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Figure 16.11. Pseudoknot structure of the polycistronic S10 mRNA region recognised by ribosomal protein S4 acting as a translational repressor. The Shine-Dalgarno sequence and initiation codon (GUG) of S10 cistron are marked. Arrows indicate the polarity of the mRNA chain and the bond between two adjacent nucleotide residues. (Reproduced from C. Portier & M. Grunberg-Manago, in "Translational Regulation of Gene Expression 2", J. Ilan, ed., p.p. 23-47, 1993, Plenum Press, New York, with permission).

hairpins can be formed within this region (Fig. 16.12 A). The hairpins can interact with each other and be rearranged into a pseudoknot structure with the Shine-Dalgarno sequence and the initiation codon being freed (Fig. 16.12 B). It seems that the two-hairpin structure and the pseudoknot structure are in equilibrium. Apparently, it is the pseudoknot conformation that binds the initiating ribosomal particle. At the same time, protein S15 also recognises and thus stabilises the pseudoknot structure. The 16S ribosomal RNA acts as an antirepressor of the S15 mRNA suggesting the existence of a structural similarity between the operator on the mRNA and the protein S15 binding site on the 16S RNA. Indeed, such a similarity can be perceived from the comparison of the structures (Fig. 16.12 C). From all this it could be assumed that protein S15 and the initiating ribosomal particle would compete with each other for the common binding site. It has been found, however, that protein S15 does not prevent the binding of the 30S ribosomal particle to the RBS and the subsequent association of the initiator tRNA but rather stabilises the 30S:mRNA or 30S:mRNA:F-Met-tRNA complex. The model has been suggested that the stabilisation of the pseudoknot structure by protein S15 traps the initiating ribosomal particle at the RBS because of the difficulty to overcome the helix adjacent to the initiation codon during transition from initiation to elongation, while in the absence of the repressor the pseudoknot structure is capable of rearranging into a less stable conformation.

The hypothesis that a repressory ribosomal protein, at least in most cases, employs a common active center for binding to ribosomal RNA in the course of ribosome self-assembly, and for binding to mRNA operators in the

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