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All bacterial and archaeal TIRs have an initiation codon, which is recognized by a dedicated initiator tRNA. This tRNA is always aminoacylated with methionine by methionyl-tRNA synthetase, and the methionine is further modified by addition of a formyl group (Figure 2.26). The three bases in initiator codons are usually AUG or GUG but in rare cases are UUG or CUG. Regardless of which amino acid these sequences call for in the genetic code (Table 2.2), they encode methionine (actually formylmethionine) as the N-terminal amino acid if they are serving as initiation codons. After translation, this methionine is often cut off by an aminopeptidase (see below). Notice that for the initiation codons, the first position of the codon can mispair with the tRNA anticodon, which always matches AUG; this differs from “wobble” during translation elongation, which involves mismatches at the third position of the codon (see below).

The initiation codon does not have to be the first sequence in the mRNA chain. In fact, the 5′ end of the mRNA may be some distance from the initiation codon of the first coding region in a transcript; this intervening region is called the 5′ untranslated region (5′-UTR) or leader region. In bacteria, many transcripts contain multiple coding regions. The translation initiation complex binds internally to the mRNA to identify the TIR for each coding region. This is different from translation in eukaryotes, where the translation initiation complex usually binds to the 5′ end of the transcript and initiates translation at the first AUG codon it encounters that is accessible (see below).

Figure 2.26 Conversion of methionine (Met) to N-formyl-methionine (fMet) by transformylase.