Uaaaaggcaucauggcuucagaaaaua

whereas the atpG has been predicted to possess a stable secondary structure both upstream of the Shine-Dalgarno sequence and in the region of the initiation codon and downstream:

Thus, the availability and affinity of initiation regions of different messages signify their "strength" in initiation and hence determine, at least in some degree, the ratio of protein production from them. This can be considered as an example of a fixed (constitutive) translational control of the proper proportions in protein synthesis products.

16.3. Translational Coupling

The fully independent translation initiation of different messages (cistrons) of a polycistronic mRNA, which determines a fixed proportion of encoded protein products according to the intrinsic initiation "strengths" of the cistrons, is just an extreme case among the ways how polycistronic mRNAs can be read out by ribosomes. In most instances the translation initiation of downstream cistrons depends on the translation of upstream messages of a polycistronic mRNA (translational coupling). The cases of such a dependent initiation of translation within a polycistonic mRNA can be classified into two groups:

(1) Initiation induced by upstream translation: translation of an upstream cistron is required for binding of free ribosomal particles at RBS of an internal cistron and thus for the initiation of translation of a downstream message. Here the RBS of an internal cistron may be conformationally hidden, and the unfolding of mRNA as a result of translation of a preceding cistron opens it and thus makes accessible for free ribosomes. A long ago known example is the dependence of initiation of replicase synthesis on translation of the preceding coat protein cistron in the systems directed by RNA's of bacteriophages of the MS2 or Qb type.

(2) Sequential translation via reinitiation: ribosomes associate with mRNA only at an upstream cistron (at its RBS) and then reinitiate at each subsequent cistron without dissociation after termination. In these cases free ribosomal particles are incapable to associate with and initiate translation at downstream cistrons. Polycistronic mRNAs encoding for ribosomal proteins are typical examples of this case.

The three situations discussed above (marked by bold face) are sketched in Fig. 16.1. It should be mentioned that their combinations and intermediate situations are also possible. For example, the independent initiation at the cistrons of the proton ATPase mRNA (see the preceding Section 16.2) is accompanied by an incomplete translational coupling of various degrees between some cistron pairs. Thus, initiation at the atpA cistron has been shown to be significantly enhanced by the translation of the preceding atpH cistron, while the initiation of the atpG cistron is only slightly increased by the translation of the preceding atpA cistron (Hellmuth et al., 1991).

16.3.1.Initiation Induced by Translation of Upstream Cistron

When full-sized polycistronic RNA of bacteriophage MS2 (see below, Section 16.4.1, Fig. 16.4) encounters free bacterial ribosomes, the initiation occurs only at the RBS of the second cistron C encoding for the phage coat protein. Despite the presence of a good Shine-Dalgarno sequence, a strong initiation codon (AUG) and an optimal distance between them, no initiation takes place at the cistron S encoding for the replicase subunit. The RBS of the S cistron is found unavailable for ribosomes due to its involvement in the long-range interaction with the upstream parts of the RNA (see below, Fig. 16.6 helix I). When ribosomes reading out the upstream C cistron reach the interacting section of the C cistron message, they melt this structure and thus open the RBS of the S cistron for binding with free ribosomes from surroundings (see Lodish & Robertson, 1969; Wiessmann et al., 1973).

Translation of the polycistronic transcript of rplJ-rplL operon encoding for ribosomal proteins L10 and L7/L12, as well as b and b' subunits of RNA polymerase (see below, Section 16.4.2, Fig. 16.7), is another remarkable example of this type of translational coupling (Friesen et al., 1980; Yates et al., 1981; Petersen, 1989). Here the RBS of the rplL (L7/L12) cistron is blocked by a long-range base-pairing of this region with the region located more than 500 nucleotides upstream, in the beginning of the preceding rplJ

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