Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm

Journal of Molecular Biology

Volumn 276, Issue 1, 1998, Pages 43-55

  Gultyaev, Alexander P ^a,b   Van Batenburg, F H D ^b   Pleij, Cornelis W A ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

Author keywords

Genetic algorithm; Potato spindle tuber viroid (PSTVd); RNA structure; Viroids

Indexed keywords

VIRUS RNA;

ALGORITHM; ARTICLE; COMPUTER SIMULATION; NONHUMAN; PRIORITY JOURNAL; RNA CONFORMATION; VIROID;

POTATO SPINDLE TUBER VIROID; SOLANUM TUBEROSUM; VIROIDS;

EID: 0032512621     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1384     Document Type: Article

References (48)

1. Abrahams J.P., van der Berg M., van Batenburg F.H.D., Pleij C.W.A. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucl. Acids Res. 18:1990;3035-3044
2. van Batenburg F.H.D., Gultyaev A.P., Pleij C.W.A. An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J. Theoret. Biol. 174:1995;269-280
3. Baumstark T., Riesner D. Only one of four possible secondary structures of the central conserved region of the potato spindle tuber viroid is a substrate for processing in a potato nuclear extract. Nucl. Acids Res. 23:1995;4246-4254
4. Berkhout B., Klaver B., Das A.T. Forced evolution of a regulatory RNA helix in the HIV-1 genome. Nucl. Acids Res. 25:1997;940-947
5. Biebricher C.K., Luce R. In vitro recombination and terminal elongation of RNA by Qβ replicase. EMBO J. 11:1992;5129-5135
6. Branch A.D., Robertson H.D. A replication cycle for viroids and other small infectious RNA's. Science. 223:1984;450-455
7. Bussiere F., Lafontaine D., Perreault J.P. Compilation and analysis of viroid and viroid-like RNA sequences. Nucl. Acids Res. 24:1996;1793-1798
8. Diener T.O. Viroids. Advan. Virus Res. 28:1983;241-283
9. Eigen M. The origin of genetic information viruses as models. Gene. 135:1993;37-47
10. Elena S.F., Dopazo J., Flores R., Diener T.O., Moya A. Phylogeny of viroids, viroidlike satellite RNAs, and the viroidlike domain of hepatitis δ virus RNA. Proc. Natl Acad. Sci. USA. 88:1991;5631-5634
11. Forrest S. Genetic algorithms: principles of natural selection applied to computation. Science. 261:1993;872-878
12. Freier S.M., Kierzek R., Jaeger J.A., Sugimoto N., Caruthers M.H., Neilson T., Turner D.H. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA. 83:1986;9373-9377
13. Gast F.U., Kempe D., Spieker R.L., Sanger H.L. Secondary structure probing of potato spindle tuber viroid (PSTVd) and sequence comparison with other small pathogenic RNA replicons provides evidence for central non-canonical base-pairs, large A-rich loops, and a terminal branch. J. Mol. Biol. 262:1996;652-670
14. Góra-Sochacka A., Kierzek A., Candresse T., Zagórski W. The genetic stability of potato spindle tuber viroid (PSTVd) molecular variants. RNA. 3:1997;68-74
15. Groeneveld H., Thimon K., van Duin J. Translational control of maturation-protein synthesis in phage MS2 a role for the kinetics of RNA folding? RNA. 1:1995;79-88
16. Gruner R., Fels A., Qu F., Zimmat R., Steger G., Riesner D. Interdependence of pathogenicity and replicability with potato spindle tuber viroid. Virology. 209:1995;60-69
17. Gultyaev A.P., van Batenburg F.H.D., Pleij C.W.A. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:1995;37-51
18. Gultyaev A.P., van Batenburg F.H.D., Pleij C.W.A. The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics. Nucl. Acids Res. 23:1995;3718-3725
19. Hammond R.W. Analysis of the virulence modulating region of potato spindle tuber viroid (PSTVd) by site-directed mutagenesis. Virology. 187:1992;654-662
20. Hecker R., Wang Z., Steger G., Riesner D. Analysis of RNA structures by temperature-gradient gel electrophoresis viroid replication and processing. Gene. 72:1988;59-74
21. Hernandez C., Elena S.F., Moya A., Flores R. Pear blister canker viroid is a member of the apple scar skin subgroup (apscaviroids) and also has sequence homology with viroids from other subgroups. J. Gen. Virol. 73:1992;2503-2507
22. Hu Y., Feldstein P.A., Bottino P.J., Owens R.A. Role of the variable domain in modulating potato spindle tuber viroid replication. Virology. 219:1996;45-56
23. Huynen M.A., Stadler P.F., Fontana W. Smoothness within ruggedness: the role of neutrality in adaptation. Proc. Natl Acad. Sci. USA. 93:1996;397-401
24. Jaeger J.A., Turner D.H., Zuker M. Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA. 86:1989;7706-7710
25. Keese P., Visvader J.E., Symons R.H. Sequence variability in plant viroid RNAs. Domingo E., Holland J.J., Ahlquist P. RNA genetics. vol. III:1988;71-98 CRC Press, Boca Raton
26. Klaff P., Riesner D., Steger G. RNA structure and the regulation of gene expression. Plant Mol. Biol. 32:1996;89-106
27. Klaver B., Berkhout B. Evolution of a disrupted TAR RNA hairpin structure in the HIV-1 virus. EMBO J. 13:1994;2650-2659
28. Klovins J., Tsareva N.A., de Smit M.H., Berzins V., van Duin J. Rapid evolution of translational control mechanisms in RNA genomes. J. Mol. Biol. 265:1997;372-384
29. Koltunow A.M., Rezaian M.A. A scheme for viroid classification. Intervirology. 30:1989;194-201
30. Loss P., Schmitz M., Steger G., Riesner D. Formation of a thermodynamically metastable structure containing hairpin II is critical for infectivity of potato spindle tuber viroid RNA. EMBO J. 10:1991;719-727
31. Ma C.K., Kolesnikow T., Rayner J.C., Simons E.L., Yim H., Simons R.W. Control of translation by mRNA secondary structure: the importance of the kinetics of structure formation. Mol. Microbiol. 14:1994;1033-1047
32. Martinez-Soriano J.P., Galindo-Alonso J., Maroon C.J.M., Yucel I., Smith D.R., Diener T.O. Mexican papita viroid putative ancestor of crop viroids. Proc. Natl Acad. Sci. USA. 93:1996;9397-9401
33. Olsthoorn R.C.L., van Duin J. Evolutionary reconstruction of a hairpin deleted from the genome of an RNA virus. Proc. Natl Acad. Sci. USA. 93:1996;12256-12261
34. Olsthoorn R.C.L., Licis N., van Duin J. Leeway and constraints in the forced evolution of a regulatory RNA helix. EMBO J. 13:1994;2660-2668
35. Owens R.A., Chen W., Hu Y., Hsu Y.-H. Suppression of potato spindle viroid replication and symptom expression by mutations which stabilize the pathogenicity domain. Virology. 208:1995;554-564
36. Owens R.A., Steger G., Hu Y., Fels A., Hammond R.W., Riesner D. RNA structural features responsible for potato spindle tuber viroid pathogenicity. Virology. 222:1996;144-158
37. Qu F., Heinrich C., Loss P., Steger G., Tien P., Riesner D. Multiple pathways of reversion in viroids for conservation of structural elements. EMBO J. 12:1993;2129-2139
38. Riesner D., Gross H.J. Viroids. Annu. Rev. Biochem. 54:1985;531-564
39. Riesner D., Baumstark T., Qu F., Klahn T., Loss P., Rosenbaum V., Schmitz M., Steger G. Physical basis and biological examples of metastable RNA structures. Lilley D.M.J., Heumann H., Suck D. Structural Tools for the Analysis of Protein - Nucleic Acid Complexes. 1992;401-435 Birkhauser, Basel
40. Rosenbaum V., Klahn T., Lundberg U., Holmgren E., von Gabain A., Riesner D. Co-existing structures of an mRNA stability determinant the 5′ region of the Escherichia coli andSerratia marcescens ompA mRNA. J. Mol. Biol. 229:1993;656-670
41. Schmitz M., Steger G. Description of RNA folding by "simulated annealing" J. Mol. Biol. 255:1996;254-266
42. Schnolzer M., Haas B., Ramm K., Hofmann H., Sanger H.L. Correlation between structure and pathogenicity of potato spindle tuber viroid (PSTV). EMBO J. 4:1985;2181-2190
43. Schuster P., Fontana W., Stadler P.F., Hofacker I.L. From sequences to shapes and back a case study in RNA secondary structures. Proc. Roy Soc. London ser. B. 255:1994;279-284
44. Steger G., Hofmann H., Fortsch J., Gross H.J., Randles J.W., Sanger H.L., Riesner D. Conformational transitions in viroids and virusoids comparison of results from energy minimization algorithm and from experimental data. J. Biomol. Struct. Dynam. 2:1984;543-571
45. Visvader J.E., Symons R.H. Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity. Nucl. Acids Res. 13:1985;2907-2920
46. Walter A.E., Turner D.H., Kim J., Lyttle M.H., Muller P., Mathews D.H., Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl Acad. Sci. USA. 91:1994;9218-9222
47. Wassenegger M., Heimes S., Sanger H.L. An infectious viroid RNA replicon evolved from an in vitro- generated non-infectious viroid deletion mutant via a complementary deletion in vivo. EMBO J. 13:1994;6172-6177
48. Wassenegger M., Spieker R.L., Thalmeir S., Gast F.-U., Riedel L., Sanger H.L. A single nucleotide substitution converts potato spindle tuber viroid (PSTVd) from a nonifectious to an infectious RNA for Nicotiana tabacum. Virology. 226:1996;191-197