Shine-Dalgarno sequence

The Shine-Dalgarno (SD) sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA (mRNA) to initiate protein synthesis by aligning the ribosome with the start codon.

The Shine-Dalgarno sequence exists both in bacteria and archaea. It is also present in some chloroplast and transcripts. The six-base consensus sequence is AGGAGG; in Escherichia coli, for example, the sequence is AGGAGGU, while subsequence GAGG dominates in E. coli virus T4 early genes.

The Shine-Dalgarno sequence was proposed by Australian scientists John Shine (b. 1946) and Lynn Dalgarno (b. 1935).

Using a method developed by Hunt, Shine and Dalgarno showed that the nucleotide tract at the 3' end of E. coli 16S ribosomal RNA (rRNA) is pyrimidine-rich and has the sequence -PyACCUCCUUA 3' OH. They proposed that these ribosomal nucleotides recognize the complementary purine-rich sequence AGGAGGU, which is found upstream of the start codon AUG in a number mRNAs found in viruses that affect E. coli. Many studies have confirmed that base pairing between the Shine-Dalgarno sequence in mRNA and the 3' end of 16S rRNA is of prime importance for initiation of translation by bacterial ribosomes.

Given the complementary relationship between rRNA and the Shine-Dalgarno sequence in mRNA, it was proposed that the sequence at the 3'-end of the rRNA determines the capacity of the prokaryotic ribosome to translate a particular gene in an mRNA. Base pairing between the 3'-end of the rRNA and the Shine-Dalgarno sequence in mRNA is a mechanism by which the cell can distinguish between initiator AUGs and internal and/or out-of-frame AUG sequences. The degree of base pairing also plays a role in determining the rate of initiation at different AUG initiator codons.

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