Shine-Dalgarno sequence

The Shine-Dalgarno sequence, 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. 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. Eukaryotic equivalent of the Shine-Dalgarno sequence is called 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.

Shine-Dalgarno sequence vs. ribosomal S1 protein
In Gram-negative bacteria, however, Shine-Dalgarno sequence presence is not obligatory for ribosome to locate initiator codon, since 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.