Importance of structural differences between complementary RNA molecules to control of replication of an IncB plasmid

Journal of Bacteriology

Volumn 179, Issue 3, 1997, Pages 742-753

  Wilson, I W ^a,b   Siemering, K R ^a,c   Praszkier, J ^a   Pittard, A J ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b GEOPHYSICAL LABORATORY   (United States)

^c MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; DNA; MESSENGER RNA; PROTEIN;

ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENE; GENE EXPRESSION; MUTATION; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA BINDING; RNA TRANSLATION;

EID: 0031019457     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.179.3.742-753.1997     Document Type: Article

References (39)

1. Asano, K., A, Kato, H. Moriwaki, C. Hama, K. Shiba, and K. Mizobuchi. 1991. Positive and negative regulations of plasmid ColIb-P9 repZ gene expression at the translational level. J. Biol. Chem. 266:3774-3781.
2. Asano, K., H. Moriwaki, and K. Mizobuchi. 1991. An induced mRNA secondary structure enhances repZ translation in plasmid ColIb-P9. J. Biol. Chem. 266:24549-24556.
3. Athanasopoulos, V., J. Praszkier, and A. J. Pittard. 1995. The replication of iin IncL/M plasmid is subject to antisense control. J. Bacteriol. 177:4730-4741.
4. Athanusopoulos, V., J. Praszkier, and A. J. Pittard. 1996. Unpublished data.
5. Bird, P. I., and J. Pittard. 1983. Demonstration of a third incompatibility function on plasmids already incompatible with group P and group I plasmids. Plasmid 9:191-200.
6. Craig, M. E., D. M. Crothers, and P. Doty. 1971. Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. Mol. Biol. 62:383-401.
7. Davey, R. B. D., P. I. Bird, S. M. Nikoletti, J. Praszkier, and J. Pittard. 1984. The use of mini-Gal plasmids for the rapid incompatibility grouping of conjugative R plasmids. Plasmid 11:234-242.
8. Gil, D., and J.-P. Bouché. 1991. ColE1-type vectors with fully repressible replication. Gene 105:17-22.
9. Groebe, D. R., and O. C. Uhlenbeck. 1988. Characterization of RNA hairpin loop stability. Nucleic Acids Res. 16:11725-11735.
10. Hjalt, T., and E. G. H. Wagner. 1992. The effect of loop size in antisense and target RNAs on the efficiency of antisense RNA control. Nucleic Acids Res. 20:6723-6732.
11. Hjalt, T. H., and E. G. H. Wagner. 1995. Bulged-out nucleotides in an antisense RNA are required for rapid target RNA binding in vitro and inhibition in vivo. Nucleic Acids Res. 23:580-587.
12. Jaeger, J. A., D. H. Turner, and M. Zuker. 1989. Improved predictions of secondary structures for RNA. Proc. Natl. Acad. Sci. USA 86:7706-7710.
13. Jaeger, J. A., D. H. Turner, and M. Zuker. 1990. Predicting optimal and suboptimal secondary structures for RNA. Methods Enzymol. 183:281-306.
14. Kieny, M. P., R. Lathe, and J. P. Lecocq. 1983. New versatile cloning and sequencing vectors based on bacteriophage M13. Gene 26:91-99.
15. Messing, J. 1983. New M13 vectors for cloning. Methods Enzymol. 101:20-78.
16. Miller, J. H. 1972. Experiments in molecular genetics, p. 352-355. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
17. Monod, J., G. Cohen-Bazire, and M. Cohen. 1951. Sur la biosynthése de la β-gulactosidase (lactase) chez Escherichia coli. La specificité de l'induction. Biochim Biophys. Acta 7:585-599.
18. Nikoletti, S., P. Bird, J. Praszkier, and J. Pittard. 1988. Analysis of the incompatibility determinants of I-complex plasmids. J. Bacteriol. 170:1311-1318.
19. Persson, C., E. G. H. Wagner, and K. Nordström. 1988. Control of replication of plasmid R1: kinetics of in vitro interaction between the antisense RNA, CopA, and its target, CopT. EMBO J. 7:3279-3288.
20. Pörschke, D., and M. Eigen. 1971. Co-operative non-enzymic base recognition. III. Kinetics of the helix-coil transition of the oligoribouridylic · oligori- boadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J. Mol. Biol. 62:361-381.
21. Praszkier, J., P. Bird, S. Nikoletti, and A. J. Pittard. 1989. Rule of counter-transcript RNA in the copy number control system of an IncB miniplasmid. J. Bacteriol. 171:5056-3064.
22. Praszkier, J., P. Bird, K. Siemering, and J. Pittard. 1991. Comparative analysis of the replication regions of the IncB, IncK, and IncZ plasmids. J. Bacteriol. 173:2393-2397.
23. Praszkier, J., I. W. Wilson, and A. J. Pittard. 1992. Mutations affecting translational coupling between the rep genes of an IncB miniplasmid. J. Bacteriol. 174:2376-2383.
24. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
25. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
26. Santa Lucia, J., Jr., R. Kierzek, and D. H. Turner. 1991. Stabilities of consecutive A · C, C · C, G · G, U · C, and U · U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U · U and C · C+ pairs. Biochemistry 30:8242-8251.
27. Siemering, K. R., J. Praszkier, and A. J. Pittard. 1993. Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication. J. Bacteriol. 175:2895-2906.
28. Siemering, K. R., J. Praszkier, and A. J. Pittard. 1994. Mechanism of binding of the antisense and target RNAs involved in the regulation of the IncB plasmid replication. J. Bacteriol. 176:2677-2688.
29. Sutcliffe, J. G. 1979. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harbor Symp. Quant. Biol. 43:77-90.
30. Tinoco, I., P. N. Borer, B. Dengler, M. D. Levine, O. C. Uhlenbeck, D. M. Crothers, and J. Gralla. 1973. Improved estimation of secondary structure in ribonucleic acids. Nature (London) New Biol. 246:40-41.
31. Tomizawa, J. 1984. Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript. Cell 38:861-870.
32. Vandeyar, M. A., M. P. Weiner, C. J. Hutton, and C. A. Batt. 1988. A simple and rapid method for the selection of oligodeoxynucleotide-directed mutants. Gene 65:129-133.
33. Wagner, E. G. H., and K. Nordström. 1986. Structural analysis of an RNA molecule involved in replication control of plasmid R1. Nucleic Acids Res. 14:2523-2538.
34. Wilson, I. W. 1995. Molecular analysis of the replication control system of IncB plasmids. Ph.D. thesis. The University of Melbourne, Parkville, Australia.
35. Wilson, I. W., P. J., and A. J. Pittard. 1993. Mutations affecting pseudoknot control of the replication of B group plasmids. J. Bacteriol. 175:6476-6483.
36. Wilson, I. W., J. Praszkier, and A. J. Pittard. 1994. Molecular analysis of RNAI control of repB translation in IncB plasmids. J. Bacteriol. 176:6497-6508.
37. Glu as indicated by different nuclase digestion patterns. J. Biol. Chem. 254:9608-9616.
38. Yang, J., S. Ganesan, J. Sarsero, and A. J. Pittard. 1993. A genetic analysis of various functions of the TyrR protein of Escherichia coli. J. Bacteriol. 175:1767-1776.
39. Zuker, M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244:48-52.