Figure 6–75 binding sites for antibiotics on the bacterial ribosome. The small (left) and large (right) subunits of the ribosome are arranged as though the ribosome has been opened like a book. Antibiotic binding sites are marked with colored spheres, and the bound tRNA molecules are shown in purple (see Figure 6–62). Most of the antibiotics shown bind directly to pockets formed by the ribosomal RNA molecules. Hygromycin B induces errors in translation, spectinomycin blocks the translocation of the peptidyl-tRNA from the A site to the P site, and streptogramin B prevents elongation of nascent peptides. Table 6–4 lists the inhibitory mechanisms of the other antibiotics shown in the figure. (Adapted from J. Poehlsgaard and S. Douthwaite, Nat. Rev. Microbiol. 3:870–881, 2005. With permission from Macmillan Publishers Ltd.) translating damaged or incompletely processed mRNAs (which would produce truncated or otherwise aberrant proteins) is apparently so great that the cell has several backup measures to prevent this from happening. To avoid translating broken mRNAs, for example, the 5ʹ cap and the poly-A tail are both recognized by the translation-initiation machinery before translation begins (see Figure 6–70).
The most powerful mRNA surveillance system, called nonsense-mediated mRNA decay, eliminates defective mRNAs before they move away from the nucleus. This mechanism is brought into play when the cell determines that an mRNA molecule has a nonsense (stop) codon (UAA, UAG, or UGA) in the “wrong” place. This situation is likely to arise in an mRNA molecule that has been improperly spliced, because aberrant splicing will usually result in the random introduction of a nonsense codon into the reading frame of the mRNA—especially in organisms, such as humans, that have a large average intron size (see Figure 6–31B).
The nonsense-mediated mRNA decay mechanism begins as an mRNA molecule is being transported from the nucleus to the cytosol. As its 5ʹ end emerges from a nuclear pore, the mRNA is met by a ribosome, which begins to translate it. As translation proceeds, the exon junction complexes (EJCs) that are bound to the mRNA at each splice site are displaced by the moving ribosome. The normal stop codon will lie within the last exon, so by the time the ribosome reaches it and stalls, no more EJCs will be bound to the mRNA. In this case, the mRNA “passes inspection” and is released to the cytosol where it can be translated in earnest (Figure 6–76). However, if the ribosome reaches a stop codon earlier, when EJCs remain bound, the mRNA molecule is rapidly degraded. In this way, the first round of translation allows the cell to test the fitness of each mRNA molecule as it exits the nucleus.
Nonsense-mediated decay may have been especially important in evolution, allowing eukaryotic cells to more easily explore new genes formed by DNA rearrangements, mutations, or alternative patterns of splicing—by selecting only those mRNAs for translation that can produce a full-length protein. Nonsense-mediated decay is also important in cells of the developing immune system, where the extensive DNA rearrangements that occur (see Figure 24–28) often generate mRNA SURVIVES, EFFICIENT TRANSLATION Upf TRIGGERS mRNA DEGRADATION