Читать книгу Snyder and Champness Molecular Genetics of Bacteria - Tina M. Henkin - Страница 186

Not all methionine codons serve as initiation codons, because methionine can be found within polypeptide sequences and not only at the N-terminal end. Furthermore, the fact that some of the initiation codons (like GUG) code for amino acids other than methionine when internal to a coding region demonstrates that the presence of one codon is clearly not enough to define a TIR. These sequences also may occur out of frame or in an mRNA sequence that is not translated at all. Obviously, sequences in addition to these three bases must help to define them as a place to begin translation.

Most bacterial genes have a second component for recognizing a translational start site within the TIR. This sequence, named the Shine-Dalgarno (S-D) sequence after the two scientists who first noticed it, is located 5 to 10 nucleotides on the 5′ side (upstream) of the initiation codon and is complementary to a short sequence near the 3′ end of the 16S RNA. Figure 2.27 shows an example of a typical bacterial TIR with a characteristic S-D sequence. By pairing with their complementary sequences on the 16S rRNA, S-D sequences help define TIRs by properly aligning the mRNA on the ribosome. However, these sequences are not always easy to identify because they can be very short and exhibit considerable variability. Moreover, not all bacterial genes have S-D sequences. The initiation codon sometimes resides at the extreme 5′ end of the mRNA (in “leaderless mRNAs”), leaving no room for an S-D sequence. In such cases, translation initiation may occur by a somewhat different mechanism (see below).

Figure 2.27 Structure of a typical bacterial translational initiation region (TIR) showing the pairing between the Shine-Dalgarno (S-D) sequence in the mRNA and a short sequence complementary to the S-D sequence that is located close to the 3′ end of the 16S rRNA. The initiation codon, typically AUG or GUG, is 5 to 10 bases downstream of the S-D sequence. N represents any base.

Because of this lack of universality, often the only way to be certain that translation is initiated at a particular initiation codon is to sequence the N terminus of the polypeptide to see if the N-terminal amino acids correspond to the codons immediately following the putative initiation codon. Protein sequencing will also reveal whether the methionine encoded by the initiation codon remains on the mature protein or is removed.