Biopolym. Cell. 2007; 23(3):243-249.
The Shine-Dalgarno hybrid during initiation of translation and elongation
1Maraschio D., 1La Teana A., 2Volpe P.
  1. Institute of Biochemistry of the University of Ancona
    Via Ranieri, 60131 Ancona, Italy
  2. 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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