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. 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 ShineDalgarno sequence is called the Kozak sequence. The Shine-Dalgarno sequence in E. coli, for example, is
AGGAGGA.
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 antiShine-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.
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 ShineDalgarno 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.