Chapter 3 : Plasmid Replication Control by Antisense RNAs

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This chapter reviews antisense-RNA-mediated regulation of plasmid replication. Antisense-RNA control in plasmid replication works through a negative control circuit: Antisense RNAs are constitutively synthesized and metabolically unstable. Antisense-RNA-mediated transcriptional attenuation is another mechanism, which has, so far, only been detected in plasmids of gram-positive bacteria (18 family and pT181 family). For antisense-RNA-controlled plasmids that replicate by the theta mechanism, the data on origin characterization and replication mechanism are briefly summarized in this chapter. A three-dimensional model of the N-terminal 63 amino acids (aa) of CopR was constructed, and amino acids involved in DNA binding and dimerization were localized: Arg29 and Arg34 within the HTH-motif are involved in specific recognition of the operator-DNA. Recently, the author showed experimentally that replication control mechanism principally functions in , albeit with a much lower efficiency than in or . The interaction between two highly structured antisense and sense RNAs, initiating by defined loop-loop contacts as shown for plasmid R1, is a recurrent one and valid for most cases of plasmid replication control. The degradation pathway of CopA has been studied in detail. A mechanism that involves RNA-RNA interactions in a manner that interferes with translation was also suggested for pC194 and pUBHO, two other RCR-type plasmids. The chapter talks about inhibition of primer formation and pseudoknot formation.

Citation: Brantl S. 2004. Plasmid Replication Control by Antisense RNAs, p 47-62. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch3

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DNA Synthesis
Genetic Elements
Antisense RNA
DNA Polymerase I
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Figure 1

Mechanisms of antisense-RNA-mediated plasmid copy-number control. Antisense RNAs are drawn in black, sense RNAs in gray. ORFs encoding essential replication initiator proteins are shown as hatched boxes, and ORFs encoding transcriptional repressor proteins are shown as checked boxes. Promoters are symbolized by black triangles and replication origins by black ovals. + indicates positive interaction, - indicates repression. Small black arrows symbolize the interaction between sense and antisense RNAs. (A) Transcriptional attenuation: plasmid pIP501. (Upper part) Working model on regulation of plP501 replication. The minimal replicon with the and genes is shown, separated by the 329-nt-long leader region (white). CopR represses transcription from the promoter pll and, at the same time, indirectly increases transcription initiation from the antisense promoter pill. The antisense RNA causes premature termination of (sense) RNA transcription at the attenuator (Lower part) Mechanism of transcriptional attenuation. For details, see text. Complementary sequence elements are designated A, B, a, and b. (B) Translatioi.nl inhibition. (Upper part) Inhibition of leader peptide translation: plasmid RI. Translation of the leader peptide (black box) is required for efficient translation. The CopB protein represses transcription from the but not from the promoter. Ribosomes are symbolized in black. (Lower part) Direct inhibition of translation: plasmid pMV158. The antisense RNA is complementary to the SD sequence and, therefore, directly inhibits ribosomc binding. The CopG protein represses transcription from the and from the promoter. (C) Inhibition of primer maturation: plasmid ColEl. (Upper part) Schematic representation of the minimal replicon. {Lower part) Mechanism of inhibition of primer maturation. Cross-hatched circle, RNA polymerase; black, newly synthesized DNA strand. For details, see text. (D) Inhibition of pseudoknot formation: plasmid ColIb-P9. (Upper part) The minimal replicon with the (leader peptide) (black box) and genes is shown. White, leader region of mRNA, (Lower part) Genes for and arc translationally coupled. On the mRNA, the SD sequence is exposed, whereas structure HI sequesters both the SD sequence (gray rectangle) and the 5′-rCGCC-3′ sequence (thick black line) and, thereby, translation. Inc (indicated by a bracket), region complementary to the antisense RNA; closed circle, start codon; open circle, codon. Unfolding of structure II by the ribosome stalling at the repY stop codon results in formation of a pseudoknot by base-pairing between the 5′-rGGCCG-3′ and 5′-CGCC-3′ (thick black line in the loop of structure 1) sequences distantly separated, and allows the ribosome to access the RBS. Binding of Inc RNA to the loop of structure 1 directly inhibits formation of the pseudoknot and the subsequent IncRNA-repZ-mRNA duplex formation inhibits rt?/;Y translation.

Citation: Brantl S. 2004. Plasmid Replication Control by Antisense RNAs, p 47-62. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch3
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