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 to bacterial sequences, although internal ribosome entry sites (IRES) have been described in mRNAs of eukaryotic cells or viruses that infect eukaryotes . Ribosome recruitment in eukaryotes is generally mediated by the 5' cap present on eukaryotic mRNAs.
18-659: Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices . There are many variants of the tetraloop. The published ones include ANYA, CUYG, GNRA, UNAC and UNCG. Three types of tetraloops are common in ribosomal RNA : GNRA, UNCG and CUUG, in which the N could be either uracil , adenine , cytosine , or guanine , and the R is either guanine or adenine. These three sequences form stable and conserved tetraloops that play an important role in structural stability and biological function of 16S rRNA. This molecular biology article
36-508: A codon during the translation process is located on one of the unpaired loops in the tRNA. Two nested stem-loop structures occur in RNA pseudoknots , where the loop of one structure forms part of the second stem. Many ribozymes also feature stem-loop structures. The self-cleaving hammerhead ribozyme contains three stem-loops that meet in a central unpaired region where the cleavage site lies. The hammerhead ribozyme's basic secondary structure
54-523: A complementarity is known to paradoxically decrease the rate of translation as the ribosome then happens to be bound too tightly to proceed downstream. The optimal distance between the RBS and the start codon is variable - it depends on the portion of the SD sequence encoded in the actual RBS and its distance to the start site of a consensus SD sequence. Optimal spacing increases the rate of translation initiation once
72-402: A double helix that ends in a loop of unpaired nucleotides. Stem-loops are most commonly found in RNA, and are a key building block of many RNA secondary structures . Stem-loops can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins , and serve as a substrate for enzymatic reactions . The formation of a stem-loop
90-443: A ribosome has been bound. The composition of nucleotides in the spacer region itself was also found to affect the rate of translation initiation in one study. Secondary structures formed by the RBS can affect the translational efficiency of mRNA, generally inhibiting translation. These secondary structures are formed by H-bonding of the mRNA base pairs and are sensitive to temperature. At a higher-than-usual temperature (~42 °C),
108-419: Is a stub . You can help Misplaced Pages by expanding it . Hairpin loop Stem-loops are nucleic acid secondary structural elements which form via intramolecular base pairing in single-stranded DNA or RNA . They are also referred to as hairpins or hairpin loops. A stem-loop occurs when two regions of the same nucleic acid strand, usually complementary in nucleotide sequence, base-pair to form
126-610: Is dependent on the stability of the helix and loop regions. The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability of this helix is determined by its length, the number of mismatches or bulges it contains (a small number are tolerable, especially in a long helix), and the base composition of the paired region. Pairings between guanine and cytosine have three hydrogen bonds and are more stable compared to adenine - uracil pairings, which have only two. In RNA, adenine-uracil pairings featuring two hydrogen bonds are equal to
144-400: Is not dependent on the full set of translation initiation factors (although this depends on the specific IRES) and is commonly found in the translation of viral mRNA. The identification of RBSs is used to determine the site of translation initiation in an unannotated sequence. This is referred to as N-terminal prediction. This is especially useful when multiple start codons are situated around
162-532: Is required for self-cleavage activity. Hairpin loops are often elements found within the 5'UTR of prokaryotes. These structures are often bound by proteins or cause the attenuation of a transcript in order to regulate translation. The mRNA stem-loop structure forming at the ribosome binding site may control an initiation of translation . Stem-loop structures are also important in prokaryotic rho-independent transcription termination . The hairpin loop forms in an mRNA strand during transcription and causes
180-559: The RNA polymerase to become dissociated from the DNA template strand. This process is known as rho-independent or intrinsic termination, and the sequences involved are called terminator sequences. Ribosome binding site The RBS in prokaryotes is a region upstream of the start codon. This region of the mRNA has the consensus 5'-AGGAGG-3', also called the Shine-Dalgarno (SD) sequence. The complementary sequence (CCUCCU), called
198-474: The RBS secondary structure of heat shock proteins becomes undone thus allowing ribosomes to bind and initiate translation. This mechanism allows a cell to quickly respond to an increase in temperature. Ribosome recruitment in eukaryotes happens when eukaryote initiation factors elF4F and poly(A)-binding protein (PABP) recognize the 5' capped mRNA and recruit the 43S ribosome complex at that location. Translation initiation happens following recruitment of
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#1732765659790216-399: The RBS. Increasing the concentration of adenine upstream of the RBS will increase the rate of ribosome recruitment. The level of complementarity of the mRNA SD sequence to the ribosomal ASD greatly affects the efficiency of translation initiation. Richer complementarity results in higher initiation efficiency. It is worth noting that this only holds up to a certain point - having too rich of
234-534: The adenine- thymine bond of DNA. Base stacking interactions, which align the pi bonds of the bases' aromatic rings in a favorable orientation, also promote helix formation. The stability of the loop also influences the formation of the stem-loop structure. Optimal loop length tends to be about 4-8 bases long; loops that are fewer than three bases long are sterically impossible and thus do not form, and large loops with no secondary structure of their own (such as pseudoknot pairing) are unstable. One common loop with
252-725: The anti-Shine-Dalgarno (ASD) is contained in the 3’ end of the 16S region of the smaller (30S) ribosomal subunit. Upon encountering the Shine-Dalgarno sequence, the ASD of the ribosome base pairs with it, after which translation is initiated. Variations of the 5'-AGGAGG-3' sequence have been found in Archaea as highly conserved 5′-GGTG-3′ regions, 5 basepairs upstream of the start site. Additionally, some bacterial initiation regions, such as rpsA in E.coli completely lack identifiable SD sequences. Prokaryotic ribosomes begin translation of
270-514: The mRNA transcript while DNA is still being transcribed. Thus translation and transcription are parallel processes. Bacterial mRNA are usually polycistronic and contain multiple ribosome binding sites. Translation initiation is the most highly regulated step of protein synthesis in prokaryotes. The rate of translation depends on two factors: The RBS sequence affects both of these factors. The ribosomal protein S1 binds to adenine sequences upstream of
288-479: The potential start site of the protein coding sequence. Identification of RBSs is particularly difficult, because they tend to be highly degenerated. One approach to identifying RBS in E.coli is using neural networks . Another approach is using the Gibbs sampling method. The Shine-Dalgarno sequence, of the prokaryotic RBS, was discovered by John Shine and Lynn Dalgarno in 1975. The Kozak consensus sequence
306-513: The ribosome, at the start codon (underlined) found within the Kozak consensus sequence ACC AUG G. Since the Kozak sequence itself is not involved in the recruitment of the ribosome, it is not considered a ribosome binding site. Eukaryotic ribosomes are known to bind to transcripts in a mechanism unlike the one involving the 5' cap, at a sequence called the internal ribosome entry site . This process
324-405: The sequence UUCG is known as the " tetraloop ," and is particularly stable due to the base-stacking interactions of its component nucleotides. Therefore, such loops can form on the microsecond time scale. Stem-loops occur in pre- microRNA structures and most famously in transfer RNA , which contain three true stem-loops and one stem that meet in a cloverleaf pattern. The anticodon that recognizes
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