The Shine–Dalgarno (SD) sequence is a

ribosomal binding site A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of translation. Mostly, RBS refers ...

in bacterial and archaeal

messenger RNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein. mRNA is created during the p ...

, generally located around 8 bases

upstream Upstream may refer to: * Upstream (bioprocess) * ''Upstream'' (film), a 1927 film by John Ford * Upstream (networking) * ''Upstream'' (newspaper), a newspaper covering the oil and gas industry * Upstream (petroleum industry) * Upstream (software ...

of the

start codon The start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon always codes for methionine in eukaryotes and Archaea and a N-formylmethionine (fMet) in bacteria, mitochondria and plastids. The ...

AUG. The RNA sequence helps recruit the

ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to ...

to the

(mRNA) to initiate

protein synthesis Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside Cell (biology), cells, homeostasis, balancing the loss of cellular proteins (via Proteolysis, degradation or Protein targeting, export) through the product ...

by aligning the ribosome with the start codon. Once recruited,

tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino ac ...

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 Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

, but rarer in

archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

. It is also present in some

chloroplast A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...

and

mitochondrial A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is use ...

transcripts. The six-base

consensus sequence In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated order of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It serves as a simplified r ...

is AGGAGG; in ''

Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...

'', for example, the sequence is AGGAGGU, while the shorter dominates in ''E. coli'' virus T4 early genes. The Shine–Dalgarno sequence was proposed by

Australia Australia, officially the Commonwealth of Australia, is a Sovereign state, sovereign country comprising the mainland of the Australia (continent), Australian continent, the island of Tasmania, and numerous List of islands of Australia, sma ...

n scientists

John Shine John Shine (born 3 July 1946) is an Australian biochemist and molecular biologist. Shine and Lynn Dalgarno discovered the nucleotide sequence, called the Shine-Dalgarno sequence, necessary for the initiation and termination of protein synth ...

and

Lynn Dalgarno Lynn Dalgarno (born 12 November 1935) is an Australian geneticist known for the discovery of the Shine-Dalgarno sequence with his graduate student, John Shine. Early life and education Dalgarno was awarded a B.Sc.(Agr.) in 1958, conducting ...

Recognition

Translation start sites

Using a method developed by Hunt, Shine and Dalgarno showed that the nucleotide tract at the

3' end Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide pentose-sugar-ri ...

of ''E. coli''

16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S rRNA ...

(rRNA) (that is, the end where

translation Translation is the communication of the Meaning (linguistic), meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The ...

begins) is pyrimidine-rich and has the specific sequence . They proposed that these ribosomal nucleotides recognize the complementary purine-rich sequence , 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.

Translation termination

In 1973 Dalgarno and Shine proposed that in

eukaryotes Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacte ...

, 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 Ff phages (for ''F'' specific ''f''ilamentous phages) is a group of almost identical filamentous bacteriophage, filamentous phage (genus ''Inovirus'') including phages F1 phage, f1, fd, M13 phage, M13 and ZJ/2, which infect Gram-negative bacteria, ...

, 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

Mutation In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mi ...

s in the Shine–Dalgarno sequence can reduce or increase

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.

References

External links

* https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=eurekah.section.19320 {{DEFAULTSORT:Shine-Dalgarno sequence Protein biosynthesis