of the mRNA between the two codons cause the ribosome to hop. In the case of gene 60 of T4, the hopping occurs almost 100% of the time, and the protein that results is the normal product of the gene. In the E. coli trpR gene, the hopping is less efficient, and the physiological significance of the hopped form is unknown.
High-level readthrough of termination codons can also give rise to more than one protein from the same ORF. Instead of stopping at a particular termination codon, the ribosome sometimes continues making a longer protein, in addition to the shorter one. Examples are the synthesis of the head proteins Qβ and the synthesis of Gag and Pol proteins in some retroviruses. Many plant vituses also make readthrough proteins. Again, it seems to be the sequence around the termination codon that promotes high-level readthrough. However, it is important to emphasize that these are all exceptions, and normally, the codons on an mRNA are translated faithfully one after the other from the TIR until a termination codon is encountered.
References
Baranov PV, Fayet O, Hendrix RW, Atkins JF. 2006. Recoding in bacteriophages and bacterial IS elements. Trends Genet 22:174–181.
Böck A, Forchhammer K, Heider J, Leinfelder W, Sawers G, Veprek B, Zinoni F. 1991. Selenocysteine: the 21st amino acid. Mol Microbiol 5:515–520.
Gaston MA, Jiang R, Krzycki JA. 2011. Functional context, biosynthesis, and genetic encoding of pyrrolysine. Curr Opin Microbiol 14:342–349.
Maldonado R, Herr AJ. 1998. Efficiency of T4 gene 60 translational bypassing. J Bacteriol 180:1822–1830.
Young TS, Schultz PG. 2010. Beyond the canonical 20 amino acids: expanding the genetic lexicon. J Biol Chem 285:11039–11044.
WOBBLE
Codons that encode the same amino acid often differ only by their third base, which is why they tend to be together in the same column when the code is presented as in Table 2.2. This pattern of redundancy in the code is due to less stringent pairing, or wobble, between the last (3′) base in the codon on the mRNA and the first (5′) base in the anticodon on the tRNA (remember that RNA sequences are always given 5′ to 3′ and that the pairing of strands of RNA, like that of DNA, is antiparallel [Figure 2.25]). As a consequence of wobble, the same tRNA can pair with more than one of the codons for a particular amino acid, so there can be fewer types of tRNA than there are codons. For example, even though there are two codons for lysine, AAA and AAG, E. coli has only one tRNA for lysine, which, because of wobble, can pair with both lysine codons.
While the term “wobble” may suggest that the process is random or that there is a lack of stringency inherent in the system, this is not really the whole story. As indicated earlier in the chapter, base pairing in RNA is different than in DNA, and modification of the anticodon itself contributes to alternative base-pairing rules, resulting in a process in which fewer tRNAs can be utilized to accurately recognize more codons (Figure 2.33). For example, wobble allows a G in the first position of the anticodon to pair with either a C or a U in the third position of the codon but not with an A or a G; this explains why UAU and UAC, but not UAA or UAG, are codons for tyrosine and can be recognized by a single tRNA with a GUA anticodon sequence. Similarly, a U in the first position of the anticodon can pair with either an A or a G in the third position of the codon (corresponding to the fact that both CAA and CAG are glutamine codons and can be recognized by a single tRNA with a UUG anticodon sequence). The rules for wobble are complicated by the fact that the bases in tRNA are sometimes modifed, and a modified base in the first position of an anticodon can have altered pairing properties. Inosine, which is a purine base found only in tRNA, can pair with any residue, so a single tRNA with inosine at the first position of the anticodon can recognize multiple codons (UCU, UCA, and UCC in Figure 2.33C, all of which encode serine). In other cases, an organism may use multiple tRNAs to recognize different codons that specify the same amino acid.
Figure 2.33 Wobble pairing between the anticodon on the tRNA and the codon in the mRNA. Non-Watson-Crick pairing interactions are possible in the third position of the codon. Alternative pairings for the anticodon base are shown: (A) guanine to cytosine or uracil; (B) uracil to adenine or guanine; and (C) inosine (a purine base found only in tRNAs) to adenine, cytosine, or uracil. This allows a single tRNA to recognize multiple codons.
TERMINATION CODONS
As noted above, not all codons stipulate an amino acid; of the 64 possible nucleotide combinations, only 61 actually encode an amino acid. The other three (UAA, UAG, and UGA) are termination (or nonsense) codons in most organisms. The termination codons are usually used to terminate translation at the end of genes (see “Translation Termination” above).
AMBIGUITY
In general, each codon specifies a single amino acid, but some can specify a different amino acid, depending on where they are in the mRNA. For example, the codons AUG and GUG encode formylmethionine if they are at the beginning of the coding region but encode methionine or valine, respectively, if they are internal to the coding region. The codons CUG, UUG, and even AUU also sometimes encode formylmethionine if they are at the beginning of a coding sequence.
The codon UGA is another exception. This codon is usually used for termination but encodes the amino acid selenocysteine in a few positions in genes (Box 2.5) and encodes tryptophan in some types of bacteria. Similarly, UAG is usually used for termination but can be used to encode the novel amino acid pyrrolysine in certain organisms.
CODON USAGE
Just because more than one codon can encode an amino acid does not mean that all the codons are used equally in all organisms. The same amino acid may be preferentially encoded by different codons in different organisms. This codon preference may reflect higher concentrations of certain tRNAs or may be related to the base composition of the DNA of the organism. While mammals have an average G+C content of about 50% (so that there are about as many AT base pairs in the DNA as there are GC base pairs), some bacteria and their viruses have very high or very low G+C contents. How the G+C content can influence codon preference is illustrated by some members of the genera Pseudomonas and Streptomyces. These organisms have G+C contents of almost 75%. To maintain such high G+C contents, the codon usage of these bacteria favors the codons that have the most G’s and C’s for each amino acid.
Polycistronic mRNA
In eukaryotes, each mRNA normally encodes only a single polypeptide. In contrast, in bacteria and archaea, one mRNA can encode either one polypeptide (monocistronic mRNAs) or more than one polypeptide (polycistronic mRNAs). Polycistronic mRNAs must have a separate TIR for each coding sequence to allow them to be translated.
The name “polycistronic” is derived from “cistron,” which is the genetic definition of the coding region for each polypeptide, and “poly,” which means many. Similarly, “monocistronic”