Di-codon organization links tRNA modifications to cancer cell proteome composition

Hormone-signalling modulates levels of tRNA-modifying enzymes, including ELP3, in cancer cells. Here we show that ELP3 is required to sustain proliferation in prostate cancer cells. Intriguingly, although ELP3 modifies tRNA at the U34-position, the ELP3-sensitive proteome was poorly explained by frequencies of codons requiring U34-modified tRNA for decoding. Instead, we identified six codon pairs (herein denoted ELP3 down di-codons "E3dDCs") that, in concert with local sequence context and 5UTR features affecting translation initiation, explain ELP3-sensitive protein expression. Moreover, despite activation of the canonical integrated stress response upon ELP3 suppression, the associated expression program was paradoxically suppressed in a fashion correlating with higher E3dDC frequencies. E3dDCs were also enriched in mitotic regulators, and ELP3-suppression caused mitotic defects that limited proliferation. Therefore, ELP3 regulates proteome composition via E3dDCs that, depending on their local sequence context and translation initiation activity, determine protein expression and downstream cellular phenotypes upon reduced levels of U34-modified tRNA.