4 The Mechanism of Translation Initiation in Eukaryotes

Standard translation initiation in eukaryotes is the process that leads to assembly of an 80S ribosome on an mRNA in which the initiation codon is base-paired to the CAU anticodon of aminoacylated initiator methionyl-transfer RNA (Met-tRNA i Met ) in the ribosomal peptidyl (P) site. The process requires separated small (40S) and large (60S) ribosomal subunits and involves at least 12 eukaryotic initiation factors (eIFs) and the binding and hydrolysis of ATP and GTP. The resulting 80S initiation complex is competent to enter the elongation phase of translation. This chapter describes the canonical mechanism of 5′-end-dependent initiation, with a bias toward the initiation process in higher eukaryotes. This process differs in detail from that in plants and yeast, in which the subunit structure and composition of some factors differ substantially. For a more detailed review of initiation in yeast and in plants, see Chapters 9 and 26, respectively. For a review of mechanisms dependent on internal ribosome entry, see Chapters 5 and 6. STRUCTURE OF EUKARYOTIC CYTOPLASMIC mRNAs The translational efficiency of eukaryotic mRNAs is limited by the rate of initiation (see, e.g., Palmiter 1972), which is in turn determined by structural features of mRNAs that influence ribosomal recruitment, scanning to the initiation codon, and initiation codon recognition. Eukaryotic mRNAs associate dynamically with proteins that mediate nuclear export, subcellular localization, stability, and translational repression, and therefore exist in cells as messenger ribonucleoproteins (mRNPs) rather than as free polynucleotides. The influence of mRNP proteins on initiation is outside the scope of this review. Almost...