Translation factor control of ribosome conformation during start codon selection

Abstract

Eukaryotic translation initiation factors (eIFs) function at multiple steps. They enable the small 40S ribosome subunit to bind to initiator tRNA and mRNA, and scan to and select an initiation codon on the mRNA. They facilitate joining of the large 60S ribosome subunit, at which point the initiation phase of translation ends with the initiator tRNA in the P (peptidyl) site, and the ribosome poised to accept a tRNA into its A (aminoacyl) site (Kapp and Lorsch 2004; Pestova et al. 2007). There are at least 10 eIFs, and many of them (eIF1, eIF1A, eIF2, eIF3, eIF4F, eIF5, and eIF5B) are direct components of the ribosomal preinitiation complex (PIC). eIF2 and eIF3 are well-characterized multimeric factors that bind directly to Met-tRNAi Met and the 40S subunit, respectively. While considered relatively large, the 40S subunit has only a limited functional space to bind translation factors. eIF1 and eIF1A are small single-polypeptide factors that bind directly to the ribosome at or near the decoding site. They are thought to directly regulate ribosome conformation. An elegant combination of genetic and biochemical studies reported in the previous issue of Genes & Development from the Hinnebusch, Lorsch, and Pestova laboratories (Cheung et al. 2007) provides substantial evidence that these factors indeed regulate the ribosome conformational rearrangement in response to start codon selection. This report and other recent reports on the structures and functions of yeast initiation factors lead to a deeper understanding of how eIFs bind the ribosome productively, communicate with each other to enable initiation, and regulate the ribosome’s conformation and activity to maintain initiation fidelity. The salient points concerning translation initiation via scanning (outlined in Fig. 1) that are important for considering the functions of eIFs in start site selection can be summarized as follows. The ternary complex (TC) is composed of eIF2, GTP, and Met-tRNAi . It associates with the 40S ribosome subunit with the assistance of eIF1, eIF1A, and eIF3. TC, eIF1, eIF3, and eIF5 together can be isolated as a multifactor complex (MFC) in yeast (Asano et al. 2000); a similar complex may be present in mammals (LeFebvre et al. 2006). There are at least two possible pathways for 43S assembly as depicted in Figure 1, one of which involves preformed MFC. The 43S PIC that is formed by these interactions is composed of the 40S subunit, MFC, and eIF1A. The 43S PIC is recruited to the mRNA by eIF4F, which is associated with the mRNA mG-cap and poly(A) tail through association with poly(A)-binding protein; the PIC in association with mRNA becomes the 48S PIC [eIF4F, poly(A), and PABP are not shown in Fig. 1]. eIF3 also is important for PIC binding to mRNA (Kolupaeva et al. 2005; Siridechadilok et al. 2005; Hinnebusch 2006; Jivotovskaya et al. 2006). The PIC scans the mRNA; upon determining it has reached a start codon, it releases the Pi formed by hydrolysis of GTP in the TC, and also releases eIF2·GDP, leaving Met-tRNAi Met positioned at the start codon. As discussed below, eIF1 also dissociates from the ribosome during selection of the start codon. A second GTP-binding factor, eIF5B, then facilitates 60S subunit joining. The guanine nucleotide exchange factor eIF2B recycles eIF2•GDP to eIF2•GTP, because only the latter binds Met-tRNAi .