Automatic detection of conserved base pairing patterns in RNA virus genomes

Computers and Chemistry

Volumn 23, Issue 3-4, 1999, Pages 401-414

  Hofacker, Ivo L ^a   Stadler, Peter F ^a,b  

^a UNIVERSITY OF VIENNA   (Austria)

^b SANTA FE INSTITUTE   (United States)

Author keywords

Compensatory mutations; Conserved substructures; RNA secondary structure prediction; RNA virus genomes; Structure alignment

Indexed keywords

VIRUS RNA;

ALGORITHM; ARTICLE; BASE PAIRING; CHEMISTRY; CONFORMATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; RNA VIRUS; VIRUS GENOME;

ALGORITHMS; BASE PAIRING; BASE SEQUENCE; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA VIRUSES; RNA, VIRAL;

EID: 0033563463     PISSN: 00978485     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0097-8485(99)00013-3     Document Type: Article

References (62)

1. Baudin, F., Marquet, R., Isel, C., Darlix, J.L., Ehresmann, B., Ehresmann, C., 1993. Functional sites in the 5′ region of human immunodeficiency virus type 1 RNA form defined structural domains. J. Mol. Biol 229, 382-397.
2. Biebricher, C., 1994. The role of RNA structure in RNA replication. Ber. Bunsenges. Phys. Chem 98, 1122-1126.
3. Brown, E.A., Zhang, H., Ping, L.-H., Lemon, S.M., 1992. Secondary structure of the 5′ nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. Nucl. Acids Res 20, 5041-5045.
4. Corodkin, J., Heyer, L.J., Stormo, G.D., 1997. Finding common sequences and structure motifs in a set of RNA molecules. In: Gaasterland, T., Karp, P., Karplus, K., Ouzounis, C., Sander, C., Valencia, A. (Eds.), Proceedings of the ISMB-97. AAAI Press, Menlo Park, CA, pp. 120-123.
5. Dandekar, T., Hentze, M.W., 1995. Finding the hairpin in the haystack: searching for RNA motifs. Trends. Genet 11, 45-50.
6. Dayton, E.T., Konings, D.A.M., Powell, D.M., Shapiro, B.A., Butini, L., Maizel, J.V., Dayton, A.I., 1992. Extensive sequence-specific information throughout the CAR/RRE, the target sequence of the human immunodeficiency virus type 1 Rev protein. J. Virol 66, 1139-1151.
7. Deng, R., Brock, K.V., 1993. 5′ and 3′ untranslated regions of pestivirus genome: primary and secondary structure analyses. Nucl. Acids Res 21, 1949-1957.
8. Domingo, E., Holland, J.J., Biebricher, C.K., Eigen, M., 1995. Quasispecies: The concept and the word. In: Gibbs, A., Calisher, C.H., García-Arenal, G. (Eds.), Molecular Basis of Virus Evolution. Cambridge University Press, Cambridge, UK, pp. 171-180.
9. Drake, J.W., 1993. Rates of spontaneous mutations among RNA viruses. Proc. Natl. Acad. Sci., USA 90, 4171-4175.
10. Duke, G.M., Hoffman, A.M., Palmenberg, A.C., 1992. Sequence and structural elements that contribute to efficient encephalomyocarditis virus RNA translation. J. Virol 66, 1602-1609.
11. Elliott, R.M., Schmaljohn, C.S., Collett, M.S., 1991. Bunyavirus genome structure and gene expression. Current Topics in Microbiology and Immunology 169, 91-141.
12. Fontana, W., Konings, D.A.M., Stadler, P.F., Schuster, P., 1993. Statistics of RNA secondary structures. Biopolymers 33, 1389-1404.
13. Gautheret, D., Major, F., Cedergren, R., 1990. Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA. Comput. Appl. Biosci 6, 325-331.
14. Gultyaev, A.P., vanbatenburg, F.H.D., Pleij, C.W.A., 1995. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol 250, 37-51.
15. Gutell, R.R., 1993. Evolutionary characteristics of RNA: Inferring higher-order structure from patterns of sequence variation. Curr. Opin. Struct. Biol 3, 313-322.
16. Higgs, P., 1998. The influence of RNA secondary structure on the rates of substitution in RNA-encoding genes. Preprint, University of Manchester.
17. Hofacker, I.L., Fekete, M., Flamm, C., Huynen, M.A., Rauscher, S., Stolorz, P.E., Stadler, P.F., 1998. Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucl. Acids Res 26, 3825-3836.
18. Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, S., Tacker, M., Schuster, P., 1994. Fast folding and comparison of RNA secondary structures. Monatsh. Chem 125, 167-188.
19. Hofacker, I.L., Huynen, M.A., Stadler, P.F., Stolorz, P.E., 1996a. Knowledge discovery in RNA sequence families of HIV using scalable computers. In: Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining, Portland, OR. AAAI Press, Portland, OR, pp. 20-25.
20. Hofacker, I.L., Huynen, M.A., Stadler, P.F., Stolorz, P.E., 1996b. RNA folding and parallel computers: the minimum free energy structures of complete HIV genomes. Technical Report # 95-10-089, SFI Santa Fe, New Mexico.
21. Hoffman, M.A., Palmenberg, A.C., 1995. Mutational analysis of the J-K stem-loop region of the encephalomyocarditis-virus IRES. J. Virol 69, 4399-4406.
22. Hogeweg, P., Hesper, B., 1984. Energy directed folding of RNA sequences. Nucl. Acids Res 12, 67-74.
23. Huynen, M., Konings, D., 1998. Questions about RNA structures in HIV and HPV. In: Myers, G.L. (Ed.), Viral Regulatory Structures and Their Degeneracy, Volume XXVIII of Santa Fe Institute Studies in the Sciences of Complexity. Addison Wesley, Longman, Reading, MA, pp. 69-82.
24. Huynen, M.A., Gutell, R., Konings, D.A.M., 1997. Assessing the reliability of RNA folding using statistical mechanics. J. Mol. Biol 267, 1104-1112.
25. Huynen, M.A., Perelson, A.S., Vieira, W.A., Stadler, P.F., 1996. Base pairing probabilities in a complete HIV-1 RNA. J. Comp. Biol 3, 253-274.
26. Jackson, R.J., Kaminski, A., 1995. Internal initiation of translation in eukaryotes: the picornavirus paradigm and beyond. RNA 1, 985-1000.
27. Konings, D., Gutell, R., 1995. A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA 1, 559-574.
28. Konings, D.A.M., Hogeweg, P., 1989. Pattern analysis of RNA secondary structure, similarity and consensus of minimal-energy folding. J. Mol. Biol 207, 597-614.
29. Le, S.-Y., Chen, J.-H., Currey, K., Maizel, J., 1988. A program for predicting significant RNA secondary structures. Comp. Appl. Biosci 4, 153-159.
30. Le, S.Y., Chen, J.H., Sonenberg, N., Maizel Jr., J.V., 1993. Conserved tertiary structural elements in the 5′ nontranslated region of cardiovirus, aphthovirus and hepatitis A virus RNAs. Nucl. Acids Res 21, 2445-2451.
31. Lück, R., Steger, G., Riesner, D., 1996. Thermodynamic prediction of conserved secondary structure: Application to the RRE element of HIV, the tRNA-like element of CMV, and the mRNA of prion protein. J. Mol. Biol 258, 813-826.
32. Mandl, C.W., Holzmann, H., Meixner, T., Rauscher, S., Stadler, P.F., Allison, S.L., Heinz, F.X., 1998. Spontaneous and engineered deletions in the 3′-noncoding region of tick-borne encephalitis virus: construction of highly attenuated mutants of flavivirus. J. Virology 72, 2132-2140.
33. Mann, D., Mikaelian, I., Zemmel, R., Green, S., Lowe, A., Kimura, T., Singh, M., Butler, P., Gait, M., Karn, J., 1994. A molecular rheostat. Co-operative rev binding to stem I of the rev-response element modulates human immunodeficiency virus type-1 late gene expression. J. Mol. Biol 241, 193-207.
34. McCaskill, J.S., 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119.
35. Michel, F., Westhof, E., 1990. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol 216, 585-610.
36. Mironov, A.A., Dyakonova, L.P., Kister, A.E., 1985. A kinetic approach to the prediction of RNA secondary structures. Journal of Biomolecular Structure and Dynamics 2, 953.
37. Monath, T.P., Heinz, F.X., 1996. Flaviviruses. In: Fields, B.N., Knipe, D.M., Howley, P.M., Chanock, R.M., Melnick, J.L., Monath, T.P., Roizmann, B., Straus, S.E. (Eds.), Fields Virology, 3rd ed. Lippincott-Raven, Philadelphia, pp. 961-1034.
38. Morgenstern, B., Frech, K., Dress, A.W.M., Werner, T., 1998. DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics 14, 290-294.
39. Paradigon, N.P.V., Girard, M., Bouloy, M., 1982. Panhandles and hairpin structures at the termini of germiston virus RNAs (bunyavirus). Virology 122, 191-197.
40. Nussinov, R., Piecznik, G., Griggs, J.R., Kleitman, D.J., 1978. Algorithms for loop matching. SIAM J. Appl. Math 35 (1), 68-82.
41. Olsthoorn, R.C.L., Garde, G., Dayhuff, T., Atkins, J.F., van Duin, J., 1995. Nucleotide sequence of a single-stranded RNA phage from pseudomonas aeruginosa: Kinship to coliphages and conservation of regulatory RNA structures. Virology 206, 611-625.
42. Pilipenko, E.V., Blinov, V.M., Romanova, L.I., Sinyakov, A.N., Maslova, S.V., Agol, V.I., 1989. Conserved structural domains in the 5′-untranslated region of picornaviral genomes: an analysis of the segment controlling translation and neurovirulence. Virology 168, 201-209.
43. Proutski, V., Gaunt, M.W., Gould, E.A., Holmes, E.C., 1997a. Secondary structure of the 3′ untranslated region of yellow fever virus: implications for virulence, attenuation and vaccine development. J. Gen. Virol 78, 1543-1549.
44. Proutski, V., Gould, E.A., Holmes, E.C., 1997b. Secondary structure of the 3′ untranslated region of flaviviruses: similarities and differences. Nucl. Acids Res 25, 1195-1202.
45. Rauscher, S., Flamm, C., Mandl, C., Heinz, F.X., Stadler, P.F., 1997. Secondary structure of the 3′-non-coding region of flavivirus genomes: comparative analysis of base pairing probabilities. RNA 3, 779-791.
46. Rivera, V.M., Welsh, J.D., Maizel Jr, J.V., 1988. Comparative sequence analysis of the 5′ noncoding region of the enteroviruses and rhinoviruses. Virology 165, 42-50.
47. Sankoff, D., 1985. Simultaneous solution of the RNA folding, alignment, and protosequence problems. SIAM J. Appl. Math 45, 810-825.
48. Schmaljohn, C.S., Jennings, G.B., Hay, J., Dalrymple, J.M., 1986. Coding strategy of the S genome segment of hantaan virus. Virology 155, 633-643.
49. Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L., 1994. From sequences to shapes and back: a case study in RNA secondary structures. Proc. Royal Society London B 255, 279-284.
50. Shi, P.-Y., Brinton, M.A., Veal, J.M., Zhong, Y.Y., Wilson, W.D., 1996. Evidence for the existence of a pseudoknot structure at the 3′ terminus of the flavivirus genomic RNA. Biochemistry 35, 4222-4230.
51. Specht, T., Wolters, J., Erdmann, V.A., 1991. Compilation of 5S rRNA and 5S rRNA gene sequences. Nucl. Acids Res. (Supplem.) 19, 2189-2191 http://userpage.chemie.fu-berlin.de/fb_chemie/ibc/agerdmann/5S_rRNA.html.
52. Tabaska, J.E., Stormo, G.D., 1997. Automated alignment of RNA sequences to pseudoknotted structures. In: Gaasterland, T., Karp, P., Karplus, K., Ouzounis, C., Sander, C., Valencia, A. (Eds.), Proceedings of the ISMB-97. AAAI Press, Menlo Park, CA, pp. 311-318.
53. Tanaka, T, Kato, N., Cho, M.-J., Sugiyama, K., Shimotohno, K., 1996. Structure of the 3′ terminus of the hepatitis C virus genome. J. Virol 70, 3307-3312.
54. Thompson, J.D., Higgs, D.G., Gibson, T.J., 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucl. Acids. Res 22, 4673-4680.
55. Wang, K., Choo, Q., Weiner, A., Ou, J., Najarian, R., Thayer, R., Mullenbach, G., Denniston, K., Gerin, J., Houghton, M., 1986. Structure, sequence and expression of the hepatitis delta (delta) viral genome. Nature 323 (6088), 508-514.
56. Waterman, M.S., 1978. Secondary structure of single-stranded nucleic acids. Adv. Math. Suppl. Studies 1, 167-212.
57. Weiser, B., Noller, H., 1995. XRNA. ftp://fangio.ucsc.edu/ pub/XRNA/. (Public Domain Software).
58. Wills, P.R., Hughes, A.J., 1990. Stem loops in HIV and prion protein mRNAs. J. AIDS 3, 95-97.
59. Winker, S., Overbeek, R., Woese, C.R., Olsen, G.J., Pfluger, N., 1990. Structure detection through automated covariance search. Comput. Appl. Biosci 6, 365-371.
60. Wuchty, S., Fontana, W., Hofacker, I.L., Schuster, P., 1999. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49, 145-165.
61. Zuker, M., 1989. The use of dynamic programming algorithms in RNA secondary structure prediction. In: Waterman, M.S. (Ed.), Mathematical Methods for DNA Sequences. CRC Press, Boca Roton, pp. 159-184.
62. Zuker, M., Stiegler, P., 1981. Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res 9, 133-148.