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Modified bases affect anticodon-codon pairing


KEY CONCEPTS:
  • Modifications in the anticodon affect the pattern of wobble pairing and therefore are important in determining tRNA specificity.
The most direct effect of modification is seen in the anticodon, where change of sequence influences the ability to pair with the codon, thus determining the meaning of the tRNA. Modifications elsewhere in the vicinity of the anticodon also influence its pairing.

When bases in the anticodon are modified, further pairing patterns become possible in addition to those predicted by the regular and wobble pairing involving A, C, U, and G. Figure 7.8 shows the use of inosine (I), which is often present at the first position of the anticodon. Inosine can pair with any one of three bases, U, C, and A.
This ability is especially important in the isoleucine codons, where AUA codes for isoleucine, while AUG codes for methionine. Because with the usual bases it is not possible to recognize A alone in the third position, any tRNA with U starting its anticodon would have to recognize AUG as well as AUA. So AUA must be read together with AUU and AUC, a problem that is solved by the existence of tRNA with I in the anticodon.
Actually, some of the predicted regular combinations do not occur, because some bases are always modified. There seems to be an absolute ban on the employment of A; usually it is converted to I. And U at the first position of the anticodon is usually converted to a modified form that has altered pairing properties.
Some modifications create preferential readings of some codons with respect to others. Anticodons with uridine-5-oxyacetic acid and 5-methoxyuridine in the first position recognize A and G efficiently as third bases of the codon, but recognize U less efficiently. Another case in which multiple pairings can occur, but with some preferred to others, is provided by the series of queuosine and its derivatives. These modified G bases continue to recognize both C and U, but pair with U more readily.

A restriction not allowed by the usual rules can be achieved by the employment of 2-thiouridine in the anticodon. Figure 7.9 shows that its modification allows the base to continue to pair with A, but prevents it from indulging in wobble pairing with G (for review see Bjork, 1987).
These and other pairing relationships make the general point that there are multiple ways to construct a set of tRNAs able to recognize all the 61 codons representing amino acids. No particular pattern predominates in any given organism, although the absence of a certain pathway for modification can prevent the use of some recognition patterns. So a particular codon family is read by tRNAs with different anticodons in different organisms.
Often the tRNAs will have overlapping responses, so that a particular codon is read by more than one tRNA. In such cases there may be differences in the efficiencies of the alternative recognition reactions. (As a general rule, codons that are commonly used tend to be more efficiently read.) And in addition to the construction of a set of tRNAs able to recognize all the codons, there may be multiple tRNAs that respond to the same codons.
The predictions of wobble pairing accord very well with the observed abilities of almost all tRNAs. But there are exceptions in which the codons recognized by a tRNA differ from those predicted by the wobble rules. Such effects probably result from the influence of neighboring bases and/or the conformation of the anticodon loop in the overall tertiary structure of the tRNA. Indeed, the importance of the structure of the anticodon loop is inherent in the idea of the wobble hypothesis itself. Further support for the influence of the surrounding structure is provided by the isolation of occasional mutants in which a change in a base in some other region of the molecule alters the ability of the anticodon to recognize codons.
Another unexpected pairing reaction is presented by the ability of the bacterial initiator, fMet-tRNAf, to recognize both AUG and GUG. This misbehavior involves the third base of the anticodon.