it and the mRNA from the ribosome. An attractive model to explain how this could happen is suggested by the observation that the release factors mimic aa-tRNA (Box 2.4). If the release factor is occupying the A site, then the peptidyltransferase might try to transfer the polypeptide chain to the release factor rather than to the amino acid on a tRNA normally occupying the A site. When EF-G then tries to translocate the release factor with the polypeptide attached to the P site, it may trigger a series of reactions that release the polypeptide. The role of ribosome release factor in this process is uncertain, but it might be involved in releasing the mRNA after termination.
REMOVAL OF THE FORMYL GROUP AND THE N-TERMINAL METHIONINE
Normally, polypeptides do not have a formyl group attached to their N termini. In fact, they usually do not even have methionine as their N-terminal amino acid. The formyl group is removed from the completed polypeptide by a special enzyme called peptide deformylase (Figure 2.31). The N-terminal methionine or entire N-formylmethionine is also often removed by an enzyme called methionine aminopeptidase, so that methionine is usually not the N-terminal amino acid in a mature polypeptide.
Mimicry in Translation
The ribosome is a very busy place during translation, with numerous factors and tRNAs cycling quickly through the A and P sites. Different factors have to enter the ribosome for each of the steps and then leave when they have finished their functions. One way the complexity of the system seems to be reduced is by having the various factors and tRNAs mimic each other′s structure, which allows them to bind to the same sites on the ribosome. For example, the translation factor EF-G seems to be roughly the same shape as the translation factor EF-Tu bound to an aa-tRNA. This may allow EF-G to enter the A site, displace the tRNA (now attached to the growing polypeptide), and move it to the P site. Another example is the mimicry between the tRNAs and the release factors. The release factors resemble tRNAs in shape, but they seem to bind to specific terminator codons through interactions between amino acids in the release factors and nucleotide bases in the termination codon, rather than through base pairing between the codon and the anticodon on a tRNA. When the peptidyltransferase attempts to transfer the polypeptide to the release factor in the A site, it sets in motion the string of events that cause translation to be terminated and the polypeptide and mRNA to be released from the ribosome. It is an attractive idea that the release factors replaced what were once terminator tRNAs that responded to these terminator codons. Perhaps, in the earliest forms of life, everything in translation was done by RNA; now, RNA is used to make proteins, and the proteins, being more versatile, play many of the roles previously played by RNA.
References
Clark BFC, Thirup S, Kjeldgaard M, Nyborg J. 1999. Structural information for explaining the molecular mechanism of protein biosynthesis. FEBS Lett 452:41–46.
Nakamura Y, Ito K. 2011. tRNA mimicry in translation termination and beyond. Wiley Interdiscip Rev RNA 2:647–668.
Nyborg J, Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Clark BFC. 1996. Structure of the ternary complex of EF-Tu: macromolecular mimicry in translation. Trends Biochem Sci 21:81–82.
Figure 2.30 Termination of translation at a nonsense codon. In the absence of a tRNA with an anticodon capable of pairing with the nonsense codon at the A site, the ribosome stalls, and a specific release factor interacts with the A site, possibly through a specific interaction between amino acids in the release factor and the UAA nonsense codon. Translocation by translation elongation factor G (EF-G) (brown) causes dissociation of the ribosome and release factor from the mRNA, with the assistance of the ribosome release factor.
Figure 2.31 Removal of the N-terminal formyl group by peptide deformylase (A) and of the N-terminal methionine by methionine aminopeptidase (B).
trans-TRANSLATION (tmRNA)
A problem occurs when the ribosome reaches the 3′ end of an mRNA without encountering a termination codon. This might happen fairly often, because mRNA is constantly being cleaved or degraded (often from the 3′ end), and transcription may terminate prematurely, resulting in a truncated mRNA. The release factors can function only at a termination codon, so the ribosome will stall on a truncated mRNA. Not only would this cause a traffic jam and sequester ribosomes in a nonfunctional state, but also the protein that is made will be defective because it is shorter than normal, and accumulation of defective proteins may cause problems for the cell. This is where a small RNA called transfer-messenger RNA (tmRNA) comes to the rescue. As the name implies, tmRNA is both a tRNA and an mRNA, as shown in Figure 2.32. It can be aminoacylated with alanine by alanyl-tRNA synthetase like an alanyl-tRNA, and it also contains a short open reading frame (ORF) that terminates in a termination codon like an mRNA. If the ribosome reaches the end of an mRNA without encountering a termination codon, tm-RNA (together with an accessory protein) enters the A site of the stalled ribosome, and alanine is inserted as the next amino acid of the polypeptide. Then, by a process that is not well understood, the ribosome shifts from translating the ORF on the mRNA to translating the ORF on the tmRNA, where it soon encounters the termination codon at the end of the ORF. The release factors then release the ribosome and the truncated polypeptide, which now contains a short additional “tag” sequence of about 10 amino acids encoded by the tmRNA. The tag sequence that has been attached to the carboxy end of the truncated polypeptide is recognized by the ClpXP protease (see below), which degrades the entire defective polypeptide. In some cases, tmRNA-mediated degradation may play a regulatory role, allowing the targeted degradation of proteins until they are needed (see Keiler and Feaga, Suggested Reading).
The Genetic Code
As mentioned above, the genetic code determines which amino acid will be inserted into a protein for each 3-nucleotide set, or codon, in the mRNA. More precisely, the genetic code is the assignment of each possible combination of 3 nucleotides to 1 of the 20 amino acids or to serve as a signal to stop translation. The code is universal, with a few minor exceptions (Box 2.5), meaning that it is the same in all organisms from bacteria to humans. The assignment of each codon to its amino acid appears in Table 2.2.
REDUNDANCY
In the genetic code, more than one codon often encodes the same amino acid. This feature of the code is called redundancy.