Plant Cell (1998) [Pubmed]
  9. Transgenic potato expressing a double-stranded RNA-specific ribonuclease is resistant to potato spindle tuber viroid. Sano, T., Nagayama, A., Ogawa, T., Ishida, I., Okada, Y. Nat. Biotechnol. (1997) [Pubmed]
  10. Separation and infectivity of circular and linear forms of potato spindle tuber viroid. Owens, R.A., Erbe, E., Hadidi, A., Steere, R.L., Diener, T.O. Proc. Natl. Acad. Sci. U.S.A. (1977) [Pubmed]
  11. Generation of viroid conformational isomers that are stable to incubation with magnesium ions and in a nuclear extract from tomato plants. Pace, U., Branch, A.D., Robertson, H.D. Nucleic Acids Res. (1992) [Pubmed]
  12. In vitro and in vivo self-cleavage of a viroid RNA with a mutation in the hammerhead catalytic pocket. Ambrós, S., Flores, R. Nucleic Acids Res. (1998) [Pubmed]
  13. Inosine 5'-triphosphate can dramatically increase the yield of NASBA products targeting GC-rich and intramolecular base-paired viroid RNA. Nakahara, K., Hataya, T., Uyeda, I. Nucleic Acids Res. (1998) [Pubmed]
  14. Ribonuclease T1 generates circular RNA molecules from viroid-specific RNA transcripts by cleavage and intramolecular ligation. Tsagris, M., Tabler, M., Sänger, H.L. Nucleic Acids Res. (1991) [Pubmed]
  15. Studies on the primary and secondary structure of potato spindle tuber viroid: products of digestion with ribonuclease A and ribonuclease T1, and modification with bisulfite. Domdey, H., Jank, P., Sänger, L., Gross, H.J. Nucleic Acids Res. (1978) [Pubmed]
  16. Two chloroplastic viroids induce the accumulation of small RNAs associated with posttranscriptional gene silencing. Martínez de Alba, A.E., Flores, R., Hernández, C. J. Virol. (2002) [Pubmed]
  17. In vitro 32P-labelling of viroid RNA for hybridization studies. Negruk, V.I., Grill, L.K., Semancik, J.S. J. Virol. Methods (1980) [Pubmed]
  18. A new sequence variant of Coleus blumei viroid 1 from the Coleus blumei cultivar "Rainbow Gold'. Spieker, R.L. Arch. Virol. (1996) [Pubmed]
  19. An extra nucleotide in the consensus catalytic core of a viroid hammerhead ribozyme: implications for the design of more efficient ribozymes. De la Peña, M., Flores, R. J. Biol. Chem. (2001) [Pubmed]
  20. Common structural features of different viroids: serial arrangement of double helical sections and internal loops. Langowski, J., Henco, K., Riesner, D., Sänger, H.L. Nucleic Acids Res. (1978) [Pubmed]
  21. Structure of viroid replicative intermediates: physico-chemical studies on SP6 transcripts of cloned oligomeric potato spindle tuber viroid. Steger, G., Tabler, M., Brüggemann, W., Colpan, M., Klotz, G., Sänger, H.L., Riesner, D. Nucleic Acids Res. (1986) [Pubmed]
  22. Nucleotide sequence and secondary structure of apple scar skin viroid. Hashimoto, J., Koganezawa, H. Nucleic Acids Res. (1987) [Pubmed]
  23. Sensitive detection of potato spindle tuber and temperate fruit tree viroids by reverse transcription-polymerase chain reaction-probe capture hybridization. Shamloul, A.M., Hadidi, A. J. Virol. Methods (1999) [Pubmed]
  24. Detection of avocado sunblotch viroid in chloroplasts of avocado leaves by in situ hybridization. Lima, M.I., Fonseca, M.E., Flores, R., Kitajima, E.W. Arch. Virol. (1994) [Pubmed]
  25. Synthesis of infectious viroids and other circular RNAs. Rezaian, M.A. Current issues in molecular biology. (1999) [Pubmed]
  26. Potato spindle tuber viroid: circular dichroism spectrum and physical chemical studies of its interaction with ethidium bromide. Singh, R.P., Williams, R.E. Can. J. Biochem. (1978) [Pubmed]
 
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