Shine-Delgarno sequence

Translation in prokaryotes begins with the formation of the ribosome complex at a defined position on the mRNA, termed the Shine-Delgamo sequence, or the ribosome binding site (RBS). In prokaryotic mRNA, this is a relatively small (4-7 nucleotides) region rich in purine nucleotides located less than 10 nucleotides to the 5 side of the translational start site (Fig. 23-3). This Shine-Delgarno sequence is complementary to the 16S ribosomal RNA (rRNA) associated with the 30S ribosomal subunit, and directs it to bind the mRNA at that position. The 3 OS ribosomal subunit will not bind this region on the mRNA without the aid of an associated protein called initiation factor 3 (IF-3). The 30S ribosomal subunit will bind the mRNA in such a manner that the peptidyl (P) site of the complex is occupied by a specialized codon with the sequence, AUG. It is at this AUG start codon where translation will eventually begin. 

Another difference between prokaryotic and eukaryotic translation is the nucleic acid sequences that recruit the small ribosomal subunit to the mRNA. As stated earlier, the Shine-Delgarno sequence interacts with the 16S rRNA of the 3 OS ribosomal subunit in the prokaryotic system, the critical step in translation initiation. In the eukaryotic... 

In vitro, the fidelity of translation is strongly influenced by the concentration of Mg2 + ions in the reaction. In the range from 1 to 4 mM Mg2 +, the ribosome will require a Shine-Delgarno sequence (prokaryotic) or a 7-methyl-guanosine cap (eukaryotic) on the mRNA before translation will initiate. For this reason, in vitro translation experiments performed with naturally occurring mRNAs are most... 

From the sequence analysis it was learned, that the narB gene codes for a protein of 715 or 729 aminoacids with a molecular weight of about 80 kD. There are two possible startcodons, the first having a truncated Shine-Delgarno sequence, the second having non at all (fig. 1C). 

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