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Protein biosynthesis in eukaryotic cells is tightly regulated. Translation of a certain mRNA is affected by many external stimuli, in particular by low molecular weight drugs used in therapy of humans and other animals. We have developed a method to analyze immediate effects caused by addition of protein synthesis inhibitors and stress inducing small molecule into the growth medium on translation of transfected reporter mRNAs in cultured cells. The method is based on fleeting mRNA transfection (FLERT) and provides data how a particular inhibitor acts on several mRNAs which differ in translation initiation mechanism. Using this method we have found that therapeutic doses of some antibiotics – inhibitors of peptidyl-transferase center of a eukaryotic ribosome – differentially affect translation of a set of luciferase mRNAs which possess different 5’ untranslated regions (but are identical in other parts of the transcripts). We speculate that effects of certain “classical” antibiotics (which are routinely used in cancer or inflammation therapy) are not limited to inhibition of translation elongation, but are primary linked to differential downregulation of expression of different cellular mRNA species at the level of translation initiation and to the consequent cytoplasmic protein imbalance.