Figure 1. Examples of antisense RNA inhibition mechanisms in plasmids. (a) Mechanisms used by plasmids related to ColE1. The antisense RNA binds to its target (pre-primer) during transcription to induce a folding change that is incompatible with primer maturation. (b) A mechanism used by plasmids similar to R1, ColIbP9, and many others. Antisense RNA binds to a region within a rep mRNA and blocks translation. (c) The transcriptional attenuation mechanism of, for example, pIP501 and pT181. Antisense RNA binds to nascent rep mRNA to induce the formation of a terminator stem–loop.

Figure 2. Experimentally determined or predicted secondary structures of regulatory RNAs. (a, b) Antisense RNAs that control copy numbers of plasmid R1 (a) and of plasmid ColE1 (b). (c) Antisense RNA of the hok/sok killer system of R1. (d) Antisense regulator of IS10 transposition. (e) Antisense regulator of conjugation of plasmid F. (f, g, h) Stress response regulators OxyS (f), MicF (g) and DsrA (h) from Escherichia coli. (i, j) Antisense RNAs controlling lysogeny in Salmonella typhimurium phage P22 Sar (i) and coliphages P1/P7 (j). (k, l, m) The short antisense RNA lin-4 in its proposed complex with one of the lin-14 target elements (grey letters; repeat 4) (k), and regulatory RNAs from adenovirus (l) and Epstein–Barr virus (m). The RNAs a–c and i are fully complementary to their target RNAs, RNA-OUT (d) is fully complementary only in its 5¢ half. Pink boxes indicate examples of known sites at which target binding initiates. Blue boxes show regions of target complementarity in ‘trans’-encoded antisense RNAs. Only one of two such regions is shown for DsrA (h).

Figure 3. Two examples of antisense-target RNA binding pathways. (a) The proposed binding pathway of CopA to CopT, the target of plasmid R1. Binding initiates between loops on top of bulged stems, proceeds by helix extension (asymmetrically) and results in the major inhibitory complex (lower, left). The unidirectional broken arrow indicates that subsequent duplex formation is slow and biologically not important. (b) The binding pathway of Sok and hok mRNA. Here, binding initiates between the single-stranded 5¢ tail of Sok and a target stem–loop. A complicated binding intermediate (third structure from left) suffices for inhibition, but is converted to a full duplex.

Figure 4. Models for different regulatory mechanisms used – the OxyS and DsrA cases. (a) Two proposed mechanisms for OxyS function. OxyS inhibition of fhlA translation is mediated by an antisense effect (upper), and OxyS repression of rpoS translation is due to binding of the translational activator Hfq. (b) Two antisense mechanisms proposed for DsrA: binding of DsrA to the hns mRNA blocks translation, and DsrA binding to an anti-RBS segment of the rpoS mRNA activates translation.