Ribosome binding site
Molecular Biology · Synthetic Biology
Say it: RY-buh-sohm BYND-ing SYTE
A ribosome binding site is a short stretch of messenger RNA just before the start codon where a ribosome attaches to begin translating a bacterial gene.
Also: ribosomal binding site, ribosome-binding site, ribosome binding sites
Definition
What is a ribosome binding site?
A ribosome binding site is the region of a messenger RNA, encoded in the DNA just ahead of a gene's coding sequence, where the small ribosomal subunit docks to start protein synthesis in bacteria and archaea. Its core is the Shine–Dalgarno sequence, a purine-rich motif close to the consensus AGGAGG that lies a few bases upstream of the AUG start codon. It base-pairs with a complementary sequence near the 3' end of the 16S ribosomal RNA, which positions the ribosome with the start codon ready for the first transfer RNA.
The site's strength largely sets how often each messenger RNA is translated. Strong pairing with the ribosomal RNA, suitable spacing from the start codon and the absence of RNA folding that hides the site all raise the rate of initiation. When one messenger RNA carries several genes, as in an operon, each gene can have its own site. Eukaryotes work differently: the ribosome usually binds the 5' cap and scans to a start codon, helped by the surrounding Kozak sequence.
In synthetic biology the ribosome binding site is a standard part. Swapping in stronger or weaker versions can change protein output over a very wide range without altering the protein, and design tools predict a sequence's strength from the energies of these RNA interactions.
Word parts
Where does the term “ribosome binding site” come from?
- ribo-
- from ribose, the sugar of RNAGerman Ribose, an altered form of arabinose
- -some
- bodyGreek soma
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Terms that go with it
- RibosomeA ribosome is a molecular machine of RNA and protein that reads messenger RNA and joins amino acids in the order it specifies to build a protein.
- TranslationTranslation is the process in which a ribosome reads the codons of a messenger RNA and links amino acids in that order to build a protein.
- Messenger RNAMessenger RNA is the RNA copy of a gene that carries protein-building instructions from DNA to the ribosomes, where it is read in three-base codons.
- CodonA codon is a sequence of three nucleotides in DNA or messenger RNA that stands for one amino acid or tells the ribosome to stop.
- OperonAn operon is a cluster of genes in bacteria that share one promoter, are switched on and off together and are copied into a single messenger RNA.
- Genetic circuitA genetic circuit is a designed set of genes and regulatory DNA that lets a cell sense inputs and respond in a programmed way, like an electronic circuit.
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Checked against
Written for biofideX in plain words, after checking these references:
- OpenStax Biology 2e, 15.5 Ribosomes and Protein Synthesis
- OpenStax Microbiology, 11.4 Protein Synthesis (Translation)
- Salis, Mirsky and Voigt (2009), Automated design of synthetic ribosome binding sites to control protein expression, Nature Biotechnology
- Wen et al. (2020), The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation, RNA Biology
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