Secondary structure model for the first three domains of Qβ RNA. Control of A-protein synthesis

Journal of Molecular Biology

Volumn 256, Issue 1, 1996, Pages 8-19

  Beekwilder, Jules ^a   Nieuwenhuizen, Rob ^a   Poot, Raymond ^a   Van Duin, Jan ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

Author keywords

Phylogenetic comparison; RNA coliphages; RNA replication; RNA secondary structure; Translational control

Indexed keywords

VIRUS RNA;

ARTICLE; BASE PAIRING; COLIPHAGE; MOLECULAR MODEL; MS2 VIRUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN SYNTHESIS REGULATION; RNA SEQUENCE; RNA STRUCTURE; SYSTEM ANALYSIS; TRANSLATION REGULATION;

EID: 0029911755     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0064     Document Type: Article

References (34)

1. Adhin, M. R., Avots, A., Berzin, V., Overbeek, G. P. & van Duin, J. (1990). Complete nucleotide sequence of the group I RNA bacteriophage fr. Biochim. Biophys. Acta, 1050, 104-109.
2. Barrera, I., Schuppli, D., Sogo, J. M. & Weber, H. (1993). Different mechanisms of recognition of bacteriophage Qβ plus and minus strand RNAs by Qβ replicase. J. Mol. Biol. 232, 512-521.
3. Beekwilder, M. J., Nieuwenhuizen, R. & van Duin, J. (1995). Secondary structure model for the last two domains of single-stranded RNA phage Qβ. J. Mol. Biol. 247, 903-917.
4. Biebricher, C. K. & Luce, R. (1993). Sequence analysis of RNA species synthesized by Qβ replicase without template. Biochemistry, 32, 4848-4854.
5. Chan, L., Zuker, M. & Jacobson, A. B. (1991). A computer method for finding common base paired helices in aligned sequences: application to the analysis of random sequences. Nucleic Acids Res. 19, 353-358.
6. Frohman, M. A. (1990). RACE: rapid amplification of cDNA ends. In PCR Protocols: A Guide to Methods and Applications, (Innis, M. A., Gelfand, D. H., Sninsky, J. J. & White, T. J., eds), pp. 28-38, Academic Press, San Diego, CA.
7. Furuse, K. (1987). Distribution of coliphages in the environment: general considerations. In: Phage Ecology (Goyal, S. M., Gerba, C. P. & Bitton, G., eds), pp. 87-124, Wiley & Sons, New York.
8. Furuse, K., Ando, A. & Watanabe, I. (1975). Isolation and grouping of RNA-phages. VII. A survey in Peru, Bolivia, Mexico, Kuwait, France, Australia and the United States of America. J. Keio Med. Soc. 52, 355-361.
9. Genetics Computer Group (1991). Program manual for the GCG package, version 7, Genetics Computer Group, Madison, WI.
10. Groeneveld, H., Thimon, K. & van Duin, J. (1995). Translational control of maturation protein synthesis in phage MS2: a role for the kinetics of RNA folding? RNA, 1, 79-88.
11. Gultyaev, A. P. (1991) The computer simulation of RNA folding involving pseudoknot formation. Nucleic Acids Res. 19, 2489-2494.
12. Havelaar, A. H., Furuse, K. & Hogeboom, W. M. (1986). Bacteriophages and indicator bacteria in human and animal faeces. J. Appl. Bacteriol. 60, 255-262.
13. Heus, H. A. & Pardi, A. (1991). Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science, 253, 191-194.
14. Hirashima, A., Inokuchi, Y., Hiragai, H., Furuse, K. and Watanabe, I. (1983). Biochemical characterization of RNA coliphage MX1. J. Gen. Virol. 64, 939-946.
15. Inokuchi, Y., Jacobson, A. B., Hirose, T., Inayama, S. & Hirashima, A. (1988). Analysis of the complete nucleotide sequence of the group IV coliphage SP. Nucl. Acids Res. 16, 6205-6221.
16. Jacobson, A. B. & Zuker, M. (1993). Structural analysis by energy dot plot of a large messenger RNA. J. Mol. Biol. 233, 261-269.
17. James, B. D., Olsen, G. J. & Pace, N. R. (1989). Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol. 180, 227-239.
18. Karnik, S. & Billeter, M. (1983). The lysis function of RNA bacteriophage Qβ is mediated by the maturation protein. EMBO J. 2, 1521-1526
19. Mekler, P. (1981). Determination of nucleotide sequence of the bacteriophage Qβ genome: organization and evolution of an RNA virus. PhD thesis, University of Zurich.
20. Miller, J. H., Ganem, D., Lu, P. & Schmitz, A. (1977). Genetic studies of the lac repressor. I. Correlation of mutational sites with specific amino acid residues: construction of a colinear gene-protein map. J. Mol. Biol. 109, 275-301.
21. Mills, D. R., Priano, C., Merz, P. & Binderow, B. R. (1990). Qβ RNA bacteriophage: mapping cis-acting elements within an RNA genome. J. Virol. 64, 3872-3881.
22. Olsthoorn, R. C. L., Licis, N. & van Duin J. (1994). Leeway and constraints in the forced evolution of a regulatory RNA helix. EMBO J. 13, 2660-2668.
23. 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.
24. Priano, C., Kramer, F. R. & Mills, D. R. (1987). Evolution of the RNA-coliphages: The role of secondary structures during RNA replication. Cold Spring Harbor Symp. Quant. Biol. 52, 321-339.
25. Reiss, J., Krawczak, M., Schloesser, M., Wagner, M. & Cooper, D. N. (1990). The effect of replication errors in the mismatch analysis of PCR-amplified DNA. Nucl. Acids Res. 18, 973-978.
26. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning, A Laboratory Manual. 2nd edit., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
27. Schuppli, D., Barrera, I. & Weber, H. (1995) Recognition elements on bacteriophage Qβ minus strand RNA that are essential for template activity with Qβ replicase. J. Mol. Biol. 243, 811-815.
28. Shiba, T. & Miyake, T. (1975). New type of infectious complex of E. coli RNA phage. Nature, 254, 157-158
29. Skripkin, E. A., Adhin, M. R., de Smit, M. H. & van Duin, J. (1990). Secondary structure of bacteriophage MS2. Conservation and biological significance. J. Mol. Biol. 211, 447-463.
30. Staples, D. H., Hindley, J., Billeter, M. A. & Weissmann, C. (1971). Localization of Qβ maturation cistron ribosome binding site. Nature New Biol. 234, 202-204.
31. Taniguchi, T., Palmieri, M. & Weissmann, C. (1978). Qβ DNA-containing hybrid plasmids give rise to Qβ phage formation in the bacterial host. Nature, 274, 223-228.
32. Tuerk, C., Gauss, P., Thermes, C., Groebe, D. R., Gayle, M., Guild, N., Stormo, G., d'Aubenton-Carafa, Y., Uhlenbeck, O. C., Tinoco, I., Jr, Brody, E. & Gold, L. (1988). CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. Natl Acad. Sci. USA, 85, 1364-1368.
33. 2) protein leads to cell lysis. Cell, 33, 877-885.
34. Zuker, M. (1989) On finding all suboptimal foldings of an RNA molecule. Science, 244, 48-52.