2 Structure of the Bacterial Ribosome and Some Implications for Translational Regulation

Translational regulation is based on modulation of translational function, most often involving the initiation phase. Not surprisingly, regulation of protein synthesis differs markedly between bacteria and eukarya, reflecting the many differences between their respective mechanisms of initiation. Although the structures of all ribosomes share commonly conserved cores, which are responsible for the main processes of translational elongation, many of the molecular components involved in translational initiation are specific to the different phylogenetic domains. These include the initiation factors, the Shine-Dalgarno sequence, formylation of the methionyl initiator tRNA, the ability to reinitiate on polycistronic mRNAs, and so on. Thus, it is not at all clear how far our knowledge of 70S (prokaryotic) ribosome structure will go toward providing insight into the mechanisms of eukaryotic translational regulation. Nevertheless, this information will help to understand prokaryotic initiation, and at least provide a starting point for interpreting the emerging structures of eukaryotic ribosomes. Most of the steps of protein synthesis appear to be based on RNA, including the many interactions between mRNA, tRNA, and rRNA that occur during the elongation phase. The roles of the proteins, such as the elongation factors and ribosomal proteins, may be to refine underlying RNA-based mechanisms, optimizing the speed and accuracy of translation. Translational initiation, at least in part, is therefore likely to involve modulation of RNA-based processes by proteins such as the initiation factors. We are beginning to understand how some of these processes work, from several decades of biochemical and genetic studies combined with the more recent...