Correlation between bending of the VM region and pathogenicity of different Potato Spindle Tuber Viroid strains

RNA

Volumn 4, Issue 10, 1998, Pages 1295-1303

  Schmitz, Axel ^a   Riesner, Detlev ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

DsRNA activated protein kinase (PKR); Mg2+ induced conformational change; Native PAGE; RNA three dimensional structure; RNA protein interactions

Indexed keywords

AGRICULTURE; ARTICLE; CORRELATION FUNCTION; NONHUMAN; PATHOGENICITY; POTATO; PRIORITY JOURNAL; STRAIN DIFFERENCE; VIROID; VIRULENCE;

BASE SEQUENCE; LYCOPERSICON ESCULENTUM; MAGNESIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PLANT VIRUSES; RNA, VIRAL; SOLANUM TUBEROSUM; VIROIDS; VIRULENCE;

POTATO SPINDLE TUBER VIROID; SOLANUM TUBEROSUM; VIROIDS;

EID: 0031717532     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838298980815     Document Type: Article

References (53)

1. Allain FHT, Howe PWA, Neuhaus D, Varani G. 1997. Structural basis of the RNA-binding specificity of human U1A protein. EMBO J 16:5764-5774.
2. Baumstark T, Schröder ARW, Riesner D. 1997. Viroid processing: Switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation. EMBO J 16:599-610.
3. Bevilacqua PC, Cech TR. 1996. Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR. Biochemistry 35:9983-9994.
4. Bhattacharyya A, Lilley DMJ. 1989. The contrasting structures of mismatched DNA sequences containing looped-out bases (bulges) and multiple mismatches (bubbles). Nucleic Acids Res 17:6821-6840.
5. Bhattacharyya A, Murchie AIH, Lilley DMJ. 1990. RNA bulges and the helical periodicity of double-stranded RNA. Nature 343:484-487.
6. Branch AD, Robertson HD. 1984. A replication cycle for viroids and other small infectious RNAs. Science 223:450-455.
7. Chu WM, Ballard R, Carpick BW Williams BRG, Schmid CW. 1998. Potential Alu function: Regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol 18:58-68.
8. Circle DA, Neel OD, Robertson HD, Clarke PA, Mathews MB. 1997. Surprising specificity of PKR binding to delta agent genomic RNA. RNA 3:438-448.
9. Clarke PA, Mathews MB. 1995. Interactions between the double-stranded RNA binding motif and RNA: Definition of the binding site for the interferon-induced protein kinase DAI (PKR) on adenovirus VA RNA. RNA 1:7-20.
10. Diener TO. 1971. Potato Spindle Tuber "Virus", IV. A replicating, low molecular weight RNA. Virology 45:411-428.
11. Diener TO, 1979. Viroids and viroid diseases. New York: Wiley.
12. Diener TO, ed. 1987. The viroids. New York: Plenum Publishing Corporation.
13. r 68000 protein kinase by viroid strains of varying pathogenicity. Biochimie 75:533-538.
14. Diener TO, Raymer WB. 1967. Potato Spindle Tuber Virus: A plant virus with properties of a free nucleic acid. Science 158:378-381.
15. Grainger RJ, Murchie AIH, Norman DG, Lilley DMJ. 1997. Severe axial bending of RNA induced by the U1A binding element present in the 3′ untranslated region of the U1A mRNA. J Mol Biol 273: 84-92.
16. Gross HJ, Domdey H, Lossow C, Jank P, Raba M, Alberty H, Sänger HL. 1978. Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature 273:203-208.
17. Gruner R, Fels A, Qu F, Zimmat R, Steger G, Riesner D. 1995. Interdependence of pathogenicity and replicability with potato spindle tuber viroid. Virology 209:60-69.
18. Hammond R. 1992. Analysis of the virulence modulating region of Potato Spindle Tuber Viroid (PSTVd) by site-directed mutagenesis. Virology 187:654-662.
19. Harders J, Lukács N, Robert-Nicoud M, Jovin TM, Riesner D. 1989. Imaging of viroids in nuclei from tomato leaf tissue by in situ hybridization and confocal laser scanning microscopy. EMBO J 8:3941-3949.
20. Hiddinga HJ, Crum CJ, Hu J, Roth DA. 1988. Viroid-induced phosphorylation of a host protein related to a dsRNA-dependent protein kinase. Science 241:451-453.
21. 1 in adenovirus-2-infected HeLa cells. J Cell Sci 106:11-22.
22. Kahn JD, Yun E, Crothers DM. 1994. Detection of localized DNA flexibility. Nature 368:163-166.
23. Keese P, Symons RH. 1985. Domains in viroids: Evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci USA 82:4582-4586.
24. Krupp G. 1988. RNA synthesis: Strategies for the use of bacteriophage RNA polymerases. Gene 72:75-89.
25. Kumar A, Yang YL, Flati V, Der S, Kadereit S, Deb A, Haque J, Reis L, Weissmann C, Williams BRG. 1997. Deficient cytokine signaling in mouse embryo fibroblasts with a targeted deletion in the PKR gene: Role of IRF-1 and NF-κB. EMBO J 16:406-416.
26. Laing LG, Gluick TC, Draper DE. 1994. Stabilization of RNA structure by Mg ions. Specific and non-specific effects. J Mol Biol 237:577-587.
27. Langland JO, Jin S, Jacobs BL, Roth DA. 1995. Identification of a plant-encoded analog of PKR, the mammalian double-stranded RNA-dependent protein kinase. Plant Physiol 108:1259-1267.
28. Langland JO, Langland LA, Browning KS, Roth DA. 1996. Phosphorylation of plant eukaryotic initiation factor-2 by the plant-encoded double-stranded RNA-dependent protein kinase, pPKR, and inhibition of protein synthesis in vitro. J Biol Chem 271:4539-4544.
29. Langland JO, Langland L, Zeman C, Saha D, Roth DA. 1997. Developmental regulation of a plant encoded inhibitor of eukaryotic initiation factor 2α phosphorylation. Plant J 12:393-400.
30. Lee SB, Esteban M. 1994. The interferon-induced double-stranded RNA-activated protein kinase induces apoptosis. Virology 199: 491-496.
31. Li JH, Yu ZP, Lomiany DJ, Petryshyn RA. 1997. Characterization of a cellular RNA that activates PKR in 3T3 F442 A cells. Inter J Oncol 11:685-695.
32. Manche L, Green SR, Schmedt C, Mathews MB. 1992. Interactions between double-stranded RNA regulators and the protein kinase DAI. Mol Cell Biol 12:5238-5248.
33. Minks MA, West DK, Benvin S, Baglioni C. 1979. Structural requirements of double-stranded RNA for the activation of 2′,5′-oligo(A) polymerase and protein kinase of interferon-treated HeLa cells. J Biol Chem 254:10180-10183.
34. Owens RA, Steger G, Hu Y, Fels A, Hammond RW, Riesner D. 1996. RNA structural features responsible for potato spindle tuber viroid pathogenicity. Virology 222:144-158.
35. Petryshyn RA, Li J, Judware R. 1994. Activation of the dsRNA-dependent kinase. Progr Mol Subcell Biol 14:1-14.
36. Rice JA, Crothers DM. 1989. DNA bending by the bulge defect. Biochemistry 28:4512-4516.
37. Riesner D, Gross HJ. 1985. Viroids. Annu Rev Biochem 54:531-564.
38. Robertson HD, Manche L, Mathews MB. 1996. Paradoxical interactions between human delta hepatitis agent RNA and the cellular protein kinase PKR. J Virol 70:5611-5617.
39. Roth DA, He X. 1994. Viral-dependent phosphorylation of a dsRNA-dependent kinase. Prog Mol Subcell Biol 14:28-46.
40. Schindler IM, Mühlbach HP. 1992. Involvement of nuclear DNA-dependent RNA polymerases in potato spindle tuber viroid replication: A reevaluation. Plant Science 84:221-229.
41. Schmitz M. 1989. Experimentelle und theoretische Untersuchungen an partiell basengepaarten Bereichen in Nukleinsäuren [thesis]. Heinrich-Heine-Universität Düsseldorf.
42. Schmitz M, Steger G. 1992. Base-pair probability profiles of RNA secondary structures. Comp Appl Biosci 8:389-399.
43. Schnölzer M, Haas B, Ramm K, Hofmann H, Sänger HL. 1985. Correlation between structure and pathogenicity of potato spindle tuber viroid (PSTV). EMBO J 4:2181-2190.
44. Schumacher J, Sänger HL, Riesner D. 1983. Subcellular localization of viroids in highly purified nuclei from tomato leaf tissue. EMBO J 2:1549-1555.
45. Semancik JS, ed. 1987. Viroids and viroid-like pathogens. Boca Raton, Florida: CRC Press.
46. Singh RP, Boucher A, Haas B, Sänger HL. 1991. Differential migration during polyacrylamide gel electrophoresis suggests conformational differences among strains of potato spindle tuber viroid. Can J Plant Pathol 13:202-211.
47. Srivastava SP, Kumar KU, Kaufman RJ. 1998. Phosphorylation of eukaryotic translation factor 2 mediates apoptosis in response to activation of the double-stranded RNA-dependent protein kinase. J Biol Chem 273:2416-2423.
48. Symons RH, ed. 1990. Viroids and related pathogenic RNAs. Semin Virol 1.
49. Tang RS, Draper DE. 1990. Bulge loops used to measure the helical twist of RNA in solution. Biochemistry 29:5232-5236.
50. Visvader JA, Symons RH. 1985. Eleven new sequence variants of citrus exocortis viroid and correlation of sequence with pathogenicity. Nucleic Acids Res 13:2907-2920.
51. Wyatt JR, Chastain M, Puglisi JD. 1991. Synthesis and purification of large amounts of RNA oligonucleotides. BioTechniques 11:764-769.
52. Zacharias M, Hagerman PJ. 1995. Bulge-induced bends in RNA: Quantification by transient electric birefringence. J Mol Biol 247: 486-500.
53. Zacharias M, Hagerman PJ. 1996. The influence of symmetric internal loops on the flexibility of RNA. J Mol Biol 257:276-289.