Aptamers to the Peptide Antibiotic Viomycin

A very interesting family of RNA-binding antibiotics are the tuberactinomycins, whose most prominent member, viomycin, is shown in Table 5.1. Viomycin is a basic peptide composed of six amino acids - two serines and four unusual amino acids, derivatives of alanine, arginine, lysine, and propionic acid. Its core structure forms a 16-membered ring with an intramolecular hydrogen bond between the a-amide proton of the guanidine moiety and the carboxyl oxygen of the serine residue 1. These peptides are not synthesized by the translational machinery, but by non-ribosomal peptide synthetases, a large family of complex and fascinating enzymes existing in microorganisms (Walsh, 2004). Viomycin is a member of the tuberactinomycin family of antibiotics, which were mainly used to fight tuberculosis. Viomycin has a single binding site at the interface of the ri-bosomal subunits and interferes with several stages of protein synthesis. It inhibits translation initiation, tRNA binding and translocation (Liou and Tanaka, 1976; Modolell and Vazquez, 1977; Wurmbach and Nierhaus, 1983). It also prevents ribosomal subunit dissociation. In addition to inhibiting the ribosome, viomycin is also a competitive inhibitor of group I intron splicing (Wank et al., 1994) and the human hepatitis delta virus ribozyme in vitro (Rogers et al., 1996). The

5.7 Aptamers to the Peptide Antibiotic Viomycin | 127

diversity of the RNA target sites recognized by this antibiotic requested a more detailed analysis of how viomycin binds to RNA. Therefore, aptamers against viomycin were selected.


The in vitro selection of viomycin-binding RNAs, performed with the same pool as the selection for streptomycin and neomycin, resulted in a number of RNAs, of which 90% had a highly conserved region of 14 nucleotides (Wallis et al., 1997). Determination of the minimal binding motif and secondary structure analysis revealed a hairpin structure, whose loop is involved in a longrange pairing interaction forming a pseudoknot (Table 5.1). The most interesting aspect of this selection is that all known viomycin-binding sites are pseudo-knots, although all these pseudo-knots have different topologies. No high-resolution structure has been determined for this aptamer and therefore it is unknown how this drug interacts with RNA in detail.

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