Adaptation of human cells to protein synthesis errors

Protein synthesis is a highly regulated process and maintenance of its fidelity is essential to life. Alterations in the components of the protein synthesis machinery, namely RNAs, aminoacyl-tRNA synthetases (aaRS) or tRNA modifying enzymes, increase the level of protein synthesis errors (PSE), and are associated with several conditions, from cancer to neurodegeneration. Still, the cause-effect mechanisms remain to be elucidated in many conditions. In order to have a global picture of how human cells respond and adapt in culture we created stable HEK293 cell lines that express mutant tRNAs. For this, we modified the anticodon of a human serine transfer RNA (tRNASer), to incorporate the amino acid serine (Ser) at various non-cognate sites and overexpressed the wild type tRNASer to evaluate the effects of tRNA misexpression. DNA microarrays were then performed to identify the transcriptional deregulation induced by PSE of cells in culture at different time points (cells passages). HEK293 cells were stably transfected with a plasmid carrying modified tRNAs and five cell lines were created; Mock (empty plasmid, our control), tRNASer(S) (carrying the wild type serine tRNA); tRNASer(A) (carrying a serine tRNA with Alanine anticodon); tRNASer(L) (carrying a serine tRNA with Leucine anticodon) and tRNASer(H) (carrying a serine tRNA with Histidine anticodon). After the creation of stable cell lines (designed passage 1, P1), cells were kept in culture dishes and subcultured ever 3 days using the same dilution (1/6) until passage 30. Three biological replicates of each of the five cell lines was extracted at three time points; P1 (cells passage 1, after the creation of the stable cell lines); P15 (cells passage 15, an intermediary time point) and P30 (cells passage 30, end of evolution experiment). All 45 samples were hybridized in Sure Print G3 Human Gene Expression 8x60k v2 microarrays (Agilent Technologies, Cat.G4851B).