Pseudoknot-dependent translational coupling in repBA genes of the IncB plasmid pMU720 involves reinitiation

Journal of Bacteriology

Volumn 184, Issue 20, 2002, Pages 5772-5780

  Praszkier, J ^a   Pittard, A J ^a  

^a UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; GENE PRODUCT; PROTEIN REPA; PROTEIN REPBA; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; GENE REPLICATION; GENE SEQUENCE; NONHUMAN; PLASMID; PLASMID PMU720; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RIBOSOME; SEQUENCE ANALYSIS; TRANSLATION REGULATION;

BACTERIAL PROTEINS; BASE PAIRING; BASE SEQUENCE; CODON, INITIATOR; CODON, TERMINATOR; DNA HELICASES; DNA REPLICATION; DNA-BINDING PROTEINS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; MUTATION; PLASMIDS; PROTEIN BIOSYNTHESIS; PROTEINS; RIBOSOMES; RNA, BACTERIAL; RNA, MESSENGER; TRANS-ACTIVATORS;

EID: 0036786920     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.184.20.5772-5780.2002     Document Type: Article

References (43)

1. Adhin, M. R., and J. van Duin. 1990. Scanning model for translational reinitiation in eubacteria. J. Mol. Biol. 213:811-818.
2. Asano, K., C. Hama, S.-I. Inoue, H. Moriwaki, and K. Mizobuchi. 1999. The plasmid ColIb-P9 antisense Inc RNA controls expression of the RepZ replication protein and its positive regulator repY with different mechanisms. J. Biol. Chem. 274:17924-17933.
3. 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.
4. Asano, K., and K. Mizobuchi. 1998. Copy number control of IncIα plasmid ColIb-P9 by competition between pseudoknot formation and antisense RNA binding at a specific RNA site. EMBO J. 17:5201-5213.
5. Asano, K., and K. Mizobuchi. 1998. An RNA pseudoknot as the molecular switch for translation of the repZ gene encoding the replication initiator of IncIα plasmid ColIb-P9. J. Biol. Chem. 273:11815-11825.
6. Asano, K., and K. Mizobuchi. 2000. Structural analysis of late intermediate complex formed between plasmid ColIb-P9 Inc RNA and its target RNA. J. Biol. Chem. 275:1269-1274.
7. 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.
8. Asano, K., T. Niimi, S. Yokoyama, and K. Mizobuchi. 1998. Structural basis for binding of the plasmid ColIb-P9 antisense Inc RNA to its target RNA with the 5′-rUUGGCG-3′ motif in the loop sequence. J. Biol. Chem. 19: 11826-11838.
9. Athanasopoulos, V. 1999. Analysis of replication control in IncL/M plasmids. Ph.D. dissertation. The University of Melbourne, Melbourne, Australia.
10. Athanasopoulos, V., J. Praszkier, and A. J. Pittard. 1995. The replication of an IncL/M plasmid is subject to antisense control. J. Bacteriol. 177:4730-4741.
11. Athanasopoulos, V., J. Praszkier, and A. J. Pittard. 1999. Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid. J. Bacteriol. 181:1811-1819.
12. Berkhout, B., R. A. Kastelein, and J. van Duin. 1985. Translational interference at overlapping reading frames in prokaryotic messenger RNA. Gene 37:171-179.
13. Berkhout, B., B. F. Schmidt, A. van Strien, J. van Boom, J. van Westrenen, and J. van Duin. 1987. Lysis gene of bacteriophage MS2 is activated by translation termination at the overlapping coat gene. J. Mol. Biol. 195:517-524.
14. Bird, P. I., and J. Pittard. 1983. Demonstration of a third incompatibility function on plasmids already incompatible with group P and group 1 plasmids. Plasmid 9:191-200.
15. Brink, M. F., M. P. Verbeet, and H. A. de Boer. 1995. Specialized ribosomes: highly specific translation in vivo of a single targeted mRNA species. Gene 156:215-222.
16. Das, A., and C. Yanofsky. 1984. A ribosome binding site sequence is necessary for efficient expression of the distal gene of a translationally-coupled gene pair. Nucleic Acids Res. 12:4757-4768.
17. de Smit, M. H. 1998. Translational control by mRNA structure in eubacteria: molecular biology and physical chemistry, p. 495-540. In R. W. Simons and M. Grunberg-Manago (ed.), RNA structure and function. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
18. Draper, D. E., T. C. Gluick, and P. J. Schlax. 1998. Pseudoknots, RNA folding, and translational regulation, p. 415-436. In R. W. Simons and M. Grunberg-Manago (ed.), RNA structure and function. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
19. Govantes, F., E. Andujar, and E. Santero. 1998. Mechanism of translational coupling in the nifLA operon of Klebsiella pneumoniae. EMBO J. 17:2368-2377.
20. Hui, A., and H. de Boer. 1987. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. Proc. Natl. Acad. Sci. USA 84:4762-4766.
21. Hui, A., P. Jhurani, and H. A. de Boer. 1987. Directing ribosomes to a single mRNA species: method to study ribosomal RNA mutations and their effects on translation of a single messenger in Escherichia coli. Methods Enzymol. 153:432-452.
22. Kieny, M. P., R. Lathe, and J. P. Lecocq. 1983. New versatile cloning and sequencing vectors based on bacteriophage M13. Gene 26:91-99.
23. Mathews, D. H., J. Sabina, M. Zuker, and D. H. Turner. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary, structure. J. Mol. Biol. 288:911-940.
24. Messing, J. 1993. New M13 vectors for cloning. Methods Enzymol. 101:20-78.
25. Miller, J. H. 1972. Experiments in molecular genetics, p. 352-355. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
26. Monod, J., G. Cohen-Bazire, and M. Cohen. 1951. Sur la biosynthèse de la β-galactosidase (lactase) chez Escherichia coli. La specificité de l'induction. Biochim. Biophys. Acta 7:585-599.
27. Pavlov, M. Y., D. V. Freistroffer, J. MacDougall, R. H. Buckingham, and M. Ehrenberg. 1997. Fast recycling of Escherichia coli ribosomes requires both ribosome recycling factor (RRF) and release factor RF3. EMBO J. 16:4134-4141.
28. Praszkier, J., P. Bird, S. Nikoletti, and A. J. Pittard. 1989. Role of countertranscript RNA in the copy number control system of an IncB miniplasmid. J. Bacteriol. 171:5056-5064.
29. 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.
30. Sambrook, J., and D. W. Russell (ed.). 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
31. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
32. Schmidt, B. F., B. Berkhout, G. P. Overbeek, A. van Strien, and J. van Duin. 1987. Determination of the RNA secondary structure that regulates lysis gene expression in bacteriophage MS2. J. Mol. Biol. 195:505-516.
33. Schottel, J. L., J. J. Sninsky, and S. N. Cohen. 1984. Effects of alterations in the translation control region on bacterial gene expression: use of cat gene constructs transcribed from the lac promoter as a model system. Gene 28:177-193.
34. 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.
35. Siemering, K. R., J. Praszkier, and A. J. Pittard. 1994. Mechanism of binding of the antisense and target RNAs involved in the regulation of IncB plasmid replication. J. Bacteriol. 176:2677-2688.
36. Spanjaard, R. A., and J. van Duin. 1989. Translation reinitiation in the presence and absence of a Shine and Dalgarno sequence. Nucleic Acids Res. 17:5501-5507.
37. Springer, M., C. Portier, and M. Grunberg-Manago. 1998. RNA mimicry in the translational apparatus, p. 377-413. In R. W. Simons and M. Grunberg-Manago (ed.), RNA structure and function. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
38. 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.
39. Wilson, I. W. 1995. Molecular analysis of the replication control system of IncB plasmids. Ph.D. dissertation. The University of Melbourne, Melbourne, Australia.
40. Wilson, I. W., J. Praszkier, and A. J. Pittard. 1993. Mutations affecting pseudoknot control of the replication of B group plasmids. J. Bacteriol. 175:6476-6483.
41. 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.
42. Yu, J. S., S. Madison-Antenucci, and D. A. Steege. 2001. Translation at higher than an optimal level interferes with coupling at an intercistronic junction. Mol. Microbiol. 42:821-834.
43. Zuker, M., D. H. Mathews, and D. H. Turner. 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide, p. 11-43. In J. A. C. Barciszewski and B. F. C. Clark (ed.), RNA biochemistry and biotechnology. Kluwer Academic Publishers, Dordrecht, The Netherlands.