Chapter 6 : Plasmid Replication Control by Antisense RNAs

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Small regulatory RNAs (sRNAs) from bacterial chromosomes came into focus in 2001, when two groups independently discovered many small RNAs from intergenic regions of the genome by a combination of computational and experimental approaches ( ). By now, >140 sRNAs have been found in and hundreds in other prokaryotic species, and it is estimated that an average bacterial genome encodes ≈200 to 300 riboregulators ( ). They can be classified into - and -encoded base-pairing sRNAs, sRNAs acting via protein binding, and sensory RNA modules like RNA thermometers and riboswitches.

Citation: Brantl S. 2015. Plasmid Replication Control by Antisense RNAs, p 83-103. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0001-2013
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Figure 1

Mechanisms of antisense-RNA-mediated plasmid copy number control. Antisense RNAs are drawn in red; sense RNAs are drawn in blue. ORFs encoding essential replication initiator proteins are shown as orange boxes; ORFs encoding transcriptional repressor proteins are shown as brown boxes. SD sequences for ORFs are blue rectangles. Promoters are symbolized by black triangles and replication origins by dark grey ovals. Arrows indicate positive interaction; black bars indicate repression. Ribosomes are in light yellow. () Transcriptional attenuation: plasmid pIP501. () Working model on regulation of pIP501 replication. The minimal replicon with the and genes is shown, separated by the 329-nt-long leader region. CopR represses transcription from the promoter pII and, at the same time, indirectly increases transcription initiation from the antisense promoter pIII. The antisense RNA causes premature termination of (sense) RNA transcription at the attenuator (). () Mechanism of transcriptional attenuation. For details see text. Complementary sequence elements are designated A, B, a, and b. Green arrow, RNase III. () Inhibition of primer maturation: plasmid ColE1. () Schematic representation of the minimal replicon. () Mechanism of inhibition of primer maturation. Violet circle, RNA polymerase. For details, see text. () Inhibition of pseudoknot formation: plasmid ColIb-P9. () The minimal replicon with the leader peptide (dark grey) and genes is shown. White: leader region of mRNA. () Genes for and are translationally coupled. On the mRNA, the SD sequence is exposed, whereas structure III sequesters both the SD sequence (black rectangle) and the 5′-rCGCC-3′ sequence (thick black line) and, thereby, translation. Inc is the region complementary to the antisense RNA; black circle, start codon; grey circle, stop codon. Unfolding of structure II by the ribosome stalling at the stop codon results in formation of a pseudoknot by base paring between the 5′-rGGCCG-3′ and 5′-CGCC-3′ (thick black lines) sequences distantly separated, and allows the ribosome to access the RBS. Binding of Inc RNA to the loop of structure I of RNA directly inhibits formation of the pseudoknot and the subsequent IncRNA--mRNA duplex formation inhibits translation. () Translation inhibition by inhibition of ribosome binding. () Working model on regulation of plasmid pMV158 replication. () The antisense RNA binds directly upstream of the extended non-SD sequence (light blue circle) 5′ of the start codon and prevents binding of the 30S ribosomal subunit. The CopG protein represses transcription from the c-promoter and from the promoter. () Inhibition of leader peptide translation. () Working model on regulation of plasmid R1 replication. () Translation of the leader peptide (black box) is required for efficient translation. The CopB protein represses transcription from the , but not from the promoter. () Translational attenuation. () Working model on regulation of plasmid pSK41 replication. () The antisense RNA interacts via three loops with the nascent mRNA resulting in a stem-loop structure that sequesters the ribosome binding site. In the absence of RNAI, the mRNA refolds into an alternative structure that exposes the ribosome binding site, allowing translation.

Citation: Brantl S. 2015. Plasmid Replication Control by Antisense RNAs, p 83-103. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0001-2013
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