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Translational Control by mRNA Structure In Eubacteria: Molecular Biology and Physical Chemistry

Maarten H. De Smit


To any living cell, it is crucial that the correct proteins are produced in the proper amounts at the right time in its life cycle. This is achieved through a multitude of mechanisms, operating at different points in the chain of events leading from the genetic code in the DNA to the appearance of a functional protein. This chapter is concerned with the initiation step of translation in prokaryotes and focuses on the role of the secondary structure of the mRNA in its control.

The question of how a 30S ribosomal subunit recognizes the beginning of a coding sequence has been the subject of extensive research over the past three decades and is still not resolved to full satisfaction. The emerging picture, however, is that the selectivity of ribosome binding is only for a small part defined by specific recognition signals in the mRNA. Primarily, non-initiator sites that could bind ribosomes spuriously are rendered harmless by hiding them in secondary structure (Ganoza et al. 1987).

30S subunits bind to RNA through various contacts of different kinds. The primary interaction is presumably through protein-RNA contacts, and is largely non-sequence-specific. This is the type of interaction that allows in vitro initiation on synthetic messengers like poly(U), and one of the main contributors is ribosomal protein S1 (van Dieijen et al. 1978; Boni et al. 1991; Hartz et al. 1991a; Ringquist et al. 1995).

Of the potential mRNA-rRNA interactions, only the Shine-Dalgarno (SD) interaction has been analyzed in sufficient detail to...

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