biology

Shine–Dalgarno sequence

Shine–Dalgarno sequence is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Shine–Dalgarno sequence rather than just read about it. In short: The Shine–Dalgarno (SD) sequence is, sometimes partially, part of a ribosomal binding site in bacterial and archaeal messenger RNA. It is generally located around 8 bases upstream of the start codon AUG.

Key takeaways

Shine–Dalgarno sequence belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Shine–Dalgarno sequence to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Shine–Dalgarno sequence from memory before moving on to harder problems.

Reference excerpt

The Shine–Dalgarno (SD) sequence is, sometimes partially, part of a ribosomal binding site in bacterial and archaeal messenger RNA. It is 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. Once recruited, tRNA may add amino acids in sequence as dictated by the codons, moving downstream from the translational start site. The Shine–Dalgarno sequence is common in bacteria, but rarer in 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 the shorter GAGG dominates in E. coli virus T4 early genes. The Shine–Dalgarno sequence was proposed by Australian scientists John Shine and Lynn Dalgarno in 1973.

Recognition

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 5'-YACCUCCUUA-3'. They proposed that these ribosomal nucleotides recognize the complementary purine-rich sequence 5'-AGGAGGU-3', which is found upstream of the start codon AUG in a number of 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.

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. 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. 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.

See also Kozak consensus sequence, the sequence that targets the ribosome to the initiation codon in Eukaryotes. Bacterial translation Archaeal translation

References

Further reading 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 JE (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. PMC 11115079. PMID 21076851. S2CID 31720000. 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. hdl:11511/55531. PMID 23011788. S2CID 45230872.{{cite journal}}: CS1 maint: multiple names: authors list (link)

External links nih.gov

Illustrations

Worked examples

Example 1 — a first encounter with Shine–Dalgarno sequence

Start with the simplest possible case. Write down what Shine–Dalgarno sequence claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Shine–Dalgarno sequence before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Shine–Dalgarno sequence ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Shine–Dalgarno sequence

In research: Shine–Dalgarno sequence appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Shine–Dalgarno sequence in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Shine–Dalgarno sequence is common in secondary-school and first-year university syllabi. It links to neighbouring topics Protein biosynthesis, so understanding it makes those chapters shorter.
In everyday life: Look for Shine–Dalgarno sequence outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Shine–Dalgarno sequence in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Shine–Dalgarno sequence means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
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Frequently asked questions

What is Shine–Dalgarno sequence in simple terms?

Why does Shine–Dalgarno sequence matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Shine–Dalgarno sequence?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Shine–Dalgarno sequence.