Biopolym. Cell. 2007; 23(3):243-249.
The Shine-Dalgarno hybrid during initiation of translation and elongation
- Institute of Biochemistry of the University of Ancona
Via Ranieri, 60131 Ancona, Italy
- Department of Biology of the University of Rome "Tor Vergata"
Via della Ricerca Scientifica 1, 00133 Rome, Italy
It was unknown whether a synthetic Shine-Dalgarno (SD) oligonucleotide labelled with 32P at its 5'-end ([32P]oct) would be able to reach the anti-SD sequence of 16S rRNA at the early stages of translation only or during elongation. To verify this, [32P]oct was incubated with 30S ribosomal subunits (RSUs), 70S ribosomes and polysomes, separately, while the SD/anti-SD binding was checked in them through sucrose gradients. The anti-SD sequence resulted highly available in 30S RSUs and sufficiently available in ribosomes. In both 30S RSUs and ribosomes, the addition of a model 002 mRNA in equimolar proportions displaced [32P]oct for about 50 %. However, in ribosomes the presence of initiation factors (IFs) and fMet-tRNA influence neither the binding of [32P]oct nor the competition coming from mRNA. In polysomes, [32P]oct was unable to hybridize the anti-SD sequence, in agreement with the hypothesis that mRNA and 16S rRNA are involved in the SD/anti-SD interaction also during elongation.
Keywords: ribosomal machinery, mRNA/16S rRNA recognition, peptide bond formation, polysomal conformation, translational state
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