When the activity of a general translation factor (such as the eIF2 discussed above) is reduced, one might expect that the translation of all mRNAs would be reduced equally. Contrary to this expectation, however, the phosphorylation of eIF2 can have selective effects, even enhancing the translation of specific mRNAs that contain uORFs. This can enable cells, for example, to adapt to starvation for specific nutrients by shutting down the synthesis of all proteins except those that are required for synthesis of the missing nutrients. The details of this mechanism have been worked out for a specific yeast mRNA that encodes a protein called Gcn4, a transcription regulator that activates many genes that encode proteins that are important for amino acid synthesis.
The Gcn4 mRNA contains several short uORFs, and when amino acids are abundant, ribosomes translate the uORFs and generally dissociate before they reach the Gcn4 coding region. A global decrease in eIF2 activity brought about by amino acid starvation makes it more likely that a scanning small ribosomal subunit will move across the uORFs (without translating them) before it acquires a molecule of eIF2 (see Figure 6–70). Such a ribosomal subunit is then free to initiate translation on the actual Gcn4 sequences. The increased level of this transcription regulator increases production of the amino acid biosynthetic enzymes.
Although approximately 90% of eukaryotic mRNAs are translated beginning with the first AUG downstream from the 5ʹ cap, certain AUGs, as we saw in the previous section, can be skipped over during the scanning process. In this section, we discuss yet another way that cells can initiate translation at positions distant from the 5ʹ end of the mRNA, using a specialized type of RNA sequence called an internal ribosome entry site (IRES). In some cases, two distinct protein-coding sequences are carried in tandem on the same eukaryotic mRNA; translation of the first occurs by the usual scanning mechanism, and translation of the second occurs through an IRES. IRESs are typically several hundred nucleotides in length and fold into specific structures that bind many, but not all, of the same proteins that are used to initiate normal 5ʹ cap-dependent translation (Figure 7–68). In fact, different IRESs require different subsets of initiation factors. However, all of them bypass the need for a 5ʹ cap structure and the translation initiation factor that recognizes it, eIF4E.
Figure 7–68 Two mechanisms of translation initiation. (A) the normal, cap-dependent mechanism requires a set of initiation factors whose assembly on the mrnA is stimulated by the presence of a 5ʹ cap and a poly-A tail (see also figure 6–70).
(B) the ireS-dependent mechanism, seen mainly in viruses, requires only a subset of the normal translation initiating factors, and these assemble directly on the folded ireS. (Adapted from A. Sachs, Cell 101:243–245, 2000. with permission from elsevier.)
Some viruses use IRESs as part of a strategy to get their own mRNA molecules translated while blocking normal 5ʹ cap-dependent translation of host mRNAs. On infection, these viruses produce a protease (encoded in the viral genome) that cleaves the host-cell translation factor eIF4G, rendering it unable to bind to eIF4E, the cap-binding complex. This shuts down most of the host cell’s translation and effectively diverts the translation machinery to the IRES sequences present on the viral mRNAs. (The truncated eIF4G remains competent to initiate translation at these internal sites.)
The many ways in which viruses manipulate their host’s protein-synthesis machinery for their own advantage continue to surprise cell biologists. Studying this “arms race” between humans and pathogens has led to many fundamental insights into the workings of the cell, and we revisit this topic in more detail in Chapter 23.