TRNA wobble

Slany, R. K., Bosl, M., Crain, R, and Kersten, H. (1993). A new function of S-adenosyl-methionine The ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine. Biochemistry 32, 7811-7817. 

There are 64 different three-letter codons, but we don t have to have 64 different tRNA molecules. Some of the anticodon loops of some of the tRNAs can recognize (bind to) more than one condon in the mRNA. The anticodon loops of the various tRNAs may also contain modified bases that can read (pair with) multiple normal bases in the RNA. This turns out to be the reason for the wobble hypothesis, in which the first two letters of a codon are more significant than the last letter. Look in a codon table and you ll see that changing the last base in a codon often doesn t change the identity of the amino acid. A tRNA that could recognize any base in codon position 3 would translate all four codons as the same amino acid. If you ve actually bothered to look over a codon table, you realize that it s not quite so simple. Some amino acids have single codons (such as AUG for Met), some amino acids have only two codons, and some have four. 

Clearly, the results emerging suggested that at least two nucleotides were modified, the absolute sequence position within the tRNA had yet to be established. Ching etalP showed that a Se U residue was present in the wobble position of the tRNA " from C. sticklandii. This study confirmed a notion that the modification probably affects the translation efficiency of certain transcripts, based on the level of modification by selenium. The authors speculated that the modification to seleno-tRNA (GAG) allowed for more efficient use of this tRNA species as compared to the tRNA (GAA). Even today, no definitive data exist to show that this modification alters the translation efficiency in these bacterial model systems. Nonetheless, these studies had established the chemical forms of Se U and mnm Se U, and established that they were derived from modifications to nucleotides that first required sulfur (S U and mnm S U), the mechanism by which selenium was inserted into the tRNA would not be definitively answered until many years later. 

We now have clear evidence that selenium can be introduced specifically into proteins as selenocysteine and into a subset of tRNA species as mnm Se U or Se2U. The pathways and molecular mechanisms for insertion of selenium into these molecules have been well established in several model systems, the best studied being E. coli. The role for selenium in selenoproteins (i.e., the need for selenium over sulfur) is thought to be its ability to act as a more reactive nucleophile and perhaps a more rapid catalyst. However, a void in our knowledge exists for the specific need for selenium-modified tRNAs. Mutation of either selD or ybbB did not alter the growth characteristics of E. coli- however, no thorough analysis of the bacterial stress response has been carried out in any of these mutants. Clearly, further study is needed to better define the role for selenium in wobble codon usage for a subset of tRNA species. 

Figure 3 Cognate and near-cognate codon-anticodon interactions. The anticodon ioop of tRNA is shown as an example interacting with various codons on the mRNA. In correct, cognate codon-anticodon pairings, two Watson-Crick base pairs can be formed in the first two positions while the third position contains either a Watson-Crick or a wobble base pair.

Many amino acids are specified by more than one codon (redundancy). Frequently, a tRNA can translate more than one of these codons, sparing the ceE from making multiple tRNAs to carry the same amino acid. For instance, in Figure 1-4-6 the arg-tRNA shown can translate both the CGA and the CGG codons that specify arginine. This phenomenon is known as Wobble" and can be summarized as follows ... 

There are not 64 different tRNAs, one for each codon, but instead the tRNAs are capable of unconventional base pairing ( wobble ) with the codons during translation of the mRNA. 

Figure 12-1. Codon-anticodon base pairing. Special wobble base-pairing rules apply to the third (3 ) position of the codon. The first (S ) position of the tRNA anticodon is frequently inosine (I) to provide this flexibility in hydrogen bonding.

Wobble Allows Some tRNAs to Recognize More than One Codon... 

The wobble (or third) base of the codon contributes to specificity, but, because it pairs only loosely with its corresponding base in the anticodon, it permits rapid dissociation of the tRNA from its codon during protein synthesis. If all three bases of a codon engaged in strong Watson-Crick pairing with the three... 

TABLE 27-4 How the Wobble Base of the Anticodon Determines the Number of Codons a tRNA Can Recognize... 

Terms in bold are defined aminoacyl-tRNA 1035 aminoacyl-tRNA synthetases 1035 translation 1035 codon 1035 reading frame 1036 initiation codon 1038 termination codons 1038 open reading frame (ORF) 1039 anticodon 1039 wobble 1041... 

The "wobble" hypothesis states that the first (5 ) base of the anticodon is not as spatially defined as the other two bases. Movement of that first base allows nontraditional base-pairing with the last (31) base of the codon, thus allowing a single tRNA to recognize more than one codon for a specific amino acid. 

Another pairing that occurs in tRNAs allows guanine to pair with uracil, e.g., G4 with U69. This was originally proposed to account for codon-anticodon interactions betweentRNA molecules and messenger RNA (Chapter 29). It is commonly called wobble pairing because the uracil must wobble away from its orientation in the normal Watson-Crick pair.27 37... 

While tRNAs consist largely of loops and stems containing Watson-Crick base pairs, they also contain Hoogsteen pairs, wobble pairs, and triplets such as the following. 

Selenium is found to a minor extent wherever sulfur exists in nature. This includes the sulfur-containing modified bases of tRNA molecules. In addition to a small amount of nonspecific incorporation of Se into all S-containing bases there are, at least in bacteria, specific Se-containing tRNAs. In E. coli one of these is specific for lysine and one for glutamate. One of the modified bases has been identified as 5-methyl-amino-methyl-2-selenouridine.570 It is present at the first position of the anticodon, the "wobble" position.571... 

A careful comparison of the wobble rules with the genetic code indicates that the minimum number of tRNAs required to translate all 61 codons is 31. With the addition of tRNAjMet the total comes to 32. Most cells contain many more than this minimum number of tRNA types. 

The enzyme tRNA-guanine transglycosylase (TGT) catalyzes the complete exchange of a base in tRNA [25, 26]. Upon reaction, guanine in the wobble position of tRNAs with the anticodon sequence GUN is replaced by the modified bases... 

Y3. Yasukawa, T., Suzuki, T., Ishii, N., Ohta, S., and Watanabe, K., Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease. EMBO J. 20,4794-4802 (2001). 

Codons that specify the same amino acid are called synonyms. Most synonyms differ only in the third base of the codon for example GUU, GUC, GUA and GUG all code for valine. During protein synthesis, each codon is recognized by a triplet of bases, called an anticodon, in a specific tRNA molecule (see Topics G10 and H2). Each base in the codon base pairs with its complementary base in the anticodon. However, the pairing of the third base of a codon is less stringent than for the first two bases (i.e. there is some wobble base-pairing ) so that in some cases a single tRNA may base-pair with more than one codon. For example, phenylalanine tRNA, which has the anticodon GAA, recognizes both of the codons UUU and UUC. The third position of the codon is therefore also called the wobble position. 

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