Figure 16.9. Comparison of the predicted secondary structure of the bicistronic L11-L1 mRNA leader recognised by ribosomal protein L1 acting as a translational repressor (left) with that of the L1rrrrprotected region of 23S ribosomal RNA (right). The identical sequence in the side loop of both RNA is marked by grey box. (Reproduced, with minor modifications, from D.E. Draper, in "Translational Regulation of Gene Expression", J. Ilan, ed., p.p. 1-26, 1987, Plenum Press, New York, with permission).

prevent initiation; however, when the specific repressor protein recognises this structure and binds to it, the structure becomes stable and makes the RBS inaccessible for interactions with the ribosome and the initiator tRNA. Indeed, the regions of mRNA structurally homologous to the protein-binding regions of ribosomal RNA generally include the RBS (see Figs. 16.8 and 16.9).

In the case of the L10 mRNA (Fig. 16.7, the sixth line) the operator region has been shown to be located rather distantly upstream of the RBS, at positions about -145 to -200 and in no way overlaps the Shine-Dalgarno sequence and the initiation codon. The secondary structure element protected by protein L10 or the pentameric complex L10:(L7/L12)4 on the mRNA, in comparison with the region of the 23S ribosomal RNA protected by the L10:(L7/L12)4 complex, is shown in Fig. 16.10. Again their structural similarity can be observed. The mechanism of the repression, however, is somewhat different: instead of directly blocking the RBS, the binding of the repressory protein seems to induce a large-scale rearrangement of the secondary/tertiary structure of the leader sequence resulting in the inaccessibility of the RBS to the initiating ribosomal particles.

The case of the control of initiation of the S13 mRNA by protein S4 (Fig. 16.7, the forth line) represents a more complicated mechanism. The operator comprises the beginning of the S13 protein cistron and the preceding 75-nucleotide-long sequence in mRNA; it folds into a complex tertiary structure consisting of two entangled pseudoknots, with the Shine-Dalgarno sequence and the initiation codon GUG being not involved in secondary and tertiary interactions (Fig. 16.11). The pseudoknot structure does not hinder the interaction of the initiating ribosomal particle with the RBS. No similarity of this structure with the binding site of protein S4 on the ribosomal 16S RNA has been noticed. The most remarkable fact is that the binding of the repressory protein (S4) to the operator does not prevent the binding of the initiating ribosomal particle to the RBS. It seems that the binding of the repressor affects the structure of mRNA around the RBS resulting in trapping the initiation complex at the initiation site, and no direct or indirect competitions between the repressor and the ribosomal particle exists in this case.

The ribosomal protein S15 is coded by the first cistron of a bicistronic message that comprises also the polynucleotide phosphorylase-encoding cistron. The translation of the S15 mRNA is regulated by protein S15, independently of the second cistron. Like some other ribosomal proteins, the protein S15 is a repressor of translation of its own mRNA (for review, see Portier & Grunberg-Manago, 1993). The operator region on the mRNA overlaps the RBS and extends upstream up to position about -60. Two mRNA 23S RNA

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