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Inhibition system

asRNAs are short non-coding RNAs that can inhibit mRNA translation by binding to the 5’ untranslated region (UTR) of that mRNA. This, therefore, can be an effective way to inhibit the expression of a great amount of genes.

That is the case of the Salmonella OmpN gene, whose translation is inhibited by the conserved RybB asRNA, which forms a short duplex with the ompN CDS. Bouvier et al.(2008), studied this inhibition of ompN gene by RybB asRNA and they concluded that RybB does not sequester the ompN SD or AUG sequences, but the interaction takes place inside the CDS. Using probing experiments, supported by prediction with the RNAhybrid algorithm (Rehmsmeier et al., 2004) they determined the interaction model.

Figure 1. Taken from Bouvier et al.(2008).

As we can see in Figure 1, RybB forms a 4+11 bp RNA duplex with the ompN CDS, that inhibits its translation. Furthermore, by chemical synthesis of the first 16 nucleotides of RybB, they proved that this fragment was enough to inhibit the translation of ompN, this inhibition being even 4-fold higher than that with the full-length RybB RNA. The remaining nucleotides of the asRNA form the rho-independent terminator of the RNA transcription. In Figure 2 we can see the full-length RybB RNA.

Figure 2. Full-length RybB aligned with two chimera asRNAs. The ompN target site is also shown. Taken from Bouvier et al.(2008).