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Motif: RBS_E_coli (RM00014)

Description: Shine-Dalgarno sequences of the Escherichia coli sub-type


Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Shine-Dalgarno sequence. More...

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.[1] 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][1]

The Shine-Dalgarno sequence was proposed by Australian scientists John Shine and Lynn Dalgarno.


Translation start sites

Using a method developed by Hunt,[2][3] 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.[1] 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.[4][5]

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.[6] 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.

Translation termination

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.[7] 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.[8] 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.[citation needed] 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][9] 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.[10]

Sequence and protein expression

Mutations in the Shine-Dalgarno sequence can reduce or increase[11] 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.

See also


  1. ^ a b c 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.
  2. ^ 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.
  3. ^ 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.
  4. ^ 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.
  5. ^ 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.
  6. ^ Shine J, Dalgarno L (1975). "Determinant of cistron specificity in bacterial ribosomes". Nature. 254 (5495): 34–38. doi:10.1038/254034a0. PMID 803646.
  7. ^ Dalgarno L, Shine J (1973). "Conserved terminal sequence in 18S rRNA may represent terminator anticodons". Nature. 245: 261–262. doi:10.1038/newbio245261a0.
  8. ^ 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.
  9. ^ 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.
  10. ^ Anon (1976). "Signals for protein synthesis". Nature. 260: 12–13. doi:10.1038/260012a0.
  11. ^ 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.

Further reading

External links

This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.


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Alignment format:

Family matches

There are 11 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...

Original order Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF00503 RNAIII 3 0.300 43.3 Match Image
3 RF01471 Listeria sRNA rliB 2 0.500 33.2 Match Image
3 RF01473 Listeria sRNA rli41 6 1.000 111.4 Match Image
3 RF01492 Listeria sRNA rli28 2 0.095 32.7 Match Image
3 RF01570 Dictyostelium signal recognition particle 2 0.667 39.4 Match Image
3 RF01766 cspA thermoregulator 3 0.200 51.6 Match Image
3 RF01824 RNA of unknown function 20 2 0.333 28.6 Match Image
3 RF01888 Embryonic ventral forebrain RNA 1 conserved region 2 10 0.526 146.7 Match Image
3 RF02052 Enterobacterial sRNA STnc630 8 0.800 123.8 Match Image
3 RF02574 Rickettsia sRNA 10 2 0.667 32.7 Match Image
3 RF02644 S. pyogenes small RNA Spy490380c 4 1.000 65.6 Match Image


This section shows the database cross-references that we have for this Rfam motif.

Literature references

  1. Shine J, Dalgarno L Nature. 1975;254:34-38. Determinant of cistron specificity in bacterial ribosomes. PUBMED:803646

External database links

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
Structure source N/A
Type Specific Recognition Motif
Author Gardner PP
Alignment details
Alignment Number of
Average length Sequence
identity (%)
seed 202 39.00 41

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate --mpi --seed 1 CM
Gathering cutoff 14.0
Covariance model Download the Infernal CM for the motif here