Regulation of DNA replication: "target" determinant of the replication control elements of plasmid R6-5 lies within a control element gene.

Danbara, Hirofumi; Brady, Ged; Timmis, J. K.; Timmis, Kenneth N.

doi:10.1073/pnas.78.8.4699

Cited by 30 publications

(30 citation statements)

References 36 publications

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“…Previous studies of the IncFII, ColEl, and IncIl antisense molecules have shown that nucleotides in the hairpin loops are important for effective antisense function (1,5,10,20,26,40,48). When sequences in the 6-base hairpin loop of the IncB RNA I were analyzed, substitution of any nucleotide in the 3-base sequence G37-C38-C39 was found to have a profound effect on the ability of RNA I to inhibit repA-lacZ expression.…”

Section: Discussionmentioning

confidence: 99%

“…In each case, both the antisense RNAs and their target regions are capable of assuming stable stem and loop structures (22,28,42,53). When mutant plasmids isolated on the basis of increased copy number or altered incompatibility specificity were analyzed, many were found to contain a base substitution within a region of the antisense gene coding for a hairpin loop (5,10,20,40,48). This genetic evidence led to the suggestion that base pairing between complementary hairpin loops plays an important role in an initial "kissing" interaction between the antisense and target RNAs.…”

mentioning

confidence: 99%

“…For the IncFII, IncIl, and ColEl groups, genetic studies of the loop-loop kissing interaction between antisense and target molecules have largely been restricted to the analysis of mutant plasmids with distinct and selectable phenotypes (1,5,10,20,26,40,48). In this paper, we describe the use of site-directed mutagenesis to systematically evaluate the importance of each nucleotide in the loop and upper stem of RNA I and RNA II to the loop-loop kissing interaction between the two molecules.…”

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confidence: 99%

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Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication

1993

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Physical analysis of RNA I, the small antisense RNA which regulates the replication of IncB miniplasmid pMU720, showed that it is a highly structured molecule containing an imperfectly paired stem closed by a 6-base hairpin loop. Mutational studies revealed that a 3-base sequence in the hairpin loop is critical to the interaction between RNA I and its complementary target in the RepA mRNA (RNA II). Furthermore, a 2-base interior loop in the upper stem was found to play an important role in facilitating effective binding between RNA I and RNA II. From these analyses, a model describing the molecular mechanism of binding between RNA I and RNA II is proposed.

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Section: Discussionmentioning

confidence: 99%

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Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication

1993

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“…This RNA, which is identical among R100, Rl, and R6, is transcribed within the leader transcript of repAl, but in the opposite direction. The target of inc RNA is known to be the repAl mRNA in the region of complementarity (10,44,45). By analogy to RepFIIA, the sequence of RepFIC shows the existence of a similar RNA at an equivalent position (Fig.…”

Section: Rg1mentioning

confidence: 99%

Nucleotide sequence analysis of RepFIC, a basic replicon present in IncFI plasmids P307 and F, and its relation to the RepA replicon of IncFII plasmids

Saadi¹,

Maas²,

Hill³

et al. 1987

J Bacteriol

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RepFIC is a basic replicon of IncFI plasmid P307 which is located within a 3.09-kilobase SmaI fragment. The nucleotide sequence of this region has been determined and shown to be homologous with the RepFIIA replicon of IncFII plasmids. The two replicons share three homologous regions, HRI, HRII, and HRIII, which are flanked by two nonhomologous regions, NHRI and NHRII. A comparison of coding regions reveals that the two replicons have several features in common. RepFIC, like RepFIIA, codes for a repA2 protein with its amino-terminal codons in HRI and its carboxy-terminal codons in NHRI. Although the codons for the repAl proteins are located in NHRII, the DNA region containing a putative promoter, ribosomal binding site, and initiation codons is located in HRII. This region also codes for an inc RNA. There are nine base-pair differences between the inc RNA of RepFIIA and that of RepFIC, and as a result, RepFIC and RepFIIA replicons are compatible. An EcoRI fragment from the F plasmid which shows homology with RepFIC of P307 has also been sequenced. This fragment contains only a portion of RepFIC, including the genes for the putative repA2 protein and inc RNA. The region coding for a putative repAl protein is interrupted by the transposon TnlO00 and shows no homology with the repAl region of RepFIA and RepFIC of P307. Our comparative and structural analyses suggest that RepFIC and RepFIIA, although different, have a similar replication mechanism and thus can be assigned to the same replicon family, which we designate the RepFIA family.

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“…In each case, both the antisense and target RNAs assume stable stem and loop structures (11,17,29,37). Genetic analyses of mutant ColEl (9,33) and IncFII (5,6,27) plasmids led to the suggestion that the specificity of the interaction between the antisense and target RNAs resides in the single-stranded loops of the respective molecules. This notion was supported by observations that even single base substitutions in these loops result in significantly altered antisense-target binding rates in vitro (18,30).…”

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confidence: 99%

Mechanism of binding of the antisense and target RNAs involved in the regulation of IncB plasmid replication

1994

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The replication frequency of the IncB miniplasmid pMU720 is dependent upon the expression of the repA gene. Binding of a small, highly structured, antisense RNA (RNA I) to its complementary target in the RepA mRNA (RNA II) inhibits repA expression and thus regulates replication. Analyses of binding of RNA I to RNA II indicated that the reaction consists of three major steps. The first step, initial kissing complex formation, involves base pairing between complementary sequences in the hairpin loops of RNA I and RNA II. The second step is facilitated by interior loop structures in the upper stems of RNA I and RNA II and involves intrastrand melting and interstrand pairing of the upper stem regions to form an extended kissing complex. This complex was shown to be sufficient for inhibition ofrepA expression. The third step involves stabilization of the extended kissing complex by pairing between complementary single-stranded tail regions of RNA I and RNA II. Thus, the final product of RNA I-RNA II binding is not a full duplex between the two molecules.

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Regulation of DNA replication: "target" determinant of the replication control elements of plasmid R6-5 lies within a control element gene.

Cited by 30 publications

References 36 publications

Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication

Interaction between the antisense and target RNAs involved in the regulation of IncB plasmid replication

Nucleotide sequence analysis of RepFIC, a basic replicon present in IncFI plasmids P307 and F, and its relation to the RepA replicon of IncFII plasmids

Mechanism of binding of the antisense and target RNAs involved in the regulation of IncB plasmid replication

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