(A) eIF2α phosphorylation determines the concentration of ternary complex and consequently the rate of translation initiation. Under normal or post-stress conditions (left), levels of phosphorylated eIF2α are kept at low levels in the cell due to expression of regulatory subunits of the phosphatase PP1 (GADD34 and CReP), which complex with PP1 and direct PP1 phosphatase activity to eIF2α. The drug salubrinal is a selective inhibitor of the PP1 complex and prevents dephosphorylation of eIF2α-P (Boyce et al., 2005). eIF2B, which catalyzes the exchange of GDP for GTP on the γ subunit of eIF2, freely binds to and dissociates from unphosphorylated eIF2α in the eIF2 complex. In its GTP form, eIF2 assembles into a ternary complex along with methionine-charged tRNA (eIF2 GTP Met-tRNAi). The ternary complex binds to the 40S ribosomal subunit to form the 43S preinitiation complex, which is then capable of initiating translation at an AUG sequence of the appropriate context on an mRNA transcript. Recognition of the start codon catalyzes GTP to GDP on eIF2, which is then released from the 40S subunit for another cycle of translation initiation. When eIF2α-P levels are low, ternary complex concentration is high and normal mRNA transcripts with short 5’ UTRs are translated with high efficiency. However, transcripts like BACE1 with long, uORF-containing, secondary structure-rich 5’UTRs are inefficiently translated. Under stress conditions (right), eIF2α is phosphorylated by one of four different kinases in response to various stimuli. In this case, eIF2B does not readily dissociate from phosphorylated eIF2α in the eIF2α complex, inhibiting the exchange of GDP for GTP on the γ-subunit of eIF2 and effectively reducing the concentration of ternary complex. In this case, the translation of normal mRNA transcripts is inhibited, while transcripts with long, uORF-containing, structured 5’UTRs are paradoxically translated with increased efficiency (de-repression). (B) Model for eIF2α phosphorylation-dependent de-repression of BACE1 mRNA translation, based on yeast GCN4 mRNA translational regulation (Schroder and Kaufman, 2006). The BACE1 5’ UTR is 453 nucleotides long, has three uORFs (numbered boxes), and has predicted stable secondary structure with a free energy of -215.3 kcal/mol (Lammich et al., 2004). uORF2 has been shown to be the major uORF that inhibits BACE1 mRNA translation under normal conditions (Mihailovich et al., 2007; Zhou and Song, 2006). A stable stem-loop structure (indicated by the hair-pin) is predicted downstream of uORF 2 (Fig. S5B). The AUGs of the three ORFs are in favorable contexts, and reports indicate that they are translated (De Pietri Tonelli et al., 2004; Mihailovich et al., 2007; Zhou and Song, 2006). In our model, ribosomes would bind to the BACE1 mRNA cap, scan down the 5’ UTR, and initiate translation first at uORF1. After translation of uORF1 is terminated and the 60S subunits dissociate, a proportion of 40S subunits remain attached and continue to scan along the BACE1 mRNA 5’ UTR. Under normal conditions, levels of phosphorylated eIF2α are low (left) and ternary complex concentrations are high. In this case, 40S subunits are efficiently reloaded with ternary complexes, 43S preinitiation complexes are rapidly formed, and translation reinitiation occurs at uORF2. A rare proline codon at the 3’ end of uORF2 (boxed P; Fig. S5A) and downstream stable secondary structure (Fig. S5B) increase dissociation of ribosomes from the BACE1 mRNA, reducing the proportion of 40S subunits that scan through the BACE1 mRNA 5’ UTR and reach the authentic BACE1 start codon for reinitiation. As a consequence, translation of the BACE1 ORF is inefficient under normal conditions. In contrast, under cellular stress conditions, phosphorylated eIF2α levels are high (right) and ternary complex concentrations are low. Translation initiation is still predicted to occur first at uORF1. Following termination of uORF1 translation, a proportion of 40S subunits remain attached and continue scanning the 5’ UTR, as in low eIF2α-P conditions. However, when eIF2α-P is high, decreased ternary complex availability causes the 40S subunit to spend more time scanning before becoming reloaded to form the 43S preinitiation complex. As a result, a higher proportion of 40S subunits scan through uORF2-3 and reach the authentic BACE1 AUG to reinitiate translation at the BACE1 ORF. Thus, BACE1 mRNA translation is more efficient under stress conditions than normal. (C) Common risk factors for Alzheimer’s disease such as age, high cholesterol, cardiovascular disease, traumatic brain injury, and ApoE4 genotype may lead to a state of impaired energy metabolism in the brain. Reduced energy availability activates the eIF2α-P stress-response pathway in neurons. Phosphorylation of eIF2α augments the translation of specific stress response proteins such as BACE1. Increased production of these stress-response proteins presumably enhances the ability of neurons to survive under low-energy conditions. However, if the stress persists, eIF2α phosphorylation and BACE1 levels remain chronically elevated, leading to increased Aβ production. Even a small increase in Aβ generation may have a significant impact on amyloid accumulation over the many years apparently required for AD development. Elevated Aβ levels may, in turn, cause neuronal dysfunction and stress, feeding back and further activating the eIF2α-P stress-response pathway. Over time, and in combination with other exacerbating factors such as impaired Aβ clearance/degradation, Aβ begins to accumulate in the brain and plaques form. Aβ accumulation may trigger downstream pathology, (e.g., tau hyperphosphorylation), ultimately leading to neurodegeneration associated with sporadic Alzheimer’s disease. (UPR = unfolded protein response).