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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 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.[further explanation needed]
Translation start sites
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) (that is, the end where translation begins) is pyrimidine-rich and has the specific sequence PyACCUCCUUA.[further explanation needed] 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.
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, Saccharomyces cerevisiae, and rabbit cells 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. In F1 phage, a class of viruses that infect bacteria, the sequence coding for the first few amino acids often contains termination triplets in the two unused reading frames.[further explanation needed] 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.
Sequence and protein expression
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 compensatory mutations in the 3'-terminal 16S rRNA sequence can restore translation.
- Kozak consensus sequence, the sequence that targets the ribosome to the initiation codon in eukaryotes.
- Prokaryotic translation
- 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. doi:10.1042/bj1200353. PMC 1179605.
- 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. doi:10.1016/0022-2836(73)90528-7.
- Dahlberg A E (1989). "The functional role of ribosomal RNA in protein synthesis". Cell. 57: 525–529. doi:10.1016/0092-8674(89)90122-0.
- 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 Natl Acad Sci USA. 72: 4734–4738. doi:10.1073/pnas.72.12.4734. PMC 388805. PMID 1107998.
- Shine J, Dalgarno L (1975). "Determinant of cistron specificity in bacterial ribosomes". Nature. 254 (5495): 34–38. doi:10.1038/254034a0. PMID 803646.
- Dalgarno L, Shine J (1973). "Conserved terminal sequence in 18S rRNA may represent terminator anticodons". Nature. 245: 261–262. doi:10.1038/newbio245261a0.
- 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. doi:10.1042/bj0950541.
- Pieczenik G, Model P, Robertson HD (1974). "Sequence and symmetry in ribosome binding sites of bacteriophage f1RNA". Journal of Molecular Biology. 90 (2): 191–214. doi:10.1016/0022-2836(74)90368-4.
- Anon (1976). "Signals for protein synthesis". Nature. 260: 12–13. doi:10.1038/260012a0.
- 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. PMC 207852. PMID 1826903.
- 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.
- Cicek Mustafa, Mutlu Ozal, Erdemir Aysegul, Ozkan Ebru, Saricay Yunus, Turgut-Balik Dilek (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. doi:10.1007/s12033-012-9602-z.
You can either download the motif alignment or view it directly in your browser window. More...
You can download (or view in your browser) a text representation of a Rfam alignment in various formats:
- Gapped FASTA
- Ungapped FASTA
You can view or download motif alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".
There are 5 Rfam families which match this motif.
This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...
To annotate the family with a motif model, the seed sequence was first filtered using a 0.9 fraction identity cut-off. The filtered seed was then scanned using Infernal cmscan (v1.1) with a concatenated CM file containing each of the motifs. Significance of hits between a seed sequence and the CM was based on a gathering threshold that was individually set for each motif. Only motifs where more than two and at least 10% of seed sequences scored higher than the gathering threshold were included for the next stage of processing. These subsets of motifs were then rescanned against the entire (non-filtered) seed to generate matches.
Number of Hits: the number of sequences in the family seed that score above the gathering threshold from motif.
Fraction of Hits: the fraction of sequences in the family seed that score above the gathering threshold from motif.
Sum of Bits: the sum of the bit scores of matches between the motif and the family seed sequence.
Image: plot illustrating where on the consensus secondary structure matches occur between seed sequences and the motif model.
|Original order||Family Accession||Family Description||Number of Hits||Fraction of Hits||Sum of Bits||Image|
|3||RF01472||Listeria sRNA rli40||4||1.000||79.9|
|3||RF01473||Listeria sRNA rli41||6||1.000||222.3|
|3||RF01824||RNA of unknown function 20||2||0.333||43.7|
|3||RF02414||Listeria sRNA rli60||4||0.364||79.1|
This section shows the database cross-references that we have for this Rfam motif.
Shine J, Dalgarno L Nature. 1975;254:34-38. Determinant of cistron specificity in bacterial ribosomes. PUBMED:803646
External database links
|External sites:|| 1: http://rnafrabase.cs.put.poznan.pl/?act=pdbdetails&id=3Q1Q
Curation and motif details
This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.
|Seed source||Predicted; Gardner PP|
|Type||Specific Recognition Motif|
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
|Covariance model||Download the Infernal CM for the motif here|