Control of replication in I-complex plasmids

Adhin, 1990, Scanning model for translational reinitiation in eubacteria, J. Mol. Biol., 213, 811, 10.1016/S0022-2836(05)80265-7

Asano, 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, 10.1093/emboj/17.17.5201

Asano, 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, 10.1074/jbc.273.19.11815

Asano, 2000, Structural analysis of late intermediate complex formed between plasmid ColIb-P9 Inc RNA and its target RNA, J. Biol. Chem., 275, 1269, 10.1074/jbc.275.2.1269

Asano, 1991, An induced mRNA secondary structure enhances repZ translation in plasmid ColIb-P9, J. Biol. Chem., 266, 24549, 10.1016/S0021-9258(18)54264-2

Asano, 1998, Structural basis for binding of the plasmid ColIb-P9 antisense Inc RNA to its target RNA with the5′-rUUGGCG-3′ motif in the loop sequence, J. Biol. Chem., 19, 11826, 10.1074/jbc.273.19.11826

Asano, 1991, Positive and negative regulations of plasmid CoLIb-P9 repZ gene expression at the translational level, J. Biol. Chem., 266, 3774, 10.1016/S0021-9258(19)67862-2

Ashraf, 1999, The uridine in U-turn: contributions to tRNA-ribosomal binding, Rna, 5, 503, 10.1017/S1355838299981931

Athanasopoulos, V., 1999. Analysis of replication control in IncL/M plasmids. Ph.D. Thesis, Department of Microbiology and Immunology, The University of Melbourne, Australia

Athanasopoulos, 1995, The replication of an IncL/M plasmid is subject to antisense control, J. Bacteriol., 177, 4730, 10.1128/jb.177.16.4730-4741.1995

Athanasopoulos, 1999, Analysis of elements involved in pseudoknot-dependent expression and regulation of the repA gene of an IncL/M plasmid, J. Bacteriol., 181, 1811, 10.1128/JB.181.6.1811-1819.1999

Betteridge, 2003, Interaction of the initiator protein of an IncB plasmid with its origin of DNA replication, J. Bacteriol., 185, 2210, 10.1128/JB.185.7.2210-2218.2003

Betteridge, 2004, Role of RepA and DnaA proteins in the opening of the origin of DNA replication of an IncB plasmid, J. Bacteriol., 186, 3785, 10.1128/JB.186.12.3785-3793.2004

Blomberg, 1992, Replication control of plasmid R1: RepA synthesis is regulated by CopA RNA through inhibition of leader peptide translation, EMBO J., 11, 2675, 10.1002/j.1460-2075.1992.tb05333.x

Brantl, 1994, Antisense RNA-mediated transcriptional attenuation occurs faster than stable antisense/target RNA pairing: an in vitro study of plasmid pIP501, EMBO J., 13, 3599, 10.1002/j.1460-2075.1994.tb06667.x

Chen, 1994, Determination of the optimal aligned spacing between the Shine–Dalgarno sequence and the translational codon of Escherichia coli mRNAs, Nucleic Acids Res., 22, 4953, 10.1093/nar/22.23.4953

Craig, 1971, Relaxation kinetics of dimer formation by self complementary oligonucleotides, J. Mol. Biol., 62, 383, 10.1016/0022-2836(71)90434-7

del Solar, 1998, Replication and control of circular bacterial plasmids, Microbiol. Mol. Biol. Rev., 62, 434, 10.1128/MMBR.62.2.434-464.1998

Dong, 1985, Regulation of transcription of the repA1 gene in the replication control region of the Inc FII plasmid NR1 by gene dosage of the repA2 transcription repressor protein, J. Bacteriol., 161, 544, 10.1128/JB.161.2.544-551.1985

Eguchi, 1990, Complex formed by complimentary RNA stem–loops and its stabilization by a protein: function of ColE1 Rom protein, Cell, 60, 199, 10.1016/0092-8674(90)90736-X

Franch, 2000, U-turns and regulatory RNAs, Curr. Opin. Microbiol., 3, 159, 10.1016/S1369-5274(00)00069-2

Franch, 1999, Antisense RNA regulation in prokaryotes: rapid RNA/RNA interaction facilitated by a general U-turn loop structure, J. Mol. Biol., 294, 1115, 10.1006/jmbi.1999.3306

Grosjean, 1976, Studies of the complex between transfer RNAs with complementary anticodons. I. Origins of enhanced affinity between complementary triplets, J. Mol. Biol., 103, 499, 10.1016/0022-2836(76)90214-X

Hama, 1990, Role of leader peptide synthesis in repZ gene expression of the ColIb-P9 plasmid, J. Biol. Chem., 265, 10666, 10.1016/S0021-9258(18)86998-8

Hama, 1990, Organization of the replication control region of plasmid ColIb-P9, J. Bacteriol., 172, 1983, 10.1128/jb.172.4.1983-1991.1990

Kim, 1986, Copy-number of a broad host-range plasmid R1162 is regulated by a small RNA, Nucleic Acids Res., 14, 8027, 10.1093/nar/14.20.8027

Kolb, 2001, Four-way junctions in antisense RNA–mRNA complexes involved in plasmid replication control: a common theme?, J. Mol. Biol., 309, 605, 10.1006/jmbi.2001.4677

Kolb, 2000, An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment, RNA, 6, 311, 10.1017/S135583820099215X

Kolb, 2000, Progression of a loop–loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA, EMBO J., 19, 5905, 10.1093/emboj/19.21.5905

Light, 1983, Post-transcriptional control of expression of the repA1 gene of plasmid R1 mediated by a small RNA molecule, EMBO J., 2, 93, 10.1002/j.1460-2075.1983.tb01387.x

Light, 1985, Transcription and its regulation in the basic replicon region of plasmid R1, Mol. Gen. Genet., 198, 503, 10.1007/BF00332947

Masukata, 1986, Control of primer formation for ColE1 plasmid replication. Conformational change of the primer transcript, Cell, 44, 125, 10.1016/0092-8674(86)90491-5

Mathews, 1999, Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, J. Mol. Biol., 288, 911, 10.1006/jmbi.1999.2700

Nikoletti, 1988, Analysis of the incompatibility determinants of I-complex plasmids, J. Bacteriol., 170, 1311, 10.1128/jb.170.3.1311-1318.1988

Novick, 1989, pT181 plasmid replication is regulated by a countertranscript-driven transcriptional terminator, Cell, 59, 395, 10.1016/0092-8674(89)90300-0

Persson, 1990, Control of replication of plasmid R1: formation of an initial transient complex is rate-limiting for antisense RNA–target RNA pairing, EMBO J., 9, 3777, 10.1002/j.1460-2075.1990.tb07591.x

Pörschke, 1971, Co-operative non-enzymic base recognition. III. Kinetics of the helix-coil transition of the oligoribouridylic–oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH, J. Mol. Biol., 62, 361, 10.1016/0022-2836(71)90433-5

Praszkier, 2002, Pseudoknot-dependent translational coupling in repBA genes of the IncB plasmid pMU720 involves reinitiation, J. Bacteriol., 184, 5772, 10.1128/JB.184.20.5772-5780.2002

Praszkier, 1992, Mutations affecting translational coupling between the rep genes of an IncB miniplasmid, J. Bacteriol., 174, 2376, 10.1128/jb.174.7.2376-2383.1992

Praszkier, 1989, Role of countertranscript RNA in the copy number control system of an IncB miniplasmid, J. Bacteriol., 171, 5056, 10.1128/jb.171.9.5056-5064.1989

Praszkier, 1991, Comparative analysis of the replication regions of the IncB, IncK, and IncZ plasmids, J. Bacteriol., 173, 2393, 10.1128/jb.173.7.2393-2397.1991

Pritchard, 1978, Control of DNA replication in bacteria, 1

Pritchard, 1969, Control of DNA synthesis in bacteria, Symp. Soc. Gen. Microbiol., 19, 263

Quigley, 1976, Structural domains of transfer RNA molecules, Science, 194, 796, 10.1126/science.790568

Schmidt, 1987, Determination of the RNA secondary structure that regulates lysis gene expression in bacteriophage MS2, J. Mol. Biol., 195, 505, 10.1016/0022-2836(87)90179-3

Shiba, 1990, Posttranscriptional control of plasmid ColIb-P9 repZ gene expression by a small RNA, J. Bacteriol., 172, 1992, 10.1128/jb.172.4.1992-1997.1990

Siemering, K.R., 1995. Interaction between the antisense and target RNAs involved in IncB plasmid replication. Ph.D. Thesis, Department of Microbiology, The University of Melbourne

Siemering, 1993, Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication, J. Bacteriol., 175, 2895, 10.1128/jb.175.10.2895-2906.1993

Siemering, 1994, Mechanism of binding of the antisense and target RNAs involved in the regulation of IncB plasmid replication, J. Bacteriol., 176, 2677, 10.1128/jb.176.9.2677-2688.1994

Slagter-Jager, 2003, Loop swapping in an antisense RNA/target RNA pair changes directionality of helix progression, J. Biol. Chem., 278, 35558, 10.1074/jbc.M304867200

Spanjaard, 1989, Translational reinitiation in the presence and absence of a Shine and Dalgarno sequence, Nucleic Acids Res., 17, 5501, 10.1093/nar/17.14.5501

Stougaard, 1982, Convergent transcription interferes with expression of the copy number control gene copA, from plasmid R1, EMBO J., 1, 323, 10.1002/j.1460-2075.1982.tb01168.x

Tomizawa, 1986, Control of ColE1 plasmid replication: binding of RNAI to RNAII and inhibition of primer formation, Cell, 47, 89, 10.1016/0092-8674(86)90369-7

Tomizawa, 1981, Inhibition of ColE1 RNA primer formation by a plasmid-specified small RNA, Proc. Natl. Acad. Sci. USA, 78, 1421, 10.1073/pnas.78.3.1421

Wilson, I.W., 1995. Molecular analysis of the replication control system of IncB Plasmids. Ph.D. Thesis, Department of Microbiology and Immunology, The University of Melbourne, Australia

Wilson, 1993, Mutations affecting pseudoknot control of the replication of B group plasmids, J. Bacteriol., 175, 6476, 10.1128/jb.175.20.6476-6483.1993

Wilson, 1994, Molecular analysis of RNAI control of repB translation in IncB plasmids, J. Bacteriol., 176, 6497, 10.1128/jb.176.21.6497-6508.1994

Wilson, 1997, Importance of structural differences between complementary RNA molecules to control of replication of an IncB plasmid, J. Bacteriol., 179, 742, 10.1128/jb.179.3.742-753.1997

Womble, 1985, Transcription of the replication control region of the IncFII R-plasmid NR1 in vitro and in vivo, J. Bacteriol., 181, 395

Wu, 1992, Expression of the repA1 gene of the IncFII plasmid NR1 is translationally coupled to expression of an overlapping leader peptide, J. Bacteriol., 174, 7620, 10.1128/jb.174.23.7620-7628.1992

Zuker, M., Mathews, D.H., Turner, D.H., 1999. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski, J.A.C., Clark, B.F.C. (Eds), RNA Biochemistry and Biotechnology. Kluwer Academic Publishers, pp. 11–43