initiator-codon

Shine-Dalgarno sequence

The Shine-Dalgarno sequence (or Shine-Dalgarno box), proposed by Australian scientists John Shine and Lynn Dalgarno, is a ribosomal binding site generally located 6-7 nucleotides upstream of the start codon AUG. The Shine-Dalgarno sequence exists only in prokaryotes. The six-base consensus sequence is AGGAGG; in E. coli, for example, the sequence is AGGAGGA. This sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon. The complementary sequence (CCUCCU), is called the anti-Shine-Dalgarno sequence and is located at the 3' end of the 16S rRNA in the ribosome. The eukaryotic equivalent of the Shine-Dalgarno sequence is called the Kozak sequence.

Mutations in the Shine-Dalgarno sequence can reduce translation. This reduction is due to a reduced mRNA-ribosome pairing efficiency, as evidenced by the fact that complementary mutations in the anti-Shine-Dalgarno sequence can restore translation.

When the Shine-Dalgarno sequence and the anti-Shine-Dalgarno sequence pair, the translation initiation factors IF2-GTP, IF1, IF3, as well as the initiator tRNA fMet-tRNA(fMET) are recruited to the ribosome.

The ribosomal S1 protein in Gram-negative bacteria

In Gram-negative bacteria, the presence of a Shine-Dalgarno sequence is not obligatory for the ribosome to locate the initiator codon. For example, it has been shown that deletion of Anti-Shine-Dalgarno sequence from 16S rRNA doesn't lead to translation initiation at non-authentic sites. Moreover, numerous prokaryotic mRNAs don't possess Shine-Dalgarno sequences at all. What principally attracts ribosome to mRNA initiation region is apparently ribosomal protein S1, which binds to AU-rich sequences found in many prokaryotic mRNAs 15-30 nucleotides upstream of start-codon. It should be noted, that S1 is only present in Gram-negative bacteria, being absent from Gram-positive species.