The Shine-Dalgarno (SD) sequence, proposed by Australian scientists John Shine (b. 1946) and Lynn Dalgarno (b. 1935), is a ribosomal binding site in prokaryotic mRNA, generally located around 8 bases upstream of the start codon AUG. The Shine-Dalgarno sequence exists both in bacteria and archaea, being also present in some chloroplast and mitochondrial 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 helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon.
- 1 The 3' terminus of the small ribosomal RNA and the recognition of translation start sites in prokaryotic mRNA
- 2 The Shine-Dalgarno sequence and protein synthesis in prokaryotic expression systems
- 3 SD-Sequences in Chloroplasts
- 4 The 3'-terminus of the small ribosomal RNA and the recognition of termination codons in messenger RNA
- 5 See also
- 6 References
- 7 External links
The 3' terminus of the small ribosomal RNA and the recognition of translation start sites in prokaryotic mRNA 
Using a stepwise degradation and terminal labelling procedure developed by Hunt, Shine and Dalgarno showed that the nucleotide tract at the 3' terminus of E. coli 16S ribosomal RNA (rRNA) is pyrimidine-rich and has the sequence -PyACCUCCUUA 3' OH . They proposed that this stretch of nucleotides recognises a complementary purine-rich sequence (AGGAGGU) in the region upstream of the correct initiator AUG found in the ribosome binding sites of a variety of coliphage mRNAs (Ref 1).
The 3' terminal sequences of 16S rRNA from Pseudomonas aeruginosa, Bacillus stearothermophilus and Caulobacter crescentus are also pyrimidine-rich, but differ one from the other and from the E.coli sequence. On the basis of complementarity relationships between these sequences and the purine-rich sequence in the ribosome binding site of different bacterial mRNA species it was proposed that the precise sequence at the 3'-end of the rRNA determines the intrinsic capacity of the prokaryotic ribosome to translate a particular cistron in a mRNA. The specific base pairing between the 3'-end of the rRNA and the sequence preceding an initiator AUG provides a mechanism by which the cell can distinguish between initiator AUGs and internal and/or out-of-phase AUG sequences. The degree of base pairing also plays a role in determining the rate of initiation at different AUG initiator codons in polycistronic mRNAs.
This hypothesis was strengthened by the demonstration that E.coli ribosomes use base pairing to identify start sites for translation of bacteriophage mRNA. This study took advantage of the antibiotic colicin E3 which induces the rapid shut down of protein synthesis in susceptible E.coli due to the removal of about 50 nucleotides from the 3'-end of 16S RNA as a result of a single endonucleolytic cleavage. Using colicin E3, a hydrogen bonded mRNA-rRNA complex was isolated after the formation of initiation complexes between E.coli ribosomes and a phage R17 initiator region. This complex included the last 50 nucleotides of 16S rRNA and melted at a temperature consistent with the predicted structure (Ref 5).
Many studies have confirmed that base pairing between the SD sequence in mRNA and the 3' end of 16S rRNA is of prime importance for initiation of translation by bacterial ribosomes.
The level of 3'-terminal adenylation of Ps. aeruginosa 16S rRNA is a function of bacterial growth rate.
The Shine-Dalgarno sequence and protein synthesis in prokaryotic expression systems
Mutations in the Shine-Dalgarno sequence can reduce or increase translation in prokaryotes. This change is due to a reduced or increased mRNA-ribosome pairing efficiency, as evidenced by the fact that complementary mutations in the 3'-terminal 16S rRNA sequence can restore translation.
SD-Sequences in Chloroplasts
The 3'-terminus of the small ribosomal RNA and the recognition of termination codons in messenger RNA 
In 1973 Dalgarno and Shine proposed that in eukaryotes, the 3'-end of the small 18S rRNA may play a role in the termination of protein synthesis by complementary base pairing with termination codons. This came from their observation that the 3' terminal sequences of 18S rRNA from Drosophila melanogaster (Ref 12), Saccharomyces cerevisiae (Ref 12) and rabbit reticulocytes are identical: GAUCAUUA -3'OH. The conservation of this sequence between such distantly related eukaryotes implied that this nucleotide tract played an important role in the cell. Since this conserved sequence contained the complement of each of the three eukaryotic termination codons (UAA, UAG and UGA) it was proposed to have a role in the termination of protein synthesis in eukaryotes. A similar role for the 3' end of 16S rRNA in recognising termination triplets in E.coli was proposed in 1974 by Shine and Dalgarno on the basis of complementarity relationships between the 3'-terminal UUA-OH in 16S rRNA and E.coli termination codons (Ref 1). In phage f1, the sequence coding for the first few amino acids often contains termination triplets in the two unused reading frames. In a commentary on this paper, it was noted that complementary base pairing with the 3'-terminus of 16S rRNA might serve to abort peptide bond formation after out-of-phase initiation.
- Kozak consensus sequence, the sequence that targets the ribosome to the initiation codon in eukaryotes.
- Prokaryotic translation
- Shine J, Dalgarno L (1974) The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Nat Acad Sci. USA, 71, 1342-1346.
- Malys N (2012). "Shine-Dalgarno sequence of bacteriophage T4: GAGG prevails in early genes". Molecular Biology Reports 39 (1): 33–9. doi:10.1007/s11033-011-0707-4. PMID 21533668.
- Hunt J A (1970) Terminal-sequence studies of high-molecular-weight ribonucleic acid. The 3'-termini of rabbit reticulocyte ribosomal RNA. Biochemical Journal. 120, 353-363.
- Shine J, Dalgarno L (1973) Occurrence of heat-dissociable ribosomal RNA in insects: the presence of three polynucleotide chains in 26S RNA from cultured Aedes aegypti cells. Journal of Molecular Biology, 75, 57-72.
- Shine J, Dalgarno L (1975) Determinant of cistron specificity in bacterial ribosomes. Nature 254 (5495) 34-38.
- Steitz J A, Jakes K (1975) How ribosomes select initiator regions in mRNA: base pair formation between the 3'-terminus of 16S rRNA and the mRNA during the initiation of protein synthesis in Escherichia coli. Proc Nat Acad Sci USA 72, 4734-4738.
- Bowman CM, Dahlberg JE, Ikemura T, Konisky J, Nomura M. (1971) Specific inactivation of 16S ribosomal RNA induced by colicin E3 in vivo. Proc Nat Acad Sci, USA 68, 964-968.
- Konisky J, Nomura M (1967) Interaction of colicins with bacterial cells. II. Specific alteration of Escherichia coli ribosomes induced by colicin E3 in vivo. J. Mol Biol, 26, 181-195.
- Dahlberg A E (1989) The functional role of ribosomal RNA in protein synthesis. Cell 57, 525-529.
- Shine J, Dalgarno L (1975) Growth dependant changes in terminal heterogeneity involving 3'-adenylate of bacterial 16S ribosomal RNA. Nature 256, 232-233.
- Johnson G (1991). "Interference with phage lambda development by the small subunit of the phage 21 terminase, gp1". Journal of Bacteriology 173(9): 2733–2738. PMID 1826903.
- Fargo DC, Zhang M, Gillham NW, Boynton JE. (1998). "Shine-Dalgarno-like sequences are not required for translation of chloroplast mRNAs in Chlamydomonas reinhardtii chloroplasts or in Escherichia coli". Mol Gen Genet 257 (3): 271–82. doi:10.1007/s004380050648. PMID 9520261.
- Dalgarno L, Shine J (1973) Conserved terminal sequence in 18S rRNA may represent terminator anticodons. Nature 245, 261-262
- Hunt J A (1965) Terminal-sequence studies of high-molecular-weight ribonucleic acid. The reaction of periodate-oxidized ribonucleosides, 5'-ribonucleotides and ribonucleic acid with isoniazid. Biochemical Journal. 95, 541-51.
- Pieczenik G, Model P, Robertson HD (1974) Sequence and symmetry in ribosome binding sites of bacteriophage f1RNA. Journal of Molecular Biology 90(2), 191-124
- Anon (1976) Signals for protein synthesis. Nature 260, 12-13.
- Voet D and Voet J (2004). Biochemistry (3rd ed.). John Wiley and Sons Inc. pp. 1321–1322 and 1342–1343.
- Hale WG, Margham JP, Saunders VA eds (1995) Collins Dictionary of Biology, (2nd ed) Shine-Dalgarno (SD) sequence. p 565.
- Lewin, B. (1994) Genes V. Oxford University Press. pp 179, 269.
- Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD (1994) The Molecular Biology of the Cell (3rd ed.) pp 237, 461.
- Malys N, McCarthy JEG (2011). "Translation initiation: variations in the mechanism can be anticipated". Cellular and Molecular Life Sciences 68 (6): 991–1003. doi:10.1007/s00018-010-0588-z. PMID 21076851.
- Mustafa Cicek, Ozal Mutlu, Aysegul Erdemir, Ebru Ozkan, Yunus Saricay, Dilek Turgut-Balik (2013), "Single Mutation in Shine-Dalgarno-Like Sequence Present in the Amino Terminal of Lactate Dehydrogenase of Plasmodium Effects the Production of an Eukaryotic Protein Expressed in a Prokaryotic System". Molecular Biotechnology 54(2): 602-608. http://link.springer.com/article/10.1007/s12033-012-9602-z